shared stream\n ret = pRegExp.match(line)\n if ret:\n l = self.readPMacro(ret.group(1), mmfFile)\n if l: \n line = l\n continue\n \n # ~s macro? -> shared state distribution\n ret = sRegExp.match(line)\n if ret:\n l = self.readSMacro(ret.group(1), mmfFile)\n if l: \n line = l\n continue\n \n \n # ~h section has begun? from now on only ~h definitions \n # ~h \"v^schwa-h+schwa=m@1_2/A:0_0_4/B:0-0-2@1-2&2-7#1-1$1-1!0-0;0-0|0/C:0+0+3/D:det_1/E:content+2@2+3&1+2#0+1/F:content_4/G:0_0/H:7=4@1=1|0/I:0=0/J:7+4-1\" \n ret = hRegExp.match(line)\n if ret:\n currentLabel = LabelEntry(ret.group(1)) \n self.labelList.append(currentLabel)\n self.labelDict[ ret.group(1) ] = currentLabel\n \n \n # we are already in the ~h section\n elif currentLabel:\n \n # link to a ~p macro which is then associated with the ~h macro \n # <STATE> 2\n # ~w \"SWeightall\"\n # <STREAM> 1\n # ~p \"mcep_s2_72\" \n ret = pRegExp.match(line)\n # or link to a ~s macro \n if not ret:\n ret = sRegExp.match(line)\n if ret:\n currentLabel.associatedMacroNames.append(ret.group(1))\n \n # fill macroToLabels\n if ret.group(1) in self.macroToLabels:\n self.macroToLabels[ ret.group(1) ].append(currentLabel)\n else:\n self.macroToLabels[ ret.group(1) ] = [ currentLabel ]\n \n \n line = mmfFile.readline()\n mmfFile.close()\n #print 'done: ' + str(len( self.macroToLabels ))\n #print self.macroToLabels","def update_macros(self, root_p, macros):\n layers_len = len([p for p in root_p.iterdir() if re.search('[lL]\\d+', p.name)])\n MacroInfo = namedtuple('MacroInfo', ['dim', 'len'])\n d = {macro.id : MacroInfo(i+layers_len, len(macro)) for i, macro in enumerate(macros)}\n self.macros_dict = d","def parse_movie(self, line):\n pass","def dump_macrosizes_action(driver: HammerDriver, append_error_func: Callable[[str], None]) -> Optional[str]:\n macro_json = list(map(lambda m: m.to_setting(), driver.tech.get_macro_sizes()))\n return json.dumps(macro_json, indent=4)","def setup_parser(self) -> Dict[str, Any]:\n\n\t# % year,doy, RH(m), Month, day, azimuth(deg),freq, satNu, LSP amp,pk2noise,UTC(hr) \n\t# 2021 9 4.888 1 9 225.3 1 2 9.51 3.23 10.08\n\t# 2021 9 5.018 1 9 181.3 1 15 7.79 2.84 15.67\n\t# 2021 9 5.123 1 9 185.4 1 16 6.27 3.01 0.68\n #----+----0----+----1----+----2----+----3----+----4----+----5----+----6----+----7\n return dict(\n skip_header=1,\n names=(\n \"year\",\n \"doy\",\n \"reflection_height\",\n \"month\",\n \"day\",\n \"azimuth\",\n \"frequency\",\n \"satellite\",\n \"amplitude\",\n \"peak2noise\",\n \"hour\",\n ),\n dtype=(\"f8\", \"f8\", \"f8\", \"f8\", \"f8\", \"f8\", \"f8\", \"f8\", \"f8\", \"f8\", \"f8\"),\n )","def generate_initial_siaf_aperture_definitions(instrument):\n siaf_detector_layout = iando.read.read_siaf_detector_layout()\n\n prd_siaf = pysiaf.Siaf(instrument)\n siaf_definitions = Table()\n\n\n for attribute_name in 'AperName AperType XDetRef YDetRef XSciSize YSciSize XSciRef YSciRef'.split():\n siaf_definitions[attribute_name] = [getattr(prd_siaf[aperture_name], attribute_name) for aperture_name in prd_siaf.apertures]\n\n parent_apertures = [None]*len(siaf_definitions)\n dependency_type = [None]*len(siaf_definitions)\n\n if instrument == 'NIRISS':\n for i,aperture_name in enumerate(siaf_definitions['AperName']):\n if aperture_name != 'NIS_CEN':\n parent_apertures[i] = 'NIS_CEN'\n if '_OSS' in aperture_name:\n dependency_type[i] = 'oss_default'\n elif aperture_name != 'NIS_CEN':\n dependency_type[i] = 'default'\n\n elif instrument == 'FGS':\n for i,aperture_name in enumerate(siaf_definitions['AperName']):\n if aperture_name not in ['FGS1_FULL', 'FGS2_FULL']:\n parent_apertures[i] = '{}_FULL'.format(aperture_name.split('_')[0])\n else:\n dependency_type[i] = 'master'\n if '_OSS' in aperture_name:\n dependency_type[i] = 'oss_default'\n elif aperture_name not in ['FGS1_FULL', 'FGS2_FULL']:\n dependency_type[i] = 'default'\n\n elif instrument == 'NIRSpec':\n for i,aperture_name in enumerate(siaf_definitions['AperName']):\n if siaf_definitions['AperType'][i] == 'TRANSFORM':\n continue\n\n if '_OSS' in aperture_name:\n dependency_type[i] = 'oss_default'\n parent_apertures[i] = aperture_name.split('_OSS')[0]\n elif 'NRS_IFU' in aperture_name:\n parent_apertures[i] = 'NRS1_FULL'\n dependency_type[i] = 'default'\n elif aperture_name in ['NRS_S200B1_SLIT']:\n parent_apertures[i] = 'NRS2_FULL'\n dependency_type[i] = 'default'\n elif aperture_name in 'NRS_S200A1_SLIT NRS_S200A2_SLIT NRS_S400A1_SLIT NRS_S1600A1_SLIT NRS_FULL_IFU'.split():\n parent_apertures[i] = 'NRS1_FULL'\n dependency_type[i] = 'default'\n elif ('_MSA1' in aperture_name) or ('_MSA2' in aperture_name):\n parent_apertures[i] = 'NRS2_FULL'\n dependency_type[i] = 'default'\n elif ('_MSA3' in aperture_name) or ('_MSA4' in aperture_name):\n parent_apertures[i] = 'NRS1_FULL'\n dependency_type[i] = 'default'\n elif aperture_name in ['NRS1_FP1MIMF']:\n parent_apertures[i] = 'NRS_S1600A1_SLIT'\n dependency_type[i] = 'FP1MIMF'\n elif 'MIMF' in aperture_name:\n parent_apertures[i] = aperture_name.split('_')[0]+'_FULL'\n dependency_type[i] = 'default'\n\n\n # if aperture_name not 'NIS_CEN':\n # parent_apertures[i] = 'NIS_CEN'\n # elif aperture_name != 'NIS_CEN':\n # dependency_type[i] = 'default'\n\n elif instrument == 'NIRCam':\n for i,aperture_name in enumerate(siaf_definitions['AperName']):\n\n # Master apertures\n if aperture_name in siaf_detector_layout['AperName']:\n dependency_type[i] = 'master'\n\n elif siaf_definitions['AperType'][i] in ['SUBARRAY', 'FULLSCA', 'ROI']:\n if 'MASK' in aperture_name:\n # Coronagraphic apertures with wedge offset\n dependency_type[i] = 'wedge'\n elif 'DHSPIL_WEDGES' in aperture_name:\n dependency_type[i] = 'dhspil_wedge'\n else:\n dependency_type[i] = 'default'\n sca_name = aperture_name[0:5]\n parent_apertures[i] = '{}_FULL'.format(sca_name)\n\n # OSS apertures\n elif siaf_definitions['AperType'][i] in ['OSS']:\n dependency_type[i] = 'default'\n parent_apertures[i] = aperture_name.split('_OSS')[0]\n\n elif (siaf_definitions['AperType'][i] in ['SLIT', 'COMPOUND']) and ('GRISM' in aperture_name) and ('WFSS' in aperture_name):\n dependency_type[i] = 'grism_wfss'\n sca_name = aperture_name.split('_')[0]\n # sca_name = aperture_name[0:5]\n parent_apertures[i] = '{}_FULL'.format(sca_name)\n\n # elif 'MASK' in aperture_name:\n # dependency_type[i] = 'wedge'\n # sca_name = aperture_name[0:5]\n # parent_apertures[i] = '{}_FULL'.format(sca_name)\n\n\n\n elif aperture_name in 'NRCALL_FULL NRCAS_FULL NRCBS_FULL'.split():\n dependency_type[i] = 'nircam_compound'\n if aperture_name == 'NRCALL_FULL':\n parent_apertures[i] = '; '.join(['NRCA1_FULL', 'NRCB2_FULL', 'NRCB1_FULL', 'NRCA2_FULL'])\n elif aperture_name == 'NRCAS_FULL':\n parent_apertures[i] = '; '.join(['NRCA1_FULL', 'NRCA3_FULL', 'NRCA4_FULL', 'NRCA2_FULL'])\n elif aperture_name == 'NRCBS_FULL':\n parent_apertures[i] = '; '.join(['NRCB4_FULL', 'NRCB2_FULL', 'NRCB1_FULL', 'NRCB3_FULL'])\n\n\n\n siaf_definitions['parent_apertures'] = parent_apertures\n siaf_definitions['dependency_type'] = dependency_type\n\n siaf_definitions.pprint()\n\n\n siaf_definitions_file_name = os.path.join(JWST_SOURCE_DATA_ROOT, instrument,\n '{}_siaf_aperture_definition.txt'.format(instrument.lower()))\n\n comments = []\n comments.append('{} aperture definition file for SIAF'.format(instrument))\n comments.append('')\n comments.append('This file contains all the necessary aperture information to generate the full SIAF given the necessary reference files (focal plane alignment, distortion) and auxiliary information (DDC mapping, wedge offsets, ...)')\n comments.append('This file also defines the order in which the apertures are presented.')\n comments.append('')\n comments.append('Originally based on {}.'.format(JWST_PRD_VERSION))\n comments.append('')\n comments.append('Generated {} {}'.format(timestamp.isot, timestamp.scale))\n comments.append('{}'.format(username))\n comments.append('')\n siaf_definitions.meta['comments'] = comments\n siaf_definitions.write(siaf_definitions_file_name, format='ascii.fixed_width', delimiter=',',\n delimiter_pad=' ', bookend=False)","def parseheader(self):\n for line in self.rawheader.split(\"\\n\"):\n pat = \"QUITTING\"\n if pat in line:\n self.prefix = line\n continue\n\n pat = \"VERSION NUMBER\"\n if pat in line:\n self.softvers = line[28:].strip()\n continue\n\n pat = \"DATE/TIME IS\"\n if pat in line:\n meta = line[22:].strip()\n matchobj = dtpat.match(meta)\n if matchobj:\n try:\n self.dumpdt = datetime.strptime(meta, moddtfmt)\n except:\n self.nodump = True\n self.comment += (\n \" *** Cannot read module date/time: {}\\n\".format(meta)\n )\n continue\n\n pat = \"NUMBER RECORDS IS\"\n if pat in line:\n self.ndumprec = line[22:].strip()\n continue\n\n pat = \"MODULE TYPE IS\"\n if pat in line:\n self.modtype = line[22:].strip()\n continue\n\n pat = \"SERIAL NUMBER IS\"\n if pat in line:\n self.modserial = line[22:].strip()\n continue\n\n pat = \"COND S/N IS\"\n if pat in line:\n meta = line[22:].strip()\n serials = meta.split(\"/\")\n self.cellserial = serials[1]\n self.ioserial = serials[0]\n continue\n\n pat = \"SAMPLING INTERVAL IS\"\n if pat in line:\n meta = line[22:].strip()\n self.sampintv = meta\n if meta == \"00:01:00\":\n self.nodump = False\n self.comment += \" *** Sample interval is {}\\n\".format(meta)\n elif meta != \"00:02:00\":\n self.nodump = True\n self.comment += \" *** Sample interval is {}\\n\".format(meta)\n continue\n\n pat = \"AVERAGE INTERVAL IS\"\n if pat in line:\n self.avgintv = line[22:].strip()\n if int(self.avgintv) != 24:\n self.nodump = True\n self.comment += \" *** Average interval is {}\\n\".format(meta)\n continue\n\n pat = \"BATTERY VOLTAGE IS\"\n if pat in line:\n self.voltage = line[22:].strip()\n continue\n\n return self.modserial","def parseGard(kh, aln, o, logger):\n\tlBP = []\n\tf = open(kh, \"r\")\n\tlLine = f.readline()\n\twhile lLine:\n\t if lLine.find(\"\\\"breakpoints\\\"\")!=-1:\n\t lLine = f.readline()\n\t lLine=lLine[lLine.find(\"[\")+1:lLine.find(\"]\")]\n\t lBP=list(map(int, lLine.split(\",\")))\n\t break\n\t lLine = f.readline()\n\tf.close()\n\tindex = 0\n\t\n\t#If there are breakpoints, add it in lBP\n\tif len(lBP) > 0:\n\t\tlogger.info(\"There are {:d} significant breakpoints in alignement {:s} at positions {}\".format(len(lBP), aln, lBP))\n\telse:\n\t\tlogger.info(\"There are no significant breakpoints in alignement {:s}.\".format(aln))\n\t\treturn []\n \n\t#If there're breakpoint(s), cut sequence in subsequences according to breakpoints\n\tif len(lBP) > 0:\n\t\tdFname2Fseq = {}\n\t\tfor fasta in SeqIO.parse(open(aln),'fasta'):\n\t\t\tdFname2Fseq[fasta.id] = str(fasta.seq)\n\t\t\n\t\t#Creation of a dico where atgc in sequence has been replace by 1 and - by 0\n\t\tlSeqBin = []\n\t\tlNameGene = []\n\t\tfor fastaSeq in dFname2Fseq:\n\t\t\tlSeqBin.append(dFname2Fseq[fastaSeq].lower().replace(\"a\", \"1\").replace(\"t\", \"1\").replace(\"c\", \"1\").replace(\"g\", \"1\").replace(\"-\", \"0\"))\n\t\t\tlNameGene.append(fastaSeq)\n\n\t\t#looking for a multiple of 3 (number of letter) (subsequence ends on or after the breakpoint)\n\t\tnbSeq = len(lNameGene)\n\t\tlenSeq = len(lSeqBin[0])\n\t\tlPos = [0]\n\t\tlBPprec = [0 for i in range(len(lSeqBin))]\n\t\tlFrag = []\n\t\tfor bp in lBP:\n\t\t\twhile bp%3 != 0:\n\t\t\t\tbp += 1\n\t\t\tlPos.append(bp)\n\t\t\tlFrag += [ dFname2Fseq[lNameGene[j]][lPos[-2]:lPos[-1]] for j in range(nbSeq) ]\n\t\t\n\t\t#Adding subsequences that start at the last breakpoint to the end\n\t\tlFrag += [dFname2Fseq[lNameGene[i]][lPos[-1]:] for i in range(nbSeq)]\n\n\t\tlBP = lPos+[lenSeq]\n\t\tlOutFrag = []\n\t\tindex = 0\n\t\tfor x in range(1,len(lBP)):\n\t\t\tdFrag = {}\n\t\t\tif lBP[x-1] == 0:\n\t\t\t\textension = \"_{:d}_{:d}\".format(lBP[x-1], lBP[x])\n\t\t\telse:\n\t\t\t\textension = \"_{:d}_{:d}\".format(lBP[x-1]-1, lBP[x])\n\n\t\t\toutFrag = o+aln.split(\"/\")[-1].split(\".\")[0]+\"_frag\"+extension+\".best.fas\"\n\t\t\tfor name in lNameGene:\n\t\t\t\tdFrag[name] = lFrag[index]\n\t\t\t\tindex += 1\n\t\t\twith open(outFrag, \"w\") as outF:\n\t\t\t outF.write(FastaResFunc.dict2fasta(dFrag))\n\t\t\t logger.info(\"\\tNew alignment: %s\"%{outFrag})\n\t\t\t outF.close()\n\t\t\t lOutFrag.append(outFrag)\n\n\t\treturn lOutFrag\n\telse:\n\t\treturn []","def _parse_motion(block, **kwargs):\n _, fa_length, time_step, name, fmt = parse_fixed_width(\n [(5, int), (5, int), (10, float), (30, to_str), (30, to_str)],\n block\n )\n\n scale, pga, _, header_lines, _ = parse_fixed_width(\n 3 * [(10, to_float)] + 2 * [(5, int)],\n block\n )\n\n m = re.search(r'(\\d+)\\w(\\d+)\\.\\d+', fmt)\n count_per_line = int(m.group(1))\n width = int(m.group(2))\n\n fname = os.path.join(os.path.dirname(kwargs['fname']), name)\n accels = np.genfromtxt(\n fname,\n delimiter=(count_per_line * [width]),\n skip_header=header_lines,\n )\n\n if np.isfinite(scale):\n pass\n elif np.isfinite(pga):\n scale = pga / np.abs(accels).max()\n else:\n scale = 1.\n\n accels *= scale\n m = motion.TimeSeriesMotion(fname, '', time_step, accels, fa_length)\n\n return m","def evaluateMacro(compiled_expression):","def parse_beam(self):\n # AIPS FITS file; stored in the history section\n beam_regex = re.compile(r'''\n BMAJ\n \\s*=\\s*\n (?P<bmaj>[-\\d\\.eE]+)\n \\s*\n BMIN\n \\s*=\\s*\n (?P<bmin>[-\\d\\.eE]+)\n \\s*\n BPA\n \\s*=\\s*\n (?P<bpa>[-\\d\\.eE]+)\n ''', re.VERBOSE)\n\n bmaj, bmin, bpa = None, None, None\n header = self.header\n try:\n # MIRIAD FITS file\n bmaj = header['BMAJ']\n bmin = header['BMIN']\n bpa = header['BPA']\n except KeyError:\n\n def get_history(hdr):\n \"\"\"\n Returns all history cards in FITS header hdr as a list of strings.\n \"\"\"\n return hdr['HISTORY']\n\n for hist_entry in get_history(header):\n results = beam_regex.search(hist_entry)\n if results:\n bmaj, bmin, bpa = [float(results.group(key)) for\n key in ('bmaj', 'bmin', 'bpa')]\n break\n\n return bmaj, bmin, bpa","def macros(self):\r\n return macros.Macros(self)","def magic_macro(self,parameter_s = ''):\n\n args = parameter_s.split()\n name,ranges = args[0], args[1:]\n #print 'rng',ranges # dbg\n cmds = self.extract_input_slices(ranges)\n macro = Macro(cmds)\n self.user_ns.update({name:macro})\n print 'Macro `%s` created. To execute, type its name (without quotes).' % name\n print 'Macro contents:'\n print str(macro).rstrip(),","def _expand_macros(self, macro_ids) -> None:\n if macro_ids is None:\n return\n\n for macro_id in macro_ids:\n macro_cfg = self._app_cfg['macros'][macro_id]\n\n self._sweep_stages.extend(macro_cfg.get('sweeps', []))\n self._reset_stages.extend(macro_cfg.get('resets', []))\n self._process_stages.extend(macro_cfg.get('processes', []))","def parse_misc(self,ins):\n if ins.instr == 'nop':\n if len(ins.args) != 0:\n raise Exception(\"Invalid number of args for ins: \", ins.instr)\n elif ins.instr == 'syscall':\n if len(ins.args) != 0:\n raise Exception(\"Invalid number of args for ins: \", ins.instr)\n elif ins.instr == 'break':\n if len(ins.args) != 0:\n raise Exception(\"Invalid number of args for ins: \", ins.instr)\n elif ins.instr == 'mflo': \n if len(ins.args) == 1:\n self.gen = [ins.args[0]]\n self.need = [Register(\"$lo\")]\n else:\n raise Exception(\"Invalid number of args for ins: \", ins.instr)\n \n elif ins.instr == 'mtlo': \n if len(ins.args) == 1:\n self.gen = [Register(\"$lo\")]\n self.need = [ins.args[0]]\n else:\n raise Exception(\"Invalid number of args for ins: \", ins.instr)\n \n elif ins.instr == 'mfhi': \n if len(ins.args) == 1:\n self.gen = [ins.args[0]]\n self.need = [Register(\"$hi\")]\n else:\n raise Exception(\"Invalid number of args for ins: \", ins.instr) \n \n elif ins.instr == 'mthi': \n if len(ins.args) == 1:\n self.gen = [Register(\"$hi\")]\n self.need = [ins.args[0]]\n else:\n raise Exception(\"Invalid number of args for ins: \", ins.instr)\n \n elif ins.instr == 'mtc1': \n if len(ins.args) == 2:\n self.gen = [ins.args[1]]\n self.need = [ins.args[0]]\n else:\n raise Exception(\"Invalid number of args for ins: \", ins.instr) \n \n elif ins.instr == 'mfc1': \n if len(ins.args) == 2:\n self.gen = [ins.args[0]]\n self.need = [ins.args[1]]\n else:\n raise Exception(\"Invalid number of args for ins: \", ins.instr) \n \n elif ins.instr == 'la': \n if len(ins.args) == 2:\n self.gen = [ins.args[0]]\n self.ival = ins.args[1]\n else:\n raise Exception(\"Invalid number of args for ins: \", ins.instr)\n \n elif ins.instr == 'lui': \n if len(ins.args) == 2:\n self.gen = [ins.args[0]]\n self.ival = ins.args[1]\n else:\n raise Exception(\"Invalid number of args for ins: \", ins.instr)","def _compat_parse_magic(self):\n def warning(magic, option):\n LOG.warning(\"Deprecated \\\"magic\\\" option \\\"{m}\\\" found. Please use new-style option \\\"{o}\\\" instead (see user manual).\".format(m=magic, o=option))\n\n magic_auto_backports = re.search(r\"\\*\\s*MINI_BUILDD:\\s*AUTO_BACKPORTS:\\s*([^*.\\[\\]]+)\", self._top_changes)\n if magic_auto_backports:\n warning(\"AUTO_BACKPORTS\", \"auto-ports\")\n self._set(\"auto-ports\", magic_auto_backports.group(1))\n\n magic_backport_mode = re.search(r\"\\*\\s*MINI_BUILDD:\\s*BACKPORT_MODE\", self._top_changes)\n if magic_backport_mode:\n warning(\"BACKPORT_MODE\", \"ignore-lintian\")\n self._set(\"ignore-lintian\", \"true\")","def test_make_macrobes(self):\n basic_test_runner(self, 'macrobes')","def initialize(self):\n print(\"Initializing macro \" + self.name + \"...\")\n\n self.initTime = wpilib.Timer.getFPGATimestamp() #get the current time\n self.f = open(\"/home/lvuser/py/macros/\"+self.name, \"w\")\n fields = [\"Drive_Y\",\n \"Drive_Twist\",\n \"Ears\",\n \"Hat\",\n \"Tilt\",\n \"Time\"]\n self.writer = csv.DictWriter(self.f, fieldnames=fields)\n self.writer.writeheader()","def resolve_macros(lines: List[SourceLine]) -> List[SourceLine]:\n macros: Dict[str, Dict[str, Any]] = {}\n found_macro = None\n lines_to_remove = []\n for idx, srcline in enumerate(lines):\n if found_macro is None:\n match = re.match(mipsRE.MACRO, srcline.line)\n if match:\n found_macro = match[1]\n macros[match[1]] = {\n \"args\": [a.strip() for a in match[2].split(\", \")] if match[2] else None,\n \"lines\": [],\n }\n lines_to_remove.append(idx)\n else:\n if \".end_macro\" in srcline.line:\n found_macro = None\n lines_to_remove.append(idx)\n else:\n macros[found_macro][\"lines\"].append(srcline)\n lines_to_remove.append(idx)\n\n lines = [l for i, l in enumerate(lines) if i not in lines_to_remove]\n\n for idx, srcline in enumerate(lines):\n for macro, macro_info in macros.items():\n if macro in srcline.line:\n if macro_info[\"args\"] is None:\n lines[idx] = macro_info[\"lines\"]\n else:\n macro_with_args(idx, lines, macro, macro_info, srcline)\n\n return flatten(lines)","def finalize(content):\n def add_usetypes(text):\n # TODO: get rid of this fian.py copypasta\n def header_starts(line): # TODO: now requires exactly one space after \"end\"\n for objtype in (\"function\", \"subroutine\"):\n p_notend = r\"(?<!\\bend\\b\\s)\" # (?<!...) is \"match if not preceded by\" (see help(re))\n p_objtype = r\"\\b{objtype}\\b\".format(objtype=objtype)\n pattern = r\"{notend}{objtype}\".format(notend=p_notend,\n objtype=p_objtype)\n matches = re.findall(pattern, line)\n assert len(matches) <= 1 # should be at most one match for the whole regex\n if len(matches) > 0:\n return True\n return False\n\n # FIXME: brittle: we assume the return type decl contains no \")\"\n def header_ends(line):\n matches = re.findall(r\"\\)\", line)\n return (len(matches) > 0)\n\n from enum import Enum\n class ReaderState(Enum):\n SCANNING = 0\n PROCESSING = 1\n\n state = ReaderState.SCANNING\n out = []\n for line in text.split(\"\\n\"):\n if state not in (ReaderState.SCANNING, ReaderState.PROCESSING):\n assert False, \"Unknown reader state '{}'\".format(state)\n doitnow = False\n if state is ReaderState.SCANNING:\n if header_starts(line):\n state = ReaderState.PROCESSING\n if state is ReaderState.PROCESSING:\n if header_ends(line):\n doitnow = True\n state = ReaderState.SCANNING\n out.append(line)\n if doitnow:\n out.append(\"use types\") # Elmer-specific\n if state != ReaderState.SCANNING:\n class ReaderError(ValueError):\n pass\n raise ReaderError(\"unexpected end of file (incomplete function or subroutine declaration?)\")\n return \"\\n\".join(out)\n\n content = add_usetypes(content)\n content = re.sub(r\"([0-9.]+)[DdEe]([+-]?[0-9]+)\", r\"\\1e\\2_dp\", content)\n content = re.sub(r\"REAL\\*8\", r\"REAL(KIND=dp)\", content)\n return content","def parse( self, exprlist ):\n t = self.prop[\"DSEC\"]\n E = self.prop[\"ELE\"]\n V = self.prop[\"VOL\"]\n T = self.prop[\"TEMP\"]\n C = self.prop[\"CONC\"]\n S = self.prop[\"SPEC\"]\n pH = E\n row = []\n for i in exprlist:\n i = i.replace(\"A\", \"self.absorbance\")\n exec 'row.append(' + i + ')'\n return row","def read_abinit(filename='abinit.in'):\n\n from ase import Atoms, units\n\n if isinstance(filename, str):\n f = open(filename)\n else: # Assume it's a file-like object\n f = filename\n\n lines = f.readlines()\n if type(filename) == str:\n f.close()\n\n full_file = ''\n for line in lines:\n if '#' in line:\n meat, comment = line.split('#')\n else:\n meat = line\n full_file = full_file + meat + ' '\n\n full_file.strip()\n tokens = full_file.lower().split()\n\n # note that the file can not be scanned sequentially\n\n index = tokens.index(\"acell\")\n unit = 1.0\n if(tokens[index+4].lower()[:3] != 'ang'):\n unit = units.Bohr\n acell = [unit*float(tokens[index+1]),\n unit*float(tokens[index+2]),\n unit*float(tokens[index+3])]\n\n index = tokens.index(\"natom\")\n natom = int(tokens[index+1])\n\n index = tokens.index(\"ntypat\")\n ntypat = int(tokens[index+1])\n\n index = tokens.index(\"typat\")\n typat = []\n for i in range(natom):\n typat.append(int(tokens[index+1+i]))\n\n index = tokens.index(\"znucl\")\n znucl = []\n for i in range(ntypat):\n znucl.append(int(tokens[index+1+i]))\n\n index = tokens.index(\"rprim\")\n rprim = []\n for i in range(3):\n rprim.append([acell[i]*float(tokens[index+3*i+1]),\n acell[i]*float(tokens[index+3*i+2]),\n acell[i]*float(tokens[index+3*i+3])])\n\n # create a list with the atomic numbers\n numbers = []\n for i in range(natom):\n ii = typat[i] - 1\n numbers.append(znucl[ii])\n\n # now the positions of the atoms\n if \"xred\" in tokens:\n index = tokens.index(\"xred\")\n xred = []\n for i in range(natom):\n xred.append([float(tokens[index+3*i+1]),\n float(tokens[index+3*i+2]),\n float(tokens[index+3*i+3])])\n atoms = Atoms(cell=rprim, scaled_positions=xred, numbers=numbers,\n pbc=True)\n else:\n if \"xcart\" in tokens:\n index = tokens.index(\"xcart\")\n unit = units.Bohr\n elif \"xangst\" in tokens:\n unit = 1.0\n index = tokens.index(\"xangst\")\n else:\n raise IOError(\n \"No xred, xcart, or xangs keyword in abinit input file\")\n\n xangs = []\n for i in range(natom):\n xangs.append([unit*float(tokens[index+3*i+1]),\n unit*float(tokens[index+3*i+2]),\n unit*float(tokens[index+3*i+3])])\n atoms = Atoms(cell=rprim, positions=xangs, numbers=numbers, pbc=True)\n \n try:\n i = tokens.index('nsppol')\n except ValueError:\n nsppol = None\n else:\n nsppol = int(tokens[i + 1])\n\n if nsppol == 2:\n index = tokens.index('spinat')\n magmoms = [float(tokens[index + 3 * i + 3]) for i in range(natom)]\n atoms.set_initial_magnetic_moments(magmoms)\n\n return atoms","def macro_with_args(idx: int, lines: List[SourceLine], macro: str, macroinfo: Dict[str, Any], srcline: SourceLine):\n macroregex = fr\"{macro}\\((.+)\\)\"\n match = re.match(macroregex, srcline.line)\n if match:\n values = match[1].split(\", \")\n argsmap = {arg: val for arg, val in zip(macroinfo[\"args\"], values)}\n expanded_macro = []\n for s in macroinfo[\"lines\"]:\n modified_line = s.line\n for a, v in argsmap.items():\n modified_line = modified_line.replace(a, v)\n expanded_macro.append(SourceLine(line=modified_line, lineno=s.lineno, filename=s.filename))\n lines[idx] = expanded_macro # type: ignore","def test_parse_multiple_procedures(self):\n source_code = dedent(\"\"\"\\\n #include <stdbool.h>\n\n /**\n * helper method to decide things\n */\n bool helper()\n {\n return true;\n }\n\n /**\n * this is a doc comment that stretches over\n * more than one line\n */\n int main()\n {\n return 0;\n }\n \"\"\")\n result = self.parser.parse(source_code.splitlines())\n assert_equal(result, {\n \"bool helper()\": \"helper method to decide things\",\n \"int main()\": (\"this is a doc comment that stretches over \"\n \"more than one line\")})","def parser(path):\n\t\n\tdata = Arff()\n\tdata.read_arff(path)\n\t\n\treturn data","def macro_func(macro_name, arg_string, body, is_block, environ):\n global macros_set_up\n args, kwargs = parse_args(arg_string)\n if macro_name == 'intro' and body:\n return intro_tag(body)\n if not macros_set_up:\n app = get_application()\n for extension in app.markup_extensions:\n macros[extension.name] = make_macro(extension)\n macros_set_up = True\n if macro_name in macros:\n return macros[macro_name](body, args, kwargs, is_block, environ)","def __initMacroActions(self):\n self.macroActGrp = createActionGroup(self)\n\n self.macroStartRecAct = E5Action(\n QCoreApplication.translate(\n 'ViewManager', 'Start Macro Recording'),\n QCoreApplication.translate(\n 'ViewManager', 'S&tart Macro Recording'),\n 0, 0, self.macroActGrp, 'vm_macro_start_recording')\n self.macroStartRecAct.setStatusTip(QCoreApplication.translate(\n 'ViewManager', 'Start Macro Recording'))\n self.macroStartRecAct.setWhatsThis(QCoreApplication.translate(\n 'ViewManager',\n \"\"\"<b>Start Macro Recording</b>\"\"\"\n \"\"\"<p>Start recording editor commands into a new macro.</p>\"\"\"\n ))\n self.macroStartRecAct.triggered.connect(self.__macroStartRecording)\n self.macroActions.append(self.macroStartRecAct)\n \n self.macroStopRecAct = E5Action(\n QCoreApplication.translate('ViewManager', 'Stop Macro Recording'),\n QCoreApplication.translate('ViewManager', 'Sto&p Macro Recording'),\n 0, 0, self.macroActGrp, 'vm_macro_stop_recording')\n self.macroStopRecAct.setStatusTip(QCoreApplication.translate(\n 'ViewManager', 'Stop Macro Recording'))\n self.macroStopRecAct.setWhatsThis(QCoreApplication.translate(\n 'ViewManager',\n \"\"\"<b>Stop Macro Recording</b>\"\"\"\n \"\"\"<p>Stop recording editor commands into a new macro.</p>\"\"\"\n ))\n self.macroStopRecAct.triggered.connect(self.__macroStopRecording)\n self.macroActions.append(self.macroStopRecAct)\n \n self.macroRunAct = E5Action(\n QCoreApplication.translate('ViewManager', 'Run Macro'),\n QCoreApplication.translate('ViewManager', '&Run Macro'),\n 0, 0, self.macroActGrp, 'vm_macro_run')\n self.macroRunAct.setStatusTip(QCoreApplication.translate(\n 'ViewManager', 'Run Macro'))\n self.macroRunAct.setWhatsThis(QCoreApplication.translate(\n 'ViewManager',\n \"\"\"<b>Run Macro</b>\"\"\"\n \"\"\"<p>Run a previously recorded editor macro.</p>\"\"\"\n ))\n self.macroRunAct.triggered.connect(self.__macroRun)\n self.macroActions.append(self.macroRunAct)\n \n self.macroDeleteAct = E5Action(\n QCoreApplication.translate('ViewManager', 'Delete Macro'),\n QCoreApplication.translate('ViewManager', '&Delete Macro'),\n 0, 0, self.macroActGrp, 'vm_macro_delete')\n self.macroDeleteAct.setStatusTip(QCoreApplication.translate(\n 'ViewManager', 'Delete Macro'))\n self.macroDeleteAct.setWhatsThis(QCoreApplication.translate(\n 'ViewManager',\n \"\"\"<b>Delete Macro</b>\"\"\"\n \"\"\"<p>Delete a previously recorded editor macro.</p>\"\"\"\n ))\n self.macroDeleteAct.triggered.connect(self.__macroDelete)\n self.macroActions.append(self.macroDeleteAct)\n \n self.macroLoadAct = E5Action(\n QCoreApplication.translate('ViewManager', 'Load Macro'),\n QCoreApplication.translate('ViewManager', '&Load Macro'),\n 0, 0, self.macroActGrp, 'vm_macro_load')\n self.macroLoadAct.setStatusTip(QCoreApplication.translate(\n 'ViewManager', 'Load Macro'))\n self.macroLoadAct.setWhatsThis(QCoreApplication.translate(\n 'ViewManager',\n \"\"\"<b>Load Macro</b>\"\"\"\n \"\"\"<p>Load an editor macro from a file.</p>\"\"\"\n ))\n self.macroLoadAct.triggered.connect(self.__macroLoad)\n self.macroActions.append(self.macroLoadAct)\n \n self.macroSaveAct = E5Action(\n QCoreApplication.translate('ViewManager', 'Save Macro'),\n QCoreApplication.translate('ViewManager', '&Save Macro'),\n 0, 0, self.macroActGrp, 'vm_macro_save')\n self.macroSaveAct.setStatusTip(QCoreApplication.translate(\n 'ViewManager', 'Save Macro'))\n self.macroSaveAct.setWhatsThis(QCoreApplication.translate(\n 'ViewManager',\n \"\"\"<b>Save Macro</b>\"\"\"\n \"\"\"<p>Save a previously recorded editor macro to a file.</p>\"\"\"\n ))\n self.macroSaveAct.triggered.connect(self.__macroSave)\n self.macroActions.append(self.macroSaveAct)\n \n self.macroActGrp.setEnabled(False)","def HandlePredefines(predefines, app):\n selecteddefine = None\n if predefines == \"archive\":\n selecteddefine = types_archive\n elif predefines == \"text\":\n selecteddefine = types_text\n elif predefines == \"audio\":\n selecteddefine = types_audio\n # Set types if app is defined\n if app:\n Mime_Set_All(selecteddefine, app)\n # Query types\n Mime_Query_All(selecteddefine)","def test_reads_photomodeler_sigmas_from_report() -> None:\n imgsz = (4288, 2848)\n sigmas = {\n \"focal\": 0.001,\n \"xp\": 0.001,\n \"yp\": 7.1e-004,\n \"fw\": 1.7e-004,\n \"fh\": 0.0,\n \"k1\": 2.0e-007,\n \"k2\": 1.2e-009,\n \"k3\": 0.0,\n \"p1\": 3.5e-007,\n \"p2\": 0.0,\n }\n path = os.path.join(\"tests\", \"CalibrationReport.txt\")\n xcam_auto = PhotoModeler.from_report(path, imgsz=imgsz, sigmas=True)\n xcam_manual = PhotoModeler(imgsz=imgsz, **sigmas)\n assert vars(xcam_auto) == vars(xcam_manual)","def readAMBERTop(self, phys, filename):\r\n\r\n def skipLine(data):\r\n nl = data.index('\\n')\r\n return data[nl+1:len(data)]\r\n\r\n def jumpTo(data, target):\r\n fp = data.index(target)\r\n return data[fp:len(data)]\r\n\r\n def readRemove(data, size):\r\n retval = data[0:size-1]\r\n return data[size:len(data)]\r\n\r\n def getInteger(data):\r\n pos = 0\r\n retval = \"\"\r\n while (not data[pos].isdigit()):\r\n pos = pos + 1\r\n while (data[pos].isdigit()):\r\n retval = retval + data[pos]\r\n pos = pos + 1\r\n data = data[pos:len(data)]\r\n return int(retval), data\r\n\r\n def parse(data, arr, str, count, dtype, tupsize=1):\r\n data = jumpTo(data, \"%FLAG \"+str)\r\n data = jumpTo(data, \"%FORMAT\")\r\n numPerLine, data = getInteger(data)\r\n fieldsize, data = getInteger(data)\r\n data = skipLine(data) \r\n \r\n arr2 = []\r\n numread = 0\r\n for j in range(0, (tupsize*count-1) / numPerLine + 1):\r\n for i in range(0, numPerLine):\r\n if (tupsize == 1):\r\n arr.append(dtype(data[0:fieldsize].strip()))\r\n else:\r\n arr2.append(dtype(data[0:fieldsize].strip()))\r\n if (len(arr2) == tupsize):\r\n arr.append(arr2)\r\n arr2 = []\r\n numread += 1\r\n data = data[fieldsize:len(data)]\r\n if (numread == tupsize*count):\r\n break\r\n data = skipLine(data) \r\n return data\r\n\r\n def scan(data, str):\r\n return (data.count(str) != 0)\r\n\r\n\r\n f = open(filename, 'r')\r\n data = f.read()\r\n\r\n # First Line: VERSION ...\r\n data = skipLine(data)\r\n\r\n # Go To: %FLAG POINTERS\r\n data = jumpTo(data, '%FLAG POINTERS')\r\n\r\n data = jumpTo(data, '%FORMAT')\r\n numPerLine, data = getInteger(data)\r\n fieldsize, data = getInteger(data)\r\n data = skipLine(data)\r\n \r\n temp = []\r\n numread = 0\r\n for j in range(0, 31 / numPerLine + 1):\r\n for i in range(0, numPerLine):\r\n temp.append(int(data[0:8]))\r\n data = data[8:len(data)]\r\n numread += 1\r\n if (numread == 31):\r\n break\r\n data = skipLine(data)\r\n \r\n [natoms, ntypes, nbonh, mbona, ntheth, mtheta, nphih, mphia, nhparm, nparm, nnb, nres, nbona, ntheta, nphia, numbnd, numang, nptra, natyp, nphb, ifpert, nbper, ngper, ndper, mbper, mgper, mdper, ifbox, nmxrs, ifcap, numextra] = temp \r\n\r\n\r\n #################################################\r\n # Read AtomTypes\r\n atomnames = []\r\n charges = []\r\n masses = []\r\n atindex = []\r\n exclusions = []\r\n nparams = []\r\n reslabels = []\r\n respointers = []\r\n forceconstants = [[], [], []] # bond, angle, dihedral\r\n equilvals = [[], [], [[], []]] # bond, angle, dihedral\r\n scee_scales = []\r\n scnb_scales = []\r\n solty = []\r\n lj_acoef = []\r\n lj_bcoef = []\r\n\r\n data = parse(data, atomnames, \"ATOM_NAME\", natoms, str) \r\n data = parse(data, charges, \"CHARGE\", natoms, float)\r\n data = parse(data, masses, \"MASS\", natoms, float)\r\n data = parse(data, atindex, \"ATOM_TYPE_INDEX\", natoms, int)\r\n data = parse(data, exclusions, \"NUMBER_EXCLUDED_ATOMS\", natoms, int)\r\n data = parse(data, nparams, \"NONBONDED_PARM_INDEX\", ntypes*ntypes, int)\r\n data = parse(data, reslabels, \"RESIDUE_LABEL\", nres, str)\r\n data = parse(data, respointers, \"RESIDUE_POINTER\", nres, int)\r\n data = parse(data, forceconstants[0], \"BOND_FORCE_CONSTANT\", numbnd, float)\r\n data = parse(data, equilvals[0], \"BOND_EQUIL_VALUE\", numbnd, float)\r\n data = parse(data, forceconstants[1], \"ANGLE_FORCE_CONSTANT\", numang, float)\r\n data = parse(data, equilvals[1], \"ANGLE_EQUIL_VALUE\", numang, float)\r\n data = parse(data, forceconstants[2], \"DIHEDRAL_FORCE_CONSTANT\", nptra, float)\r\n data = parse(data, equilvals[2][0], \"DIHEDRAL_PERIODICITY\", nptra, float)\r\n data = parse(data, equilvals[2][1], \"DIHEDRAL_PHASE\", nptra, float)\r\n if (scan(data, \"SCEE_SCALE_FACTOR\")):\r\n data = parse(data, scee_scales, \"SCEE_SCALE_FACTORS\", nptra, float)\r\n else:\r\n for i in range(0, nptra):\r\n scee_scales.append(1.2) # Default \r\n if (scan(data, \"SCNB_SCALE_FACTOR\")):\r\n data = parse(data, scnb_scales, \"SCNB_SCALE_FACTORS\", nptra, float)\r\n else:\r\n for i in range(0, nptra):\r\n scnb_scales.append(2.0) # Default \r\n\r\n data = parse(data, solty, \"SOLTY\", natyp, float)\r\n data = parse(data, lj_acoef, \"LENNARD_JONES_ACOEF\", ntypes*(ntypes+1)/2, float)\r\n data = parse(data, lj_bcoef, \"LENNARD_JONES_BCOEF\", ntypes*(ntypes+1)/2, float)\r\n\r\n\r\n ##########################################################\r\n # STRUCTURE\r\n\r\n bonds = [[], []] # With H, Without H\r\n angles = [[], []] # With H, Without H\r\n dihedrals = [[], []] # With H, Without H\r\n impropers = [[], []] # With H, Without H\r\n excluded_atoms = [] \r\n hbond_acoef = []\r\n hbond_bcoef = []\r\n hbcut = []\r\n amber_atom_types = []\r\n tree_chain = []\r\n join_array = []\r\n irotat = []\r\n radii = []\r\n screen = []\r\n\r\n data = parse(data, bonds[0], \"BONDS_INC_HYDROGEN\", nbonh, int, 3)\r\n data = parse(data, bonds[1], \"BONDS_WITHOUT_HYDROGEN\", nbona, int, 3)\r\n data = parse(data, angles[0], \"ANGLES_INC_HYDROGEN\", ntheth, int, 4)\r\n data = parse(data, angles[1], \"ANGLES_WITHOUT_HYDROGEN\", ntheta, int, 4)\r\n data = parse(data, dihedrals[0], \"DIHEDRALS_INC_HYDROGEN\", nphih, int, 5)\r\n data = parse(data, dihedrals[1], \"DIHEDRALS_WITHOUT_HYDROGEN\", nphia, int, 5)\r\n \r\n # MERGE ARRAYS - PM HANDLES THE H+\r\n final_bonds = bonds[0] + bonds[1]\r\n final_angles = angles[0] + angles[1]\r\n final_dihedrals = dihedrals[0] + dihedrals[1]\r\n final_impropers = []\r\n \r\n # CLEAN UP THE TRASH\r\n del(bonds)\r\n del(angles)\r\n del(dihedrals)\r\n \r\n\r\n # Move impropers into their own array\r\n i = 0\r\n while (i < len(final_dihedrals)):\r\n if (final_dihedrals[i][2] < 0): # 1-4 exclusions are handled by our back end\r\n final_dihedrals[i][2] *= -1\r\n if (final_dihedrals[i][3] < 0):\r\n final_dihedrals[i][3] *= -1 # Make + again\r\n final_impropers.append(final_dihedrals[i])\r\n final_dihedrals.remove(final_dihedrals[i])\r\n i -= 1\r\n i += 1\r\n\r\n # Convert charge units\r\n for i in range(0, len(charges)):\r\n charges[i] /= 18.223\r\n\r\n\r\n data = parse(data, excluded_atoms, \"EXCLUDED_ATOMS_LIST\", nnb, int)\r\n data = parse(data, hbond_acoef, \"HBOND_ACOEF\", nphb, float)\r\n data = parse(data, hbond_bcoef, \"HBOND_BCOEF\", nphb, float)\r\n data = parse(data, hbcut, \"HBCUT\", nphb, float)\r\n data = parse(data, amber_atom_types, \"AMBER_ATOM_TYPE\", natoms, str)\r\n data = parse(data, tree_chain, \"TREE_CHAIN_CLASSIFICATION\", natoms, str)\r\n data = parse(data, join_array, \"JOIN_ARRAY\", natoms, int)\r\n data = parse(data, irotat, \"IROTAT\", natoms, int)\r\n data = parse(data, radii, \"RADII\", natoms, float)\r\n data = parse(data, screen, \"SCREEN\", natoms, float)\r\n\r\n # Further process dihedrals and impropers\r\n # Deal with multiplicity\r\n # A bit ugly, but the fastest for now\r\n # forceconstants[2][dihedrals[0][i][4]-1], int(equilvals[2][0][dihedrals[0][i][4]-1]), equilvals[2][1][dihedrals[0][i][4]-1]\r\n\r\n mult_di = dict()\r\n mult_im = dict()\r\n for i in range(0, len(final_dihedrals)):\r\n di_id = str(final_dihedrals[i][0])+' '+str(final_dihedrals[i][1])+' '+str(final_dihedrals[i][2])+' '+str(final_dihedrals[i][3])\r\n if (not mult_di.has_key(di_id)):\r\n mult_di[di_id] = [1, False, [forceconstants[2][final_dihedrals[i][4]-1]], [int(equilvals[2][0][final_dihedrals[i][4]-1])], [equilvals[2][1][final_dihedrals[i][4]-1]]]\r\n else:\r\n mult_di[di_id][0] += 1\r\n mult_di[di_id][2].append(forceconstants[2][final_dihedrals[i][4]-1])\r\n mult_di[di_id][3].append(int(equilvals[2][0][final_dihedrals[i][4]-1]))\r\n mult_di[di_id][4].append(equilvals[2][1][final_dihedrals[i][4]-1])\r\n \r\n for i in range(0, len(final_impropers)):\r\n im_id = str(final_impropers[i][0])+' '+str(final_impropers[i][1])+' '+str(final_impropers[i][2])+' '+str(final_impropers[i][3])\r\n if (not mult_im.has_key(di_id)):\r\n mult_im[im_id] = [1, False, [forceconstants[2][final_impropers[i][4]-1]], [int(equilvals[2][0][final_impropers[i][4]-1])], [equilvals[2][1][final_impropers[i][4]-1]]]\r\n else:\r\n mult_im[im_id][0] += 1\r\n mult_im[im_id][2].append(forceconstants[2][final_impropers[i][4]-1])\r\n mult_im[im_id][3].append(int(equilvals[2][0][final_impropers[i][4]-1]))\r\n mult_im[im_id][4].append(equilvals[2][1][final_impropers[i][4]-1])\r\n\r\n\r\n\r\n \r\n #[natoms, ntypes, nbonh, mbona, ntheth, mtheta, nphih, mphia, nhparm, nparm, nnb, nres, nbona, ntheta, nphia, numbnd, numang, nptra, natyp, nphb, ifpert, nbper, ngper, ndper, mbper, mgper, mdper, ifbox, nmxrs, ifcap, numextra] = temp \r\n #phys.myPSF.createAll(natoms, nbonh+mbona, ntheth+mtheta,\r\n # len(dihedrals[0])+len(dihedrals[1]),\r\n # len(impropers[0])+len(impropers[1]),\r\n # 0, 0, 0, 0)\r\n \r\n # Add atoms\r\n curres = 1\r\n for i in range(0, natoms):\r\n phys.myPSF.addAtom(i, 'SIM', curres, reslabels[curres-1],\r\n atomnames[i], atomnames[i], charges[i],\r\n masses[i]) \r\n if (curres != nres and i >= respointers[curres]):\r\n curres += 1\r\n\r\n # Add bonds\r\n for i in range(0, nbonh+nbona):\r\n phys.myPSF.addBond(i+1, final_bonds[i][0]/3+1, final_bonds[i][1]/3+1)\r\n phys.myPAR.addBond(i+1, atomnames[final_bonds[i][0]/3], atomnames[final_bonds[i][1]/3], forceconstants[0][final_bonds[i][2]/3], equilvals[0][final_bonds[i][2]/3])\r\n \r\n # Add angles\r\n for i in range(0, ntheth+ntheta):\r\n phys.myPSF.addAngle(i+1, final_angles[i][0]/3+1, final_angles[i][1]/3+1, final_angles[i][2]/3+1)\r\n phys.myPAR.addAngle(i+1, atomnames[final_angles[i][0]/3], atomnames[final_angles[i][1]/3], atomnames[final_angles[i][2]/3], forceconstants[1][final_angles[i][3]/3], equilvals[1][final_angles[i][3]/3])\r\n \r\n # Add dihedrals\r\n for i in range(0, len(final_dihedrals)):\r\n di_id = str(final_dihedrals[i][0])+' '+str(final_dihedrals[i][1])+' '+str(final_dihedrals[i][2])+' '+str(final_dihedrals[i][3])\r\n mult = mult_di[di_id][0]\r\n checked = mult_di[di_id][1]\r\n print di_id, \" \", mult\r\n if (not checked):\r\n if (mult == 1):\r\n phys.myPSF.addDihedral(i+1, final_dihedrals[i][0]/3+1, final_dihedrals[i][1]/3+1, int(numpy.abs(final_dihedrals[i][2]))/3+1, final_dihedrals[i][3]/3+1)\r\n phys.myPAR.addDihedral(i+1, atomnames[final_dihedrals[i][0]/3], atomnames[final_dihedrals[i][1]/3], atomnames[int(numpy.abs(final_dihedrals[i][2]))/3], atomnames[final_dihedrals[i][3]/3], forceconstants[2][final_dihedrals[i][4]-1], int(equilvals[2][0][final_dihedrals[i][4]-1]), equilvals[2][1][final_dihedrals[i][4]-1])\r\n else:\r\n mult_di[di_id][1] = True\r\n # Add dihedral with the appropriate multiplicity\r\n # Force constants, periodicity and phase shifts are in [2], [3], and [4] respectively\r\n fcvec = PARReader.VectorOfDouble()\r\n periodvec = PARReader.VectorOfInt()\r\n phasevec = PARReader.VectorOfDouble() \r\n for j in range(0, len(mult_di[di_id][2])):\r\n fcvec.push_back(mult_di[di_id][2][j])\r\n periodvec.push_back(mult_di[di_id][3][j])\r\n phasevec.push_back(mult_di[di_id][4][j])\r\n phys.myPSF.addDihedral(i+1, final_dihedrals[i][0]/3+1, final_dihedrals[i][1]/3+1, int(numpy.abs(final_dihedrals[i][2]))/3+1, final_dihedrals[i][3]/3+1)\r\n phys.myPAR.addDihedral(i+1, atomnames[final_dihedrals[i][0]/3], atomnames[final_dihedrals[i][1]/3], atomnames[int(numpy.abs(final_dihedrals[i][2]))/3], atomnames[final_dihedrals[i][3]/3], mult, fcvec, periodvec, phasevec)\r\n \r\n\r\n\r\n\r\n for i in range(0, len(final_impropers)):\r\n im_id = str(final_impropers[i][0])+' '+str(final_impropers[i][1])+' '+str(final_impropers[i][2])+' '+str(final_impropers[i][3])\r\n mult = mult_im[im_id][0]\r\n checked = mult_im[im_id][1]\r\n print im_id, \" \", mult\r\n if (not checked):\r\n if (mult == 1):\r\n phys.myPSF.addImproper(i+1, final_impropers[i][0]/3+1, final_impropers[i][1]/3+1, int(numpy.abs(final_impropers[i][2]))/3+1, final_impropers[i][3]/3+1)\r\n phys.myPAR.addImproper(i+1, atomnames[final_impropers[i][0]/3], atomnames[final_impropers[i][1]/3], atomnames[int(numpy.abs(final_impropers[i][2]))/3], atomnames[final_impropers[i][3]/3], forceconstants[2][final_impropers[i][4]-1], int(equilvals[2][0][final_impropers[i][4]-1]), equilvals[2][1][final_impropers[i][4]-1])\r\n else:\r\n mult_im[im_id][1] = True\r\n # Add dihedral with the appropriate multiplicity\r\n # Force constants, periodicity and phase shifts are in [2], [3], and [4] respectively\r\n fcvec = PARReader.VectorOfDouble()\r\n periodvec = PARReader.VectorOfInt()\r\n phasevec = PARReader.VectorOfDouble() \r\n for j in range(0, len(mult_im[im_id][2])):\r\n fcvec.push_back(mult_im[im_id][2][j])\r\n periodvec.push_back(mult_im[im_id][3][j])\r\n phasevec.push_back(mult_im[im_id][4][j])\r\n phys.myPSF.addImproper(i+1, final_impropers[i][0]/3+1, final_impropers[i][1]/3+1, int(numpy.abs(final_impropers[i][2]))/3+1, final_impropers[i][3]/3+1)\r\n phys.myPAR.addImproper(i+1, atomnames[final_impropers[i][0]/3], atomnames[final_impropers[i][1]/3], atomnames[int(numpy.abs(final_impropers[i][2]))/3], atomnames[final_impropers[i][3]/3], mult, fcvec, periodvec, phasevec)\r\n\r\n \r\n # Need to add garbage nonbonded stuff for now\r\n for i in range(0, natoms):\r\n phys.myPAR.addNonbonded(i, atomnames[i], 1, 1, 1, 1, 1, 1)\r\n\r\n # Add VDW parameters\r\n # AMBER has the Aij and Bij already in the parameter file\r\n # This actually makes life easier.\r\n # CHARMM does not, they simply have the original sigma and epsilon.\r\n # To compensate for this, for now we will leave the nonbondeds empty in phys.myPAR\r\n # We will then access the LennardJones parameter table in Topology directly\r\n k = 0\r\n phys.myTop.resizeLennardJonesParameters(ntypes)\r\n for i in range(0, ntypes):\r\n for j in range(i, ntypes):\r\n params = GenericTopology.LennardJonesParameters(lj_acoef[k], lj_bcoef[k])\r\n k += 1\r\n phys.myTop.setLennardJonesParameters(i, j, params)\r\n \r\n phys.myPAR.readFlag = 1\r\n phys.build()","def get_parser():\n\tparser = argparse.ArgumentParser('cgm_plot_pha.py',\n\t\tformatter_class=argparse.RawDescriptionHelpFormatter,\n\t\tdescription=\"\"\"\nplot pha spectrum from an event fitsfile.\n\t\t\"\"\"\n\t\t)\n\tversion = '%(prog)s ' + __version__\n\tparser.add_argument('--version', '-v', action='version', version=version,\n\t\thelp='show version of this command.')\n\tparser.add_argument('input_evtfits', type=str, \n\t\thelp='input fits-format event file.')\n\tparser.add_argument('--pha_min', type=int, default=None,\n\t\thelp='pha_min')\t\n\tparser.add_argument('--pha_max', type=int, default=None,\n\t\thelp='pha_max')\t\n\tparser.add_argument('--tbin', type=float, default=None,\n\t\thelp='tbin')\n\tparser.add_argument('--threshold', type=float, default=None,\n\t\thelp='threshold')\t\t\t\t\t\t\n\treturn parser","def function_macro(self, platform, stack):\n initial_pos = self.pos\n try:\n identifier = self.match_type(Identifier)\n if identifier in stack:\n raise ParseError('Cannot expand token')\n\n self.match_value(Punctuator, \"(\")\n args = self.__arg_list()\n self.match_value(Punctuator, \")\")\n except ParseError:\n self.pos = initial_pos\n raise ParseError(\"Not a function-like macro.\")\n\n macro = platform.get_macro(str(identifier))\n if not macro:\n raise ParseError(\"Not a function-like macro.\")\n\n # Argument pre-scan\n # Macro arguments are macro-expanded before substitution\n expanded_args = [MacroExpander(arg).expand(platform) for arg in args]\n\n # Combine variadic arguments into one, separated by commas\n va_args = None\n if macro.is_variadic():\n va_args = util.interleave(expanded_args[len(macro.args) - 1:],\n Punctuator(\"EXPANSION\", -1, False, \",\"))\n va_args = va_args[:-1] # Remove final comma\n\n # Substitute each occurrence of an argument in the expansion\n substituted_tokens = []\n for token in macro.expansion:\n\n substitution = []\n\n # If a token matches an argument, it is substituted;\n # otherwise it passes through\n try:\n substitution = expanded_args[macro.args.index(token.token)]\n except (ValueError, ParseError):\n substitution = token\n\n # If a token matches the variable argument, substitute\n # precomputed va_args\n if macro.is_variadic() and token.token == macro.variable_argument() and va_args:\n\n # Whether the token was preceded by whitespace should be\n # tracked through substitution\n for t in va_args[0]:\n t.prev_white = token.prev_white\n substitution = va_args\n\n self.grow_token_list(substituted_tokens, substitution)\n\n # Check the expansion for macros to expand\n stack.push(identifier)\n expansion = MacroExpander(substituted_tokens).expand(platform, stack)\n stack.pop()\n return expansion","def _parse_preset(self, xmldata):\r\n\r\n raise NotImplementedError","def pre_processor(self):","def generate_parser():\n description = \"%(prog)s -- Data handling, normalization, manipulation, and plotting for HiC and 5C experimental data\"\n epilog = \"For command line options of each command, type: %(prog)s <COMMAND> -h\"\n parser = ap.ArgumentParser(description=description, epilog=epilog)\n parser.add_argument(\"--version\", action=\"version\", version=\"%(prog)s %(version_num)s\" % {'prog':parser.prog, 'version_num':VERSION})\n subparsers = parser.add_subparsers(dest='subcommand')\n\n add_connect_subparser(subparsers)\n add_fragments_subparser(subparsers)\n add_fivecdataset_subparser(subparsers)\n add_fivecproject_subparser(subparsers)\n add_fivecnormalize_subparser(subparsers)\n add_complete_fivec_subparser(subparsers)\n add_fivec_heatmap_subparser(subparsers)\n add_fivec_interval_subparser(subparsers)\n add_fivec_combine_replicates_subparser(subparsers)\n add_fends_subparser(subparsers)\n add_hicdataset_subparser(subparsers)\n add_hicproject_subparser(subparsers)\n add_hicnormalize_subparser(subparsers)\n add_complete_hic_subparser(subparsers)\n add_hic_heatmap_subparser(subparsers)\n add_hic_mrheatmap_subparser(subparsers)\n add_hic_interval_subparser(subparsers)\n add_hic_combine_replicates_subparser(subparsers)\n add_quasar_subparser(subparsers)\n return parser","def spec_parser(subparser):\n parser = subparser.add_parser('spec',\\\n help='will print information about a spectral file (also SELAFIN),'\\\n 'such as frequencies, periodes, etc.')\n parser = add_arg(parser, 'xvars')\n parser = add_arg(parser, 'core')\n parser = add_arg(parser, 'time')\n parser = add_arg(parser, 'accuracy')\n parser.add_argument(\"input_files\", metavar='Spectrum SELAFIN file',\n nargs=\"+\")\n\n return subparser","def arg_parser(self):\n print\n\n parser = argparse.ArgumentParser()\n subparsers = parser.add_subparsers()\n\n status = subparsers.add_parser('status', help=self.viewer.status.__doc__)\n status.set_defaults(func=self.viewer.status)\n\n view_catalog = subparsers.add_parser('catalog', help=self.viewer.view_full_catalog.__doc__)\n view_catalog.set_defaults(func=self.viewer.view_full_catalog)\n\n view_tags = subparsers.add_parser('tags', help=self.viewer.view_all_tags.__doc__)\n view_tags.add_argument('-a', '--alpha', action='store_true', help=\"List tags alphabetically\")\n view_tags.set_defaults(func=self.viewer.view_all_tags)\n\n search = subparsers.add_parser('search', help=self.viewer.search_tags.__doc__)\n search.add_argument('-t', '--tags', nargs='+', required=True, help=\"Tags to search for\")\n search.add_argument('-o', action='store_true', help=\"Search using 'or' logic ('and' logic by default)\")\n search.set_defaults(func=self.viewer.search_tags) \n\n add_file = subparsers.add_parser('addfile', help=self.editor.add_files.__doc__)\n add_file.add_argument('filename', help=\"Name of file to add catalog\")\n add_file.set_defaults(func=self.editor.add_files)\n\n add_tags = subparsers.add_parser('addtags', help=self.editor.add_tag.__doc__)\n add_tags.add_argument('filename', help=\"Name of file to add catalog\")\n add_tags.add_argument('-t', '--tags', nargs='+', help=\"Tags to add to catalog\")\n add_tags.set_defaults(func=self.editor.add_tag)\n\n edit_entry = subparsers.add_parser('edit', help=self.editor.edit_entry.__doc__)\n edit_entry.add_argument('filename', help=\"Name of file to add catalog\")\n edit_entry.set_defaults(func=self.editor.edit_entry)\n\n clean_catalog = subparsers.add_parser('clean', help=self.editor.clean_catalog.__doc__)\n clean_catalog.add_argument('-t', '--tags', nargs='+', help=\"Tags to be deleted from catalog entirely\")\n clean_catalog.set_defaults(func=self.editor.clean_catalog)\n\n delete_entry = subparsers.add_parser('delete', help=self.editor.delete_entry.__doc__)\n delete_entry.add_argument('filename', help=\"File from which to delete specified tags\")\n delete_entry.add_argument('-t', '--tags', nargs='+', help=\"Tags to be deleted\")\n delete_entry.set_defaults(func=self.editor.delete_entry)\n\n merge_tags = subparsers.add_parser('merge', help=self.editor.merge_tags.__doc__)\n merge_tags.add_argument('--source', required=True, help=\"File from which tags are being taken\")\n merge_tags.add_argument('--dest', required=True, help=\"Destination file to which tags from --source are added\")\n merge_tags.set_defaults(func=self.editor.merge_tags)\n\n \n args = parser.parse_args()\n\n args.func(args)","def parseArguments():\n # Create argument parser\n #parser = argparse.ArgumentParser()\n parser = ArgumentParser()\n\n\n # Positional mandatory arguments\n parser.add_argument(\"input\", nargs='+',help=\"Input Image with .fits ending. A folder or multiple Images also work\", type=str)\n parser.add_argument(\"-c\", \"--catalog\", help=\"Catalog to use for position reference ('PS', '2MASS' or 'GAIA') or name of local file\", type=str, default=\"PS\")\n\n parser.add_argument(\"-s\", \"--save_images\", help=\"Set True to create _image_before.pdf and _image_after.pdf\", type=bool, default=False)\n parser.add_argument(\"-p\", \"--images\", help=\"Set 0 to not create the plots.\", type=int, default=1)\n\n parser.add_argument(\"-v\", \"--verbose\", help=\"More console output about what is happening. Helpfull for debugging.\", type=bool, default=False)\n parser.add_argument(\"-silent\", \"--silent\", help=\"Almost no console output. Use when running many files. turns verbose off, turns plots off, turns ignore warning on. \", type=bool, default=False)\n\n\n\n parser.add_argument(\"-w\", \"--ignore_warnings\", help=\"Set False to see all Warnings about the header if there is problems. Default is to ignore most warnings.\", type=bool, default=True)\n\n parser.add_argument(\"-ra\", \"--ra\", help=\"Set ra by hand in degrees. Should not be necessary if the info is in the fits header.\", type=float, default=None)\n parser.add_argument(\"-dec\", \"--dec\", help=\"Set dec by hand in degrees. Should not be necessary if the info is in the fits header.\", type=float, default=None)\n\n parser.add_argument(\"-proj1\", \"--projection_ra\", help=\"Set the projection by hand. Should not be necessary if the info is in the fits header. example: -proj1 RA---TAN -proj2 DEC--TAN\", type=str, default=None)\n parser.add_argument(\"-proj2\", \"--projection_dec\", help=\"Set the projection by hand. Should not be necessary if the info is in the fits header. example: -proj1 RA---TAN -proj2 DEC--TAN\", type=str, default=None)\n\n\n parser.add_argument(\"-rot_scale\", \"--rotation_scaling\", help=\"By default rotation and scaling is determined. If wcs already contains this info and the fit fails you can try deactivating this part by setting it to 0\", type=int, default=1)\n parser.add_argument(\"-xy_trafo\", \"--xy_transformation\", help=\"By default the x and y offset is determined. If wcs already contains this info and the fit fails you can try deactivating this part by setting it to 0\", type=int, default=1)\n parser.add_argument(\"-fine\", \"--fine_transformation\", help=\"By default a fine transformation is applied in the end. You can try deactivating this part by setting it to 0\", type=int, default=1)\n\n parser.add_argument(\"-vignette\", \"--vignette\", help=\"Do not use corner of the image. Only use the data in a circle around the center with certain radius. Default: not used. Set to 1 for circle that touches the sides. Less to cut off more\", type=float, default=3)\n parser.add_argument(\"-vignette_rec\", \"--vignette_rectangular\", help=\"Do not use corner of the image. Cutoff 1- <value> on each side of the image. Default: not used. 1 uses the full image, 0.9 cuts 10%% on each side\", type=float, default=1.)\n\n parser.add_argument(\"-cutout\", \"--cutout\", help=\"Cutout bad recangle from Image. Specify corners in pixel as -cutout xstart xend ystart yend. You can give multiple cutouts \", nargs='+',action=\"append\", type=int)\n\n parser.add_argument(\"-ignore_header_rot\", \"--ignore_header_rot\", help=\"Set to 0 to ignore rotation information contained in header\", type=int, default=0)\n\n parser.add_argument(\"-r\", \"--radius\", help=\"Change the download radius for how many catalog objects should be downloaded in arcmin. \", type=float, default=-1)\n parser.add_argument(\"-save_bad_result\", \"--save_bad_result\", help=\"Save result even when it is considered bad by setting this to 1. By default bad results will not be saved\", type=int, default=0)\n\n parser.add_argument(\"-sigma_threshold_for_source_detection\", \"--sigma_threshold_for_source_detection\", help=\"Sigma threshold for source detection on the image\", type=float, default=5)\n parser.add_argument(\"-seeing\", \"--seeing\", help=\"Average FWHM of sources. Default 4px\", type=float, default=4)\n\n parser.add_argument(\"-high_res\", \"--high_resolution\", help=\"Set true to indicate higher resolution image like HST to allow larger steps for fine transformation. Default False for smaller telescopes\", type=bool, default=False)\n parser.add_argument(\"-hdul_idx\", \"--hdul_idx\", help=\"Index of the image data in the fits file. Default 0\", type=int, default=0)\n parser.add_argument(\"-filename_for_sources\", \"--filename_for_sources\", help=\"Save the sky positions of the sources to file to calibrate another image with it. Set to the filename without extension. Default: not used\", type=str, default=None)\n\n # Print version\n parser.add_argument(\"--version\", action=\"version\", version='%%(prog)s - Version 1.5') #\n #changelog\n #version 0.0 proof of concept\n #version 0.1 alpha version\n #version 1.0 first public version\n #version 1.2 included option to not show images\n #version 1.3 improved support for high resolution images\n #version 1.4 bugfixes and ability to calibrate based on another image\n #version 1.5 added compatibility with photutils v1.4\n\n # Parse arguments\n args = parser.parse_args()\n\n return args","def parse_args(argv=None):\n description = textwrap.dedent('''Panacea - \n \n This script does ... (Fill in Later)\n \n ''')\n \n parser = ap.ArgumentParser(description=description,\n formatter_class=ap.RawTextHelpFormatter)\n \n parser.add_argument(\"-rt\",\"--reduce_twi\", \n help='''Reduce Twighlight frames for calibration''',\n action=\"count\", default=0)\n\n parser.add_argument(\"-c\",\"--custom\", \n help='''Execute custom function''',\n action=\"count\", default=0)\n\n parser.add_argument(\"-s\",\"--save_sci_fibers\", \n help='''Save Science Fibers''',\n action=\"count\", default=0)\n\n parser.add_argument(\"-sa\",\"--save_sci_amplifier\", \n help='''Save Science Amplifier''',\n action=\"count\", default=0)\n\n parser.add_argument(\"-rs\",\"--reduce_sci\", \n help='''Reduce Science frames''',\n action=\"count\", default=0)\n\n parser.add_argument(\"-mb\",\"--make_masterbias\", \n help='''Make MasterBias frames''',\n action=\"count\", default=0)\n \n parser.add_argument(\"-md\",\"--make_masterdark\", \n help='''Make MasterDark frames''',\n action=\"count\", default=0)\n \n parser.add_argument(\"-uos\",\"--use_other_sky\", \n help='''Use another frame for the sky_spectrum''',\n action=\"count\", default=0)\n\n parser.add_argument(\"-at\",\"--adjust_trace\", \n help='''Adjust trace using science frame.''',\n action=\"count\", default=0)\n \n parser.add_argument(\"-rff\",\"--refit_fiber_to_fiber\", \n help='''Using the sky spectrum, refit the fiber to\n fiber.''',\n action=\"count\", default=0)\n\n parser.add_argument(\"-utr\",\"--use_trace_ref\", \n help='''Using trace reference files to recover all\n fibers.''',\n action=\"count\", default=0)\n \n parser.add_argument(\"--fiber_date\", nargs='?', type=str, \n help='''Date for Fiber_Locations''', default = None) \n\n parser.add_argument(\"-p\",\"--pixelflats\", \n help='''Turn off using pixel flats.''',\n action=\"count\", default=0)\n\n parser.add_argument(\"-sfs\",\"--start_from_scratch\", \n help='''Re-fiberextract, sky-subtract, cosmic ray reject.''',\n action=\"count\", default=0)\n \n parser.add_argument(\"--specid\", nargs='?', type=str, \n help='''List of SPECID's for processing. [REQUIRED]\n Ex: \"020,008\".''', default = None)\n\n parser.add_argument(\"--instr\", nargs='?', type=str, \n help='''Instrument to process. \n Default: \"virus\"\n Ex: \"camra\" for lab data,\n \"lrs2\" for lrs2.''', default = \"virus\")\n \n parser.add_argument(\"--instr_side\", nargs='?', type=str, \n help='''Instrument side to process. \n Default: \"blue\"\n Ex: \"blue\" for LRS2B,\n \"red\" for LRS2R.''', default = \"blue\")\n\n parser.add_argument(\"--output\", nargs='?', type=str, \n help='''Output Directory\n Default: \\\"reductions\"''', \n default=\"reductions\")\n \n parser.add_argument(\"--rootdir\", nargs='?', type=str, \n help='''Root Directory\n Default: \\\"/work/03946/hetdex/maverick\\\"''', \n default=\"/work/03946/hetdex/maverick\")\n\n parser.add_argument(\"--configdir\", nargs='?', type=str, \n help='''Config Directory\n Default: \\\"/work/03946/hetdex/maverick/virus_config\\\"''', \n default=\"/work/03946/hetdex/maverick/virus_config\")\n\n parser.add_argument(\"--biasdir\", type=str,\n help='''Bias Library\n Default: \\\"/work/03946/hetdex/maverick/virus_config/lib_bias\\\"''', \n default=\"/work/03946/hetdex/maverick/virus_config/lib_bias\")\n \n parser.add_argument(\"--darkdir\", type=str,\n help='''Dark Library\n Default: \\\"/work/03946/hetdex/maverick/virus_config/lib_dark\\\"''',\n default=\"/work/03946/hetdex/maverick/virus_config/lib_dark\")\n \n parser.add_argument(\"-sd\",\"--scidir_date\", nargs='?', type=str,\n help='''Science Directory Date. [REQUIRED, if --reduce_sci]\n Ex: \\\"20160412\\\"''', default=None)\n\n parser.add_argument(\"-so\",\"--scidir_obsid\", nargs='?', type=str,\n help='''Science Directory ObsID. [REQUIRED, if --reduce_sci]\n Ex: \\\"3\\\" or \\\"102\\\"''', default=None)\n \n parser.add_argument(\"-se\",\"--scidir_expnum\", nargs='?', type=str,\n help='''Science Directory exposure number.\n Ex: \\\"1\\\" or \\\"05\\\"''', default=None) \n\n parser.add_argument(\"-bd\",\"--biadir_date\", nargs='?', type=str,\n help='''Science Directory Date. [REQUIRED, if --reduce_sci]\n Ex: \\\"20160412\\\"''', default=None)\n\n parser.add_argument(\"-bo\",\"--biadir_obsid\", nargs='?', type=str,\n help='''Science Directory ObsID. [REQUIRED, if --reduce_sci]\n Ex: \\\"3\\\" or \\\"102\\\"''', default=None)\n \n parser.add_argument(\"-be\",\"--biadir_expnum\", nargs='?', type=str,\n help='''Science Directory exposure number.\n Ex: \\\"1\\\" or \\\"05\\\"''', default=None) \n\n parser.add_argument(\"--bias_outfolder\", nargs='?', type=str, \n help='''Output folder name for bias library\n Default: \\\"default\"''', \n default=\"default\")\n\n parser.add_argument(\"-dd\",\"--drkdir_date\", nargs='?', type=str,\n help='''Science Directory Date. [REQUIRED, if --reduce_sci]\n Ex: \\\"20160412\\\"''', default=None)\n\n parser.add_argument(\"-do\",\"--drkdir_obsid\", nargs='?', type=str,\n help='''Science Directory ObsID. [REQUIRED, if --reduce_sci]\n Ex: \\\"3\\\" or \\\"102\\\"''', default=None)\n \n parser.add_argument(\"-de\",\"--drkdir_expnum\", nargs='?', type=str,\n help='''Science Directory exposure number.\n Ex: \\\"1\\\" or \\\"05\\\"''', default=None) \n\n parser.add_argument(\"--dark_outfolder\", nargs='?', type=str, \n help='''Output folder name for dark library\n Default: \\\"default\"''', \n default=\"default\")\n\n parser.add_argument(\"-td\",\"--twidir_date\", nargs='?', type=str,\n help='''Twi Directory Date. [REQUIRED, if --reduce_twi]\n Ex: \\\"20160412\\\"''', default=None)\n\n parser.add_argument(\"-to\",\"--twidir_obsid\", nargs='?', type=str,\n help='''Twi Directory ObsID. [REQUIRED, if --reduce_twi]\n Ex: \\\"3\\\" or \\\"102\\\"''', default=None)\n \n parser.add_argument(\"-te\",\"--twidir_expnum\", nargs='?', type=str,\n help='''Twi Directory exposure number.\n Ex: \\\"1\\\" or \\\"05\\\"''', default=None) \n\n parser.add_argument(\"-skd\",\"--skydir_date\", nargs='?', type=str,\n help='''Sky Directory Date. [REQUIRED, --use_other_sky]\n Ex: \\\"20160412\\\"''', default=None)\n\n parser.add_argument(\"-sko\",\"--skydir_obsid\", nargs='?', type=str,\n help='''Sky Directory ObsID. [REQUIRED, --use_other_sky]\n Ex: \\\"3\\\" or \\\"102\\\"''', default=None)\n \n parser.add_argument(\"-ske\",\"--skydir_expnum\", nargs='?', type=str,\n help='''Sky Directory exposure number.\n Ex: \\\"1\\\" or \\\"05\\\"''', default=None) \n\n parser.add_argument(\"-d\",\"--debug\", help='''Debug.''',\n action=\"count\", default=0)\n \n args = parser.parse_args(args=argv)\n\n # Check that the arguments are filled\n if args.specid:\n args.specid = args.specid.replace(\" \", \"\").split(',')\n else:\n msg = 'No SPECID was provided.'\n parser.error(msg) \n \n\n \n if args.instr.lower() == 'virus':\n instr = 'virus_'\n if args.instr.lower() == 'lrs2':\n if args.instr_side.lower() == 'blue':\n instr = 'lrs2b_'\n if args.instr.lower() == 'lrs2':\n if args.instr_side.lower() == 'red':\n instr = 'lrs2r_'\n if args.instr.lower() == 'virusw':\n instr = 'virusw_' \n for con in config.config_dict:\n setattr(args, con, getattr(config, instr+config.config_dict[con]))\n\n\n labels = ['dir_date', 'dir_obsid', 'dir_expnum']\n observations=[]\n args.check_if_twi_exists=False\n if args.reduce_sci:\n observations.append('sci')\n if not args.reduce_twi:\n observations.append('twi')\n args.check_if_twi_exists = True\n if args.reduce_twi:\n observations.append('twi')\n if args.use_other_sky:\n observations.append('sky')\n if args.make_masterbias:\n observations.append('bia')\n if args.make_masterdark:\n observations.append('drk')\n for obs in observations:\n for label in labels[:2]:\n getattr(args, obs+label)\n if getattr(args, obs+label) is None:\n msg = '%s%s was not provided' %(obs, label)\n parser.error(msg) \n else:\n setattr(args, obs+label, \n getattr(args, obs+label).replace(\" \", \"\").split(','))\n if getattr(args, obs+labels[2]) is not None:\n setattr(args, obs+labels[2], \n getattr(args, obs+labels[2]).replace(\" \", \"\").split(','))\n DF = pd.DataFrame(columns=['Files', 'Output', 'Amp', 'Specid', \n 'Ifuslot', 'Ifuid']) \n cnt=0\n for date in getattr(args, obs+labels[0]):\n for obsid in getattr(args, obs+labels[1]):\n if getattr(args, obs+labels[2]) is not None: \n for expnum in getattr(args, obs+labels[2]):\n folder = op.join(date, \n args.instr, \n \"{:s}{:07d}\".format(args.instr,int(obsid)), \n \"exp{:02d}\".format(int(expnum)),\n args.instr)\n files = sorted(glob.glob(op.join(args.rootdir, folder, '*')))\n if files:\n mkpath(op.join(args.output,folder)) \n for fn in files:\n F = fits.open(fn)\n outfolder = op.join(args.output,folder) \n amp = (F[0].header['CCDPOS'].replace(' ', '') \n + F[0].header['CCDHALF'].replace(' ', ''))\n sp = '%03d' %F[0].header['SPECID']\n ifuid = F[0].header['IFUID'].replace(' ', '')\n ifuslot = '%03d' %F[0].header['IFUSLOT']\n DF.loc[cnt] = pd.Series({'Files':fn, \n 'Output':outfolder, \n 'Specid':sp,\n 'Ifuslot': ifuslot,\n 'Ifuid': ifuid, \n 'Amp': amp})\n cnt+=1\n else:\n folder = op.join(date, args.instr,\n \"{:s}{:07d}\".format(args.instr,int(obsid)))\n files = sorted(glob.glob(op.join(args.rootdir, folder, '*', args.instr, \n '*')))\n if files:\n nfiles = sorted(glob.glob(op.join(args.output, folder, '*')))\n for nfile in nfiles:\n mkpath(op.join(nfile, args.instr))\n for fn in files:\n F = fits.open(fn)\n exp = op.basename(op.dirname(op.dirname(fn)))\n outfolder = op.join(args.output,folder, exp, args.instr)\n amp = (F[0].header['CCDPOS'].replace(' ', '') \n + F[0].header['CCDHALF'].replace(' ', ''))\n sp = '%03d' %F[0].header['SPECID']\n ifuid = F[0].header['IFUID'].replace(' ', '')\n ifuslot = '%03d' %F[0].header['IFUSLOT']\n DF.loc[cnt] = pd.Series({'Files':fn, 'Output':outfolder, \n 'Specid':sp, 'Ifuslot': ifuslot,\n 'Ifuid': ifuid, 'Amp': amp})\n cnt+=1\n setattr(args, obs+'_df', DF)\n \n if args.reduce_sci:\n cals=['twi']\n if args.use_other_sky:\n cals.append('sky')\n else: \n args.sky_dir = None\n for cal in cals:\n if getattr(args, cal+labels[0]) is None:\n print(\"Please provide one \"+cal+labels[0])\n sys.exit(1) \n if len(getattr(args, cal+labels[0]))>1:\n print(\"Please provide only one \"+cal+labels[0])\n print(\"I am cowardly quitting instead of making a smart program.\")\n sys.exit(1)\n if getattr(args, cal+labels[1]) is None:\n print(\"Please provide one \"+cal+labels[1])\n sys.exit(1) \n if len(getattr(args, cal+labels[1]))>1:\n print(\"Please provide only one \"+cal+labels[1])\n print(\"I am cowardly quitting instead of making a smart program.\")\n sys.exit(1)\n if getattr(args, cal+labels[2]) is None:\n print(\"Please provide one \"+cal+labels[2])\n sys.exit(1) \n if len(getattr(args, cal+labels[2]))>1:\n print(\"Please provide only one \"+cal+labels[2])\n print(\"I am cowardly quitting instead of making a smart program.\")\n sys.exit(1) \n for date in getattr(args, cal+labels[0]):\n for obsid in getattr(args, cal+labels[1]):\n if getattr(args, cal+labels[2]) is not None: \n for expnum in getattr(args, cal+labels[2]):\n setattr(args, cal+'_dir', op.join(args.output, date, args.instr, \n \"{:s}{:07d}\".format(args.instr,int(obsid)), \n \"exp{:02d}\".format(int(expnum)),\n args.instr))\n \n \n\n return args","def intf_MMTEST(E):\n macro= \"10 10 0 p dup 100 10 0 p dup rot l drop 50 100 0 p dup rot l drop l drop\"\n oblistcontent= list()\n for s in macro.split(' '):\n try:\n s= float(s)\n except ValueError:\n pass\n if type(s) == type('str'):\n oblistcontent.append(objectifier.StackOB_SYM(s))\n else:\n oblistcontent.append(objectifier.StackOB_VAL(s))\n testmacro= objectifier.StackOB_LST(oblistcontent) \n testmacro.dead= False\n E.The.StackPush(testmacro)","def parseGerber(self, fullname, layername, updateExtents = 0):\n\n GAT = config.GAT\n GAMT = config.GAMT\n # First construct reverse GAT/GAMT, mapping definition to code\n RevGAT = config.buildRevDict(GAT) # RevGAT[hash] = aperturename\n RevGAMT = config.buildRevDict(GAMT) # RevGAMT[hash] = aperturemacroname\n\n #print 'Reading data from %s ...' % fullname\n\n fid = file(fullname, 'rt')\n currtool = None\n\n self.apxlat[layername] = {}\n self.apmxlat[layername] = {}\n self.commands[layername] = []\n self.apertures[layername] = []\n\n # These divisors are used to scale (X,Y) co-ordinates. We store\n # everything as integers in hundred-thousandths of an inch (i.e., M.5\n # format). If we get something in M.4 format, we must multiply by\n # 10. If we get something in M.6 format we must divide by 10, etc.\n x_div = 1.0\n y_div = 1.0\n\n # Drawing commands can be repeated with X or Y omitted if they are\n # the same as before. These variables store the last X/Y value as\n # integers in hundred-thousandths of an inch.\n last_x = last_y = 0\n\n # Last modal G-code. Some G-codes introduce \"modes\", such as circular interpolation\n # mode, and we want to remember what mode we're in. We're interested in:\n # G01 -- linear interpolation, cancels all circular interpolation modes\n # G36 -- Turn on polygon area fill\n # G37 -- Turn off polygon area fill\n last_gmode = 1 # G01 by default, linear interpolation\n\n # We want to know whether to do signed (G75) or unsigned (G74) I/J offsets. These\n # modes are independent of G01/G02/G03, e.g., Protel will issue multiple G03/G01\n # codes all in G75 mode.\n # G74 -- Single-quadrant circular interpolation (disables multi-quadrant interpolation)\n # G02/G03 codes set clockwise/counterclockwise arcs in a single quadrant only\n # using X/Y/I/J commands with UNSIGNED (I,J).\n # G75 -- Multi-quadrant circular interpolation --> X/Y/I/J with signed (I,J)\n # G02/G03 codes set clockwise/counterclockwise arcs in all 4 quadrants\n # using X/Y/I/J commands with SIGNED (I,J).\n circ_signed = True # Assume G75...make sure this matches canned header we write out\n\n # If the very first flash/draw is a shorthand command (i.e., without an Xxxxx or Yxxxx)\n # component then we don't really \"see\" the first point X00000Y00000. To account for this\n # we use the following Boolean flag as well as the isLastShorthand flag during parsing\n # to manually insert the point X000000Y00000 into the command stream.\n firstFlash = True\n\n for line in fid:\n # Get rid of CR characters (0x0D) and leading/trailing blanks\n line = string.replace(line, '\\x0D', '').strip()\n\n # Old location of format_pat search. Now moved down into the sub-line parse loop below.\n\n # RS-274X statement? If so, echo it. Currently, only the \"LP\" statement is expected\n # (from Protel, of course). These will be distinguished from D-code and G-code\n # commands by the fact that the first character of the string is '%'.\n match = layerpol_pat.match(line)\n if match:\n self.commands[layername].append(line)\n continue\n \n # See if this is an aperture definition, and if so, map it.\n match = apdef_pat.match(line)\n if match:\n if currtool:\n raise RuntimeError, \"File %s has an aperture definition that comes after drawing commands.\" % fullname\n\n A = aptable.parseAperture(line, self.apmxlat[layername])\n if not A:\n raise RuntimeError, \"Unknown aperture definition in file %s\" % fullname\n\n hash = A.hash()\n if not RevGAT.has_key(hash):\n #print line\n #print self.apmxlat\n #print RevGAT\n raise RuntimeError, 'File %s has aperture definition \"%s\" not in global aperture table.' % (fullname, hash)\n\n # This says that all draw commands with this aperture code will\n # be replaced by aperture self.apxlat[layername][code].\n self.apxlat[layername][A.code] = RevGAT[hash]\n continue\n\n # Ignore %AMOC8* from Eagle for now as it uses a macro parameter, which\n # is not yet supported in GerbMerge.\n if line[:7]=='%AMOC8*':\n continue\n\n # See if this is an aperture macro definition, and if so, map it.\n M = amacro.parseApertureMacro(line,fid)\n if M:\n if currtool:\n raise RuntimeError, \"File %s has an aperture macro definition that comes after drawing commands.\" % fullname\n\n hash = M.hash()\n if not RevGAMT.has_key(hash):\n raise RuntimeError, 'File %s has aperture macro definition not in global aperture macro table:\\n%s' % (fullname, hash)\n\n # This says that all aperture definition commands that reference this macro name\n # will be replaced by aperture macro name self.apmxlat[layername][macroname].\n self.apmxlat[layername][M.name] = RevGAMT[hash]\n continue\n\n # From this point on we may have more than one match on this line, e.g.:\n # G54D11*X22400Y22300D02*X22500Y22200D01*\n sub_line = line\n while sub_line:\n # Handle \"comment\" G-codes first\n match = comment_pat.match(sub_line)\n if match:\n sub_line = sub_line[match.end():]\n continue\n\n # See if this is a format statement, and if so, map it. In version 1.3 this was moved down\n # from the line-only parse checks above (see comment) to handle OrCAD lines like\n # G74*%FSLAN2X34Y34*%\n match = format_pat.match(sub_line) # Used to be format_pat.search\n if match:\n sub_line = sub_line[match.end():]\n for item in match.groups():\n if item is None: continue # Optional group didn't match\n\n if item[0] in \"LA\": # omit leading zeroes and absolute co-ordinates\n continue\n\n if item[0]=='T': # omit trailing zeroes\n raise RuntimeError, \"Trailing zeroes not supported in RS274X files\"\n if item[0]=='I': # incremental co-ordinates\n raise RuntimeError, \"Incremental co-ordinates not supported in RS274X files\"\n\n if item[0]=='N': # Maximum digits for N* commands...ignore it\n continue\n\n if item[0]=='X': # M.N specification for X-axis.\n fracpart = int(item[2])\n x_div = 10.0**(5-fracpart)\n if item[0]=='Y': # M.N specification for Y-axis.\n fracpart = int(item[2])\n y_div = 10.0**(5-fracpart)\n continue\n\n # Parse and interpret G-codes\n match = gcode_pat.match(sub_line)\n if match:\n sub_line = sub_line[match.end():]\n gcode = int(match.group(1))\n\n # Determine if this is a G-Code that should be ignored because it has no effect\n # (e.g., G70 specifies \"inches\" which is already in effect).\n if gcode in [54, 70, 90]:\n continue\n\n # Determine if this is a G-Code that we have to emit because it matters.\n if gcode in [1, 2, 3, 36, 37, 74, 75]:\n self.commands[layername].append(\"G%02d\" % gcode)\n\n # Determine if this is a G-code that sets a new mode\n if gcode in [1, 36, 37]:\n last_gmode = gcode\n\n # Remember last G74/G75 code so we know whether to do signed or unsigned I/J\n # offsets.\n if gcode==74:\n circ_signed = False\n elif gcode==75:\n circ_signed = True\n \n continue\n\n raise RuntimeError, \"G-Code 'G%02d' is not supported\" % gcode\n\n # See if this is a tool change (aperture change) command\n match = tool_pat.match(sub_line)\n if match:\n currtool = match.group(1)\n\n # Protel likes to issue random D01, D02, and D03 commands instead of aperture\n # codes. We can ignore D01 because it simply means to move to the current location\n # while drawing. Well, that's drawing a point. We can ignore D02 because it means\n # to move to the current location without drawing. Truly pointless. We do NOT want\n # to ignore D03 because it implies a flash. Protel very inefficiently issues a D02\n # move to a location without drawing, then a single-line D03 to flash. However, a D02\n # terminates a polygon in G36 mode, so keep D02's in this case.\n if currtool=='D01' or (currtool=='D02' and (last_gmode != 36)):\n sub_line = sub_line[match.end():]\n continue\n\n if (currtool == 'D03') or (currtool=='D02' and (last_gmode == 36)):\n self.commands[layername].append(currtool)\n sub_line = sub_line[match.end():]\n continue\n\n # Map it using our translation table\n if not self.apxlat[layername].has_key(currtool):\n raise RuntimeError, 'File %s has tool change command \"%s\" with no corresponding translation' % (fullname, currtool)\n\n currtool = self.apxlat[layername][currtool]\n\n # Add it to the list of things to write out\n self.commands[layername].append(currtool)\n\n # Add it to the list of all apertures needed by this layer\n self.apertures[layername].append(currtool)\n\n # Move on to next match, if any\n sub_line = sub_line[match.end():]\n continue\n\n # Is it a simple draw command?\n I = J = None # For circular interpolation drawing commands\n match = drawXY_pat.match(sub_line)\n isLastShorthand = False # By default assume we don't make use of last_x and last_y\n if match:\n x, y, d = map(__builtin__.int, match.groups())\n else:\n match = drawX_pat.match(sub_line)\n if match:\n x, d = map(__builtin__.int, match.groups())\n y = last_y\n isLastShorthand = True # Indicate we're making use of last_x/last_y\n else:\n match = drawY_pat.match(sub_line)\n if match:\n y, d = map(__builtin__.int, match.groups())\n x = last_x\n isLastShorthand = True # Indicate we're making use of last_x/last_y\n\n # Maybe it's a circular interpolation draw command with IJ components\n if match is None:\n match = cdrawXY_pat.match(sub_line)\n if match:\n x, y, I, J, d = map(__builtin__.int, match.groups())\n else:\n match = cdrawX_pat.match(sub_line)\n if match:\n x, I, J, d = map(__builtin__.int, match.groups())\n y = last_y\n isLastShorthand = True # Indicate we're making use of last_x/last_y\n else:\n match = cdrawY_pat.match(sub_line)\n if match:\n y, I, J, d = map(__builtin__.int, match.groups())\n x = last_x\n isLastShorthand = True # Indicate we're making use of last_x/last_y\n\n if match:\n if currtool is None:\n # It's OK if this is an exposure-off movement command (specified with D02).\n # It's also OK if we're in the middle of a G36 polygon fill as we're only defining\n # the polygon extents.\n if (d != 2) and (last_gmode != 36):\n raise RuntimeError, 'File %s has draw command %s with no aperture chosen' % (fullname, sub_line)\n\n # Save last_x/y BEFORE scaling to 2.5 format else subsequent single-ordinate\n # flashes (e.g., Y with no X) will be scaled twice!\n last_x = x\n last_y = y\n\n # Corner case: if this is the first flash/draw and we are using shorthand (i.e., missing Xxxx\n # or Yxxxxx) then prepend the point X0000Y0000 into the commands as it is actually the starting\n # point of our layer. We prepend the command X0000Y0000D02, i.e., a move to (0,0) without drawing.\n if (isLastShorthand and firstFlash):\n self.commands[layername].append((0,0,2))\n if updateExtents:\n self.minx = min(self.minx,0)\n self.maxx = max(self.maxx,0)\n self.miny = min(self.miny,0)\n self.maxy = max(self.maxy,0)\n\n x = int(round(x*x_div))\n y = int(round(y*y_div))\n if I is not None:\n I = int(round(I*x_div))\n J = int(round(J*y_div))\n self.commands[layername].append((x,y,I,J,d,circ_signed))\n else:\n self.commands[layername].append((x,y,d))\n firstFlash = False\n\n # Update dimensions...this is complicated for circular interpolation commands\n # that span more than one quadrant. For now, we ignore this problem since users\n # should be using a border layer to indicate extents.\n if updateExtents:\n if x < self.minx: self.minx = x\n if x > self.maxx: self.maxx = x\n if y < self.miny: self.miny = y\n if y > self.maxy: self.maxy = y\n\n # Move on to next match, if any\n sub_line = sub_line[match.end():]\n continue\n\n # If it's none of the above, it had better be on our ignore list.\n for pat in IgnoreList:\n match = pat.match(sub_line)\n if match:\n break\n else:\n raise RuntimeError, 'File %s has uninterpretable line:\\n %s' % (fullname, line)\n\n sub_line = sub_line[match.end():]\n # end while still things to match on this line\n # end of for each line in file\n\n fid.close()\n if 0:\n print layername\n print self.commands[layername]","def __gen_token_anno_file(self, top_level_layer):\n base_paula_id = '{}.{}.tok'.format(self.corpus_name, self.name)\n paula_id = '{}.{}.{}.tok_multiFeat'.format(top_level_layer,\n self.corpus_name,\n self.name)\n E, tree = gen_paula_etree(paula_id)\n mflist = E('multiFeatList',\n {XMLBASE: base_paula_id+'.xml'})\n\n for token_id in self.dg.tokens:\n mfeat = E('multiFeat',\n {XLINKHREF: '#{}'.format(token_id)})\n token_dict = self.dg.node[token_id]\n for feature in token_dict:\n # TODO: highly inefficient! refactor!1!!\n if feature not in IGNORED_TOKEN_ATTRIBS \\\n and feature.startswith(top_level_layer):\n mfeat.append(E('feat',\n {'name': feature,\n 'value': token_dict[feature]}))\n\n if self.human_readable: # adds token string as a <!-- comment -->\n mfeat.append(Comment(token_dict[self.dg.ns+':token']))\n mflist.append(mfeat)\n\n tree.append(mflist)\n self.files[paula_id] = tree\n self.file2dtd[paula_id] = PaulaDTDs.multifeat\n return paula_id","def compile_customization(data):\n data=data.split(\" \")\n optional_data=data[1:]\n data = data[0].split(\"@\")\n return_dict = {}\n return_dict['resize_type']=data[0]\n return_dict['width']=int(data[1])\n return_dict['height']=int(data[2])\n return_dict['padding_type']='reflect'\n return_dict['constant_color']=[255,0,0]\n\n if len(optional_data)!=0:\n optional_data=optional_data[0]\n if \",\" in optional_data:\n return_dict['padding_type']='constant'\n color_list=optional_data.split(\",\")\n return_dict['constant_color']=tuple([int(i) for i in color_list])\n else:\n return_dict['padding_type']=optional_data\n return return_dict","def parse_illumina_line(l, barcode_length, rev_comp_barcode,\r\n barcode_in_sequence=False):\r\n fields = l.strip().split(':')\r\n\r\n y_position_subfields = fields[4].split('#')\r\n y_position = int(y_position_subfields[0])\r\n sequence = fields[5]\r\n qual_string = fields[6]\r\n\r\n if barcode_in_sequence:\r\n barcode = sequence[:barcode_length]\r\n sequence = sequence[barcode_length:]\r\n qual_string = qual_string[barcode_length:]\r\n else:\r\n barcode = y_position_subfields[1][:barcode_length]\r\n\r\n if rev_comp_barcode:\r\n barcode = str(DNA(barcode).rc())\r\n\r\n result = {\r\n 'Full description': ':'.join(fields[:5]),\r\n 'Machine Name': fields[0],\r\n 'Channel Number': int(fields[1]),\r\n 'Tile Number': int(fields[2]),\r\n 'X Position': int(fields[3]),\r\n 'Y Position': y_position,\r\n 'Barcode': barcode,\r\n 'Full Y Position Field': fields[4],\r\n 'Sequence': sequence,\r\n 'Quality Score': qual_string}\r\n\r\n return result","def _parse(self, data):\n pe = construct.PEFILE_HEADER.parse(data)\n\n # Convert Container classes to use ours, so we can deepcopy.\n pe = Container.from_container(pe)\n\n # Convert the FlagEnums into list of constants.\n for section in pe.SectionTable:\n if isinstance(section.Characteristics, dict):\n section.Characteristics = [flag for flag, value in section.Characteristics.items() if value]\n section.data = data[section.PointerToRawData:section.PointerToRawData + section.SizeOfRawData]\n file_header = pe.NTHeaders.FileHeader\n if isinstance(file_header.Characteristics, dict):\n file_header.Characteristics = [\n flag for flag, value in file_header.Characteristics.items() if value]\n optional_header = pe.NTHeaders.OptionalHeader\n if isinstance(optional_header.DllCharacteristics, dict):\n optional_header.DllCharacteristics = [\n flag for flag, value in optional_header.DllCharacteristics.items() if value]\n\n self.update(pe)","def parse(self, filehandle):\n l = filehandle.readline()\n if l.split()[0] != '##maf':\n return\n else:\n self.setpar(l.split()[1:])\n\n l=filehandle.readline()\n while l:\n la = l.split()\n## print la\n if(len(la)==0 or la[0]=='#'):\n## print \"skipping\"\n 1\n elif(la[0]=='a'):\n## print \"reading alignment\"\n self.readalign(la[1:], filehandle)\n else:\n## print \"end of records\"\n return\n\n l=filehandle.readline()","def read_kitti_cal(calfile):\n\n text_file = open(calfile, 'r')\n\n p2pat = re.compile(('(P2:)\\s+(fpat)\\s+(fpat)\\s+(fpat)\\s+(fpat)\\s+(fpat)\\s+(fpat)\\s+(fpat)\\s+(fpat)\\s+(fpat)' +\n '\\s+(fpat)\\s+(fpat)\\s+(fpat)\\s*\\n').replace('fpat', '[-+]?[\\d]+\\.?[\\d]*[Ee](?:[-+]?[\\d]+)?'))\n\n for line in text_file:\n\n parsed = p2pat.fullmatch(line)\n\n # bbGt annotation in text format of:\n # cls x y w h occ x y w h ign ang\n if parsed is not None:\n p2 = np.zeros([4, 4], dtype=float)\n p2[0, 0] = parsed.group(2)\n p2[0, 1] = parsed.group(3)\n p2[0, 2] = parsed.group(4)\n p2[0, 3] = parsed.group(5)\n p2[1, 0] = parsed.group(6)\n p2[1, 1] = parsed.group(7)\n p2[1, 2] = parsed.group(8)\n p2[1, 3] = parsed.group(9)\n p2[2, 0] = parsed.group(10)\n p2[2, 1] = parsed.group(11)\n p2[2, 2] = parsed.group(12)\n p2[2, 3] = parsed.group(13)\n\n p2[3, 3] = 1\n\n text_file.close()\n\n return p2","def construct_parser_preprocessor(subparser) -> None:\n\n def within_percent_interval(interval_str: str) -> float:\n \"\"\"\n Checks whether or not the given string representation of a floating\n point number is in the interval [0, 1].\n\n Parameters\n ----------\n interval_str: str :\n The string that needs to be checked for a valid value\n\n Returns\n -------\n float\n If valid, the number representation of interval_str\n\n Raises\n ------\n ValueError\n If interval_str cannot be converted to a floating pointer number\n ArgumentTypeError\n If the number is not within the interval [0, 1]\n \"\"\"\n interval = float(interval_str)\n if interval < 0 or interval > 1:\n raise ArgumentTypeError(\"Input given is out of bounds!\")\n\n return interval\n \"\"\"\n if subparser:\n preprocess_parser = subparser.add_parser(\n \"preprocess\",\n formatter_class=argparse.ArgumentDefaultsHelpFormatter,\n help=\"Preprocess given dataset\",\n )\n else:\n preprocess_parser = argparse.ArgumentParser(\n description='Preprocess given dataset',\n formatter_class=argparse.ArgumentDefaultsHelpFormatter\n )\n \"\"\"\n\n subparser.add_argument(\n 'input_dir', type=str, default=\"data_clean\", metavar=\"input-dir\",\n help='Input directory to preprocess'\n )\n\n subparser.add_argument(\n '-o', '--output-dir', type=str, default=\"filtered_data_clean\",\n help='Output directory to hold preprocessed data_clean'\n )\n\n subparser.add_argument(\n '--stopwords', type=str, default=None,\n help='Path to the .csv stop words file'\n )\n\n # Make file generation options mutually exclusive\n # Note, all 3 of the flags appear. However, we only want 1 of them to\n # appear.\n subparser.add_argument(\n '--export', type=str, default=\"single\",\n choices=[\"single\", \"split\", \"fasttext\", \"all\"],\n help='Indicate whether you only want a single file holding all of the '\n 'preprocessed data_clean, or both. If \"split\\\" was chosen, it '\n 'utilizes the \"--train-split\" argument to know how big to make the '\n 'training and testing sets. If fasttext is given, it utilizes the '\n '\"--slice-length\" argument to know how big to make each slice'\n )\n\n subparser.add_argument(\n '--slice_length', type=int, default=25,\n help=\"Number of tokens to have per slice of a file.\"\n )\n\n subparser.add_argument(\n '--train-split', type=within_percent_interval, default=.8,\n metavar=\"[0-1]\",\n help=\"Percentage in interval [0,1] of total data_clean going to the \\\n training dataset.\"\n )\n\n subparser.set_defaults(run=run_preprocessor)","def parse_inputs():\n\n parser = argparse.ArgumentParser(description=\"Command line argument handler for ugaudio spectral_average program.\",\n formatter_class=argparse.ArgumentDefaultsHelpFormatter)\n\n # a group of args for verbosity\n group = parser.add_mutually_exclusive_group()\n group.add_argument('-v', '--verbose', action='store_true')\n group.add_argument('-q', '--quiet', action='store_true')\n\n # nfiles\n help_nfiles = 'nfiles to preview (ONLY for testing)'\n parser.add_argument('-g', '--nfiles', default=DEFAULT_NFILES, type=nfiles_int, help=help_nfiles)\n\n # nfft\n help_nfft = 'Nfft'\n parser.add_argument('-n', '--nfft', default=DEFAULT_NFFT, type=nfft_int, help=help_nfft)\n\n # sample rate\n help_rate = 'sample rate (sa/sec)'\n parser.add_argument('-r', '--rate', default=DEFAULT_RATE, type=rate_str, help=help_rate)\n\n # cutoff\n help_cutoff = 'cutoff'\n parser.add_argument('-c', '--cutoff', default=DEFAULT_CUTOFF, type=cutoff_str, help=help_cutoff)\n\n # sensors\n help_sensors = 'sensors'\n parser.add_argument('-s', '--sensors', default=DEFAULT_SENSORS, type=sensors_list, help=help_sensors)\n\n # PAD directory\n help_paddir = 'PAD dir'\n parser.add_argument('-p', '--paddir', default=DEFAULT_PADDIR, type=folder_str, help=help_paddir)\n\n # output directory\n help_outdir = 'output dir'\n parser.add_argument('-o', '--outdir', default=DEFAULT_OUTDIR, type=outdir_str, help=help_outdir)\n\n # start date\n help_start = 'start date'\n parser.add_argument('-d', '--start', default=DEFAULT_START, type=dtm_date, help=help_start)\n\n # end date\n help_end = 'end date'\n parser.add_argument('-e', '--end', default=DEFAULT_END, type=dtm_date, help=help_end)\n\n # parse arguments\n module_logger.debug('calling parse_args')\n args = parser.parse_args()\n\n return args","def main():\n dir_path='.'\n meas_file='magic_measurements.txt'\n samp_file=\"er_samples.txt\"\n out_file='magic_measurements.txt'\n if '-h' in sys.argv:\n print(main.__doc__)\n sys.exit()\n if '-WD' in sys.argv:\n ind = sys.argv.index('-WD')\n dir_path=sys.argv[ind+1]\n if '-f' in sys.argv:\n ind = sys.argv.index('-f')\n meas_file=sys.argv[ind+1]\n if '-fsa' in sys.argv:\n ind = sys.argv.index('-fsa')\n samp_file=sys.argv[ind+1]\n if '-F' in sys.argv:\n ind = sys.argv.index('-F')\n out_file=sys.argv[ind+1]\n # read in measurements file\n meas_file=dir_path+'/'+meas_file\n out_file=dir_path+'/'+out_file\n samp_file=dir_path+'/'+samp_file\n data,file_type=pmag.magic_read(meas_file)\n samps,file_type=pmag.magic_read(samp_file)\n MeasRecs=[]\n sampnames,sflag=[],0\n for rec in data:\n for samp in samps:\n if samp['er_sample_name'].lower()==rec['er_sample_name'].lower():\n if samp['er_sample_name'] not in sampnames:sampnames.append(samp['er_sample_name'].lower())\n rec['er_site_name']=samp['er_site_name']\n rec['er_location_name']=samp['er_location_name']\n MeasRecs.append(rec)\n break\n if rec['er_sample_name'].lower() not in sampnames:\n sampnames.append(rec['er_sample_name'].lower())\n sflag=1\n SampRec={}\n for key in list(samps[0].keys()):SampRec[key]=\"\"\n SampRec['er_sample_name']=rec['er_sample_name']\n SampRec['er_citation_names']=\"This study\"\n SampRec['er_site_name']='MISSING'\n SampRec['er_location_name']='MISSING'\n SampRec['sample_desription']='recorded added by update_measurements - edit as needed'\n samps.append(SampRec)\n print(rec['er_sample_name'],' missing from er_samples.txt file - edit orient.txt file and re-import')\n rec['er_site_name']='MISSING'\n rec['er_location_name']='MISSING'\n MeasRecs.append(rec)\n pmag.magic_write(out_file,MeasRecs,'magic_measurements')\n print(\"updated measurements file stored in \", out_file)\n if sflag==1:\n pmag.magic_write(samp_file,samps,'er_samples')\n print(\"updated sample file stored in \", samp_file)","def sequence_macros(macros):\n\n def foo():\n for m in macros:\n m()\n\n return foo","def generate_parser(renamer):\n parser = ShlexArgumentParser(\n formatter_class=RawDescriptionHelpFormatter,\n prog=\"brp\",\n usage=\"cmd [args ...]\",\n add_help=False,\n exit_on_error=False,\n )\n subparsers = parser.add_subparsers(\n title=\"commands\",\n description=\"actions to take on the filenames\",\n )\n\n _help = [\n _help_parser((\"help\", \"h\", \"?\"), subparsers, renamer),\n _save_parser((\"save\", \"s\"), subparsers, renamer),\n _quit_parser((\"quit\", \"q\", \"exit\"), subparsers, renamer),\n _save_quit_parser((\"write\", \"w\"), subparsers, renamer),\n _print_parser((\"list\", \"ls\", \"l\"), subparsers, renamer),\n _history_parser((\"history\", \"hist\", \"past\"), subparsers, renamer),\n _undo_parser((\"undo\", \"u\"), subparsers, renamer),\n _reset_parser((\"reset\", \"over\", \"o\"), subparsers, renamer),\n _automate_parser((\"automate\", \"a\", \"auto\"), subparsers, renamer),\n _find_replace_parser((\"replace\", \"r\", \"re\", \"reg\", \"regex\"), subparsers, renamer),\n _append_parser((\"append\", \"ap\"), subparsers, renamer),\n _prepend_parser((\"prepend\", \"p\", \"pre\"), subparsers, renamer),\n _insert_parser((\"insert\", \"i\", \"in\"), subparsers, renamer),\n _case_parser((\"case\", \"c\"), subparsers, renamer),\n _extension_parser((\"extension\", \"x\", \"ext\"), subparsers, renamer),\n ]\n\n return parser, _help","def _m4_file_analysis(self, fin):\n # imp.reload(m4_macros_analysis)\n raw_data = fin.read()\n\n mylexer = m4_macros_analysis.M4Lexer()\n mylexer.build()\n lexer = mylexer.clone()\n generator = mylexer.get_token_iter(raw_data, lexer=lexer)\n cache_generator = m4_macros_analysis.CacheGenerator(generator, origin_data=raw_data)\n\n self._m4_analyzer.functions_analyze(cache_generator, fin.name)","def _fusion_legacy_handler(_, __, tokens):\n if RANGE_5P not in tokens:\n tokens[RANGE_5P] = {FUSION_MISSING: \"?\"}\n if RANGE_3P not in tokens:\n tokens[RANGE_3P] = {FUSION_MISSING: \"?\"}\n return tokens","def process_declaration(self, decl,datatype):\n # Looping character by character in the string which contains only the part where variables are mentioned(without the datatype keyword).\n filename = \"sym.csv\"\n name = \"\"\n i=0\n pos=-1\n flag=0 #used to track identifiers with having digits\n with open(filename, 'a') as csvfile:\n csvwriter = csv.writer(csvfile)\n for c in decl:\n \n pos += 1\n i=0\n # Checking if the variable mentioned is an array declaration. This will be executed only if '[' character has been encountered earlier.\n if self.flag_array:\n # Checks if the '[' has a matching ']'\n if (c == \"]\"):\n self.structure += c # Saving the current status of the array structure.\n self.flag_array = False # Setting flag to say that the array declaration has been processed completely.\n self.array_structure[self.identifiers[-1]] = self.structure # Saving the array structure(or dimension) into a dictionary.\n continue # Jumping into the next iteration.\n # Checks if next variable is going to be declared.\n elif (c == \",\"):\n continue # Jumping to the next iteration.\n # Checks if declaration statement is ending.\n elif (c == \";\"):\n print(self.structure)\n break # Breaking out of the loop. It can also be return.\n # If none of the conditions match then it is the dimension being mentioned.\n else:\n self.structure += c # Saving the dimension into the variable that is used for saving the overall structure of the array.\n continue # Jumping to the next iteration.\n\n # Checking if the variable is being assigned with a value during the declaration.\n \n if c == \"=\":\n flag=1 #this means the encountered digits are values\n self.identifiers += self.temp # Saving the characters parsed so far as an identifier, since '=' operator marks the end of the identifier and beginning of the value.\n\n if(len(name.strip())>0 and re.search(r\"[a-zA-Z_][a-zA-Z_0-9]*\",name.strip()) and not(self.check(name.strip()))):\n if(re.search(r\"[0-9]\", decl).start()):\n indexValue = re.search(r\"[0-9\\.]+\", decl[pos:]).start()\n lastValue = re.search(r\"[0-9\\.]+\", decl[pos:]).end()\n value = decl[pos+indexValue:pos+lastValue]\n csvwriter.writerow(['Identifier',datatype,name.strip(),value,''])\n name=\"\"\n \n continue\n csvwriter.writerow(['Identifier',datatype,name.strip(),'',''])\n name = \"\"\n \n \n\n # Checking if an array is being declared.\n elif c == \"[\":\n self.identifiers += self.temp # String read so far is saved as an identifier, since '[' marks the end of identifier name and begin of the dimension.\n self.temp = \"\" # Emptying the string which contained the name of the identifier.\n if len(name.strip())>0 and re.search(r\"[a-zA-Z_][a-zA-Z_0-9]*\",name.strip()) and not(self.check(name.strip())):\n csvwriter.writerow(['Identifer',datatype+\"Array\",name.strip(),'',''])\n name = \"\"\n self.structure += c # Adding '[' into the structure variable.\n self.flag_array = True # Marking the beginning of dimension.\n\n # Checking if the declaration is for a function.\n elif c == \"(\":\n self.temp = \"\" # Emptying the string which holds the identifier name since it is a function name and not that of any variable.\n break\n\n # Checking if the declaration is marking end of a variable name.\n elif c == \",\":\n flag=0 #after \",\" it's possible that identifier has digit in it. So, make flag 0 again\n self.identifiers += self.temp # Adding the name parsed so far into the list of all variables.\n self.temp = \"\" # Emptying the string which holds the name of the identifier.\n if len(name.strip())>0 and re.search(r\"[a-zA-Z_][a-zA-Z_0-9]*\",name.strip()) and not(self.check(name.strip())):\n # if(re.search())\n \n csvwriter.writerow(['Identifer',datatype,name.strip(),'',''])\n name = \"\"\n continue\n\n # Checking if the statement has ended.\n elif c == \";\":\n self.identifiers += self.temp # Adding the string parsed so far into the list of identifiers.\n self.temp = \"\" # Emptying the string that holds the name of the identifier.\n if len(name.strip())>0 and re.search(r\"[a-zA-Z_][a-zA-Z_0-9]*\",name.strip()) and not(self.check(name.strip())):\n csvwriter.writerow(['Identifer',datatype,name.strip(),'',''])\n name = \"\"\n break\n\n # Checking for whitespaces within the line.\n elif c == \" \":\n continue\n #Doesn't take values as identifier names\n elif(re.search(r'[0-9]',c)):\n if(flag == 1): #check if it's value or identifier\n continue\n else:\n self.temp += c\n name += c\n\n # If none of the conditions satisfy, then the character is part of the identifier name. Hence adding it to the name string.\n else:\n self.temp += c\n name += c","def xephemFormat(self):\n line = []\n #Field 1: names\n names = [self.getName()]\n identifiers = self.getIdentifiers()\n if identifiers[0] is not None:\n names.append(identifiers[0])\n for i in range(1,4):\n if identifiers[i] is not None:\n names.extend(identifiers[i])\n line.append(\"|\".join(names))\n\n #Field 2: type designation\n objType = self.getType()\n if objType in (\"Galaxy Pair\", \"Galaxy Triplet\", \"Group of galaxies\"):\n line.append(\"f|A\")\n elif objType == \"Globular Cluster\":\n line.append(\"f|C\")\n elif objType == \"Double star\":\n line.append(\"f|D\")\n elif objType in (\"HII Ionized region\", \"Nebula\"):\n line.append(\"f|F\")\n elif objType == \"Galaxy\":\n if self.getHubble().startswith(\"S\"):\n line.append(\"f|G\")\n else:\n line.append(\"f|H\")\n elif objType == \"Dark Nebula\":\n line.append(\"f|K\")\n elif objType in (\"Emission Nebula\", \"Reflection Nebula\"):\n line.append(\"f|N\")\n elif objType in (\"Association of stars\", \"Open Cluster\"):\n line.append(\"f|O\")\n elif objType == \"Planetary Nebula\":\n line.append(\"f|P\")\n elif objType == \"Supernova remnant\":\n line.append(\"f|R\")\n elif objType == \"Star\":\n line.append(\"f|S\")\n elif objType == \"Star cluster + Nebula\":\n line.append(\"f|U\")\n else:\n line.append(\"f\")\n\n #Field 3: Right Ascension\n line.append(self.getRA())\n\n #Field 4: Declination\n line.append(self.getDec())\n\n #Field 5: Magnitude\n #We use the first available magnitude in the sequence b,v,j,h,k\n for mag in self.getMagnitudes():\n if mag is not None:\n line.append(str(mag))\n break\n\n #Field 6: optional Epoch, we let it empty\n line.append(\"\")\n\n #Field 7: Dimensions\n dimensions = []\n #Xephem format wants axes espressed in arcsec, we have arcmin\n for value in (self.getDimensions()[0],self.getDimensions()[1]):\n if value is not None:\n dimensions.append(str(value*60))\n else:\n dimensions.append(\"\")\n if self.getDimensions()[2] is not None:\n dimensions.append(str(value))\n else:\n dimensions.append(\"\")\n line.append(\"|\".join(dimensions))\n\n return \",\".join(line)","def parse(token):\n\n pass","def _prepare_registration(self, record):\n logging.debug('.. generate macros before registration experiment')\n # set the paths for this experiment\n path_dir = self._get_path_reg_dir(record)\n path_im_ref, path_im_move, _, _ = self._get_paths(record)\n name_im_ref, name_im_move = [os.path.basename(p)\n for p in [path_im_ref, path_im_move]]\n path_regist = os.path.join(path_dir, os.path.basename(path_im_move))\n\n with open(self.params['path_config_bUnwarpJ'], 'r') as fp:\n lines = fp.readlines()\n # merge lines into one string\n config_bunwarpj = ' '.join(l.strip() for l in lines)\n # define set of all possible parameters for macros generating\n dict_params = {\n 'source': path_im_move, 'target': path_im_ref,\n 'name_source': name_im_move, 'name_target': name_im_ref,\n 'config_bUnwarpJ': config_bunwarpj, 'output': path_dir,\n 'warp': path_regist}\n\n # if config for SIFT is defined add SIFT extraction\n if 'path_config_IJ_SIFT' in self.params:\n with open(self.params['path_config_IJ_SIFT'], 'r') as fp:\n lines = fp.readlines()\n dict_params['config_SIFT'] = ' '.join(l.strip() for l in lines)\n dict_params['SIFT'] = MACRO_SIFT % dict_params\n else:\n dict_params['SIFT'] = ''\n\n # if config for MOPS is defined add MOPS extraction\n if 'path_config_IJ_MOPS' in self.params:\n with open(self.params['path_config_IJ_MOPS'], 'r') as fp:\n lines = fp.readlines()\n dict_params['config_MOPS'] = ' '.join(l.strip() for l in lines)\n dict_params['MOPS'] = MACRO_MOPS % dict_params\n else:\n dict_params['MOPS'] = ''\n\n # generate the registration macro\n macro_regist = MACRO_REGISTRATION % dict_params\n with open(os.path.join(path_dir, NAME_MACRO_REGISTRATION), 'w') as fp:\n fp.write(macro_regist)\n\n return record","def sample_vcf():\n file_content = b\"\"\"##fileformat=VCFv4.2\n##hailversion=0.2.100-2ea2615a797a\n##INFO=<ID=QUALapprox,Number=1,Type=Integer,Description=\"\">\n##INFO=<ID=SB,Number=.,Type=Integer,Description=\"\">\n##INFO=<ID=MQ,Number=1,Type=Float,Description=\"\">\n##INFO=<ID=MQRankSum,Number=1,Type=Float,Description=\"\">\n##INFO=<ID=VarDP,Number=1,Type=Integer,Description=\"\">\n##INFO=<ID=AS_ReadPosRankSum,Number=1,Type=Float,Description=\"\">\n##INFO=<ID=AS_pab_max,Number=1,Type=Float,Description=\"\">\n##INFO=<ID=AS_QD,Number=1,Type=Float,Description=\"\">\n##INFO=<ID=AS_MQ,Number=1,Type=Float,Description=\"\">\n##INFO=<ID=QD,Number=1,Type=Float,Description=\"\">\n##INFO=<ID=AS_MQRankSum,Number=1,Type=Float,Description=\"\">\n##INFO=<ID=FS,Number=1,Type=Float,Description=\"\">\n##INFO=<ID=AS_FS,Number=1,Type=Float,Description=\"\">\n##INFO=<ID=ReadPosRankSum,Number=1,Type=Float,Description=\"\">\n##INFO=<ID=AS_QUALapprox,Number=1,Type=Integer,Description=\"\">\n##INFO=<ID=AS_SB_TABLE,Number=.,Type=Integer,Description=\"\">\n##INFO=<ID=AS_VarDP,Number=1,Type=Integer,Description=\"\">\n##INFO=<ID=AS_SOR,Number=1,Type=Float,Description=\"\">\n##INFO=<ID=SOR,Number=1,Type=Float,Description=\"\">\n##INFO=<ID=singleton,Number=0,Type=Flag,Description=\"\">\n##INFO=<ID=transmitted_singleton,Number=0,Type=Flag,Description=\"\">\n##INFO=<ID=omni,Number=0,Type=Flag,Description=\"\">\n##INFO=<ID=mills,Number=0,Type=Flag,Description=\"\">\n##INFO=<ID=monoallelic,Number=0,Type=Flag,Description=\"\">\n##INFO=<ID=AS_VQSLOD,Number=1,Type=Float,Description=\"\">\n##INFO=<ID=InbreedingCoeff,Number=1,Type=Float,Description=\"\">\n##FILTER=<ID=AC0,Description=\"Allele count is zero after filtering out low-confidence genotypes (GQ < 20; DP < 10; and AB < 0.2 for het calls)\">\n##FILTER=<ID=AS_VQSR,Description=\"Failed VQSR filtering thresholds of -2.7739 for SNPs and -1.0606 for indels\">\n##contig=<ID=chr1,length=248956422,assembly=GRCh38>\n#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\nchr1\t10330\t.\tCCCCTAACCCTAACCCTAACCCTACCCTAACCCTAACCCTAACCCTAACCCTAA\tC\t.\tPASS\tQUALapprox=21493;SB=325,1077,113,694;MQ=32.1327;MQRankSum=0.720000;VarDP=2236;AS_ReadPosRankSum=-0.736000;AS_pab_max=1.00000;AS_QD=5.17857;AS_MQ=29.5449;QD=9.61225;AS_MQRankSum=0.00000;FS=8.55065;AS_FS=.;ReadPosRankSum=0.727000;AS_QUALapprox=145;AS_SB_TABLE=325,1077,2,5;AS_VarDP=28;AS_SOR=0.311749;SOR=1.48100;singleton;AS_VQSLOD=13.4641;InbreedingCoeff=-0.000517845\"\"\"\n file = io.BytesIO(file_content)\n return file","def parse_part(self):\n parts = []\n for part in re.split(r'\\*\\*\\* ([A-Z- ]+) \\*\\*\\*', self.hand_file): # return [ 'part1', 'splitter1', 'part2',..\n parts.append(part)\n\n for i in range(0, len(parts)):\n if i == 0:\n self.part_dict['HEADER'] = parts[i]\n if i % 2 != 0: # number is odd\n self.part_dict[parts[i]] = parts[i + 1]","def parser(raw_seq, date):\n taxon_id = int(raw_seq.features[0].qualifiers['db_xref'][0][6:])\n organism = raw_seq.annotations['organism']\n accession = raw_seq.annotations['accessions'][0]\n gene = []\n records = []\n frag_type = 'whole'\n begin = 1\n end = len(raw_seq)\n sequence = str(raw_seq.seq)\n name = organism\n strand = 1\n rec = [taxon_id, organism, accession, name, frag_type, begin, end, strand, sequence, date]\n records.append(rec)\n for i in raw_seq.features:\n if i.type == 'gene' and 'gene' in i.qualifiers:\n if i.location_operator != 'join':\n frag_type = 'gene'\n begin = int(i.location.start)\n end = int(i.location.end)\n sequence = str(raw_seq.seq[begin:end])\n name = str(i.qualifiers['gene'][0])\n strand = str(i.location.strand)\n rec = [taxon_id, organism, accession, name, frag_type, begin, end, strand, sequence, date]\n elif i.location_operator == 'join':\n frag_type = 'gene'\n begin = int(i.sub_features[0].location.start)\n end = int(i.sub_features[0].location.end)\n name = str(i.qualifiers['gene'][0])\n strand = str(i.location.strand)\n sequence = ''\n rec = [taxon_id, organism, accession, name, frag_type, begin, end, strand, sequence, date]\n gene.append(rec)\n begin = int(i.sub_features[1].location.start)\n end = int(i.sub_features[1].location.end)\n sequence = ''.join([str(raw_seq.seq[begin:end]), str(raw_seq.seq[begin:end])])\n rec = [taxon_id, organism, accession, name, frag_type, begin, end, strand, sequence, date]\n elif i.type == 'CDS' and 'gene' in i.qualifiers:\n frag_type = 'cds'\n begin = int(i.location.start)\n end = int(i.location.end)\n sequence = str(raw_seq.seq[begin:end])\n name = str(i.qualifiers['gene'][0]).replace(' ', '_')\n strand = str(i.location.strand)\n rec = [taxon_id, organism, accession, name, frag_type, begin, end, strand, sequence, date]\n elif i.type == 'tRNA' and 'gene' in i.qualifiers:\n frag_type = 'tRNA'\n begin = int(i.location.start)\n end = int(i.location.end)\n sequence = str(raw_seq.seq[begin:end])\n if len(sequence) >= 100:\n sequence = ''\n name = str(i.qualifiers['gene'][0]).replace(' ', '_')\n strand = str(i.location.strand)\n rec = [taxon_id, organism, accession, name, frag_type, begin, end, strand, sequence, date]\n elif i.type == 'rRNA':\n frag_type = 'rRNA'\n begin = int(i.location.start)\n end = int(i.location.end)\n sequence = str(raw_seq.seq[begin:end])\n name = str(i.qualifiers['product'][0]).replace(' ', '_')\n strand = str(i.location.strand)\n rec = [taxon_id, organism, accession, name, frag_type, begin, end, strand, sequence, date]\n elif i.type == 'exon' and 'gene' in i.qualifiers:\n frag_type = 'exon'\n begin = int(i.location.start)\n end = int(i.location.end)\n sequence = str(raw_seq.seq[begin:end])\n if 'number' in i.qualifiers:\n name = '{0}_exon_{1}'.format(i.qualifiers['gene'][0],\n i.qualifiers['number'][0])\n else:\n name = '{0}_exon'.format(i.qualifiers['gene'][0])\n strand = int(i.location.strand)\n rec = [taxon_id, organism, accession, name, frag_type, begin, end, strand, sequence, date]\n elif i.type == 'intron' and 'gene' in i.qualifiers:\n frag_type = 'intron'\n begin = int(i.location.start)\n end = int(i.location.end)\n sequence = str(raw_seq.seq[begin:end])\n strand = str(i.location.strand)\n if 'number' in i.qualifiers:\n name = '{0}_{1}_intron'.format(i.qualifiers['gene'][0],\n i.qualifiers['number'][0])\n else:\n name = '{0}_intron'.format(i.qualifiers['gene'][0])\n rec = [taxon_id, organism, accession, name, frag_type, begin, end, strand, sequence, date]\n\n records.append(rec)\n gene.sort(key=lambda x: x[5])\n\n for i in range(len(gene) - 1):\n frag_type = 'spacer'\n now = gene[i]\n then = gene[i + 1]\n tail = now[6] + 1\n head = then[5] - 1\n sequence = str(raw_seq.seq[tail:head])\n name = '{0}-{1}_spacer'.format(now[3], then[3])\n strand = 0\n rec = [taxon_id, organism, accession, name, frag_type, begin, end, strand, sequence, date]\n records.append(rec)\n records.extend(gene)\n\n database.extend(records)","def _parse(self):\n with open(self.input) as f:\n for line in f:\n if not line.lstrip().startswith(\"#\"): # comment\n stripped_line=line.split(\"#\")[0].strip()\n \n # Initialise an empty option dictionary with some good defaults\n if \"[\" in stripped_line:\n molname=stripped_line.split()[1]\n self.options[molname]=self.empty_option_dict.copy() # dict1=dict2 does not copy!\n self.options[molname][\"MolName\"]=molname\n if \":\" in stripped_line: \n # now process line by line\n if \"{\" not in stripped_line:\n key,value=[i.strip() for i in stripped_line.split(\":\")]\n\n if key not in self.options[molname].keys():\n raise BaseException(\"Option \\\"{}\\\" not known, please check your input file\".format(key))\n self.options[molname][key]=value \n else:\n # This is to define special lines that are given by a dictionary\n key,value=stripped_line.split(\":\",1) # split on first occurence\n if key==\"Addon\": # additional atoms to be added per molecule\n addondict=self.empty_addon_dict.copy()\n addondict_string = value.split(\"}\",-1)[0].split(\"{\",1)[1]\n for pair in addondict_string.split(\",\"):\n addonkey,addonvalue=[i.strip() for i in pair.split(\":\")]\n if addonkey not in addondict.keys():\n raise BaseException(\"Option \\\"{}\\\" in Addon section of molecule {} not known, please check your input file\".format(addonkey,molname))\n addondict[addonkey]=addonvalue\n value=addondict\n # Since addon keyword can be used many times, this is a list\n self.options[molname][key].append(value) \n self._check()","def pat_parse():\n\tfn = abs_path(sdict['sfn'], path)\n\n\t#read the data\n\tskiprows = None\n\t#if 'skiprows' in sdict: skiprows = sdict['skiprows']\n\traw = pd.read_excel(fn, skiprows= skiprows, header = None)\n\n\t#clean up \n\tcols = raw.loc[0].combine_first(raw.loc[1]).copy() #combines split header rows\n\traw.columns = cols\n\n\traw.drop(s['junkcols'], inplace = True, #loses any intersperced cols we don't need\n\t\t axis = 1) \n\traw = raw.iloc[2:, :-2] #drops the header and last 2 cols\n\traw.replace(missing, 0, inplace = True)\n\n\traw = raw.astype('float64', #convert any col we can to a numeric type\n\t\t errors = 'ignore')\n\traw = fix_non_ascii_df(raw) #fix non-ascii chars in text\n\n\traw.columns.rename(s['col_renames'], inplace = True) #standardize company, industry names\n\n\traw.insert(0, firmid_col, #look up and insert FirmID\n\t\t get_firmid_from_vendor_name(raw[coname_col]) )\n\n\taggregate\n\t\"\"\"\n company, ticker, GICS industry, inventions by year, sum(inventions by year), CAGR\n\n tabs: [\"No of inventions\", Quality of patents\", \"Rate of abandonment\", \"R&D spending\"]\n\n need:\n - replace \"-\" with 0 (not NaN)\n - get FirmID\n - good ind averages \"\"\"\n\ta = 1","def build_parser(self):\n parser = argparse.ArgumentParser(\n description=\"Run Crystal Matching algorithm attempting to translate co-ordinates \"\n \"on an input image to the coordinate-space of an output image while \"\n \"accounting for possible movement of crystals in the sample.\")\n\n if sys.version_info[0] < 3:\n parser.add_argument('Formulatrix_image',\n metavar=\"Formulatrix_image_path\",\n type=file,\n help='Image file from the Formulatrix - selected_point should correspond to co-ordinates on '\n 'this image.')\n else:\n parser.add_argument('Formulatrix_image',\n metavar=\"Formulatrix_image_path\",\n type=argparse.FileType('r'),\n help='Image file from the Formulatrix - selected_point should correspond to co-ordinates on '\n 'this image.')\n parser.add_argument('beamline_stack_path',\n metavar=\"beamline_stack_path\",\n help=\"A path pointing at a directory which stores images to be stacked or a path to a stacked image.\")\n parser.add_argument('selected_points',\n metavar=\"x,y\",\n nargs='*',\n help=\"Comma-separated co-ordinates of selected points to be translated from the marked image \"\n \"to the target image.\")\n parser.add_argument('-o','--output',\n metavar=\"focused_image_path\",\n help=\"Specify directory for the stacked image. \"\n \"A file called 'processed.tif' will be created in the directory.\"\n \"'processed.tif' will be created in log directory if this is not set.\")\n parser.add_argument('--config',\n metavar=\"path\",\n action=ReadableConfigDir,\n default=join(self.get_script_path(), readable_config_dir.CONFIG_DIR_NAME),\n help=\"Sets the configuration directory.\")\n parser.add_argument('--scale',\n metavar=\"scale\",\n help=\"The scale between the Formulatrix and beamline image given as the resolution of each \"\n \"image separated by a colon. Note this is relative (1:2 is the same as 2:4) and a value \"\n \"must be specified for each image using the format \"\n \"'[Formulatrix_image_resolution]:[beamline_image_resolution]'.\")\n parser.add_argument('-j', '--job',\n metavar=\"job_id\",\n help=\"Specify a job_id - this will be reported in the output to help identify this run.\")\n parser.add_argument('--to_json',\n action='store_true',\n help=\"Output a JSON object.\")\n parser.add_argument('--version',\n action='version',\n version=VersionHandler.version_string())\n parser.add_argument('--log',\n metavar=\"path\",\n help=\"Write log files to the directory specified by path.\")\n self.parser = parser","def base_gate_sequence_and_macros(model, basic_gates_macros: dict = None):\n prep_fiducials, meas_fiducials, germs = (\n model.prep_fiducials(),\n model.meas_fiducials(),\n model.germs(),\n )\n\n # create minimal generating gate sequence\n base_gate_sequence = list({k.str.split(\"@\")[0] for k in prep_fiducials + germs + meas_fiducials})\n base_gate_sequence.remove(\"{}\")\n base_gate_sequence.sort(key=len, reverse=True)\n\n if basic_gates_macros:\n # create generating gate sequence macros\n base_gate_sequence_macros = [s.split(\"G\") for s in base_gate_sequence]\n for i, s in enumerate(base_gate_sequence_macros):\n s = [basic_gates_macros[k] for k in s if basic_gates_macros.get(k) is not None]\n base_gate_sequence_macros[i] = sequence_macros(s)\n return base_gate_sequence, base_gate_sequence_macros\n else:\n return base_gate_sequence","def parse_qasm(qasm):\n\n lines = qasm.split('\\n')\n n = int(lines[0])\n\n # turn into tuples of python types\n gates = [\n tuple(map(_convert_ints_and_floats, line.strip().split(\" \")))\n for line in lines[1:] if line\n ]\n\n # put registers/parameters in standard order and detect if gate round used\n gates = tuple(map(_put_registers_last, gates))\n round_specified = isinstance(gates[0][0], numbers.Integral)\n\n return {\n 'n': n,\n 'gates': gates,\n 'n_gates': len(gates),\n 'round_specified': round_specified,\n }","def parseCommandLine():\n parser = OptionParser(usage=\"%prog \", version=\"%prog \" + __version__,\n description='''\n This program calculates omegaAB value from a hexagonal lattice trajectory\n stored in xyz file (see for more details)''')\n parser.add_option(\"-f\", \"--traj\", dest=\"inXyzFilename\",default = \"hexTraj.xyz\",\n help=\"xyz input trajectory file (default traj.xyz)\", metavar=\"INXYZFILE\")\n parser.add_option(\"-r\", \"--reference\", dest=\"symbol\",default = \"P11\",\n help=\"reference particle name\", metavar=\"ADATOM\")\n parser.add_option(\"-o\", \"--output\", dest=\"outDatFilename\", default=\"omega.dat\",\n help=\"output dat file with omega values for each frame. WARNING: it will be overriden\", metavar=\"OUTXYZFILE\")\n \n parser.add_option(\"-q\", \"--quiet\",\n action=\"store_false\", dest=\"verbose\", default=True,\n help=\"don't print status messages to stdout\")\n\n (options, _) = parser.parse_args()\n\n return options","def _parseFileHeader(self):\n self.fileheader = FileHeader()\n self.fileheader.parse(self.f)\n #print('Parsed fileheader')","def parse_scan_args(file_path: str) -> dict:\n log = ess_factory(fullpath=file_path, check_for_errors=False)\n scan_args = {'scan': None, 'freeze': [],\n 'step': 0, 'step_size': 0, 'n_atom': 0}\n if isinstance(log, GaussianLog):\n try:\n # g09, g16\n scan_blk = parse_str_blocks(file_path, 'The following ModRedundant input section has been read:',\n 'Isotopes and Nuclear Properties', regex=False)[0][1:-1]\n except IndexError: # Cannot find any block\n # g03\n scan_blk_1 = parse_str_blocks(file_path, 'The following ModRedundant input section has been read:',\n 'GradGradGradGrad', regex=False)[0][1:-2]\n scan_blk_2 = parse_str_blocks(file_path, 'NAtoms=',\n 'One-electron integrals computed', regex=False)[0][:1]\n scan_blk = scan_blk_1 + scan_blk_2\n scan_pat = r'[DBA]?(\\s+\\d+){2,4}\\s+S\\s+\\d+[\\s\\d.]+'\n frz_pat = r'[DBA]?(\\s+\\d+){2,4}\\s+F'\n value_pat = r'[\\d.]+'\n for line in scan_blk:\n if re.search(scan_pat, line.strip()):\n values = re.findall(value_pat, line)\n scan_len = len(values) - 2 # atom indexes + step + stepsize\n scan_args['scan'] = [int(values[i]) for i in range(scan_len)]\n scan_args['step'] = int(values[-2])\n scan_args['step_size'] = float(values[-1])\n if re.search(frz_pat, line.strip()):\n values = re.findall(value_pat, line)\n scan_args['freeze'].append([int(values[i]) for i in range(len(values))])\n if 'NAtoms' in line:\n scan_args['n_atom'] = int(line.split()[1])\n else:\n raise NotImplementedError(f'parse_scan_args() can currently only parse Gaussian output '\n f'files, got {log}')\n return scan_args"],"string":"[\n \"def __parse_macro(self, buffer):\\n\\t\\t\\n\\t\\t# Parse an optional id\\n\\t\\tspell = self.__read_number(buffer)\\n\\t\\t\\n\\t\\t##\\n\\t\\t# FIXME technically, the effects do not exist, as\\n\\t\\t# WoW parses the identifier alphanumerically\\n\\t\\t# Do we really want that? It's easier to go back.\\n\\t\\t\\n\\t\\t# Parse an alphabetic identifier\\n\\t\\tidentifier = self.__read_alpha(buffer)\\n\\t\\t\\n\\t\\t# effect id should be the next char\\n\\t\\teffect = buffer.read(1)\\n\\t\\t\\n\\t\\t# However it's optional. If it's not here\\n\\t\\t# we have to go back one char.\\n\\t\\tif effect and effect not in (\\\"1\\\", \\\"2\\\", \\\"3\\\"):\\n\\t\\t\\tbuffer.seek(-1, SEEK_CUR)\\n\\t\\t\\teffect = \\\"\\\"\\n\\t\\t\\n\\t\\treturn spell, identifier, effect\",\n \"def parse_afos(self):\\n # at most, only look at the top four lines\\n data = \\\"\\\\n\\\".join([line.strip()\\n for line in self.sections[0].split(\\\"\\\\n\\\")[:4]])\\n tokens = re.findall(\\\"^([A-Z0-9 ]{4,6})$\\\", data, re.M)\\n if tokens:\\n self.afos = tokens[0]\",\n \"def get_macros(self, text):\\n if text is None:\\n return\\n \\n # join and split so we can accept a list or string. \\n text = ''.join(text)\\n for m in text.splitlines():\\n name, body = m.split(None, 1)\\n name, args = name.split('(', 1)\\n args = '(%s' % args\\n self.all[name] = c_ast.Macro(name, args, body)\",\n \"def __expand_macros(self, text, macros):\\n #print macros.items()\\n for k, v in macros.items():\\n text = re.sub(r'\\\\$\\\\(({key}|{key},[^)]*)\\\\)'.format(key=k),v, text)\\n\\n return text\",\n \"def parseIntoChunks(self, content):\\n p = re.compile(asmChunk)\\n\\n def categorizeChunk(match):\\n groupDict = match.groupdict()\\n if groupDict[\\\"macrodef\\\"] is not None:\\n assert groupDict[\\\"macrodefname\\\"], \\\"spairo: error: macro def has no name\\\"\\n print(\\\"spairo: warn: macro definition found: {}.\\\".format(groupDict[\\\"macrodefname\\\"]), file=sys.stderr)\\n self.macroNames.add(groupDict[\\\"macrodefname\\\"])\\n self.chunks.append(AsmChunk(index=len(self.chunks), unitType=\\\"macrodef\\\", isTextSection=self.isTextSection, text=match.group(\\\"macrodef\\\"), filename=self.filename, lineNum=self.currLine))\\n log.info(\\\"Found macro: name: {}, content: {}\\\".format(groupDict[\\\"macrodefname\\\"], groupDict[\\\"macrodef\\\"]))\\n return match.group(\\\"macrodef\\\")\\n\\n if groupDict[\\\"label\\\"] is not None:\\n self.chunks.append(AsmChunk(index=len(self.chunks), unitType=\\\"label\\\", isTextSection=self.isTextSection, text=match.group(\\\"label\\\"), filename=self.filename, lineNum=self.currLine))\\n return match.group(\\\"label\\\")\\n\\n elif groupDict[\\\"popln\\\"] is not None:\\n self.detectTextSection(match.group(\\\"popln\\\"))\\n self.chunks.append(AsmChunk(index=len(self.chunks), unitType=\\\"popln\\\", isTextSection=self.isTextSection, text=match.group(\\\"popln\\\"), filename=self.filename, lineNum=self.currLine))\\n return match.group(\\\"popln\\\")\\n\\n elif groupDict[\\\"instr\\\"] is not None:\\n assert groupDict[\\\"instrname\\\"], \\\"spairo: error: instr/macro has no name\\\"\\n # is it a macro use?\\n if groupDict[\\\"instrname\\\"] in self.macroNames:\\n # its a macro\\n print(\\\"spairo: warn: use of macro found: {}\\\".format(groupDict[\\\"instrname\\\"]), file=sys.stderr)\\n log.info(\\\"macro used: name: {}, content: {}\\\".format(groupDict[\\\"instrname\\\"], groupDict[\\\"instr\\\"]))\\n self.chunks.append(AsmChunk(index=len(self.chunks), unitType=\\\"macrouse\\\", isTextSection=self.isTextSection, text=match.group(\\\"instr\\\"), filename=self.filename, lineNum=self.currLine))\\n return match.group(\\\"instr\\\") # macro is a (set of) instruction(s)\\n else:\\n # its an instruction\\n self.chunks.append(AsmChunk(index=len(self.chunks), unitType=\\\"instr\\\", isTextSection=self.isTextSection, text=match.group(\\\"instr\\\"), filename=self.filename, lineNum=self.currLine))\\n return match.group(\\\"instr\\\")\\n\\n elif groupDict[\\\"comment\\\"] is not None:\\n self.chunks.append(AsmChunk(index=len(self.chunks), unitType=\\\"comment\\\", isTextSection=self.isTextSection, text=match.group(\\\"comment\\\").strip(), filename=self.filename, lineNum=self.currLine))\\n self.currLine += int(groupDict[\\\"lines\\\"])\\n return match.group(\\\"instr\\\")\\n\\n elif groupDict[\\\"ws\\\"] is not None:\\n self.chunks.append(\\n AsmChunk(index=len(self.chunks), unitType=\\\"ws\\\", isTextSection=self.isTextSection, text=match.group(\\\"ws\\\"), filename=self.filename, lineNum=self.currLine))\\n self.currLine += groupDict[\\\"ws\\\"].count(\\\"\\\\n\\\")\\n return match.group(\\\"ws\\\")\\n\\n elif groupDict[\\\"app\\\"] is not None:\\n self.chunks.append(\\n AsmChunk(index=len(self.chunks), unitType=\\\"app\\\", isTextSection=self.isTextSection, text=match.group(\\\"app\\\"), filename=self.filename, lineNum=self.currLine))\\n return match.group(\\\"app\\\")\\n\\n elif groupDict[\\\"nws\\\"] is not None:\\n print(\\\"AD: not white space: '{}', file: {}, line: {}\\\".format(groupDict[\\\"nws\\\"], self.filename, self.currLine))\\n assert False\\n # self.chunks.append((\\\"nws\\\", match.group(\\\"nws\\\")))\\n return match.group(\\\"nws\\\")\\n\\n else:\\n assert False, \\\"No group identified {}\\\".format(groupDict)\\n\\n p.sub(categorizeChunk, content)\",\n \"def _expand_macros(tokdict,macrodict):\\r\\n def macro_value(m):\\r\\n return '(?:%s)' % macrodict[m.groupdict()['macro']]\\r\\n for key, value in tokdict.items():\\r\\n while re.search(r'{[a-z][a-z0-9-]*}', value):\\r\\n value = re.sub(r'{(?P<macro>[a-z][a-z0-9-]*)}',\\r\\n macro_value, value)\\r\\n tokdict[key] = value\\r\\n return tokdict\",\n \"def _parse_assembler_text(text):\\n tokens = parser.findall(text)\\n factor = tokens[0]\\n lambda_variable_name = tokens[1]\\n function_id = tokens[2]\\n par_name = tokens[3]\\n\\n return \\\"lambda %s: %s * %s[%s].%s\\\" % \\\\\\n (lambda_variable_name,\\n factor,\\n lambda_variable_name,\\n function_id,\\n par_name)\",\n \"def convert_macro(macro):\\n convert_dict = {\\n 'CONTACTNAME' : 'user.name',\\n 'CONTACTALIAS' : 'user.display_name',\\n 'CONTACTEMAIL' : 'user.email',\\n 'CONTACTPAGER' : 'user.pager',\\n 'SERVICEDESC' : 'service.name',\\n 'SERVICEDISPLAYNAME' : 'service.display_name',\\n 'SERVICECHECKCOMMAND' : 'service.check_command',\\n 'SERVICESTATE' : 'service.state',\\n 'SERVICESTATEID' : 'service.state_id',\\n 'SERVICESTATETYPE' : 'service.state_type',\\n 'SERVICEATTEMPT' : 'service.check_attempt',\\n 'MAXSERVICEATTEMPT' : 'service.max_check_attempts',\\n 'LASTSERVICESTATE' : 'service.last_state',\\n 'LASTSERVICESTATEID' : 'service.last_state_id',\\n 'LASTSERVICESTATETYPE' : 'service.last_state_type',\\n 'LASTSERVICESTATECHANGE' : 'service.last_state_change',\\n 'SERVICEDOWNTIME' : 'service.downtime_depth',\\n 'SERVICEDURATIONSEC' : 'service.duration_sec',\\n 'SERVICELATENCY' : 'service.latency',\\n 'SERVICEEXECUTIONTIME' : 'service.execution_time',\\n 'SERVICEOUTPUT' : 'service.output',\\n 'SERVICEPERFDATA' : 'service.perfdata',\\n 'LASTSERVICECHECK' : 'service.last_check',\\n 'SERVICENOTES' : 'service.notes',\\n 'SERVICENOTESURL' : 'service.notes_url',\\n 'SERVICEACTIONURL' : 'service.action_url',\\n 'HOSTNAME' : 'host.name',\\n 'HOSTADDRESS' : 'host.address',\\n 'HOSTADDRESS6' : 'host.address6',\\n 'HOSTDISPLAYNAME' : 'host.display_name',\\n 'HOSTALIAS' : 'host.display_name',\\n 'HOSTCHECKCOMMAND' : 'host.check_command',\\n 'HOSTSTATE' : 'host.state',\\n 'HOSTSTATEID' : 'host.state_id',\\n 'HOSTSTATETYPE' : 'host.state_type',\\n 'HOSTATTEMPT' : 'host.check_attempt',\\n 'MAXHOSTATTEMPT' : 'host.max_check_attempts',\\n 'LASTHOSTSTATE' : 'host.last_state',\\n 'LASTHOSTSTATEID' : 'host.last_state_id',\\n 'LASTHOSTSTATETYPE' : 'host.last_state_type',\\n 'LASTHOSTSTATECHANGE' : 'host.last_state_change',\\n 'HOSTDOWNTIME' : 'host.downtime_depth',\\n 'HOSTDURATIONSEC' : 'host.duration_sec',\\n 'HOSTLATENCY' : 'host.latency',\\n 'HOSTEXECUTIONTIME' : 'host.execution_time',\\n 'HOSTOUTPUT' : 'host.output',\\n 'HOSTPERFDATA' : 'host.perfdata',\\n 'LASTHOSTCHECK' : 'host.last_check',\\n 'HOSTNOTES' : 'host.notes',\\n 'HOSTNOTESURL' : 'host.notes_url',\\n 'HOSTACTIONURL' : 'host.action_url',\\n 'TOTALSERVICES' : 'host.num_services',\\n 'TOTALSERVICESOK' : 'host.num_services_ok',\\n 'TOTALSERVICESWARNING' : 'host.num_services_warning',\\n 'TOTALSERVICESUNKNOWN' : 'host.num_services_unknown',\\n 'TOTALSERVICESCRITICAL' : 'host.num_services_critical',\\n 'COMMANDNAME' : 'command.name',\\n 'NOTIFICATIONTYPE' : 'notification.type',\\n 'NOTIFICATIONAUTHOR' : 'notification.author',\\n 'NOTIFICATIONCOMMENT' : 'notification.comment',\\n 'NOTIFICATIONAUTHORNAME' : 'notification.author',\\n 'NOTIFICATIONAUTHORALIAS' : 'notification.author',\\n 'TIMET' : 'icinga.timet',\\n 'LONGDATETIME' : 'icinga.long_date_time',\\n 'SHORTDATETIME' : 'icinga.short_date_time',\\n 'DATE' : 'icinga.date',\\n 'TIME' : 'icinga.time',\\n 'PROCESSSTARTTIME' : 'icinga.uptime',\\n 'TOTALHOSTSUP' : 'icinga.num_hosts_up',\\n 'TOTALHOSTSDOWN' : 'icinga.num_hosts_down',\\n 'TOTALHOSTSUNREACHABLE' : 'icinga.num_hosts_unreachable',\\n 'TOTALHOSTSDOWNUNHANDLED' : '-',\\n 'TOTALHOSTSUNREACHABLEUNHANDLED' : '-',\\n 'TOTALHOSTPROBLEMS' : 'down',\\n 'TOTALHOSTPROBLEMSUNHANDLED' : 'down-(downtime+acknowledged)',\\n 'TOTALSERVICESOK' : 'icinga.num_services_ok',\\n 'TOTALSERVICESWARNING' : 'icinga.num_services_warning',\\n 'TOTALSERVICESCRITICAL' : 'icinga.num_services_critical',\\n 'TOTALSERVICESUNKNOWN' : 'icinga.num_services_unknown',\\n 'TOTALSERVICESWARNINGUNHANDLED' : '-',\\n 'TOTALSERVICESCRITICALUNHANDLED' : '-',\\n 'TOTALSERVICESUNKNOWNUNHANDLED' : '-',\\n 'TOTALSERVICEPROBLEMS' : 'ok+warning+critical+unknown',\\n 'TOTALSERVICEPROBLEMSUNHANDLED' : 'warning+critical+unknown-(downtime+acknowledged)',\\n 'CHANGE_CUSTOM_CONTACT_VAR' : 'CHANGE_CUSTOM_USER_VAR',\\n }\\n\\n #The following external commands are not supported:\\n unsupported = [\\n 'CHANGE_*MODATTR',\\n 'CHANGE_CONTACT_HOST_NOTIFICATION_TIMEPERIOD',\\n 'CHANGE_HOST_NOTIFICATION_TIMEPERIOD',\\n 'CHANGE_SVC_NOTIFICATION_TIMEPERIOD',\\n 'DEL_DOWNTIME_BY_HOSTGROUP_NAME',\\n 'DEL_DOWNTIME_BY_START_TIME_COMMENT',\\n 'DISABLE_ALL_NOTIFICATIONS_BEYOND_HOST',\\n 'DISABLE_CONTACT_HOST_NOTIFICATIONS',\\n 'DISABLE_CONTACT_SVC_NOTIFICATIONS',\\n 'DISABLE_CONTACTGROUP_HOST_NOTIFICATIONS',\\n 'DISABLE_CONTACTGROUP_SVC_NOTIFICATIONS',\\n 'DISABLE_FAILURE_PREDICTION',\\n 'DISABLE_HOST_AND_CHILD_NOTIFICATIONS',\\n 'DISABLE_HOST_FRESHNESS_CHECKS',\\n 'DISABLE_NOTIFICATIONS_EXPIRE_TIME',\\n 'DISABLE_SERVICE_FRESHNESS_CHECKS',\\n 'ENABLE_ALL_NOTIFICATIONS_BEYOND_HOST',\\n 'ENABLE_CONTACT_HOST_NOTIFICATIONS',\\n 'ENABLE_CONTACT_SVC_NOTIFICATIONS',\\n 'ENABLE_CONTACTGROUP_HOST_NOTIFICATIONS',\\n 'ENABLE_CONTACTGROUP_SVC_NOTIFICATIONS',\\n 'ENABLE_FAILURE_PREDICTION',\\n 'ENABLE_HOST_AND_CHILD_NOTIFICATIONS',\\n 'ENABLE_HOST_FRESHNESS_CHECKS',\\n 'ENABLE_SERVICE_FRESHNESS_CHECKS',\\n 'READ_STATE_INFORMATION',\\n 'SAVE_STATE_INFORMATION',\\n 'SET_HOST_NOTIFICATION_NUMBER',\\n 'SET_SVC_NOTIFICATION_NUMBER',\\n 'START_ACCEPTING_PASSIVE_HOST_CHECKS',\\n 'START_ACCEPTING_PASSIVE_SVC_CHECKS',\\n 'START_OBSESSING_OVER_HOST',\\n 'START_OBSESSING_OVER_HOST_CHECKS',\\n 'START_OBSESSING_OVER_SVC',\\n 'START_OBSESSING_OVER_SVC_CHECKS',\\n 'STOP_ACCEPTING_PASSIVE_HOST_CHECKS',\\n 'STOP_ACCEPTING_PASSIVE_SVC_CHECKS',\\n 'STOP_OBSESSING_OVER_HOST',\\n 'STOP_OBSESSING_OVER_HOST_CHECKS',\\n 'STOP_OBSESSING_OVER_SVC',\\n 'STOP_OBSESSING_OVER_SVC_CHECKS',\\n]\\n # Strip the $$\\n sane_macro = macro.translate(None, '$')\\n #debug(sane_macro)\\n # Return true when it's a global parameter\\n if sane_macro in convert_dict:\\n return False, '$' + convert_dict[sane_macro] + '$'\\n elif sane_macro in unsupported:\\n return False, 'UNSUPPORTED'\\n elif not sane_macro in ['ARG1','ARG2','ARG3','ARG4','ARG5','ARG6']:\\n return True, sane_macro.title()\\n else:\\n return False, ''\",\n \"def parse_aperture_mask(\\n tpf,\\n sap_mask=\\\"pipeline\\\",\\n aper_radius=None,\\n percentile=None,\\n verbose=False,\\n threshold_sigma=None,\\n):\\n if verbose:\\n if sap_mask == \\\"round\\\":\\n print(\\n \\\"aperture photometry mask: {} (r={} pix)\\\\n\\\".format(\\n sap_mask, aper_radius\\n )\\n )\\n elif sap_mask == \\\"square\\\":\\n print(\\n \\\"aperture photometry mask: {0} ({1}x{1} pix)\\\\n\\\".format(\\n sap_mask, aper_radius\\n )\\n )\\n elif sap_mask == \\\"percentile\\\":\\n print(\\n \\\"aperture photometry mask: {} ({}%)\\\\n\\\".format(\\n sap_mask, percentile\\n )\\n )\\n else:\\n print(\\\"aperture photometry mask: {}\\\\n\\\".format(sap_mask))\\n\\n # stacked_img = np.median(tpf.flux,axis=0)\\n if (sap_mask == \\\"pipeline\\\") or (sap_mask is None):\\n errmsg = \\\"tpf does not have pipeline mask\\\"\\n assert tpf.pipeline_mask is not None, errmsg\\n mask = tpf.pipeline_mask # default\\n elif sap_mask == \\\"all\\\":\\n mask = np.ones((tpf.shape[1], tpf.shape[2]), dtype=bool)\\n elif sap_mask == \\\"round\\\":\\n assert aper_radius is not None, \\\"supply aper_radius\\\"\\n mask = make_round_mask(tpf.flux[0], radius=aper_radius)\\n elif sap_mask == \\\"square\\\":\\n assert aper_radius is not None, \\\"supply aper_radius/size\\\"\\n mask = make_square_mask(tpf.flux[0], size=aper_radius, angle=None)\\n elif sap_mask == \\\"threshold\\\":\\n assert threshold_sigma is not None, \\\"supply threshold_sigma\\\"\\n # FIXME: make sure aperture is contiguous\\n mask = tpf.create_threshold_mask(threshold_sigma)\\n elif sap_mask == \\\"percentile\\\":\\n assert percentile is not None, \\\"supply percentile\\\"\\n median_img = np.nanmedian(tpf.flux, axis=0)\\n mask = median_img > np.nanpercentile(median_img, percentile)\\n else:\\n raise ValueError(\\\"Unknown aperture mask\\\")\\n return mask\",\n \"def _parse_program(raw_program: list):\\n curr_mask = dict()\\n masks = list()\\n splitter = ' = '\\n\\n for p in raw_program:\\n if 'mask' in p:\\n split_pea = p.split(splitter)\\n mask = split_pea[1]\\n if curr_mask:\\n masks.append(curr_mask)\\n curr_mask = dict()\\n curr_mask['mask'] = mask\\n else:\\n split_memory = p.split(splitter)\\n mem = int(split_memory[0][4:-1])\\n val = int(split_memory[1])\\n curr_mask[mem] = val\\n\\n if curr_mask:\\n masks.append(curr_mask)\\n\\n return masks\",\n \"def macro_definition(self):\\n identifier = self.match_type(Identifier)\\n\\n # Match function-like macro definitions\\n arg_pos = self.pos\\n try:\\n # Read a list of arguments between parentheses.\\n # whitespace is NOT permitted before the opening paren.\\n punctuator = self.match_value(Punctuator, \\\"(\\\")\\n if punctuator.prev_white:\\n raise ParseError(\\\"Not a function-like macro.\\\")\\n args = self.__arg_list()\\n punctuator = self.match_value(Punctuator, \\\")\\\")\\n except ParseError:\\n args = None\\n self.pos = arg_pos\\n\\n return (identifier, args)\",\n \"def process_macro(parent, macro, style_macros, reference):\\n mlist = [process_node(parent, style_node, style_macros, reference) \\n for style_node in macro]\\n return(mlist)\",\n \"def _parse_prefix(i, doc):\\n\\n assert isinstance(i, int)\\n assert isinstance(doc, List)\\n\\n i, guard_macro = parse_pattern(i, doc, \\\"#ifndef (\\\\S+)$\\\")\\n i, define_macro = parse_pattern(i, doc, \\\"#define (\\\\S+)$\\\")\\n if guard_macro != define_macro:\\n raise ParseFailure(i, f\\\"guard macro mismatch: {guard_macro} / {define_macro}\\\")\\n i, = parse_pattern(i, doc, \\\"// <<< Use Configuration Wizard in Context Menu >>>\\\")\\n i, = parse_pattern(i, doc, \\\"#ifdef USE_APP_CONFIG\\\")\\n i, = parse_pattern(i, doc, '#include \\\"app_config.h\\\"')\\n i, = parse_pattern(i, doc, \\\"#endif\\\")\\n\\n return i, guard_macro\",\n \"def edit_template(self, template):\\n macro = []\\n for line in template:\\n search_result = re.search(line_to_edit, line)\\n if search_result != None:\\n line = line[(search_result.start()+1):]\\n if line.find(\\\"/rat/procset\\\") >= 0:\\n parts = line.split(\\\" \\\")\\n new_line = parts[0] + \\\" \\\" + parts[1] + \\\" \\\\\\\"\\\"\\n new_line += self._path\\n new_line += \\\"\\\\\\\"\\\\n\\\"\\n line = new_line\\n if line.find(\\\"/generator/add\\\") >= 0:\\n parts = line.split(\\\" \\\")\\n new_line = parts[0] + \\\" \\\" + parts[1] + \\\" \\\"\\n parts2 = parts[2].split(\\\":\\\")\\n new_line += self._generator.get_generator() + \\\":\\\" + parts2[1]\\n new_line += \\\"\\\\n\\\"\\n line = new_line\\n if line.find(\\\"/generator/vtx/set\\\") >= 0:\\n parts = line.split(\\\" \\\")\\n new_line = parts[0] + \\\" \\\"\\n new_line += self._generator.get_type() + \\\" \\\"\\n new_line += self._generator.get_isotope().get_name() + \\\" \\\"\\n new_line += str(int(self._generator.get_level())) + \\\" \\\"\\n new_line += str(int(self._generator.get_mode())) + \\\" \\\"\\n new_line += str(self._generator.get_e_lo()) + \\\" \\\"\\n new_line += str(self._generator.get_e_hi())\\n new_line += \\\"\\\\n\\\"\\n line = new_line\\n try:\\n assert(re.match\\\\\\n (r\\\"^.*\\\\s[0-9]{1,2}?\\\\s[0-9]{1,2}?\\\\s\\\"\\n \\\"[0-9]+\\\\.[0-9]+\\\\s[0-9]+\\\\.[0-9]+$\\\", line)\\\\\\n != None),\\\\\\n \\\"/generator/vtx/set line has incorrect format\\\"\\n except AssertionError as detail:\\n print \\\"generate_spectrum.edit_template: error,\\\", detail\\n sys.exit(1)\\n if line.find(\\\"/rat/run/start\\\") >= 0:\\n parts = line.split(\\\" \\\")\\n new_line = parts[0] + \\\" \\\" + str(self._n_events)\\n new_line += \\\"\\\\n\\\"\\n line = new_line\\n macro.append(line)\\n return macro\",\n \"def readMaf( options, data ):\\n regex = 's\\\\s+([\\\\w\\\\d\\\\-]+?)\\\\.([\\\\w\\\\d\\\\.\\\\+\\\\-]+?)\\\\s+(\\\\d+)\\\\s+(\\\\d+)\\\\s+([-+])\\\\s+(\\\\d+)\\\\s+([\\\\-actgurykmswbdhvnACTGURYKMSWBDHVN]+)'\\n pat = re.compile( regex )\\n mf = open( options.maf )\\n mafLineList = []\\n order = -1\\n hplList = []\\n hpl = ''\\n five = ''\\n three = ''\\n for line in mf:\\n if line.startswith('#HPL'):\\n d = line.split(' ')\\n # example line: \\\"#HPL=12049 5=1 3=1 SPL=123412 S5=0 S3=12\\\"\\n # there will be one hpl line per options.other line\\n # in blocks that contain the options.ref\\n hpl = int( d[0][5:] ) # comment at start of this field\\n hFive = int( d[1][2] )\\n hThree = int( d[2][2] )\\n spl = int( d[3][4:] ) # no comment at start of this field\\n hplList.append( { 'hpl': hpl, 'hFive': hFive, \\n 'hThree': hThree, 'spl': spl } )\\n continue\\n if line.startswith('s'):\\n line = line.strip()\\n ml, order = extractMafLine( line, order, pat, options, data )\\n if ml is None:\\n sys.stderr.write( 'regexp fail on file %s line: \\\\'%s\\\\'\\\\n'\\n 'Regex: \\\\'%s\\\\'\\\\n' % ( options.maf, line, regex ) )\\n sys.exit( 1 )\\n if ml == 'notOurGenome':\\n continue\\n if ml.length != len( ml.sequence ):\\n sys.stderr.write( 'Error while working on file %s :\\\\n '\\n 'printed sequence length (%d) not equal to actual sequence '\\n 'length (%d) ref genome:%s other genome:%s line below:\\\\n%s\\\\n' % \\n ( options.maf, ml.length, len( ml.sequence ), options.ref, options.other, line ) )\\n sys.exit( 1 )\\n mafLineList.append( ml )\\n else:\\n # end of the block\\n if len( mafLineList ) > 0:\\n extractBlockPairs( mafLineList, hplList, options, data )\\n mafLineList = []\\n order = -1\\n hplList = []\\n hpl = ''\\n five = ''\\n three = ''\\n if len( mafLineList ) > 0:\\n extractBlockPairs( mafLineList, hplList, options, data )\",\n \"def read_macroctd(self, data_file):\\n if type(data_file) == str:\\n fid = open(data_file)\\n elif type(data_file) == file:\\n fid = data_file\\n initial_file_location = fid.tell()\\n\\n self.header_lines = []\\n\\n buf = fid.readline()\\n self.header_lines.append(buf)\\n buf = fid.readline()\\n self.header_lines.append(buf)\\n self.serial_number = buf.split(',')[3]\\n\\n while buf:\\n if buf[0:9] == '@AVERAGES':\\n break\\n\\n if buf[0:11] == '@DEPLOYMENT':\\n self.site_name = buf.split(None, 1)[-1].strip('\\\"\\\\r\\\\n')\\n\\n self.header_lines.append(buf)\\n buf = fid.readline()\\n\\n fields = ['Date', 'Time', 'Battery', 'Temperature', 'EC', 'Pressure']\\n params = fields[2:]\\n units = ['volts', 'degC', 'mS/cm', 'psi']\\n\\n data = np.genfromtxt(fid, delimiter=',', dtype=None, names=fields)\\n\\n if type(data_file) == str:\\n fid.close()\\n else:\\n fid.seek(initial_file_location)\\n\\n self.dates = np.array(\\n [datetime.datetime.strptime(d + t, '%m/%d/%y%H:%M')\\n for d, t in zip(data['Date'], data['Time'])])\\n\\n #atm pressure correction for macroctd\\n data['Pressure'] -= 14.7\\n #assign param & unit names\\n for param, unit in zip(params, units):\\n self.num_params += 1\\n self.parameters.append(Parameter(param.strip(), unit.strip()))\\n\\n for ii in range(self.num_params):\\n param = self.parameters[ii].name\\n self.parameters[ii].data = data[param]\",\n \"def macros(self) -> Dict[str, List[str]]:\\n\\n result: Dict[str, List[str]] = {}\\n for spec in self.specs.values():\\n result[spec.name] = []\\n for macro in spec.macros.values():\\n result[spec.name].append(macro[0])\\n return result\",\n \"def special_defmacro(self, form):\\n if not len(form) >= 3:\\n raise SyntaxError(\\\"Not enough forms\\\")\\n #print form\\n form[0] = I('def')\\n #print \\\"Macro s-exps:\\\", form\\n fun = self.compileModule([form])\\n #print \\\"macro-function:\\\", fun\\n code = self.getCode(fun, mode='exec')\\n ns = makeNS({})\\n #print \\\"EVALING\\\", code, \\\"IN\\\", ns\\n eval(code, ns)\\n self.macros[form[1][0].name] = ns[form[1][0].name]\\n #print \\\"GOT THE MACRO!\\\", ns[form[1].name]\",\n \"def haar_parser():\\n\\n tree = ET.parse('haarcascade_frontalface_alt.xml')\\n root = tree.getroot()\\n stage_number = 0\\n\\n for haar_data in root.findall('haarcascade_frontalface_alt'):\\n for stage in haar_data.findall('stages'):\\n for underscore in stage.findall('_'):\\n for tree in underscore.findall('trees'):\\n feature_number = 0\\n\\n STAGE_THRESH = float(sci_notation_to_float(underscore.find('stage_threshold').text))\\n\\n # print the data in form: `define STAGE_THRESH_stage# value\\n # f'{variable:.20f}' is used to suppress the default convention of Python to print floats in sci notation\\n print (\\\"`define STAGE_THRESH_\\\" + str(stage_number) + \\\" \\\" + str(f'{STAGE_THRESH:.20f}') + \\\";\\\")\\n for underscore_1 in tree.findall('_'):\\n for underscore_2 in underscore_1.findall('_'):\\n\\n # get the desired data\\n FEATURE_THRESH = float(sci_notation_to_float(underscore_2.find('threshold').text))\\n LEFT = float(sci_notation_to_float(underscore_2.find('left_val').text))\\n RIGHT = float(sci_notation_to_float(underscore_2.find('right_val').text))\\n\\n # print the data in the form: `define VARIABLE_stage#_feature# value\\n print (\\\"`define FEATURE_THRESH_\\\" + str(stage_number) + \\\"_\\\" + str(feature_number) + \\\" \\\" + str(f'{FEATURE_THRESH:.20f}') + \\\";\\\")\\n print (\\\"`define LEFT_\\\" + str(stage_number) + \\\"_\\\" + str(feature_number) + \\\" \\\" + str(f'{LEFT:.20f}') + \\\";\\\")\\n print (\\\"`define RIGHT_\\\" + str(stage_number) + \\\"_\\\" + str(feature_number) + \\\" \\\" + str(f'{RIGHT:.20f}') + \\\";\\\")\\n\\n # get the desired data from rectangles\\n for feature in underscore_2.findall('feature'):\\n for rects in feature.findall('rects'):\\n rectangle_number = 0\\n for rect in rects.findall('_'):\\n first_space = rect.text.find(\\\" \\\")\\n second_space = rect.text.find(\\\" \\\", first_space + 1)\\n third_space = rect.text.find(\\\" \\\", second_space + 1)\\n fourth_space = rect.text.find(\\\" \\\", third_space + 1)\\n\\n print (\\\"`define X_COORD_\\\" + str(stage_number) + \\\"_\\\" + str(feature_number) + \\\"_\\\" + str(rectangle_number) + \\\" \\\" + rect.text[0:first_space] + \\\";\\\")\\n print (\\\"`define Y_COORD_\\\" + str(stage_number) + \\\"_\\\" + str(feature_number) + \\\"_\\\" + str(rectangle_number) + rect.text[first_space:second_space] + \\\";\\\")\\n print (\\\"`define WIDTH_\\\" + str(stage_number) + \\\"_\\\" + str(feature_number) + \\\"_\\\" + str(rectangle_number) + rect.text[second_space:third_space] + \\\";\\\")\\n print (\\\"`define HEIGHT_\\\" + str(stage_number) + \\\"_\\\" + str(feature_number) + \\\"_\\\" + str(rectangle_number) + rect.text[third_space:fourth_space] + \\\";\\\")\\n\\n rectangle_number += 1\\n\\n feature_number += 1\\n\\n stage_number += 1\",\n \"def parse_design(self, detailed_design_file):\",\n \"def _parse(self, content):\\n os.environ['ASTER_VERSION_DIR'] = self.dirn\\n cfg = {}\\n self._content = content\\n for l in split_endlines(self._content):\\n if not re.search('^[ ]*#', l):\\n try:\\n typ, nam, ver, val = l.split('|')\\n #print '========>', typ, '//', nam, '//', ver, '//', val\\n typ = re.sub('^[ ]*', '', re.sub('[ ]*$', '', typ)).strip()\\n val = re.sub('^[ ]*', '', re.sub('[ ]*$', '', val)).strip()\\n if val != '':\\n val = osp.expandvars(val)\\n if cfg.has_key(typ):\\n cfg[typ].append(val)\\n else:\\n cfg[typ] = [val]\\n except ValueError:\\n pass\\n return cfg\",\n \"def enrich_macro(self):\\n if self.multi is True:\\n # The macro has no inputs\\n rxp = '\\\\\\\\' + self.macro_name + '\\\\s*(.*$)'\\n else:\\n # The macro has one or more inputs\\n rxp = '\\\\\\\\' + self.macro_name + '(?![a-zA-Z])'\\n return rxp\",\n \"def parse_directive(line):\\n composite = list()\\n pointer = line.find(\\\"#\\\")\\n composite.append(line[0: pointer])\\n composite.append(line[pointer + 1: len(line) - 1])\\n return composite\",\n \"def setup_parser(self) -> Dict[str, Any]:\\n\\n\\n # % GALAT - SPP Single Point Positioning\\n # % -------------------------------------\\n # % Processing Option\\n # % ------------------\\n # % GNSS system(s) : GALILEO\\n # % Orbit type : Broadcast - INAV\\n # % Solution type : SPP\\n # % Frequency : E1\\n # % Elevation mask : 5.0 deg\\n # % Time interval : 30.0 s\\n # % Ionosphere opt : NeQuick-G\\n # % Troposhere opt : GMF with GPT\\n # % Obs start : 2020/01/04 00:00:00.0 GPST (week 2086 518400.0s)\\n # % Obs end : 2020/01/04 23:59:30.0 GPST (week 2086 604770.0s)\\n # % Epoch expected : 2880\\n # % Epoch have : 2880\\n # %\\n # % Input file(s) : KOUG00GUF_R_20200040000_01D_30S_MO.rnx\\n # % Input file(s) : CNES0030.20L\\n # % Input file(s) : CNES0040.20L\\n # % Input file(s) : igs14.atx\\n # %\\n # % RINEX header info\\n # % ------------------\\n # % Marker : KOUG 97301M402\\n # % Receiver T/V/# : SEPT POLARX5TR 5.3.0 17323022503\\n # % Antenna T/ /# : LEIAR25.R3 LEIT 10180007\\n # % Position XYZ : 3855263.3407 -5049731.9986 563040.4252\\n # % Antenna H/E/N : 0.0000 0.0000 0.0000\\n self._parse_header()\\n\\n # ----+----1----+----2----+----3----+----4----+----5----+----6----+----7----+----8----+----9----+----0----+--\\n # 2020/01/04 00:00:00 5.098466365 -52.639742999 106.8901 -0.603 -0.821 -0.349 1.018 0.349 \\n # 2020/01/04 00:00:30 5.098466094 -52.639742684 107.4962 -0.633 -0.856 0.257 1.065 0.257 \\n # 2020/01/04 00:01:00 5.098466030 -52.639740961 107.6125 -0.640 -1.047 0.373 1.228 0.373 \\n return dict(\\n names=(\\n \\\"yyyymmdd\\\", \\n \\\"hhmmss\\\", \\n \\\"latitude\\\", \\n \\\"longitude\\\", \\n \\\"height\\\", \\n \\\"dlatitude\\\", \\n \\\"dlongitude\\\", \\n \\\"dheight\\\",\\n \\\"hpe\\\",\\n \\\"vpe\\\",\\n \\\"site_vel_3d\\\",\\n \\\"pdop\\\",\\n \\\"num_satellite_available\\\",\\n \\\"num_satellite_used\\\",\\n ),\\n comments=\\\"%\\\",\\n delimiter=(10, 9, 15, 15, 10, 9, 9, 9, 9, 9, 9, 6, 4, 4),\\n dtype=(\\\"U10\\\", \\\"U9\\\", \\\"f8\\\", \\\"f8\\\", \\\"f8\\\", \\\"f8\\\", \\\"f8\\\", \\\"f8\\\", \\\"f8\\\", \\\"f8\\\", \\\"f8\\\", \\\"f8\\\", \\\"f8\\\", \\\"f8\\\"),\\n autostrip=True,\\n )\",\n \"def parse(source):\\r\\n #remove shared indentation\\r\\n source = dedent(source)\\r\\n print source\\r\\n\\r\\n structure = structure_parse(source)\\r\\n\\r\\n print structure.signature\\r\\n print structure.annotation\\r\\n print structure.body\\r\\n\\r\\n\\r\\n signature = signature_parse(structure.signature)\\r\\n\\r\\n kernel = kernel_parse(signature.kernel)\\r\\n inputs = input_parse(signature.input)\\r\\n\\r\\n print signature.kernel\\r\\n print signature.input\\r\\n print signature.output\\r\\n\\r\\n\\r\\n quit()\",\n \"def parse(self, content):\\n self._sections = {}\\n self._filters = []\\n section = None\\n\\n def error(msg):\\n print('autodl.cfg: line {}: {}'.format(i + 1, msg))\\n # log('autodl.cfg: line {}: {}'.format(i + 1, msg))\\n\\n first_prog = re.compile(ur'^\\\\[\\\\s*([\\\\w\\\\-]+)\\\\s*(?:([^\\\\]]+))?\\\\s*]$')\\n second_prog = re.compile(ur'^([\\\\w\\\\-]+)\\\\s*=(.*)$')\\n lines = content['data'].split('\\\\n')\\n for line in lines:\\n i = 0\\n line = line.strip()\\n if line == '':\\n continue\\n\\n first_array = first_prog.match(line)\\n second_array = second_prog.match(line)\\n if line[0] == '#':\\n if section:\\n section.add_comment(line)\\n elif first_array:\\n _type = first_array.group(1).strip().lower()\\n try:\\n _name = first_array.group(2).strip().lower()\\n except AttributeError:\\n _name = None\\n section = self.get_section(_type, _name)\\n elif second_array:\\n if section is None:\\n error('Missing a [section]')\\n else:\\n _option = second_array.group(1).strip().lower()\\n _value = second_array.group(2).strip().lower()\\n section.add_option(_option, _value)\\n else:\\n error('Ignoring line')\\n i += 1\",\n \"def parse_hand(self):\\n self.parse_part()\\n self.parse_header()\\n self.parse_setup()\\n self.parse_preflop()\\n self.parse_flop()\\n self.parse_turn()\\n self.parse_river()\\n self.parse_showdown()\\n self.conclude_hand()\",\n \"def _parse_definition_V4X(par, parfile):\\n line = None\\n while line != '':\\n pos = parfile.tell()\\n line = parfile.readline().strip()\\n #Parse the useful parts of the definition entry:\\n #the identifier-valid name, the number of columns, and the type\\n m = re.search(r'# ([^<>\\\\(\\\\)\\\\[\\\\]]*[a-zA-Z]).*\\\\((\\\\d+)?[\\\\*]?(\\\\w+)\\\\)', line)\\n if not m:\\n if not par.fields:\\n continue\\n else:\\n parfile.seek(pos)\\n break\\n var_descrip, type_len, type_descrip = m.group(1, 2, 3)\\n var_name = _sanitize_to_identifer(var_descrip).lower()\\n if type_len:\\n type_len = int(type_len)\\n else:\\n type_len = 1\\n #'string' should be interpreted as integer regardless\\n if type_descrip == 'integer' or type_descrip == 'string':\\n type_code = np.int64\\n elif type_descrip == 'float':\\n type_code = np.float64 # Same as MATLAB double\\n else:\\n raise ValueError(descrip)\\n #Sub variables exist for variables that have size > 1\\n #We add an underscore plus the name of the sub variable\\n #i.e. image_angulation_x, image_angulation_y, image_angulation_z\\n if type_len > 1:\\n par.fields.extend(tuple((var_name + '_' + s, type_code)\\n for s in _SUBVAR_NAMES[var_name]))\\n else:\\n par.fields.append((var_name, type_code))\\n par.field_len = len(par.fields)\\n return par.fields\",\n \"def parse_defines(self):\\n for line in self.header.splitlines():\\n if line.lower().startswith(\\\"#define\\\"):\\n _, line = line.strip().split(None, 1) # remove #define\\n if \\\" \\\" in line:\\n symbol, value = line.split(None, 1)\\n if value.isdigit():\\n value = int(value)\\n elif value.startswith(\\\"0x\\\"):\\n value = int(value, 16)\\n elif value in self.types:\\n self.types[symbol] = self.types[value]\\n else:\\n symbol = line\\n value = \\\"\\\"\\n self.constants[symbol] = value\\n return self.constants\",\n \"def make_parser(actions=None):\\n if actions is None:\\n actions = {}\\n\\n # Start off with the imported pijnu library functions:\\n toolset = globals().copy()\\n\\n parser = Parser()\\n state = parser.state\\n\\n### title: preprocessor ###\\n \\n \\n def toolset_from_grammar():\\n \\\"\\\"\\\"Return a map of toolset functions hard-coded into the grammar.\\\"\\\"\\\"\\n ### <toolset>\\n def replace_by_space(node):\\n node.value = ' '\\n \\n \\n return locals().copy()\\n \\n toolset.update(toolset_from_grammar())\\n toolset.update(actions)\\n \\n ### <definition>\\n # recursive pattern(s)\\n inline = Recursive(name='inline')\\n # Codes\\n \\n LF = Char('\\\\n', expression=\\\"'\\\\\\\\x0a'\\\", name='LF')\\n CR = Char('\\\\r', expression=\\\"'\\\\\\\\x0d'\\\", name='CR')\\n EOL = Choice([LF, CR], expression='LF / CR', name='EOL')\\n TAB = Word('\\\\t', expression='\\\"\\\\t\\\"', name='TAB')\\n L_BRACKET = Word('[', expression='\\\"[\\\"', name='L_BRACKET')\\n R_BRACKET = Word(']', expression='\\\"\\\\\\\\]\\\"', name='R_BRACKET')\\n L_BRACE = Word('{', expression='\\\"{\\\"', name='L_BRACE')(toolset['drop'])\\n R_BRACE = Word('}', expression='\\\"}\\\"', name='R_BRACE')(toolset['drop'])\\n SPACE = Word(' ', expression='\\\" \\\"', name='SPACE')(toolset['drop'])\\n SPACETAB = Choice([SPACE, TAB], expression='SPACE / TAB', name='SPACETAB')(toolset['drop'])\\n SPACETABEOL = Choice([SPACE, TAB, EOL], expression='SPACE / TAB / EOL', name='SPACETABEOL')(toolset['drop'])\\n PIPE = Word('|', expression='\\\"|\\\"', name='PIPE')(toolset['drop'])\\n BANG = Word('!', expression='\\\"!\\\"', name='BANG')(toolset['drop'])\\n EQUAL = Word('=', expression='\\\"=\\\"', name='EQUAL')(toolset['drop'])\\n LT = Word('<', expression='\\\"<\\\"', name='LT')(toolset['drop'])\\n GT = Word('>', expression='\\\">\\\"', name='GT')(toolset['drop'])\\n HASH = Word('#', expression='\\\"#\\\"', name='HASH')(toolset['drop'])\\n DASH = Word('-', expression='\\\"-\\\"', name='DASH')(toolset['drop'])\\n AMP = Word('&', expression='\\\"&\\\"', name='AMP')(toolset['drop'])\\n COLON = Word(':', expression='\\\":\\\"', name='COLON')(toolset['drop'])\\n SEMICOLON = Word(';', expression='\\\";\\\"', name='SEMICOLON')(toolset['drop'])\\n TEMPLATE_BEGIN = Repetition(L_BRACE, numMin=2, numMax=2, expression='L_BRACE{2}', name='TEMPLATE_BEGIN')(toolset['drop'])\\n TEMPLATE_END = Repetition(R_BRACE, numMin=2, numMax=2, expression='R_BRACE{2}', name='TEMPLATE_END')(toolset['drop'])\\n PARAMETER_BEGIN = Repetition(L_BRACE, numMin=3, numMax=3, expression='L_BRACE{3}', name='PARAMETER_BEGIN')(toolset['drop'])\\n PARAMETER_END = Repetition(R_BRACE, numMin=3, numMax=3, expression='R_BRACE{3}', name='PARAMETER_END')(toolset['drop'])\\n \\n # Predefined tags\\n \\n NOWIKI_BEGIN = Word('<nowiki>', expression='\\\"<nowiki>\\\"', name='NOWIKI_BEGIN')\\n NOWIKI_END = Word('</nowiki>', expression='\\\"</nowiki>\\\"', name='NOWIKI_END')\\n PRE_BEGIN = Word('<pre>', expression='\\\"<pre>\\\"', name='PRE_BEGIN')\\n PRE_END = Word('</pre>', expression='\\\"</pre>\\\"', name='PRE_END')\\n special_tag = Choice([NOWIKI_BEGIN, NOWIKI_END, PRE_BEGIN, PRE_END], expression='NOWIKI_BEGIN/NOWIKI_END/PRE_BEGIN/PRE_END', name='special_tag')\\n \\n # Characters\\n \\n any_char = Choice([Klass(u' !\\\"#$%&\\\\'()*+,-./0123456789:;<=>?@ABCDEFGHIJKLMNOPQRSTUVWXYZ[\\\\\\\\]^_`abcdefghijklmnopqrstuvwxyz{|}~\\\\x7f\\\\x80\\\\x81\\\\x82\\\\x83\\\\x84\\\\x85\\\\x86\\\\x87\\\\x88\\\\x89\\\\x8a\\\\x8b\\\\x8c\\\\x8d\\\\x8e\\\\x8f\\\\x90\\\\x91\\\\x92\\\\x93\\\\x94\\\\x95\\\\x96\\\\x97\\\\x98\\\\x99\\\\x9a\\\\x9b\\\\x9c\\\\x9d\\\\x9e\\\\x9f\\\\xa0\\\\xa1\\\\xa2\\\\xa3\\\\xa4\\\\xa5\\\\xa6\\\\xa7\\\\xa8\\\\xa9\\\\xaa\\\\xab\\\\xac\\\\xad\\\\xae\\\\xaf\\\\xb0\\\\xb1\\\\xb2\\\\xb3\\\\xb4\\\\xb5\\\\xb6\\\\xb7\\\\xb8\\\\xb9\\\\xba\\\\xbb\\\\xbc\\\\xbd\\\\xbe\\\\xbf\\\\xc0\\\\xc1\\\\xc2\\\\xc3\\\\xc4\\\\xc5\\\\xc6\\\\xc7\\\\xc8\\\\xc9\\\\xca\\\\xcb\\\\xcc\\\\xcd\\\\xce\\\\xcf\\\\xd0\\\\xd1\\\\xd2\\\\xd3\\\\xd4\\\\xd5\\\\xd6\\\\xd7\\\\xd8\\\\xd9\\\\xda\\\\xdb\\\\xdc\\\\xdd\\\\xde\\\\xdf\\\\xe0\\\\xe1\\\\xe2\\\\xe3\\\\xe4\\\\xe5\\\\xe6\\\\xe7\\\\xe8\\\\xe9\\\\xea\\\\xeb\\\\xec\\\\xed\\\\xee\\\\xef\\\\xf0\\\\xf1\\\\xf2\\\\xf3\\\\xf4\\\\xf5\\\\xf6\\\\xf7\\\\xf8\\\\xf9\\\\xfa\\\\xfb\\\\xfc\\\\xfd\\\\xfe\\\\xff', expression='[\\\\\\\\x20..\\\\\\\\xff]'), Char('/', expression=\\\"'/'\\\")], expression=\\\"[\\\\\\\\x20..\\\\\\\\xff] / '/'\\\", name='any_char')\\n esc_char = Choice([L_BRACKET, R_BRACKET, PIPE, L_BRACE, R_BRACE, LT, GT, AMP, SEMICOLON], expression='L_BRACKET/R_BRACKET/PIPE/L_BRACE/R_BRACE/LT/GT/AMP/SEMICOLON', name='esc_char')\\n raw_char = Sequence([NextNot(esc_char, expression='!esc_char'), any_char], expression='!esc_char any_char', name='raw_char')\\n raw_text = Repetition(Choice([raw_char, TAB], expression='raw_char / TAB'), numMin=1, numMax=False, expression='(raw_char / TAB)+', name='raw_text')(toolset['join'])\\n numeral = Klass(u'0123456789', expression='[0..9]', name='numeral')\\n number = Sequence([Option(Word('-', expression='\\\"-\\\"'), expression='\\\"-\\\"?'), Repetition(numeral, numMin=1, numMax=False, expression='numeral+')], expression='\\\"-\\\"? numeral+', name='number')(toolset['join'])\\n \\n # HTML comments\\n # HTML comments are totally ignored and do not appear in the final text\\n \\n comment_content = Repetition(Choice([Repetition(Sequence([NextNot(Sequence([Repetition(DASH, numMin=2, numMax=2, expression='DASH{2}'), GT], expression='DASH{2} GT'), expression='!(DASH{2} GT)'), Klass(u' !\\\"#$%&\\\\'()*+,-./0123456789:;<=>?@ABCDEFGHIJKLMNOPQRSTUVWXYZ[\\\\\\\\]^_`abcdefghijklmnopqrstuvwxyz{|}~\\\\x7f\\\\x80\\\\x81\\\\x82\\\\x83\\\\x84\\\\x85\\\\x86\\\\x87\\\\x88\\\\x89\\\\x8a\\\\x8b\\\\x8c\\\\x8d\\\\x8e\\\\x8f\\\\x90\\\\x91\\\\x92\\\\x93\\\\x94\\\\x95\\\\x96\\\\x97\\\\x98\\\\x99\\\\x9a\\\\x9b\\\\x9c\\\\x9d\\\\x9e\\\\x9f\\\\xa0\\\\xa1\\\\xa2\\\\xa3\\\\xa4\\\\xa5\\\\xa6\\\\xa7\\\\xa8\\\\xa9\\\\xaa\\\\xab\\\\xac\\\\xad\\\\xae\\\\xaf\\\\xb0\\\\xb1\\\\xb2\\\\xb3\\\\xb4\\\\xb5\\\\xb6\\\\xb7\\\\xb8\\\\xb9\\\\xba\\\\xbb\\\\xbc\\\\xbd\\\\xbe\\\\xbf\\\\xc0\\\\xc1\\\\xc2\\\\xc3\\\\xc4\\\\xc5\\\\xc6\\\\xc7\\\\xc8\\\\xc9\\\\xca\\\\xcb\\\\xcc\\\\xcd\\\\xce\\\\xcf\\\\xd0\\\\xd1\\\\xd2\\\\xd3\\\\xd4\\\\xd5\\\\xd6\\\\xd7\\\\xd8\\\\xd9\\\\xda\\\\xdb\\\\xdc\\\\xdd\\\\xde\\\\xdf\\\\xe0\\\\xe1\\\\xe2\\\\xe3\\\\xe4\\\\xe5\\\\xe6\\\\xe7\\\\xe8\\\\xe9\\\\xea\\\\xeb\\\\xec\\\\xed\\\\xee\\\\xef\\\\xf0\\\\xf1\\\\xf2\\\\xf3\\\\xf4\\\\xf5\\\\xf6\\\\xf7\\\\xf8\\\\xf9\\\\xfa\\\\xfb\\\\xfc\\\\xfd\\\\xfe\\\\xff', expression='[\\\\\\\\x20..\\\\\\\\xff]')], expression='!(DASH{2} GT) [\\\\\\\\x20..\\\\\\\\xff]'), numMin=1, numMax=False, expression='(!(DASH{2} GT) [\\\\\\\\x20..\\\\\\\\xff])+'), SPACETABEOL], expression='(!(DASH{2} GT) [\\\\\\\\x20..\\\\\\\\xff])+ / SPACETABEOL'), numMin=False, numMax=False, expression='((!(DASH{2} GT) [\\\\\\\\x20..\\\\\\\\xff])+ / SPACETABEOL)*', name='comment_content')\\n html_comment = Sequence([LT, BANG, Repetition(DASH, numMin=2, numMax=2, expression='DASH{2}'), comment_content, Repetition(DASH, numMin=2, numMax=2, expression='DASH{2}'), GT], expression='LT BANG DASH{2} comment_content DASH{2} GT', name='html_comment')(toolset['drop'])\\n \\n # Text\\n \\n page_name = Repetition(raw_char, numMin=1, numMax=False, expression='raw_char+', name='page_name')(toolset['join'])\\n \\n # Template parameters\\n # Those parameters should be substituted by their value when the current page is a template\\n # or by their optional default value in any case\\n \\n parameter_id = Repetition(raw_char, numMin=1, numMax=False, expression='raw_char+', name='parameter_id')(toolset['join'])\\n parameter_value = Option(inline, expression='inline?', name='parameter_value')(toolset['keep'])\\n optional_default_value = Sequence([Option(Sequence([PIPE, Repetition(SPACETABEOL, numMin=False, numMax=False, expression='SPACETABEOL*'), parameter_value], expression='PIPE SPACETABEOL* parameter_value'), expression='(PIPE SPACETABEOL* parameter_value)?'), Repetition(SPACETABEOL, numMin=False, numMax=False, expression='SPACETABEOL*')], expression='(PIPE SPACETABEOL* parameter_value)? SPACETABEOL*', name='optional_default_value')(toolset['liftNode'])\\n template_parameter = Sequence([PARAMETER_BEGIN, parameter_id, optional_default_value, PARAMETER_END], expression='PARAMETER_BEGIN parameter_id optional_default_value PARAMETER_END', name='template_parameter')(toolset['substitute_template_parameter'])\\n \\n # Links\\n \\n LINK_PIPE = Clone(PIPE, expression='PIPE', name='LINK_PIPE')(toolset['restore'])\\n internal_link = Sequence([Repetition(L_BRACKET, numMin=2, numMax=2, expression='L_BRACKET{2}'), inline, Repetition(Sequence([LINK_PIPE, inline], expression='LINK_PIPE inline'), numMin=False, numMax=False, expression='(LINK_PIPE inline)*'), Repetition(R_BRACKET, numMin=2, numMax=2, expression='R_BRACKET{2}')], expression='L_BRACKET{2} inline (LINK_PIPE inline)* R_BRACKET{2}', name='internal_link')(toolset['join'])\\n external_link = Sequence([L_BRACKET, inline, Repetition(Sequence([SPACE, inline], expression='SPACE inline'), numMin=False, numMax=False, expression='(SPACE inline)*'), R_BRACKET], expression='L_BRACKET inline (SPACE inline)* R_BRACKET', name='external_link')(toolset['join'])\\n link = Choice([internal_link, external_link], expression='internal_link / external_link', name='link')\\n \\n # Templates\\n \\n value_content = Repetition(Choice([inline, Sequence([NextNot(Sequence([Repetition(SPACETABEOL, numMin=False, numMax=False, expression='SPACETABEOL*'), Choice([TEMPLATE_END, PIPE], expression='TEMPLATE_END / PIPE')], expression='SPACETABEOL* (TEMPLATE_END / PIPE)'), expression='!(SPACETABEOL* (TEMPLATE_END / PIPE))'), Choice([any_char, EOL], expression='any_char / EOL')], expression='!(SPACETABEOL* (TEMPLATE_END / PIPE)) (any_char / EOL)')], expression='inline / (!(SPACETABEOL* (TEMPLATE_END / PIPE)) (any_char / EOL))'), numMin=False, numMax=False, expression='(inline / (!(SPACETABEOL* (TEMPLATE_END / PIPE)) (any_char / EOL)))*', name='value_content')(toolset['keep'])\\n parameter_value = Sequence([value_content, Repetition(SPACETABEOL, numMin=False, numMax=False, expression='SPACETABEOL*')], expression='value_content SPACETABEOL*', name='parameter_value')\\n optional_value = Option(parameter_value, expression='parameter_value?', name='optional_value')\\n parameter_equal = Sequence([Repetition(SPACETABEOL, numMin=False, numMax=False, expression='SPACETABEOL*'), EQUAL, Repetition(SPACETABEOL, numMin=False, numMax=False, expression='SPACETABEOL*')], expression='SPACETABEOL* EQUAL SPACETABEOL*', name='parameter_equal')\\n parameter_name = Repetition(Sequence([NextNot(Choice([esc_char, parameter_equal], expression='esc_char/parameter_equal'), expression='!(esc_char/parameter_equal)'), raw_char], expression='!(esc_char/parameter_equal) raw_char'), numMin=1, numMax=False, expression='(!(esc_char/parameter_equal) raw_char)+', name='parameter_name')(toolset['join'])\\n named_parameter = Sequence([parameter_name, parameter_equal, optional_value], expression='parameter_name parameter_equal optional_value', name='named_parameter')\\n standalone_parameter = Option(value_content, expression='value_content?', name='standalone_parameter')(toolset['join'])\\n parameter = Sequence([Repetition(SPACETABEOL, numMin=False, numMax=False, expression='SPACETABEOL*'), PIPE, Repetition(SPACETABEOL, numMin=False, numMax=False, expression='SPACETABEOL*'), Choice([named_parameter, standalone_parameter], expression='named_parameter/standalone_parameter')], expression='SPACETABEOL* PIPE SPACETABEOL* (named_parameter/standalone_parameter)', name='parameter')(toolset['liftValue'])\\n parameters = Repetition(parameter, numMin=False, numMax=False, expression='parameter*', name='parameters')\\n template = Sequence([TEMPLATE_BEGIN, page_name, parameters, Repetition(SPACETABEOL, numMin=False, numMax=False, expression='SPACETABEOL*'), TEMPLATE_END], expression='TEMPLATE_BEGIN page_name parameters SPACETABEOL* TEMPLATE_END', name='template')(toolset['substitute_template'])\\n \\n # inline allows to have templates/links inside templates/links\\n \\n structure = Choice([link, template, template_parameter], expression='link / template / template_parameter', name='structure')\\n inline **= Repetition(Choice([structure, raw_text], expression='structure / raw_text'), numMin=1, numMax=False, expression='(structure / raw_text)+', name='inline')\\n numbered_entity = Sequence([AMP, HASH, Repetition(Klass(u'0123456789', expression='[0..9]'), numMin=1, numMax=False, expression='[0..9]+'), SEMICOLON], expression='AMP HASH [0..9]+ SEMICOLON', name='numbered_entity')(toolset['substitute_numbered_entity'])\\n named_entity = Sequence([AMP, Repetition(Klass(u'abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ', expression='[a..zA..Z]'), numMin=1, numMax=False, expression='[a..zA..Z]+'), SEMICOLON], expression='AMP [a..zA..Z]+ SEMICOLON', name='named_entity')(toolset['substitute_named_entity'])\\n entity = Choice([named_entity, numbered_entity], expression='named_entity / numbered_entity', name='entity')\\n \\n # wildcard in templates\\n divider = Clone(COLON, expression='COLON', name='divider')(toolset['keep'])\\n wildcard = Sequence([Repetition(L_BRACE, numMin=4, numMax=4, expression='L_BRACE{4}'), Option(number, expression='number?'), divider, Option(number, expression='number?'), Repetition(R_BRACE, numMin=4, numMax=4, expression='R_BRACE{4}')], expression='L_BRACE{4} number? divider number? R_BRACE{4}', name='wildcard')(toolset['substitute_template_wildcard'])\\n \\n # Pre and nowiki tags\\n # Preformatted acts like nowiki (disables wikitext parsing)\\n # We allow any char without parsing them as long as the tag is not closed\\n \\n pre_text = Repetition(Sequence([NextNot(PRE_END, expression='!PRE_END'), any_char], expression='!PRE_END any_char'), numMin=False, numMax=False, expression='(!PRE_END any_char)*', name='pre_text')(toolset['join'])\\n preformatted = Sequence([PRE_BEGIN, pre_text, PRE_END], expression='PRE_BEGIN pre_text PRE_END', name='preformatted')(toolset['liftValue'])\\n eol_to_space = Repetition(EOL, numMin=False, numMax=False, expression='EOL*', name='eol_to_space')(toolset['replace_by_space'])\\n nowiki_text = Repetition(Sequence([NextNot(NOWIKI_END, expression='!NOWIKI_END'), Choice([any_char, eol_to_space], expression='any_char/eol_to_space')], expression='!NOWIKI_END (any_char/eol_to_space)'), numMin=False, numMax=False, expression='(!NOWIKI_END (any_char/eol_to_space))*', name='nowiki_text')(toolset['join'])\\n nowiki = Sequence([NOWIKI_BEGIN, nowiki_text, NOWIKI_END], expression='NOWIKI_BEGIN nowiki_text NOWIKI_END', name='nowiki')(toolset['liftValue'])\\n \\n # Text types\\n \\n styled_text = Choice([template, template_parameter, entity, wildcard], expression='template / template_parameter / entity / wildcard', name='styled_text')\\n not_styled_text = Choice([html_comment, preformatted, nowiki], expression='html_comment / preformatted / nowiki', name='not_styled_text')\\n allowed_char = Repetition(esc_char, numMin=1, numMax=1, expression='esc_char{1}', name='allowed_char')(toolset['restore'], toolset['liftValue'])\\n allowed_text = Choice([raw_text, allowed_char], expression='raw_text / allowed_char', name='allowed_text')\\n wikitext = Repetition(Choice([not_styled_text, styled_text, allowed_text, EOL], expression='not_styled_text / styled_text / allowed_text / EOL'), numMin=1, numMax=False, expression='(not_styled_text / styled_text / allowed_text / EOL)+', name='wikitext')(toolset['join'])\\n\\n symbols = locals().copy()\\n symbols.update(actions)\\n parser._recordPatterns(symbols)\\n parser._setTopPattern(\\\"wikitext\\\")\\n parser.grammarTitle = \\\"preprocessor\\\"\\n parser.filename = \\\"preprocessorParser.py\\\"\\n\\n return parser\",\n \"def test_macro_sizes(self) -> None:\\n import hammer_config\\n\\n tech_dir, tech_dir_base = HammerToolTestHelpers.create_tech_dir(\\\"dummy28\\\")\\n tech_json_filename = os.path.join(tech_dir, \\\"dummy28.tech.json\\\")\\n\\n def add_lib_with_lef(d: Dict[str, Any]) -> Dict[str, Any]:\\n with open(os.path.join(tech_dir, 'my_vendor_lib.lef'), 'w') as f:\\n f.write(\\\"\\\"\\\"VERSION 5.8 ;\\nBUSBITCHARS \\\"[]\\\" ;\\nDIVIDERCHAR \\\"/\\\" ;\\n\\nMACRO my_awesome_macro\\n CLASS BLOCK ;\\n ORIGIN -0.435 607.525 ;\\n FOREIGN my_awesome_macro 0.435 -607.525 ;\\n SIZE 810.522 BY 607.525 ;\\n SYMMETRY X Y R90 ;\\nEND my_awesome_macro\\n\\nEND LIBRARY\\n \\\"\\\"\\\")\\n r = deepdict(d)\\n r['libraries'].append({\\n 'name': 'my_vendor_lib',\\n 'lef file': 'test/my_vendor_lib.lef'\\n })\\n return r\\n\\n HammerToolTestHelpers.write_tech_json(tech_json_filename, add_lib_with_lef)\\n sys.path.append(tech_dir_base)\\n tech_opt = hammer_tech.HammerTechnology.load_from_dir(\\\"dummy28\\\", tech_dir)\\n if tech_opt is None:\\n self.assertTrue(False, \\\"Unable to load technology\\\")\\n return\\n else:\\n tech = tech_opt # type: hammer_tech.HammerTechnology\\n tech.cache_dir = tech_dir\\n\\n tech.logger = HammerVLSILogging.context(\\\"\\\")\\n\\n database = hammer_config.HammerDatabase()\\n tech.set_database(database)\\n\\n # Test that macro sizes can be read out of the LEF.\\n self.assertEqual(tech.get_macro_sizes(), [\\n hammer_tech.MacroSize(library='my_vendor_lib', name='my_awesome_macro',\\n width=Decimal(\\\"810.522\\\"), height=Decimal(\\\"607.525\\\"))\\n ])\\n\\n # Cleanup\\n shutil.rmtree(tech_dir_base)\",\n \"def __init__(self, macro_name, macro_content):\\n self._macro_name = process_for_latex(macro_name)\\n self._macro_content = macro_content\",\n \"def loadFullMMF(self, path):\\n \\n logger.info('Loading macro file %s', path)\\n \\n mmfFile = open(path)\\n \\n currentLabel = None\\n hRegExp = re.compile(\\\"~h \\\\\\\"(.+)\\\\\\\"\\\")\\n pRegExp = re.compile(\\\"~p \\\\\\\"(.+)\\\\\\\"\\\")\\n sRegExp = re.compile(\\\"~s \\\\\\\"(.+)\\\\\\\"\\\") # ~s \\\"dur_s2_102\\\"\\n \\n # read file line by line\\n line = mmfFile.readline() \\n while line:\\n #print line\\n \\n # no ~h section till now, macro definitions?\\n if currentLabel is None:\\n \\n # ~p macro? -> shared stream\\n ret = pRegExp.match(line)\\n if ret:\\n l = self.readPMacro(ret.group(1), mmfFile)\\n if l: \\n line = l\\n continue\\n \\n # ~s macro? -> shared state distribution\\n ret = sRegExp.match(line)\\n if ret:\\n l = self.readSMacro(ret.group(1), mmfFile)\\n if l: \\n line = l\\n continue\\n \\n \\n # ~h section has begun? from now on only ~h definitions \\n # ~h \\\"v^schwa-h+schwa=m@1_2/A:0_0_4/B:0-0-2@1-2&2-7#1-1$1-1!0-0;0-0|0/C:0+0+3/D:det_1/E:content+2@2+3&1+2#0+1/F:content_4/G:0_0/H:7=4@1=1|0/I:0=0/J:7+4-1\\\" \\n ret = hRegExp.match(line)\\n if ret:\\n currentLabel = LabelEntry(ret.group(1)) \\n self.labelList.append(currentLabel)\\n self.labelDict[ ret.group(1) ] = currentLabel\\n \\n \\n # we are already in the ~h section\\n elif currentLabel:\\n \\n # link to a ~p macro which is then associated with the ~h macro \\n # <STATE> 2\\n # ~w \\\"SWeightall\\\"\\n # <STREAM> 1\\n # ~p \\\"mcep_s2_72\\\" \\n ret = pRegExp.match(line)\\n # or link to a ~s macro \\n if not ret:\\n ret = sRegExp.match(line)\\n if ret:\\n currentLabel.associatedMacroNames.append(ret.group(1))\\n \\n # fill macroToLabels\\n if ret.group(1) in self.macroToLabels:\\n self.macroToLabels[ ret.group(1) ].append(currentLabel)\\n else:\\n self.macroToLabels[ ret.group(1) ] = [ currentLabel ]\\n \\n \\n line = mmfFile.readline()\\n mmfFile.close()\\n #print 'done: ' + str(len( self.macroToLabels ))\\n #print self.macroToLabels\",\n \"def update_macros(self, root_p, macros):\\n layers_len = len([p for p in root_p.iterdir() if re.search('[lL]\\\\d+', p.name)])\\n MacroInfo = namedtuple('MacroInfo', ['dim', 'len'])\\n d = {macro.id : MacroInfo(i+layers_len, len(macro)) for i, macro in enumerate(macros)}\\n self.macros_dict = d\",\n \"def parse_movie(self, line):\\n pass\",\n \"def dump_macrosizes_action(driver: HammerDriver, append_error_func: Callable[[str], None]) -> Optional[str]:\\n macro_json = list(map(lambda m: m.to_setting(), driver.tech.get_macro_sizes()))\\n return json.dumps(macro_json, indent=4)\",\n \"def setup_parser(self) -> Dict[str, Any]:\\n\\n\\t# % year,doy, RH(m), Month, day, azimuth(deg),freq, satNu, LSP amp,pk2noise,UTC(hr) \\n\\t# 2021 9 4.888 1 9 225.3 1 2 9.51 3.23 10.08\\n\\t# 2021 9 5.018 1 9 181.3 1 15 7.79 2.84 15.67\\n\\t# 2021 9 5.123 1 9 185.4 1 16 6.27 3.01 0.68\\n #----+----0----+----1----+----2----+----3----+----4----+----5----+----6----+----7\\n return dict(\\n skip_header=1,\\n names=(\\n \\\"year\\\",\\n \\\"doy\\\",\\n \\\"reflection_height\\\",\\n \\\"month\\\",\\n \\\"day\\\",\\n \\\"azimuth\\\",\\n \\\"frequency\\\",\\n \\\"satellite\\\",\\n \\\"amplitude\\\",\\n \\\"peak2noise\\\",\\n \\\"hour\\\",\\n ),\\n dtype=(\\\"f8\\\", \\\"f8\\\", \\\"f8\\\", \\\"f8\\\", \\\"f8\\\", \\\"f8\\\", \\\"f8\\\", \\\"f8\\\", \\\"f8\\\", \\\"f8\\\", \\\"f8\\\"),\\n )\",\n \"def generate_initial_siaf_aperture_definitions(instrument):\\n siaf_detector_layout = iando.read.read_siaf_detector_layout()\\n\\n prd_siaf = pysiaf.Siaf(instrument)\\n siaf_definitions = Table()\\n\\n\\n for attribute_name in 'AperName AperType XDetRef YDetRef XSciSize YSciSize XSciRef YSciRef'.split():\\n siaf_definitions[attribute_name] = [getattr(prd_siaf[aperture_name], attribute_name) for aperture_name in prd_siaf.apertures]\\n\\n parent_apertures = [None]*len(siaf_definitions)\\n dependency_type = [None]*len(siaf_definitions)\\n\\n if instrument == 'NIRISS':\\n for i,aperture_name in enumerate(siaf_definitions['AperName']):\\n if aperture_name != 'NIS_CEN':\\n parent_apertures[i] = 'NIS_CEN'\\n if '_OSS' in aperture_name:\\n dependency_type[i] = 'oss_default'\\n elif aperture_name != 'NIS_CEN':\\n dependency_type[i] = 'default'\\n\\n elif instrument == 'FGS':\\n for i,aperture_name in enumerate(siaf_definitions['AperName']):\\n if aperture_name not in ['FGS1_FULL', 'FGS2_FULL']:\\n parent_apertures[i] = '{}_FULL'.format(aperture_name.split('_')[0])\\n else:\\n dependency_type[i] = 'master'\\n if '_OSS' in aperture_name:\\n dependency_type[i] = 'oss_default'\\n elif aperture_name not in ['FGS1_FULL', 'FGS2_FULL']:\\n dependency_type[i] = 'default'\\n\\n elif instrument == 'NIRSpec':\\n for i,aperture_name in enumerate(siaf_definitions['AperName']):\\n if siaf_definitions['AperType'][i] == 'TRANSFORM':\\n continue\\n\\n if '_OSS' in aperture_name:\\n dependency_type[i] = 'oss_default'\\n parent_apertures[i] = aperture_name.split('_OSS')[0]\\n elif 'NRS_IFU' in aperture_name:\\n parent_apertures[i] = 'NRS1_FULL'\\n dependency_type[i] = 'default'\\n elif aperture_name in ['NRS_S200B1_SLIT']:\\n parent_apertures[i] = 'NRS2_FULL'\\n dependency_type[i] = 'default'\\n elif aperture_name in 'NRS_S200A1_SLIT NRS_S200A2_SLIT NRS_S400A1_SLIT NRS_S1600A1_SLIT NRS_FULL_IFU'.split():\\n parent_apertures[i] = 'NRS1_FULL'\\n dependency_type[i] = 'default'\\n elif ('_MSA1' in aperture_name) or ('_MSA2' in aperture_name):\\n parent_apertures[i] = 'NRS2_FULL'\\n dependency_type[i] = 'default'\\n elif ('_MSA3' in aperture_name) or ('_MSA4' in aperture_name):\\n parent_apertures[i] = 'NRS1_FULL'\\n dependency_type[i] = 'default'\\n elif aperture_name in ['NRS1_FP1MIMF']:\\n parent_apertures[i] = 'NRS_S1600A1_SLIT'\\n dependency_type[i] = 'FP1MIMF'\\n elif 'MIMF' in aperture_name:\\n parent_apertures[i] = aperture_name.split('_')[0]+'_FULL'\\n dependency_type[i] = 'default'\\n\\n\\n # if aperture_name not 'NIS_CEN':\\n # parent_apertures[i] = 'NIS_CEN'\\n # elif aperture_name != 'NIS_CEN':\\n # dependency_type[i] = 'default'\\n\\n elif instrument == 'NIRCam':\\n for i,aperture_name in enumerate(siaf_definitions['AperName']):\\n\\n # Master apertures\\n if aperture_name in siaf_detector_layout['AperName']:\\n dependency_type[i] = 'master'\\n\\n elif siaf_definitions['AperType'][i] in ['SUBARRAY', 'FULLSCA', 'ROI']:\\n if 'MASK' in aperture_name:\\n # Coronagraphic apertures with wedge offset\\n dependency_type[i] = 'wedge'\\n elif 'DHSPIL_WEDGES' in aperture_name:\\n dependency_type[i] = 'dhspil_wedge'\\n else:\\n dependency_type[i] = 'default'\\n sca_name = aperture_name[0:5]\\n parent_apertures[i] = '{}_FULL'.format(sca_name)\\n\\n # OSS apertures\\n elif siaf_definitions['AperType'][i] in ['OSS']:\\n dependency_type[i] = 'default'\\n parent_apertures[i] = aperture_name.split('_OSS')[0]\\n\\n elif (siaf_definitions['AperType'][i] in ['SLIT', 'COMPOUND']) and ('GRISM' in aperture_name) and ('WFSS' in aperture_name):\\n dependency_type[i] = 'grism_wfss'\\n sca_name = aperture_name.split('_')[0]\\n # sca_name = aperture_name[0:5]\\n parent_apertures[i] = '{}_FULL'.format(sca_name)\\n\\n # elif 'MASK' in aperture_name:\\n # dependency_type[i] = 'wedge'\\n # sca_name = aperture_name[0:5]\\n # parent_apertures[i] = '{}_FULL'.format(sca_name)\\n\\n\\n\\n elif aperture_name in 'NRCALL_FULL NRCAS_FULL NRCBS_FULL'.split():\\n dependency_type[i] = 'nircam_compound'\\n if aperture_name == 'NRCALL_FULL':\\n parent_apertures[i] = '; '.join(['NRCA1_FULL', 'NRCB2_FULL', 'NRCB1_FULL', 'NRCA2_FULL'])\\n elif aperture_name == 'NRCAS_FULL':\\n parent_apertures[i] = '; '.join(['NRCA1_FULL', 'NRCA3_FULL', 'NRCA4_FULL', 'NRCA2_FULL'])\\n elif aperture_name == 'NRCBS_FULL':\\n parent_apertures[i] = '; '.join(['NRCB4_FULL', 'NRCB2_FULL', 'NRCB1_FULL', 'NRCB3_FULL'])\\n\\n\\n\\n siaf_definitions['parent_apertures'] = parent_apertures\\n siaf_definitions['dependency_type'] = dependency_type\\n\\n siaf_definitions.pprint()\\n\\n\\n siaf_definitions_file_name = os.path.join(JWST_SOURCE_DATA_ROOT, instrument,\\n '{}_siaf_aperture_definition.txt'.format(instrument.lower()))\\n\\n comments = []\\n comments.append('{} aperture definition file for SIAF'.format(instrument))\\n comments.append('')\\n comments.append('This file contains all the necessary aperture information to generate the full SIAF given the necessary reference files (focal plane alignment, distortion) and auxiliary information (DDC mapping, wedge offsets, ...)')\\n comments.append('This file also defines the order in which the apertures are presented.')\\n comments.append('')\\n comments.append('Originally based on {}.'.format(JWST_PRD_VERSION))\\n comments.append('')\\n comments.append('Generated {} {}'.format(timestamp.isot, timestamp.scale))\\n comments.append('{}'.format(username))\\n comments.append('')\\n siaf_definitions.meta['comments'] = comments\\n siaf_definitions.write(siaf_definitions_file_name, format='ascii.fixed_width', delimiter=',',\\n delimiter_pad=' ', bookend=False)\",\n \"def parseheader(self):\\n for line in self.rawheader.split(\\\"\\\\n\\\"):\\n pat = \\\"QUITTING\\\"\\n if pat in line:\\n self.prefix = line\\n continue\\n\\n pat = \\\"VERSION NUMBER\\\"\\n if pat in line:\\n self.softvers = line[28:].strip()\\n continue\\n\\n pat = \\\"DATE/TIME IS\\\"\\n if pat in line:\\n meta = line[22:].strip()\\n matchobj = dtpat.match(meta)\\n if matchobj:\\n try:\\n self.dumpdt = datetime.strptime(meta, moddtfmt)\\n except:\\n self.nodump = True\\n self.comment += (\\n \\\" *** Cannot read module date/time: {}\\\\n\\\".format(meta)\\n )\\n continue\\n\\n pat = \\\"NUMBER RECORDS IS\\\"\\n if pat in line:\\n self.ndumprec = line[22:].strip()\\n continue\\n\\n pat = \\\"MODULE TYPE IS\\\"\\n if pat in line:\\n self.modtype = line[22:].strip()\\n continue\\n\\n pat = \\\"SERIAL NUMBER IS\\\"\\n if pat in line:\\n self.modserial = line[22:].strip()\\n continue\\n\\n pat = \\\"COND S/N IS\\\"\\n if pat in line:\\n meta = line[22:].strip()\\n serials = meta.split(\\\"/\\\")\\n self.cellserial = serials[1]\\n self.ioserial = serials[0]\\n continue\\n\\n pat = \\\"SAMPLING INTERVAL IS\\\"\\n if pat in line:\\n meta = line[22:].strip()\\n self.sampintv = meta\\n if meta == \\\"00:01:00\\\":\\n self.nodump = False\\n self.comment += \\\" *** Sample interval is {}\\\\n\\\".format(meta)\\n elif meta != \\\"00:02:00\\\":\\n self.nodump = True\\n self.comment += \\\" *** Sample interval is {}\\\\n\\\".format(meta)\\n continue\\n\\n pat = \\\"AVERAGE INTERVAL IS\\\"\\n if pat in line:\\n self.avgintv = line[22:].strip()\\n if int(self.avgintv) != 24:\\n self.nodump = True\\n self.comment += \\\" *** Average interval is {}\\\\n\\\".format(meta)\\n continue\\n\\n pat = \\\"BATTERY VOLTAGE IS\\\"\\n if pat in line:\\n self.voltage = line[22:].strip()\\n continue\\n\\n return self.modserial\",\n \"def parseGard(kh, aln, o, logger):\\n\\tlBP = []\\n\\tf = open(kh, \\\"r\\\")\\n\\tlLine = f.readline()\\n\\twhile lLine:\\n\\t if lLine.find(\\\"\\\\\\\"breakpoints\\\\\\\"\\\")!=-1:\\n\\t lLine = f.readline()\\n\\t lLine=lLine[lLine.find(\\\"[\\\")+1:lLine.find(\\\"]\\\")]\\n\\t lBP=list(map(int, lLine.split(\\\",\\\")))\\n\\t break\\n\\t lLine = f.readline()\\n\\tf.close()\\n\\tindex = 0\\n\\t\\n\\t#If there are breakpoints, add it in lBP\\n\\tif len(lBP) > 0:\\n\\t\\tlogger.info(\\\"There are {:d} significant breakpoints in alignement {:s} at positions {}\\\".format(len(lBP), aln, lBP))\\n\\telse:\\n\\t\\tlogger.info(\\\"There are no significant breakpoints in alignement {:s}.\\\".format(aln))\\n\\t\\treturn []\\n \\n\\t#If there're breakpoint(s), cut sequence in subsequences according to breakpoints\\n\\tif len(lBP) > 0:\\n\\t\\tdFname2Fseq = {}\\n\\t\\tfor fasta in SeqIO.parse(open(aln),'fasta'):\\n\\t\\t\\tdFname2Fseq[fasta.id] = str(fasta.seq)\\n\\t\\t\\n\\t\\t#Creation of a dico where atgc in sequence has been replace by 1 and - by 0\\n\\t\\tlSeqBin = []\\n\\t\\tlNameGene = []\\n\\t\\tfor fastaSeq in dFname2Fseq:\\n\\t\\t\\tlSeqBin.append(dFname2Fseq[fastaSeq].lower().replace(\\\"a\\\", \\\"1\\\").replace(\\\"t\\\", \\\"1\\\").replace(\\\"c\\\", \\\"1\\\").replace(\\\"g\\\", \\\"1\\\").replace(\\\"-\\\", \\\"0\\\"))\\n\\t\\t\\tlNameGene.append(fastaSeq)\\n\\n\\t\\t#looking for a multiple of 3 (number of letter) (subsequence ends on or after the breakpoint)\\n\\t\\tnbSeq = len(lNameGene)\\n\\t\\tlenSeq = len(lSeqBin[0])\\n\\t\\tlPos = [0]\\n\\t\\tlBPprec = [0 for i in range(len(lSeqBin))]\\n\\t\\tlFrag = []\\n\\t\\tfor bp in lBP:\\n\\t\\t\\twhile bp%3 != 0:\\n\\t\\t\\t\\tbp += 1\\n\\t\\t\\tlPos.append(bp)\\n\\t\\t\\tlFrag += [ dFname2Fseq[lNameGene[j]][lPos[-2]:lPos[-1]] for j in range(nbSeq) ]\\n\\t\\t\\n\\t\\t#Adding subsequences that start at the last breakpoint to the end\\n\\t\\tlFrag += [dFname2Fseq[lNameGene[i]][lPos[-1]:] for i in range(nbSeq)]\\n\\n\\t\\tlBP = lPos+[lenSeq]\\n\\t\\tlOutFrag = []\\n\\t\\tindex = 0\\n\\t\\tfor x in range(1,len(lBP)):\\n\\t\\t\\tdFrag = {}\\n\\t\\t\\tif lBP[x-1] == 0:\\n\\t\\t\\t\\textension = \\\"_{:d}_{:d}\\\".format(lBP[x-1], lBP[x])\\n\\t\\t\\telse:\\n\\t\\t\\t\\textension = \\\"_{:d}_{:d}\\\".format(lBP[x-1]-1, lBP[x])\\n\\n\\t\\t\\toutFrag = o+aln.split(\\\"/\\\")[-1].split(\\\".\\\")[0]+\\\"_frag\\\"+extension+\\\".best.fas\\\"\\n\\t\\t\\tfor name in lNameGene:\\n\\t\\t\\t\\tdFrag[name] = lFrag[index]\\n\\t\\t\\t\\tindex += 1\\n\\t\\t\\twith open(outFrag, \\\"w\\\") as outF:\\n\\t\\t\\t outF.write(FastaResFunc.dict2fasta(dFrag))\\n\\t\\t\\t logger.info(\\\"\\\\tNew alignment: %s\\\"%{outFrag})\\n\\t\\t\\t outF.close()\\n\\t\\t\\t lOutFrag.append(outFrag)\\n\\n\\t\\treturn lOutFrag\\n\\telse:\\n\\t\\treturn []\",\n \"def _parse_motion(block, **kwargs):\\n _, fa_length, time_step, name, fmt = parse_fixed_width(\\n [(5, int), (5, int), (10, float), (30, to_str), (30, to_str)],\\n block\\n )\\n\\n scale, pga, _, header_lines, _ = parse_fixed_width(\\n 3 * [(10, to_float)] + 2 * [(5, int)],\\n block\\n )\\n\\n m = re.search(r'(\\\\d+)\\\\w(\\\\d+)\\\\.\\\\d+', fmt)\\n count_per_line = int(m.group(1))\\n width = int(m.group(2))\\n\\n fname = os.path.join(os.path.dirname(kwargs['fname']), name)\\n accels = np.genfromtxt(\\n fname,\\n delimiter=(count_per_line * [width]),\\n skip_header=header_lines,\\n )\\n\\n if np.isfinite(scale):\\n pass\\n elif np.isfinite(pga):\\n scale = pga / np.abs(accels).max()\\n else:\\n scale = 1.\\n\\n accels *= scale\\n m = motion.TimeSeriesMotion(fname, '', time_step, accels, fa_length)\\n\\n return m\",\n \"def evaluateMacro(compiled_expression):\",\n \"def parse_beam(self):\\n # AIPS FITS file; stored in the history section\\n beam_regex = re.compile(r'''\\n BMAJ\\n \\\\s*=\\\\s*\\n (?P<bmaj>[-\\\\d\\\\.eE]+)\\n \\\\s*\\n BMIN\\n \\\\s*=\\\\s*\\n (?P<bmin>[-\\\\d\\\\.eE]+)\\n \\\\s*\\n BPA\\n \\\\s*=\\\\s*\\n (?P<bpa>[-\\\\d\\\\.eE]+)\\n ''', re.VERBOSE)\\n\\n bmaj, bmin, bpa = None, None, None\\n header = self.header\\n try:\\n # MIRIAD FITS file\\n bmaj = header['BMAJ']\\n bmin = header['BMIN']\\n bpa = header['BPA']\\n except KeyError:\\n\\n def get_history(hdr):\\n \\\"\\\"\\\"\\n Returns all history cards in FITS header hdr as a list of strings.\\n \\\"\\\"\\\"\\n return hdr['HISTORY']\\n\\n for hist_entry in get_history(header):\\n results = beam_regex.search(hist_entry)\\n if results:\\n bmaj, bmin, bpa = [float(results.group(key)) for\\n key in ('bmaj', 'bmin', 'bpa')]\\n break\\n\\n return bmaj, bmin, bpa\",\n \"def macros(self):\\r\\n return macros.Macros(self)\",\n \"def magic_macro(self,parameter_s = ''):\\n\\n args = parameter_s.split()\\n name,ranges = args[0], args[1:]\\n #print 'rng',ranges # dbg\\n cmds = self.extract_input_slices(ranges)\\n macro = Macro(cmds)\\n self.user_ns.update({name:macro})\\n print 'Macro `%s` created. To execute, type its name (without quotes).' % name\\n print 'Macro contents:'\\n print str(macro).rstrip(),\",\n \"def _expand_macros(self, macro_ids) -> None:\\n if macro_ids is None:\\n return\\n\\n for macro_id in macro_ids:\\n macro_cfg = self._app_cfg['macros'][macro_id]\\n\\n self._sweep_stages.extend(macro_cfg.get('sweeps', []))\\n self._reset_stages.extend(macro_cfg.get('resets', []))\\n self._process_stages.extend(macro_cfg.get('processes', []))\",\n \"def parse_misc(self,ins):\\n if ins.instr == 'nop':\\n if len(ins.args) != 0:\\n raise Exception(\\\"Invalid number of args for ins: \\\", ins.instr)\\n elif ins.instr == 'syscall':\\n if len(ins.args) != 0:\\n raise Exception(\\\"Invalid number of args for ins: \\\", ins.instr)\\n elif ins.instr == 'break':\\n if len(ins.args) != 0:\\n raise Exception(\\\"Invalid number of args for ins: \\\", ins.instr)\\n elif ins.instr == 'mflo': \\n if len(ins.args) == 1:\\n self.gen = [ins.args[0]]\\n self.need = [Register(\\\"$lo\\\")]\\n else:\\n raise Exception(\\\"Invalid number of args for ins: \\\", ins.instr)\\n \\n elif ins.instr == 'mtlo': \\n if len(ins.args) == 1:\\n self.gen = [Register(\\\"$lo\\\")]\\n self.need = [ins.args[0]]\\n else:\\n raise Exception(\\\"Invalid number of args for ins: \\\", ins.instr)\\n \\n elif ins.instr == 'mfhi': \\n if len(ins.args) == 1:\\n self.gen = [ins.args[0]]\\n self.need = [Register(\\\"$hi\\\")]\\n else:\\n raise Exception(\\\"Invalid number of args for ins: \\\", ins.instr) \\n \\n elif ins.instr == 'mthi': \\n if len(ins.args) == 1:\\n self.gen = [Register(\\\"$hi\\\")]\\n self.need = [ins.args[0]]\\n else:\\n raise Exception(\\\"Invalid number of args for ins: \\\", ins.instr)\\n \\n elif ins.instr == 'mtc1': \\n if len(ins.args) == 2:\\n self.gen = [ins.args[1]]\\n self.need = [ins.args[0]]\\n else:\\n raise Exception(\\\"Invalid number of args for ins: \\\", ins.instr) \\n \\n elif ins.instr == 'mfc1': \\n if len(ins.args) == 2:\\n self.gen = [ins.args[0]]\\n self.need = [ins.args[1]]\\n else:\\n raise Exception(\\\"Invalid number of args for ins: \\\", ins.instr) \\n \\n elif ins.instr == 'la': \\n if len(ins.args) == 2:\\n self.gen = [ins.args[0]]\\n self.ival = ins.args[1]\\n else:\\n raise Exception(\\\"Invalid number of args for ins: \\\", ins.instr)\\n \\n elif ins.instr == 'lui': \\n if len(ins.args) == 2:\\n self.gen = [ins.args[0]]\\n self.ival = ins.args[1]\\n else:\\n raise Exception(\\\"Invalid number of args for ins: \\\", ins.instr)\",\n \"def _compat_parse_magic(self):\\n def warning(magic, option):\\n LOG.warning(\\\"Deprecated \\\\\\\"magic\\\\\\\" option \\\\\\\"{m}\\\\\\\" found. Please use new-style option \\\\\\\"{o}\\\\\\\" instead (see user manual).\\\".format(m=magic, o=option))\\n\\n magic_auto_backports = re.search(r\\\"\\\\*\\\\s*MINI_BUILDD:\\\\s*AUTO_BACKPORTS:\\\\s*([^*.\\\\[\\\\]]+)\\\", self._top_changes)\\n if magic_auto_backports:\\n warning(\\\"AUTO_BACKPORTS\\\", \\\"auto-ports\\\")\\n self._set(\\\"auto-ports\\\", magic_auto_backports.group(1))\\n\\n magic_backport_mode = re.search(r\\\"\\\\*\\\\s*MINI_BUILDD:\\\\s*BACKPORT_MODE\\\", self._top_changes)\\n if magic_backport_mode:\\n warning(\\\"BACKPORT_MODE\\\", \\\"ignore-lintian\\\")\\n self._set(\\\"ignore-lintian\\\", \\\"true\\\")\",\n \"def test_make_macrobes(self):\\n basic_test_runner(self, 'macrobes')\",\n \"def initialize(self):\\n print(\\\"Initializing macro \\\" + self.name + \\\"...\\\")\\n\\n self.initTime = wpilib.Timer.getFPGATimestamp() #get the current time\\n self.f = open(\\\"/home/lvuser/py/macros/\\\"+self.name, \\\"w\\\")\\n fields = [\\\"Drive_Y\\\",\\n \\\"Drive_Twist\\\",\\n \\\"Ears\\\",\\n \\\"Hat\\\",\\n \\\"Tilt\\\",\\n \\\"Time\\\"]\\n self.writer = csv.DictWriter(self.f, fieldnames=fields)\\n self.writer.writeheader()\",\n \"def resolve_macros(lines: List[SourceLine]) -> List[SourceLine]:\\n macros: Dict[str, Dict[str, Any]] = {}\\n found_macro = None\\n lines_to_remove = []\\n for idx, srcline in enumerate(lines):\\n if found_macro is None:\\n match = re.match(mipsRE.MACRO, srcline.line)\\n if match:\\n found_macro = match[1]\\n macros[match[1]] = {\\n \\\"args\\\": [a.strip() for a in match[2].split(\\\", \\\")] if match[2] else None,\\n \\\"lines\\\": [],\\n }\\n lines_to_remove.append(idx)\\n else:\\n if \\\".end_macro\\\" in srcline.line:\\n found_macro = None\\n lines_to_remove.append(idx)\\n else:\\n macros[found_macro][\\\"lines\\\"].append(srcline)\\n lines_to_remove.append(idx)\\n\\n lines = [l for i, l in enumerate(lines) if i not in lines_to_remove]\\n\\n for idx, srcline in enumerate(lines):\\n for macro, macro_info in macros.items():\\n if macro in srcline.line:\\n if macro_info[\\\"args\\\"] is None:\\n lines[idx] = macro_info[\\\"lines\\\"]\\n else:\\n macro_with_args(idx, lines, macro, macro_info, srcline)\\n\\n return flatten(lines)\",\n \"def finalize(content):\\n def add_usetypes(text):\\n # TODO: get rid of this fian.py copypasta\\n def header_starts(line): # TODO: now requires exactly one space after \\\"end\\\"\\n for objtype in (\\\"function\\\", \\\"subroutine\\\"):\\n p_notend = r\\\"(?<!\\\\bend\\\\b\\\\s)\\\" # (?<!...) is \\\"match if not preceded by\\\" (see help(re))\\n p_objtype = r\\\"\\\\b{objtype}\\\\b\\\".format(objtype=objtype)\\n pattern = r\\\"{notend}{objtype}\\\".format(notend=p_notend,\\n objtype=p_objtype)\\n matches = re.findall(pattern, line)\\n assert len(matches) <= 1 # should be at most one match for the whole regex\\n if len(matches) > 0:\\n return True\\n return False\\n\\n # FIXME: brittle: we assume the return type decl contains no \\\")\\\"\\n def header_ends(line):\\n matches = re.findall(r\\\"\\\\)\\\", line)\\n return (len(matches) > 0)\\n\\n from enum import Enum\\n class ReaderState(Enum):\\n SCANNING = 0\\n PROCESSING = 1\\n\\n state = ReaderState.SCANNING\\n out = []\\n for line in text.split(\\\"\\\\n\\\"):\\n if state not in (ReaderState.SCANNING, ReaderState.PROCESSING):\\n assert False, \\\"Unknown reader state '{}'\\\".format(state)\\n doitnow = False\\n if state is ReaderState.SCANNING:\\n if header_starts(line):\\n state = ReaderState.PROCESSING\\n if state is ReaderState.PROCESSING:\\n if header_ends(line):\\n doitnow = True\\n state = ReaderState.SCANNING\\n out.append(line)\\n if doitnow:\\n out.append(\\\"use types\\\") # Elmer-specific\\n if state != ReaderState.SCANNING:\\n class ReaderError(ValueError):\\n pass\\n raise ReaderError(\\\"unexpected end of file (incomplete function or subroutine declaration?)\\\")\\n return \\\"\\\\n\\\".join(out)\\n\\n content = add_usetypes(content)\\n content = re.sub(r\\\"([0-9.]+)[DdEe]([+-]?[0-9]+)\\\", r\\\"\\\\1e\\\\2_dp\\\", content)\\n content = re.sub(r\\\"REAL\\\\*8\\\", r\\\"REAL(KIND=dp)\\\", content)\\n return content\",\n \"def parse( self, exprlist ):\\n t = self.prop[\\\"DSEC\\\"]\\n E = self.prop[\\\"ELE\\\"]\\n V = self.prop[\\\"VOL\\\"]\\n T = self.prop[\\\"TEMP\\\"]\\n C = self.prop[\\\"CONC\\\"]\\n S = self.prop[\\\"SPEC\\\"]\\n pH = E\\n row = []\\n for i in exprlist:\\n i = i.replace(\\\"A\\\", \\\"self.absorbance\\\")\\n exec 'row.append(' + i + ')'\\n return row\",\n \"def read_abinit(filename='abinit.in'):\\n\\n from ase import Atoms, units\\n\\n if isinstance(filename, str):\\n f = open(filename)\\n else: # Assume it's a file-like object\\n f = filename\\n\\n lines = f.readlines()\\n if type(filename) == str:\\n f.close()\\n\\n full_file = ''\\n for line in lines:\\n if '#' in line:\\n meat, comment = line.split('#')\\n else:\\n meat = line\\n full_file = full_file + meat + ' '\\n\\n full_file.strip()\\n tokens = full_file.lower().split()\\n\\n # note that the file can not be scanned sequentially\\n\\n index = tokens.index(\\\"acell\\\")\\n unit = 1.0\\n if(tokens[index+4].lower()[:3] != 'ang'):\\n unit = units.Bohr\\n acell = [unit*float(tokens[index+1]),\\n unit*float(tokens[index+2]),\\n unit*float(tokens[index+3])]\\n\\n index = tokens.index(\\\"natom\\\")\\n natom = int(tokens[index+1])\\n\\n index = tokens.index(\\\"ntypat\\\")\\n ntypat = int(tokens[index+1])\\n\\n index = tokens.index(\\\"typat\\\")\\n typat = []\\n for i in range(natom):\\n typat.append(int(tokens[index+1+i]))\\n\\n index = tokens.index(\\\"znucl\\\")\\n znucl = []\\n for i in range(ntypat):\\n znucl.append(int(tokens[index+1+i]))\\n\\n index = tokens.index(\\\"rprim\\\")\\n rprim = []\\n for i in range(3):\\n rprim.append([acell[i]*float(tokens[index+3*i+1]),\\n acell[i]*float(tokens[index+3*i+2]),\\n acell[i]*float(tokens[index+3*i+3])])\\n\\n # create a list with the atomic numbers\\n numbers = []\\n for i in range(natom):\\n ii = typat[i] - 1\\n numbers.append(znucl[ii])\\n\\n # now the positions of the atoms\\n if \\\"xred\\\" in tokens:\\n index = tokens.index(\\\"xred\\\")\\n xred = []\\n for i in range(natom):\\n xred.append([float(tokens[index+3*i+1]),\\n float(tokens[index+3*i+2]),\\n float(tokens[index+3*i+3])])\\n atoms = Atoms(cell=rprim, scaled_positions=xred, numbers=numbers,\\n pbc=True)\\n else:\\n if \\\"xcart\\\" in tokens:\\n index = tokens.index(\\\"xcart\\\")\\n unit = units.Bohr\\n elif \\\"xangst\\\" in tokens:\\n unit = 1.0\\n index = tokens.index(\\\"xangst\\\")\\n else:\\n raise IOError(\\n \\\"No xred, xcart, or xangs keyword in abinit input file\\\")\\n\\n xangs = []\\n for i in range(natom):\\n xangs.append([unit*float(tokens[index+3*i+1]),\\n unit*float(tokens[index+3*i+2]),\\n unit*float(tokens[index+3*i+3])])\\n atoms = Atoms(cell=rprim, positions=xangs, numbers=numbers, pbc=True)\\n \\n try:\\n i = tokens.index('nsppol')\\n except ValueError:\\n nsppol = None\\n else:\\n nsppol = int(tokens[i + 1])\\n\\n if nsppol == 2:\\n index = tokens.index('spinat')\\n magmoms = [float(tokens[index + 3 * i + 3]) for i in range(natom)]\\n atoms.set_initial_magnetic_moments(magmoms)\\n\\n return atoms\",\n \"def macro_with_args(idx: int, lines: List[SourceLine], macro: str, macroinfo: Dict[str, Any], srcline: SourceLine):\\n macroregex = fr\\\"{macro}\\\\((.+)\\\\)\\\"\\n match = re.match(macroregex, srcline.line)\\n if match:\\n values = match[1].split(\\\", \\\")\\n argsmap = {arg: val for arg, val in zip(macroinfo[\\\"args\\\"], values)}\\n expanded_macro = []\\n for s in macroinfo[\\\"lines\\\"]:\\n modified_line = s.line\\n for a, v in argsmap.items():\\n modified_line = modified_line.replace(a, v)\\n expanded_macro.append(SourceLine(line=modified_line, lineno=s.lineno, filename=s.filename))\\n lines[idx] = expanded_macro # type: ignore\",\n \"def test_parse_multiple_procedures(self):\\n source_code = dedent(\\\"\\\"\\\"\\\\\\n #include <stdbool.h>\\n\\n /**\\n * helper method to decide things\\n */\\n bool helper()\\n {\\n return true;\\n }\\n\\n /**\\n * this is a doc comment that stretches over\\n * more than one line\\n */\\n int main()\\n {\\n return 0;\\n }\\n \\\"\\\"\\\")\\n result = self.parser.parse(source_code.splitlines())\\n assert_equal(result, {\\n \\\"bool helper()\\\": \\\"helper method to decide things\\\",\\n \\\"int main()\\\": (\\\"this is a doc comment that stretches over \\\"\\n \\\"more than one line\\\")})\",\n \"def parser(path):\\n\\t\\n\\tdata = Arff()\\n\\tdata.read_arff(path)\\n\\t\\n\\treturn data\",\n \"def macro_func(macro_name, arg_string, body, is_block, environ):\\n global macros_set_up\\n args, kwargs = parse_args(arg_string)\\n if macro_name == 'intro' and body:\\n return intro_tag(body)\\n if not macros_set_up:\\n app = get_application()\\n for extension in app.markup_extensions:\\n macros[extension.name] = make_macro(extension)\\n macros_set_up = True\\n if macro_name in macros:\\n return macros[macro_name](body, args, kwargs, is_block, environ)\",\n \"def __initMacroActions(self):\\n self.macroActGrp = createActionGroup(self)\\n\\n self.macroStartRecAct = E5Action(\\n QCoreApplication.translate(\\n 'ViewManager', 'Start Macro Recording'),\\n QCoreApplication.translate(\\n 'ViewManager', 'S&tart Macro Recording'),\\n 0, 0, self.macroActGrp, 'vm_macro_start_recording')\\n self.macroStartRecAct.setStatusTip(QCoreApplication.translate(\\n 'ViewManager', 'Start Macro Recording'))\\n self.macroStartRecAct.setWhatsThis(QCoreApplication.translate(\\n 'ViewManager',\\n \\\"\\\"\\\"<b>Start Macro Recording</b>\\\"\\\"\\\"\\n \\\"\\\"\\\"<p>Start recording editor commands into a new macro.</p>\\\"\\\"\\\"\\n ))\\n self.macroStartRecAct.triggered.connect(self.__macroStartRecording)\\n self.macroActions.append(self.macroStartRecAct)\\n \\n self.macroStopRecAct = E5Action(\\n QCoreApplication.translate('ViewManager', 'Stop Macro Recording'),\\n QCoreApplication.translate('ViewManager', 'Sto&p Macro Recording'),\\n 0, 0, self.macroActGrp, 'vm_macro_stop_recording')\\n self.macroStopRecAct.setStatusTip(QCoreApplication.translate(\\n 'ViewManager', 'Stop Macro Recording'))\\n self.macroStopRecAct.setWhatsThis(QCoreApplication.translate(\\n 'ViewManager',\\n \\\"\\\"\\\"<b>Stop Macro Recording</b>\\\"\\\"\\\"\\n \\\"\\\"\\\"<p>Stop recording editor commands into a new macro.</p>\\\"\\\"\\\"\\n ))\\n self.macroStopRecAct.triggered.connect(self.__macroStopRecording)\\n self.macroActions.append(self.macroStopRecAct)\\n \\n self.macroRunAct = E5Action(\\n QCoreApplication.translate('ViewManager', 'Run Macro'),\\n QCoreApplication.translate('ViewManager', '&Run Macro'),\\n 0, 0, self.macroActGrp, 'vm_macro_run')\\n self.macroRunAct.setStatusTip(QCoreApplication.translate(\\n 'ViewManager', 'Run Macro'))\\n self.macroRunAct.setWhatsThis(QCoreApplication.translate(\\n 'ViewManager',\\n \\\"\\\"\\\"<b>Run Macro</b>\\\"\\\"\\\"\\n \\\"\\\"\\\"<p>Run a previously recorded editor macro.</p>\\\"\\\"\\\"\\n ))\\n self.macroRunAct.triggered.connect(self.__macroRun)\\n self.macroActions.append(self.macroRunAct)\\n \\n self.macroDeleteAct = E5Action(\\n QCoreApplication.translate('ViewManager', 'Delete Macro'),\\n QCoreApplication.translate('ViewManager', '&Delete Macro'),\\n 0, 0, self.macroActGrp, 'vm_macro_delete')\\n self.macroDeleteAct.setStatusTip(QCoreApplication.translate(\\n 'ViewManager', 'Delete Macro'))\\n self.macroDeleteAct.setWhatsThis(QCoreApplication.translate(\\n 'ViewManager',\\n \\\"\\\"\\\"<b>Delete Macro</b>\\\"\\\"\\\"\\n \\\"\\\"\\\"<p>Delete a previously recorded editor macro.</p>\\\"\\\"\\\"\\n ))\\n self.macroDeleteAct.triggered.connect(self.__macroDelete)\\n self.macroActions.append(self.macroDeleteAct)\\n \\n self.macroLoadAct = E5Action(\\n QCoreApplication.translate('ViewManager', 'Load Macro'),\\n QCoreApplication.translate('ViewManager', '&Load Macro'),\\n 0, 0, self.macroActGrp, 'vm_macro_load')\\n self.macroLoadAct.setStatusTip(QCoreApplication.translate(\\n 'ViewManager', 'Load Macro'))\\n self.macroLoadAct.setWhatsThis(QCoreApplication.translate(\\n 'ViewManager',\\n \\\"\\\"\\\"<b>Load Macro</b>\\\"\\\"\\\"\\n \\\"\\\"\\\"<p>Load an editor macro from a file.</p>\\\"\\\"\\\"\\n ))\\n self.macroLoadAct.triggered.connect(self.__macroLoad)\\n self.macroActions.append(self.macroLoadAct)\\n \\n self.macroSaveAct = E5Action(\\n QCoreApplication.translate('ViewManager', 'Save Macro'),\\n QCoreApplication.translate('ViewManager', '&Save Macro'),\\n 0, 0, self.macroActGrp, 'vm_macro_save')\\n self.macroSaveAct.setStatusTip(QCoreApplication.translate(\\n 'ViewManager', 'Save Macro'))\\n self.macroSaveAct.setWhatsThis(QCoreApplication.translate(\\n 'ViewManager',\\n \\\"\\\"\\\"<b>Save Macro</b>\\\"\\\"\\\"\\n \\\"\\\"\\\"<p>Save a previously recorded editor macro to a file.</p>\\\"\\\"\\\"\\n ))\\n self.macroSaveAct.triggered.connect(self.__macroSave)\\n self.macroActions.append(self.macroSaveAct)\\n \\n self.macroActGrp.setEnabled(False)\",\n \"def HandlePredefines(predefines, app):\\n selecteddefine = None\\n if predefines == \\\"archive\\\":\\n selecteddefine = types_archive\\n elif predefines == \\\"text\\\":\\n selecteddefine = types_text\\n elif predefines == \\\"audio\\\":\\n selecteddefine = types_audio\\n # Set types if app is defined\\n if app:\\n Mime_Set_All(selecteddefine, app)\\n # Query types\\n Mime_Query_All(selecteddefine)\",\n \"def test_reads_photomodeler_sigmas_from_report() -> None:\\n imgsz = (4288, 2848)\\n sigmas = {\\n \\\"focal\\\": 0.001,\\n \\\"xp\\\": 0.001,\\n \\\"yp\\\": 7.1e-004,\\n \\\"fw\\\": 1.7e-004,\\n \\\"fh\\\": 0.0,\\n \\\"k1\\\": 2.0e-007,\\n \\\"k2\\\": 1.2e-009,\\n \\\"k3\\\": 0.0,\\n \\\"p1\\\": 3.5e-007,\\n \\\"p2\\\": 0.0,\\n }\\n path = os.path.join(\\\"tests\\\", \\\"CalibrationReport.txt\\\")\\n xcam_auto = PhotoModeler.from_report(path, imgsz=imgsz, sigmas=True)\\n xcam_manual = PhotoModeler(imgsz=imgsz, **sigmas)\\n assert vars(xcam_auto) == vars(xcam_manual)\",\n \"def readAMBERTop(self, phys, filename):\\r\\n\\r\\n def skipLine(data):\\r\\n nl = data.index('\\\\n')\\r\\n return data[nl+1:len(data)]\\r\\n\\r\\n def jumpTo(data, target):\\r\\n fp = data.index(target)\\r\\n return data[fp:len(data)]\\r\\n\\r\\n def readRemove(data, size):\\r\\n retval = data[0:size-1]\\r\\n return data[size:len(data)]\\r\\n\\r\\n def getInteger(data):\\r\\n pos = 0\\r\\n retval = \\\"\\\"\\r\\n while (not data[pos].isdigit()):\\r\\n pos = pos + 1\\r\\n while (data[pos].isdigit()):\\r\\n retval = retval + data[pos]\\r\\n pos = pos + 1\\r\\n data = data[pos:len(data)]\\r\\n return int(retval), data\\r\\n\\r\\n def parse(data, arr, str, count, dtype, tupsize=1):\\r\\n data = jumpTo(data, \\\"%FLAG \\\"+str)\\r\\n data = jumpTo(data, \\\"%FORMAT\\\")\\r\\n numPerLine, data = getInteger(data)\\r\\n fieldsize, data = getInteger(data)\\r\\n data = skipLine(data) \\r\\n \\r\\n arr2 = []\\r\\n numread = 0\\r\\n for j in range(0, (tupsize*count-1) / numPerLine + 1):\\r\\n for i in range(0, numPerLine):\\r\\n if (tupsize == 1):\\r\\n arr.append(dtype(data[0:fieldsize].strip()))\\r\\n else:\\r\\n arr2.append(dtype(data[0:fieldsize].strip()))\\r\\n if (len(arr2) == tupsize):\\r\\n arr.append(arr2)\\r\\n arr2 = []\\r\\n numread += 1\\r\\n data = data[fieldsize:len(data)]\\r\\n if (numread == tupsize*count):\\r\\n break\\r\\n data = skipLine(data) \\r\\n return data\\r\\n\\r\\n def scan(data, str):\\r\\n return (data.count(str) != 0)\\r\\n\\r\\n\\r\\n f = open(filename, 'r')\\r\\n data = f.read()\\r\\n\\r\\n # First Line: VERSION ...\\r\\n data = skipLine(data)\\r\\n\\r\\n # Go To: %FLAG POINTERS\\r\\n data = jumpTo(data, '%FLAG POINTERS')\\r\\n\\r\\n data = jumpTo(data, '%FORMAT')\\r\\n numPerLine, data = getInteger(data)\\r\\n fieldsize, data = getInteger(data)\\r\\n data = skipLine(data)\\r\\n \\r\\n temp = []\\r\\n numread = 0\\r\\n for j in range(0, 31 / numPerLine + 1):\\r\\n for i in range(0, numPerLine):\\r\\n temp.append(int(data[0:8]))\\r\\n data = data[8:len(data)]\\r\\n numread += 1\\r\\n if (numread == 31):\\r\\n break\\r\\n data = skipLine(data)\\r\\n \\r\\n [natoms, ntypes, nbonh, mbona, ntheth, mtheta, nphih, mphia, nhparm, nparm, nnb, nres, nbona, ntheta, nphia, numbnd, numang, nptra, natyp, nphb, ifpert, nbper, ngper, ndper, mbper, mgper, mdper, ifbox, nmxrs, ifcap, numextra] = temp \\r\\n\\r\\n\\r\\n #################################################\\r\\n # Read AtomTypes\\r\\n atomnames = []\\r\\n charges = []\\r\\n masses = []\\r\\n atindex = []\\r\\n exclusions = []\\r\\n nparams = []\\r\\n reslabels = []\\r\\n respointers = []\\r\\n forceconstants = [[], [], []] # bond, angle, dihedral\\r\\n equilvals = [[], [], [[], []]] # bond, angle, dihedral\\r\\n scee_scales = []\\r\\n scnb_scales = []\\r\\n solty = []\\r\\n lj_acoef = []\\r\\n lj_bcoef = []\\r\\n\\r\\n data = parse(data, atomnames, \\\"ATOM_NAME\\\", natoms, str) \\r\\n data = parse(data, charges, \\\"CHARGE\\\", natoms, float)\\r\\n data = parse(data, masses, \\\"MASS\\\", natoms, float)\\r\\n data = parse(data, atindex, \\\"ATOM_TYPE_INDEX\\\", natoms, int)\\r\\n data = parse(data, exclusions, \\\"NUMBER_EXCLUDED_ATOMS\\\", natoms, int)\\r\\n data = parse(data, nparams, \\\"NONBONDED_PARM_INDEX\\\", ntypes*ntypes, int)\\r\\n data = parse(data, reslabels, \\\"RESIDUE_LABEL\\\", nres, str)\\r\\n data = parse(data, respointers, \\\"RESIDUE_POINTER\\\", nres, int)\\r\\n data = parse(data, forceconstants[0], \\\"BOND_FORCE_CONSTANT\\\", numbnd, float)\\r\\n data = parse(data, equilvals[0], \\\"BOND_EQUIL_VALUE\\\", numbnd, float)\\r\\n data = parse(data, forceconstants[1], \\\"ANGLE_FORCE_CONSTANT\\\", numang, float)\\r\\n data = parse(data, equilvals[1], \\\"ANGLE_EQUIL_VALUE\\\", numang, float)\\r\\n data = parse(data, forceconstants[2], \\\"DIHEDRAL_FORCE_CONSTANT\\\", nptra, float)\\r\\n data = parse(data, equilvals[2][0], \\\"DIHEDRAL_PERIODICITY\\\", nptra, float)\\r\\n data = parse(data, equilvals[2][1], \\\"DIHEDRAL_PHASE\\\", nptra, float)\\r\\n if (scan(data, \\\"SCEE_SCALE_FACTOR\\\")):\\r\\n data = parse(data, scee_scales, \\\"SCEE_SCALE_FACTORS\\\", nptra, float)\\r\\n else:\\r\\n for i in range(0, nptra):\\r\\n scee_scales.append(1.2) # Default \\r\\n if (scan(data, \\\"SCNB_SCALE_FACTOR\\\")):\\r\\n data = parse(data, scnb_scales, \\\"SCNB_SCALE_FACTORS\\\", nptra, float)\\r\\n else:\\r\\n for i in range(0, nptra):\\r\\n scnb_scales.append(2.0) # Default \\r\\n\\r\\n data = parse(data, solty, \\\"SOLTY\\\", natyp, float)\\r\\n data = parse(data, lj_acoef, \\\"LENNARD_JONES_ACOEF\\\", ntypes*(ntypes+1)/2, float)\\r\\n data = parse(data, lj_bcoef, \\\"LENNARD_JONES_BCOEF\\\", ntypes*(ntypes+1)/2, float)\\r\\n\\r\\n\\r\\n ##########################################################\\r\\n # STRUCTURE\\r\\n\\r\\n bonds = [[], []] # With H, Without H\\r\\n angles = [[], []] # With H, Without H\\r\\n dihedrals = [[], []] # With H, Without H\\r\\n impropers = [[], []] # With H, Without H\\r\\n excluded_atoms = [] \\r\\n hbond_acoef = []\\r\\n hbond_bcoef = []\\r\\n hbcut = []\\r\\n amber_atom_types = []\\r\\n tree_chain = []\\r\\n join_array = []\\r\\n irotat = []\\r\\n radii = []\\r\\n screen = []\\r\\n\\r\\n data = parse(data, bonds[0], \\\"BONDS_INC_HYDROGEN\\\", nbonh, int, 3)\\r\\n data = parse(data, bonds[1], \\\"BONDS_WITHOUT_HYDROGEN\\\", nbona, int, 3)\\r\\n data = parse(data, angles[0], \\\"ANGLES_INC_HYDROGEN\\\", ntheth, int, 4)\\r\\n data = parse(data, angles[1], \\\"ANGLES_WITHOUT_HYDROGEN\\\", ntheta, int, 4)\\r\\n data = parse(data, dihedrals[0], \\\"DIHEDRALS_INC_HYDROGEN\\\", nphih, int, 5)\\r\\n data = parse(data, dihedrals[1], \\\"DIHEDRALS_WITHOUT_HYDROGEN\\\", nphia, int, 5)\\r\\n \\r\\n # MERGE ARRAYS - PM HANDLES THE H+\\r\\n final_bonds = bonds[0] + bonds[1]\\r\\n final_angles = angles[0] + angles[1]\\r\\n final_dihedrals = dihedrals[0] + dihedrals[1]\\r\\n final_impropers = []\\r\\n \\r\\n # CLEAN UP THE TRASH\\r\\n del(bonds)\\r\\n del(angles)\\r\\n del(dihedrals)\\r\\n \\r\\n\\r\\n # Move impropers into their own array\\r\\n i = 0\\r\\n while (i < len(final_dihedrals)):\\r\\n if (final_dihedrals[i][2] < 0): # 1-4 exclusions are handled by our back end\\r\\n final_dihedrals[i][2] *= -1\\r\\n if (final_dihedrals[i][3] < 0):\\r\\n final_dihedrals[i][3] *= -1 # Make + again\\r\\n final_impropers.append(final_dihedrals[i])\\r\\n final_dihedrals.remove(final_dihedrals[i])\\r\\n i -= 1\\r\\n i += 1\\r\\n\\r\\n # Convert charge units\\r\\n for i in range(0, len(charges)):\\r\\n charges[i] /= 18.223\\r\\n\\r\\n\\r\\n data = parse(data, excluded_atoms, \\\"EXCLUDED_ATOMS_LIST\\\", nnb, int)\\r\\n data = parse(data, hbond_acoef, \\\"HBOND_ACOEF\\\", nphb, float)\\r\\n data = parse(data, hbond_bcoef, \\\"HBOND_BCOEF\\\", nphb, float)\\r\\n data = parse(data, hbcut, \\\"HBCUT\\\", nphb, float)\\r\\n data = parse(data, amber_atom_types, \\\"AMBER_ATOM_TYPE\\\", natoms, str)\\r\\n data = parse(data, tree_chain, \\\"TREE_CHAIN_CLASSIFICATION\\\", natoms, str)\\r\\n data = parse(data, join_array, \\\"JOIN_ARRAY\\\", natoms, int)\\r\\n data = parse(data, irotat, \\\"IROTAT\\\", natoms, int)\\r\\n data = parse(data, radii, \\\"RADII\\\", natoms, float)\\r\\n data = parse(data, screen, \\\"SCREEN\\\", natoms, float)\\r\\n\\r\\n # Further process dihedrals and impropers\\r\\n # Deal with multiplicity\\r\\n # A bit ugly, but the fastest for now\\r\\n # forceconstants[2][dihedrals[0][i][4]-1], int(equilvals[2][0][dihedrals[0][i][4]-1]), equilvals[2][1][dihedrals[0][i][4]-1]\\r\\n\\r\\n mult_di = dict()\\r\\n mult_im = dict()\\r\\n for i in range(0, len(final_dihedrals)):\\r\\n di_id = str(final_dihedrals[i][0])+' '+str(final_dihedrals[i][1])+' '+str(final_dihedrals[i][2])+' '+str(final_dihedrals[i][3])\\r\\n if (not mult_di.has_key(di_id)):\\r\\n mult_di[di_id] = [1, False, [forceconstants[2][final_dihedrals[i][4]-1]], [int(equilvals[2][0][final_dihedrals[i][4]-1])], [equilvals[2][1][final_dihedrals[i][4]-1]]]\\r\\n else:\\r\\n mult_di[di_id][0] += 1\\r\\n mult_di[di_id][2].append(forceconstants[2][final_dihedrals[i][4]-1])\\r\\n mult_di[di_id][3].append(int(equilvals[2][0][final_dihedrals[i][4]-1]))\\r\\n mult_di[di_id][4].append(equilvals[2][1][final_dihedrals[i][4]-1])\\r\\n \\r\\n for i in range(0, len(final_impropers)):\\r\\n im_id = str(final_impropers[i][0])+' '+str(final_impropers[i][1])+' '+str(final_impropers[i][2])+' '+str(final_impropers[i][3])\\r\\n if (not mult_im.has_key(di_id)):\\r\\n mult_im[im_id] = [1, False, [forceconstants[2][final_impropers[i][4]-1]], [int(equilvals[2][0][final_impropers[i][4]-1])], [equilvals[2][1][final_impropers[i][4]-1]]]\\r\\n else:\\r\\n mult_im[im_id][0] += 1\\r\\n mult_im[im_id][2].append(forceconstants[2][final_impropers[i][4]-1])\\r\\n mult_im[im_id][3].append(int(equilvals[2][0][final_impropers[i][4]-1]))\\r\\n mult_im[im_id][4].append(equilvals[2][1][final_impropers[i][4]-1])\\r\\n\\r\\n\\r\\n\\r\\n \\r\\n #[natoms, ntypes, nbonh, mbona, ntheth, mtheta, nphih, mphia, nhparm, nparm, nnb, nres, nbona, ntheta, nphia, numbnd, numang, nptra, natyp, nphb, ifpert, nbper, ngper, ndper, mbper, mgper, mdper, ifbox, nmxrs, ifcap, numextra] = temp \\r\\n #phys.myPSF.createAll(natoms, nbonh+mbona, ntheth+mtheta,\\r\\n # len(dihedrals[0])+len(dihedrals[1]),\\r\\n # len(impropers[0])+len(impropers[1]),\\r\\n # 0, 0, 0, 0)\\r\\n \\r\\n # Add atoms\\r\\n curres = 1\\r\\n for i in range(0, natoms):\\r\\n phys.myPSF.addAtom(i, 'SIM', curres, reslabels[curres-1],\\r\\n atomnames[i], atomnames[i], charges[i],\\r\\n masses[i]) \\r\\n if (curres != nres and i >= respointers[curres]):\\r\\n curres += 1\\r\\n\\r\\n # Add bonds\\r\\n for i in range(0, nbonh+nbona):\\r\\n phys.myPSF.addBond(i+1, final_bonds[i][0]/3+1, final_bonds[i][1]/3+1)\\r\\n phys.myPAR.addBond(i+1, atomnames[final_bonds[i][0]/3], atomnames[final_bonds[i][1]/3], forceconstants[0][final_bonds[i][2]/3], equilvals[0][final_bonds[i][2]/3])\\r\\n \\r\\n # Add angles\\r\\n for i in range(0, ntheth+ntheta):\\r\\n phys.myPSF.addAngle(i+1, final_angles[i][0]/3+1, final_angles[i][1]/3+1, final_angles[i][2]/3+1)\\r\\n phys.myPAR.addAngle(i+1, atomnames[final_angles[i][0]/3], atomnames[final_angles[i][1]/3], atomnames[final_angles[i][2]/3], forceconstants[1][final_angles[i][3]/3], equilvals[1][final_angles[i][3]/3])\\r\\n \\r\\n # Add dihedrals\\r\\n for i in range(0, len(final_dihedrals)):\\r\\n di_id = str(final_dihedrals[i][0])+' '+str(final_dihedrals[i][1])+' '+str(final_dihedrals[i][2])+' '+str(final_dihedrals[i][3])\\r\\n mult = mult_di[di_id][0]\\r\\n checked = mult_di[di_id][1]\\r\\n print di_id, \\\" \\\", mult\\r\\n if (not checked):\\r\\n if (mult == 1):\\r\\n phys.myPSF.addDihedral(i+1, final_dihedrals[i][0]/3+1, final_dihedrals[i][1]/3+1, int(numpy.abs(final_dihedrals[i][2]))/3+1, final_dihedrals[i][3]/3+1)\\r\\n phys.myPAR.addDihedral(i+1, atomnames[final_dihedrals[i][0]/3], atomnames[final_dihedrals[i][1]/3], atomnames[int(numpy.abs(final_dihedrals[i][2]))/3], atomnames[final_dihedrals[i][3]/3], forceconstants[2][final_dihedrals[i][4]-1], int(equilvals[2][0][final_dihedrals[i][4]-1]), equilvals[2][1][final_dihedrals[i][4]-1])\\r\\n else:\\r\\n mult_di[di_id][1] = True\\r\\n # Add dihedral with the appropriate multiplicity\\r\\n # Force constants, periodicity and phase shifts are in [2], [3], and [4] respectively\\r\\n fcvec = PARReader.VectorOfDouble()\\r\\n periodvec = PARReader.VectorOfInt()\\r\\n phasevec = PARReader.VectorOfDouble() \\r\\n for j in range(0, len(mult_di[di_id][2])):\\r\\n fcvec.push_back(mult_di[di_id][2][j])\\r\\n periodvec.push_back(mult_di[di_id][3][j])\\r\\n phasevec.push_back(mult_di[di_id][4][j])\\r\\n phys.myPSF.addDihedral(i+1, final_dihedrals[i][0]/3+1, final_dihedrals[i][1]/3+1, int(numpy.abs(final_dihedrals[i][2]))/3+1, final_dihedrals[i][3]/3+1)\\r\\n phys.myPAR.addDihedral(i+1, atomnames[final_dihedrals[i][0]/3], atomnames[final_dihedrals[i][1]/3], atomnames[int(numpy.abs(final_dihedrals[i][2]))/3], atomnames[final_dihedrals[i][3]/3], mult, fcvec, periodvec, phasevec)\\r\\n \\r\\n\\r\\n\\r\\n\\r\\n for i in range(0, len(final_impropers)):\\r\\n im_id = str(final_impropers[i][0])+' '+str(final_impropers[i][1])+' '+str(final_impropers[i][2])+' '+str(final_impropers[i][3])\\r\\n mult = mult_im[im_id][0]\\r\\n checked = mult_im[im_id][1]\\r\\n print im_id, \\\" \\\", mult\\r\\n if (not checked):\\r\\n if (mult == 1):\\r\\n phys.myPSF.addImproper(i+1, final_impropers[i][0]/3+1, final_impropers[i][1]/3+1, int(numpy.abs(final_impropers[i][2]))/3+1, final_impropers[i][3]/3+1)\\r\\n phys.myPAR.addImproper(i+1, atomnames[final_impropers[i][0]/3], atomnames[final_impropers[i][1]/3], atomnames[int(numpy.abs(final_impropers[i][2]))/3], atomnames[final_impropers[i][3]/3], forceconstants[2][final_impropers[i][4]-1], int(equilvals[2][0][final_impropers[i][4]-1]), equilvals[2][1][final_impropers[i][4]-1])\\r\\n else:\\r\\n mult_im[im_id][1] = True\\r\\n # Add dihedral with the appropriate multiplicity\\r\\n # Force constants, periodicity and phase shifts are in [2], [3], and [4] respectively\\r\\n fcvec = PARReader.VectorOfDouble()\\r\\n periodvec = PARReader.VectorOfInt()\\r\\n phasevec = PARReader.VectorOfDouble() \\r\\n for j in range(0, len(mult_im[im_id][2])):\\r\\n fcvec.push_back(mult_im[im_id][2][j])\\r\\n periodvec.push_back(mult_im[im_id][3][j])\\r\\n phasevec.push_back(mult_im[im_id][4][j])\\r\\n phys.myPSF.addImproper(i+1, final_impropers[i][0]/3+1, final_impropers[i][1]/3+1, int(numpy.abs(final_impropers[i][2]))/3+1, final_impropers[i][3]/3+1)\\r\\n phys.myPAR.addImproper(i+1, atomnames[final_impropers[i][0]/3], atomnames[final_impropers[i][1]/3], atomnames[int(numpy.abs(final_impropers[i][2]))/3], atomnames[final_impropers[i][3]/3], mult, fcvec, periodvec, phasevec)\\r\\n\\r\\n \\r\\n # Need to add garbage nonbonded stuff for now\\r\\n for i in range(0, natoms):\\r\\n phys.myPAR.addNonbonded(i, atomnames[i], 1, 1, 1, 1, 1, 1)\\r\\n\\r\\n # Add VDW parameters\\r\\n # AMBER has the Aij and Bij already in the parameter file\\r\\n # This actually makes life easier.\\r\\n # CHARMM does not, they simply have the original sigma and epsilon.\\r\\n # To compensate for this, for now we will leave the nonbondeds empty in phys.myPAR\\r\\n # We will then access the LennardJones parameter table in Topology directly\\r\\n k = 0\\r\\n phys.myTop.resizeLennardJonesParameters(ntypes)\\r\\n for i in range(0, ntypes):\\r\\n for j in range(i, ntypes):\\r\\n params = GenericTopology.LennardJonesParameters(lj_acoef[k], lj_bcoef[k])\\r\\n k += 1\\r\\n phys.myTop.setLennardJonesParameters(i, j, params)\\r\\n \\r\\n phys.myPAR.readFlag = 1\\r\\n phys.build()\",\n \"def get_parser():\\n\\tparser = argparse.ArgumentParser('cgm_plot_pha.py',\\n\\t\\tformatter_class=argparse.RawDescriptionHelpFormatter,\\n\\t\\tdescription=\\\"\\\"\\\"\\nplot pha spectrum from an event fitsfile.\\n\\t\\t\\\"\\\"\\\"\\n\\t\\t)\\n\\tversion = '%(prog)s ' + __version__\\n\\tparser.add_argument('--version', '-v', action='version', version=version,\\n\\t\\thelp='show version of this command.')\\n\\tparser.add_argument('input_evtfits', type=str, \\n\\t\\thelp='input fits-format event file.')\\n\\tparser.add_argument('--pha_min', type=int, default=None,\\n\\t\\thelp='pha_min')\\t\\n\\tparser.add_argument('--pha_max', type=int, default=None,\\n\\t\\thelp='pha_max')\\t\\n\\tparser.add_argument('--tbin', type=float, default=None,\\n\\t\\thelp='tbin')\\n\\tparser.add_argument('--threshold', type=float, default=None,\\n\\t\\thelp='threshold')\\t\\t\\t\\t\\t\\t\\n\\treturn parser\",\n \"def function_macro(self, platform, stack):\\n initial_pos = self.pos\\n try:\\n identifier = self.match_type(Identifier)\\n if identifier in stack:\\n raise ParseError('Cannot expand token')\\n\\n self.match_value(Punctuator, \\\"(\\\")\\n args = self.__arg_list()\\n self.match_value(Punctuator, \\\")\\\")\\n except ParseError:\\n self.pos = initial_pos\\n raise ParseError(\\\"Not a function-like macro.\\\")\\n\\n macro = platform.get_macro(str(identifier))\\n if not macro:\\n raise ParseError(\\\"Not a function-like macro.\\\")\\n\\n # Argument pre-scan\\n # Macro arguments are macro-expanded before substitution\\n expanded_args = [MacroExpander(arg).expand(platform) for arg in args]\\n\\n # Combine variadic arguments into one, separated by commas\\n va_args = None\\n if macro.is_variadic():\\n va_args = util.interleave(expanded_args[len(macro.args) - 1:],\\n Punctuator(\\\"EXPANSION\\\", -1, False, \\\",\\\"))\\n va_args = va_args[:-1] # Remove final comma\\n\\n # Substitute each occurrence of an argument in the expansion\\n substituted_tokens = []\\n for token in macro.expansion:\\n\\n substitution = []\\n\\n # If a token matches an argument, it is substituted;\\n # otherwise it passes through\\n try:\\n substitution = expanded_args[macro.args.index(token.token)]\\n except (ValueError, ParseError):\\n substitution = token\\n\\n # If a token matches the variable argument, substitute\\n # precomputed va_args\\n if macro.is_variadic() and token.token == macro.variable_argument() and va_args:\\n\\n # Whether the token was preceded by whitespace should be\\n # tracked through substitution\\n for t in va_args[0]:\\n t.prev_white = token.prev_white\\n substitution = va_args\\n\\n self.grow_token_list(substituted_tokens, substitution)\\n\\n # Check the expansion for macros to expand\\n stack.push(identifier)\\n expansion = MacroExpander(substituted_tokens).expand(platform, stack)\\n stack.pop()\\n return expansion\",\n \"def _parse_preset(self, xmldata):\\r\\n\\r\\n raise NotImplementedError\",\n \"def pre_processor(self):\",\n \"def generate_parser():\\n description = \\\"%(prog)s -- Data handling, normalization, manipulation, and plotting for HiC and 5C experimental data\\\"\\n epilog = \\\"For command line options of each command, type: %(prog)s <COMMAND> -h\\\"\\n parser = ap.ArgumentParser(description=description, epilog=epilog)\\n parser.add_argument(\\\"--version\\\", action=\\\"version\\\", version=\\\"%(prog)s %(version_num)s\\\" % {'prog':parser.prog, 'version_num':VERSION})\\n subparsers = parser.add_subparsers(dest='subcommand')\\n\\n add_connect_subparser(subparsers)\\n add_fragments_subparser(subparsers)\\n add_fivecdataset_subparser(subparsers)\\n add_fivecproject_subparser(subparsers)\\n add_fivecnormalize_subparser(subparsers)\\n add_complete_fivec_subparser(subparsers)\\n add_fivec_heatmap_subparser(subparsers)\\n add_fivec_interval_subparser(subparsers)\\n add_fivec_combine_replicates_subparser(subparsers)\\n add_fends_subparser(subparsers)\\n add_hicdataset_subparser(subparsers)\\n add_hicproject_subparser(subparsers)\\n add_hicnormalize_subparser(subparsers)\\n add_complete_hic_subparser(subparsers)\\n add_hic_heatmap_subparser(subparsers)\\n add_hic_mrheatmap_subparser(subparsers)\\n add_hic_interval_subparser(subparsers)\\n add_hic_combine_replicates_subparser(subparsers)\\n add_quasar_subparser(subparsers)\\n return parser\",\n \"def spec_parser(subparser):\\n parser = subparser.add_parser('spec',\\\\\\n help='will print information about a spectral file (also SELAFIN),'\\\\\\n 'such as frequencies, periodes, etc.')\\n parser = add_arg(parser, 'xvars')\\n parser = add_arg(parser, 'core')\\n parser = add_arg(parser, 'time')\\n parser = add_arg(parser, 'accuracy')\\n parser.add_argument(\\\"input_files\\\", metavar='Spectrum SELAFIN file',\\n nargs=\\\"+\\\")\\n\\n return subparser\",\n \"def arg_parser(self):\\n print\\n\\n parser = argparse.ArgumentParser()\\n subparsers = parser.add_subparsers()\\n\\n status = subparsers.add_parser('status', help=self.viewer.status.__doc__)\\n status.set_defaults(func=self.viewer.status)\\n\\n view_catalog = subparsers.add_parser('catalog', help=self.viewer.view_full_catalog.__doc__)\\n view_catalog.set_defaults(func=self.viewer.view_full_catalog)\\n\\n view_tags = subparsers.add_parser('tags', help=self.viewer.view_all_tags.__doc__)\\n view_tags.add_argument('-a', '--alpha', action='store_true', help=\\\"List tags alphabetically\\\")\\n view_tags.set_defaults(func=self.viewer.view_all_tags)\\n\\n search = subparsers.add_parser('search', help=self.viewer.search_tags.__doc__)\\n search.add_argument('-t', '--tags', nargs='+', required=True, help=\\\"Tags to search for\\\")\\n search.add_argument('-o', action='store_true', help=\\\"Search using 'or' logic ('and' logic by default)\\\")\\n search.set_defaults(func=self.viewer.search_tags) \\n\\n add_file = subparsers.add_parser('addfile', help=self.editor.add_files.__doc__)\\n add_file.add_argument('filename', help=\\\"Name of file to add catalog\\\")\\n add_file.set_defaults(func=self.editor.add_files)\\n\\n add_tags = subparsers.add_parser('addtags', help=self.editor.add_tag.__doc__)\\n add_tags.add_argument('filename', help=\\\"Name of file to add catalog\\\")\\n add_tags.add_argument('-t', '--tags', nargs='+', help=\\\"Tags to add to catalog\\\")\\n add_tags.set_defaults(func=self.editor.add_tag)\\n\\n edit_entry = subparsers.add_parser('edit', help=self.editor.edit_entry.__doc__)\\n edit_entry.add_argument('filename', help=\\\"Name of file to add catalog\\\")\\n edit_entry.set_defaults(func=self.editor.edit_entry)\\n\\n clean_catalog = subparsers.add_parser('clean', help=self.editor.clean_catalog.__doc__)\\n clean_catalog.add_argument('-t', '--tags', nargs='+', help=\\\"Tags to be deleted from catalog entirely\\\")\\n clean_catalog.set_defaults(func=self.editor.clean_catalog)\\n\\n delete_entry = subparsers.add_parser('delete', help=self.editor.delete_entry.__doc__)\\n delete_entry.add_argument('filename', help=\\\"File from which to delete specified tags\\\")\\n delete_entry.add_argument('-t', '--tags', nargs='+', help=\\\"Tags to be deleted\\\")\\n delete_entry.set_defaults(func=self.editor.delete_entry)\\n\\n merge_tags = subparsers.add_parser('merge', help=self.editor.merge_tags.__doc__)\\n merge_tags.add_argument('--source', required=True, help=\\\"File from which tags are being taken\\\")\\n merge_tags.add_argument('--dest', required=True, help=\\\"Destination file to which tags from --source are added\\\")\\n merge_tags.set_defaults(func=self.editor.merge_tags)\\n\\n \\n args = parser.parse_args()\\n\\n args.func(args)\",\n \"def parseArguments():\\n # Create argument parser\\n #parser = argparse.ArgumentParser()\\n parser = ArgumentParser()\\n\\n\\n # Positional mandatory arguments\\n parser.add_argument(\\\"input\\\", nargs='+',help=\\\"Input Image with .fits ending. A folder or multiple Images also work\\\", type=str)\\n parser.add_argument(\\\"-c\\\", \\\"--catalog\\\", help=\\\"Catalog to use for position reference ('PS', '2MASS' or 'GAIA') or name of local file\\\", type=str, default=\\\"PS\\\")\\n\\n parser.add_argument(\\\"-s\\\", \\\"--save_images\\\", help=\\\"Set True to create _image_before.pdf and _image_after.pdf\\\", type=bool, default=False)\\n parser.add_argument(\\\"-p\\\", \\\"--images\\\", help=\\\"Set 0 to not create the plots.\\\", type=int, default=1)\\n\\n parser.add_argument(\\\"-v\\\", \\\"--verbose\\\", help=\\\"More console output about what is happening. Helpfull for debugging.\\\", type=bool, default=False)\\n parser.add_argument(\\\"-silent\\\", \\\"--silent\\\", help=\\\"Almost no console output. Use when running many files. turns verbose off, turns plots off, turns ignore warning on. \\\", type=bool, default=False)\\n\\n\\n\\n parser.add_argument(\\\"-w\\\", \\\"--ignore_warnings\\\", help=\\\"Set False to see all Warnings about the header if there is problems. Default is to ignore most warnings.\\\", type=bool, default=True)\\n\\n parser.add_argument(\\\"-ra\\\", \\\"--ra\\\", help=\\\"Set ra by hand in degrees. Should not be necessary if the info is in the fits header.\\\", type=float, default=None)\\n parser.add_argument(\\\"-dec\\\", \\\"--dec\\\", help=\\\"Set dec by hand in degrees. Should not be necessary if the info is in the fits header.\\\", type=float, default=None)\\n\\n parser.add_argument(\\\"-proj1\\\", \\\"--projection_ra\\\", help=\\\"Set the projection by hand. Should not be necessary if the info is in the fits header. example: -proj1 RA---TAN -proj2 DEC--TAN\\\", type=str, default=None)\\n parser.add_argument(\\\"-proj2\\\", \\\"--projection_dec\\\", help=\\\"Set the projection by hand. Should not be necessary if the info is in the fits header. example: -proj1 RA---TAN -proj2 DEC--TAN\\\", type=str, default=None)\\n\\n\\n parser.add_argument(\\\"-rot_scale\\\", \\\"--rotation_scaling\\\", help=\\\"By default rotation and scaling is determined. If wcs already contains this info and the fit fails you can try deactivating this part by setting it to 0\\\", type=int, default=1)\\n parser.add_argument(\\\"-xy_trafo\\\", \\\"--xy_transformation\\\", help=\\\"By default the x and y offset is determined. If wcs already contains this info and the fit fails you can try deactivating this part by setting it to 0\\\", type=int, default=1)\\n parser.add_argument(\\\"-fine\\\", \\\"--fine_transformation\\\", help=\\\"By default a fine transformation is applied in the end. You can try deactivating this part by setting it to 0\\\", type=int, default=1)\\n\\n parser.add_argument(\\\"-vignette\\\", \\\"--vignette\\\", help=\\\"Do not use corner of the image. Only use the data in a circle around the center with certain radius. Default: not used. Set to 1 for circle that touches the sides. Less to cut off more\\\", type=float, default=3)\\n parser.add_argument(\\\"-vignette_rec\\\", \\\"--vignette_rectangular\\\", help=\\\"Do not use corner of the image. Cutoff 1- <value> on each side of the image. Default: not used. 1 uses the full image, 0.9 cuts 10%% on each side\\\", type=float, default=1.)\\n\\n parser.add_argument(\\\"-cutout\\\", \\\"--cutout\\\", help=\\\"Cutout bad recangle from Image. Specify corners in pixel as -cutout xstart xend ystart yend. You can give multiple cutouts \\\", nargs='+',action=\\\"append\\\", type=int)\\n\\n parser.add_argument(\\\"-ignore_header_rot\\\", \\\"--ignore_header_rot\\\", help=\\\"Set to 0 to ignore rotation information contained in header\\\", type=int, default=0)\\n\\n parser.add_argument(\\\"-r\\\", \\\"--radius\\\", help=\\\"Change the download radius for how many catalog objects should be downloaded in arcmin. \\\", type=float, default=-1)\\n parser.add_argument(\\\"-save_bad_result\\\", \\\"--save_bad_result\\\", help=\\\"Save result even when it is considered bad by setting this to 1. By default bad results will not be saved\\\", type=int, default=0)\\n\\n parser.add_argument(\\\"-sigma_threshold_for_source_detection\\\", \\\"--sigma_threshold_for_source_detection\\\", help=\\\"Sigma threshold for source detection on the image\\\", type=float, default=5)\\n parser.add_argument(\\\"-seeing\\\", \\\"--seeing\\\", help=\\\"Average FWHM of sources. Default 4px\\\", type=float, default=4)\\n\\n parser.add_argument(\\\"-high_res\\\", \\\"--high_resolution\\\", help=\\\"Set true to indicate higher resolution image like HST to allow larger steps for fine transformation. Default False for smaller telescopes\\\", type=bool, default=False)\\n parser.add_argument(\\\"-hdul_idx\\\", \\\"--hdul_idx\\\", help=\\\"Index of the image data in the fits file. Default 0\\\", type=int, default=0)\\n parser.add_argument(\\\"-filename_for_sources\\\", \\\"--filename_for_sources\\\", help=\\\"Save the sky positions of the sources to file to calibrate another image with it. Set to the filename without extension. Default: not used\\\", type=str, default=None)\\n\\n # Print version\\n parser.add_argument(\\\"--version\\\", action=\\\"version\\\", version='%%(prog)s - Version 1.5') #\\n #changelog\\n #version 0.0 proof of concept\\n #version 0.1 alpha version\\n #version 1.0 first public version\\n #version 1.2 included option to not show images\\n #version 1.3 improved support for high resolution images\\n #version 1.4 bugfixes and ability to calibrate based on another image\\n #version 1.5 added compatibility with photutils v1.4\\n\\n # Parse arguments\\n args = parser.parse_args()\\n\\n return args\",\n \"def parse_args(argv=None):\\n description = textwrap.dedent('''Panacea - \\n \\n This script does ... (Fill in Later)\\n \\n ''')\\n \\n parser = ap.ArgumentParser(description=description,\\n formatter_class=ap.RawTextHelpFormatter)\\n \\n parser.add_argument(\\\"-rt\\\",\\\"--reduce_twi\\\", \\n help='''Reduce Twighlight frames for calibration''',\\n action=\\\"count\\\", default=0)\\n\\n parser.add_argument(\\\"-c\\\",\\\"--custom\\\", \\n help='''Execute custom function''',\\n action=\\\"count\\\", default=0)\\n\\n parser.add_argument(\\\"-s\\\",\\\"--save_sci_fibers\\\", \\n help='''Save Science Fibers''',\\n action=\\\"count\\\", default=0)\\n\\n parser.add_argument(\\\"-sa\\\",\\\"--save_sci_amplifier\\\", \\n help='''Save Science Amplifier''',\\n action=\\\"count\\\", default=0)\\n\\n parser.add_argument(\\\"-rs\\\",\\\"--reduce_sci\\\", \\n help='''Reduce Science frames''',\\n action=\\\"count\\\", default=0)\\n\\n parser.add_argument(\\\"-mb\\\",\\\"--make_masterbias\\\", \\n help='''Make MasterBias frames''',\\n action=\\\"count\\\", default=0)\\n \\n parser.add_argument(\\\"-md\\\",\\\"--make_masterdark\\\", \\n help='''Make MasterDark frames''',\\n action=\\\"count\\\", default=0)\\n \\n parser.add_argument(\\\"-uos\\\",\\\"--use_other_sky\\\", \\n help='''Use another frame for the sky_spectrum''',\\n action=\\\"count\\\", default=0)\\n\\n parser.add_argument(\\\"-at\\\",\\\"--adjust_trace\\\", \\n help='''Adjust trace using science frame.''',\\n action=\\\"count\\\", default=0)\\n \\n parser.add_argument(\\\"-rff\\\",\\\"--refit_fiber_to_fiber\\\", \\n help='''Using the sky spectrum, refit the fiber to\\n fiber.''',\\n action=\\\"count\\\", default=0)\\n\\n parser.add_argument(\\\"-utr\\\",\\\"--use_trace_ref\\\", \\n help='''Using trace reference files to recover all\\n fibers.''',\\n action=\\\"count\\\", default=0)\\n \\n parser.add_argument(\\\"--fiber_date\\\", nargs='?', type=str, \\n help='''Date for Fiber_Locations''', default = None) \\n\\n parser.add_argument(\\\"-p\\\",\\\"--pixelflats\\\", \\n help='''Turn off using pixel flats.''',\\n action=\\\"count\\\", default=0)\\n\\n parser.add_argument(\\\"-sfs\\\",\\\"--start_from_scratch\\\", \\n help='''Re-fiberextract, sky-subtract, cosmic ray reject.''',\\n action=\\\"count\\\", default=0)\\n \\n parser.add_argument(\\\"--specid\\\", nargs='?', type=str, \\n help='''List of SPECID's for processing. [REQUIRED]\\n Ex: \\\"020,008\\\".''', default = None)\\n\\n parser.add_argument(\\\"--instr\\\", nargs='?', type=str, \\n help='''Instrument to process. \\n Default: \\\"virus\\\"\\n Ex: \\\"camra\\\" for lab data,\\n \\\"lrs2\\\" for lrs2.''', default = \\\"virus\\\")\\n \\n parser.add_argument(\\\"--instr_side\\\", nargs='?', type=str, \\n help='''Instrument side to process. \\n Default: \\\"blue\\\"\\n Ex: \\\"blue\\\" for LRS2B,\\n \\\"red\\\" for LRS2R.''', default = \\\"blue\\\")\\n\\n parser.add_argument(\\\"--output\\\", nargs='?', type=str, \\n help='''Output Directory\\n Default: \\\\\\\"reductions\\\"''', \\n default=\\\"reductions\\\")\\n \\n parser.add_argument(\\\"--rootdir\\\", nargs='?', type=str, \\n help='''Root Directory\\n Default: \\\\\\\"/work/03946/hetdex/maverick\\\\\\\"''', \\n default=\\\"/work/03946/hetdex/maverick\\\")\\n\\n parser.add_argument(\\\"--configdir\\\", nargs='?', type=str, \\n help='''Config Directory\\n Default: \\\\\\\"/work/03946/hetdex/maverick/virus_config\\\\\\\"''', \\n default=\\\"/work/03946/hetdex/maverick/virus_config\\\")\\n\\n parser.add_argument(\\\"--biasdir\\\", type=str,\\n help='''Bias Library\\n Default: \\\\\\\"/work/03946/hetdex/maverick/virus_config/lib_bias\\\\\\\"''', \\n default=\\\"/work/03946/hetdex/maverick/virus_config/lib_bias\\\")\\n \\n parser.add_argument(\\\"--darkdir\\\", type=str,\\n help='''Dark Library\\n Default: \\\\\\\"/work/03946/hetdex/maverick/virus_config/lib_dark\\\\\\\"''',\\n default=\\\"/work/03946/hetdex/maverick/virus_config/lib_dark\\\")\\n \\n parser.add_argument(\\\"-sd\\\",\\\"--scidir_date\\\", nargs='?', type=str,\\n help='''Science Directory Date. [REQUIRED, if --reduce_sci]\\n Ex: \\\\\\\"20160412\\\\\\\"''', default=None)\\n\\n parser.add_argument(\\\"-so\\\",\\\"--scidir_obsid\\\", nargs='?', type=str,\\n help='''Science Directory ObsID. [REQUIRED, if --reduce_sci]\\n Ex: \\\\\\\"3\\\\\\\" or \\\\\\\"102\\\\\\\"''', default=None)\\n \\n parser.add_argument(\\\"-se\\\",\\\"--scidir_expnum\\\", nargs='?', type=str,\\n help='''Science Directory exposure number.\\n Ex: \\\\\\\"1\\\\\\\" or \\\\\\\"05\\\\\\\"''', default=None) \\n\\n parser.add_argument(\\\"-bd\\\",\\\"--biadir_date\\\", nargs='?', type=str,\\n help='''Science Directory Date. [REQUIRED, if --reduce_sci]\\n Ex: \\\\\\\"20160412\\\\\\\"''', default=None)\\n\\n parser.add_argument(\\\"-bo\\\",\\\"--biadir_obsid\\\", nargs='?', type=str,\\n help='''Science Directory ObsID. [REQUIRED, if --reduce_sci]\\n Ex: \\\\\\\"3\\\\\\\" or \\\\\\\"102\\\\\\\"''', default=None)\\n \\n parser.add_argument(\\\"-be\\\",\\\"--biadir_expnum\\\", nargs='?', type=str,\\n help='''Science Directory exposure number.\\n Ex: \\\\\\\"1\\\\\\\" or \\\\\\\"05\\\\\\\"''', default=None) \\n\\n parser.add_argument(\\\"--bias_outfolder\\\", nargs='?', type=str, \\n help='''Output folder name for bias library\\n Default: \\\\\\\"default\\\"''', \\n default=\\\"default\\\")\\n\\n parser.add_argument(\\\"-dd\\\",\\\"--drkdir_date\\\", nargs='?', type=str,\\n help='''Science Directory Date. [REQUIRED, if --reduce_sci]\\n Ex: \\\\\\\"20160412\\\\\\\"''', default=None)\\n\\n parser.add_argument(\\\"-do\\\",\\\"--drkdir_obsid\\\", nargs='?', type=str,\\n help='''Science Directory ObsID. [REQUIRED, if --reduce_sci]\\n Ex: \\\\\\\"3\\\\\\\" or \\\\\\\"102\\\\\\\"''', default=None)\\n \\n parser.add_argument(\\\"-de\\\",\\\"--drkdir_expnum\\\", nargs='?', type=str,\\n help='''Science Directory exposure number.\\n Ex: \\\\\\\"1\\\\\\\" or \\\\\\\"05\\\\\\\"''', default=None) \\n\\n parser.add_argument(\\\"--dark_outfolder\\\", nargs='?', type=str, \\n help='''Output folder name for dark library\\n Default: \\\\\\\"default\\\"''', \\n default=\\\"default\\\")\\n\\n parser.add_argument(\\\"-td\\\",\\\"--twidir_date\\\", nargs='?', type=str,\\n help='''Twi Directory Date. [REQUIRED, if --reduce_twi]\\n Ex: \\\\\\\"20160412\\\\\\\"''', default=None)\\n\\n parser.add_argument(\\\"-to\\\",\\\"--twidir_obsid\\\", nargs='?', type=str,\\n help='''Twi Directory ObsID. [REQUIRED, if --reduce_twi]\\n Ex: \\\\\\\"3\\\\\\\" or \\\\\\\"102\\\\\\\"''', default=None)\\n \\n parser.add_argument(\\\"-te\\\",\\\"--twidir_expnum\\\", nargs='?', type=str,\\n help='''Twi Directory exposure number.\\n Ex: \\\\\\\"1\\\\\\\" or \\\\\\\"05\\\\\\\"''', default=None) \\n\\n parser.add_argument(\\\"-skd\\\",\\\"--skydir_date\\\", nargs='?', type=str,\\n help='''Sky Directory Date. [REQUIRED, --use_other_sky]\\n Ex: \\\\\\\"20160412\\\\\\\"''', default=None)\\n\\n parser.add_argument(\\\"-sko\\\",\\\"--skydir_obsid\\\", nargs='?', type=str,\\n help='''Sky Directory ObsID. [REQUIRED, --use_other_sky]\\n Ex: \\\\\\\"3\\\\\\\" or \\\\\\\"102\\\\\\\"''', default=None)\\n \\n parser.add_argument(\\\"-ske\\\",\\\"--skydir_expnum\\\", nargs='?', type=str,\\n help='''Sky Directory exposure number.\\n Ex: \\\\\\\"1\\\\\\\" or \\\\\\\"05\\\\\\\"''', default=None) \\n\\n parser.add_argument(\\\"-d\\\",\\\"--debug\\\", help='''Debug.''',\\n action=\\\"count\\\", default=0)\\n \\n args = parser.parse_args(args=argv)\\n\\n # Check that the arguments are filled\\n if args.specid:\\n args.specid = args.specid.replace(\\\" \\\", \\\"\\\").split(',')\\n else:\\n msg = 'No SPECID was provided.'\\n parser.error(msg) \\n \\n\\n \\n if args.instr.lower() == 'virus':\\n instr = 'virus_'\\n if args.instr.lower() == 'lrs2':\\n if args.instr_side.lower() == 'blue':\\n instr = 'lrs2b_'\\n if args.instr.lower() == 'lrs2':\\n if args.instr_side.lower() == 'red':\\n instr = 'lrs2r_'\\n if args.instr.lower() == 'virusw':\\n instr = 'virusw_' \\n for con in config.config_dict:\\n setattr(args, con, getattr(config, instr+config.config_dict[con]))\\n\\n\\n labels = ['dir_date', 'dir_obsid', 'dir_expnum']\\n observations=[]\\n args.check_if_twi_exists=False\\n if args.reduce_sci:\\n observations.append('sci')\\n if not args.reduce_twi:\\n observations.append('twi')\\n args.check_if_twi_exists = True\\n if args.reduce_twi:\\n observations.append('twi')\\n if args.use_other_sky:\\n observations.append('sky')\\n if args.make_masterbias:\\n observations.append('bia')\\n if args.make_masterdark:\\n observations.append('drk')\\n for obs in observations:\\n for label in labels[:2]:\\n getattr(args, obs+label)\\n if getattr(args, obs+label) is None:\\n msg = '%s%s was not provided' %(obs, label)\\n parser.error(msg) \\n else:\\n setattr(args, obs+label, \\n getattr(args, obs+label).replace(\\\" \\\", \\\"\\\").split(','))\\n if getattr(args, obs+labels[2]) is not None:\\n setattr(args, obs+labels[2], \\n getattr(args, obs+labels[2]).replace(\\\" \\\", \\\"\\\").split(','))\\n DF = pd.DataFrame(columns=['Files', 'Output', 'Amp', 'Specid', \\n 'Ifuslot', 'Ifuid']) \\n cnt=0\\n for date in getattr(args, obs+labels[0]):\\n for obsid in getattr(args, obs+labels[1]):\\n if getattr(args, obs+labels[2]) is not None: \\n for expnum in getattr(args, obs+labels[2]):\\n folder = op.join(date, \\n args.instr, \\n \\\"{:s}{:07d}\\\".format(args.instr,int(obsid)), \\n \\\"exp{:02d}\\\".format(int(expnum)),\\n args.instr)\\n files = sorted(glob.glob(op.join(args.rootdir, folder, '*')))\\n if files:\\n mkpath(op.join(args.output,folder)) \\n for fn in files:\\n F = fits.open(fn)\\n outfolder = op.join(args.output,folder) \\n amp = (F[0].header['CCDPOS'].replace(' ', '') \\n + F[0].header['CCDHALF'].replace(' ', ''))\\n sp = '%03d' %F[0].header['SPECID']\\n ifuid = F[0].header['IFUID'].replace(' ', '')\\n ifuslot = '%03d' %F[0].header['IFUSLOT']\\n DF.loc[cnt] = pd.Series({'Files':fn, \\n 'Output':outfolder, \\n 'Specid':sp,\\n 'Ifuslot': ifuslot,\\n 'Ifuid': ifuid, \\n 'Amp': amp})\\n cnt+=1\\n else:\\n folder = op.join(date, args.instr,\\n \\\"{:s}{:07d}\\\".format(args.instr,int(obsid)))\\n files = sorted(glob.glob(op.join(args.rootdir, folder, '*', args.instr, \\n '*')))\\n if files:\\n nfiles = sorted(glob.glob(op.join(args.output, folder, '*')))\\n for nfile in nfiles:\\n mkpath(op.join(nfile, args.instr))\\n for fn in files:\\n F = fits.open(fn)\\n exp = op.basename(op.dirname(op.dirname(fn)))\\n outfolder = op.join(args.output,folder, exp, args.instr)\\n amp = (F[0].header['CCDPOS'].replace(' ', '') \\n + F[0].header['CCDHALF'].replace(' ', ''))\\n sp = '%03d' %F[0].header['SPECID']\\n ifuid = F[0].header['IFUID'].replace(' ', '')\\n ifuslot = '%03d' %F[0].header['IFUSLOT']\\n DF.loc[cnt] = pd.Series({'Files':fn, 'Output':outfolder, \\n 'Specid':sp, 'Ifuslot': ifuslot,\\n 'Ifuid': ifuid, 'Amp': amp})\\n cnt+=1\\n setattr(args, obs+'_df', DF)\\n \\n if args.reduce_sci:\\n cals=['twi']\\n if args.use_other_sky:\\n cals.append('sky')\\n else: \\n args.sky_dir = None\\n for cal in cals:\\n if getattr(args, cal+labels[0]) is None:\\n print(\\\"Please provide one \\\"+cal+labels[0])\\n sys.exit(1) \\n if len(getattr(args, cal+labels[0]))>1:\\n print(\\\"Please provide only one \\\"+cal+labels[0])\\n print(\\\"I am cowardly quitting instead of making a smart program.\\\")\\n sys.exit(1)\\n if getattr(args, cal+labels[1]) is None:\\n print(\\\"Please provide one \\\"+cal+labels[1])\\n sys.exit(1) \\n if len(getattr(args, cal+labels[1]))>1:\\n print(\\\"Please provide only one \\\"+cal+labels[1])\\n print(\\\"I am cowardly quitting instead of making a smart program.\\\")\\n sys.exit(1)\\n if getattr(args, cal+labels[2]) is None:\\n print(\\\"Please provide one \\\"+cal+labels[2])\\n sys.exit(1) \\n if len(getattr(args, cal+labels[2]))>1:\\n print(\\\"Please provide only one \\\"+cal+labels[2])\\n print(\\\"I am cowardly quitting instead of making a smart program.\\\")\\n sys.exit(1) \\n for date in getattr(args, cal+labels[0]):\\n for obsid in getattr(args, cal+labels[1]):\\n if getattr(args, cal+labels[2]) is not None: \\n for expnum in getattr(args, cal+labels[2]):\\n setattr(args, cal+'_dir', op.join(args.output, date, args.instr, \\n \\\"{:s}{:07d}\\\".format(args.instr,int(obsid)), \\n \\\"exp{:02d}\\\".format(int(expnum)),\\n args.instr))\\n \\n \\n\\n return args\",\n \"def intf_MMTEST(E):\\n macro= \\\"10 10 0 p dup 100 10 0 p dup rot l drop 50 100 0 p dup rot l drop l drop\\\"\\n oblistcontent= list()\\n for s in macro.split(' '):\\n try:\\n s= float(s)\\n except ValueError:\\n pass\\n if type(s) == type('str'):\\n oblistcontent.append(objectifier.StackOB_SYM(s))\\n else:\\n oblistcontent.append(objectifier.StackOB_VAL(s))\\n testmacro= objectifier.StackOB_LST(oblistcontent) \\n testmacro.dead= False\\n E.The.StackPush(testmacro)\",\n \"def parseGerber(self, fullname, layername, updateExtents = 0):\\n\\n GAT = config.GAT\\n GAMT = config.GAMT\\n # First construct reverse GAT/GAMT, mapping definition to code\\n RevGAT = config.buildRevDict(GAT) # RevGAT[hash] = aperturename\\n RevGAMT = config.buildRevDict(GAMT) # RevGAMT[hash] = aperturemacroname\\n\\n #print 'Reading data from %s ...' % fullname\\n\\n fid = file(fullname, 'rt')\\n currtool = None\\n\\n self.apxlat[layername] = {}\\n self.apmxlat[layername] = {}\\n self.commands[layername] = []\\n self.apertures[layername] = []\\n\\n # These divisors are used to scale (X,Y) co-ordinates. We store\\n # everything as integers in hundred-thousandths of an inch (i.e., M.5\\n # format). If we get something in M.4 format, we must multiply by\\n # 10. If we get something in M.6 format we must divide by 10, etc.\\n x_div = 1.0\\n y_div = 1.0\\n\\n # Drawing commands can be repeated with X or Y omitted if they are\\n # the same as before. These variables store the last X/Y value as\\n # integers in hundred-thousandths of an inch.\\n last_x = last_y = 0\\n\\n # Last modal G-code. Some G-codes introduce \\\"modes\\\", such as circular interpolation\\n # mode, and we want to remember what mode we're in. We're interested in:\\n # G01 -- linear interpolation, cancels all circular interpolation modes\\n # G36 -- Turn on polygon area fill\\n # G37 -- Turn off polygon area fill\\n last_gmode = 1 # G01 by default, linear interpolation\\n\\n # We want to know whether to do signed (G75) or unsigned (G74) I/J offsets. These\\n # modes are independent of G01/G02/G03, e.g., Protel will issue multiple G03/G01\\n # codes all in G75 mode.\\n # G74 -- Single-quadrant circular interpolation (disables multi-quadrant interpolation)\\n # G02/G03 codes set clockwise/counterclockwise arcs in a single quadrant only\\n # using X/Y/I/J commands with UNSIGNED (I,J).\\n # G75 -- Multi-quadrant circular interpolation --> X/Y/I/J with signed (I,J)\\n # G02/G03 codes set clockwise/counterclockwise arcs in all 4 quadrants\\n # using X/Y/I/J commands with SIGNED (I,J).\\n circ_signed = True # Assume G75...make sure this matches canned header we write out\\n\\n # If the very first flash/draw is a shorthand command (i.e., without an Xxxxx or Yxxxx)\\n # component then we don't really \\\"see\\\" the first point X00000Y00000. To account for this\\n # we use the following Boolean flag as well as the isLastShorthand flag during parsing\\n # to manually insert the point X000000Y00000 into the command stream.\\n firstFlash = True\\n\\n for line in fid:\\n # Get rid of CR characters (0x0D) and leading/trailing blanks\\n line = string.replace(line, '\\\\x0D', '').strip()\\n\\n # Old location of format_pat search. Now moved down into the sub-line parse loop below.\\n\\n # RS-274X statement? If so, echo it. Currently, only the \\\"LP\\\" statement is expected\\n # (from Protel, of course). These will be distinguished from D-code and G-code\\n # commands by the fact that the first character of the string is '%'.\\n match = layerpol_pat.match(line)\\n if match:\\n self.commands[layername].append(line)\\n continue\\n \\n # See if this is an aperture definition, and if so, map it.\\n match = apdef_pat.match(line)\\n if match:\\n if currtool:\\n raise RuntimeError, \\\"File %s has an aperture definition that comes after drawing commands.\\\" % fullname\\n\\n A = aptable.parseAperture(line, self.apmxlat[layername])\\n if not A:\\n raise RuntimeError, \\\"Unknown aperture definition in file %s\\\" % fullname\\n\\n hash = A.hash()\\n if not RevGAT.has_key(hash):\\n #print line\\n #print self.apmxlat\\n #print RevGAT\\n raise RuntimeError, 'File %s has aperture definition \\\"%s\\\" not in global aperture table.' % (fullname, hash)\\n\\n # This says that all draw commands with this aperture code will\\n # be replaced by aperture self.apxlat[layername][code].\\n self.apxlat[layername][A.code] = RevGAT[hash]\\n continue\\n\\n # Ignore %AMOC8* from Eagle for now as it uses a macro parameter, which\\n # is not yet supported in GerbMerge.\\n if line[:7]=='%AMOC8*':\\n continue\\n\\n # See if this is an aperture macro definition, and if so, map it.\\n M = amacro.parseApertureMacro(line,fid)\\n if M:\\n if currtool:\\n raise RuntimeError, \\\"File %s has an aperture macro definition that comes after drawing commands.\\\" % fullname\\n\\n hash = M.hash()\\n if not RevGAMT.has_key(hash):\\n raise RuntimeError, 'File %s has aperture macro definition not in global aperture macro table:\\\\n%s' % (fullname, hash)\\n\\n # This says that all aperture definition commands that reference this macro name\\n # will be replaced by aperture macro name self.apmxlat[layername][macroname].\\n self.apmxlat[layername][M.name] = RevGAMT[hash]\\n continue\\n\\n # From this point on we may have more than one match on this line, e.g.:\\n # G54D11*X22400Y22300D02*X22500Y22200D01*\\n sub_line = line\\n while sub_line:\\n # Handle \\\"comment\\\" G-codes first\\n match = comment_pat.match(sub_line)\\n if match:\\n sub_line = sub_line[match.end():]\\n continue\\n\\n # See if this is a format statement, and if so, map it. In version 1.3 this was moved down\\n # from the line-only parse checks above (see comment) to handle OrCAD lines like\\n # G74*%FSLAN2X34Y34*%\\n match = format_pat.match(sub_line) # Used to be format_pat.search\\n if match:\\n sub_line = sub_line[match.end():]\\n for item in match.groups():\\n if item is None: continue # Optional group didn't match\\n\\n if item[0] in \\\"LA\\\": # omit leading zeroes and absolute co-ordinates\\n continue\\n\\n if item[0]=='T': # omit trailing zeroes\\n raise RuntimeError, \\\"Trailing zeroes not supported in RS274X files\\\"\\n if item[0]=='I': # incremental co-ordinates\\n raise RuntimeError, \\\"Incremental co-ordinates not supported in RS274X files\\\"\\n\\n if item[0]=='N': # Maximum digits for N* commands...ignore it\\n continue\\n\\n if item[0]=='X': # M.N specification for X-axis.\\n fracpart = int(item[2])\\n x_div = 10.0**(5-fracpart)\\n if item[0]=='Y': # M.N specification for Y-axis.\\n fracpart = int(item[2])\\n y_div = 10.0**(5-fracpart)\\n continue\\n\\n # Parse and interpret G-codes\\n match = gcode_pat.match(sub_line)\\n if match:\\n sub_line = sub_line[match.end():]\\n gcode = int(match.group(1))\\n\\n # Determine if this is a G-Code that should be ignored because it has no effect\\n # (e.g., G70 specifies \\\"inches\\\" which is already in effect).\\n if gcode in [54, 70, 90]:\\n continue\\n\\n # Determine if this is a G-Code that we have to emit because it matters.\\n if gcode in [1, 2, 3, 36, 37, 74, 75]:\\n self.commands[layername].append(\\\"G%02d\\\" % gcode)\\n\\n # Determine if this is a G-code that sets a new mode\\n if gcode in [1, 36, 37]:\\n last_gmode = gcode\\n\\n # Remember last G74/G75 code so we know whether to do signed or unsigned I/J\\n # offsets.\\n if gcode==74:\\n circ_signed = False\\n elif gcode==75:\\n circ_signed = True\\n \\n continue\\n\\n raise RuntimeError, \\\"G-Code 'G%02d' is not supported\\\" % gcode\\n\\n # See if this is a tool change (aperture change) command\\n match = tool_pat.match(sub_line)\\n if match:\\n currtool = match.group(1)\\n\\n # Protel likes to issue random D01, D02, and D03 commands instead of aperture\\n # codes. We can ignore D01 because it simply means to move to the current location\\n # while drawing. Well, that's drawing a point. We can ignore D02 because it means\\n # to move to the current location without drawing. Truly pointless. We do NOT want\\n # to ignore D03 because it implies a flash. Protel very inefficiently issues a D02\\n # move to a location without drawing, then a single-line D03 to flash. However, a D02\\n # terminates a polygon in G36 mode, so keep D02's in this case.\\n if currtool=='D01' or (currtool=='D02' and (last_gmode != 36)):\\n sub_line = sub_line[match.end():]\\n continue\\n\\n if (currtool == 'D03') or (currtool=='D02' and (last_gmode == 36)):\\n self.commands[layername].append(currtool)\\n sub_line = sub_line[match.end():]\\n continue\\n\\n # Map it using our translation table\\n if not self.apxlat[layername].has_key(currtool):\\n raise RuntimeError, 'File %s has tool change command \\\"%s\\\" with no corresponding translation' % (fullname, currtool)\\n\\n currtool = self.apxlat[layername][currtool]\\n\\n # Add it to the list of things to write out\\n self.commands[layername].append(currtool)\\n\\n # Add it to the list of all apertures needed by this layer\\n self.apertures[layername].append(currtool)\\n\\n # Move on to next match, if any\\n sub_line = sub_line[match.end():]\\n continue\\n\\n # Is it a simple draw command?\\n I = J = None # For circular interpolation drawing commands\\n match = drawXY_pat.match(sub_line)\\n isLastShorthand = False # By default assume we don't make use of last_x and last_y\\n if match:\\n x, y, d = map(__builtin__.int, match.groups())\\n else:\\n match = drawX_pat.match(sub_line)\\n if match:\\n x, d = map(__builtin__.int, match.groups())\\n y = last_y\\n isLastShorthand = True # Indicate we're making use of last_x/last_y\\n else:\\n match = drawY_pat.match(sub_line)\\n if match:\\n y, d = map(__builtin__.int, match.groups())\\n x = last_x\\n isLastShorthand = True # Indicate we're making use of last_x/last_y\\n\\n # Maybe it's a circular interpolation draw command with IJ components\\n if match is None:\\n match = cdrawXY_pat.match(sub_line)\\n if match:\\n x, y, I, J, d = map(__builtin__.int, match.groups())\\n else:\\n match = cdrawX_pat.match(sub_line)\\n if match:\\n x, I, J, d = map(__builtin__.int, match.groups())\\n y = last_y\\n isLastShorthand = True # Indicate we're making use of last_x/last_y\\n else:\\n match = cdrawY_pat.match(sub_line)\\n if match:\\n y, I, J, d = map(__builtin__.int, match.groups())\\n x = last_x\\n isLastShorthand = True # Indicate we're making use of last_x/last_y\\n\\n if match:\\n if currtool is None:\\n # It's OK if this is an exposure-off movement command (specified with D02).\\n # It's also OK if we're in the middle of a G36 polygon fill as we're only defining\\n # the polygon extents.\\n if (d != 2) and (last_gmode != 36):\\n raise RuntimeError, 'File %s has draw command %s with no aperture chosen' % (fullname, sub_line)\\n\\n # Save last_x/y BEFORE scaling to 2.5 format else subsequent single-ordinate\\n # flashes (e.g., Y with no X) will be scaled twice!\\n last_x = x\\n last_y = y\\n\\n # Corner case: if this is the first flash/draw and we are using shorthand (i.e., missing Xxxx\\n # or Yxxxxx) then prepend the point X0000Y0000 into the commands as it is actually the starting\\n # point of our layer. We prepend the command X0000Y0000D02, i.e., a move to (0,0) without drawing.\\n if (isLastShorthand and firstFlash):\\n self.commands[layername].append((0,0,2))\\n if updateExtents:\\n self.minx = min(self.minx,0)\\n self.maxx = max(self.maxx,0)\\n self.miny = min(self.miny,0)\\n self.maxy = max(self.maxy,0)\\n\\n x = int(round(x*x_div))\\n y = int(round(y*y_div))\\n if I is not None:\\n I = int(round(I*x_div))\\n J = int(round(J*y_div))\\n self.commands[layername].append((x,y,I,J,d,circ_signed))\\n else:\\n self.commands[layername].append((x,y,d))\\n firstFlash = False\\n\\n # Update dimensions...this is complicated for circular interpolation commands\\n # that span more than one quadrant. For now, we ignore this problem since users\\n # should be using a border layer to indicate extents.\\n if updateExtents:\\n if x < self.minx: self.minx = x\\n if x > self.maxx: self.maxx = x\\n if y < self.miny: self.miny = y\\n if y > self.maxy: self.maxy = y\\n\\n # Move on to next match, if any\\n sub_line = sub_line[match.end():]\\n continue\\n\\n # If it's none of the above, it had better be on our ignore list.\\n for pat in IgnoreList:\\n match = pat.match(sub_line)\\n if match:\\n break\\n else:\\n raise RuntimeError, 'File %s has uninterpretable line:\\\\n %s' % (fullname, line)\\n\\n sub_line = sub_line[match.end():]\\n # end while still things to match on this line\\n # end of for each line in file\\n\\n fid.close()\\n if 0:\\n print layername\\n print self.commands[layername]\",\n \"def __gen_token_anno_file(self, top_level_layer):\\n base_paula_id = '{}.{}.tok'.format(self.corpus_name, self.name)\\n paula_id = '{}.{}.{}.tok_multiFeat'.format(top_level_layer,\\n self.corpus_name,\\n self.name)\\n E, tree = gen_paula_etree(paula_id)\\n mflist = E('multiFeatList',\\n {XMLBASE: base_paula_id+'.xml'})\\n\\n for token_id in self.dg.tokens:\\n mfeat = E('multiFeat',\\n {XLINKHREF: '#{}'.format(token_id)})\\n token_dict = self.dg.node[token_id]\\n for feature in token_dict:\\n # TODO: highly inefficient! refactor!1!!\\n if feature not in IGNORED_TOKEN_ATTRIBS \\\\\\n and feature.startswith(top_level_layer):\\n mfeat.append(E('feat',\\n {'name': feature,\\n 'value': token_dict[feature]}))\\n\\n if self.human_readable: # adds token string as a <!-- comment -->\\n mfeat.append(Comment(token_dict[self.dg.ns+':token']))\\n mflist.append(mfeat)\\n\\n tree.append(mflist)\\n self.files[paula_id] = tree\\n self.file2dtd[paula_id] = PaulaDTDs.multifeat\\n return paula_id\",\n \"def compile_customization(data):\\n data=data.split(\\\" \\\")\\n optional_data=data[1:]\\n data = data[0].split(\\\"@\\\")\\n return_dict = {}\\n return_dict['resize_type']=data[0]\\n return_dict['width']=int(data[1])\\n return_dict['height']=int(data[2])\\n return_dict['padding_type']='reflect'\\n return_dict['constant_color']=[255,0,0]\\n\\n if len(optional_data)!=0:\\n optional_data=optional_data[0]\\n if \\\",\\\" in optional_data:\\n return_dict['padding_type']='constant'\\n color_list=optional_data.split(\\\",\\\")\\n return_dict['constant_color']=tuple([int(i) for i in color_list])\\n else:\\n return_dict['padding_type']=optional_data\\n return return_dict\",\n \"def parse_illumina_line(l, barcode_length, rev_comp_barcode,\\r\\n barcode_in_sequence=False):\\r\\n fields = l.strip().split(':')\\r\\n\\r\\n y_position_subfields = fields[4].split('#')\\r\\n y_position = int(y_position_subfields[0])\\r\\n sequence = fields[5]\\r\\n qual_string = fields[6]\\r\\n\\r\\n if barcode_in_sequence:\\r\\n barcode = sequence[:barcode_length]\\r\\n sequence = sequence[barcode_length:]\\r\\n qual_string = qual_string[barcode_length:]\\r\\n else:\\r\\n barcode = y_position_subfields[1][:barcode_length]\\r\\n\\r\\n if rev_comp_barcode:\\r\\n barcode = str(DNA(barcode).rc())\\r\\n\\r\\n result = {\\r\\n 'Full description': ':'.join(fields[:5]),\\r\\n 'Machine Name': fields[0],\\r\\n 'Channel Number': int(fields[1]),\\r\\n 'Tile Number': int(fields[2]),\\r\\n 'X Position': int(fields[3]),\\r\\n 'Y Position': y_position,\\r\\n 'Barcode': barcode,\\r\\n 'Full Y Position Field': fields[4],\\r\\n 'Sequence': sequence,\\r\\n 'Quality Score': qual_string}\\r\\n\\r\\n return result\",\n \"def _parse(self, data):\\n pe = construct.PEFILE_HEADER.parse(data)\\n\\n # Convert Container classes to use ours, so we can deepcopy.\\n pe = Container.from_container(pe)\\n\\n # Convert the FlagEnums into list of constants.\\n for section in pe.SectionTable:\\n if isinstance(section.Characteristics, dict):\\n section.Characteristics = [flag for flag, value in section.Characteristics.items() if value]\\n section.data = data[section.PointerToRawData:section.PointerToRawData + section.SizeOfRawData]\\n file_header = pe.NTHeaders.FileHeader\\n if isinstance(file_header.Characteristics, dict):\\n file_header.Characteristics = [\\n flag for flag, value in file_header.Characteristics.items() if value]\\n optional_header = pe.NTHeaders.OptionalHeader\\n if isinstance(optional_header.DllCharacteristics, dict):\\n optional_header.DllCharacteristics = [\\n flag for flag, value in optional_header.DllCharacteristics.items() if value]\\n\\n self.update(pe)\",\n \"def parse(self, filehandle):\\n l = filehandle.readline()\\n if l.split()[0] != '##maf':\\n return\\n else:\\n self.setpar(l.split()[1:])\\n\\n l=filehandle.readline()\\n while l:\\n la = l.split()\\n## print la\\n if(len(la)==0 or la[0]=='#'):\\n## print \\\"skipping\\\"\\n 1\\n elif(la[0]=='a'):\\n## print \\\"reading alignment\\\"\\n self.readalign(la[1:], filehandle)\\n else:\\n## print \\\"end of records\\\"\\n return\\n\\n l=filehandle.readline()\",\n \"def read_kitti_cal(calfile):\\n\\n text_file = open(calfile, 'r')\\n\\n p2pat = re.compile(('(P2:)\\\\s+(fpat)\\\\s+(fpat)\\\\s+(fpat)\\\\s+(fpat)\\\\s+(fpat)\\\\s+(fpat)\\\\s+(fpat)\\\\s+(fpat)\\\\s+(fpat)' +\\n '\\\\s+(fpat)\\\\s+(fpat)\\\\s+(fpat)\\\\s*\\\\n').replace('fpat', '[-+]?[\\\\d]+\\\\.?[\\\\d]*[Ee](?:[-+]?[\\\\d]+)?'))\\n\\n for line in text_file:\\n\\n parsed = p2pat.fullmatch(line)\\n\\n # bbGt annotation in text format of:\\n # cls x y w h occ x y w h ign ang\\n if parsed is not None:\\n p2 = np.zeros([4, 4], dtype=float)\\n p2[0, 0] = parsed.group(2)\\n p2[0, 1] = parsed.group(3)\\n p2[0, 2] = parsed.group(4)\\n p2[0, 3] = parsed.group(5)\\n p2[1, 0] = parsed.group(6)\\n p2[1, 1] = parsed.group(7)\\n p2[1, 2] = parsed.group(8)\\n p2[1, 3] = parsed.group(9)\\n p2[2, 0] = parsed.group(10)\\n p2[2, 1] = parsed.group(11)\\n p2[2, 2] = parsed.group(12)\\n p2[2, 3] = parsed.group(13)\\n\\n p2[3, 3] = 1\\n\\n text_file.close()\\n\\n return p2\",\n \"def construct_parser_preprocessor(subparser) -> None:\\n\\n def within_percent_interval(interval_str: str) -> float:\\n \\\"\\\"\\\"\\n Checks whether or not the given string representation of a floating\\n point number is in the interval [0, 1].\\n\\n Parameters\\n ----------\\n interval_str: str :\\n The string that needs to be checked for a valid value\\n\\n Returns\\n -------\\n float\\n If valid, the number representation of interval_str\\n\\n Raises\\n ------\\n ValueError\\n If interval_str cannot be converted to a floating pointer number\\n ArgumentTypeError\\n If the number is not within the interval [0, 1]\\n \\\"\\\"\\\"\\n interval = float(interval_str)\\n if interval < 0 or interval > 1:\\n raise ArgumentTypeError(\\\"Input given is out of bounds!\\\")\\n\\n return interval\\n \\\"\\\"\\\"\\n if subparser:\\n preprocess_parser = subparser.add_parser(\\n \\\"preprocess\\\",\\n formatter_class=argparse.ArgumentDefaultsHelpFormatter,\\n help=\\\"Preprocess given dataset\\\",\\n )\\n else:\\n preprocess_parser = argparse.ArgumentParser(\\n description='Preprocess given dataset',\\n formatter_class=argparse.ArgumentDefaultsHelpFormatter\\n )\\n \\\"\\\"\\\"\\n\\n subparser.add_argument(\\n 'input_dir', type=str, default=\\\"data_clean\\\", metavar=\\\"input-dir\\\",\\n help='Input directory to preprocess'\\n )\\n\\n subparser.add_argument(\\n '-o', '--output-dir', type=str, default=\\\"filtered_data_clean\\\",\\n help='Output directory to hold preprocessed data_clean'\\n )\\n\\n subparser.add_argument(\\n '--stopwords', type=str, default=None,\\n help='Path to the .csv stop words file'\\n )\\n\\n # Make file generation options mutually exclusive\\n # Note, all 3 of the flags appear. However, we only want 1 of them to\\n # appear.\\n subparser.add_argument(\\n '--export', type=str, default=\\\"single\\\",\\n choices=[\\\"single\\\", \\\"split\\\", \\\"fasttext\\\", \\\"all\\\"],\\n help='Indicate whether you only want a single file holding all of the '\\n 'preprocessed data_clean, or both. If \\\"split\\\\\\\" was chosen, it '\\n 'utilizes the \\\"--train-split\\\" argument to know how big to make the '\\n 'training and testing sets. If fasttext is given, it utilizes the '\\n '\\\"--slice-length\\\" argument to know how big to make each slice'\\n )\\n\\n subparser.add_argument(\\n '--slice_length', type=int, default=25,\\n help=\\\"Number of tokens to have per slice of a file.\\\"\\n )\\n\\n subparser.add_argument(\\n '--train-split', type=within_percent_interval, default=.8,\\n metavar=\\\"[0-1]\\\",\\n help=\\\"Percentage in interval [0,1] of total data_clean going to the \\\\\\n training dataset.\\\"\\n )\\n\\n subparser.set_defaults(run=run_preprocessor)\",\n \"def parse_inputs():\\n\\n parser = argparse.ArgumentParser(description=\\\"Command line argument handler for ugaudio spectral_average program.\\\",\\n formatter_class=argparse.ArgumentDefaultsHelpFormatter)\\n\\n # a group of args for verbosity\\n group = parser.add_mutually_exclusive_group()\\n group.add_argument('-v', '--verbose', action='store_true')\\n group.add_argument('-q', '--quiet', action='store_true')\\n\\n # nfiles\\n help_nfiles = 'nfiles to preview (ONLY for testing)'\\n parser.add_argument('-g', '--nfiles', default=DEFAULT_NFILES, type=nfiles_int, help=help_nfiles)\\n\\n # nfft\\n help_nfft = 'Nfft'\\n parser.add_argument('-n', '--nfft', default=DEFAULT_NFFT, type=nfft_int, help=help_nfft)\\n\\n # sample rate\\n help_rate = 'sample rate (sa/sec)'\\n parser.add_argument('-r', '--rate', default=DEFAULT_RATE, type=rate_str, help=help_rate)\\n\\n # cutoff\\n help_cutoff = 'cutoff'\\n parser.add_argument('-c', '--cutoff', default=DEFAULT_CUTOFF, type=cutoff_str, help=help_cutoff)\\n\\n # sensors\\n help_sensors = 'sensors'\\n parser.add_argument('-s', '--sensors', default=DEFAULT_SENSORS, type=sensors_list, help=help_sensors)\\n\\n # PAD directory\\n help_paddir = 'PAD dir'\\n parser.add_argument('-p', '--paddir', default=DEFAULT_PADDIR, type=folder_str, help=help_paddir)\\n\\n # output directory\\n help_outdir = 'output dir'\\n parser.add_argument('-o', '--outdir', default=DEFAULT_OUTDIR, type=outdir_str, help=help_outdir)\\n\\n # start date\\n help_start = 'start date'\\n parser.add_argument('-d', '--start', default=DEFAULT_START, type=dtm_date, help=help_start)\\n\\n # end date\\n help_end = 'end date'\\n parser.add_argument('-e', '--end', default=DEFAULT_END, type=dtm_date, help=help_end)\\n\\n # parse arguments\\n module_logger.debug('calling parse_args')\\n args = parser.parse_args()\\n\\n return args\",\n \"def main():\\n dir_path='.'\\n meas_file='magic_measurements.txt'\\n samp_file=\\\"er_samples.txt\\\"\\n out_file='magic_measurements.txt'\\n if '-h' in sys.argv:\\n print(main.__doc__)\\n sys.exit()\\n if '-WD' in sys.argv:\\n ind = sys.argv.index('-WD')\\n dir_path=sys.argv[ind+1]\\n if '-f' in sys.argv:\\n ind = sys.argv.index('-f')\\n meas_file=sys.argv[ind+1]\\n if '-fsa' in sys.argv:\\n ind = sys.argv.index('-fsa')\\n samp_file=sys.argv[ind+1]\\n if '-F' in sys.argv:\\n ind = sys.argv.index('-F')\\n out_file=sys.argv[ind+1]\\n # read in measurements file\\n meas_file=dir_path+'/'+meas_file\\n out_file=dir_path+'/'+out_file\\n samp_file=dir_path+'/'+samp_file\\n data,file_type=pmag.magic_read(meas_file)\\n samps,file_type=pmag.magic_read(samp_file)\\n MeasRecs=[]\\n sampnames,sflag=[],0\\n for rec in data:\\n for samp in samps:\\n if samp['er_sample_name'].lower()==rec['er_sample_name'].lower():\\n if samp['er_sample_name'] not in sampnames:sampnames.append(samp['er_sample_name'].lower())\\n rec['er_site_name']=samp['er_site_name']\\n rec['er_location_name']=samp['er_location_name']\\n MeasRecs.append(rec)\\n break\\n if rec['er_sample_name'].lower() not in sampnames:\\n sampnames.append(rec['er_sample_name'].lower())\\n sflag=1\\n SampRec={}\\n for key in list(samps[0].keys()):SampRec[key]=\\\"\\\"\\n SampRec['er_sample_name']=rec['er_sample_name']\\n SampRec['er_citation_names']=\\\"This study\\\"\\n SampRec['er_site_name']='MISSING'\\n SampRec['er_location_name']='MISSING'\\n SampRec['sample_desription']='recorded added by update_measurements - edit as needed'\\n samps.append(SampRec)\\n print(rec['er_sample_name'],' missing from er_samples.txt file - edit orient.txt file and re-import')\\n rec['er_site_name']='MISSING'\\n rec['er_location_name']='MISSING'\\n MeasRecs.append(rec)\\n pmag.magic_write(out_file,MeasRecs,'magic_measurements')\\n print(\\\"updated measurements file stored in \\\", out_file)\\n if sflag==1:\\n pmag.magic_write(samp_file,samps,'er_samples')\\n print(\\\"updated sample file stored in \\\", samp_file)\",\n \"def sequence_macros(macros):\\n\\n def foo():\\n for m in macros:\\n m()\\n\\n return foo\",\n \"def generate_parser(renamer):\\n parser = ShlexArgumentParser(\\n formatter_class=RawDescriptionHelpFormatter,\\n prog=\\\"brp\\\",\\n usage=\\\"cmd [args ...]\\\",\\n add_help=False,\\n exit_on_error=False,\\n )\\n subparsers = parser.add_subparsers(\\n title=\\\"commands\\\",\\n description=\\\"actions to take on the filenames\\\",\\n )\\n\\n _help = [\\n _help_parser((\\\"help\\\", \\\"h\\\", \\\"?\\\"), subparsers, renamer),\\n _save_parser((\\\"save\\\", \\\"s\\\"), subparsers, renamer),\\n _quit_parser((\\\"quit\\\", \\\"q\\\", \\\"exit\\\"), subparsers, renamer),\\n _save_quit_parser((\\\"write\\\", \\\"w\\\"), subparsers, renamer),\\n _print_parser((\\\"list\\\", \\\"ls\\\", \\\"l\\\"), subparsers, renamer),\\n _history_parser((\\\"history\\\", \\\"hist\\\", \\\"past\\\"), subparsers, renamer),\\n _undo_parser((\\\"undo\\\", \\\"u\\\"), subparsers, renamer),\\n _reset_parser((\\\"reset\\\", \\\"over\\\", \\\"o\\\"), subparsers, renamer),\\n _automate_parser((\\\"automate\\\", \\\"a\\\", \\\"auto\\\"), subparsers, renamer),\\n _find_replace_parser((\\\"replace\\\", \\\"r\\\", \\\"re\\\", \\\"reg\\\", \\\"regex\\\"), subparsers, renamer),\\n _append_parser((\\\"append\\\", \\\"ap\\\"), subparsers, renamer),\\n _prepend_parser((\\\"prepend\\\", \\\"p\\\", \\\"pre\\\"), subparsers, renamer),\\n _insert_parser((\\\"insert\\\", \\\"i\\\", \\\"in\\\"), subparsers, renamer),\\n _case_parser((\\\"case\\\", \\\"c\\\"), subparsers, renamer),\\n _extension_parser((\\\"extension\\\", \\\"x\\\", \\\"ext\\\"), subparsers, renamer),\\n ]\\n\\n return parser, _help\",\n \"def _m4_file_analysis(self, fin):\\n # imp.reload(m4_macros_analysis)\\n raw_data = fin.read()\\n\\n mylexer = m4_macros_analysis.M4Lexer()\\n mylexer.build()\\n lexer = mylexer.clone()\\n generator = mylexer.get_token_iter(raw_data, lexer=lexer)\\n cache_generator = m4_macros_analysis.CacheGenerator(generator, origin_data=raw_data)\\n\\n self._m4_analyzer.functions_analyze(cache_generator, fin.name)\",\n \"def _fusion_legacy_handler(_, __, tokens):\\n if RANGE_5P not in tokens:\\n tokens[RANGE_5P] = {FUSION_MISSING: \\\"?\\\"}\\n if RANGE_3P not in tokens:\\n tokens[RANGE_3P] = {FUSION_MISSING: \\\"?\\\"}\\n return tokens\",\n \"def process_declaration(self, decl,datatype):\\n # Looping character by character in the string which contains only the part where variables are mentioned(without the datatype keyword).\\n filename = \\\"sym.csv\\\"\\n name = \\\"\\\"\\n i=0\\n pos=-1\\n flag=0 #used to track identifiers with having digits\\n with open(filename, 'a') as csvfile:\\n csvwriter = csv.writer(csvfile)\\n for c in decl:\\n \\n pos += 1\\n i=0\\n # Checking if the variable mentioned is an array declaration. This will be executed only if '[' character has been encountered earlier.\\n if self.flag_array:\\n # Checks if the '[' has a matching ']'\\n if (c == \\\"]\\\"):\\n self.structure += c # Saving the current status of the array structure.\\n self.flag_array = False # Setting flag to say that the array declaration has been processed completely.\\n self.array_structure[self.identifiers[-1]] = self.structure # Saving the array structure(or dimension) into a dictionary.\\n continue # Jumping into the next iteration.\\n # Checks if next variable is going to be declared.\\n elif (c == \\\",\\\"):\\n continue # Jumping to the next iteration.\\n # Checks if declaration statement is ending.\\n elif (c == \\\";\\\"):\\n print(self.structure)\\n break # Breaking out of the loop. It can also be return.\\n # If none of the conditions match then it is the dimension being mentioned.\\n else:\\n self.structure += c # Saving the dimension into the variable that is used for saving the overall structure of the array.\\n continue # Jumping to the next iteration.\\n\\n # Checking if the variable is being assigned with a value during the declaration.\\n \\n if c == \\\"=\\\":\\n flag=1 #this means the encountered digits are values\\n self.identifiers += self.temp # Saving the characters parsed so far as an identifier, since '=' operator marks the end of the identifier and beginning of the value.\\n\\n if(len(name.strip())>0 and re.search(r\\\"[a-zA-Z_][a-zA-Z_0-9]*\\\",name.strip()) and not(self.check(name.strip()))):\\n if(re.search(r\\\"[0-9]\\\", decl).start()):\\n indexValue = re.search(r\\\"[0-9\\\\.]+\\\", decl[pos:]).start()\\n lastValue = re.search(r\\\"[0-9\\\\.]+\\\", decl[pos:]).end()\\n value = decl[pos+indexValue:pos+lastValue]\\n csvwriter.writerow(['Identifier',datatype,name.strip(),value,''])\\n name=\\\"\\\"\\n \\n continue\\n csvwriter.writerow(['Identifier',datatype,name.strip(),'',''])\\n name = \\\"\\\"\\n \\n \\n\\n # Checking if an array is being declared.\\n elif c == \\\"[\\\":\\n self.identifiers += self.temp # String read so far is saved as an identifier, since '[' marks the end of identifier name and begin of the dimension.\\n self.temp = \\\"\\\" # Emptying the string which contained the name of the identifier.\\n if len(name.strip())>0 and re.search(r\\\"[a-zA-Z_][a-zA-Z_0-9]*\\\",name.strip()) and not(self.check(name.strip())):\\n csvwriter.writerow(['Identifer',datatype+\\\"Array\\\",name.strip(),'',''])\\n name = \\\"\\\"\\n self.structure += c # Adding '[' into the structure variable.\\n self.flag_array = True # Marking the beginning of dimension.\\n\\n # Checking if the declaration is for a function.\\n elif c == \\\"(\\\":\\n self.temp = \\\"\\\" # Emptying the string which holds the identifier name since it is a function name and not that of any variable.\\n break\\n\\n # Checking if the declaration is marking end of a variable name.\\n elif c == \\\",\\\":\\n flag=0 #after \\\",\\\" it's possible that identifier has digit in it. So, make flag 0 again\\n self.identifiers += self.temp # Adding the name parsed so far into the list of all variables.\\n self.temp = \\\"\\\" # Emptying the string which holds the name of the identifier.\\n if len(name.strip())>0 and re.search(r\\\"[a-zA-Z_][a-zA-Z_0-9]*\\\",name.strip()) and not(self.check(name.strip())):\\n # if(re.search())\\n \\n csvwriter.writerow(['Identifer',datatype,name.strip(),'',''])\\n name = \\\"\\\"\\n continue\\n\\n # Checking if the statement has ended.\\n elif c == \\\";\\\":\\n self.identifiers += self.temp # Adding the string parsed so far into the list of identifiers.\\n self.temp = \\\"\\\" # Emptying the string that holds the name of the identifier.\\n if len(name.strip())>0 and re.search(r\\\"[a-zA-Z_][a-zA-Z_0-9]*\\\",name.strip()) and not(self.check(name.strip())):\\n csvwriter.writerow(['Identifer',datatype,name.strip(),'',''])\\n name = \\\"\\\"\\n break\\n\\n # Checking for whitespaces within the line.\\n elif c == \\\" \\\":\\n continue\\n #Doesn't take values as identifier names\\n elif(re.search(r'[0-9]',c)):\\n if(flag == 1): #check if it's value or identifier\\n continue\\n else:\\n self.temp += c\\n name += c\\n\\n # If none of the conditions satisfy, then the character is part of the identifier name. Hence adding it to the name string.\\n else:\\n self.temp += c\\n name += c\",\n \"def xephemFormat(self):\\n line = []\\n #Field 1: names\\n names = [self.getName()]\\n identifiers = self.getIdentifiers()\\n if identifiers[0] is not None:\\n names.append(identifiers[0])\\n for i in range(1,4):\\n if identifiers[i] is not None:\\n names.extend(identifiers[i])\\n line.append(\\\"|\\\".join(names))\\n\\n #Field 2: type designation\\n objType = self.getType()\\n if objType in (\\\"Galaxy Pair\\\", \\\"Galaxy Triplet\\\", \\\"Group of galaxies\\\"):\\n line.append(\\\"f|A\\\")\\n elif objType == \\\"Globular Cluster\\\":\\n line.append(\\\"f|C\\\")\\n elif objType == \\\"Double star\\\":\\n line.append(\\\"f|D\\\")\\n elif objType in (\\\"HII Ionized region\\\", \\\"Nebula\\\"):\\n line.append(\\\"f|F\\\")\\n elif objType == \\\"Galaxy\\\":\\n if self.getHubble().startswith(\\\"S\\\"):\\n line.append(\\\"f|G\\\")\\n else:\\n line.append(\\\"f|H\\\")\\n elif objType == \\\"Dark Nebula\\\":\\n line.append(\\\"f|K\\\")\\n elif objType in (\\\"Emission Nebula\\\", \\\"Reflection Nebula\\\"):\\n line.append(\\\"f|N\\\")\\n elif objType in (\\\"Association of stars\\\", \\\"Open Cluster\\\"):\\n line.append(\\\"f|O\\\")\\n elif objType == \\\"Planetary Nebula\\\":\\n line.append(\\\"f|P\\\")\\n elif objType == \\\"Supernova remnant\\\":\\n line.append(\\\"f|R\\\")\\n elif objType == \\\"Star\\\":\\n line.append(\\\"f|S\\\")\\n elif objType == \\\"Star cluster + Nebula\\\":\\n line.append(\\\"f|U\\\")\\n else:\\n line.append(\\\"f\\\")\\n\\n #Field 3: Right Ascension\\n line.append(self.getRA())\\n\\n #Field 4: Declination\\n line.append(self.getDec())\\n\\n #Field 5: Magnitude\\n #We use the first available magnitude in the sequence b,v,j,h,k\\n for mag in self.getMagnitudes():\\n if mag is not None:\\n line.append(str(mag))\\n break\\n\\n #Field 6: optional Epoch, we let it empty\\n line.append(\\\"\\\")\\n\\n #Field 7: Dimensions\\n dimensions = []\\n #Xephem format wants axes espressed in arcsec, we have arcmin\\n for value in (self.getDimensions()[0],self.getDimensions()[1]):\\n if value is not None:\\n dimensions.append(str(value*60))\\n else:\\n dimensions.append(\\\"\\\")\\n if self.getDimensions()[2] is not None:\\n dimensions.append(str(value))\\n else:\\n dimensions.append(\\\"\\\")\\n line.append(\\\"|\\\".join(dimensions))\\n\\n return \\\",\\\".join(line)\",\n \"def parse(token):\\n\\n pass\",\n \"def _prepare_registration(self, record):\\n logging.debug('.. generate macros before registration experiment')\\n # set the paths for this experiment\\n path_dir = self._get_path_reg_dir(record)\\n path_im_ref, path_im_move, _, _ = self._get_paths(record)\\n name_im_ref, name_im_move = [os.path.basename(p)\\n for p in [path_im_ref, path_im_move]]\\n path_regist = os.path.join(path_dir, os.path.basename(path_im_move))\\n\\n with open(self.params['path_config_bUnwarpJ'], 'r') as fp:\\n lines = fp.readlines()\\n # merge lines into one string\\n config_bunwarpj = ' '.join(l.strip() for l in lines)\\n # define set of all possible parameters for macros generating\\n dict_params = {\\n 'source': path_im_move, 'target': path_im_ref,\\n 'name_source': name_im_move, 'name_target': name_im_ref,\\n 'config_bUnwarpJ': config_bunwarpj, 'output': path_dir,\\n 'warp': path_regist}\\n\\n # if config for SIFT is defined add SIFT extraction\\n if 'path_config_IJ_SIFT' in self.params:\\n with open(self.params['path_config_IJ_SIFT'], 'r') as fp:\\n lines = fp.readlines()\\n dict_params['config_SIFT'] = ' '.join(l.strip() for l in lines)\\n dict_params['SIFT'] = MACRO_SIFT % dict_params\\n else:\\n dict_params['SIFT'] = ''\\n\\n # if config for MOPS is defined add MOPS extraction\\n if 'path_config_IJ_MOPS' in self.params:\\n with open(self.params['path_config_IJ_MOPS'], 'r') as fp:\\n lines = fp.readlines()\\n dict_params['config_MOPS'] = ' '.join(l.strip() for l in lines)\\n dict_params['MOPS'] = MACRO_MOPS % dict_params\\n else:\\n dict_params['MOPS'] = ''\\n\\n # generate the registration macro\\n macro_regist = MACRO_REGISTRATION % dict_params\\n with open(os.path.join(path_dir, NAME_MACRO_REGISTRATION), 'w') as fp:\\n fp.write(macro_regist)\\n\\n return record\",\n \"def sample_vcf():\\n file_content = b\\\"\\\"\\\"##fileformat=VCFv4.2\\n##hailversion=0.2.100-2ea2615a797a\\n##INFO=<ID=QUALapprox,Number=1,Type=Integer,Description=\\\"\\\">\\n##INFO=<ID=SB,Number=.,Type=Integer,Description=\\\"\\\">\\n##INFO=<ID=MQ,Number=1,Type=Float,Description=\\\"\\\">\\n##INFO=<ID=MQRankSum,Number=1,Type=Float,Description=\\\"\\\">\\n##INFO=<ID=VarDP,Number=1,Type=Integer,Description=\\\"\\\">\\n##INFO=<ID=AS_ReadPosRankSum,Number=1,Type=Float,Description=\\\"\\\">\\n##INFO=<ID=AS_pab_max,Number=1,Type=Float,Description=\\\"\\\">\\n##INFO=<ID=AS_QD,Number=1,Type=Float,Description=\\\"\\\">\\n##INFO=<ID=AS_MQ,Number=1,Type=Float,Description=\\\"\\\">\\n##INFO=<ID=QD,Number=1,Type=Float,Description=\\\"\\\">\\n##INFO=<ID=AS_MQRankSum,Number=1,Type=Float,Description=\\\"\\\">\\n##INFO=<ID=FS,Number=1,Type=Float,Description=\\\"\\\">\\n##INFO=<ID=AS_FS,Number=1,Type=Float,Description=\\\"\\\">\\n##INFO=<ID=ReadPosRankSum,Number=1,Type=Float,Description=\\\"\\\">\\n##INFO=<ID=AS_QUALapprox,Number=1,Type=Integer,Description=\\\"\\\">\\n##INFO=<ID=AS_SB_TABLE,Number=.,Type=Integer,Description=\\\"\\\">\\n##INFO=<ID=AS_VarDP,Number=1,Type=Integer,Description=\\\"\\\">\\n##INFO=<ID=AS_SOR,Number=1,Type=Float,Description=\\\"\\\">\\n##INFO=<ID=SOR,Number=1,Type=Float,Description=\\\"\\\">\\n##INFO=<ID=singleton,Number=0,Type=Flag,Description=\\\"\\\">\\n##INFO=<ID=transmitted_singleton,Number=0,Type=Flag,Description=\\\"\\\">\\n##INFO=<ID=omni,Number=0,Type=Flag,Description=\\\"\\\">\\n##INFO=<ID=mills,Number=0,Type=Flag,Description=\\\"\\\">\\n##INFO=<ID=monoallelic,Number=0,Type=Flag,Description=\\\"\\\">\\n##INFO=<ID=AS_VQSLOD,Number=1,Type=Float,Description=\\\"\\\">\\n##INFO=<ID=InbreedingCoeff,Number=1,Type=Float,Description=\\\"\\\">\\n##FILTER=<ID=AC0,Description=\\\"Allele count is zero after filtering out low-confidence genotypes (GQ < 20; DP < 10; and AB < 0.2 for het calls)\\\">\\n##FILTER=<ID=AS_VQSR,Description=\\\"Failed VQSR filtering thresholds of -2.7739 for SNPs and -1.0606 for indels\\\">\\n##contig=<ID=chr1,length=248956422,assembly=GRCh38>\\n#CHROM\\tPOS\\tID\\tREF\\tALT\\tQUAL\\tFILTER\\tINFO\\nchr1\\t10330\\t.\\tCCCCTAACCCTAACCCTAACCCTACCCTAACCCTAACCCTAACCCTAACCCTAA\\tC\\t.\\tPASS\\tQUALapprox=21493;SB=325,1077,113,694;MQ=32.1327;MQRankSum=0.720000;VarDP=2236;AS_ReadPosRankSum=-0.736000;AS_pab_max=1.00000;AS_QD=5.17857;AS_MQ=29.5449;QD=9.61225;AS_MQRankSum=0.00000;FS=8.55065;AS_FS=.;ReadPosRankSum=0.727000;AS_QUALapprox=145;AS_SB_TABLE=325,1077,2,5;AS_VarDP=28;AS_SOR=0.311749;SOR=1.48100;singleton;AS_VQSLOD=13.4641;InbreedingCoeff=-0.000517845\\\"\\\"\\\"\\n file = io.BytesIO(file_content)\\n return file\",\n \"def parse_part(self):\\n parts = []\\n for part in re.split(r'\\\\*\\\\*\\\\* ([A-Z- ]+) \\\\*\\\\*\\\\*', self.hand_file): # return [ 'part1', 'splitter1', 'part2',..\\n parts.append(part)\\n\\n for i in range(0, len(parts)):\\n if i == 0:\\n self.part_dict['HEADER'] = parts[i]\\n if i % 2 != 0: # number is odd\\n self.part_dict[parts[i]] = parts[i + 1]\",\n \"def parser(raw_seq, date):\\n taxon_id = int(raw_seq.features[0].qualifiers['db_xref'][0][6:])\\n organism = raw_seq.annotations['organism']\\n accession = raw_seq.annotations['accessions'][0]\\n gene = []\\n records = []\\n frag_type = 'whole'\\n begin = 1\\n end = len(raw_seq)\\n sequence = str(raw_seq.seq)\\n name = organism\\n strand = 1\\n rec = [taxon_id, organism, accession, name, frag_type, begin, end, strand, sequence, date]\\n records.append(rec)\\n for i in raw_seq.features:\\n if i.type == 'gene' and 'gene' in i.qualifiers:\\n if i.location_operator != 'join':\\n frag_type = 'gene'\\n begin = int(i.location.start)\\n end = int(i.location.end)\\n sequence = str(raw_seq.seq[begin:end])\\n name = str(i.qualifiers['gene'][0])\\n strand = str(i.location.strand)\\n rec = [taxon_id, organism, accession, name, frag_type, begin, end, strand, sequence, date]\\n elif i.location_operator == 'join':\\n frag_type = 'gene'\\n begin = int(i.sub_features[0].location.start)\\n end = int(i.sub_features[0].location.end)\\n name = str(i.qualifiers['gene'][0])\\n strand = str(i.location.strand)\\n sequence = ''\\n rec = [taxon_id, organism, accession, name, frag_type, begin, end, strand, sequence, date]\\n gene.append(rec)\\n begin = int(i.sub_features[1].location.start)\\n end = int(i.sub_features[1].location.end)\\n sequence = ''.join([str(raw_seq.seq[begin:end]), str(raw_seq.seq[begin:end])])\\n rec = [taxon_id, organism, accession, name, frag_type, begin, end, strand, sequence, date]\\n elif i.type == 'CDS' and 'gene' in i.qualifiers:\\n frag_type = 'cds'\\n begin = int(i.location.start)\\n end = int(i.location.end)\\n sequence = str(raw_seq.seq[begin:end])\\n name = str(i.qualifiers['gene'][0]).replace(' ', '_')\\n strand = str(i.location.strand)\\n rec = [taxon_id, organism, accession, name, frag_type, begin, end, strand, sequence, date]\\n elif i.type == 'tRNA' and 'gene' in i.qualifiers:\\n frag_type = 'tRNA'\\n begin = int(i.location.start)\\n end = int(i.location.end)\\n sequence = str(raw_seq.seq[begin:end])\\n if len(sequence) >= 100:\\n sequence = ''\\n name = str(i.qualifiers['gene'][0]).replace(' ', '_')\\n strand = str(i.location.strand)\\n rec = [taxon_id, organism, accession, name, frag_type, begin, end, strand, sequence, date]\\n elif i.type == 'rRNA':\\n frag_type = 'rRNA'\\n begin = int(i.location.start)\\n end = int(i.location.end)\\n sequence = str(raw_seq.seq[begin:end])\\n name = str(i.qualifiers['product'][0]).replace(' ', '_')\\n strand = str(i.location.strand)\\n rec = [taxon_id, organism, accession, name, frag_type, begin, end, strand, sequence, date]\\n elif i.type == 'exon' and 'gene' in i.qualifiers:\\n frag_type = 'exon'\\n begin = int(i.location.start)\\n end = int(i.location.end)\\n sequence = str(raw_seq.seq[begin:end])\\n if 'number' in i.qualifiers:\\n name = '{0}_exon_{1}'.format(i.qualifiers['gene'][0],\\n i.qualifiers['number'][0])\\n else:\\n name = '{0}_exon'.format(i.qualifiers['gene'][0])\\n strand = int(i.location.strand)\\n rec = [taxon_id, organism, accession, name, frag_type, begin, end, strand, sequence, date]\\n elif i.type == 'intron' and 'gene' in i.qualifiers:\\n frag_type = 'intron'\\n begin = int(i.location.start)\\n end = int(i.location.end)\\n sequence = str(raw_seq.seq[begin:end])\\n strand = str(i.location.strand)\\n if 'number' in i.qualifiers:\\n name = '{0}_{1}_intron'.format(i.qualifiers['gene'][0],\\n i.qualifiers['number'][0])\\n else:\\n name = '{0}_intron'.format(i.qualifiers['gene'][0])\\n rec = [taxon_id, organism, accession, name, frag_type, begin, end, strand, sequence, date]\\n\\n records.append(rec)\\n gene.sort(key=lambda x: x[5])\\n\\n for i in range(len(gene) - 1):\\n frag_type = 'spacer'\\n now = gene[i]\\n then = gene[i + 1]\\n tail = now[6] + 1\\n head = then[5] - 1\\n sequence = str(raw_seq.seq[tail:head])\\n name = '{0}-{1}_spacer'.format(now[3], then[3])\\n strand = 0\\n rec = [taxon_id, organism, accession, name, frag_type, begin, end, strand, sequence, date]\\n records.append(rec)\\n records.extend(gene)\\n\\n database.extend(records)\",\n \"def _parse(self):\\n with open(self.input) as f:\\n for line in f:\\n if not line.lstrip().startswith(\\\"#\\\"): # comment\\n stripped_line=line.split(\\\"#\\\")[0].strip()\\n \\n # Initialise an empty option dictionary with some good defaults\\n if \\\"[\\\" in stripped_line:\\n molname=stripped_line.split()[1]\\n self.options[molname]=self.empty_option_dict.copy() # dict1=dict2 does not copy!\\n self.options[molname][\\\"MolName\\\"]=molname\\n if \\\":\\\" in stripped_line: \\n # now process line by line\\n if \\\"{\\\" not in stripped_line:\\n key,value=[i.strip() for i in stripped_line.split(\\\":\\\")]\\n\\n if key not in self.options[molname].keys():\\n raise BaseException(\\\"Option \\\\\\\"{}\\\\\\\" not known, please check your input file\\\".format(key))\\n self.options[molname][key]=value \\n else:\\n # This is to define special lines that are given by a dictionary\\n key,value=stripped_line.split(\\\":\\\",1) # split on first occurence\\n if key==\\\"Addon\\\": # additional atoms to be added per molecule\\n addondict=self.empty_addon_dict.copy()\\n addondict_string = value.split(\\\"}\\\",-1)[0].split(\\\"{\\\",1)[1]\\n for pair in addondict_string.split(\\\",\\\"):\\n addonkey,addonvalue=[i.strip() for i in pair.split(\\\":\\\")]\\n if addonkey not in addondict.keys():\\n raise BaseException(\\\"Option \\\\\\\"{}\\\\\\\" in Addon section of molecule {} not known, please check your input file\\\".format(addonkey,molname))\\n addondict[addonkey]=addonvalue\\n value=addondict\\n # Since addon keyword can be used many times, this is a list\\n self.options[molname][key].append(value) \\n self._check()\",\n \"def pat_parse():\\n\\tfn = abs_path(sdict['sfn'], path)\\n\\n\\t#read the data\\n\\tskiprows = None\\n\\t#if 'skiprows' in sdict: skiprows = sdict['skiprows']\\n\\traw = pd.read_excel(fn, skiprows= skiprows, header = None)\\n\\n\\t#clean up \\n\\tcols = raw.loc[0].combine_first(raw.loc[1]).copy() #combines split header rows\\n\\traw.columns = cols\\n\\n\\traw.drop(s['junkcols'], inplace = True, #loses any intersperced cols we don't need\\n\\t\\t axis = 1) \\n\\traw = raw.iloc[2:, :-2] #drops the header and last 2 cols\\n\\traw.replace(missing, 0, inplace = True)\\n\\n\\traw = raw.astype('float64', #convert any col we can to a numeric type\\n\\t\\t errors = 'ignore')\\n\\traw = fix_non_ascii_df(raw) #fix non-ascii chars in text\\n\\n\\traw.columns.rename(s['col_renames'], inplace = True) #standardize company, industry names\\n\\n\\traw.insert(0, firmid_col, #look up and insert FirmID\\n\\t\\t get_firmid_from_vendor_name(raw[coname_col]) )\\n\\n\\taggregate\\n\\t\\\"\\\"\\\"\\n company, ticker, GICS industry, inventions by year, sum(inventions by year), CAGR\\n\\n tabs: [\\\"No of inventions\\\", Quality of patents\\\", \\\"Rate of abandonment\\\", \\\"R&D spending\\\"]\\n\\n need:\\n - replace \\\"-\\\" with 0 (not NaN)\\n - get FirmID\\n - good ind averages \\\"\\\"\\\"\\n\\ta = 1\",\n \"def build_parser(self):\\n parser = argparse.ArgumentParser(\\n description=\\\"Run Crystal Matching algorithm attempting to translate co-ordinates \\\"\\n \\\"on an input image to the coordinate-space of an output image while \\\"\\n \\\"accounting for possible movement of crystals in the sample.\\\")\\n\\n if sys.version_info[0] < 3:\\n parser.add_argument('Formulatrix_image',\\n metavar=\\\"Formulatrix_image_path\\\",\\n type=file,\\n help='Image file from the Formulatrix - selected_point should correspond to co-ordinates on '\\n 'this image.')\\n else:\\n parser.add_argument('Formulatrix_image',\\n metavar=\\\"Formulatrix_image_path\\\",\\n type=argparse.FileType('r'),\\n help='Image file from the Formulatrix - selected_point should correspond to co-ordinates on '\\n 'this image.')\\n parser.add_argument('beamline_stack_path',\\n metavar=\\\"beamline_stack_path\\\",\\n help=\\\"A path pointing at a directory which stores images to be stacked or a path to a stacked image.\\\")\\n parser.add_argument('selected_points',\\n metavar=\\\"x,y\\\",\\n nargs='*',\\n help=\\\"Comma-separated co-ordinates of selected points to be translated from the marked image \\\"\\n \\\"to the target image.\\\")\\n parser.add_argument('-o','--output',\\n metavar=\\\"focused_image_path\\\",\\n help=\\\"Specify directory for the stacked image. \\\"\\n \\\"A file called 'processed.tif' will be created in the directory.\\\"\\n \\\"'processed.tif' will be created in log directory if this is not set.\\\")\\n parser.add_argument('--config',\\n metavar=\\\"path\\\",\\n action=ReadableConfigDir,\\n default=join(self.get_script_path(), readable_config_dir.CONFIG_DIR_NAME),\\n help=\\\"Sets the configuration directory.\\\")\\n parser.add_argument('--scale',\\n metavar=\\\"scale\\\",\\n help=\\\"The scale between the Formulatrix and beamline image given as the resolution of each \\\"\\n \\\"image separated by a colon. Note this is relative (1:2 is the same as 2:4) and a value \\\"\\n \\\"must be specified for each image using the format \\\"\\n \\\"'[Formulatrix_image_resolution]:[beamline_image_resolution]'.\\\")\\n parser.add_argument('-j', '--job',\\n metavar=\\\"job_id\\\",\\n help=\\\"Specify a job_id - this will be reported in the output to help identify this run.\\\")\\n parser.add_argument('--to_json',\\n action='store_true',\\n help=\\\"Output a JSON object.\\\")\\n parser.add_argument('--version',\\n action='version',\\n version=VersionHandler.version_string())\\n parser.add_argument('--log',\\n metavar=\\\"path\\\",\\n help=\\\"Write log files to the directory specified by path.\\\")\\n self.parser = parser\",\n \"def base_gate_sequence_and_macros(model, basic_gates_macros: dict = None):\\n prep_fiducials, meas_fiducials, germs = (\\n model.prep_fiducials(),\\n model.meas_fiducials(),\\n model.germs(),\\n )\\n\\n # create minimal generating gate sequence\\n base_gate_sequence = list({k.str.split(\\\"@\\\")[0] for k in prep_fiducials + germs + meas_fiducials})\\n base_gate_sequence.remove(\\\"{}\\\")\\n base_gate_sequence.sort(key=len, reverse=True)\\n\\n if basic_gates_macros:\\n # create generating gate sequence macros\\n base_gate_sequence_macros = [s.split(\\\"G\\\") for s in base_gate_sequence]\\n for i, s in enumerate(base_gate_sequence_macros):\\n s = [basic_gates_macros[k] for k in s if basic_gates_macros.get(k) is not None]\\n base_gate_sequence_macros[i] = sequence_macros(s)\\n return base_gate_sequence, base_gate_sequence_macros\\n else:\\n return base_gate_sequence\",\n \"def parse_qasm(qasm):\\n\\n lines = qasm.split('\\\\n')\\n n = int(lines[0])\\n\\n # turn into tuples of python types\\n gates = [\\n tuple(map(_convert_ints_and_floats, line.strip().split(\\\" \\\")))\\n for line in lines[1:] if line\\n ]\\n\\n # put registers/parameters in standard order and detect if gate round used\\n gates = tuple(map(_put_registers_last, gates))\\n round_specified = isinstance(gates[0][0], numbers.Integral)\\n\\n return {\\n 'n': n,\\n 'gates': gates,\\n 'n_gates': len(gates),\\n 'round_specified': round_specified,\\n }\",\n \"def parseCommandLine():\\n parser = OptionParser(usage=\\\"%prog \\\", version=\\\"%prog \\\" + __version__,\\n description='''\\n This program calculates omegaAB value from a hexagonal lattice trajectory\\n stored in xyz file (see for more details)''')\\n parser.add_option(\\\"-f\\\", \\\"--traj\\\", dest=\\\"inXyzFilename\\\",default = \\\"hexTraj.xyz\\\",\\n help=\\\"xyz input trajectory file (default traj.xyz)\\\", metavar=\\\"INXYZFILE\\\")\\n parser.add_option(\\\"-r\\\", \\\"--reference\\\", dest=\\\"symbol\\\",default = \\\"P11\\\",\\n help=\\\"reference particle name\\\", metavar=\\\"ADATOM\\\")\\n parser.add_option(\\\"-o\\\", \\\"--output\\\", dest=\\\"outDatFilename\\\", default=\\\"omega.dat\\\",\\n help=\\\"output dat file with omega values for each frame. WARNING: it will be overriden\\\", metavar=\\\"OUTXYZFILE\\\")\\n \\n parser.add_option(\\\"-q\\\", \\\"--quiet\\\",\\n action=\\\"store_false\\\", dest=\\\"verbose\\\", default=True,\\n help=\\\"don't print status messages to stdout\\\")\\n\\n (options, _) = parser.parse_args()\\n\\n return options\",\n \"def _parseFileHeader(self):\\n self.fileheader = FileHeader()\\n self.fileheader.parse(self.f)\\n #print('Parsed fileheader')\",\n \"def parse_scan_args(file_path: str) -> dict:\\n log = ess_factory(fullpath=file_path, check_for_errors=False)\\n scan_args = {'scan': None, 'freeze': [],\\n 'step': 0, 'step_size': 0, 'n_atom': 0}\\n if isinstance(log, GaussianLog):\\n try:\\n # g09, g16\\n scan_blk = parse_str_blocks(file_path, 'The following ModRedundant input section has been read:',\\n 'Isotopes and Nuclear Properties', regex=False)[0][1:-1]\\n except IndexError: # Cannot find any block\\n # g03\\n scan_blk_1 = parse_str_blocks(file_path, 'The following ModRedundant input section has been read:',\\n 'GradGradGradGrad', regex=False)[0][1:-2]\\n scan_blk_2 = parse_str_blocks(file_path, 'NAtoms=',\\n 'One-electron integrals computed', regex=False)[0][:1]\\n scan_blk = scan_blk_1 + scan_blk_2\\n scan_pat = r'[DBA]?(\\\\s+\\\\d+){2,4}\\\\s+S\\\\s+\\\\d+[\\\\s\\\\d.]+'\\n frz_pat = r'[DBA]?(\\\\s+\\\\d+){2,4}\\\\s+F'\\n value_pat = r'[\\\\d.]+'\\n for line in scan_blk:\\n if re.search(scan_pat, line.strip()):\\n values = re.findall(value_pat, line)\\n scan_len = len(values) - 2 # atom indexes + step + stepsize\\n scan_args['scan'] = [int(values[i]) for i in range(scan_len)]\\n scan_args['step'] = int(values[-2])\\n scan_args['step_size'] = float(values[-1])\\n if re.search(frz_pat, line.strip()):\\n values = re.findall(value_pat, line)\\n scan_args['freeze'].append([int(values[i]) for i in range(len(values))])\\n if 'NAtoms' in line:\\n scan_args['n_atom'] = int(line.split()[1])\\n else:\\n raise NotImplementedError(f'parse_scan_args() can currently only parse Gaussian output '\\n f'files, got {log}')\\n return scan_args\"\n]","isConversational":false},"negative_scores":{"kind":"list like","value":["0.58941257","0.5843007","0.5546842","0.53140604","0.5287681","0.5214822","0.5029532","0.49508327","0.49250644","0.49058402","0.49010736","0.4891424","0.48260668","0.48217857","0.48092648","0.48078823","0.48026338","0.48020837","0.4797323","0.47908527","0.4788812","0.47760877","0.47434953","0.4736973","0.47157913","0.469151","0.46807024","0.46766588","0.46642333","0.46631378","0.46599367","0.45879662","0.45855948","0.45804912","0.4576338","0.45726842","0.45716384","0.45620513","0.45602965","0.4560268","0.455976","0.45523098","0.4548983","0.45394322","0.45286122","0.45214736","0.45212492","0.45104456","0.45084777","0.45059767","0.4502123","0.4483457","0.44812602","0.4461989","0.44510645","0.4450172","0.44480196","0.4445296","0.44452432","0.44441897","0.4441705","0.44399583","0.44393244","0.44355148","0.44353792","0.4411709","0.44099265","0.44097555","0.44009456","0.43864673","0.43587837","0.43515277","0.43454933","0.43450302","0.43443224","0.4342509","0.43208605","0.431919","0.43177542","0.43098536","0.43040192","0.43012518","0.4300499","0.42986688","0.42902547","0.42870563","0.42856994","0.42809826","0.42740315","0.4271547","0.42632365","0.4255809","0.42522147","0.42515242","0.42497405","0.42482018","0.42476505","0.42470592","0.42466116","0.42433643","0.42425245"],"string":"[\n \"0.58941257\",\n \"0.5843007\",\n \"0.5546842\",\n \"0.53140604\",\n \"0.5287681\",\n \"0.5214822\",\n \"0.5029532\",\n \"0.49508327\",\n \"0.49250644\",\n \"0.49058402\",\n \"0.49010736\",\n \"0.4891424\",\n \"0.48260668\",\n \"0.48217857\",\n \"0.48092648\",\n \"0.48078823\",\n \"0.48026338\",\n \"0.48020837\",\n \"0.4797323\",\n \"0.47908527\",\n \"0.4788812\",\n \"0.47760877\",\n \"0.47434953\",\n \"0.4736973\",\n \"0.47157913\",\n \"0.469151\",\n \"0.46807024\",\n \"0.46766588\",\n \"0.46642333\",\n \"0.46631378\",\n \"0.46599367\",\n \"0.45879662\",\n \"0.45855948\",\n \"0.45804912\",\n \"0.4576338\",\n \"0.45726842\",\n \"0.45716384\",\n \"0.45620513\",\n \"0.45602965\",\n \"0.4560268\",\n \"0.455976\",\n \"0.45523098\",\n \"0.4548983\",\n \"0.45394322\",\n \"0.45286122\",\n \"0.45214736\",\n \"0.45212492\",\n \"0.45104456\",\n \"0.45084777\",\n \"0.45059767\",\n \"0.4502123\",\n \"0.4483457\",\n \"0.44812602\",\n \"0.4461989\",\n \"0.44510645\",\n \"0.4450172\",\n \"0.44480196\",\n \"0.4445296\",\n \"0.44452432\",\n \"0.44441897\",\n \"0.4441705\",\n \"0.44399583\",\n \"0.44393244\",\n \"0.44355148\",\n \"0.44353792\",\n \"0.4411709\",\n \"0.44099265\",\n \"0.44097555\",\n \"0.44009456\",\n \"0.43864673\",\n \"0.43587837\",\n \"0.43515277\",\n \"0.43454933\",\n \"0.43450302\",\n \"0.43443224\",\n \"0.4342509\",\n \"0.43208605\",\n \"0.431919\",\n \"0.43177542\",\n \"0.43098536\",\n \"0.43040192\",\n \"0.43012518\",\n \"0.4300499\",\n \"0.42986688\",\n \"0.42902547\",\n \"0.42870563\",\n \"0.42856994\",\n \"0.42809826\",\n \"0.42740315\",\n \"0.4271547\",\n \"0.42632365\",\n \"0.4255809\",\n \"0.42522147\",\n \"0.42515242\",\n \"0.42497405\",\n \"0.42482018\",\n \"0.42476505\",\n \"0.42470592\",\n \"0.42466116\",\n \"0.42433643\",\n \"0.42425245\"\n]","isConversational":false},"document_score":{"kind":"string","value":"0.0"},"document_rank":{"kind":"string","value":"-1"}}},{"rowIdx":16584,"cells":{"query":{"kind":"string","value":"Parse a batch of gerber files in a zip file."},"document":{"kind":"string","value":"def test_zip_batch(self):\n assert self.design.layout.layers[0].name == 'top'"},"metadata":{"kind":"string","value":"{\n \"objective\": {\n \"self\": [],\n \"paired\": [],\n \"triplet\": [\n [\n \"query\",\n \"document\",\n \"negatives\"\n ]\n ]\n }\n}"},"negatives":{"kind":"list like","value":["def _add_tag_files(\n zip_file, dir_name, payload_info_list, payload_byte_count, payload_file_count\n):\n tag_info_list = []\n _add_tag_file(zip_file, dir_name, tag_info_list, _gen_bagit_text_file_tup())\n _add_tag_file(\n zip_file,\n dir_name,\n tag_info_list,\n _gen_bag_info_file_tup(payload_byte_count, payload_file_count),\n )\n _add_tag_file(\n zip_file, dir_name, tag_info_list, _gen_pid_mapping_file_tup(payload_info_list)\n )\n return tag_info_list","def load_zip_files(zip_path):\n zd = zipfile.ZipFile(zip_path)\n paths = sorted(zd.filelist, key=lambda x: x.date_time)\n for path in paths:\n with zd.open(path, 'r') as fd:\n try:\n data = json.load(fd)\n yield File.Ok(fd.name, data)\n except (json.JSONDecodeError, UnicodeDecodeError) as exc:\n fd.seek(0)\n yield File.Err(fd.name, fd.read(), str(exc))","def parse_gzipped_directory(input_dir, start_date, end_date, infos, backup_stamps):\n try:\n file_names = sorted(os.listdir(input_dir)) \n for file_name in file_names:\n if file_name.endswith(\".manifest.gz\") or file_name.endswith(\".manifest\"):\n tmp = parse_file(input_dir + \"/\" + file_name, start_date, end_date, backup_stamps)\n backup_stamps[tmp[\"backup_label\"]] = tmp[\"backup_timestamp_stop_ts\"]\n if tmp:\n infos.append(tmp)\n except OSError as e:\n logging.error(\"Failed to open directory\", exc_info=True)\n exit(1)\n except:\n raise","def parse_file(file_name: str, delims='\\n', encoding='utf-8', zip_type=None):\n try:\n decoder = codecs.getincrementaldecoder(encoding)()\n except LookupError as e:\n print(str(e))\n return\n\n read_buffer_size = 10*1024\n max_line_size = 100*1024\n\n if not zip_type:\n open_f = open\n elif zip_type == 'gz':\n open_f = gzip.open\n else:\n raise NotImplementedError()\n\n with open_f(file_name, 'rb') as fp:\n buffered_str = ''\n for bs in iter(partial(fp.read, read_buffer_size), b''):\n decoded_str = decoder.decode(bs)\n # FIXME: i don't think current implementation is efficient enough...\n for c in decoded_str:\n if c in delims:\n if len(buffered_str) > 0:\n yield buffered_str\n buffered_str = ''\n else:\n buffered_str += c\n if len(buffered_str) >= max_line_size:\n yield buffered_str\n buffered_str = ''\n if len(buffered_str) > 0:\n yield buffered_str","def add_zip(self, zipfile, valid_extensions=('txt', 'csv', 'xls', 'xlsx'), encoding='utf8',\n doc_label_fmt_txt='{path}-{basename}', doc_label_path_join='_', doc_label_fmt_tabular='{basename}-{id}',\n force_unix_linebreaks=True, **kwargs):\n\n tmpdir = mkdtemp()\n\n read_size = kwargs.pop('read_size', -1)\n\n with ZipFile(zipfile) as zipobj:\n for member in zipobj.namelist():\n path_parts = path_recursive_split(member)\n\n if not path_parts:\n continue\n\n dirs, fname = path_parts[:-1], path_parts[-1]\n\n basename, ext = os.path.splitext(fname)\n basename = basename.strip()\n\n if ext:\n ext = ext[1:]\n\n if ext in valid_extensions:\n tmpfile = zipobj.extract(member, tmpdir)\n\n if ext in {'csv', 'xls', 'xlsx'}:\n self.add_tabular(tmpfile, encoding=encoding, doc_label_fmt=doc_label_fmt_tabular,\n force_unix_linebreaks=force_unix_linebreaks, **kwargs)\n else:\n doclabel = doc_label_fmt_txt.format(path=doc_label_path_join.join(dirs),\n basename=basename,\n ext=ext)\n\n if doclabel.startswith('-'):\n doclabel = doclabel[1:]\n\n self.add_files(tmpfile, doc_labels=[doclabel], encoding=encoding, read_size=read_size,\n force_unix_linebreaks=force_unix_linebreaks)\n\n return self","def fromZip(self, zip_location,extract_location):\n zip_file = zipfile.ZipFile(zip_location,'r')\n zip_file.extractall(extract_location)","def _extract_zip(self, zipfile):\n zf = ZipFile(zipfile)\n d = {}\n for n in zf.namelist():\n d[n] = zf.read(n)\n return d","def unpack_HCP_zips(zipsfolder, LR_path, RL_path):\n listing = os.listdir(zipsfolder)\n for files in listing:\n if files.endswith('_3T_tfMRI_EMOTION_preproc.zip'):\n with open(zipsfolder + files, 'rb') as fileobj:\n with zipfile.ZipFile(fileobj) as z:\n subject = z.filename[len(zipsfolder):int(len(zipsfolder) + 6)]\n for zip_info in z.infolist():\n if zip_info.filename[-22:].endswith('fMRI_EMOTION_LR.nii.gz'):\n zip_info.filename = subject + '_' + os.path.basename(zip_info.filename)\n z.extract(zip_info, path=LR_path)\n print(f'Subject {subject} LR.nii.gz data extracted...')\n if zip_info.filename[-22:].endswith('fMRI_EMOTION_RL.nii.gz'):\n zip_info.filename = subject + '_' + os.path.basename(zip_info.filename)\n z.extract(zip_info, path=RL_path)\n print(f'Subject {subject} RL.nii.gz data extracted...')\n fileobj.close()","def load_zip_codes():\n logger.info('Loading zip code data')\n read_zips()","def extractall(self, *args, **kwargs):\n self.zipfile.extractall(*args, **kwargs)","def unzip_citibike_data(zip_dir):\n# zip_dir = \"data/citibike-tripdata-nyc/\"\n# csv_dir = \"data/citibike-tripdata-nyc/csv\"\n extension = \".zip\"\n\n # for each zip file in zip_dir extract data\n for item in os.listdir(zip_dir):\n if item.endswith(extension):\n\n # create zipfile object and extract\n file_name = zip_dir + item\n with zipfile.ZipFile(file_name, \"r\") as zip_ref:\n zip_ref.extractall(zip_dir)\n print(item + \" done\")","def _add_manifest_files(zip_file, dir_name, payload_info_list, tag_info_list):\n for checksum_algorithm in _get_checksum_algorithm_set(payload_info_list):\n _add_tag_file(\n zip_file,\n dir_name,\n tag_info_list,\n _gen_manifest_file_tup(payload_info_list, checksum_algorithm),\n )","def extractZipFiles(rootDir, zipDir):\n for root, dirs, files in os.walk(zipDir, topdown=False):\n for name in files:\n \n zipFiles = os.path.join(root, name)\n \n #Check file extension here\n if \".zip\" not in zipFiles:\n continue\n \n else:\n zipPath = zipfile.ZipFile(zipFiles, 'r')\n #print(zipPath) \n \n filesInZip = zipPath.namelist()\n i = 0 \n for i in range(len(filesInZip)):\n #print(filesInZip[i])\n #print(zipPath.getinfo(filesInZip[i]))\n \n if \".mp3\" in filesInZip[i]:\n zipPath.extract(filesInZip[i], rootDir)\n print(\"{0} extracted to {1}\".format(filesInZip[i], rootDir))\n\n elif \".m4a\" in filesInZip[i]:\n zipPath.extract(filesInZip[i], rootDir)\n print(\"{0} extracted to {1}\".format(filesInZip[i], rootDir))\n\n elif \".mp4\" in filesInZip[i]:\n zipPath.extract(filesInZip[i], rootDir)\n print(\"{0} extracted to {1}\".format(filesInZip[i], rootDir))\n\n elif \".png\" in filesInZip[i]:\n zipPath.extract(filesInZip[i], rootDir)\n print(\"{0} extracted to {1}\".format(filesInZip[i], rootDir))\n\n elif \".jpg\" in filesInZip[i]:\n zipPath.extract(filesInZip[i], rootDir)\n print(\"{0} extracted to {1}\".format(filesInZip[i], rootDir))\n \n elif \".pdf\" in filesInZip[i]:\n zipPath.extract(filesInZip[i], rootDir)\n print(\"{0} extracted to {1}\".format(filesInZip[i], rootDir))\n\n else:\n print(\"No media found in zip file {0}\".format(name))\n \n zipPath.close()","def zipstreams(filename):\r\n with open(filename, 'rb') as fh:\r\n data = fh.read()\r\n i = 0\r\n while i < len(data):\r\n try:\r\n zo = zlib.decompressobj()\r\n yield i, zo.decompress(data[i:])\r\n i += len(data[i:]) - len(zo.unused_data)\r\n except zlib.error:\r\n i += 1","def gen_stats_zip(filename_list, zipfilename, tier='tier2', csv_processor='ICOS-ETC', zip_processor='LBL_AMP', ts_format=\"%Y-%m-%d %H:%M:%S\"):\n log.info(\"Generating ZIP and stats for: {z}\".format(z=zipfilename))\n\n if not filename_list:\n return [], []\n\n today = datetime.now().strftime(ts_format)\n output_zip = zip_file_list(filename_list=filename_list, zipfilename=zipfilename)\n\n if output_zip != zipfilename:\n raise ONEFluxError(\"ZIP filenames differ: {i} {o}\".format(i=zipfilename, o=output_zip))\n\n size, md5sum, _ = file_stat(filename=zipfilename)\n zip_entry = [['\"{e}\"'.format(e=os.path.basename(zipfilename)),\n '{e}'.format(e=format(size)),\n '\"{e}\"'.format(e=md5sum),\n '\"{e}\"'.format(e=len(filename_list)),\n '\"{e}\"'.format(e=tier),\n '\"{e}\"'.format(e=zip_processor),\n '\"{e}\"'.format(e=today)], ]\n csv_entries = []\n for filename in filename_list:\n f_size, f_md5sum, f_timestamp_change = file_stat(filename=filename)\n f_today = f_timestamp_change.strftime(ts_format)\n entry = ['\"{e}\"'.format(e=os.path.basename(zipfilename)),\n '\"{e}\"'.format(e=os.path.basename(filename)),\n '{e}'.format(e=f_size),\n '\"{e}\"'.format(e=f_md5sum),\n '\"{e}\"'.format(e=csv_processor),\n '\"{e}\"'.format(e=f_today)]\n csv_entries.append(entry)\n\n return zip_entry, csv_entries","def quickScanZip(args, fh):\n # 100 bytes is the smallest .zip possible\n\n fh.seek(0, 2)\n fsize = fh.tell()\n if fsize==0:\n print(\"Empty file\")\n return\n if fsize<100:\n print(\"Zip too small: %d bytes, minimum zip is 100 bytes\" % fsize)\n return\n fh.seek(-100, 2)\n\n eoddata = fh.read()\n iEND = eoddata.find(b'PK\\x05\\x06')\n if iEND==-1:\n # try with larger chunk\n ofs = max(fh.tell()-0x10100, 0)\n fh.seek(ofs, 0)\n eoddata = fh.read()\n iEND = eoddata.find(b'PK\\x05\\x06')\n if iEND==-1:\n print(\"expected PK0506 - probably not a PKZIP file\")\n return\n else:\n ofs = fh.tell()-0x100\n eod = EndOfCentralDir(ofs, eoddata, iEND+4)\n yield eod\n\n dirofs = eod.dirOffset\n for _ in range(eod.thisEntries):\n fh.seek(dirofs)\n dirdata = fh.read(46)\n if dirdata[:4] != b'PK\\x01\\x02':\n print(\"expected PK0102\")\n return\n dirent = CentralDirEntry(dirofs, dirdata, 4)\n\n yield dirent\n dirofs = dirent.endOffset","def parse_region_data(self, region):\n\n #downloads newest data\n self.download_data()\n\n TmpList = [[] for i in range(65)]\n\n #goes through all the files and saves their data to the variable\n for zipName in self.ListOfZipFiles:\n with zipfile.ZipFile(\"./\"+self.folder+\"/\"+zipName, 'r') as zf:\n if self.getCsvFileByRegion(region) == None:\n print(\"ERROR: neznamy nazev kraje: \" + region, file=sys.stderr)\n return None\n #opens zip file for reading\n with zf.open(self.getCsvFileByRegion(region), \"r\") as f:\n reader = f.read().decode(\"iso 8859-2\")\n reader = StringIO(reader)\n reader = csv.reader(reader, delimiter = \";\")\n #saves every row of file\n for row in reader:\n TmpList[0].append(region)\n i=1\n #saves every column separated because of their types\n for item in row:\n if item != \"\":\n if (i>0 and i<4) or (i>4 and i<6) or (i>6 and i<32) or (i>32 and i<35) or (i>35 and i<46) or i==61 or i==64:\n if not re.search(\"^[-]{0,1}[0-9]*$\", item):\n item = None\n else:\n item=int(item)\n elif i>45 and i<52:\n if not re.search(\"^[-]{0,1}[0-9]*[,.]{0,1}[0-9]+$\", item):\n item = None\n else:\n item = item.replace(\",\", \".\")\n if re.search(\"^[-]{1}.*$\", item):\n item = item.replace(\"-\", \"\")\n item = -(float(item))\n else:\n item = float(item)\n elif i==6:\n if not re.search(\"^[-]{0,1}[0-9]*$\", item):\n item = None\n else:\n if (len(item) == 4):\n #cas nijak neupravuji, jen rozdeluji minuty od hodin\n #policie uz nastavila hodnoty podle nich pozname nevalidni hodnotu\n #pro minuty tato hodnota je 60\n #pro hodiny tato hodnota je 25\n #dle meho nazoru mi prislo zbytecne na misto techto dvou hdonot davat nejakou jinou nevalidni hodnotu (napr. NaN, -1)\n #prepsal bych nevalidni vystup na jiny nevalidni vystup\n item = item[:2] + \":\" + item[2:]\n else:\n item = None\n TmpList[i].append(item)\n else:\n TmpList[i].append(None)\n i+=1\n\n ListNpArrays = [[] for i in range(65)]\n\n #transforms into numpy.ndarray\n for x in range(0, 65):\n ListNpArrays[x] = np.array(TmpList[x], dtype=object)\n\n return (self.headers, ListNpArrays)","def _get_stream_readers_for_zip(fh, tmp_dir):\n fasta_zip = zipfile.ZipFile(fh, 'r')\n rval = []\n for member in fasta_zip.namelist():\n fasta_zip.extract(member, tmp_dir)\n rval.append(open(os.path.join(tmp_dir, member), 'rb'))\n return rval","def iterator(dataset_fn, sections=None, lang=None, field_indices=None):\n files = filelist(lang=lang, sections=sections)\n\n with TarFile.open(dataset_fn, 'r:gz') as f:\n for member in f:\n if member.isfile() and os.path.basename(member.name) in files:\n logging.info('parsing %s ...' % member.name)\n m_f = f.extractfile(member)\n\n for sentence in parse_conll(m_f, field_indices=field_indices):\n yield sentence\n\n m_f.close()","def _unzip_files(self) -> None:\n for file in self.input_path.iterdir():\n if is_zipfile(file):\n with ZipFile(file, mode=\"r\") as archive:\n archive.extractall(path=self.temp_path)","def process_lucidchart_zip(zip_path, format, outdir, overwrite=False):\n\n if outdir.exists():\n if overwrite:\n shutil.rmtree(outdir)\n else:\n raise Exception(f\"outdir={outdir} must not exist\")\n\n outdir.mkdir()\n\n with ZipFile(zip_path, 'r') as zf:\n\n namemap = {f\"Page {idx+1}.{format}\": name for idx, name in enumerate(names_in_page_order)}\n\n # ensure 1:1 mapping\n exist_pages = set(zf.namelist())\n desired_pages = set(namemap.keys())\n if exist_pages != desired_pages:\n raise Exception(f\"\"\"unexpected content in zip file\n exist_pages={exist_pages}\n desired_pages={desired_pages}\n exist - desired={exist_pages - desired_pages}\n desired - exist={desired_pages - exist_pages}\n \"\"\")\n\n paths = []\n for ep in exist_pages:\n dest_name = namemap[ep]\n dest_path = outdir / f\"{dest_name}.{format}\"\n dest_path.write_bytes(zf.open(ep).read())\n paths += [dest_path]\n return paths","def zip_parse(html_file):\n zpf = html_file.replace('.html', '.zip')\n summhead = []\n datahead = []\n rv_summary = []\n rv_data = []\n with zipfile.ZipFile(zpf, 'r') as Z:\n summfile = [x for x in Z.namelist()\n if x.endswith(\"summary.txt\")][0]\n datafile = summfile.replace('summary.txt', 'fastqc_data.txt')\n\n summ = Z.read(summfile).decode('ASCII')\n data = Z.read(datafile).decode('ASCII')\n\n for line in summ.split(\"\\n\"):\n ls = line.strip().split(\"\\t\")\n if len(ls) < 3:\n continue\n summhead.append(ls[1])\n rv_summary.append(ls[0])\n\n for line in data.split(\"\\n\"):\n if \">>END_MODULE\" in line:\n break\n if line.startswith(\"#\"):\n continue\n if line.startswith(\">\"):\n continue\n ls = line.strip().split(\"\\t\")\n if ls[0] == 'Filename':\n continue\n datahead.append(ls[0])\n rv_data.append(ls[1])\n\n return dict(zip(summhead, rv_summary)), \\\n dict(zip(datahead, rv_data))","def gen_glogs(zipname, ref_hashes, extraction, verbose=True, **extraction_kwargs):\n with ZipFile(zipname, 'r') as z:\n # sort files according to reference hash list\n filenames = sort_files(z.namelist(), ref_hashes)\n if verbose:\n filenames = tqdm(filenames)\n\n # load and return glog\n for filename in filenames:\n with io.BytesIO(z.read(filename)) as buffer:\n glog = buffer.getvalue()\n yield extraction(glog, **extraction_kwargs)","def get_list_of_files_in_zip(zip_files):\n files = {k: [] for k in zip_files}\n for zip_file in zip_files:\n print('[ INFO ] Loading: %s' % zip_file)\n try:\n with ZipFile(join(zip_file), 'r') as z:\n files[zip_file] = files[zip_file] + z.namelist()\n except Exception as e:\n print(e)\n return files","def tag_file_process(self, multiple_files):\n # the path is now becoming a string since it goes through the UI\n # text entry box, not a list or tuple any more, so we turn it to a\n # list of paths\n file_list = multiple_files.split(' ')\n # the main dictionary to store all tags\n tag_dict = dict()\n rows = []\n # now for all the tag file under the folder(root directory), we load\n # the data into the dictionary\n if len(file_list) == 0:\n tk.messagebox.showwarning('warning', 'no files chosen')\n else:\n for file_path in file_list:\n if os.path.isfile(file_path):\n with open(file_path, 'r', encoding='utf-8') as \\\n current_tag_file:\n # initialize the dictionary and the inner dictionary\n reader = csv.reader(current_tag_file)\n for row in reader:\n # the encode, decode is use to resolve the \"\\ueffa\"\n # BOM-utf8 problem\n row[0] = row[0].encode('utf-8').decode('utf-8-sig')\n tag_dict[row[0]] = dict()\n rows.append(row)\n # store the tag into the dictionary\n for row in rows:\n # the 1st column is the main key(mob fact col name)\n # the 2nd column is the tag id\n # the 3rd column is the tag with real meaning\n tag_dict[row[0]][row[1]] = row[2]\n\n else:\n tk.messagebox.showinfo('warning', 'can not obtain: ' +\n file_path)\n return tag_dict","def add_zip(manager, zipfile, incref=False):\n from .core.cache.buffer_cache import empty_dict_checksum, empty_list_checksum\n result = []\n for checksum in zipfile.namelist():\n if checksum in (empty_dict_checksum, empty_list_checksum):\n continue\n checksum2 = bytes.fromhex(checksum)\n buffer = zipfile.read(checksum)\n checksum3 = calculate_checksum(buffer)\n if checksum3 != checksum2:\n raise ValueError(\"Incorrect checksum for zipped file '{}'\".format(checksum))\n buffer_cache.cache_buffer(checksum2, buffer)\n if incref:\n buffer_cache.incref(checksum2, authoritative=False)\n result.append(checksum)\n return result","def extract(zip_file_path: str) -> List[bytes]:\n\n with ZipFile(zip_file_path, 'r') as zip_file:\n files_extracted = zip_file.namelist()\n try:\n assert len(files_extracted) == 1, f\"{zip_file_path} contains more than one file: \"\n except:\n logging.info(f\"{zip_file_path} contains more than one file: {files_extracted}\")\n with zip_file.open(files_extracted[0], 'r') as f:\n return f.readlines()","def _extract_data(inputs):\n filename, split = inputs\n for name, fobj in tfds.download.iter_archive(\n filename, tfds.download.ExtractMethod.TAR_STREAM\n ):\n split_name = name.split(\"_\")\n if len(split_name) > 2 and split_name[2] == split:\n yield [name, fobj.read()]","def load(folder, number_of_files=None, verbose=False):\n files = list_files(folder, number_of_files)\n\n lemmatized_sentences = []\n original_sentences = []\n for zipped_file in files:\n if verbose:\n print(\"Parsing \" + zipped_file)\n file = unzip(zipped_file)\n (lemmas, originals) = parse(file)\n original_sentences += originals\n lemmatized_sentences += lemmas\n\n return lemmatized_sentences, original_sentences","def peak_file_parser(infile):\n # Open file and make sure supported\n pfile = open_zipped(infile)\n file_parsers = {'bed': bed_file}\n file_parser = None\n if pfile.name == '<stdin>':\n file_parser = bed_file\n else:\n for n in file_parsers:\n if in_name(pfile, n):\n file_parser = file_parsers[n]\n if not file_parser:\n nm = pfile.name\n pfile.close()\n raise Exception('Unknown file type: {}'.format(nm))\n\n # Return the iterator\n return file_parser(pfile)","def parse_files():\n pfuncs = [ # parse py files : add #\n parse_test_files,\n parse_model_files,\n parse_url_files,\n parse_route_files,\n parse_settings_files,\n parse_setup_files,\n ]\n\n while PY_FILES:\n for _ in range(len(pfuncs)):\n a_func = pfuncs.pop()\n a_func()\n break","def parse_region_data(self, region):\r\n \r\n self.download_data()\r\n region_filename = self.__get_region_filename(region)\r\n list_str = [\"region\", \"p1\", \"p36\", \"p37\", \"p2a\", \"weekday(p2a)\", \"p2b\", \"p6\", \"p7\", \"p8\", \"p9\", \"p10\", \r\n \"p11\", \"p12\", \"p13a\", \"p13b\", \"p13c\", \"p14\", \"p15\", \"p16\", \"p17\", \"p18\",\"p19\", \"p20\", \"p21\", \r\n \"p22\", \"p23\", \"p24\", \"p27\", \"p28\", \"p34\", \"p35\", \"p39\", \"p44\", \"p45a\", \"p47\", \"p48a\", \"p49\", \r\n \"p50a\", \"p50b\", \"p51\", \"p52\", \"p53\", \"p55a\", \"p57\", \"p58\", \"a\", \"b\", \"d\", \"e\", \"f\", \"g\", \"h\", \r\n \"i\", \"j\", \"k\", \"l\", \"m\", \"n\", \"o\", \"p\", \"q\", \"r\", \"s\", \"t\", \"p5a\"]\r\n \r\n row_count = self.__get_files_row_count(region)\r\n list_arrays = [np.zeros(row_count, dtype=dt) for dt in self.__types]\r\n row_index = 0\r\n for file in self.__files:\r\n file_to_parse = os.path.join(self.__folder, os.path.basename(file))\r\n with zipfile.ZipFile(file_to_parse, \"r\") as zf:\r\n with zf.open(region_filename, 'r') as csv_file:\r\n reader = csv.reader(TextIOWrapper(csv_file, 'windows-1250'), delimiter=';', quotechar='\"')\r\n for row in reader:\r\n list_arrays[0][row_index] = region\r\n for col_index, col in enumerate(row):\r\n try:\r\n list_arrays[col_index + 1][row_index] = col\r\n except ValueError:\r\n if list_arrays[col_index + 1][row_index].dtype == np.int64:\r\n list_arrays[col_index + 1][row_index] = -1\r\n elif list_arrays[col_index + 1][row_index].dtype == 'datetime64[D]':\r\n print('Error2:', col)\r\n elif list_arrays[col_index + 1][row_index].dtype == np.float64:\r\n if type(col) != str:\r\n list_arrays[col_index + 1][row_index] = col.replace(',', '.')\r\n else:\r\n list_arrays[col_index + 1][row_index] = float(\"nan\")\r\n row_index += 1\r\n \r\n return (list_str, list_arrays)","def _unpack_archive(self, dir, filters):\n ext = os.path.splitext(self.path)[1]\n if ext in [\".zip\", \".xpi\"]:\n if filters:\n raise GbpError(\"Can only filter tar archives: %s\", (ext, self.path))\n self._unpack_zip(dir)\n else:\n self._unpack_tar(dir, filters)","def load_zip(data):\n zip_codes = [address['postalCode'] for address in data]\n zip_codes_objects = [Zip(data=zip_code)\n for zip_code\n in zip_codes]\n Zip.objects.bulk_create(zip_codes_objects)","def parse_records(self):\n for record in sp.parse(gzip.open(\n \"./human_uniprot_04_07_20.gz\", 'rt')):\n # print(record.taxonomy_id)\n # if record.organism != \"Homo sapiens\":\n # continue\n # print(record.features[0])\n # for comment in record.comments:\n # if comment.startswith(\"SUBCELLULAR LOCATION\"):\n # print(comment)\n self.extract_features_to_dict(record)\n self.extract_localization(record)","def processfile(args, fh):\n if args.quick:\n scanner = quickScanZip(args, fh)\n else:\n scanner = findPKHeaders(args, fh)\n\n def checkarg(arg, ent):\n if not arg:\n return False\n return '*' in arg or ent.name in arg\n def checkname(a, b):\n if a and '*' in a: return True\n if b and '*' in b: return True\n l = 0\n if a: l += len(a)\n if b: l += len(b)\n return l > 1\n\n if args.verbose and not (args.cat or args.raw or args.save):\n print(\" 0304 need flgs mth stamp --crc-- compsize fullsize nlen xlen namofs xofs datofs endofs\")\n print(\" 0102 crea need flgs mth stamp --crc-- compsize fullsize nlen xlen clen dsk0 attr osattr datptr namofs xofs cmtofs endofs\")\n for ent in scanner:\n if args.cat or args.raw or args.save:\n if args.quick and isinstance(ent, CentralDirEntry) or \\\n not args.quick and isinstance(ent, LocalFileHeader):\n ent.loaditems(fh)\n do_cat = checkarg(args.cat, ent)\n do_raw = checkarg(args.raw, ent)\n do_save= checkarg(args.save, ent)\n\n do_name= checkname(args.cat, args.raw)\n\n if do_name:\n print(\"\\n===> \" + ent.name + \" <===\\n\")\n\n sys.stdout.flush()\n blks = zipraw(fh, ent)\n\n if args.password and ent.flags&1:\n blks = zip_decrypt(blks, args.password)\n if do_cat or do_save:\n blks = skipbytes(blks, 12, args)\n\n if do_cat:\n sys.stdout.buffer.writelines(zipcat(blks, ent))\n if do_raw:\n sys.stdout.buffer.writelines(blks)\n if do_save:\n savefile(args.outputdir, ent.name, zipcat(blks, ent))\n else:\n ent.loaditems(fh)\n if args.verbose or not args.quick:\n print(\"%08x: %s\" % (ent.pkOffset, ent))\n else:\n print(ent.summary())\n if hasattr(ent, \"comment\") and ent.comment and not args.dumpraw:\n print(ent.comment)\n if args.dumpraw and hasattr(ent, \"extraLength\") and ent.extraLength:\n print(\"%08x: XTRA: %s\" % (ent.extraOffset, binascii.b2a_hex(getbytes(fh, ent.extraOffset, ent.extraLength))))\n if args.dumpraw and hasattr(ent, \"comment\") and ent.comment:\n print(\"%08x: CMT: %s\" % (ent.commentOffset, binascii.b2a_hex(getbytes(fh, ent.commentOffset, ent.commentLength))))\n if args.dumpraw and isinstance(ent, LocalFileHeader):\n blks = zipraw(fh, ent)\n if args.password and ent.flags&1:\n blks = zip_decrypt(blks, args.password)\n\n blockdump(ent.dataOffset, blks)","def parse_files(self, filenames=\"\"):\n if self._parsed:\n raise Exception(\"Have been parsed\")\n self._parsed = True\n\n if filenames:\n if not isinstance(filenames, (list, tuple)):\n filenames = self._parse_string(filenames).strip(\", \").split(\",\")\n\n for filename in filenames:\n self._parse_file(filename)\n\n self._check_and_fix()","def load_files_info(self):\n authors = {}\n paths = sorted(self.zipfile.filelist, key=lambda x: x.date_time)\n for path in paths:\n with self.zipfile.open(path) as fd:\n try:\n data = json.load(fd)\n names = self.extract_author_name(data)\n except json.JSONDecodeError:\n fd.seek(0)\n self.invalid_files[fd.name] = fd.read()\n else:\n authors.update({name: path for name in names})\n\n return authors","def unzip_oxygen_files(zip_file):\n name_main_content = None\n name_left_menu = None\n list_img_files_to_save = list()\n\n files_unzipped = ZipFile(zip_file)\n for file_unzipped_name in files_unzipped.namelist():\n if not file_unzipped_name.startswith('__MACOSX'):\n if file_unzipped_name.endswith(\".jpeg\"):\n list_img_files_to_save.append(file_unzipped_name)\n elif file_unzipped_name.endswith(\".indexList.html\"):\n name_left_menu = file_unzipped_name\n elif file_unzipped_name.endswith(\"_xsd.html\"):\n name_main_content = file_unzipped_name\n\n return files_unzipped, name_left_menu, name_main_content, list_img_files_to_save","def _read_recs(basedir):\n for borotag in boro_tags:\n datafile = \"%s/%s.csv\" % (basedir,borotag)\n print(\"slurp '%s' ..\" % datafile)\n recs = read_recs(datafile)\n yield from (pluto.parse.normalize(r) for r in recs)","def read_data(filename):\n data=''\n with zipfile.ZipFile(filename) as f:\n \n for file in f.namelist():\n subdata = tf.compat.as_str(f.read(file))\n data+=subdata\n return nlp(data)","def process_file(filename):\n print \"Reading and Parsing File: {}\".format(filename)\n parsed_entries = file_parser(filename)\n print \"Starting to Process Entries\"\n chunked_entires = chunk_entries(parsed_entries)\n return [process_entries(entry) for entry in chunked_entires]","def _iter_dag_filelocs(fileloc: str) -> Iterator[str]:\n if fileloc.endswith(\".py\") or not zipfile.is_zipfile(fileloc):\n yield fileloc\n return\n try:\n with zipfile.ZipFile(fileloc) as z:\n for info in z.infolist():\n if might_contain_dag(info.filename, True, z):\n yield os.path.join(fileloc, info.filename)\n except zipfile.BadZipFile:\n self.log.exception(\"There was an error accessing ZIP file %s %s\", fileloc)","def unpack_landsat(inpath, outpath, bands=None, clouds=None):\r\n tfile = tarfile.open(inpath,'r:gz')\r\n if bands is None:\r\n #Extract all of the bands.\r\n tfile.extractall(outpath);\r\n else:\r\n #Extract just the bands specified.\r\n\r\n #Get the names of the members of the archive\r\n names = tfile.getnames()\r\n\r\n #Make sure the bands are given as a list\r\n bands = list(bands)\r\n\r\n #Find those elements of the archive that match the bands specified\r\n #\t(plus metadata file)\r\n members = tfile.getmembers()\r\n elements = []\r\n blist = ''.join(str(i) for i in bands)\r\n if clouds:\r\n patternStr = '.*_B[' + blist + ']\\.TIF|.*_MTL.txt|.*_band[' + blist + \\\r\n ']\\.tif|.*_cfmask.*\\.tif|.*\\.xml|.*cloud.*\\.tif'\r\n else:\r\n patternStr = '.*_B[' + blist + ']\\.TIF|.*_MTL.txt|.*_band[' + blist + \\\r\n ']\\.tif|.*_cfmask.*\\.tif|.*\\.xml'\r\n\r\n pattern = re.compile(patternStr)\r\n for i, name in enumerate(names):\r\n if pattern.match(name):\r\n elements.append(members[i])\r\n tfile.extractall(outpath,members = elements)\r\n\r\n '''\r\n Note: the below section was written with the intention of\r\n adding valuable metadata info to the .TIF files themselves.\r\n This theoretically allows easy retreival of key metadata info,\r\n but the method to set new metadata seems unreliable. Appears to\r\n be an open issue, but there may be a solution. For now, assume\r\n this does not work.\r\n\r\n #Now we loop through each output, adding important metadata.\r\n #Fetch metadata and make sure there is only one file.\r\n meta = glob.glob(outpath + '/*_MTL.txt')\r\n if len(meta) > 1:\r\n raise('MORE THAN ONE METADATA FILE FOUND!')\r\n\r\n metadata = read_metadata(meta[0])\r\n\r\n #Add the metadata.\r\n for tif in glob.glob(outpath + '*.TIF'):\r\n #Open the tif file\r\n ras = gdal.Open(tif)\r\n\r\n #Preserve any existing metadata & add important metadata from file\r\n meta = ras.GetMetadata()\r\n meta['SCENE_CENTER_TIME'] = metadata['SCENE_CENTER_TIME']\r\n meta['DATE_ACQUIRED'] = metadata['DATE_ACQUIRED']\r\n meta['LANDSAT_SCENE_ID'] = metadata['LANDSAT_SCENE_ID']\r\n\r\n #Now write the new metadata back to the tif.\r\n ras.SetMetadata(meta)\r\n ras.FlushCache()\r\n ras = None\r\n '''","def _add_tag_file(zip_file, dir_name, tag_info_list, tag_tup):\n tag_name, tag_str = tag_tup\n tag_path = d1_common.utils.filesystem.gen_safe_path(dir_name, tag_name)\n tag_iter = _create_and_add_tag_iter(zip_file, tag_path, tag_str)\n tag_info_list.append(\n {\n \"path\": tag_path,\n \"checksum\": d1_common.checksum.calculate_checksum_on_iterator(\n tag_iter, TAG_CHECKSUM_ALGO\n ),\n }\n )","def convert(self, tag=\"Data\", delimiter=\",\", noheader=False,\n limit=-1, buffer_size=1000):\n\n\n file_ctr = 0\n item_ctr = 0\n for dirName, subdirList, fileList in os.walk(self.input_directory):\n print('Found directory: %s' % dirName)\n for fname in fileList:\n print('\\t%s' % fname)\n # open the xml file for iteration\n if not fname.endswith(\".xml\"):\n continue\n #pdb.set_trace()\n \n input_file = dirName + \"/\" + fname\n self.context = ETree.iterparse(input_file, events=(\"start\", \"end\"))\n\n # iterate through the xml\n items = [{}]\n\n depth = 0\n min_depth = 0\n row_depth = -1\n n = 0\n for event, elem in self.context:\n if event == \"start\":\n depth += 1\n continue\n else:\n depth -= 1\n if depth < min_depth:\n min_depth = depth\n\n if depth < row_depth and items:\n if noheader:\n noheader = False\n else:\n # new line\n self.output_buffer.append(items)\n items = []\n # flush buffer to disk\n if len(self.output_buffer) > buffer_size:\n self._write_buffer(delimiter)\n\n plain_tag = elem.tag\n last_delim = max(elem.tag.rfind('}'), elem.tag.rfind(':'))\n if 0 < last_delim < len(elem.tag) - 1:\n plain_tag = elem.tag[last_delim + 1:]\n if tag == plain_tag:\n if n == 0:\n min_depth = depth\n elif n == 1:\n row_depth = min_depth\n n += 1\n if 0 < limit < n:\n break\n elem_name = elem.get(\"name\")\n if elem_name in self.output_dict[0].keys():\n if elem_name == 'SamS.ArchivedURL':\n if hash(elem.text) in self.item_titles.keys() and self.item_titles[hash(elem.text)] == elem.text:\n #item is repetative\n self.output_dict[item_ctr]={}\n #item_ctr-=1\n break\n else:\n self.item_titles[hash(elem.text)] = elem.text\n self.output_dict[item_ctr][elem_name]= elem.text and elem.text.encode('utf8') or ''\n\n #if (len(self.output_dict[item_ctr]) > 0 ) :\n if ('SamS.ArchivedURL' in self.output_dict[item_ctr]):\n item_ctr+=1\n self.output_dict.append({})\n else:\n self.output_dict[item_ctr] = {}\n \n file_ctr+=1 #next row in the dictionary array\n print \"processing file no \", file_ctr, \" item no\", item_ctr\n\n #pdb.set_trace()\n self._write_buffer(delimiter) # write rest of the buffer to file\n\n return n","def debianize( strFilename ):\n \n #~ data = gzip.GzipFile( strFilename ).read();\n #~ print data;\n #~ return;\n \n #~ data = gzip.open( strFilename ).read();\n #~ print data;\n #~ return; \n \n #~ uncompressedData = bz2.BZ2File(strFilename).read()\n #~ print str(uncompressedData)\n #~ return;\n \n #~ file = open( strFilename, 'rb' );\n #~ data = file.read();\n #~ file.close();\n #~ print debug.dumpHexa( data );\n \n #~ ar = tarfile.open(strFilename, 'r:*')\n #~ for item in ar:\n #~ print( str(item) );\n #~ print( \"%s:\" % item.name );\n #~ #print debug.dumpHexa(item.buf);\n #~ #print zlib.decompress(item.buf)\n #~ #print zlib.decompress(ar.extractfile(item).read())\n #~ data = ar.extractfile(item.name).read()\n #~ print data # works !\n #~ ar.close() \n #~ return;\n \n fileLists = [];\n file = open( strFilename );\n data = file.read();\n file.close();\n \n print( \"data len: %d\" % len( data ) );\n\n nDataCompressedOffset = 0; # 132\n\n # works fine on toto.gz\n #~ f = gzip.open(strFilename, 'rb')\n #~ file_content = f.read()\n #~ print file_content\n #~ f.close() \n \n #~ decompressor = bz2.BZ2Decompressor();\n #~ uncompressed = decompressor.decompress(data[nDataCompressedOffset:]);\n \n #~ uncompressed = zlib.decompress(data[nDataCompressedOffset:]);\n \n uncompressed = decompress( data );\n print( \"uncompressed: %s\" % str( uncompressed ) );","def get_extract(filename: str, importer: str) -> list[Any]:\n entries = g.ledger.ingest.extract(filename, importer)\n return list(map(serialise, entries))","def readzip(zipfile, filename=None):\n with ctxZipReader(zipfile, filename) as zipstream:\n dwg = read(zipstream, dxfversion=zipstream.dxfversion)\n dwg.filename = zipstream.dxf_file_name\n return dwg","def unzip_subtitles(self, zip_filepath):\n with ZipFile(zip_filepath, 'r') as zip_obj:\n filenames = zip_obj.namelist()\n\n subtitle_filenames = [fn for fn in filenames if fn.endswith('.srt')]\n for fn in subtitle_filenames:\n zip_obj.extract(fn, self.temp_storage_dir)\n\n return subtitle_filenames","def read_gdf_from_zip(zip_fp):\r\n with ZipFile(zip_fp) as z:\r\n # Lists all files inside the ZipFile, here assumes that there is only a single file inside\r\n layer = z.namelist()[0]\r\n data = gpd.read_file(io.BytesIO(z.read(layer)))\r\n return data","def concatenate_files(self, files):\n entries = []\n for f in files:\n tree = ETree.parse(f)\n\n root = tree.getroot()\n entries = root.findall(tags[\"entry\"])\n\n for entry in entries:\n yield entry","def process_into_zip(input_root, output_root, file_list):\n output_path = os.path.join(output_root, \"UNF_Backup.zip\")\n new_zip = zipfile.ZipFile(output_path, \"w\")\n for backup_id, backup_file in file_list.items():\n if backup_file.is_dir is not True:\n zinfo = backup_file.get_zipinfo()\n data = get_file_data(backup_file, input_root)\n if data is None:\n logging.warning(f\"Unable to find data: {backup_file.file_id} ({backup_file.relative_path})\")\n continue\n else:\n new_zip.writestr(zinfo, data)\n new_zip.close()","def load_zipped_image(zipfilename):\n\n # Read each image and append in a list\n img = []\n filenames = []\n with ZipFile(zipfilename) as archive:\n for entry in archive.infolist():\n with archive.open(entry) as file:\n tmp = Image.open(file)\n img.append(np.array(tmp))\n filenames.append(file.name)\n\n # Return the read images\n return img, filenames","def _add_payload_files(zip_file, payload_info_list):\n payload_byte_count = 0\n payload_file_count = 0\n for payload_info_dict in payload_info_list:\n zip_file.write_iter(payload_info_dict[\"path\"], payload_info_dict[\"iter\"])\n payload_byte_count += payload_info_dict[\"iter\"].size\n payload_file_count += 1\n return payload_byte_count, payload_file_count","def _parse_filelist(self):\n if not os.path.exists(self.filelist):\n print \"couldn't find \",self.filelist\n return\n\n f = open( self.filelist, 'r' )\n flist = f.readlines()\n self.larlitefilelist = []\n for f in flist:\n if \".root\" in f:\n self.larlitefilelist.append( f.strip() )","def parse(self):\n\t\tfor part in self.mail.walk():\n\t\t\tself.process_part(part)","def parse(path):\n data = gzip.open(path, 'rb')\n for byte_line in data:\n yield eval(byte_line) # return generator instance to save memory","def load_zip_archive(archive_file, \n file_list=None, \n suffix_list=['jpeg', 'jpg', 'png'],\n as_float=False):\n if type(file_list) in [str]:\n file_list = [file_list]\n\n if type(suffix_list) in [str]:\n suffix_list = [suffix_list]\n if suffix_list and type(suffix_list) not in [set]:\n suffix_list = set(suffix_list)\n\n imgs = []\n with ZipFile(archive_file, 'r') as zfa:\n for f_info in zfa.infolist():\n if f_info.is_dir():\n continue\n\n if suffix_list:\n i = f_info.filename.rfind('.')\n suffix = f_info.filename[i+1:].lower() if i >= 0 else ''\n if suffix not in suffix_list:\n continue\n\n if file_list:\n use_f = False\n for fl in file_list:\n if re.match(fl, f_info.filename):\n use_f = True\n break\n if not use_f:\n continue\n\n imgs.append((load_image(zfa.open(f_info)), f_info.filename))\n return imgs","def prepare_zip_file(self):\n # need the following:\n # 1. readme\n # 2. cleaned features file\n # 3. gene map\n # 4. clean response file\n # 5. run.yml\n # 6. combined viz scores files\n # 7. all top_genes_per_phenotype* files\n # 8. network metadata\n zip_path = os.path.join(\\\n self.job_dir_path, 'download.zip')\n with ZipFile(zip_path, 'w', ZIP_DEFLATED) as zipout:\n\n zipout.write(\\\n '/zip_readmes/README-GP.txt', 'README-GP.txt')\n\n cleaned_features_path = os.path.join(\\\n self.userfiles_dir, self.features_file_relative_path)\n zipout.write(\\\n cleaned_features_path, 'clean_genomic_matrix.txt')\n\n gene_names_map_path = os.path.join(\\\n self.userfiles_dir, self.gene_names_map_relative_path)\n zipout.write(\\\n gene_names_map_path, 'gene_map.txt')\n\n cleaned_response_path = os.path.join(\\\n self.userfiles_dir, self.response_file_relative_path)\n zipout.write(\\\n cleaned_response_path, 'clean_phenotypic_matrix.txt')\n\n zipout.write(\\\n self.yml_path, 'run_params.yml')\n\n # combine viz files\n combined_viz_path = os.path.join(self.job_dir_path, \\\n 'combined_viz.tsv')\n with open(combined_viz_path, 'w') as combo:\n for fidx, fname in enumerate(sorted(self.get_response_files())):\n fpath = os.path.join(self.results_dir_path, fname)\n with open(fpath, 'r') as vizfile:\n for lidx, line in enumerate(vizfile):\n if lidx == 0 and fidx > 0:\n # only print the column labels once\n pass\n else:\n combo.write(line)\n zipout.write(combined_viz_path, 'genes_ranked_per_phenotype.txt')\n\n top_genes_files = [f for f in os.listdir(self.results_dir_path) \\\n if f.startswith('top_genes_per_phenotype')]\n if len(top_genes_files) == 1:\n top_genes_file_path = os.path.join(\\\n self.results_dir_path, top_genes_files[0])\n zipout.write(\\\n top_genes_file_path, 'top_genes_per_phenotype_matrix.txt')\n\n if self.gg_network_metadata_full_path is not None:\n zipout.write(self.gg_network_metadata_full_path, \\\n 'interaction_network.metadata')","def test_zip_files(self):\n base_zip_files = ['whypython.txt', 'states.dbf', 'cities.kmz']\n\n text_file = os.path.join(os.getcwd(), 'test-data', 'whypython.txt')\n dbf_file = os.path.join(os.getcwd(), 'test-data', 'states.dbf')\n kml_file = os.path.join(os.getcwd(), 'test-data', 'cities.kmz')\n #non_file = os.path.join(os.getcwd(), 'test-data', 'emptyfolder')\n self.request['params'][0]['response']['docs'][0]['path'] = text_file\n self.request['params'][0]['response']['docs'][1]['path'] = dbf_file\n self.request['params'][0]['response']['docs'][2]['path'] = kml_file\n #self.request['params'][0]['response']['docs'][3]['path'] = non_file\n __import__(self.request['task'])\n getattr(sys.modules[self.request['task']], \"execute\")(self.request)\n zip_files = zipfile.ZipFile(os.path.join(self.temp_folder, 'output.zip')).namelist()\n self.assertEqual(sorted(zip_files), sorted(base_zip_files))","def extract(self, paths=None):\n\n all_files = self._get_package_files()\n if paths is None:\n extracted_files = all_files.values()\n else:\n extracted_files = [all_files[path] for path in paths]\n\n # filter already extracted file\n extracted_files = [pf for pf in extracted_files if not os.path.isfile(self.project.storage.fspath(pf.extract_path))]\n\n # group files by package\n files_by_package = defaultdict(list)\n for pf in extracted_files:\n files_by_package[pf.package].append(pf)\n\n package_files_path = f\"{self.path}/packages/files\"\n\n for package, files in files_by_package.items():\n with self.project.storage.stream(f\"{package_files_path}/{package}\") as reader:\n # sort files by offset to extract while streaming the bin file\n for pkgfile in sorted(files, key=lambda f: f.offset):\n logger.debug(f\"extracting {pkgfile.path}\")\n reader.skip_to(pkgfile.offset)\n fspath = self.project.storage.fspath(pkgfile.extract_path)\n with write_file_or_remove(fspath) as fout:\n if pkgfile.compressed:\n zobj = zlib.decompressobj(zlib.MAX_WBITS | 32)\n def writer(data):\n return fout.write(zobj.decompress(data))\n reader.copy(writer, pkgfile.size)\n fout.write(zobj.flush())\n else:\n reader.copy(fout.write, pkgfile.size)","def extract_bz2(tar_bz_f, calc_type):\n \n # we give the gaussian calculator a label that includes the directory the\n # log file is contained in, this does not affect the parsing process but\n # generate a warning as it is not an expected form for the label. To avoid\n # the profusion of warning messages in stdout we suppress warnings here.\n warnings.filterwarnings(\"ignore\")\n\n extended_xyzs = []\n\n with tarfile.open(tar_bz_f,'r:bz2') as data_tar:\n calc_logs = (log_tar for log_tar in data_tar \n if calc_type in log_tar.name and '.log' in log_tar.name)\n \n for calc_log in calc_logs:\n try:\n # extract log file (and relevant directory)\n data_tar.extract(calc_log)\n\n # convert to ASE/Gaussian format\n mol = read(calc_log.name)\n mol.set_calculator(\n Gaussian(\n label=calc_log.name.replace('.log','')\n )\n )\n\n # parse into ML readable format\n parsed_mol = ase_mol_parse(mol)\n extended_xyzs.append(parsed_mol)\n except AttributeError:\n # if the calculation didn't complete we get an empty dictionary \n # so we we keep track of these failed calculations with a blank \n # entry other than mol_id\n blank_entry = {'mol_id':calc_log.name.replace('.log','')}\n extended_xyzs.append(blank_entry)\n finally:\n # delete extracted log file\n os.remove(calc_log.name)\n\n # solves memory problem\n # http://blogs.it.ox.ac.uk/inapickle/2011/06/20/high-memory-usage-when-using-pythons-tarfile-module/ # noqa\n data_tar.members=[]\n \n dir_name = tar_bz_f.replace('.tar.bz2','')\n\n # delete extracted directory\n os.rmdir(dir_name)\n\n # search key function\n # assumes files are named xxx_frame_{frame}_mol_{no}\n def mol_no_frame(mol):\n mol_no = int(mol['mol_id'].split('_')[-1].replace('.log',''))\n mol_frame = int(mol['mol_id'].split('_')[-3])\n return mol_no,mol_frame\n\n extended_xyzs = sorted(extended_xyzs,key=mol_no_frame)\n\n with open(dir_name + '_' + calc_type + '_data.pkl', 'w') as data_f:\n dill.dump(extended_xyzs, data_f)","def file_zipper(root_dir):\n # FINDING AND ZIPPING UNZIPPED FILES\n for root, dirs, files in os.walk(root_dir, topdown=False):\n if root != \"\":\n if root[-1] != '/': root += '/'\n for current_file in files:\n filepath = \"%s/%s\"%(root, current_file)\n try:\n file_size = os.path.getsize(filepath)\n except Exception as e:\n file_size = 0\n debug.log('Error: file_zipper failed to zip following file '+filepath, e)\n # Excluding small files, gzipped files and links\n if ( file_size > 50\n and current_file[-3:] != \".gz\"\n and not os.path.islink(filepath)\n ):\n if current_file[-4:] == \".zip\":\n # Unzip file\n ec = Popen('unzip -qq \"%s\" -d %s > /dev/null 2>&1'%(filepath, root), shell=True).wait()\n if ec > 0:\n debug.log('Error: fileZipper failed to unzip following file %s'%filepath)\n continue\n else:\n ec = Popen('rm -f \"%s\" > /dev/null 2>&1'%(filepath), shell=True).wait()\n if ec > 0: debug.log('Error: fileZipper failed to delete the original zip file (%s)'%filepath)\n filepath = filepath[:-4]\n # Saving a gzipped version\n with open_(filepath, 'rb') as f, open_(filepath+\".gz\", 'wb', 9) as gz:\n gz.writelines(f)\n # Deleting old (non-zipped) file\n try: os.remove(filepath)\n except OSError as e:\n debug.log((\"WARNING! The file %s could not be \"\n \"removed!\\n%s\")%(current_file, e))","def parse(self, filename):\n infile = file(filename)\n for line in infile:\n self.parseLine(line)","def unzip_data(zip_f,data_folder_path): \n\n with zipfile.ZipFile(zip_f,\"r\") as zip_ref:\n zip_ref.extractall(data_folder_path)","def parse_file(self, domain_filename,\n gzip=False,\n fixed=True, pdf=False, output_path=None, **kargs):\n valid_file_formats = set(['fasta_style', 'dfam'])\n assert format in valid_file_formats, '{0} not in {1} valid_file_formats'.format(format, valid_file_formats)\n\n if output_path:\n if not os.path.exists(output_path):\n os.mkdir(output_path)\n self.output_path = output_path\n\n self.fixed = fixed\n self.pdf = pdf\n\n self.data = []\n\n if format == 'fasta_style':\n self.data = self.__load_fasta_style(filename, gzip)\n elif format == 'dfam':\n self.data = self.__load_dfam_style(filename, gzip)","def tar_file_and_group(data):\n for sample in data:\n assert \"stream\" in sample\n stream = tarfile.open(fileobj=sample[\"stream\"], mode=\"r|*\")\n prev_prefix = None\n example = {}\n valid = True\n for tarinfo in stream:\n name = tarinfo.name\n pos = name.rfind(\".\")\n assert pos > 0\n prefix, postfix = name[:pos], name[pos + 1 :]\n if prev_prefix is not None and prefix != prev_prefix:\n example[\"key\"] = prev_prefix\n if valid:\n yield example\n example = {}\n valid = True\n with stream.extractfile(tarinfo) as file_obj:\n try:\n if postfix == \"txt\":\n example[\"txt\"] = file_obj.read().decode(\"utf8\").strip()\n elif postfix in AUDIO_FORMAT_SETS:\n waveform, sample_rate = torchaudio.load(file_obj)\n example[\"wav\"] = waveform\n example[\"sample_rate\"] = sample_rate\n else:\n example[postfix] = file_obj.read()\n except Exception as ex:\n valid = False\n logging.warning(\"error to parse {}\".format(name))\n prev_prefix = prefix\n if prev_prefix is not None:\n example[\"key\"] = prev_prefix\n yield example\n stream.close()\n if \"process\" in sample:\n sample[\"process\"].communicate()\n sample[\"stream\"].close()","def main():\r\n\r\n #Create a list of all files that have the GPX file format\r\n fileList = glob.glob(os.path.join(inFolder,\"*.{0}\".format(inFormat)))\r\n\r\n #Create a connection to PostGIS database\r\n pgConn = createPostgisConnection(dbFormat, dbHost, dbName, dbSchema, dbUser, dbPWD)\r\n\r\n #Process each *listed* layer type from a GPS file\r\n for f in fileList:\r\n importGPX(f, gpxImportLayers, pgConn)","def main():\n processSetOfCerFiles(sys.argv[1:])","def test_pick_files(mock_zip_file):\n\n files = ['Unihan_Readings.txt', 'Unihan_Variants.txt']\n\n options = {'input_files': files, 'zip_path': str(mock_zip_file)}\n\n b = process.Packager(options)\n\n result = b.options['input_files']\n expected = files\n\n assert result == expected, 'Returns only the files picked.'","def parse_facs_files():\n\n #Load parser settings\n parser_settings = getattr(settings,'FACS_PARSER_SETTINGS')\n\n files_to_parse = [parser_settings['facs_source_directory']+f for f in os.listdir(parser_settings['facs_source_directory']) if '.exp' in f]\n\n for filename in files_to_parse: \n\n #Compute MD5 hash\n facs_file = file(filename,'rbU')\n md5hash = hashlib.md5(facs_file.read()).hexdigest()\n facs_file.close()\n \n #Skip file if previously parsed.\n if FacsFile.objects.filter(original_filename=filename,md5hash=md5hash):\n print 'Skipping ', filename\n continue\n\n #Open file, remove null bytes and prepare csv reader\n facs_file = file(filename, 'rU')\n csv_reader = csv.reader((x.replace('\\0', '') for x in facs_file),dialect=csv.excel_tab)\n\n #Reader header\n csv_header = csv_reader.next()\n facs_file_results = []\n\n #Parse the file\n for csv_row in csv_reader:\n if csv_row[0]:\n facs_file_results.append(dict(zip(csv_header,csv_row)))\n\n #Close the file\n facs_file.close()\n\n #Save the information to database and archive file\n random_ints = ''.join([str(random.randint(0,9)) for n in range(10)])\n archive_filename = parser_settings['facs_archive_directory'] + filename.split('/')[-1][:-4].split('_')[0] + '_' + random_ints + '.exp'\n shutil.move(filename, archive_filename)\n\n facs_file = FacsFile(\n original_filename = filename,\n md5hash = md5hash,\n archive_filename = archive_filename,\n )\n facs_file.save()\n\n #Remove empty elements\n for result in facs_file_results:\n for key, data in result.items():\n if data == '.' or not(data):\n del result[key]\n\n #Cache test code and interface mappings\n test_codes = []\n for testcode_mapping in TestCodeMapping.objects.filter(interface_name=parser_settings['testcode_interface_name']):\n test_code = testcode_mapping.code\n code = test_code.code\n code_mapping = testcode_mapping.code_mapping\n\n test_codes.append((code, code_mapping, test_code))\n\n #Add results to database\n for result in facs_file_results:\n\n #Parse result date\n result_date = dateutil.parser.parse(result[parser_settings['result_datetime']])\n result_error_code = getattr(result, parser_settings['error_codes'], '')\n result_identifier = result[parser_settings['sample_identifier']]\n result_cytometer = result[parser_settings['cytometer_serial']]\n\n #Create the dictionnary of result items.\n new_result_item_dict = {}\n for test_code, facs_file_column, test_code_object in test_codes:\n new_result_item_dict[test_code] = ResultItem(\n test_code = test_code_object,\n result_item_value = result[facs_file_column],\n error_code = result_error_code,\n result_item_datetime = result_date,\n )\n\n #Search for possible duplicate result\n is_duplicate = False\n for possible_duplicate in FacsResult.objects.filter(result_identifier=result_identifier):\n if possible_duplicate.get_resultitem_dict() == new_result_item_dict:\n is_duplicate = True\n break\n\n #Save result and result item to data if it is not a duplicate\n if not is_duplicate:\n \n new_result = FacsResult(\n result_identifier=result_identifier,\n result_datetime=result_date,\n origin_facs_file=facs_file,\n cytometer_serial_number=result_cytometer,\n )\n \n new_result.save()\n \n #Add the reference to the result for each item and save it to database.\n for item in new_result_item_dict.values():\n item.result = new_result\n item.save()\n\n new_result.link_to_requisition()","def get_filenames(zip_file: str) -> List:\n file_names = []\n with ZipFile(zip_file, 'r') as zipObj:\n listOfiles = zipObj.namelist()\n for elem in listOfiles:\n if \"wav\" in elem:\n file_names.append(elem)\n return file_names","def processSetOfCerFiles(files):\n printHeader()\n \n k = 0\n for f in files:\n k = k + 1\n sz = get_file_size(f)\n with open(f, 'rb') as fb:\n processCerFile(k, fb, sz=sz)","def test_find_many_files_zipped_allow(self):\n\n these_file_names = satellite_io.find_many_files(\n top_directory_name=TOP_DIRECTORY_NAME,\n first_date_string=FIRST_DATE_STRING,\n last_date_string=LAST_DATE_STRING,\n prefer_zipped=True, allow_other_format=True, test_mode=True\n )\n\n self.assertTrue(these_file_names == FILE_NAMES_UNZIPPED)","def process_files(compress, files):\n [compress.add_file(file) for file in files]\n\n compress.execute() # upload files to iLovePDF\n compress.download() # download resultant file\n print(\"Compression saved {}% of disk space.\".format(\n PDFWorkshop.__percentage_storage_saved(compress))\n )\n compress.delete_current_task()","def read_files(filenames, gram_size=1):\n assert isinstance(filenames, list), \"filenames argument must be a list\"\n parser = MorParser()\n for fn in filenames:\n for uid, speaker, ngram in generate_chunks(parser.parse(fn), gram_size):\n yield fn, uid, speaker, ngram","def extract_data(archive: ZipFile, dir_name: str) -> Data:\n with archive.open(f\"{dir_name}/caption.txt\", \"r\") as f:\n captions = f.readlines()\n data = []\n for line in captions:\n tmp = line.decode().strip().split()\n img_name = tmp[0]\n formula = tmp[1:]\n with archive.open(f\"{dir_name}/{img_name}.bmp\", \"r\") as f:\n # move image to memory immediately, avoid lazy loading, which will lead to None pointer error in loading\n img = Image.open(f).copy()\n data.append((img_name, img, formula))\n\n print(f\"Extract data from: {dir_name}, with data size: {len(data)}\")\n\n return data","def gzip_files(topDir, afni_file,localizerfile):\n\n print 'GZIPPING FILES...'\n\n command1 = \"gzip %s*BRIK\" % (topDir)\n command2 = \"gzip %s*HEAD\" % (topDir)\n command3 = \"gzip %s%s/pb00*\" % (topDir,afni_file)\n command4 = \"gzip %s%s/errts*\" % (topDir,afni_file)\n command5 = \"gzip %s%s/fitts*\" % (topDir,afni_file)\n command6 = \"gzip %s%s/*al*\" % (topDir,afni_file)\n command7 = \"gzip %s%s/*ns*\" % (topDir,afni_file)\n command8 = \"gzip %s%s/all_runs*\" % (topDir,afni_file)\n command9 = \"gzip %s%s/*mask*\" % (topDir,afni_file)\n command10 = \"gzip %s*nii\" % (topDir)\n command11 = \"gzip %s%s/pb01*\" % (topDir,afni_file)\n command12 = \"gzip %s%s/pb03*\" % (topDir,afni_file)\n command13 = \"gzip %s%s/pb02*\" % (topDir,afni_file)\n\n os.system(command1)\n os.system(command2)\n os.system(command3)\n os.system(command4)\n os.system(command5)\n os.system(command6)\n os.system(command7)\n os.system(command8)\n #os.system(command9)\n os.system(command10)\n os.system(command11)\n try:\n os.system(command12)\n except:\n print 'Could not gzip pb03 files'\n\n if localizerfile == 'facescene_loc':\n os.system(command13)","def parse(self, f):\n \n for line in f:\n self.parse_line(line)","def parse_directory(input_dir, start_date = datetime(1970,1,1), end_date = datetime(9999,12,31,23,59,59)):\n logging.debug(\"Beginning parse_directory {}\".format(input_dir))\n\n def parse_gzipped_directory(input_dir, start_date, end_date, infos, backup_stamps):\n \"\"\" Scans a gzipped directory. This one in different situation \"\"\"\n try:\n file_names = sorted(os.listdir(input_dir)) \n for file_name in file_names:\n if file_name.endswith(\".manifest.gz\") or file_name.endswith(\".manifest\"):\n tmp = parse_file(input_dir + \"/\" + file_name, start_date, end_date, backup_stamps)\n backup_stamps[tmp[\"backup_label\"]] = tmp[\"backup_timestamp_stop_ts\"]\n if tmp:\n infos.append(tmp)\n except OSError as e:\n logging.error(\"Failed to open directory\", exc_info=True)\n exit(1)\n except:\n raise\n \n if not path.isdir(input_dir):\n logging.error(\"The specified path is not a directory\")\n exit(1)\n\n infos = []\n backup_stamps = {}\n if path.exists(input_dir + \"/backup.info\"):\n\n dir_names = sorted(os.listdir(input_dir + \"/backup.history\"))\n for dir_name in dir_names:\n parse_gzipped_directory(input_dir + \"/backup.history/\" + dir_name, start_date, end_date, infos, backup_stamps)\n\n else:\n parse_gzipped_directory(input_dir, start_date, end_date, infos, backup_stamps)\n \n logging.debug(\"End parse_directory\")\n return infos","def unzip_data():\n zip_ref = zipfile.ZipFile(data_zip, 'r')\n zip_ref.extractall('')\n zip_ref.close()","def open_files(filenames):\n for filename in filenames:\n if filename.endswith('.gz') or filename.endswith('.zip'):\n yield gzip.open(filename, 'r')\n else:\n yield open(filename, 'rb')","def parse(self, *args, **kwargs):\n if self.is_gzipped:\n fin = gzip.open(self.path, 'rb')\n else:\n fin = open(self.path, 'r')\n line_num = 0\n expect_header = True\n for line in fin:\n line_num += 1\n line = line.strip()\n if not line: # skip empty lines\n continue\n if expect_header:\n if self._is_header(line):\n logger.debug(\n f\"Detected header at line {line_num}: {line!r}\")\n continue\n else:\n expect_header = False\n try:\n chrom, pos = self._parse_line(line, *args, **kwargs)\n if chrom is not None:\n yield chrom, pos\n except (IndexError, ValueError, TypeError):\n fin.close()\n raise FileFormatError(format=self.format, line_num=line_num,\n line=line)\n fin.close()","def Extract_zip_file (path_to_zip,dir_to_save_into):\n with zipfile.ZipFile(path_to_zip) as zf:\n \n for member in tqdm(zf.namelist(), desc='Extracting'):\n try:\n if ('annotations' in member) and (member.endswith('.json')): \n zf.extract(member, dir_to_save_into)\n shutil.move(os.path.join(dir_to_save_into,member),dir_to_save_into)\n if ('train' in member):\n zf.extract(member, dir_to_save_into)\n if ('test' in member):\n zf.extract(member, dir_to_save_into)\n if ('val' in member):\n zf.extract(member, dir_to_save_into)\n except zipfile.error as e:\n pass\n\n #delete zip\n os.remove(path_to_zip)\n if(os.path.isdir(os.path.join(dir_to_save_into,'annotations'))):\n # remove the tmp annotations directory\n shutil.rmtree(os.path.join(dir_to_save_into,'annotations'))","def extract_and_tag_test():\n test_untagged_path = os.getcwd() + \"/data/test/test_untagged/\"\n test_untagged_directory = os.fsencode(test_untagged_path)\n\n print(\"Tagging text. Please wait...\")\n for file in os.listdir(test_untagged_directory):\n filename = os.fsdecode(file)\n try:\n if filename.endswith(\".txt\"):\n text = entity_process.read_data(test_untagged_path, file)\n text = text.lower()\n header,body = entity_process.split_text(text)\n header_array = header.splitlines()\n\n\n start_time, end_time = entity_process.extract_time(header)\n location = entity_process.extract_location(header_array, body)\n speaker = entity_process.extract_speaker(header_array, body)\n\n entity_tagger.tag_all(filename, text, start_time, end_time, location, speaker)\n except Exception as e:\n raise e\n return \"No files found here!\"\n print(\"Tagging complete! Text saved to\" + os.getcwd() + \"/out\")","def _unpack_archive(self):\n with zipfile.ZipFile(self._archive_full_path, 'r') as zip_ref:\n zip_ref.extractall(self._storage_path)\n\n _logger.debug('Archive has been unpacked.')","def _bam_extract_impl(config: BamExtractConfig, sites: typing.List[vcf.Site]) -> None:\n for path in config.input_files:\n _bam_extract_impl_for_file(config, sites, path)","def process_file(self, filename, order=2):\n fp = open(filename)\n self.skip_gutenberg_header(fp)\n\n for line in fp:\n for word in line.rstrip().split():\n self.process_word(word, order)\n\n #print(\">>>DEBUG the suffix map\")\n #i = 0\n #for k,v in self.suffix_map.items():\n # print(\"key is {}, value is {}\".format(k, v))\n # i += 1\n # if i > 10:\n # break","def extract(self):\n self.build_path_pairs()\n self.extract_field_blocks()\n self.assert_filenames()","def unzip_nested_zip(dataset_zip, path_unzip):\r\n\r\n with zipfile.ZipFile(dataset_zip, \"r\") as zfile:\r\n try:\r\n zfile.extractall(path=path_unzip)\r\n except OSError as e:\r\n logging.warning(\r\n \"Please check the unzipped files manually. There may be some missed important files.\"\r\n )\r\n logging.warning(\"The directory is: \" + path_unzip)\r\n for root, dirs, files in os.walk(path_unzip):\r\n for filename in files:\r\n if re.search(r\"\\.zip$\", filename):\r\n file_spec = os.path.join(root, filename)\r\n new_dir = os.path.join(root, filename[0:-4])\r\n unzip_nested_zip(file_spec, new_dir)","def test_open_each(self):\n zip_paths = zip_scanner(os.getcwd())\n for zip_path in zip_paths:\n with ZipEditor(zip_path) as zed:\n self.assertEqual(zip_path, zed.file)\n zed.open()\n self.assertIsNotNone(zed.tmpdir.name)\n self.assertEqual(zed.tmpdir.name, zed.getdir())\n self.assertIsNone(zed.getdir())","def decompress_files(self):\n crx2rnx_path = os.path.join(ROOT_DIR, 'CRX2RNX')\n if not os.path.isfile(crx2rnx_path):\n raise OSError('Cannot find CRX2RNX binary in project directory!')\n\n if glob('{}/*'.format(self.__directory)):\n subprocess.run([\"gunzip\", \"-dr\", self.__directory])\n # convert Hatanaka compressed RINEX to standard RINEX\n for f in glob('{}/*.??d'.format(self.__directory)):\n subprocess.run([crx2rnx_path, f])\n else:\n raise RuntimeError(\n 'Could not decompress. No files were downloaded from FTP server.')","def bags(fondz_dir):\n fondz_dir = os.path.abspath(fondz_dir)\n results = {\n 'bags': [],\n 'num_files': 0,\n 'bytes': 0\n }\n originals_dir = os.path.join(fondz_dir, \"originals\")\n\n for bag in os.listdir(originals_dir):\n # TODO: look for other manifest types?\n bag_dir = os.path.join(originals_dir, bag)\n manifest = os.path.join(bag_dir, \"manifest-md5.txt\")\n b = {\n \"files\": [],\n \"bytes\": 0,\n }\n for line in open(manifest):\n line = line.strip()\n cols = re.split(r' +', line)\n path = os.path.join(bag_dir, cols[1])\n st = os.stat(path)\n rel_path = os.path.join(\"originals\", bag, path)\n b['bytes'] += st.st_size\n b['files'].append({\n \"path\": rel_path,\n \"bytes\": st.st_size,\n \"created\": st.st_ctime,\n \"modified\": st.st_mtime,\n \"md5\": cols[0]\n })\n results['bytes'] += b['bytes']\n results['num_files'] += len(b['files'])\n results['bags'].append(b)\n\n bags_json = os.path.join(fondz_dir, \"js\", \"bags.json\")\n write_json(results, bags_json)\n return results","def _extract_all_gz_in_dir(directory):\n for file in os.listdir(directory):\n if file.endswith(\".gz\"):\n gz_fname = os.path.join(directory, file)\n _extract_gz(gz_fname, os.path.dirname(gz_fname))\n os.remove(gz_fname)","def parse_input():\n with open(\"input_07.txt\", \"r\") as f:\n for line in f:\n Bag(line)","def create_chunks(file_names):\n\n\tnew_chunks = []\n\n\tfor name in file_names:\n\n\t\t# Find the .inf file and read the details stored within\n\t\ttry:\n\t\t\tdetails = open(name + suffix + 'inf', 'r').readline()\n\t\texcept IOError:\n\n\t\t\ttry:\n\t\t\t\tdetails = open(name + suffix + 'INF', 'r').readline()\n\t\t\texcept IOError:\n\t\t\t\tprint(\"Couldn't open information file, %s\" % name+suffix+'inf')\n\t\t\t\tsys.exit()\n\n\t\t# Parse the details\n\t\tdetails = [string.rstrip(details)]\n\n\t\tsplitters = [' ', '\\011']\n\n\t\t# Split the details up where certain whitespace characters occur\n\t\tfor s in splitters:\n\n\t\t\tnew_details = []\n\n\t\t\t# Split up each substring (list entry)\n\t\t\tfor d in details:\n\n\t\t\t\tnew_details = new_details + string.split(d, s)\n\n\t\t\tdetails = new_details\n\n\t\t# We should have details about the load and execution addresses\n\n\t\t# Open the file\n\t\ttry:\n\t\t\tin_file = open(name, 'rb')\n\t\texcept IOError:\n\t\t\tprint(\"Couldn't open file, %s\" % name)\n\t\t\tsys.exit()\n\n\t\t# Find the length of the file (don't rely on the .inf file)\n\t\tin_file.seek(0, 2)\n\t\tlength = in_file.tell()\n\t\tin_file.seek(0, 0)\n\n\t\t# Examine the name entry and take the load and execution addresses\n\t\tdot_at = string.find(details[0], '.')\n\t\tif dot_at != -1:\n\t\t\treal_name = details[0][dot_at+1:]\n\t\t\tload, exe = details[1], details[2]\n\t\telse:\n\t\t\treal_name = get_leafname(name)\n\t\t\tload, exe = details[0], details[1]\n\n\t\tload = hex2num(load)\n\t\texe = hex2num(exe)\n\n\t\tif load == None or exe == None:\n\t\t\tprint('Problem with %s: information is possibly incorrect.' % name+suffix+'inf')\n\t\t\tsys.exit()\n\n\t\t# Reset the block number to zero\n\t\tblock_number = 0\n\n\t\t# Long gap\n\t\tgap = 1\n\t\n\t\t# Write block details\n\t\twhile True:\n\t\t\tblock, last = write_block(in_file, real_name, load, exe, length, block_number)\n\n\t\t\tif gap == 1:\n\t\t\t\tnew_chunks.append((0x110, number(2,0x05dc)))\n\t\t\t\tgap = 0\n\t\t\telse:\n\t\t\t\tnew_chunks.append((0x110, number(2,0x0258)))\n\n\t\t\t# Write the block to the list of new chunks\n\n\t\t\t# For old versions, just write the block\n\t\t\tif UEF_major == 0 and UEF_minor < 9:\n\t\t\t\tnew_chunks.append((0x100, block))\n\t\t\telse:\n\t\t\t\tnew_chunks.append((0x100, block))\n\n\t\t\tif last == 1:\n\t\t\t\tbreak\n\n\t\t\t# Increment the block number\n\t\t\tblock_number = block_number + 1\n\n\t\t# Close the input file\n\t\tin_file.close()\n\n\t# Write some finishing bytes to the list of new chunks\n#\tnew_chunks.append((0x110, number(2,0x0258)))\n#\tnew_chunks.append((0x112, number(2,0x0258)))\n\n\t# Return the list of new chunks\n\treturn new_chunks","def unpack(file, path='.'):\n assert isfile(file)\n assert isdir(path)\n\n for implementor in [GzipTarredFile, ZippedFile, Bzip2TarredFile]:\n if implementor.is_valid(file):\n with console.cd(path):\n return [implementor(file).extract(), implementor]\n else:\n raise InvalidFile, 'compressed file format unknown: %s' % file","def file_package_iter(self):\n files = list()\n futures = list()\n\n amount = 0\n for file in self.file_iterator:\n if amount + self._estimate_file_size(file) > self.max_size:\n if len(files) == 0: # This file is too large for one archive, special handling\n self.pool.wait(futures)\n self._calculate_hash(file)\n yield self._finish_info_package([file])\n continue\n\n self.pool.wait(futures)\n yield self._finish_info_package(files)\n\n files = list()\n amount = 0\n\n amount += file.size\n files.append(file)\n futures.append(self.pool.add_task(self._calculate_hash, file)) # todo calc small files in-thread?\n\n if len(files) > 0:\n yield self._finish_info_package(files)","def process(self, zip_processor):\n for filename in os.listdir(zip_processor.temp_dir):\n with open(zip_processor._full_filename(filename)) as file:\n contents = file.read()\n contents = contents.replace(self.search_string, self.replace_string)\n with open(zip_processor._full_filename(filename), \"w\") as file:\n file.write(contents)","def retrieveGEOFiles(geonum, directory):\n samplelist = []\n\n ##download data https://geoparse.readthedocs.io/en/latest/GEOparse.html\n print(\"###############STARTING DOWNLOAD################ \\n\\n\\n\")\n print(geonum + '\\n\\n')\n gse = GEOparse.get_GEO(geo=geonum, destdir=directory)\n\n for gsm_name, gsm in gse.gsms.items():\n\n samplelist.append(gsm_name)\n\n filename = directory + \"/\" + gsm_name + \".txt\"\n o = open(filename, \"w\")\n o.write(\"Name: \" + gsm_name)\n o.write(\"\\nMetadata:\")\n for key, value in gsm.metadata.items():\n o.write(\"\\n - %s : %s\" % (key, \", \".join(value)))\n if key == 'supplementary_file':\n for item in value:\n wget.download(item, directory)\n o.close()\n\n for gpl_name, gpl in gse.gpls.items():\n filename = directory + \"/\" + gpl_name + \".platform\"\n o = open(filename, \"w\")\n o.write(\"Name: \" + gpl_name)\n o.write(\"\\nMetadata:\")\n for key, value in gpl.metadata.items():\n o.write(\"\\n - %s : %s\" % (key, \", \".join(value)))\n o.close()\n\n print(\" ################### FINISHED DOWNLOAD ###################### \\n\\n\")\n\n return samplelist"],"string":"[\n \"def _add_tag_files(\\n zip_file, dir_name, payload_info_list, payload_byte_count, payload_file_count\\n):\\n tag_info_list = []\\n _add_tag_file(zip_file, dir_name, tag_info_list, _gen_bagit_text_file_tup())\\n _add_tag_file(\\n zip_file,\\n dir_name,\\n tag_info_list,\\n _gen_bag_info_file_tup(payload_byte_count, payload_file_count),\\n )\\n _add_tag_file(\\n zip_file, dir_name, tag_info_list, _gen_pid_mapping_file_tup(payload_info_list)\\n )\\n return tag_info_list\",\n \"def load_zip_files(zip_path):\\n zd = zipfile.ZipFile(zip_path)\\n paths = sorted(zd.filelist, key=lambda x: x.date_time)\\n for path in paths:\\n with zd.open(path, 'r') as fd:\\n try:\\n data = json.load(fd)\\n yield File.Ok(fd.name, data)\\n except (json.JSONDecodeError, UnicodeDecodeError) as exc:\\n fd.seek(0)\\n yield File.Err(fd.name, fd.read(), str(exc))\",\n \"def parse_gzipped_directory(input_dir, start_date, end_date, infos, backup_stamps):\\n try:\\n file_names = sorted(os.listdir(input_dir)) \\n for file_name in file_names:\\n if file_name.endswith(\\\".manifest.gz\\\") or file_name.endswith(\\\".manifest\\\"):\\n tmp = parse_file(input_dir + \\\"/\\\" + file_name, start_date, end_date, backup_stamps)\\n backup_stamps[tmp[\\\"backup_label\\\"]] = tmp[\\\"backup_timestamp_stop_ts\\\"]\\n if tmp:\\n infos.append(tmp)\\n except OSError as e:\\n logging.error(\\\"Failed to open directory\\\", exc_info=True)\\n exit(1)\\n except:\\n raise\",\n \"def parse_file(file_name: str, delims='\\\\n', encoding='utf-8', zip_type=None):\\n try:\\n decoder = codecs.getincrementaldecoder(encoding)()\\n except LookupError as e:\\n print(str(e))\\n return\\n\\n read_buffer_size = 10*1024\\n max_line_size = 100*1024\\n\\n if not zip_type:\\n open_f = open\\n elif zip_type == 'gz':\\n open_f = gzip.open\\n else:\\n raise NotImplementedError()\\n\\n with open_f(file_name, 'rb') as fp:\\n buffered_str = ''\\n for bs in iter(partial(fp.read, read_buffer_size), b''):\\n decoded_str = decoder.decode(bs)\\n # FIXME: i don't think current implementation is efficient enough...\\n for c in decoded_str:\\n if c in delims:\\n if len(buffered_str) > 0:\\n yield buffered_str\\n buffered_str = ''\\n else:\\n buffered_str += c\\n if len(buffered_str) >= max_line_size:\\n yield buffered_str\\n buffered_str = ''\\n if len(buffered_str) > 0:\\n yield buffered_str\",\n \"def add_zip(self, zipfile, valid_extensions=('txt', 'csv', 'xls', 'xlsx'), encoding='utf8',\\n doc_label_fmt_txt='{path}-{basename}', doc_label_path_join='_', doc_label_fmt_tabular='{basename}-{id}',\\n force_unix_linebreaks=True, **kwargs):\\n\\n tmpdir = mkdtemp()\\n\\n read_size = kwargs.pop('read_size', -1)\\n\\n with ZipFile(zipfile) as zipobj:\\n for member in zipobj.namelist():\\n path_parts = path_recursive_split(member)\\n\\n if not path_parts:\\n continue\\n\\n dirs, fname = path_parts[:-1], path_parts[-1]\\n\\n basename, ext = os.path.splitext(fname)\\n basename = basename.strip()\\n\\n if ext:\\n ext = ext[1:]\\n\\n if ext in valid_extensions:\\n tmpfile = zipobj.extract(member, tmpdir)\\n\\n if ext in {'csv', 'xls', 'xlsx'}:\\n self.add_tabular(tmpfile, encoding=encoding, doc_label_fmt=doc_label_fmt_tabular,\\n force_unix_linebreaks=force_unix_linebreaks, **kwargs)\\n else:\\n doclabel = doc_label_fmt_txt.format(path=doc_label_path_join.join(dirs),\\n basename=basename,\\n ext=ext)\\n\\n if doclabel.startswith('-'):\\n doclabel = doclabel[1:]\\n\\n self.add_files(tmpfile, doc_labels=[doclabel], encoding=encoding, read_size=read_size,\\n force_unix_linebreaks=force_unix_linebreaks)\\n\\n return self\",\n \"def fromZip(self, zip_location,extract_location):\\n zip_file = zipfile.ZipFile(zip_location,'r')\\n zip_file.extractall(extract_location)\",\n \"def _extract_zip(self, zipfile):\\n zf = ZipFile(zipfile)\\n d = {}\\n for n in zf.namelist():\\n d[n] = zf.read(n)\\n return d\",\n \"def unpack_HCP_zips(zipsfolder, LR_path, RL_path):\\n listing = os.listdir(zipsfolder)\\n for files in listing:\\n if files.endswith('_3T_tfMRI_EMOTION_preproc.zip'):\\n with open(zipsfolder + files, 'rb') as fileobj:\\n with zipfile.ZipFile(fileobj) as z:\\n subject = z.filename[len(zipsfolder):int(len(zipsfolder) + 6)]\\n for zip_info in z.infolist():\\n if zip_info.filename[-22:].endswith('fMRI_EMOTION_LR.nii.gz'):\\n zip_info.filename = subject + '_' + os.path.basename(zip_info.filename)\\n z.extract(zip_info, path=LR_path)\\n print(f'Subject {subject} LR.nii.gz data extracted...')\\n if zip_info.filename[-22:].endswith('fMRI_EMOTION_RL.nii.gz'):\\n zip_info.filename = subject + '_' + os.path.basename(zip_info.filename)\\n z.extract(zip_info, path=RL_path)\\n print(f'Subject {subject} RL.nii.gz data extracted...')\\n fileobj.close()\",\n \"def load_zip_codes():\\n logger.info('Loading zip code data')\\n read_zips()\",\n \"def extractall(self, *args, **kwargs):\\n self.zipfile.extractall(*args, **kwargs)\",\n \"def unzip_citibike_data(zip_dir):\\n# zip_dir = \\\"data/citibike-tripdata-nyc/\\\"\\n# csv_dir = \\\"data/citibike-tripdata-nyc/csv\\\"\\n extension = \\\".zip\\\"\\n\\n # for each zip file in zip_dir extract data\\n for item in os.listdir(zip_dir):\\n if item.endswith(extension):\\n\\n # create zipfile object and extract\\n file_name = zip_dir + item\\n with zipfile.ZipFile(file_name, \\\"r\\\") as zip_ref:\\n zip_ref.extractall(zip_dir)\\n print(item + \\\" done\\\")\",\n \"def _add_manifest_files(zip_file, dir_name, payload_info_list, tag_info_list):\\n for checksum_algorithm in _get_checksum_algorithm_set(payload_info_list):\\n _add_tag_file(\\n zip_file,\\n dir_name,\\n tag_info_list,\\n _gen_manifest_file_tup(payload_info_list, checksum_algorithm),\\n )\",\n \"def extractZipFiles(rootDir, zipDir):\\n for root, dirs, files in os.walk(zipDir, topdown=False):\\n for name in files:\\n \\n zipFiles = os.path.join(root, name)\\n \\n #Check file extension here\\n if \\\".zip\\\" not in zipFiles:\\n continue\\n \\n else:\\n zipPath = zipfile.ZipFile(zipFiles, 'r')\\n #print(zipPath) \\n \\n filesInZip = zipPath.namelist()\\n i = 0 \\n for i in range(len(filesInZip)):\\n #print(filesInZip[i])\\n #print(zipPath.getinfo(filesInZip[i]))\\n \\n if \\\".mp3\\\" in filesInZip[i]:\\n zipPath.extract(filesInZip[i], rootDir)\\n print(\\\"{0} extracted to {1}\\\".format(filesInZip[i], rootDir))\\n\\n elif \\\".m4a\\\" in filesInZip[i]:\\n zipPath.extract(filesInZip[i], rootDir)\\n print(\\\"{0} extracted to {1}\\\".format(filesInZip[i], rootDir))\\n\\n elif \\\".mp4\\\" in filesInZip[i]:\\n zipPath.extract(filesInZip[i], rootDir)\\n print(\\\"{0} extracted to {1}\\\".format(filesInZip[i], rootDir))\\n\\n elif \\\".png\\\" in filesInZip[i]:\\n zipPath.extract(filesInZip[i], rootDir)\\n print(\\\"{0} extracted to {1}\\\".format(filesInZip[i], rootDir))\\n\\n elif \\\".jpg\\\" in filesInZip[i]:\\n zipPath.extract(filesInZip[i], rootDir)\\n print(\\\"{0} extracted to {1}\\\".format(filesInZip[i], rootDir))\\n \\n elif \\\".pdf\\\" in filesInZip[i]:\\n zipPath.extract(filesInZip[i], rootDir)\\n print(\\\"{0} extracted to {1}\\\".format(filesInZip[i], rootDir))\\n\\n else:\\n print(\\\"No media found in zip file {0}\\\".format(name))\\n \\n zipPath.close()\",\n \"def zipstreams(filename):\\r\\n with open(filename, 'rb') as fh:\\r\\n data = fh.read()\\r\\n i = 0\\r\\n while i < len(data):\\r\\n try:\\r\\n zo = zlib.decompressobj()\\r\\n yield i, zo.decompress(data[i:])\\r\\n i += len(data[i:]) - len(zo.unused_data)\\r\\n except zlib.error:\\r\\n i += 1\",\n \"def gen_stats_zip(filename_list, zipfilename, tier='tier2', csv_processor='ICOS-ETC', zip_processor='LBL_AMP', ts_format=\\\"%Y-%m-%d %H:%M:%S\\\"):\\n log.info(\\\"Generating ZIP and stats for: {z}\\\".format(z=zipfilename))\\n\\n if not filename_list:\\n return [], []\\n\\n today = datetime.now().strftime(ts_format)\\n output_zip = zip_file_list(filename_list=filename_list, zipfilename=zipfilename)\\n\\n if output_zip != zipfilename:\\n raise ONEFluxError(\\\"ZIP filenames differ: {i} {o}\\\".format(i=zipfilename, o=output_zip))\\n\\n size, md5sum, _ = file_stat(filename=zipfilename)\\n zip_entry = [['\\\"{e}\\\"'.format(e=os.path.basename(zipfilename)),\\n '{e}'.format(e=format(size)),\\n '\\\"{e}\\\"'.format(e=md5sum),\\n '\\\"{e}\\\"'.format(e=len(filename_list)),\\n '\\\"{e}\\\"'.format(e=tier),\\n '\\\"{e}\\\"'.format(e=zip_processor),\\n '\\\"{e}\\\"'.format(e=today)], ]\\n csv_entries = []\\n for filename in filename_list:\\n f_size, f_md5sum, f_timestamp_change = file_stat(filename=filename)\\n f_today = f_timestamp_change.strftime(ts_format)\\n entry = ['\\\"{e}\\\"'.format(e=os.path.basename(zipfilename)),\\n '\\\"{e}\\\"'.format(e=os.path.basename(filename)),\\n '{e}'.format(e=f_size),\\n '\\\"{e}\\\"'.format(e=f_md5sum),\\n '\\\"{e}\\\"'.format(e=csv_processor),\\n '\\\"{e}\\\"'.format(e=f_today)]\\n csv_entries.append(entry)\\n\\n return zip_entry, csv_entries\",\n \"def quickScanZip(args, fh):\\n # 100 bytes is the smallest .zip possible\\n\\n fh.seek(0, 2)\\n fsize = fh.tell()\\n if fsize==0:\\n print(\\\"Empty file\\\")\\n return\\n if fsize<100:\\n print(\\\"Zip too small: %d bytes, minimum zip is 100 bytes\\\" % fsize)\\n return\\n fh.seek(-100, 2)\\n\\n eoddata = fh.read()\\n iEND = eoddata.find(b'PK\\\\x05\\\\x06')\\n if iEND==-1:\\n # try with larger chunk\\n ofs = max(fh.tell()-0x10100, 0)\\n fh.seek(ofs, 0)\\n eoddata = fh.read()\\n iEND = eoddata.find(b'PK\\\\x05\\\\x06')\\n if iEND==-1:\\n print(\\\"expected PK0506 - probably not a PKZIP file\\\")\\n return\\n else:\\n ofs = fh.tell()-0x100\\n eod = EndOfCentralDir(ofs, eoddata, iEND+4)\\n yield eod\\n\\n dirofs = eod.dirOffset\\n for _ in range(eod.thisEntries):\\n fh.seek(dirofs)\\n dirdata = fh.read(46)\\n if dirdata[:4] != b'PK\\\\x01\\\\x02':\\n print(\\\"expected PK0102\\\")\\n return\\n dirent = CentralDirEntry(dirofs, dirdata, 4)\\n\\n yield dirent\\n dirofs = dirent.endOffset\",\n \"def parse_region_data(self, region):\\n\\n #downloads newest data\\n self.download_data()\\n\\n TmpList = [[] for i in range(65)]\\n\\n #goes through all the files and saves their data to the variable\\n for zipName in self.ListOfZipFiles:\\n with zipfile.ZipFile(\\\"./\\\"+self.folder+\\\"/\\\"+zipName, 'r') as zf:\\n if self.getCsvFileByRegion(region) == None:\\n print(\\\"ERROR: neznamy nazev kraje: \\\" + region, file=sys.stderr)\\n return None\\n #opens zip file for reading\\n with zf.open(self.getCsvFileByRegion(region), \\\"r\\\") as f:\\n reader = f.read().decode(\\\"iso 8859-2\\\")\\n reader = StringIO(reader)\\n reader = csv.reader(reader, delimiter = \\\";\\\")\\n #saves every row of file\\n for row in reader:\\n TmpList[0].append(region)\\n i=1\\n #saves every column separated because of their types\\n for item in row:\\n if item != \\\"\\\":\\n if (i>0 and i<4) or (i>4 and i<6) or (i>6 and i<32) or (i>32 and i<35) or (i>35 and i<46) or i==61 or i==64:\\n if not re.search(\\\"^[-]{0,1}[0-9]*$\\\", item):\\n item = None\\n else:\\n item=int(item)\\n elif i>45 and i<52:\\n if not re.search(\\\"^[-]{0,1}[0-9]*[,.]{0,1}[0-9]+$\\\", item):\\n item = None\\n else:\\n item = item.replace(\\\",\\\", \\\".\\\")\\n if re.search(\\\"^[-]{1}.*$\\\", item):\\n item = item.replace(\\\"-\\\", \\\"\\\")\\n item = -(float(item))\\n else:\\n item = float(item)\\n elif i==6:\\n if not re.search(\\\"^[-]{0,1}[0-9]*$\\\", item):\\n item = None\\n else:\\n if (len(item) == 4):\\n #cas nijak neupravuji, jen rozdeluji minuty od hodin\\n #policie uz nastavila hodnoty podle nich pozname nevalidni hodnotu\\n #pro minuty tato hodnota je 60\\n #pro hodiny tato hodnota je 25\\n #dle meho nazoru mi prislo zbytecne na misto techto dvou hdonot davat nejakou jinou nevalidni hodnotu (napr. NaN, -1)\\n #prepsal bych nevalidni vystup na jiny nevalidni vystup\\n item = item[:2] + \\\":\\\" + item[2:]\\n else:\\n item = None\\n TmpList[i].append(item)\\n else:\\n TmpList[i].append(None)\\n i+=1\\n\\n ListNpArrays = [[] for i in range(65)]\\n\\n #transforms into numpy.ndarray\\n for x in range(0, 65):\\n ListNpArrays[x] = np.array(TmpList[x], dtype=object)\\n\\n return (self.headers, ListNpArrays)\",\n \"def _get_stream_readers_for_zip(fh, tmp_dir):\\n fasta_zip = zipfile.ZipFile(fh, 'r')\\n rval = []\\n for member in fasta_zip.namelist():\\n fasta_zip.extract(member, tmp_dir)\\n rval.append(open(os.path.join(tmp_dir, member), 'rb'))\\n return rval\",\n \"def iterator(dataset_fn, sections=None, lang=None, field_indices=None):\\n files = filelist(lang=lang, sections=sections)\\n\\n with TarFile.open(dataset_fn, 'r:gz') as f:\\n for member in f:\\n if member.isfile() and os.path.basename(member.name) in files:\\n logging.info('parsing %s ...' % member.name)\\n m_f = f.extractfile(member)\\n\\n for sentence in parse_conll(m_f, field_indices=field_indices):\\n yield sentence\\n\\n m_f.close()\",\n \"def _unzip_files(self) -> None:\\n for file in self.input_path.iterdir():\\n if is_zipfile(file):\\n with ZipFile(file, mode=\\\"r\\\") as archive:\\n archive.extractall(path=self.temp_path)\",\n \"def process_lucidchart_zip(zip_path, format, outdir, overwrite=False):\\n\\n if outdir.exists():\\n if overwrite:\\n shutil.rmtree(outdir)\\n else:\\n raise Exception(f\\\"outdir={outdir} must not exist\\\")\\n\\n outdir.mkdir()\\n\\n with ZipFile(zip_path, 'r') as zf:\\n\\n namemap = {f\\\"Page {idx+1}.{format}\\\": name for idx, name in enumerate(names_in_page_order)}\\n\\n # ensure 1:1 mapping\\n exist_pages = set(zf.namelist())\\n desired_pages = set(namemap.keys())\\n if exist_pages != desired_pages:\\n raise Exception(f\\\"\\\"\\\"unexpected content in zip file\\n exist_pages={exist_pages}\\n desired_pages={desired_pages}\\n exist - desired={exist_pages - desired_pages}\\n desired - exist={desired_pages - exist_pages}\\n \\\"\\\"\\\")\\n\\n paths = []\\n for ep in exist_pages:\\n dest_name = namemap[ep]\\n dest_path = outdir / f\\\"{dest_name}.{format}\\\"\\n dest_path.write_bytes(zf.open(ep).read())\\n paths += [dest_path]\\n return paths\",\n \"def zip_parse(html_file):\\n zpf = html_file.replace('.html', '.zip')\\n summhead = []\\n datahead = []\\n rv_summary = []\\n rv_data = []\\n with zipfile.ZipFile(zpf, 'r') as Z:\\n summfile = [x for x in Z.namelist()\\n if x.endswith(\\\"summary.txt\\\")][0]\\n datafile = summfile.replace('summary.txt', 'fastqc_data.txt')\\n\\n summ = Z.read(summfile).decode('ASCII')\\n data = Z.read(datafile).decode('ASCII')\\n\\n for line in summ.split(\\\"\\\\n\\\"):\\n ls = line.strip().split(\\\"\\\\t\\\")\\n if len(ls) < 3:\\n continue\\n summhead.append(ls[1])\\n rv_summary.append(ls[0])\\n\\n for line in data.split(\\\"\\\\n\\\"):\\n if \\\">>END_MODULE\\\" in line:\\n break\\n if line.startswith(\\\"#\\\"):\\n continue\\n if line.startswith(\\\">\\\"):\\n continue\\n ls = line.strip().split(\\\"\\\\t\\\")\\n if ls[0] == 'Filename':\\n continue\\n datahead.append(ls[0])\\n rv_data.append(ls[1])\\n\\n return dict(zip(summhead, rv_summary)), \\\\\\n dict(zip(datahead, rv_data))\",\n \"def gen_glogs(zipname, ref_hashes, extraction, verbose=True, **extraction_kwargs):\\n with ZipFile(zipname, 'r') as z:\\n # sort files according to reference hash list\\n filenames = sort_files(z.namelist(), ref_hashes)\\n if verbose:\\n filenames = tqdm(filenames)\\n\\n # load and return glog\\n for filename in filenames:\\n with io.BytesIO(z.read(filename)) as buffer:\\n glog = buffer.getvalue()\\n yield extraction(glog, **extraction_kwargs)\",\n \"def get_list_of_files_in_zip(zip_files):\\n files = {k: [] for k in zip_files}\\n for zip_file in zip_files:\\n print('[ INFO ] Loading: %s' % zip_file)\\n try:\\n with ZipFile(join(zip_file), 'r') as z:\\n files[zip_file] = files[zip_file] + z.namelist()\\n except Exception as e:\\n print(e)\\n return files\",\n \"def tag_file_process(self, multiple_files):\\n # the path is now becoming a string since it goes through the UI\\n # text entry box, not a list or tuple any more, so we turn it to a\\n # list of paths\\n file_list = multiple_files.split(' ')\\n # the main dictionary to store all tags\\n tag_dict = dict()\\n rows = []\\n # now for all the tag file under the folder(root directory), we load\\n # the data into the dictionary\\n if len(file_list) == 0:\\n tk.messagebox.showwarning('warning', 'no files chosen')\\n else:\\n for file_path in file_list:\\n if os.path.isfile(file_path):\\n with open(file_path, 'r', encoding='utf-8') as \\\\\\n current_tag_file:\\n # initialize the dictionary and the inner dictionary\\n reader = csv.reader(current_tag_file)\\n for row in reader:\\n # the encode, decode is use to resolve the \\\"\\\\ueffa\\\"\\n # BOM-utf8 problem\\n row[0] = row[0].encode('utf-8').decode('utf-8-sig')\\n tag_dict[row[0]] = dict()\\n rows.append(row)\\n # store the tag into the dictionary\\n for row in rows:\\n # the 1st column is the main key(mob fact col name)\\n # the 2nd column is the tag id\\n # the 3rd column is the tag with real meaning\\n tag_dict[row[0]][row[1]] = row[2]\\n\\n else:\\n tk.messagebox.showinfo('warning', 'can not obtain: ' +\\n file_path)\\n return tag_dict\",\n \"def add_zip(manager, zipfile, incref=False):\\n from .core.cache.buffer_cache import empty_dict_checksum, empty_list_checksum\\n result = []\\n for checksum in zipfile.namelist():\\n if checksum in (empty_dict_checksum, empty_list_checksum):\\n continue\\n checksum2 = bytes.fromhex(checksum)\\n buffer = zipfile.read(checksum)\\n checksum3 = calculate_checksum(buffer)\\n if checksum3 != checksum2:\\n raise ValueError(\\\"Incorrect checksum for zipped file '{}'\\\".format(checksum))\\n buffer_cache.cache_buffer(checksum2, buffer)\\n if incref:\\n buffer_cache.incref(checksum2, authoritative=False)\\n result.append(checksum)\\n return result\",\n \"def extract(zip_file_path: str) -> List[bytes]:\\n\\n with ZipFile(zip_file_path, 'r') as zip_file:\\n files_extracted = zip_file.namelist()\\n try:\\n assert len(files_extracted) == 1, f\\\"{zip_file_path} contains more than one file: \\\"\\n except:\\n logging.info(f\\\"{zip_file_path} contains more than one file: {files_extracted}\\\")\\n with zip_file.open(files_extracted[0], 'r') as f:\\n return f.readlines()\",\n \"def _extract_data(inputs):\\n filename, split = inputs\\n for name, fobj in tfds.download.iter_archive(\\n filename, tfds.download.ExtractMethod.TAR_STREAM\\n ):\\n split_name = name.split(\\\"_\\\")\\n if len(split_name) > 2 and split_name[2] == split:\\n yield [name, fobj.read()]\",\n \"def load(folder, number_of_files=None, verbose=False):\\n files = list_files(folder, number_of_files)\\n\\n lemmatized_sentences = []\\n original_sentences = []\\n for zipped_file in files:\\n if verbose:\\n print(\\\"Parsing \\\" + zipped_file)\\n file = unzip(zipped_file)\\n (lemmas, originals) = parse(file)\\n original_sentences += originals\\n lemmatized_sentences += lemmas\\n\\n return lemmatized_sentences, original_sentences\",\n \"def peak_file_parser(infile):\\n # Open file and make sure supported\\n pfile = open_zipped(infile)\\n file_parsers = {'bed': bed_file}\\n file_parser = None\\n if pfile.name == '<stdin>':\\n file_parser = bed_file\\n else:\\n for n in file_parsers:\\n if in_name(pfile, n):\\n file_parser = file_parsers[n]\\n if not file_parser:\\n nm = pfile.name\\n pfile.close()\\n raise Exception('Unknown file type: {}'.format(nm))\\n\\n # Return the iterator\\n return file_parser(pfile)\",\n \"def parse_files():\\n pfuncs = [ # parse py files : add #\\n parse_test_files,\\n parse_model_files,\\n parse_url_files,\\n parse_route_files,\\n parse_settings_files,\\n parse_setup_files,\\n ]\\n\\n while PY_FILES:\\n for _ in range(len(pfuncs)):\\n a_func = pfuncs.pop()\\n a_func()\\n break\",\n \"def parse_region_data(self, region):\\r\\n \\r\\n self.download_data()\\r\\n region_filename = self.__get_region_filename(region)\\r\\n list_str = [\\\"region\\\", \\\"p1\\\", \\\"p36\\\", \\\"p37\\\", \\\"p2a\\\", \\\"weekday(p2a)\\\", \\\"p2b\\\", \\\"p6\\\", \\\"p7\\\", \\\"p8\\\", \\\"p9\\\", \\\"p10\\\", \\r\\n \\\"p11\\\", \\\"p12\\\", \\\"p13a\\\", \\\"p13b\\\", \\\"p13c\\\", \\\"p14\\\", \\\"p15\\\", \\\"p16\\\", \\\"p17\\\", \\\"p18\\\",\\\"p19\\\", \\\"p20\\\", \\\"p21\\\", \\r\\n \\\"p22\\\", \\\"p23\\\", \\\"p24\\\", \\\"p27\\\", \\\"p28\\\", \\\"p34\\\", \\\"p35\\\", \\\"p39\\\", \\\"p44\\\", \\\"p45a\\\", \\\"p47\\\", \\\"p48a\\\", \\\"p49\\\", \\r\\n \\\"p50a\\\", \\\"p50b\\\", \\\"p51\\\", \\\"p52\\\", \\\"p53\\\", \\\"p55a\\\", \\\"p57\\\", \\\"p58\\\", \\\"a\\\", \\\"b\\\", \\\"d\\\", \\\"e\\\", \\\"f\\\", \\\"g\\\", \\\"h\\\", \\r\\n \\\"i\\\", \\\"j\\\", \\\"k\\\", \\\"l\\\", \\\"m\\\", \\\"n\\\", \\\"o\\\", \\\"p\\\", \\\"q\\\", \\\"r\\\", \\\"s\\\", \\\"t\\\", \\\"p5a\\\"]\\r\\n \\r\\n row_count = self.__get_files_row_count(region)\\r\\n list_arrays = [np.zeros(row_count, dtype=dt) for dt in self.__types]\\r\\n row_index = 0\\r\\n for file in self.__files:\\r\\n file_to_parse = os.path.join(self.__folder, os.path.basename(file))\\r\\n with zipfile.ZipFile(file_to_parse, \\\"r\\\") as zf:\\r\\n with zf.open(region_filename, 'r') as csv_file:\\r\\n reader = csv.reader(TextIOWrapper(csv_file, 'windows-1250'), delimiter=';', quotechar='\\\"')\\r\\n for row in reader:\\r\\n list_arrays[0][row_index] = region\\r\\n for col_index, col in enumerate(row):\\r\\n try:\\r\\n list_arrays[col_index + 1][row_index] = col\\r\\n except ValueError:\\r\\n if list_arrays[col_index + 1][row_index].dtype == np.int64:\\r\\n list_arrays[col_index + 1][row_index] = -1\\r\\n elif list_arrays[col_index + 1][row_index].dtype == 'datetime64[D]':\\r\\n print('Error2:', col)\\r\\n elif list_arrays[col_index + 1][row_index].dtype == np.float64:\\r\\n if type(col) != str:\\r\\n list_arrays[col_index + 1][row_index] = col.replace(',', '.')\\r\\n else:\\r\\n list_arrays[col_index + 1][row_index] = float(\\\"nan\\\")\\r\\n row_index += 1\\r\\n \\r\\n return (list_str, list_arrays)\",\n \"def _unpack_archive(self, dir, filters):\\n ext = os.path.splitext(self.path)[1]\\n if ext in [\\\".zip\\\", \\\".xpi\\\"]:\\n if filters:\\n raise GbpError(\\\"Can only filter tar archives: %s\\\", (ext, self.path))\\n self._unpack_zip(dir)\\n else:\\n self._unpack_tar(dir, filters)\",\n \"def load_zip(data):\\n zip_codes = [address['postalCode'] for address in data]\\n zip_codes_objects = [Zip(data=zip_code)\\n for zip_code\\n in zip_codes]\\n Zip.objects.bulk_create(zip_codes_objects)\",\n \"def parse_records(self):\\n for record in sp.parse(gzip.open(\\n \\\"./human_uniprot_04_07_20.gz\\\", 'rt')):\\n # print(record.taxonomy_id)\\n # if record.organism != \\\"Homo sapiens\\\":\\n # continue\\n # print(record.features[0])\\n # for comment in record.comments:\\n # if comment.startswith(\\\"SUBCELLULAR LOCATION\\\"):\\n # print(comment)\\n self.extract_features_to_dict(record)\\n self.extract_localization(record)\",\n \"def processfile(args, fh):\\n if args.quick:\\n scanner = quickScanZip(args, fh)\\n else:\\n scanner = findPKHeaders(args, fh)\\n\\n def checkarg(arg, ent):\\n if not arg:\\n return False\\n return '*' in arg or ent.name in arg\\n def checkname(a, b):\\n if a and '*' in a: return True\\n if b and '*' in b: return True\\n l = 0\\n if a: l += len(a)\\n if b: l += len(b)\\n return l > 1\\n\\n if args.verbose and not (args.cat or args.raw or args.save):\\n print(\\\" 0304 need flgs mth stamp --crc-- compsize fullsize nlen xlen namofs xofs datofs endofs\\\")\\n print(\\\" 0102 crea need flgs mth stamp --crc-- compsize fullsize nlen xlen clen dsk0 attr osattr datptr namofs xofs cmtofs endofs\\\")\\n for ent in scanner:\\n if args.cat or args.raw or args.save:\\n if args.quick and isinstance(ent, CentralDirEntry) or \\\\\\n not args.quick and isinstance(ent, LocalFileHeader):\\n ent.loaditems(fh)\\n do_cat = checkarg(args.cat, ent)\\n do_raw = checkarg(args.raw, ent)\\n do_save= checkarg(args.save, ent)\\n\\n do_name= checkname(args.cat, args.raw)\\n\\n if do_name:\\n print(\\\"\\\\n===> \\\" + ent.name + \\\" <===\\\\n\\\")\\n\\n sys.stdout.flush()\\n blks = zipraw(fh, ent)\\n\\n if args.password and ent.flags&1:\\n blks = zip_decrypt(blks, args.password)\\n if do_cat or do_save:\\n blks = skipbytes(blks, 12, args)\\n\\n if do_cat:\\n sys.stdout.buffer.writelines(zipcat(blks, ent))\\n if do_raw:\\n sys.stdout.buffer.writelines(blks)\\n if do_save:\\n savefile(args.outputdir, ent.name, zipcat(blks, ent))\\n else:\\n ent.loaditems(fh)\\n if args.verbose or not args.quick:\\n print(\\\"%08x: %s\\\" % (ent.pkOffset, ent))\\n else:\\n print(ent.summary())\\n if hasattr(ent, \\\"comment\\\") and ent.comment and not args.dumpraw:\\n print(ent.comment)\\n if args.dumpraw and hasattr(ent, \\\"extraLength\\\") and ent.extraLength:\\n print(\\\"%08x: XTRA: %s\\\" % (ent.extraOffset, binascii.b2a_hex(getbytes(fh, ent.extraOffset, ent.extraLength))))\\n if args.dumpraw and hasattr(ent, \\\"comment\\\") and ent.comment:\\n print(\\\"%08x: CMT: %s\\\" % (ent.commentOffset, binascii.b2a_hex(getbytes(fh, ent.commentOffset, ent.commentLength))))\\n if args.dumpraw and isinstance(ent, LocalFileHeader):\\n blks = zipraw(fh, ent)\\n if args.password and ent.flags&1:\\n blks = zip_decrypt(blks, args.password)\\n\\n blockdump(ent.dataOffset, blks)\",\n \"def parse_files(self, filenames=\\\"\\\"):\\n if self._parsed:\\n raise Exception(\\\"Have been parsed\\\")\\n self._parsed = True\\n\\n if filenames:\\n if not isinstance(filenames, (list, tuple)):\\n filenames = self._parse_string(filenames).strip(\\\", \\\").split(\\\",\\\")\\n\\n for filename in filenames:\\n self._parse_file(filename)\\n\\n self._check_and_fix()\",\n \"def load_files_info(self):\\n authors = {}\\n paths = sorted(self.zipfile.filelist, key=lambda x: x.date_time)\\n for path in paths:\\n with self.zipfile.open(path) as fd:\\n try:\\n data = json.load(fd)\\n names = self.extract_author_name(data)\\n except json.JSONDecodeError:\\n fd.seek(0)\\n self.invalid_files[fd.name] = fd.read()\\n else:\\n authors.update({name: path for name in names})\\n\\n return authors\",\n \"def unzip_oxygen_files(zip_file):\\n name_main_content = None\\n name_left_menu = None\\n list_img_files_to_save = list()\\n\\n files_unzipped = ZipFile(zip_file)\\n for file_unzipped_name in files_unzipped.namelist():\\n if not file_unzipped_name.startswith('__MACOSX'):\\n if file_unzipped_name.endswith(\\\".jpeg\\\"):\\n list_img_files_to_save.append(file_unzipped_name)\\n elif file_unzipped_name.endswith(\\\".indexList.html\\\"):\\n name_left_menu = file_unzipped_name\\n elif file_unzipped_name.endswith(\\\"_xsd.html\\\"):\\n name_main_content = file_unzipped_name\\n\\n return files_unzipped, name_left_menu, name_main_content, list_img_files_to_save\",\n \"def _read_recs(basedir):\\n for borotag in boro_tags:\\n datafile = \\\"%s/%s.csv\\\" % (basedir,borotag)\\n print(\\\"slurp '%s' ..\\\" % datafile)\\n recs = read_recs(datafile)\\n yield from (pluto.parse.normalize(r) for r in recs)\",\n \"def read_data(filename):\\n data=''\\n with zipfile.ZipFile(filename) as f:\\n \\n for file in f.namelist():\\n subdata = tf.compat.as_str(f.read(file))\\n data+=subdata\\n return nlp(data)\",\n \"def process_file(filename):\\n print \\\"Reading and Parsing File: {}\\\".format(filename)\\n parsed_entries = file_parser(filename)\\n print \\\"Starting to Process Entries\\\"\\n chunked_entires = chunk_entries(parsed_entries)\\n return [process_entries(entry) for entry in chunked_entires]\",\n \"def _iter_dag_filelocs(fileloc: str) -> Iterator[str]:\\n if fileloc.endswith(\\\".py\\\") or not zipfile.is_zipfile(fileloc):\\n yield fileloc\\n return\\n try:\\n with zipfile.ZipFile(fileloc) as z:\\n for info in z.infolist():\\n if might_contain_dag(info.filename, True, z):\\n yield os.path.join(fileloc, info.filename)\\n except zipfile.BadZipFile:\\n self.log.exception(\\\"There was an error accessing ZIP file %s %s\\\", fileloc)\",\n \"def unpack_landsat(inpath, outpath, bands=None, clouds=None):\\r\\n tfile = tarfile.open(inpath,'r:gz')\\r\\n if bands is None:\\r\\n #Extract all of the bands.\\r\\n tfile.extractall(outpath);\\r\\n else:\\r\\n #Extract just the bands specified.\\r\\n\\r\\n #Get the names of the members of the archive\\r\\n names = tfile.getnames()\\r\\n\\r\\n #Make sure the bands are given as a list\\r\\n bands = list(bands)\\r\\n\\r\\n #Find those elements of the archive that match the bands specified\\r\\n #\\t(plus metadata file)\\r\\n members = tfile.getmembers()\\r\\n elements = []\\r\\n blist = ''.join(str(i) for i in bands)\\r\\n if clouds:\\r\\n patternStr = '.*_B[' + blist + ']\\\\.TIF|.*_MTL.txt|.*_band[' + blist + \\\\\\r\\n ']\\\\.tif|.*_cfmask.*\\\\.tif|.*\\\\.xml|.*cloud.*\\\\.tif'\\r\\n else:\\r\\n patternStr = '.*_B[' + blist + ']\\\\.TIF|.*_MTL.txt|.*_band[' + blist + \\\\\\r\\n ']\\\\.tif|.*_cfmask.*\\\\.tif|.*\\\\.xml'\\r\\n\\r\\n pattern = re.compile(patternStr)\\r\\n for i, name in enumerate(names):\\r\\n if pattern.match(name):\\r\\n elements.append(members[i])\\r\\n tfile.extractall(outpath,members = elements)\\r\\n\\r\\n '''\\r\\n Note: the below section was written with the intention of\\r\\n adding valuable metadata info to the .TIF files themselves.\\r\\n This theoretically allows easy retreival of key metadata info,\\r\\n but the method to set new metadata seems unreliable. Appears to\\r\\n be an open issue, but there may be a solution. For now, assume\\r\\n this does not work.\\r\\n\\r\\n #Now we loop through each output, adding important metadata.\\r\\n #Fetch metadata and make sure there is only one file.\\r\\n meta = glob.glob(outpath + '/*_MTL.txt')\\r\\n if len(meta) > 1:\\r\\n raise('MORE THAN ONE METADATA FILE FOUND!')\\r\\n\\r\\n metadata = read_metadata(meta[0])\\r\\n\\r\\n #Add the metadata.\\r\\n for tif in glob.glob(outpath + '*.TIF'):\\r\\n #Open the tif file\\r\\n ras = gdal.Open(tif)\\r\\n\\r\\n #Preserve any existing metadata & add important metadata from file\\r\\n meta = ras.GetMetadata()\\r\\n meta['SCENE_CENTER_TIME'] = metadata['SCENE_CENTER_TIME']\\r\\n meta['DATE_ACQUIRED'] = metadata['DATE_ACQUIRED']\\r\\n meta['LANDSAT_SCENE_ID'] = metadata['LANDSAT_SCENE_ID']\\r\\n\\r\\n #Now write the new metadata back to the tif.\\r\\n ras.SetMetadata(meta)\\r\\n ras.FlushCache()\\r\\n ras = None\\r\\n '''\",\n \"def _add_tag_file(zip_file, dir_name, tag_info_list, tag_tup):\\n tag_name, tag_str = tag_tup\\n tag_path = d1_common.utils.filesystem.gen_safe_path(dir_name, tag_name)\\n tag_iter = _create_and_add_tag_iter(zip_file, tag_path, tag_str)\\n tag_info_list.append(\\n {\\n \\\"path\\\": tag_path,\\n \\\"checksum\\\": d1_common.checksum.calculate_checksum_on_iterator(\\n tag_iter, TAG_CHECKSUM_ALGO\\n ),\\n }\\n )\",\n \"def convert(self, tag=\\\"Data\\\", delimiter=\\\",\\\", noheader=False,\\n limit=-1, buffer_size=1000):\\n\\n\\n file_ctr = 0\\n item_ctr = 0\\n for dirName, subdirList, fileList in os.walk(self.input_directory):\\n print('Found directory: %s' % dirName)\\n for fname in fileList:\\n print('\\\\t%s' % fname)\\n # open the xml file for iteration\\n if not fname.endswith(\\\".xml\\\"):\\n continue\\n #pdb.set_trace()\\n \\n input_file = dirName + \\\"/\\\" + fname\\n self.context = ETree.iterparse(input_file, events=(\\\"start\\\", \\\"end\\\"))\\n\\n # iterate through the xml\\n items = [{}]\\n\\n depth = 0\\n min_depth = 0\\n row_depth = -1\\n n = 0\\n for event, elem in self.context:\\n if event == \\\"start\\\":\\n depth += 1\\n continue\\n else:\\n depth -= 1\\n if depth < min_depth:\\n min_depth = depth\\n\\n if depth < row_depth and items:\\n if noheader:\\n noheader = False\\n else:\\n # new line\\n self.output_buffer.append(items)\\n items = []\\n # flush buffer to disk\\n if len(self.output_buffer) > buffer_size:\\n self._write_buffer(delimiter)\\n\\n plain_tag = elem.tag\\n last_delim = max(elem.tag.rfind('}'), elem.tag.rfind(':'))\\n if 0 < last_delim < len(elem.tag) - 1:\\n plain_tag = elem.tag[last_delim + 1:]\\n if tag == plain_tag:\\n if n == 0:\\n min_depth = depth\\n elif n == 1:\\n row_depth = min_depth\\n n += 1\\n if 0 < limit < n:\\n break\\n elem_name = elem.get(\\\"name\\\")\\n if elem_name in self.output_dict[0].keys():\\n if elem_name == 'SamS.ArchivedURL':\\n if hash(elem.text) in self.item_titles.keys() and self.item_titles[hash(elem.text)] == elem.text:\\n #item is repetative\\n self.output_dict[item_ctr]={}\\n #item_ctr-=1\\n break\\n else:\\n self.item_titles[hash(elem.text)] = elem.text\\n self.output_dict[item_ctr][elem_name]= elem.text and elem.text.encode('utf8') or ''\\n\\n #if (len(self.output_dict[item_ctr]) > 0 ) :\\n if ('SamS.ArchivedURL' in self.output_dict[item_ctr]):\\n item_ctr+=1\\n self.output_dict.append({})\\n else:\\n self.output_dict[item_ctr] = {}\\n \\n file_ctr+=1 #next row in the dictionary array\\n print \\\"processing file no \\\", file_ctr, \\\" item no\\\", item_ctr\\n\\n #pdb.set_trace()\\n self._write_buffer(delimiter) # write rest of the buffer to file\\n\\n return n\",\n \"def debianize( strFilename ):\\n \\n #~ data = gzip.GzipFile( strFilename ).read();\\n #~ print data;\\n #~ return;\\n \\n #~ data = gzip.open( strFilename ).read();\\n #~ print data;\\n #~ return; \\n \\n #~ uncompressedData = bz2.BZ2File(strFilename).read()\\n #~ print str(uncompressedData)\\n #~ return;\\n \\n #~ file = open( strFilename, 'rb' );\\n #~ data = file.read();\\n #~ file.close();\\n #~ print debug.dumpHexa( data );\\n \\n #~ ar = tarfile.open(strFilename, 'r:*')\\n #~ for item in ar:\\n #~ print( str(item) );\\n #~ print( \\\"%s:\\\" % item.name );\\n #~ #print debug.dumpHexa(item.buf);\\n #~ #print zlib.decompress(item.buf)\\n #~ #print zlib.decompress(ar.extractfile(item).read())\\n #~ data = ar.extractfile(item.name).read()\\n #~ print data # works !\\n #~ ar.close() \\n #~ return;\\n \\n fileLists = [];\\n file = open( strFilename );\\n data = file.read();\\n file.close();\\n \\n print( \\\"data len: %d\\\" % len( data ) );\\n\\n nDataCompressedOffset = 0; # 132\\n\\n # works fine on toto.gz\\n #~ f = gzip.open(strFilename, 'rb')\\n #~ file_content = f.read()\\n #~ print file_content\\n #~ f.close() \\n \\n #~ decompressor = bz2.BZ2Decompressor();\\n #~ uncompressed = decompressor.decompress(data[nDataCompressedOffset:]);\\n \\n #~ uncompressed = zlib.decompress(data[nDataCompressedOffset:]);\\n \\n uncompressed = decompress( data );\\n print( \\\"uncompressed: %s\\\" % str( uncompressed ) );\",\n \"def get_extract(filename: str, importer: str) -> list[Any]:\\n entries = g.ledger.ingest.extract(filename, importer)\\n return list(map(serialise, entries))\",\n \"def readzip(zipfile, filename=None):\\n with ctxZipReader(zipfile, filename) as zipstream:\\n dwg = read(zipstream, dxfversion=zipstream.dxfversion)\\n dwg.filename = zipstream.dxf_file_name\\n return dwg\",\n \"def unzip_subtitles(self, zip_filepath):\\n with ZipFile(zip_filepath, 'r') as zip_obj:\\n filenames = zip_obj.namelist()\\n\\n subtitle_filenames = [fn for fn in filenames if fn.endswith('.srt')]\\n for fn in subtitle_filenames:\\n zip_obj.extract(fn, self.temp_storage_dir)\\n\\n return subtitle_filenames\",\n \"def read_gdf_from_zip(zip_fp):\\r\\n with ZipFile(zip_fp) as z:\\r\\n # Lists all files inside the ZipFile, here assumes that there is only a single file inside\\r\\n layer = z.namelist()[0]\\r\\n data = gpd.read_file(io.BytesIO(z.read(layer)))\\r\\n return data\",\n \"def concatenate_files(self, files):\\n entries = []\\n for f in files:\\n tree = ETree.parse(f)\\n\\n root = tree.getroot()\\n entries = root.findall(tags[\\\"entry\\\"])\\n\\n for entry in entries:\\n yield entry\",\n \"def process_into_zip(input_root, output_root, file_list):\\n output_path = os.path.join(output_root, \\\"UNF_Backup.zip\\\")\\n new_zip = zipfile.ZipFile(output_path, \\\"w\\\")\\n for backup_id, backup_file in file_list.items():\\n if backup_file.is_dir is not True:\\n zinfo = backup_file.get_zipinfo()\\n data = get_file_data(backup_file, input_root)\\n if data is None:\\n logging.warning(f\\\"Unable to find data: {backup_file.file_id} ({backup_file.relative_path})\\\")\\n continue\\n else:\\n new_zip.writestr(zinfo, data)\\n new_zip.close()\",\n \"def load_zipped_image(zipfilename):\\n\\n # Read each image and append in a list\\n img = []\\n filenames = []\\n with ZipFile(zipfilename) as archive:\\n for entry in archive.infolist():\\n with archive.open(entry) as file:\\n tmp = Image.open(file)\\n img.append(np.array(tmp))\\n filenames.append(file.name)\\n\\n # Return the read images\\n return img, filenames\",\n \"def _add_payload_files(zip_file, payload_info_list):\\n payload_byte_count = 0\\n payload_file_count = 0\\n for payload_info_dict in payload_info_list:\\n zip_file.write_iter(payload_info_dict[\\\"path\\\"], payload_info_dict[\\\"iter\\\"])\\n payload_byte_count += payload_info_dict[\\\"iter\\\"].size\\n payload_file_count += 1\\n return payload_byte_count, payload_file_count\",\n \"def _parse_filelist(self):\\n if not os.path.exists(self.filelist):\\n print \\\"couldn't find \\\",self.filelist\\n return\\n\\n f = open( self.filelist, 'r' )\\n flist = f.readlines()\\n self.larlitefilelist = []\\n for f in flist:\\n if \\\".root\\\" in f:\\n self.larlitefilelist.append( f.strip() )\",\n \"def parse(self):\\n\\t\\tfor part in self.mail.walk():\\n\\t\\t\\tself.process_part(part)\",\n \"def parse(path):\\n data = gzip.open(path, 'rb')\\n for byte_line in data:\\n yield eval(byte_line) # return generator instance to save memory\",\n \"def load_zip_archive(archive_file, \\n file_list=None, \\n suffix_list=['jpeg', 'jpg', 'png'],\\n as_float=False):\\n if type(file_list) in [str]:\\n file_list = [file_list]\\n\\n if type(suffix_list) in [str]:\\n suffix_list = [suffix_list]\\n if suffix_list and type(suffix_list) not in [set]:\\n suffix_list = set(suffix_list)\\n\\n imgs = []\\n with ZipFile(archive_file, 'r') as zfa:\\n for f_info in zfa.infolist():\\n if f_info.is_dir():\\n continue\\n\\n if suffix_list:\\n i = f_info.filename.rfind('.')\\n suffix = f_info.filename[i+1:].lower() if i >= 0 else ''\\n if suffix not in suffix_list:\\n continue\\n\\n if file_list:\\n use_f = False\\n for fl in file_list:\\n if re.match(fl, f_info.filename):\\n use_f = True\\n break\\n if not use_f:\\n continue\\n\\n imgs.append((load_image(zfa.open(f_info)), f_info.filename))\\n return imgs\",\n \"def prepare_zip_file(self):\\n # need the following:\\n # 1. readme\\n # 2. cleaned features file\\n # 3. gene map\\n # 4. clean response file\\n # 5. run.yml\\n # 6. combined viz scores files\\n # 7. all top_genes_per_phenotype* files\\n # 8. network metadata\\n zip_path = os.path.join(\\\\\\n self.job_dir_path, 'download.zip')\\n with ZipFile(zip_path, 'w', ZIP_DEFLATED) as zipout:\\n\\n zipout.write(\\\\\\n '/zip_readmes/README-GP.txt', 'README-GP.txt')\\n\\n cleaned_features_path = os.path.join(\\\\\\n self.userfiles_dir, self.features_file_relative_path)\\n zipout.write(\\\\\\n cleaned_features_path, 'clean_genomic_matrix.txt')\\n\\n gene_names_map_path = os.path.join(\\\\\\n self.userfiles_dir, self.gene_names_map_relative_path)\\n zipout.write(\\\\\\n gene_names_map_path, 'gene_map.txt')\\n\\n cleaned_response_path = os.path.join(\\\\\\n self.userfiles_dir, self.response_file_relative_path)\\n zipout.write(\\\\\\n cleaned_response_path, 'clean_phenotypic_matrix.txt')\\n\\n zipout.write(\\\\\\n self.yml_path, 'run_params.yml')\\n\\n # combine viz files\\n combined_viz_path = os.path.join(self.job_dir_path, \\\\\\n 'combined_viz.tsv')\\n with open(combined_viz_path, 'w') as combo:\\n for fidx, fname in enumerate(sorted(self.get_response_files())):\\n fpath = os.path.join(self.results_dir_path, fname)\\n with open(fpath, 'r') as vizfile:\\n for lidx, line in enumerate(vizfile):\\n if lidx == 0 and fidx > 0:\\n # only print the column labels once\\n pass\\n else:\\n combo.write(line)\\n zipout.write(combined_viz_path, 'genes_ranked_per_phenotype.txt')\\n\\n top_genes_files = [f for f in os.listdir(self.results_dir_path) \\\\\\n if f.startswith('top_genes_per_phenotype')]\\n if len(top_genes_files) == 1:\\n top_genes_file_path = os.path.join(\\\\\\n self.results_dir_path, top_genes_files[0])\\n zipout.write(\\\\\\n top_genes_file_path, 'top_genes_per_phenotype_matrix.txt')\\n\\n if self.gg_network_metadata_full_path is not None:\\n zipout.write(self.gg_network_metadata_full_path, \\\\\\n 'interaction_network.metadata')\",\n \"def test_zip_files(self):\\n base_zip_files = ['whypython.txt', 'states.dbf', 'cities.kmz']\\n\\n text_file = os.path.join(os.getcwd(), 'test-data', 'whypython.txt')\\n dbf_file = os.path.join(os.getcwd(), 'test-data', 'states.dbf')\\n kml_file = os.path.join(os.getcwd(), 'test-data', 'cities.kmz')\\n #non_file = os.path.join(os.getcwd(), 'test-data', 'emptyfolder')\\n self.request['params'][0]['response']['docs'][0]['path'] = text_file\\n self.request['params'][0]['response']['docs'][1]['path'] = dbf_file\\n self.request['params'][0]['response']['docs'][2]['path'] = kml_file\\n #self.request['params'][0]['response']['docs'][3]['path'] = non_file\\n __import__(self.request['task'])\\n getattr(sys.modules[self.request['task']], \\\"execute\\\")(self.request)\\n zip_files = zipfile.ZipFile(os.path.join(self.temp_folder, 'output.zip')).namelist()\\n self.assertEqual(sorted(zip_files), sorted(base_zip_files))\",\n \"def extract(self, paths=None):\\n\\n all_files = self._get_package_files()\\n if paths is None:\\n extracted_files = all_files.values()\\n else:\\n extracted_files = [all_files[path] for path in paths]\\n\\n # filter already extracted file\\n extracted_files = [pf for pf in extracted_files if not os.path.isfile(self.project.storage.fspath(pf.extract_path))]\\n\\n # group files by package\\n files_by_package = defaultdict(list)\\n for pf in extracted_files:\\n files_by_package[pf.package].append(pf)\\n\\n package_files_path = f\\\"{self.path}/packages/files\\\"\\n\\n for package, files in files_by_package.items():\\n with self.project.storage.stream(f\\\"{package_files_path}/{package}\\\") as reader:\\n # sort files by offset to extract while streaming the bin file\\n for pkgfile in sorted(files, key=lambda f: f.offset):\\n logger.debug(f\\\"extracting {pkgfile.path}\\\")\\n reader.skip_to(pkgfile.offset)\\n fspath = self.project.storage.fspath(pkgfile.extract_path)\\n with write_file_or_remove(fspath) as fout:\\n if pkgfile.compressed:\\n zobj = zlib.decompressobj(zlib.MAX_WBITS | 32)\\n def writer(data):\\n return fout.write(zobj.decompress(data))\\n reader.copy(writer, pkgfile.size)\\n fout.write(zobj.flush())\\n else:\\n reader.copy(fout.write, pkgfile.size)\",\n \"def extract_bz2(tar_bz_f, calc_type):\\n \\n # we give the gaussian calculator a label that includes the directory the\\n # log file is contained in, this does not affect the parsing process but\\n # generate a warning as it is not an expected form for the label. To avoid\\n # the profusion of warning messages in stdout we suppress warnings here.\\n warnings.filterwarnings(\\\"ignore\\\")\\n\\n extended_xyzs = []\\n\\n with tarfile.open(tar_bz_f,'r:bz2') as data_tar:\\n calc_logs = (log_tar for log_tar in data_tar \\n if calc_type in log_tar.name and '.log' in log_tar.name)\\n \\n for calc_log in calc_logs:\\n try:\\n # extract log file (and relevant directory)\\n data_tar.extract(calc_log)\\n\\n # convert to ASE/Gaussian format\\n mol = read(calc_log.name)\\n mol.set_calculator(\\n Gaussian(\\n label=calc_log.name.replace('.log','')\\n )\\n )\\n\\n # parse into ML readable format\\n parsed_mol = ase_mol_parse(mol)\\n extended_xyzs.append(parsed_mol)\\n except AttributeError:\\n # if the calculation didn't complete we get an empty dictionary \\n # so we we keep track of these failed calculations with a blank \\n # entry other than mol_id\\n blank_entry = {'mol_id':calc_log.name.replace('.log','')}\\n extended_xyzs.append(blank_entry)\\n finally:\\n # delete extracted log file\\n os.remove(calc_log.name)\\n\\n # solves memory problem\\n # http://blogs.it.ox.ac.uk/inapickle/2011/06/20/high-memory-usage-when-using-pythons-tarfile-module/ # noqa\\n data_tar.members=[]\\n \\n dir_name = tar_bz_f.replace('.tar.bz2','')\\n\\n # delete extracted directory\\n os.rmdir(dir_name)\\n\\n # search key function\\n # assumes files are named xxx_frame_{frame}_mol_{no}\\n def mol_no_frame(mol):\\n mol_no = int(mol['mol_id'].split('_')[-1].replace('.log',''))\\n mol_frame = int(mol['mol_id'].split('_')[-3])\\n return mol_no,mol_frame\\n\\n extended_xyzs = sorted(extended_xyzs,key=mol_no_frame)\\n\\n with open(dir_name + '_' + calc_type + '_data.pkl', 'w') as data_f:\\n dill.dump(extended_xyzs, data_f)\",\n \"def file_zipper(root_dir):\\n # FINDING AND ZIPPING UNZIPPED FILES\\n for root, dirs, files in os.walk(root_dir, topdown=False):\\n if root != \\\"\\\":\\n if root[-1] != '/': root += '/'\\n for current_file in files:\\n filepath = \\\"%s/%s\\\"%(root, current_file)\\n try:\\n file_size = os.path.getsize(filepath)\\n except Exception as e:\\n file_size = 0\\n debug.log('Error: file_zipper failed to zip following file '+filepath, e)\\n # Excluding small files, gzipped files and links\\n if ( file_size > 50\\n and current_file[-3:] != \\\".gz\\\"\\n and not os.path.islink(filepath)\\n ):\\n if current_file[-4:] == \\\".zip\\\":\\n # Unzip file\\n ec = Popen('unzip -qq \\\"%s\\\" -d %s > /dev/null 2>&1'%(filepath, root), shell=True).wait()\\n if ec > 0:\\n debug.log('Error: fileZipper failed to unzip following file %s'%filepath)\\n continue\\n else:\\n ec = Popen('rm -f \\\"%s\\\" > /dev/null 2>&1'%(filepath), shell=True).wait()\\n if ec > 0: debug.log('Error: fileZipper failed to delete the original zip file (%s)'%filepath)\\n filepath = filepath[:-4]\\n # Saving a gzipped version\\n with open_(filepath, 'rb') as f, open_(filepath+\\\".gz\\\", 'wb', 9) as gz:\\n gz.writelines(f)\\n # Deleting old (non-zipped) file\\n try: os.remove(filepath)\\n except OSError as e:\\n debug.log((\\\"WARNING! The file %s could not be \\\"\\n \\\"removed!\\\\n%s\\\")%(current_file, e))\",\n \"def parse(self, filename):\\n infile = file(filename)\\n for line in infile:\\n self.parseLine(line)\",\n \"def unzip_data(zip_f,data_folder_path): \\n\\n with zipfile.ZipFile(zip_f,\\\"r\\\") as zip_ref:\\n zip_ref.extractall(data_folder_path)\",\n \"def parse_file(self, domain_filename,\\n gzip=False,\\n fixed=True, pdf=False, output_path=None, **kargs):\\n valid_file_formats = set(['fasta_style', 'dfam'])\\n assert format in valid_file_formats, '{0} not in {1} valid_file_formats'.format(format, valid_file_formats)\\n\\n if output_path:\\n if not os.path.exists(output_path):\\n os.mkdir(output_path)\\n self.output_path = output_path\\n\\n self.fixed = fixed\\n self.pdf = pdf\\n\\n self.data = []\\n\\n if format == 'fasta_style':\\n self.data = self.__load_fasta_style(filename, gzip)\\n elif format == 'dfam':\\n self.data = self.__load_dfam_style(filename, gzip)\",\n \"def tar_file_and_group(data):\\n for sample in data:\\n assert \\\"stream\\\" in sample\\n stream = tarfile.open(fileobj=sample[\\\"stream\\\"], mode=\\\"r|*\\\")\\n prev_prefix = None\\n example = {}\\n valid = True\\n for tarinfo in stream:\\n name = tarinfo.name\\n pos = name.rfind(\\\".\\\")\\n assert pos > 0\\n prefix, postfix = name[:pos], name[pos + 1 :]\\n if prev_prefix is not None and prefix != prev_prefix:\\n example[\\\"key\\\"] = prev_prefix\\n if valid:\\n yield example\\n example = {}\\n valid = True\\n with stream.extractfile(tarinfo) as file_obj:\\n try:\\n if postfix == \\\"txt\\\":\\n example[\\\"txt\\\"] = file_obj.read().decode(\\\"utf8\\\").strip()\\n elif postfix in AUDIO_FORMAT_SETS:\\n waveform, sample_rate = torchaudio.load(file_obj)\\n example[\\\"wav\\\"] = waveform\\n example[\\\"sample_rate\\\"] = sample_rate\\n else:\\n example[postfix] = file_obj.read()\\n except Exception as ex:\\n valid = False\\n logging.warning(\\\"error to parse {}\\\".format(name))\\n prev_prefix = prefix\\n if prev_prefix is not None:\\n example[\\\"key\\\"] = prev_prefix\\n yield example\\n stream.close()\\n if \\\"process\\\" in sample:\\n sample[\\\"process\\\"].communicate()\\n sample[\\\"stream\\\"].close()\",\n \"def main():\\r\\n\\r\\n #Create a list of all files that have the GPX file format\\r\\n fileList = glob.glob(os.path.join(inFolder,\\\"*.{0}\\\".format(inFormat)))\\r\\n\\r\\n #Create a connection to PostGIS database\\r\\n pgConn = createPostgisConnection(dbFormat, dbHost, dbName, dbSchema, dbUser, dbPWD)\\r\\n\\r\\n #Process each *listed* layer type from a GPS file\\r\\n for f in fileList:\\r\\n importGPX(f, gpxImportLayers, pgConn)\",\n \"def main():\\n processSetOfCerFiles(sys.argv[1:])\",\n \"def test_pick_files(mock_zip_file):\\n\\n files = ['Unihan_Readings.txt', 'Unihan_Variants.txt']\\n\\n options = {'input_files': files, 'zip_path': str(mock_zip_file)}\\n\\n b = process.Packager(options)\\n\\n result = b.options['input_files']\\n expected = files\\n\\n assert result == expected, 'Returns only the files picked.'\",\n \"def parse_facs_files():\\n\\n #Load parser settings\\n parser_settings = getattr(settings,'FACS_PARSER_SETTINGS')\\n\\n files_to_parse = [parser_settings['facs_source_directory']+f for f in os.listdir(parser_settings['facs_source_directory']) if '.exp' in f]\\n\\n for filename in files_to_parse: \\n\\n #Compute MD5 hash\\n facs_file = file(filename,'rbU')\\n md5hash = hashlib.md5(facs_file.read()).hexdigest()\\n facs_file.close()\\n \\n #Skip file if previously parsed.\\n if FacsFile.objects.filter(original_filename=filename,md5hash=md5hash):\\n print 'Skipping ', filename\\n continue\\n\\n #Open file, remove null bytes and prepare csv reader\\n facs_file = file(filename, 'rU')\\n csv_reader = csv.reader((x.replace('\\\\0', '') for x in facs_file),dialect=csv.excel_tab)\\n\\n #Reader header\\n csv_header = csv_reader.next()\\n facs_file_results = []\\n\\n #Parse the file\\n for csv_row in csv_reader:\\n if csv_row[0]:\\n facs_file_results.append(dict(zip(csv_header,csv_row)))\\n\\n #Close the file\\n facs_file.close()\\n\\n #Save the information to database and archive file\\n random_ints = ''.join([str(random.randint(0,9)) for n in range(10)])\\n archive_filename = parser_settings['facs_archive_directory'] + filename.split('/')[-1][:-4].split('_')[0] + '_' + random_ints + '.exp'\\n shutil.move(filename, archive_filename)\\n\\n facs_file = FacsFile(\\n original_filename = filename,\\n md5hash = md5hash,\\n archive_filename = archive_filename,\\n )\\n facs_file.save()\\n\\n #Remove empty elements\\n for result in facs_file_results:\\n for key, data in result.items():\\n if data == '.' or not(data):\\n del result[key]\\n\\n #Cache test code and interface mappings\\n test_codes = []\\n for testcode_mapping in TestCodeMapping.objects.filter(interface_name=parser_settings['testcode_interface_name']):\\n test_code = testcode_mapping.code\\n code = test_code.code\\n code_mapping = testcode_mapping.code_mapping\\n\\n test_codes.append((code, code_mapping, test_code))\\n\\n #Add results to database\\n for result in facs_file_results:\\n\\n #Parse result date\\n result_date = dateutil.parser.parse(result[parser_settings['result_datetime']])\\n result_error_code = getattr(result, parser_settings['error_codes'], '')\\n result_identifier = result[parser_settings['sample_identifier']]\\n result_cytometer = result[parser_settings['cytometer_serial']]\\n\\n #Create the dictionnary of result items.\\n new_result_item_dict = {}\\n for test_code, facs_file_column, test_code_object in test_codes:\\n new_result_item_dict[test_code] = ResultItem(\\n test_code = test_code_object,\\n result_item_value = result[facs_file_column],\\n error_code = result_error_code,\\n result_item_datetime = result_date,\\n )\\n\\n #Search for possible duplicate result\\n is_duplicate = False\\n for possible_duplicate in FacsResult.objects.filter(result_identifier=result_identifier):\\n if possible_duplicate.get_resultitem_dict() == new_result_item_dict:\\n is_duplicate = True\\n break\\n\\n #Save result and result item to data if it is not a duplicate\\n if not is_duplicate:\\n \\n new_result = FacsResult(\\n result_identifier=result_identifier,\\n result_datetime=result_date,\\n origin_facs_file=facs_file,\\n cytometer_serial_number=result_cytometer,\\n )\\n \\n new_result.save()\\n \\n #Add the reference to the result for each item and save it to database.\\n for item in new_result_item_dict.values():\\n item.result = new_result\\n item.save()\\n\\n new_result.link_to_requisition()\",\n \"def get_filenames(zip_file: str) -> List:\\n file_names = []\\n with ZipFile(zip_file, 'r') as zipObj:\\n listOfiles = zipObj.namelist()\\n for elem in listOfiles:\\n if \\\"wav\\\" in elem:\\n file_names.append(elem)\\n return file_names\",\n \"def processSetOfCerFiles(files):\\n printHeader()\\n \\n k = 0\\n for f in files:\\n k = k + 1\\n sz = get_file_size(f)\\n with open(f, 'rb') as fb:\\n processCerFile(k, fb, sz=sz)\",\n \"def test_find_many_files_zipped_allow(self):\\n\\n these_file_names = satellite_io.find_many_files(\\n top_directory_name=TOP_DIRECTORY_NAME,\\n first_date_string=FIRST_DATE_STRING,\\n last_date_string=LAST_DATE_STRING,\\n prefer_zipped=True, allow_other_format=True, test_mode=True\\n )\\n\\n self.assertTrue(these_file_names == FILE_NAMES_UNZIPPED)\",\n \"def process_files(compress, files):\\n [compress.add_file(file) for file in files]\\n\\n compress.execute() # upload files to iLovePDF\\n compress.download() # download resultant file\\n print(\\\"Compression saved {}% of disk space.\\\".format(\\n PDFWorkshop.__percentage_storage_saved(compress))\\n )\\n compress.delete_current_task()\",\n \"def read_files(filenames, gram_size=1):\\n assert isinstance(filenames, list), \\\"filenames argument must be a list\\\"\\n parser = MorParser()\\n for fn in filenames:\\n for uid, speaker, ngram in generate_chunks(parser.parse(fn), gram_size):\\n yield fn, uid, speaker, ngram\",\n \"def extract_data(archive: ZipFile, dir_name: str) -> Data:\\n with archive.open(f\\\"{dir_name}/caption.txt\\\", \\\"r\\\") as f:\\n captions = f.readlines()\\n data = []\\n for line in captions:\\n tmp = line.decode().strip().split()\\n img_name = tmp[0]\\n formula = tmp[1:]\\n with archive.open(f\\\"{dir_name}/{img_name}.bmp\\\", \\\"r\\\") as f:\\n # move image to memory immediately, avoid lazy loading, which will lead to None pointer error in loading\\n img = Image.open(f).copy()\\n data.append((img_name, img, formula))\\n\\n print(f\\\"Extract data from: {dir_name}, with data size: {len(data)}\\\")\\n\\n return data\",\n \"def gzip_files(topDir, afni_file,localizerfile):\\n\\n print 'GZIPPING FILES...'\\n\\n command1 = \\\"gzip %s*BRIK\\\" % (topDir)\\n command2 = \\\"gzip %s*HEAD\\\" % (topDir)\\n command3 = \\\"gzip %s%s/pb00*\\\" % (topDir,afni_file)\\n command4 = \\\"gzip %s%s/errts*\\\" % (topDir,afni_file)\\n command5 = \\\"gzip %s%s/fitts*\\\" % (topDir,afni_file)\\n command6 = \\\"gzip %s%s/*al*\\\" % (topDir,afni_file)\\n command7 = \\\"gzip %s%s/*ns*\\\" % (topDir,afni_file)\\n command8 = \\\"gzip %s%s/all_runs*\\\" % (topDir,afni_file)\\n command9 = \\\"gzip %s%s/*mask*\\\" % (topDir,afni_file)\\n command10 = \\\"gzip %s*nii\\\" % (topDir)\\n command11 = \\\"gzip %s%s/pb01*\\\" % (topDir,afni_file)\\n command12 = \\\"gzip %s%s/pb03*\\\" % (topDir,afni_file)\\n command13 = \\\"gzip %s%s/pb02*\\\" % (topDir,afni_file)\\n\\n os.system(command1)\\n os.system(command2)\\n os.system(command3)\\n os.system(command4)\\n os.system(command5)\\n os.system(command6)\\n os.system(command7)\\n os.system(command8)\\n #os.system(command9)\\n os.system(command10)\\n os.system(command11)\\n try:\\n os.system(command12)\\n except:\\n print 'Could not gzip pb03 files'\\n\\n if localizerfile == 'facescene_loc':\\n os.system(command13)\",\n \"def parse(self, f):\\n \\n for line in f:\\n self.parse_line(line)\",\n \"def parse_directory(input_dir, start_date = datetime(1970,1,1), end_date = datetime(9999,12,31,23,59,59)):\\n logging.debug(\\\"Beginning parse_directory {}\\\".format(input_dir))\\n\\n def parse_gzipped_directory(input_dir, start_date, end_date, infos, backup_stamps):\\n \\\"\\\"\\\" Scans a gzipped directory. This one in different situation \\\"\\\"\\\"\\n try:\\n file_names = sorted(os.listdir(input_dir)) \\n for file_name in file_names:\\n if file_name.endswith(\\\".manifest.gz\\\") or file_name.endswith(\\\".manifest\\\"):\\n tmp = parse_file(input_dir + \\\"/\\\" + file_name, start_date, end_date, backup_stamps)\\n backup_stamps[tmp[\\\"backup_label\\\"]] = tmp[\\\"backup_timestamp_stop_ts\\\"]\\n if tmp:\\n infos.append(tmp)\\n except OSError as e:\\n logging.error(\\\"Failed to open directory\\\", exc_info=True)\\n exit(1)\\n except:\\n raise\\n \\n if not path.isdir(input_dir):\\n logging.error(\\\"The specified path is not a directory\\\")\\n exit(1)\\n\\n infos = []\\n backup_stamps = {}\\n if path.exists(input_dir + \\\"/backup.info\\\"):\\n\\n dir_names = sorted(os.listdir(input_dir + \\\"/backup.history\\\"))\\n for dir_name in dir_names:\\n parse_gzipped_directory(input_dir + \\\"/backup.history/\\\" + dir_name, start_date, end_date, infos, backup_stamps)\\n\\n else:\\n parse_gzipped_directory(input_dir, start_date, end_date, infos, backup_stamps)\\n \\n logging.debug(\\\"End parse_directory\\\")\\n return infos\",\n \"def unzip_data():\\n zip_ref = zipfile.ZipFile(data_zip, 'r')\\n zip_ref.extractall('')\\n zip_ref.close()\",\n \"def open_files(filenames):\\n for filename in filenames:\\n if filename.endswith('.gz') or filename.endswith('.zip'):\\n yield gzip.open(filename, 'r')\\n else:\\n yield open(filename, 'rb')\",\n \"def parse(self, *args, **kwargs):\\n if self.is_gzipped:\\n fin = gzip.open(self.path, 'rb')\\n else:\\n fin = open(self.path, 'r')\\n line_num = 0\\n expect_header = True\\n for line in fin:\\n line_num += 1\\n line = line.strip()\\n if not line: # skip empty lines\\n continue\\n if expect_header:\\n if self._is_header(line):\\n logger.debug(\\n f\\\"Detected header at line {line_num}: {line!r}\\\")\\n continue\\n else:\\n expect_header = False\\n try:\\n chrom, pos = self._parse_line(line, *args, **kwargs)\\n if chrom is not None:\\n yield chrom, pos\\n except (IndexError, ValueError, TypeError):\\n fin.close()\\n raise FileFormatError(format=self.format, line_num=line_num,\\n line=line)\\n fin.close()\",\n \"def Extract_zip_file (path_to_zip,dir_to_save_into):\\n with zipfile.ZipFile(path_to_zip) as zf:\\n \\n for member in tqdm(zf.namelist(), desc='Extracting'):\\n try:\\n if ('annotations' in member) and (member.endswith('.json')): \\n zf.extract(member, dir_to_save_into)\\n shutil.move(os.path.join(dir_to_save_into,member),dir_to_save_into)\\n if ('train' in member):\\n zf.extract(member, dir_to_save_into)\\n if ('test' in member):\\n zf.extract(member, dir_to_save_into)\\n if ('val' in member):\\n zf.extract(member, dir_to_save_into)\\n except zipfile.error as e:\\n pass\\n\\n #delete zip\\n os.remove(path_to_zip)\\n if(os.path.isdir(os.path.join(dir_to_save_into,'annotations'))):\\n # remove the tmp annotations directory\\n shutil.rmtree(os.path.join(dir_to_save_into,'annotations'))\",\n \"def extract_and_tag_test():\\n test_untagged_path = os.getcwd() + \\\"/data/test/test_untagged/\\\"\\n test_untagged_directory = os.fsencode(test_untagged_path)\\n\\n print(\\\"Tagging text. Please wait...\\\")\\n for file in os.listdir(test_untagged_directory):\\n filename = os.fsdecode(file)\\n try:\\n if filename.endswith(\\\".txt\\\"):\\n text = entity_process.read_data(test_untagged_path, file)\\n text = text.lower()\\n header,body = entity_process.split_text(text)\\n header_array = header.splitlines()\\n\\n\\n start_time, end_time = entity_process.extract_time(header)\\n location = entity_process.extract_location(header_array, body)\\n speaker = entity_process.extract_speaker(header_array, body)\\n\\n entity_tagger.tag_all(filename, text, start_time, end_time, location, speaker)\\n except Exception as e:\\n raise e\\n return \\\"No files found here!\\\"\\n print(\\\"Tagging complete! Text saved to\\\" + os.getcwd() + \\\"/out\\\")\",\n \"def _unpack_archive(self):\\n with zipfile.ZipFile(self._archive_full_path, 'r') as zip_ref:\\n zip_ref.extractall(self._storage_path)\\n\\n _logger.debug('Archive has been unpacked.')\",\n \"def _bam_extract_impl(config: BamExtractConfig, sites: typing.List[vcf.Site]) -> None:\\n for path in config.input_files:\\n _bam_extract_impl_for_file(config, sites, path)\",\n \"def process_file(self, filename, order=2):\\n fp = open(filename)\\n self.skip_gutenberg_header(fp)\\n\\n for line in fp:\\n for word in line.rstrip().split():\\n self.process_word(word, order)\\n\\n #print(\\\">>>DEBUG the suffix map\\\")\\n #i = 0\\n #for k,v in self.suffix_map.items():\\n # print(\\\"key is {}, value is {}\\\".format(k, v))\\n # i += 1\\n # if i > 10:\\n # break\",\n \"def extract(self):\\n self.build_path_pairs()\\n self.extract_field_blocks()\\n self.assert_filenames()\",\n \"def unzip_nested_zip(dataset_zip, path_unzip):\\r\\n\\r\\n with zipfile.ZipFile(dataset_zip, \\\"r\\\") as zfile:\\r\\n try:\\r\\n zfile.extractall(path=path_unzip)\\r\\n except OSError as e:\\r\\n logging.warning(\\r\\n \\\"Please check the unzipped files manually. There may be some missed important files.\\\"\\r\\n )\\r\\n logging.warning(\\\"The directory is: \\\" + path_unzip)\\r\\n for root, dirs, files in os.walk(path_unzip):\\r\\n for filename in files:\\r\\n if re.search(r\\\"\\\\.zip$\\\", filename):\\r\\n file_spec = os.path.join(root, filename)\\r\\n new_dir = os.path.join(root, filename[0:-4])\\r\\n unzip_nested_zip(file_spec, new_dir)\",\n \"def test_open_each(self):\\n zip_paths = zip_scanner(os.getcwd())\\n for zip_path in zip_paths:\\n with ZipEditor(zip_path) as zed:\\n self.assertEqual(zip_path, zed.file)\\n zed.open()\\n self.assertIsNotNone(zed.tmpdir.name)\\n self.assertEqual(zed.tmpdir.name, zed.getdir())\\n self.assertIsNone(zed.getdir())\",\n \"def decompress_files(self):\\n crx2rnx_path = os.path.join(ROOT_DIR, 'CRX2RNX')\\n if not os.path.isfile(crx2rnx_path):\\n raise OSError('Cannot find CRX2RNX binary in project directory!')\\n\\n if glob('{}/*'.format(self.__directory)):\\n subprocess.run([\\\"gunzip\\\", \\\"-dr\\\", self.__directory])\\n # convert Hatanaka compressed RINEX to standard RINEX\\n for f in glob('{}/*.??d'.format(self.__directory)):\\n subprocess.run([crx2rnx_path, f])\\n else:\\n raise RuntimeError(\\n 'Could not decompress. No files were downloaded from FTP server.')\",\n \"def bags(fondz_dir):\\n fondz_dir = os.path.abspath(fondz_dir)\\n results = {\\n 'bags': [],\\n 'num_files': 0,\\n 'bytes': 0\\n }\\n originals_dir = os.path.join(fondz_dir, \\\"originals\\\")\\n\\n for bag in os.listdir(originals_dir):\\n # TODO: look for other manifest types?\\n bag_dir = os.path.join(originals_dir, bag)\\n manifest = os.path.join(bag_dir, \\\"manifest-md5.txt\\\")\\n b = {\\n \\\"files\\\": [],\\n \\\"bytes\\\": 0,\\n }\\n for line in open(manifest):\\n line = line.strip()\\n cols = re.split(r' +', line)\\n path = os.path.join(bag_dir, cols[1])\\n st = os.stat(path)\\n rel_path = os.path.join(\\\"originals\\\", bag, path)\\n b['bytes'] += st.st_size\\n b['files'].append({\\n \\\"path\\\": rel_path,\\n \\\"bytes\\\": st.st_size,\\n \\\"created\\\": st.st_ctime,\\n \\\"modified\\\": st.st_mtime,\\n \\\"md5\\\": cols[0]\\n })\\n results['bytes'] += b['bytes']\\n results['num_files'] += len(b['files'])\\n results['bags'].append(b)\\n\\n bags_json = os.path.join(fondz_dir, \\\"js\\\", \\\"bags.json\\\")\\n write_json(results, bags_json)\\n return results\",\n \"def _extract_all_gz_in_dir(directory):\\n for file in os.listdir(directory):\\n if file.endswith(\\\".gz\\\"):\\n gz_fname = os.path.join(directory, file)\\n _extract_gz(gz_fname, os.path.dirname(gz_fname))\\n os.remove(gz_fname)\",\n \"def parse_input():\\n with open(\\\"input_07.txt\\\", \\\"r\\\") as f:\\n for line in f:\\n Bag(line)\",\n \"def create_chunks(file_names):\\n\\n\\tnew_chunks = []\\n\\n\\tfor name in file_names:\\n\\n\\t\\t# Find the .inf file and read the details stored within\\n\\t\\ttry:\\n\\t\\t\\tdetails = open(name + suffix + 'inf', 'r').readline()\\n\\t\\texcept IOError:\\n\\n\\t\\t\\ttry:\\n\\t\\t\\t\\tdetails = open(name + suffix + 'INF', 'r').readline()\\n\\t\\t\\texcept IOError:\\n\\t\\t\\t\\tprint(\\\"Couldn't open information file, %s\\\" % name+suffix+'inf')\\n\\t\\t\\t\\tsys.exit()\\n\\n\\t\\t# Parse the details\\n\\t\\tdetails = [string.rstrip(details)]\\n\\n\\t\\tsplitters = [' ', '\\\\011']\\n\\n\\t\\t# Split the details up where certain whitespace characters occur\\n\\t\\tfor s in splitters:\\n\\n\\t\\t\\tnew_details = []\\n\\n\\t\\t\\t# Split up each substring (list entry)\\n\\t\\t\\tfor d in details:\\n\\n\\t\\t\\t\\tnew_details = new_details + string.split(d, s)\\n\\n\\t\\t\\tdetails = new_details\\n\\n\\t\\t# We should have details about the load and execution addresses\\n\\n\\t\\t# Open the file\\n\\t\\ttry:\\n\\t\\t\\tin_file = open(name, 'rb')\\n\\t\\texcept IOError:\\n\\t\\t\\tprint(\\\"Couldn't open file, %s\\\" % name)\\n\\t\\t\\tsys.exit()\\n\\n\\t\\t# Find the length of the file (don't rely on the .inf file)\\n\\t\\tin_file.seek(0, 2)\\n\\t\\tlength = in_file.tell()\\n\\t\\tin_file.seek(0, 0)\\n\\n\\t\\t# Examine the name entry and take the load and execution addresses\\n\\t\\tdot_at = string.find(details[0], '.')\\n\\t\\tif dot_at != -1:\\n\\t\\t\\treal_name = details[0][dot_at+1:]\\n\\t\\t\\tload, exe = details[1], details[2]\\n\\t\\telse:\\n\\t\\t\\treal_name = get_leafname(name)\\n\\t\\t\\tload, exe = details[0], details[1]\\n\\n\\t\\tload = hex2num(load)\\n\\t\\texe = hex2num(exe)\\n\\n\\t\\tif load == None or exe == None:\\n\\t\\t\\tprint('Problem with %s: information is possibly incorrect.' % name+suffix+'inf')\\n\\t\\t\\tsys.exit()\\n\\n\\t\\t# Reset the block number to zero\\n\\t\\tblock_number = 0\\n\\n\\t\\t# Long gap\\n\\t\\tgap = 1\\n\\t\\n\\t\\t# Write block details\\n\\t\\twhile True:\\n\\t\\t\\tblock, last = write_block(in_file, real_name, load, exe, length, block_number)\\n\\n\\t\\t\\tif gap == 1:\\n\\t\\t\\t\\tnew_chunks.append((0x110, number(2,0x05dc)))\\n\\t\\t\\t\\tgap = 0\\n\\t\\t\\telse:\\n\\t\\t\\t\\tnew_chunks.append((0x110, number(2,0x0258)))\\n\\n\\t\\t\\t# Write the block to the list of new chunks\\n\\n\\t\\t\\t# For old versions, just write the block\\n\\t\\t\\tif UEF_major == 0 and UEF_minor < 9:\\n\\t\\t\\t\\tnew_chunks.append((0x100, block))\\n\\t\\t\\telse:\\n\\t\\t\\t\\tnew_chunks.append((0x100, block))\\n\\n\\t\\t\\tif last == 1:\\n\\t\\t\\t\\tbreak\\n\\n\\t\\t\\t# Increment the block number\\n\\t\\t\\tblock_number = block_number + 1\\n\\n\\t\\t# Close the input file\\n\\t\\tin_file.close()\\n\\n\\t# Write some finishing bytes to the list of new chunks\\n#\\tnew_chunks.append((0x110, number(2,0x0258)))\\n#\\tnew_chunks.append((0x112, number(2,0x0258)))\\n\\n\\t# Return the list of new chunks\\n\\treturn new_chunks\",\n \"def unpack(file, path='.'):\\n assert isfile(file)\\n assert isdir(path)\\n\\n for implementor in [GzipTarredFile, ZippedFile, Bzip2TarredFile]:\\n if implementor.is_valid(file):\\n with console.cd(path):\\n return [implementor(file).extract(), implementor]\\n else:\\n raise InvalidFile, 'compressed file format unknown: %s' % file\",\n \"def file_package_iter(self):\\n files = list()\\n futures = list()\\n\\n amount = 0\\n for file in self.file_iterator:\\n if amount + self._estimate_file_size(file) > self.max_size:\\n if len(files) == 0: # This file is too large for one archive, special handling\\n self.pool.wait(futures)\\n self._calculate_hash(file)\\n yield self._finish_info_package([file])\\n continue\\n\\n self.pool.wait(futures)\\n yield self._finish_info_package(files)\\n\\n files = list()\\n amount = 0\\n\\n amount += file.size\\n files.append(file)\\n futures.append(self.pool.add_task(self._calculate_hash, file)) # todo calc small files in-thread?\\n\\n if len(files) > 0:\\n yield self._finish_info_package(files)\",\n \"def process(self, zip_processor):\\n for filename in os.listdir(zip_processor.temp_dir):\\n with open(zip_processor._full_filename(filename)) as file:\\n contents = file.read()\\n contents = contents.replace(self.search_string, self.replace_string)\\n with open(zip_processor._full_filename(filename), \\\"w\\\") as file:\\n file.write(contents)\",\n \"def retrieveGEOFiles(geonum, directory):\\n samplelist = []\\n\\n ##download data https://geoparse.readthedocs.io/en/latest/GEOparse.html\\n print(\\\"###############STARTING DOWNLOAD################ \\\\n\\\\n\\\\n\\\")\\n print(geonum + '\\\\n\\\\n')\\n gse = GEOparse.get_GEO(geo=geonum, destdir=directory)\\n\\n for gsm_name, gsm in gse.gsms.items():\\n\\n samplelist.append(gsm_name)\\n\\n filename = directory + \\\"/\\\" + gsm_name + \\\".txt\\\"\\n o = open(filename, \\\"w\\\")\\n o.write(\\\"Name: \\\" + gsm_name)\\n o.write(\\\"\\\\nMetadata:\\\")\\n for key, value in gsm.metadata.items():\\n o.write(\\\"\\\\n - %s : %s\\\" % (key, \\\", \\\".join(value)))\\n if key == 'supplementary_file':\\n for item in value:\\n wget.download(item, directory)\\n o.close()\\n\\n for gpl_name, gpl in gse.gpls.items():\\n filename = directory + \\\"/\\\" + gpl_name + \\\".platform\\\"\\n o = open(filename, \\\"w\\\")\\n o.write(\\\"Name: \\\" + gpl_name)\\n o.write(\\\"\\\\nMetadata:\\\")\\n for key, value in gpl.metadata.items():\\n o.write(\\\"\\\\n - %s : %s\\\" % (key, \\\", \\\".join(value)))\\n o.close()\\n\\n print(\\\" ################### FINISHED DOWNLOAD ###################### \\\\n\\\\n\\\")\\n\\n return samplelist\"\n]","isConversational":false},"negative_scores":{"kind":"list like","value":["0.635105","0.62073517","0.61985546","0.6158757","0.59900516","0.58955044","0.58135545","0.58013874","0.57838947","0.56704354","0.5652113","0.5610305","0.55248296","0.551513","0.5497405","0.549419","0.5461678","0.5454392","0.5449247","0.541069","0.54071915","0.5393547","0.5383908","0.53606355","0.5327275","0.52997386","0.52967876","0.5287174","0.52772015","0.52659124","0.526485","0.52624476","0.52619356","0.52515525","0.52429485","0.5232549","0.5228436","0.52221924","0.52184594","0.5208116","0.52054185","0.51976675","0.5183016","0.51820683","0.5176655","0.51718193","0.51567286","0.5155581","0.5151049","0.5149151","0.5136968","0.513689","0.5120048","0.51186216","0.5116506","0.5110474","0.51080495","0.51072574","0.5105606","0.51006687","0.5097277","0.5092744","0.50925004","0.5071251","0.50552994","0.5048711","0.50465983","0.5045155","0.5044352","0.50436103","0.50374824","0.5037268","0.50168514","0.5013812","0.50136334","0.50072783","0.50046957","0.5004398","0.49976704","0.49907178","0.49897188","0.49868864","0.49796006","0.49752223","0.4973241","0.49728176","0.4972098","0.4970689","0.497001","0.49679896","0.4962551","0.49512583","0.4948872","0.494673","0.4937193","0.4932376","0.4926465","0.49241674","0.4920523","0.4902308","0.49017957"],"string":"[\n \"0.635105\",\n \"0.62073517\",\n \"0.61985546\",\n \"0.6158757\",\n \"0.59900516\",\n \"0.58955044\",\n \"0.58135545\",\n \"0.58013874\",\n \"0.57838947\",\n \"0.56704354\",\n \"0.5652113\",\n \"0.5610305\",\n \"0.55248296\",\n \"0.551513\",\n \"0.5497405\",\n \"0.549419\",\n \"0.5461678\",\n \"0.5454392\",\n \"0.5449247\",\n \"0.541069\",\n \"0.54071915\",\n \"0.5393547\",\n \"0.5383908\",\n \"0.53606355\",\n \"0.5327275\",\n \"0.52997386\",\n \"0.52967876\",\n \"0.5287174\",\n \"0.52772015\",\n \"0.52659124\",\n \"0.526485\",\n \"0.52624476\",\n \"0.52619356\",\n \"0.52515525\",\n \"0.52429485\",\n \"0.5232549\",\n \"0.5228436\",\n \"0.52221924\",\n \"0.52184594\",\n \"0.5208116\",\n \"0.52054185\",\n \"0.51976675\",\n \"0.5183016\",\n \"0.51820683\",\n \"0.5176655\",\n \"0.51718193\",\n \"0.51567286\",\n \"0.5155581\",\n \"0.5151049\",\n \"0.5149151\",\n \"0.5136968\",\n \"0.513689\",\n \"0.5120048\",\n \"0.51186216\",\n \"0.5116506\",\n \"0.5110474\",\n \"0.51080495\",\n \"0.51072574\",\n \"0.5105606\",\n \"0.51006687\",\n \"0.5097277\",\n \"0.5092744\",\n \"0.50925004\",\n \"0.5071251\",\n \"0.50552994\",\n \"0.5048711\",\n \"0.50465983\",\n \"0.5045155\",\n \"0.5044352\",\n \"0.50436103\",\n \"0.50374824\",\n \"0.5037268\",\n \"0.50168514\",\n \"0.5013812\",\n \"0.50136334\",\n \"0.50072783\",\n \"0.50046957\",\n \"0.5004398\",\n \"0.49976704\",\n \"0.49907178\",\n \"0.49897188\",\n \"0.49868864\",\n \"0.49796006\",\n \"0.49752223\",\n \"0.4973241\",\n \"0.49728176\",\n \"0.4972098\",\n \"0.4970689\",\n \"0.497001\",\n \"0.49679896\",\n \"0.4962551\",\n \"0.49512583\",\n \"0.4948872\",\n \"0.494673\",\n \"0.4937193\",\n \"0.4932376\",\n \"0.4926465\",\n \"0.49241674\",\n \"0.4920523\",\n \"0.4902308\",\n \"0.49017957\"\n]","isConversational":false},"document_score":{"kind":"string","value":"0.0"},"document_rank":{"kind":"string","value":"-1"}}},{"rowIdx":16585,"cells":{"query":{"kind":"string","value":"Parse a batch of gerber files in a bz2 tarball."},"document":{"kind":"string","value":"def test_bz_batch(self):\n assert self.design.layout.layers[0].name == 'top'"},"metadata":{"kind":"string","value":"{\n \"objective\": {\n \"self\": [],\n \"paired\": [],\n \"triplet\": [\n [\n \"query\",\n \"document\",\n \"negatives\"\n ]\n ]\n }\n}"},"negatives":{"kind":"list like","value":["def extract_bz2(tar_bz_f, calc_type):\n \n # we give the gaussian calculator a label that includes the directory the\n # log file is contained in, this does not affect the parsing process but\n # generate a warning as it is not an expected form for the label. To avoid\n # the profusion of warning messages in stdout we suppress warnings here.\n warnings.filterwarnings(\"ignore\")\n\n extended_xyzs = []\n\n with tarfile.open(tar_bz_f,'r:bz2') as data_tar:\n calc_logs = (log_tar for log_tar in data_tar \n if calc_type in log_tar.name and '.log' in log_tar.name)\n \n for calc_log in calc_logs:\n try:\n # extract log file (and relevant directory)\n data_tar.extract(calc_log)\n\n # convert to ASE/Gaussian format\n mol = read(calc_log.name)\n mol.set_calculator(\n Gaussian(\n label=calc_log.name.replace('.log','')\n )\n )\n\n # parse into ML readable format\n parsed_mol = ase_mol_parse(mol)\n extended_xyzs.append(parsed_mol)\n except AttributeError:\n # if the calculation didn't complete we get an empty dictionary \n # so we we keep track of these failed calculations with a blank \n # entry other than mol_id\n blank_entry = {'mol_id':calc_log.name.replace('.log','')}\n extended_xyzs.append(blank_entry)\n finally:\n # delete extracted log file\n os.remove(calc_log.name)\n\n # solves memory problem\n # http://blogs.it.ox.ac.uk/inapickle/2011/06/20/high-memory-usage-when-using-pythons-tarfile-module/ # noqa\n data_tar.members=[]\n \n dir_name = tar_bz_f.replace('.tar.bz2','')\n\n # delete extracted directory\n os.rmdir(dir_name)\n\n # search key function\n # assumes files are named xxx_frame_{frame}_mol_{no}\n def mol_no_frame(mol):\n mol_no = int(mol['mol_id'].split('_')[-1].replace('.log',''))\n mol_frame = int(mol['mol_id'].split('_')[-3])\n return mol_no,mol_frame\n\n extended_xyzs = sorted(extended_xyzs,key=mol_no_frame)\n\n with open(dir_name + '_' + calc_type + '_data.pkl', 'w') as data_f:\n dill.dump(extended_xyzs, data_f)","def _read_recs(basedir):\n for borotag in boro_tags:\n datafile = \"%s/%s.csv\" % (basedir,borotag)\n print(\"slurp '%s' ..\" % datafile)\n recs = read_recs(datafile)\n yield from (pluto.parse.normalize(r) for r in recs)","def parse_gzipped_directory(input_dir, start_date, end_date, infos, backup_stamps):\n try:\n file_names = sorted(os.listdir(input_dir)) \n for file_name in file_names:\n if file_name.endswith(\".manifest.gz\") or file_name.endswith(\".manifest\"):\n tmp = parse_file(input_dir + \"/\" + file_name, start_date, end_date, backup_stamps)\n backup_stamps[tmp[\"backup_label\"]] = tmp[\"backup_timestamp_stop_ts\"]\n if tmp:\n infos.append(tmp)\n except OSError as e:\n logging.error(\"Failed to open directory\", exc_info=True)\n exit(1)\n except:\n raise","def debianize( strFilename ):\n \n #~ data = gzip.GzipFile( strFilename ).read();\n #~ print data;\n #~ return;\n \n #~ data = gzip.open( strFilename ).read();\n #~ print data;\n #~ return; \n \n #~ uncompressedData = bz2.BZ2File(strFilename).read()\n #~ print str(uncompressedData)\n #~ return;\n \n #~ file = open( strFilename, 'rb' );\n #~ data = file.read();\n #~ file.close();\n #~ print debug.dumpHexa( data );\n \n #~ ar = tarfile.open(strFilename, 'r:*')\n #~ for item in ar:\n #~ print( str(item) );\n #~ print( \"%s:\" % item.name );\n #~ #print debug.dumpHexa(item.buf);\n #~ #print zlib.decompress(item.buf)\n #~ #print zlib.decompress(ar.extractfile(item).read())\n #~ data = ar.extractfile(item.name).read()\n #~ print data # works !\n #~ ar.close() \n #~ return;\n \n fileLists = [];\n file = open( strFilename );\n data = file.read();\n file.close();\n \n print( \"data len: %d\" % len( data ) );\n\n nDataCompressedOffset = 0; # 132\n\n # works fine on toto.gz\n #~ f = gzip.open(strFilename, 'rb')\n #~ file_content = f.read()\n #~ print file_content\n #~ f.close() \n \n #~ decompressor = bz2.BZ2Decompressor();\n #~ uncompressed = decompressor.decompress(data[nDataCompressedOffset:]);\n \n #~ uncompressed = zlib.decompress(data[nDataCompressedOffset:]);\n \n uncompressed = decompress( data );\n print( \"uncompressed: %s\" % str( uncompressed ) );","def _decompress_tarball(*, in_fileobj, out_fileobj):\n with tarfile.open(fileobj=in_fileobj, mode=\"r\") as it, tarfile.open(\n fileobj=out_fileobj, mode=\"w|\"\n ) as ot:\n for member in it.getmembers():\n extracted = it.extractfile(member)\n ot.addfile(member, extracted)","def create_tarballs_from_xml_files_in_folder(xml_dir, download_date=\"2017.11.02\"):\n\n xml_list = glob.glob(os.path.join(xml_dir, \"*.xml\"))\n\n for xml in xml_list:\n xml_renamed = xml[:-4] + \".BLAST.xml\"\n xml_tar_gz = xml[:-4] + \".BLAST.xml.tar.gz\"\n xml_txt = xml[:-4] + \"_details.txt\"\n # xml_txt = xml[:-4] + \".BLAST_details.txt\"\n\n if not os.path.isfile(xml_tar_gz):\n copyfile(xml, xml_renamed)\n acc = os.path.basename(xml).split(\".\")[0]\n sys.stdout.write(\"{}, \".format(acc))\n sys.stdout.flush()\n # create an empty text file with the download date\n date = strftime(\"%Y%m%d\")\n with open(xml_txt, \"w\") as f:\n f.write(\"acc\\t{}\\ndownload_date\\t{}\\ndatabase\\tncbi_nr\\ne_value\\t1\\n\".format(acc, download_date))\n\n with tarfile.open(xml_tar_gz, mode='w:gz') as tar:\n # add the files to the compressed tarfile\n tar.add(xml_renamed, arcname=os.path.basename(xml_renamed))\n tar.add(xml_txt, arcname=os.path.basename(xml_txt))\n\n # delete the original files\n try:\n os.remove(xml_renamed)\n os.remove(xml_txt)\n except:\n sys.stdout.write(\"{} could not be deleted\".format(xml_renamed))","def ParserTeil2():\r\n Bags = {}\r\n for Line in Lines:\r\n Words = Line.split()\r\n Farbe = Words[0]+\" \"+Words[1]\r\n Bags[Farbe] = re.findall(r\"(\\d+?) (.+?) bags?\", Line)\r\n return Bags","def _unpack_tar(self, dir, filters):\n try:\n unpackArchive = gbpc.UnpackTarArchive(self.path, dir, filters)\n unpackArchive()\n except gbpc.CommandExecFailed:\n # unpackArchive already printed an error message\n raise GbpError","def main(args):\n # Extract keys\n logger.info(\"Extracting brass bedpe file key from tarfile...\")\n bedpe, bedpe_index = extract_tar_keys(args.results_archive)\n # process bedpe\n logger.info(\"Processing brass bedpe {0}...\".format(bedpe))\n process_bedpe(args.results_archive, bedpe, bedpe_index, args.output_prefix)","def bags(fondz_dir):\n fondz_dir = os.path.abspath(fondz_dir)\n results = {\n 'bags': [],\n 'num_files': 0,\n 'bytes': 0\n }\n originals_dir = os.path.join(fondz_dir, \"originals\")\n\n for bag in os.listdir(originals_dir):\n # TODO: look for other manifest types?\n bag_dir = os.path.join(originals_dir, bag)\n manifest = os.path.join(bag_dir, \"manifest-md5.txt\")\n b = {\n \"files\": [],\n \"bytes\": 0,\n }\n for line in open(manifest):\n line = line.strip()\n cols = re.split(r' +', line)\n path = os.path.join(bag_dir, cols[1])\n st = os.stat(path)\n rel_path = os.path.join(\"originals\", bag, path)\n b['bytes'] += st.st_size\n b['files'].append({\n \"path\": rel_path,\n \"bytes\": st.st_size,\n \"created\": st.st_ctime,\n \"modified\": st.st_mtime,\n \"md5\": cols[0]\n })\n results['bytes'] += b['bytes']\n results['num_files'] += len(b['files'])\n results['bags'].append(b)\n\n bags_json = os.path.join(fondz_dir, \"js\", \"bags.json\")\n write_json(results, bags_json)\n return results","def parse(path):\n data = gzip.open(path, 'rb')\n for byte_line in data:\n yield eval(byte_line) # return generator instance to save memory","def gbk_parse(fname):\n fhand = _open_file(gbkfname)\n unk = 1 \n\n for record in SeqIO.parse(fhand, \"genbank\"):\n\n gene_tags = dict()\n tx_tags = collections.defaultdict(list) \n exon = collections.defaultdict(list) \n cds = collections.defaultdict(list) \n mol_type, chr_id = None, None \n\n for rec in record.features:\n\n if rec.type == 'source':\n mol_type = rec.qualifiers['mol_type'][0]\n try:\n chr_id = rec.qualifiers['chromosome'][0]\n except:\n chr_id = record.name \n continue \n\n strand='-'\n strand='+' if rec.strand>0 else strand\n \n fid = None \n try:\n fid = rec.qualifiers['gene'][0]\n except:\n pass\n\n transcript_id = None\n try:\n transcript_id = rec.qualifiers['transcript_id'][0]\n except:\n pass \n\n if re.search(r'gene', rec.type):\n gene_tags[fid] = (rec.location._start.position+1, \n rec.location._end.position, \n strand,\n rec.type,\n rec.qualifiers['note'][0])\n elif rec.type == 'exon':\n exon[fid].append((rec.location._start.position+1, \n rec.location._end.position))\n elif rec.type=='CDS':\n cds[fid].append((rec.location._start.position+1, \n rec.location._end.position))\n else: \n # get all transcripts \n if transcript_id: \n tx_tags[fid].append((rec.location._start.position+1,\n rec.location._end.position, \n transcript_id,\n rec.type))\n # record extracted, generate feature table\n unk = feature_table(chr_id, mol_type, strand, gene_tags, tx_tags, cds, exon, unk)\n \n #break\n fhand.close()","def _extract_data(inputs):\n filename, split = inputs\n for name, fobj in tfds.download.iter_archive(\n filename, tfds.download.ExtractMethod.TAR_STREAM\n ):\n split_name = name.split(\"_\")\n if len(split_name) > 2 and split_name[2] == split:\n yield [name, fobj.read()]","def parse_file(path):\n if sys.platform.startswith('linux') or sys.platform.startswith('cygwin'):\n # Assume Linux has GNU objdump. This has the options:\n # -t (list symbols), -C (de-mangle symbol names)\n objdump_args = ['objdump', '-t', '-C']\n elif sys.platform.startswith('darwin'):\n # Assume OSX has LLVM objdump. This has the options:\n # -t (list symbols)\n objdump_args = ['objdump', '-t']\n objdump_args.append(path)\n with StreamingProcess(objdump_args) as proc:\n # Find the first non-blank line.\n first_line = proc.peek()\n while not first_line:\n try:\n proc.next()\n first_line = proc.peek()\n except StopIteration:\n return []\n # Is this an archive?\n match = re.match(r'^.*[Aa]rchive\\s+(.+):$', first_line)\n if match:\n # In this format we have to skip this descriptive line.\n proc.next()\n return parse_archive(match.group(1), proc)\n # Some objdumps format archives differently.\n match = re.match(r'^(.+)\\((.+)\\):\\s+file format', first_line)\n if match:\n return parse_archive(match.group(1), proc)\n # Otherwise maybe it's an object file?\n match = re.match(r'^(.+):\\s+file format', first_line)\n if match:\n return [parse_object_file(match.group(1), proc)]\n # Otherwise it's not an archive or object file.\n return []","def tar_file_and_group(data):\n for sample in data:\n assert \"stream\" in sample\n stream = tarfile.open(fileobj=sample[\"stream\"], mode=\"r|*\")\n prev_prefix = None\n example = {}\n valid = True\n for tarinfo in stream:\n name = tarinfo.name\n pos = name.rfind(\".\")\n assert pos > 0\n prefix, postfix = name[:pos], name[pos + 1 :]\n if prev_prefix is not None and prefix != prev_prefix:\n example[\"key\"] = prev_prefix\n if valid:\n yield example\n example = {}\n valid = True\n with stream.extractfile(tarinfo) as file_obj:\n try:\n if postfix == \"txt\":\n example[\"txt\"] = file_obj.read().decode(\"utf8\").strip()\n elif postfix in AUDIO_FORMAT_SETS:\n waveform, sample_rate = torchaudio.load(file_obj)\n example[\"wav\"] = waveform\n example[\"sample_rate\"] = sample_rate\n else:\n example[postfix] = file_obj.read()\n except Exception as ex:\n valid = False\n logging.warning(\"error to parse {}\".format(name))\n prev_prefix = prefix\n if prev_prefix is not None:\n example[\"key\"] = prev_prefix\n yield example\n stream.close()\n if \"process\" in sample:\n sample[\"process\"].communicate()\n sample[\"stream\"].close()","def process_lines(self):\n\n for line in self.all_lines:\n container_re = re.compile(r'(.*?) bags')\n bags_re = re.compile(r'(?:(\\d+)|no other) (.*?) bags*')\n container_name = re.match(container_re, line).group(1)\n bags = re.findall(bags_re, line)\n self.all_bags[container_name] = bags","def parse_input():\n with open(\"input_07.txt\", \"r\") as f:\n for line in f:\n Bag(line)","def unpack_landsat(inpath, outpath, bands=None, clouds=None):\r\n tfile = tarfile.open(inpath,'r:gz')\r\n if bands is None:\r\n #Extract all of the bands.\r\n tfile.extractall(outpath);\r\n else:\r\n #Extract just the bands specified.\r\n\r\n #Get the names of the members of the archive\r\n names = tfile.getnames()\r\n\r\n #Make sure the bands are given as a list\r\n bands = list(bands)\r\n\r\n #Find those elements of the archive that match the bands specified\r\n #\t(plus metadata file)\r\n members = tfile.getmembers()\r\n elements = []\r\n blist = ''.join(str(i) for i in bands)\r\n if clouds:\r\n patternStr = '.*_B[' + blist + ']\\.TIF|.*_MTL.txt|.*_band[' + blist + \\\r\n ']\\.tif|.*_cfmask.*\\.tif|.*\\.xml|.*cloud.*\\.tif'\r\n else:\r\n patternStr = '.*_B[' + blist + ']\\.TIF|.*_MTL.txt|.*_band[' + blist + \\\r\n ']\\.tif|.*_cfmask.*\\.tif|.*\\.xml'\r\n\r\n pattern = re.compile(patternStr)\r\n for i, name in enumerate(names):\r\n if pattern.match(name):\r\n elements.append(members[i])\r\n tfile.extractall(outpath,members = elements)\r\n\r\n '''\r\n Note: the below section was written with the intention of\r\n adding valuable metadata info to the .TIF files themselves.\r\n This theoretically allows easy retreival of key metadata info,\r\n but the method to set new metadata seems unreliable. Appears to\r\n be an open issue, but there may be a solution. For now, assume\r\n this does not work.\r\n\r\n #Now we loop through each output, adding important metadata.\r\n #Fetch metadata and make sure there is only one file.\r\n meta = glob.glob(outpath + '/*_MTL.txt')\r\n if len(meta) > 1:\r\n raise('MORE THAN ONE METADATA FILE FOUND!')\r\n\r\n metadata = read_metadata(meta[0])\r\n\r\n #Add the metadata.\r\n for tif in glob.glob(outpath + '*.TIF'):\r\n #Open the tif file\r\n ras = gdal.Open(tif)\r\n\r\n #Preserve any existing metadata & add important metadata from file\r\n meta = ras.GetMetadata()\r\n meta['SCENE_CENTER_TIME'] = metadata['SCENE_CENTER_TIME']\r\n meta['DATE_ACQUIRED'] = metadata['DATE_ACQUIRED']\r\n meta['LANDSAT_SCENE_ID'] = metadata['LANDSAT_SCENE_ID']\r\n\r\n #Now write the new metadata back to the tif.\r\n ras.SetMetadata(meta)\r\n ras.FlushCache()\r\n ras = None\r\n '''","def parse_blast_XML(blast_xml):\n\tblast_xml_op = open (blast_xml, 'r')\n\tfor record in NCBIXML.parse(blast_xml_op):\n\t\tfor align in record.alignments:\n\t\t\thit_id = align.hit_id.split(\"|\")\n\t\t\tprev_eval = 1\n\t\t\tcoverage = align.length / 390 ######arreglar per posar longitud sequencia\n\t\t\tfor hsp in align.hsps:\n\t\t\t\tif hsp.expect < prev_eval:\n\t\t\t\t\tprev_eval = hsp.expect\n\t\t\tefetch = Entrez.efetch(db=\"protein\", id=hit_id, rettype=\"fasta\")\n\t\t\tfor line in efetch:\n\t\t\t\tline = line.rstrip()\n\t\t\t\tif line.startswith(\">\"):\n\t\t\t\t\tid_info = line\n\t\t\t\t\tsequence = \"\"\n\t\t\t\telse:\n\t\t\t\t\tsequence += line\n\t\t\tsequence += line\n\n\t\t\torganism = id_info[id_info.find(\"[\") + 1:id_info.find(\"]\")]\n\t\t\torganism = organism.split()\n\t\t\tif len(organism) != 1:\n\t\t\t\tspecies = str(organism[0] + \"_\" + organism[1])\n\n\t\t\tyield BlastResult(hit_id[1], species, sequence, prev_eval, coverage)","def _unpack_archive(self, dir, filters):\n ext = os.path.splitext(self.path)[1]\n if ext in [\".zip\", \".xpi\"]:\n if filters:\n raise GbpError(\"Can only filter tar archives: %s\", (ext, self.path))\n self._unpack_zip(dir)\n else:\n self._unpack_tar(dir, filters)","def iterator(dataset_fn, sections=None, lang=None, field_indices=None):\n files = filelist(lang=lang, sections=sections)\n\n with TarFile.open(dataset_fn, 'r:gz') as f:\n for member in f:\n if member.isfile() and os.path.basename(member.name) in files:\n logging.info('parsing %s ...' % member.name)\n m_f = f.extractfile(member)\n\n for sentence in parse_conll(m_f, field_indices=field_indices):\n yield sentence\n\n m_f.close()","def parse(self, recursive=True):\n # Read and process the file header\n self.fh.seek(0x0, 0)\n header = struct.unpack(\"=10I\", self.fh.read(0x28))\n\n data_start_block = header[0x1]\n\n idx_table_entry_count = header[0x4]\n\n off_table_offset = header[0x5]\n off_table_addr = self.IDX_TABLE_ADDR + off_table_offset\n\n self.fh.seek(self.IDX_TABLE_ADDR, 0)\n\n # Read and populate the index table\n idx_table = []\n for idx in range(idx_table_entry_count):\n typ, num1, num2, num3, num4 = Image.parse_idx_entry(\n self.fh.read(self.IDX_TABLE_ENTRY_SIZE)\n )\n idx_table.append([typ, num1, num2, num3, num4])\n\n self.fh.seek(off_table_addr, 0)\n\n # FIXME: Not sure what 'unk' is.\n off_table_entry_count, unk = struct.unpack(\"=4x2I\", self.fh.read(0xC))\n\n # Read and populate the offset table\n off_table = {}\n for i in range(off_table_entry_count):\n idx, blk_num = Image.parse_off_entry(\n self.fh.read(self.OFF_TABLE_ENTRY_SIZE)\n )\n off_table[idx] = blk_num\n\n # Populate entries\n self.entries = []\n for idx, idx_entry in enumerate(idx_table):\n if idx not in off_table:\n self.entries.append(None)\n continue\n\n blk_num = off_table[idx]\n off = self.fh.tell()\n\n # We need to grab the actual (compressed) size from the PACKage header\n res = None\n addr = self.BLOCK_NUM_ADDR(blk_num)\n if idx_entry[0x0] == b\"PAK \":\n self.fh.seek(addr)\n (\n typ,\n cnt,\n ptr_off,\n str_table_off,\n dec_data_off,\n dec_len,\n cmp_len,\n pad_len,\n ) = Package.parse_header(self.fh.read(Package.ENTRY_SIZE))\n res = Package(FileWindow(self.filename, addr, cmp_len), idx_entry[0x3])\n else:\n res = Resource(\n idx_entry[0x0], FileWindow(self.filename, addr, idx_entry[0x1])\n )\n\n if recursive:\n res.parse(recursive)\n self.entries.append(res)\n self.fh.seek(off, 0)","def bgzip_tabix(bedbz2):\n bed = bedbz2.replace(\".bz2\", \"\")\n bedgz = bed + \".gz\"\n tbi = bedgz + \".tbi\"\n if os.path.exists(bedgz) and os.path.exists(tbi):\n print bedgz, tbi, \"has beed generated.\"\n return\n c1 = \"bzip2 -d %s\" % bedbz2\n c2 = \"bgzip %s\" % bed\n c3 = \"tabix -s 1 -b 2 -e 3 %s\" % bedgz\n call_sys([c1, c2, c3])","def readArff(filename):\n \n data = []\n labels = []\n\n def parseLine(line): # csv.reader could not do this.\n isopen = False\n current = ''\n for c in line:\n if c == \"'\":\n if isopen:\n yield current\n current = ''\n isopen = not isopen\n elif isopen:\n current += c\n\n #with filename.open() as f:\n with bz2.open(str(filename)+'.bz2', 'r') as f:\n \n line = ''\n while line != '@data':\n line = f.readline().decode().strip()\n if line.startswith(\"@attribute 'classification'\"):\n line = line[line.find('{') + 1:line.find('}')]\n classes = {i:n for n,i in enumerate(parseLine(line))}\n\n for line in f.read().decode().splitlines():\n record = list(parseLine(line))\n labels.append(classes[record[-1]])\n data.append([int(x) for x in record[:-1]])\n return numpy.array(data, dtype=float), numpy.array(labels), classes","def bz2_file_reader(path):\n return bz2.open(path, 'rt')","def decompress_bz2(filename):\n basename = os.path.basename(filename)\n newfilepath = os.path.dirname(filename) + '/' + '.'.join(basename.split('.')[0:-1]) # all but bz2\n\n with open(newfilepath, 'wb') as new_file, bz2.BZ2File(filename, 'rb') as bz2_file:\n for data in iter(lambda : bz2_file.read(100 * 1024), b''):\n new_file.write(data)\n\n return newfilepath","def decompress_bz2(filename):\n basename = os.path.basename(filename)\n newfilepath = os.path.dirname(filename) + '/' + '.'.join(basename.split('.')[0:-1]) # all but bz2\n\n with open(newfilepath, 'wb') as new_file, bz2.BZ2File(filename, 'rb') as bz2_file:\n for data in iter(lambda : bz2_file.read(100 * 1024), b''):\n new_file.write(data)\n\n return newfilepath","def convert(self, tag=\"Data\", delimiter=\",\", noheader=False,\n limit=-1, buffer_size=1000):\n\n\n file_ctr = 0\n item_ctr = 0\n for dirName, subdirList, fileList in os.walk(self.input_directory):\n print('Found directory: %s' % dirName)\n for fname in fileList:\n print('\\t%s' % fname)\n # open the xml file for iteration\n if not fname.endswith(\".xml\"):\n continue\n #pdb.set_trace()\n \n input_file = dirName + \"/\" + fname\n self.context = ETree.iterparse(input_file, events=(\"start\", \"end\"))\n\n # iterate through the xml\n items = [{}]\n\n depth = 0\n min_depth = 0\n row_depth = -1\n n = 0\n for event, elem in self.context:\n if event == \"start\":\n depth += 1\n continue\n else:\n depth -= 1\n if depth < min_depth:\n min_depth = depth\n\n if depth < row_depth and items:\n if noheader:\n noheader = False\n else:\n # new line\n self.output_buffer.append(items)\n items = []\n # flush buffer to disk\n if len(self.output_buffer) > buffer_size:\n self._write_buffer(delimiter)\n\n plain_tag = elem.tag\n last_delim = max(elem.tag.rfind('}'), elem.tag.rfind(':'))\n if 0 < last_delim < len(elem.tag) - 1:\n plain_tag = elem.tag[last_delim + 1:]\n if tag == plain_tag:\n if n == 0:\n min_depth = depth\n elif n == 1:\n row_depth = min_depth\n n += 1\n if 0 < limit < n:\n break\n elem_name = elem.get(\"name\")\n if elem_name in self.output_dict[0].keys():\n if elem_name == 'SamS.ArchivedURL':\n if hash(elem.text) in self.item_titles.keys() and self.item_titles[hash(elem.text)] == elem.text:\n #item is repetative\n self.output_dict[item_ctr]={}\n #item_ctr-=1\n break\n else:\n self.item_titles[hash(elem.text)] = elem.text\n self.output_dict[item_ctr][elem_name]= elem.text and elem.text.encode('utf8') or ''\n\n #if (len(self.output_dict[item_ctr]) > 0 ) :\n if ('SamS.ArchivedURL' in self.output_dict[item_ctr]):\n item_ctr+=1\n self.output_dict.append({})\n else:\n self.output_dict[item_ctr] = {}\n \n file_ctr+=1 #next row in the dictionary array\n print \"processing file no \", file_ctr, \" item no\", item_ctr\n\n #pdb.set_trace()\n self._write_buffer(delimiter) # write rest of the buffer to file\n\n return n","def parse(self):\n gen = self.v6_gen() # read from workers\n gen = self.tuple_gen(gen) # convert v6->tuple\n gen = self.batch_gen(gen) # assemble into batches\n for b in gen:\n yield b","def parse(self, filename: str, input_format='csv', **kwargs):\n if 'delimiter' not in kwargs:\n kwargs['delimiter'] = self._extention_types[input_format]\n if filename.endswith('.tar'):\n with tarfile.open(filename) as tar:\n for member in tar.getmembers():\n f = tar.extractfile(member)\n df = pd.read_csv(f, comment='#', **kwargs) # type: pd.DataFrame\n if member.name == 'nodes.csv':\n self.load_nodes(df)\n elif member.name == 'edges.csv':\n self.load_edges(df)\n else:\n raise Exception('Tar file contains unrecognized member {}'.format(member.name))\n else:\n df = pd.read_csv(filename, comment='#', **kwargs) # type: pd.DataFrame\n self.load(df)","def fromgroups(args):\n from jcvi.formats.bed import Bed\n\n p = OptionParser(fromgroups.__doc__)\n opts, args = p.parse_args(args)\n\n if len(args) < 2:\n sys.exit(not p.print_help())\n\n groupsfile = args[0]\n bedfiles = args[1:]\n beds = [Bed(x) for x in bedfiles]\n fp = open(groupsfile)\n groups = [row.strip().split(\",\") for row in fp]\n for b1, b2 in product(beds, repeat=2):\n extract_pairs(b1, b2, groups)","def parse(self, *args, **kwargs):\n if self.is_gzipped:\n fin = gzip.open(self.path, 'rb')\n else:\n fin = open(self.path, 'r')\n line_num = 0\n expect_header = True\n for line in fin:\n line_num += 1\n line = line.strip()\n if not line: # skip empty lines\n continue\n if expect_header:\n if self._is_header(line):\n logger.debug(\n f\"Detected header at line {line_num}: {line!r}\")\n continue\n else:\n expect_header = False\n try:\n chrom, pos = self._parse_line(line, *args, **kwargs)\n if chrom is not None:\n yield chrom, pos\n except (IndexError, ValueError, TypeError):\n fin.close()\n raise FileFormatError(format=self.format, line_num=line_num,\n line=line)\n fin.close()","def parse(fcontents, utf16=False): # TODO where does this conversion take place??\n if utf16:\n # Handle a bunch of Unicode nonsense; files appear to be in UTF-16LE\n quant_results = fcontents.split(BLOCK_DIVIDER_UTF16)[3]\\\n .decode(AWKWARD_ENCODING).encode('ascii', 'ignore').split(\"\\r\\n\")\n else:\n quant_results = fcontents.split(BLOCK_DIVIDER)[3].split(\"\\r\\n\")\n\n for res in quant_results:\n items = res.split(\"\\t\")\n if re.search(\"\\d+\", items[0]): # ignore non-digit rows\n amt = items[9]\n if amt == OUTSIDE_LADDER:\n amt = 100\n yield (int(items[0]), items[1], float(amt))","def _add_tag_files(\n zip_file, dir_name, payload_info_list, payload_byte_count, payload_file_count\n):\n tag_info_list = []\n _add_tag_file(zip_file, dir_name, tag_info_list, _gen_bagit_text_file_tup())\n _add_tag_file(\n zip_file,\n dir_name,\n tag_info_list,\n _gen_bag_info_file_tup(payload_byte_count, payload_file_count),\n )\n _add_tag_file(\n zip_file, dir_name, tag_info_list, _gen_pid_mapping_file_tup(payload_info_list)\n )\n return tag_info_list","def tarball(request):\n\n patches = (models.Patch\n .query(ancestor=request.patchset.key)\n .order(models.Patch.filename)\n .fetch(1000))\n\n temp = tempfile.TemporaryFile()\n tar = tarfile.open(mode=\"w|bz2\", fileobj=temp)\n\n def add_entry(prefix, content, patch):\n data = content.data\n if data is None:\n data = content.text\n if isinstance(data, unicode):\n data = data.encode(\"utf-8\", \"replace\")\n if data is None:\n return\n info = tarfile.TarInfo(prefix + patch.filename)\n info.size = len(data)\n # TODO(adonovan): set SYMTYPE/0755 when Rietveld supports symlinks.\n info.type = tarfile.REGTYPE\n info.mode = 0644\n # datetime->time_t\n delta = request.patchset.modified - datetime.datetime(1970, 1, 1)\n info.mtime = int(delta.days * 86400 + delta.seconds)\n tar.addfile(info, fileobj=StringIO(data))\n\n for patch in patches:\n if not patch.no_base_file:\n try:\n add_entry('a/', patch.get_content(), patch) # before\n except FetchError: # I/O problem?\n logging.exception('tarball: patch(%s, %s).get_content failed' %\n (patch.key.id(), patch.filename))\n try:\n add_entry('b/', patch.get_patched_content(), patch) # after\n except FetchError: # file deletion? I/O problem?\n logging.exception('tarball: patch(%s, %s).get_patched_content failed' %\n (patch.key.id(), patch.filename))\n\n tar.close()\n temp.flush()\n\n wrapper = FileWrapper(temp)\n response = HttpResponse(wrapper, mimetype='application/x-gtar')\n response['Content-Disposition'] = (\n 'attachment; filename=patch%s_%s.tar.bz2' % (request.issue.key.id(),\n request.patchset.key.id()))\n response['Content-Length'] = temp.tell()\n temp.seek(0)\n return response","def unpack(file, path='.'):\n assert isfile(file)\n assert isdir(path)\n\n for implementor in [GzipTarredFile, ZippedFile, Bzip2TarredFile]:\n if implementor.is_valid(file):\n with console.cd(path):\n return [implementor(file).extract(), implementor]\n else:\n raise InvalidFile, 'compressed file format unknown: %s' % file","def tarball(request):\n\n patches = (models.Patch\n .query(models.Patch.patchset_key == request.patchset.key)\n .order(models.Patch.filename)\n .fetch(1000))\n\n temp = tempfile.TemporaryFile()\n tar = tarfile.open(mode=\"w|bz2\", fileobj=temp)\n\n def add_entry(prefix, content):\n data = content.data\n if data is None:\n data = content.text\n if isinstance(data, unicode):\n data = data.encode(\"utf-8\", \"replace\")\n if data is None:\n return\n info = tarfile.TarInfo(prefix + patch.filename)\n info.size = len(data)\n # TODO(adonovan): set SYMTYPE/0755 when Rietveld supports symlinks.\n info.type = tarfile.REGTYPE\n info.mode = 0644\n # datetime->time_t\n delta = request.patchset.modified - datetime.datetime(1970, 1, 1)\n info.mtime = int(delta.days * 86400 + delta.seconds)\n tar.addfile(info, fileobj=StringIO(data))\n\n for patch in patches:\n if not patch.no_base_file:\n try:\n add_entry('a/', patch.get_content()) # before\n except FetchError: # I/O problem?\n logging.exception('tarball: patch(%s, %s).get_content failed' %\n (patch.key.id(), patch.filename))\n try:\n add_entry('b/', patch.get_patched_content()) # after\n except FetchError: # file deletion? I/O problem?\n logging.exception('tarball: patch(%s, %s).get_patched_content failed' %\n (patch.key.id(), patch.filename))\n\n tar.close()\n temp.flush()\n\n wrapper = FileWrapper(temp)\n response = HttpResponse(wrapper, mimetype='application/x-gtar')\n response['Content-Disposition'] = (\n 'attachment; filename=patch%s_%s.tar.bz2' % (request.issue.key.id(),\n request.patchset.key.id()))\n response['Content-Length'] = temp.tell()\n temp.seek(0)\n return response","def parse(self, ergFilePath):\n infoFilePath = ergFilePath + '.info'\n quantityList = self.getQuantityList(infoFilePath)\n\n # get block size\n blockSize = sum(quantity.bytes for quantity in quantityList)\n\n with open(ergFilePath, 'rb') as ergFile:\n\n # read the first 16 bytes, as they are not needed now\n ergFile.read(16)\n\n # now read the rest of the file block wise\n block = ergFile.read(blockSize)\n while len(block) == blockSize:\n for q in quantityList:\n q.values.append(np.fromstring(block[:q.bytes], q.dataType)[0])\n block = block[q.bytes:]\n block = ergFile.read(blockSize)\n\n self.quantityList = quantityList\n return quantityList","def extract_tars(file_pattern, path_in, path_out):\n for f in glob.glob(os.path.join(path_in, file_pattern)):\n shutil.unpack_archive(f, path_out)","def gzip_files(topDir, afni_file,localizerfile):\n\n print 'GZIPPING FILES...'\n\n command1 = \"gzip %s*BRIK\" % (topDir)\n command2 = \"gzip %s*HEAD\" % (topDir)\n command3 = \"gzip %s%s/pb00*\" % (topDir,afni_file)\n command4 = \"gzip %s%s/errts*\" % (topDir,afni_file)\n command5 = \"gzip %s%s/fitts*\" % (topDir,afni_file)\n command6 = \"gzip %s%s/*al*\" % (topDir,afni_file)\n command7 = \"gzip %s%s/*ns*\" % (topDir,afni_file)\n command8 = \"gzip %s%s/all_runs*\" % (topDir,afni_file)\n command9 = \"gzip %s%s/*mask*\" % (topDir,afni_file)\n command10 = \"gzip %s*nii\" % (topDir)\n command11 = \"gzip %s%s/pb01*\" % (topDir,afni_file)\n command12 = \"gzip %s%s/pb03*\" % (topDir,afni_file)\n command13 = \"gzip %s%s/pb02*\" % (topDir,afni_file)\n\n os.system(command1)\n os.system(command2)\n os.system(command3)\n os.system(command4)\n os.system(command5)\n os.system(command6)\n os.system(command7)\n os.system(command8)\n #os.system(command9)\n os.system(command10)\n os.system(command11)\n try:\n os.system(command12)\n except:\n print 'Could not gzip pb03 files'\n\n if localizerfile == 'facescene_loc':\n os.system(command13)","def main():\r\n parser = CommonArgParser(__file__)\r\n parser.add_argument('src_dir', help='Source directory')\r\n parser.add_argument(\r\n 'out_dir',\r\n default='.',\r\n help=\"\"\"The directory the files to be extracted.\r\n (Default: Current directoty\"\"\")\r\n args = parser.parse_all()\r\n for f in next_file(args.src_dir, ['*.tgz', '*.tar.gz']):\r\n untgz(f, args.out_dir)","def parse(all_blobs, all_angles):","def boldExtract(genera):\r\n # Prepare Web Service Endpoint for BOLD's Public Data Portal API\r\n # Appending BOLD's base URL to each genera from the NSR list\r\n base_url = 'http://v4.boldsystems.org/index.php/API_Public/combined?taxon='\r\n source_urls = list(map(lambda x: \"{}{}{}\".\r\n format(base_url, x, '&format=tsv'), genera))\r\n\r\n # Download sequence data from BOLD using list of url's\r\n print('Beginning sequence data retrieval...')\r\n counter = 0\r\n for url in source_urls:\r\n r = http.request('GET', url)\r\n name = genera[counter]\r\n counter += 1\r\n with open(args.outdir1+\"/\"+name+\".tsv\", \"wb\") as fcont:\r\n fcont.write(r.data)","def iter_libsvm(filepath_or_buffer, target_type=float, compression='infer'):\n\n # If a file is not opened, then we open it\n if not hasattr(filepath_or_buffer, 'read'):\n filepath_or_buffer = open_filepath(filepath_or_buffer, compression)\n\n def split_pair(pair):\n name, value = pair.split(':')\n value = float(value)\n return name, value\n\n for line in filepath_or_buffer:\n\n # Remove carriage return and whitespace\n line = line.rstrip()\n # Remove potential end of line comments\n line = line.split('#')[0]\n\n y, x = line.split(' ', maxsplit=1)\n y = target_type(y)\n x = dict([split_pair(pair) for pair in x.split(' ')])\n yield x, y","def yield_publications_metadata(tf):\n logger.info('Start yielding...')\n with gzip.GzipFile(fileobj=tf, mode='r') as json_file:\n for index, line in enumerate(json_file):\n yield build_es_bulk(line.decode('utf-8'))","def parse_archive(path, objdump):\n object_files = []\n current_file = None\n for line in objdump:\n if not line:\n continue\n match = re.match(r'^(.*[^\\)])(\\((.+)\\))?:\\s+file format', line)\n if match:\n filename = match.group(3) if match.group(3) else match.group(1)\n current_file = ObjectFile(filename, path)\n object_files.append(current_file)\n continue\n if not current_file:\n raise Exception('Archive does not specify object to attribute '\n 'symbols to ' + path)\n sym = parse_symbol(line)\n if not sym:\n if current_file.symbols:\n current_file = None\n continue\n current_file.symbols.append(sym)\n return object_files","def bz2_file_bytes_reader(path):\n return bz2.open(path, 'rb')","def LoadBatch(filename):","def parse_ensembl_genes(lines):\n LOG.info(\"Parsing ensembl genes from file\")\n header = []\n for index, line in enumerate(lines):\n # File allways start with a header line\n if index == 0:\n header = line.rstrip().split(\"\\t\")\n continue\n # After that each line represents a gene\n\n yield parse_ensembl_line(line, header)","def __init__(self, fpath, prefix, suffix, globar_year=None):\n self.fpath = fpath\n prefix_len = len(prefix)\n suffix_len = len(suffix)\n self.year = globar_year\n self.year_str = str(globar_year)\n\n # filename example : good_2005_0.pgz\n files = [f for f in listdir(fpath) if isfile(join(fpath, f)) and\n (f[-suffix_len:] == suffix and f[:prefix_len] == prefix)]\n\n pat = '{0}_{1}'.format(prefix, self.year_str)\n last_batch = \\\n list(sorted(filter(lambda f: pat in f, files)))\n first_batch = \\\n list(sorted(filter(lambda f: pat not in f, files)))\n\n logging.info('in ChunkReader.__init__() : '\n '(last_batch) {0} files : {1}'.format(len(last_batch), ' '.join(last_batch)))\n logging.info('in ChunkReader.__init__() : '\n '(first_batch) {0} files : {1}'.format(len(first_batch), ' '.join(first_batch)))\n\n first_batch.extend(last_batch)\n # queue-like usage\n self.files = first_batch[::-1]\n logging.info('in ChunkReader.__init__ : '\n 'all files {0} files : {1}'.format(len(self.files), ' '.join(self.files)))","def parseDec_GZIPLoader(self, data): # Once gziploader is decrypted, parse the 0xA9 byte config\n hardcoded_val = data[0:1]\n flag = data[1:2]\n datfile_size = int.from_bytes(data[2:6], byteorder=\"little\")\n print(\"[+] datfile size: \", datfile_size)\n dllfile_size = int.from_bytes(data[6:10], byteorder=\"little\")\n print(\"[+] dllfile size: \", dllfile_size)\n dirname = self.extractStrFromBuff(data[10:])\n print(\"[+] Directory Name:\", dirname)\n\n count = self.incNulls(data[10 + len(dirname):])\n datname = self.extractStrFromBuff(data[count + 10 + len(dirname):])\n print(\"[+] Dat Name :\", datname)\n\n count = count + 10 + len(dirname) + len(datname)\n datname = datname[1:]\n count2 = self.incNulls(data[count:])\n count = count + count2\n dllname = self.extractStrFromBuff(data[count:])\n print(\"[+] Dll Name: \", dllname)\n count += len(dllname)\n count2 = self.incNulls(data[count:])\n count += count2\n # datfile offset is now 710 bytes in\n datfile_data = data[710:710 + datfile_size]\n dllfile_start = 710 + datfile_size\n dllfile_data = data[dllfile_start:dllfile_start + dllfile_size]\n datfile_b64 = base64.b64encode(datfile_data).decode()\n dllfile_b64 = base64.b64encode(dllfile_data).decode()\n ParsedDict = {\"Directory_Name\": dirname.decode(),\n \"DatFile_Name\": datname.decode(),\n \"DllFile_Name\": dllname.decode(),\n \"DatFile\": datfile_b64,\n \"DllFile\": dllfile_b64}\n\n return ParsedDict","def untgz(tgz_filename, out_dir):\r\n logging.info(\"Source: %s\" % tgz_filename)\r\n tgz = TgzHelper(tgz_filename, out_dir)\r\n tgz.extract()","def _process_fileobj(self,\n tar_file_obj: IO[bytes],\n object_node: graph.COSObject) -> None:\n with tarfile.open(fileobj=tar_file_obj) as tar_file:\n gz_file_names = [f.name for f in tar_file.getmembers()\n if f.name.endswith('.gz')]\n for gz_file_name in gz_file_names:\n gz_file_obj = tar_file.extractfile(gz_file_name)\n if gz_file_obj:\n oem_data = self._parse_oem_data(gz_file_obj)\n aso_id = self._get_aso_id_from_file_name(gz_file_name)\n self._save_oem(oem_data, aso_id, object_node)","def archive_bag_api_messages(bags, bucket):\n for bag in bags:\n yield {\n 'type': 'Ingest',\n 'ingestType': {\n 'id': 'create',\n 'type': 'IngestType'\n },\n 'uploadUrl': f's3://{bucket}/{bag}'\n }","def read_data_with_preprocess(filename):\n\n with bz2.BZ2File(filename) as f:\n\n data = []\n file_size = os.stat(filename).st_size\n chunk_size = 1024 * 1024 # reading 1 MB at a time as the dataset is moderately large\n print('Reading data...')\n for i in range(ceil(file_size//chunk_size)+1):\n bytes_to_read = min(chunk_size,file_size-(i*chunk_size))\n file_string = f.read(bytes_to_read).decode('utf-8')\n file_string = file_string.lower()\n # tokenizes a string to words residing in a list\n file_string = nltk.word_tokenize(file_string)\n data.extend(file_string)\n return data","def parse_records(self):\n for record in sp.parse(gzip.open(\n \"./human_uniprot_04_07_20.gz\", 'rt')):\n # print(record.taxonomy_id)\n # if record.organism != \"Homo sapiens\":\n # continue\n # print(record.features[0])\n # for comment in record.comments:\n # if comment.startswith(\"SUBCELLULAR LOCATION\"):\n # print(comment)\n self.extract_features_to_dict(record)\n self.extract_localization(record)","def extract_tarball(fileobj, path, callback=None):\n tar_cmd = [\"tar\", \"-zx\", \"--directory=%s\" % path]\n tar_proc = make_subprocess(tar_cmd, stderr=True, stdin=True)\n\n try:\n while True:\n chunk = fileobj.read(CHUNK_SIZE)\n if chunk == '':\n break\n\n if callback:\n callback(chunk)\n\n tar_proc.stdin.write(chunk)\n except Exception:\n try_kill_process(tar_proc)\n raise\n\n finish_subprocess(tar_proc, tar_cmd)","def read_and_parse(path_pattern, parser, **kwargs):\n for filename in glob.glob(path_pattern):\n with open(filename, 'r') as file:\n yield filename, parser.parse(file.read(), **kwargs)","def decompress(self, chunk):\n # print(self.decompressor.eof)\n data = self.data_rem + self.decompressor.decompress(chunk)\n if data != 0: # 0 is common -- waiting for a bzip2 block\n # process dat here\n\n chunk_decoded, self.data_rem = self.decodeBytesUtf8Safe(data)\n try:\n ### A chunk might contain an incomplete game, which is difficult\n ### to produce later. Therefore incomplete strings are saved in\n ### remainder_string and concacated in the next run\n chunk_decoded = self.games_rem + chunk_decoded\n except:\n chunk_decoded = chunk_decoded\n\n ### Split chunks at the \"Event\" key as it is the indicator\n ### for a new game\n games = re.sub(\"\\n\\n\\[Event\", \"\\n\\n;[Event\", chunk_decoded).split(\"\\n\\n;\")\n\n ### Extract the last chunk as it is typically incomplete and can be\n ### concacated in the next run. Additionally, it removes the last\n ### match from chunk and leaves chunk = [], in case no further data\n ### can be extracted from the archive.\n\n self.games_rem = games.pop()\n\n self.extract_keys(games)","def parse_blast_XML(blast_xml, config_file):\n\tblast_xml_op = open (blast_xml, 'r')\n\tEntrez.email = parse_config(config_file, \"email\")\n\tdb, evalue = parse_config(config_file, \"blast\")\n\n\tfor record in NCBIXML.parse(blast_xml_op):\n\t\tfor align in record.alignments:\n\t\t\thit_id = align.hit_id.split(\"|\")\n\t\t\tprev_eval = 1\n\t\t\tfor hsp in align.hsps:\n\t\t\t\tif hsp.expect < prev_eval:\n\t\t\t\t\tprev_eval = hsp.expect\n\t\t\tefetch = Entrez.efetch(db=\"protein\", id=hit_id, rettype=\"fasta\")\n\t\t\tfor line in efetch:\n\t\t\t\tline = line.rstrip()\n\t\t\t\tif line.startswith(\">\"):\n\t\t\t\t\tid_info = line\n\t\t\t\t\tsequence = \"\"\n\t\t\t\telse:\n\t\t\t\t\tsequence += line\n\t\t\tsequence += line\n\n\t\t\torganism = id_info[id_info.find(\"[\") + 1:id_info.find(\"]\")]\n\t\t\torganism = organism.split()\n\t\t\tif len(organism) != 1:\n\t\t\t\tspecies = str(organism[0] + \"_\" + organism[1])\n\n\t\t\tif prev_eval <= float(evalue):\n\t\t\t\tyield BlastResult(hit_id[1], species, sequence, prev_eval)","def parse(self, limit=None):\n if limit is not None:\n logger.info(\"Only parsing first %d rows of each file\", limit)\n logger.info(\"Parsing files...\")\n\n if self.testOnly:\n self.testMode = True\n\n # the following will provide us the hash-lookups\n self._process_dbxref()\n self._process_cvterm()\n self._process_genotypes(limit)\n self._process_pubs(limit)\n # do this before environments to get the external ids\n self._process_environment_cvterm()\n self._process_environments()\n self._process_organisms(limit) # must be done before features\n self._process_organism_dbxref(limit)\n self._process_features(limit)\n self._process_phenotype(limit)\n self._process_phenotype_cvterm()\n # gets external mappings for features (genes, variants, etc)\n self._process_feature_dbxref(limit)\n # do this after organisms to get the right taxonomy\n self._process_stocks(limit)\n # figures out types of some of the features\n self._get_derived_feature_types(limit)\n\n # These are the associations amongst the objects above\n self._process_stockprop(limit)\n self._process_pub_dbxref(limit)\n self._process_phendesc(limit)\n self._process_feature_genotype(limit)\n self._process_feature_pub(limit)\n self._process_stock_genotype(limit)\n self._process_phenstatement(limit) # these are G2P associations\n\n self._process_feature_relationship(limit)\n\n self._process_disease_models(limit)\n # TODO add version info from file somehow\n # (in parser rather than during fetching)\n\n logger.info(\"Finished parsing.\")\n logger.info(\"Loaded %d nodes\", len(self.graph))\n return","def bzpull(request, target):\n if target.startswith(\"sha1:\"):\n target = target[5:]\n url = \"http://bitzi.com/lookup/%s?v=tventtxt\" % target\n tventtxt = urllib.urlopen(url)\n tventdict = {}\n targets_to_update = set()\n count = 0\n text = \"\"\n try:\n for line in tventtxt:\n text += '\\n'\n line = line.strip()\n text += line\n if not line:\n if 'user' in tventdict and 'target_id' in tventdict and 'when' in tventdict:\n tvent = Tvent()\n tvent.when = tventdict['when']\n tvent.user = tventdict['user']\n target, created = Target.objects.get_or_create(id=tventdict['target_id'])\n tvent.target = target\n targets_to_update.add(target.id)\n tvent.tagtext = tventdict['tagtext']\n tvent.save()\n count += 1\n else:\n # error; required field not present\n text += '\\nERROR: incomplete tvent ' + str(tventdict)\n tventdict = {}\n continue\n if line.startswith(\"=\"):\n tventdict['when'] = line[1:]\n continue\n if line.startswith(\"~\"):\n tventdict['user'] = line[1:]\n continue\n if line.startswith(\"@\"):\n tventdict['target_id'] = line[1:]\n continue\n tventdict['tagtext'] = tventdict.get('tagtext','') + line + '\\n'\n if 'user' in tventdict and 'target_id' in tventdict and 'when' in tventdict:\n # TODO: reduce duplication with above\n tvent = Tvent()\n tvent.when = tventdict['when']\n tvent.user = tventdict['user']\n target = Target.objects.get_or_create(id=tventdict['target_id'])\n tvent.target = target\n targets_to_update.add(target.id)\n # TODO: cleanup tags here? \n tvent.save()\n count += 1\n else:\n # error; required field not present\n text += '\\nERROR: incomplete tvent ' + str(tventdict)\n finally:\n tventtxt.close()\n # trigger update of any possibly-changed Target summaries\n for id in targets_to_update:\n Target.objects.get(id=id).updateFromTvents()\n return HttpResponse('Pulled %d tvents from: %s\\n %s' % (count, url, text), mimetype='text/plain')","def decompress_chunks(bstrm):\n decompressor = zlib.decompressobj()\n for chunk in iter(lambda: bstrm.read(BUFSIZE), b\"\"):\n yield decompressor.decompress(chunk)\n yield decompressor.flush()","def process_file(self, filename, order=2):\n fp = open(filename)\n self.skip_gutenberg_header(fp)\n\n for line in fp:\n for word in line.rstrip().split():\n self.process_word(word, order)\n\n #print(\">>>DEBUG the suffix map\")\n #i = 0\n #for k,v in self.suffix_map.items():\n # print(\"key is {}, value is {}\".format(k, v))\n # i += 1\n # if i > 10:\n # break","def parse(cls, bstr=None, filename=None, bytes_input=None, file_input=None,\n offset_bytes=0, headers_only=False, recursive=True):\n\n if filename:\n bstr = bs.ConstBitStream(filename=filename, offset=offset_bytes * 8)\n elif bytes_input:\n bstr = bs.ConstBitStream(bytes=bytes_input, offset=offset_bytes * 8)\n elif file_input:\n bstr = bs.ConstBitStream(auto=file_input, offset=offset_bytes * 8)\n\n log.debug(\"Starting parse\")\n log.debug(\"Size is %d bits\", bstr.len)\n\n while bstr.pos < bstr.len:\n log.debug(\"Byte pos before header: %d relative to (%d)\", bstr.bytepos, offset_bytes)\n log.debug(\"Reading header\")\n header = cls.parse_header(bstr)\n log.debug(\"Header type: %s\", header.box_type)\n log.debug(\"Byte pos after header: %d relative to (%d)\", bstr.bytepos, offset_bytes)\n\n if headers_only:\n yield header\n\n # move pointer to next header if possible\n try:\n bstr.bytepos = header.start_pos + header.box_size\n except ValueError:\n log.warning(\"Premature end of data\")\n raise\n else:\n yield cls.parse_box(bstr, header, recursive=recursive)","def main(input_file=None, decoy_tag=None, output_file=None):\n NEW_HEADERS = [\n \"Raw data location\",\n \"Spectrum ID\",\n \"Spectrum Title\",\n \"Retention Time (s)\",\n \"Rank\",\n \"Calc m/z\",\n \"Exp m/z\",\n \"Charge\",\n \"Sequence\",\n \"Modifications\",\n \"X\\!Tandem:expect\",\n \"X\\!Tandem:hyperscore\",\n \"proteinacc_start_stop_pre_post_;\",\n \"Is decoy\",\n ]\n PROTON = 1.00727646677\n protein = None\n group = None\n group_counter = 0\n protein_groups = []\n\n if input_file.endswith(\".gz\"):\n compressed = True\n # Gzipped files are not seekable\n import gzip\n\n # file_object = codecs.getreader(\"utf-8\")(\n # gzip.open(path)\n # )\n file_object = codecs.getreader(\"utf-8\")(gzip.open(input_file))\n else:\n file_object = codecs.open(input_file, mode=\"r\", encoding=\"utf-8\")\n\n csvOut = csv.DictWriter(open(output_file, \"w\", newline=\"\"), NEW_HEADERS)\n csvOut.writeheader()\n\n print(\"Converting XTandem XML into CSV: {0}\".format(input_file))\n tandemXML = iter(cElementTree.iterparse(file_object, events=(b\"start\", b\"end\")))\n\n for pos, (event, element) in enumerate(tandemXML):\n if event == b\"start\":\n if element.tag.endswith(\"bioml\"):\n raw_data_location = element.attrib[\"label\"].split(\"'\")[1]\n if element.tag.endswith(\"group\"):\n if \"mh\" in element.attrib.keys():\n group_counter = 0\n notes = ddict(set)\n notes_key = None\n group = {} # reset group\n group[\"Raw data location\"] = raw_data_location\n group[\"Charge\"] = element.attrib[\"z\"]\n group[\"Exp m/z\"] = (\n float(element.attrib[\"mh\"]) / float(group[\"Charge\"])\n ) + PROTON\n group[\"X\\!Tandem:expect\"] = element.attrib[\"expect\"]\n protein_groups = []\n domain_groups = []\n if element.attrib[\"label\"] == \"fragment ion mass spectrum\":\n notes_key = \"spectrum\"\n if element.attrib[\"label\"] == \"input parameters\":\n notes_key = \"parameters\"\n group_counter += 1\n\n elif element.tag.endswith(\"protein\"):\n protein = {} # reset protein\n notes_key = \"protein\"\n\n elif element.tag.endswith(\"domain\"):\n if \"seq\" in element.attrib.keys():\n domain = {header: \"\" for header in NEW_HEADERS} # reset domain\n domain[\"Sequence\"] = element.attrib[\"seq\"]\n domain[\"X\\!Tandem:hyperscore\"] = element.attrib[\"hyperscore\"]\n domain[\"Calc m/z\"] = (\n float(element.attrib[\"mh\"]) / float(group[\"Charge\"])\n ) + PROTON\n protein[\"Start\"] = element.attrib[\"start\"]\n protein[\"Stop\"] = element.attrib[\"end\"]\n protein[\"pre\"] = element.attrib[\"pre\"][-1]\n protein[\"post\"] = element.attrib[\"post\"][0]\n if protein[\"Start\"] == \"1\":\n protein[\"pre\"] = \"-\"\n if protein[\"post\"] == \"]\":\n protein[\"post\"] = \"-\"\n domain[\n \"proteinacc_start_stop_pre_post_;\"\n ] = \"{0}_{1}_{2}_{3}_{4};\".format(\n protein[\"Defline\"],\n protein[\"Start\"],\n protein[\"Stop\"],\n protein[\"pre\"],\n protein[\"post\"],\n )\n if protein[\"Defline\"].startswith(decoy_tag):\n domain[\"Is decoy\"] = True\n else:\n domain[\"Is decoy\"] = False\n domain[\"Rank\"] = 1\n\n elif element.tag.endswith(\"aa\"):\n if \"modified\" not in element.attrib.keys():\n continue\n mod = \"{0}:{1}\".format(\n element.attrib[\"modified\"],\n int(element.attrib[\"at\"]) - int(protein[\"Start\"]) + 1,\n )\n try:\n domain[\"Modifications\"].append(mod)\n except:\n domain[\"Modifications\"] = [mod]\n else:\n if element.tag.endswith(\"protein\"):\n protein_groups.append(protein)\n if element.tag.endswith(\"domain\"):\n for k, v in domain.items():\n if k not in protein.keys():\n protein[k] = v\n # domain_groups.append( domain )\n elif element.tag.endswith(\"note\"):\n if notes_key == \"spectrum\":\n group[\"Spectrum Title\"] = element.text.strip()\n elif notes_key == \"protein\":\n protein[\"Defline\"] = element.text.strip()\n elif element.tag.endswith(\"group\"):\n group_counter -= 1\n if group_counter == 0:\n dict2write = {}\n # proteins = []\n for protein_group in protein_groups:\n for key in NEW_HEADERS:\n # if key == 'proteinacc_start_stop_pre_post_;':\n # proteins.append(protein_group[key])\n # continue\n if key == \"Modifications\" and protein_group[key] != \"\":\n dict2write[key] = \";\".join(protein_group[key])\n continue\n try:\n dict2write[key] = group[key]\n except:\n dict2write[key] = protein_group[key]\n # dict2write['proteinacc_start_stop_pre_post_;'] = ''.join(proteins)\n csvOut.writerow(dict2write)\n protein_groups = []\n return","def uncompress_bzip2(location, target_dir):\n return uncompress(location, target_dir, decompressor=bz2.BZ2File)","def run(self):\n lineage_csv_gz = self.input_files_local[0][0]\n output_db = self.output_files_local()[0]\n log.write(f\"input: {lineage_csv_gz} output: {output_db}\")\n\n with IdSeqDictForUpdate(output_db, IdSeqDictValue.VALUE_TYPE_ARRAY) as lineage_dict:\n batch_list = {}\n with gzip.open(lineage_csv_gz, \"rt\") as gzf:\n for line in gzf:\n fields = line.rstrip().split(\",\")\n taxid = fields[0]\n species, genus, family = fields[-1:-4:-1]\n batch_list[taxid] = [species, genus, family]\n if len(batch_list) >= BATCH_INSERT_SIZE:\n lineage_dict.batch_inserts(batch_list.items())\n batch_list = {}\n lineage_dict.batch_inserts(batch_list.items())","def _parse_tx_infos(self, gtf_path):\n if os.path.exists('_tx_cache.bin'):\n with open('_tx_cache.bin', 'rb') as f:\n return pickle.load(f)\n result = []\n with gzip.open(gtf_path, 'rt') as f:\n for i, line in enumerate(f):\n if i % 1000 == 0:\n print('processed {}'.format(i), file=sys.stderr)\n if line.startswith('#'):\n continue\n if line.split('\\t', 3)[2] != 'transcript':\n continue\n record = GTFFeature.parse(line)\n if record.feature != 'transcript':\n continue\n result.append(\n TranscriptInfo(record.attrs['gene_id'],\n record.attrs['transcript_id'],\n record.attrs['transcript_type'],\n record.seqname,\n record.start,\n record.end))\n with open('_tx_cache.bin', 'wb') as g:\n pickle.dump(result, g)\n print(len(result), file=sys.stderr)\n return result","def batch_tadbit(directory, parser=None, **kwargs):\n\n matrix = []\n for f_name in listdir(directory):\n if f_name.startswith('.'):\n continue\n f_name = path.join(directory, f_name)\n if parser:\n matrix.append(parser(f_name))\n continue\n elif not path.isfile(f_name):\n continue\n matrix.append(f_name)\n return tadbit(matrix, **kwargs)","def extract_and_tag_test():\n test_untagged_path = os.getcwd() + \"/data/test/test_untagged/\"\n test_untagged_directory = os.fsencode(test_untagged_path)\n\n print(\"Tagging text. Please wait...\")\n for file in os.listdir(test_untagged_directory):\n filename = os.fsdecode(file)\n try:\n if filename.endswith(\".txt\"):\n text = entity_process.read_data(test_untagged_path, file)\n text = text.lower()\n header,body = entity_process.split_text(text)\n header_array = header.splitlines()\n\n\n start_time, end_time = entity_process.extract_time(header)\n location = entity_process.extract_location(header_array, body)\n speaker = entity_process.extract_speaker(header_array, body)\n\n entity_tagger.tag_all(filename, text, start_time, end_time, location, speaker)\n except Exception as e:\n raise e\n return \"No files found here!\"\n print(\"Tagging complete! Text saved to\" + os.getcwd() + \"/out\")","def unzipdir(path):\n filenames = fullpathlist(path)\n for filename in filenames:\n if filename.endswith(\"bz2\"):\n print \"doing\", filename\n os.system('bunzip2 \"%s\"' % filename)\n else:\n print \"skipping\", filename","def read_ptbtagged(ptbtagged_path: str) -> Iterator[Tuple[TokenSeq, PosSeq]]:\n #do this immediately (first)\n #start generating feature matrices\n \n #read file into an array \n with open(ptbtagged_path) as f:\n file_array = f.readlines()\n file_array.append(\"\\n\")\n array_of_tuples = create_tuples(file_array)\n\n return generator(array_of_tuples)","def main():\n parse_file(sys.argv[1])","def extract_betti( fname, betti_file ):\n # open and read chomp-produced data file\n with open( fname + '.cbetti', 'r' ) as fh:\n lines = fh.readlines()\n # grab the line with the Betti numbers\n if len( lines ) > 1:\n for line in lines:\n if line.startswith( 'Betti' ):\n # keep only the numbers\n betti_numbers = line.strip().split()[2:]\n # chomp output single line of betti number (the \"other\" chomp\n # version...)\n else:\n betti_numbers = lines[0].strip().split()\n max_dim = len( betti_numbers )\n # open betti file and save generators. write the same format for\n # both chomp outputs to keep things consistent\n with open( betti_file + '.betti', 'w' ) as fh:\n for i, b in enumerate( betti_numbers ):\n line = str(i) + ' ' + betti_numbers[i] +'\\n'\n fh.write( line )","def read_gz(images,labels):\n\t# Open the images with gzip in read binary mode\n\t# images = gzip.open('../MNIST-data/train-images-idx3-ubyte.gz', 'rb')\n\t# labels = gzip.open('../MNIST-data/train-labels-idx1-ubyte.gz', 'rb')\n\n\t# Read the binary data\n\n\t# We have to get big endian unsigned int. So we need '>I'\n\n\t# Get metadata for images\n\timages.read(4) # skip the magic_number\n\tnumber_of_images = images.read(4)\n\tnumber_of_images = unpack('>I', number_of_images)[0]\n\trows = images.read(4)\n\trows = unpack('>I', rows)[0]#28\n\tcols = images.read(4)\n\tcols = unpack('>I', cols)[0]#28\n\n\t# Get metadata for labels\n\tlabels.read(4) # skip the magic_number\n\tN = labels.read(4)\n\tN = unpack('>I', N)[0] #60000\n\t# print(number_of_images);\n\n\tif number_of_images != N:\n\t raise Exception('number of labels did not match the number of images')\n\n\t# Get the data\n\tx = zeros((N, rows, cols), dtype=float32) # Initialize numpy array #60000X28X28\n\ty = zeros((N, 1), dtype=uint8) # Initialize numpy array\n\tfor i in range(N):\n\t if i % 1000 == 0:\n\t print(\"i: %i\" % i)\n\t for row in range(rows):\n\t for col in range(cols):\n\t tmp_pixel = images.read(1) # Just a single byte\n\t tmp_pixel = unpack('>B', tmp_pixel)[0]\n\t x[i][row][col] = tmp_pixel\n\t tmp_label = labels.read(1)\n\t y[i] = unpack('>B', tmp_label)[0]\n\t # print(y.shape)#60000X1\n\treturn (x, y)","def parse_region_data(self, region):\r\n \r\n self.download_data()\r\n region_filename = self.__get_region_filename(region)\r\n list_str = [\"region\", \"p1\", \"p36\", \"p37\", \"p2a\", \"weekday(p2a)\", \"p2b\", \"p6\", \"p7\", \"p8\", \"p9\", \"p10\", \r\n \"p11\", \"p12\", \"p13a\", \"p13b\", \"p13c\", \"p14\", \"p15\", \"p16\", \"p17\", \"p18\",\"p19\", \"p20\", \"p21\", \r\n \"p22\", \"p23\", \"p24\", \"p27\", \"p28\", \"p34\", \"p35\", \"p39\", \"p44\", \"p45a\", \"p47\", \"p48a\", \"p49\", \r\n \"p50a\", \"p50b\", \"p51\", \"p52\", \"p53\", \"p55a\", \"p57\", \"p58\", \"a\", \"b\", \"d\", \"e\", \"f\", \"g\", \"h\", \r\n \"i\", \"j\", \"k\", \"l\", \"m\", \"n\", \"o\", \"p\", \"q\", \"r\", \"s\", \"t\", \"p5a\"]\r\n \r\n row_count = self.__get_files_row_count(region)\r\n list_arrays = [np.zeros(row_count, dtype=dt) for dt in self.__types]\r\n row_index = 0\r\n for file in self.__files:\r\n file_to_parse = os.path.join(self.__folder, os.path.basename(file))\r\n with zipfile.ZipFile(file_to_parse, \"r\") as zf:\r\n with zf.open(region_filename, 'r') as csv_file:\r\n reader = csv.reader(TextIOWrapper(csv_file, 'windows-1250'), delimiter=';', quotechar='\"')\r\n for row in reader:\r\n list_arrays[0][row_index] = region\r\n for col_index, col in enumerate(row):\r\n try:\r\n list_arrays[col_index + 1][row_index] = col\r\n except ValueError:\r\n if list_arrays[col_index + 1][row_index].dtype == np.int64:\r\n list_arrays[col_index + 1][row_index] = -1\r\n elif list_arrays[col_index + 1][row_index].dtype == 'datetime64[D]':\r\n print('Error2:', col)\r\n elif list_arrays[col_index + 1][row_index].dtype == np.float64:\r\n if type(col) != str:\r\n list_arrays[col_index + 1][row_index] = col.replace(',', '.')\r\n else:\r\n list_arrays[col_index + 1][row_index] = float(\"nan\")\r\n row_index += 1\r\n \r\n return (list_str, list_arrays)","def parse_file(file_name: str, delims='\\n', encoding='utf-8', zip_type=None):\n try:\n decoder = codecs.getincrementaldecoder(encoding)()\n except LookupError as e:\n print(str(e))\n return\n\n read_buffer_size = 10*1024\n max_line_size = 100*1024\n\n if not zip_type:\n open_f = open\n elif zip_type == 'gz':\n open_f = gzip.open\n else:\n raise NotImplementedError()\n\n with open_f(file_name, 'rb') as fp:\n buffered_str = ''\n for bs in iter(partial(fp.read, read_buffer_size), b''):\n decoded_str = decoder.decode(bs)\n # FIXME: i don't think current implementation is efficient enough...\n for c in decoded_str:\n if c in delims:\n if len(buffered_str) > 0:\n yield buffered_str\n buffered_str = ''\n else:\n buffered_str += c\n if len(buffered_str) >= max_line_size:\n yield buffered_str\n buffered_str = ''\n if len(buffered_str) > 0:\n yield buffered_str","def processfile(args, fh):\n if args.quick:\n scanner = quickScanZip(args, fh)\n else:\n scanner = findPKHeaders(args, fh)\n\n def checkarg(arg, ent):\n if not arg:\n return False\n return '*' in arg or ent.name in arg\n def checkname(a, b):\n if a and '*' in a: return True\n if b and '*' in b: return True\n l = 0\n if a: l += len(a)\n if b: l += len(b)\n return l > 1\n\n if args.verbose and not (args.cat or args.raw or args.save):\n print(\" 0304 need flgs mth stamp --crc-- compsize fullsize nlen xlen namofs xofs datofs endofs\")\n print(\" 0102 crea need flgs mth stamp --crc-- compsize fullsize nlen xlen clen dsk0 attr osattr datptr namofs xofs cmtofs endofs\")\n for ent in scanner:\n if args.cat or args.raw or args.save:\n if args.quick and isinstance(ent, CentralDirEntry) or \\\n not args.quick and isinstance(ent, LocalFileHeader):\n ent.loaditems(fh)\n do_cat = checkarg(args.cat, ent)\n do_raw = checkarg(args.raw, ent)\n do_save= checkarg(args.save, ent)\n\n do_name= checkname(args.cat, args.raw)\n\n if do_name:\n print(\"\\n===> \" + ent.name + \" <===\\n\")\n\n sys.stdout.flush()\n blks = zipraw(fh, ent)\n\n if args.password and ent.flags&1:\n blks = zip_decrypt(blks, args.password)\n if do_cat or do_save:\n blks = skipbytes(blks, 12, args)\n\n if do_cat:\n sys.stdout.buffer.writelines(zipcat(blks, ent))\n if do_raw:\n sys.stdout.buffer.writelines(blks)\n if do_save:\n savefile(args.outputdir, ent.name, zipcat(blks, ent))\n else:\n ent.loaditems(fh)\n if args.verbose or not args.quick:\n print(\"%08x: %s\" % (ent.pkOffset, ent))\n else:\n print(ent.summary())\n if hasattr(ent, \"comment\") and ent.comment and not args.dumpraw:\n print(ent.comment)\n if args.dumpraw and hasattr(ent, \"extraLength\") and ent.extraLength:\n print(\"%08x: XTRA: %s\" % (ent.extraOffset, binascii.b2a_hex(getbytes(fh, ent.extraOffset, ent.extraLength))))\n if args.dumpraw and hasattr(ent, \"comment\") and ent.comment:\n print(\"%08x: CMT: %s\" % (ent.commentOffset, binascii.b2a_hex(getbytes(fh, ent.commentOffset, ent.commentLength))))\n if args.dumpraw and isinstance(ent, LocalFileHeader):\n blks = zipraw(fh, ent)\n if args.password and ent.flags&1:\n blks = zip_decrypt(blks, args.password)\n\n blockdump(ent.dataOffset, blks)","def reagent_parser(self, filename, initial_dictlist = dict()):\n results = initial_dictlist\n\n filepath = os.path.join(self.base_dir, filename)\n\n with open(filepath, 'r') as fileobj:\n xml = fileobj.read()\n parsed = BeautifulSoup(xml, \"lxml-xml\")\n\n substances = parsed.find_all(\"substance\")\n\n # iterates for every substance in file\n for substance in substances:\n\n # pulls the Beilstein Registry number\n rn = substance.find(\"IDE.XRN\").text\n\n # finds all molfiles, indicated by \"YY.STR\"\n molfiles = substance.find_all(\"YY.STR\")\n\n # V2000 files always follow V3000 files if V3000 files are available\n # if V3000 files are not available, V2000 files are the first and only file\n # we are only using V2000 files\n try:\n\n # if possible, converts the second file (the V2000 file) to SMILES\n mymol = readstring(\"mol\", molfiles[1].text)\n smi = mymol.write(str(\"smi\")).split()[0]\n\n results[rn] = smi\n except:\n\n # occurs when only zero or one file listed for specific registry number\n try:\n\n # if possible, converts the first file (the V2000 file) to SMILES\n mymol = readstring(\"mol\", molfiles[0].text)\n smi = mymol.write(str(\"smi\")).split()[0]\n\n results[rn] = smi\n except:\n\n # if not file is listed for the registry number, skips that number\n continue\n\n return results","def parse(self, f):\n \n for line in f:\n self.parse_line(line)","def load_ineraction_files(file_prefix):\n\tbinintfile=file_prefix+'.binint.log'\n\tcollfile=file_prefix+'.collision.log'\n\tmergefile=file_prefix+'.semergedisrupt.log'\n\tunitsfile=file_prefix+'.conv.sh'\n\n\twith open(binintfile, 'r') as f:\n\t\tnum_int = sum([1 for line in f if '****' in line])\n\t\tf.seek(0) #need to count the encounters then reset the file handle\n\t\tbinints = [binint(f) for __ in range(num_int)]\n\n\twith open(mergefile,'r') as f:\n\t\tnext(f) #skip the header\n\t\tmergers = [se_merger(line) for line in f]\n\t\t\n\twith open(collfile,'r') as f:\n\t\tnext(f) #skip the header\n\t\tcollisions = [collision(line) for line in f]\n\n\tunits = conversion_file(unitsfile) \n\n\treturn (units,binints,mergers,collisions)","def process_file(filename):\n print \"Reading and Parsing File: {}\".format(filename)\n parsed_entries = file_parser(filename)\n print \"Starting to Process Entries\"\n chunked_entires = chunk_entries(parsed_entries)\n return [process_entries(entry) for entry in chunked_entires]","def __parsePackages__(self, f):\n\n\t\tp = apt_pkg.ParseTagFile(f)\n\n\t\t# Just load into memory the fields that are going to be useful\n\t\twhile p.Step() == 1:\n\t\t\tpkg = p.Section['Package']\n\n\t\t\tself.packages[pkg] = {}\n\n\t\t\tfor field in p.Section.keys():\n\t\t\t\tif field == 'Package':\n\t\t\t\t\tpass \n\t\t\t\telif ['Depends', 'Recommends', 'Suggests', 'Enhances', 'Pre-Depends', 'Conflicts', 'Provides'].count(field):\n\t\t\t\t\tvalue = p.Section.get(field, \"\")\n\t\t\t\t\tself.packages[pkg][field] = apt_pkg.ParseDepends(value)\n\t\t\t\telif ['Size', 'Installed-Size'].count(field):\n\t\t\t \t\tvalue = p.Section.get(field, \"0\")\n\t\t\t \t\tself.packages[pkg][field] = int(value)\n\t\t\t\telif field == 'Source':\n\t\t\t\t\tsrc = p.Section.get(field, pkg)\n\t\t\t\t\tidx = src.find('(')\n\t\t\t\t\tif idx != -1:\n\t\t\t\t\t\tsrc = src[:idx].strip()\n\t\t\t\t\tself.packages[pkg][field] = src\n\t\t\t\telif field == 'Provides':\n\t\t\t\t\tself.packages[pkg][\"Provides\"] = apt_pkg.ParseDepends(p.Section.get(\"Provides\", \"\"))\n\t\t\t\telse:\n\t\t\t\t\tself.packages[pkg][field] = p.Section.get(field, '')\n\n\t f.close()","def _bam_extract_impl(config: BamExtractConfig, sites: typing.List[vcf.Site]) -> None:\n for path in config.input_files:\n _bam_extract_impl_for_file(config, sites, path)","def testTarBundling(self):\n try:\n tP = os.path.join(self.__workPath, \"t0.tar.gz\")\n dirPath = os.path.join(self.__inpDirPath, \"topdir\")\n\n ok = self.__fileU.bundleTarfile(tP, [dirPath], mode=\"w:gz\", recursive=True)\n self.assertTrue(ok)\n\n numBytes = self.__fileU.size(tP)\n self.assertGreaterEqual(numBytes, 250)\n #\n md5 = self.__fileU.hash(tP, hashType=\"md5\")\n self.assertTrue(md5 is not None)\n #\n ok = self.__fileU.unbundleTarfile(tP, dirPath=self.__workPath)\n self.assertTrue(ok)\n #\n tP = os.path.join(self.__workPath, \"t1.tar.gz\")\n dirPathList = [os.path.join(self.__inpDirPath, \"topdir\", \"subdirA\"), os.path.join(self.__inpDirPath, \"topdir\", \"subdirB\")]\n\n ok = self.__fileU.bundleTarfile(tP, dirPathList, mode=\"w:gz\", recursive=True)\n self.assertTrue(ok)\n #\n ok = self.__fileU.unbundleTarfile(tP, dirPath=self.__workPath)\n self.assertTrue(ok)\n\n tP = os.path.join(self.__workPath, \"t2.tar\")\n dirPathList = [os.path.join(self.__inpDirPath, \"topdir\", \"subdirA\"), os.path.join(self.__inpDirPath, \"topdir\", \"subdirB\")]\n\n ok = self.__fileU.bundleTarfile(tP, dirPathList, mode=\"w\", recursive=True)\n self.assertTrue(ok)\n #\n ok = self.__fileU.unbundleTarfile(tP, dirPath=self.__workPath)\n self.assertTrue(ok)\n\n except Exception as e:\n logger.exception(\"Failing with %s\", str(e))\n self.fail()","def compress_bz2(filename):\n bz2_filename = filename + '.bz2'\n\n with open(filename, 'rb') as og_file, bz2.BZ2File(bz2_filename, 'wb') as bz2_file:\n for data in iter(lambda : og_file.read(100 * 1024), b''):\n bz2_file.write(data)\n\n return bz2_filename","def compress_bz2(filename):\n bz2_filename = filename + '.bz2'\n\n with open(filename, 'rb') as og_file, bz2.BZ2File(bz2_filename, 'wb') as bz2_file:\n for data in iter(lambda : og_file.read(100 * 1024), b''):\n bz2_file.write(data)\n\n return bz2_filename","def process_bedpe(archive, bedpe, bedpe_index, output_prefix):\n out_raw_bedpe = '{0}.tmp.bedpe.gz'.format(output_prefix)\n logger.info(\"Extracting raw bedpe to tmp file {0}\".format(out_raw_bedpe))\n extract_file(archive, bedpe, out_raw_bedpe)\n\n out_raw_bedpe_index = '{0}.tmp.bedpe.gz.tbi'.format(output_prefix)\n logger.info(\"Extracting raw bedpe index to tmp file {0}\".format(out_raw_bedpe_index))\n extract_file(archive, bedpe_index, out_raw_bedpe_index)\n\n out_formatted_bedpe = '{0}.bedpe.gz'.format(output_prefix)\n logger.info(\"Creating final bedpe {0}\".format(out_formatted_bedpe))\n writer = pysam.BGZFile(out_formatted_bedpe, mode='wb')\n reader = pysam.BGZFile(out_raw_bedpe, mode='rb')\n try:\n meta_line = None\n process_header = False\n hdr = []\n for line in reader:\n line = line.decode('utf-8')\n if line.startswith('#'):\n meta_line = line\n else:\n if not process_header:\n hdr = format_header(meta_line)\n assert len(hdr) == len(set(hdr)), \\\n \"Duplicate header keys {0}\".format(','.join(hdr))\n writer.write(('#' + '\\t'.join(hdr) + '\\n').encode('utf-8'))\n process_header = True\n\n dat = dict(zip(hdr, line.rstrip('\\r\\n').split('\\t')))\n dat['brass_notation'] = dat['brass_notation'].replace('Chr.chr', 'chr')\n new_line = \"\\t\".join([dat[i] for i in hdr]) + '\\n'\n writer.write(new_line.encode('utf-8'))\n finally:\n writer.close()\n reader.close()\n\n # tabix index\n logger.info(\"Creating final bedpe index {0}\".format(out_formatted_bedpe + '.tbi'))\n pysam.tabix_index( out_formatted_bedpe, preset='bed', force=True )\n\n # clean up\n logger.info(\"Cleaning up tmp files...\")\n os.remove(out_raw_bedpe)\n os.remove(out_raw_bedpe_index)","def split_batches(filenames):\n by_time = {}\n for path_name in filenames:\n file_name = path.basename(path_name)\n parsed_fn = parse_agdc_fn(file_name)\n dt = parsed_fn['datetime']\n by_time.setdefault(dt, []).append((path_name, parsed_fn))\n\n rv = list(by_time.values())\n\n for group in rv:\n # Will raise exception if group is non-homogeneous\n check_sane(parsed for _, parsed in group)\n\n return rv","def _parse_ach_file(self, contents):\n file_length = len(contents)\n\n for index in range(0, file_length, self.LINE_LENGTH):\n line = contents[index:index + self.LINE_LENGTH]\n\n if line.startswith('1'):\n self._read_header(line)\n elif line.startswith('5'):\n self._read_batch_header(line)\n elif line.startswith('6'):\n self._read_entry_detail(line)\n elif line.startswith('7'):\n self._read_addenda_record(line)\n elif line.startswith('8'):\n self._read_batch_control_record(line)\n elif line.startswith('9'):\n if line == '9' * 94:\n continue\n self._read_file_control_record(line)","def parseGRO(filename):\n\tprint(\"Cannot parse .gro files yet.\")\n\texit()","def parse(self, infile):\r\n raise NotImplementedError()","def parse_tle_bytes(f):\n lines=f.splitlines()\n\n tles=[]\n ctle=None\n state=\"none\"\n for l in lines:\n m_name=re.fullmatch(b\"^\\s*((\\S.*)?\\S)\\s*$\",l)\n m_line1=re.fullmatch(\"^\\s*(1)\\s+(\\d{1,5})(\\w)\\s+\"\\\n \"(\\d{2})(\\d{3})(\\w{0,3})\\s+(\\d{2})(\\s{0,2}\\d{1,3}\\.\\d{8})\\s+\"\\\n \"([-+ 0]\\.\\d{8})\\s+([-+ ]\\d{5}[-+]\\d)\\s+([-+ ]\\d{5}[-+]\\d)\\s+\"\\\n \"(0)\\s+(\\d{1,4})(\\d)\\s*$\",l.decode(\"ascii\"))\n m_line2=re.fullmatch(\"^\\s*(2)\\s+(\\d{1,5})\\s+\"\\\n \"(\\d{1,3}\\.\\d{4})\\s+(\\d{1,3}\\.\\d{4})\\s+(\\d{1,7})\\s+\"\\\n \"(\\d{1,3}\\.\\d{4})\\s+(\\d{1,3}\\.\\d{4})\\s+\"\\\n \"(\\d{1,2}\\.\\d{8})(\\s*\\d{1,5})(\\d)\\s*$\",l.decode(\"ascii\"))\n if (state==\"name\" and m_line1 is None) or (state==\"line1\" and m_line2 is None):\n if not _quiet:\n print(\"WARNING: Non consecutive TLE line (\"+str(l)+\\\n \"), discards partial TLE (\\\"\"+str(ctle.name)+\"\\\":\"+\\\n str(ctle.id)+\")\",file=sys.stderr)\n ctle=None\n state=\"none\"\n\n if state==\"line1\" and m_line2 is not None:\n cksum=int(m_line2.group(10))\n nsum=0\n for c in l.strip(b\" \\r\\n\\t\")[:-1].decode(\"ascii\"):\n if c.isdigit():\n nsum+=int(c)\n elif c==\"-\":\n nsum+=1\n nsum%=10\n ctle.line2valid=cksum==nsum\n if ((not _quiet) and (cksum!=nsum)):\n print(\"WARNING: checksum did not match [check(\\\"\"+\\\n l.strip(b\" \\r\\n\\t\").decode(\"ascii\")+\"\\\")=\"+\\\n str(nsum)+\"!=\"+str(cksum)+\"]\",file=sys.stderr)\n newid=int(m_line2.group(2))\n if newid!=ctle.id:\n if not _quiet:\n print(\"ERROR: unexpeced id in second line, skipping!\",\n file=sys.stderr)\n ctle=None\n state=\"none\"\n continue\n ctle.inc=float(m_line2.group(3))\n ctle.raan=float(m_line2.group(4))\n ctle.ecc=float(\"0.\"+m_line2.group(5))\n ctle.aop=float(m_line2.group(6))\n ctle.ma=float(m_line2.group(7))\n ctle.mm=float(m_line2.group(8))\n ctle.revol=int(m_line2.group(9))\n tles.append(copy.deepcopy(ctle))\n if _verbose:\n print(\"Successfully read in TLE for \\\"\"+ctle.name+\"\\\": \"+str(ctle.id),\n file=sys.stderr)\n ctle=None\n state=\"none\"\n elif state==\"name\" and m_line1 is not None:\n cksum=int(m_line1.group(14))\n nsum=0\n for c in l.strip(b\" \\r\\n\\t\")[:-1].decode(\"ascii\"):\n if c.isdigit():\n nsum+=int(c)\n elif c==\"-\":\n nsum+=1\n nsum%=10\n ctle.line1valid=cksum==nsum\n if ((not _quiet) and (cksum!=nsum)):\n print(\"WARNING: checksum did not match [check(\\\"\"+\\\n l.strip(b\" \\r\\n\\t\").decode(\"ascii\")+\"\\\")=\"+\\\n str(nsum)+\"!=\"+str(cksum)+\"]\",file=sys.stderr)\n ctle.id=int(m_line1.group(2))\n ctle.desig[\"year\"]=int(m_line1.group(4))\n ctle.desig[\"launch\"]=int(m_line1.group(5))\n ctle.desig[\"object\"]=m_line1.group(6)\n ctle.epoch[\"year\"]=int(m_line1.group(7))\n ctle.epoch[\"day\"]=float(m_line1.group(8))\n fdmm_str=m_line1.group(9)\n ctle.fdmm=float(fdmm_str[0]+\"0\"+fdmm_str[1:])\n sdmm_str=m_line1.group(10)\n ctle.sdmm=float(sdmm_str[0]+\"0.\"+sdmm_str[1:6]+\"e\"+sdmm_str[6:])\n bstar_str=m_line1.group(11)\n ctle.bstar=float(bstar_str[0]+\"0.\"+bstar_str[1:6]+\"e\"+bstar_str[6:])\n ctle.nr=int(m_line1.group(13))\n state=\"line1\"\n elif state==\"none\" and m_name is not None:\n ctle=tle()\n ctle.name=m_name.group(1).decode(\"ascii\")\n state=\"name\"\n return tles","def parse_shard(shard_path):\n with tf.io.gfile.GFile(shard_path, 'rb') as f:\n with gzip.GzipFile(fileobj=f, mode='rb') as f_gz:\n for line in f_gz: # Line-by-line.\n yield deserialize_inference_result(line)","def process(marc_filepath):\n start = datetime.datetime.utcnow()\n click.echo(\"Started transforming MARC to BF at {} for {}\".format(\n start.isoformat(),\n marc_filepath))\n for i, marc_xml in enumerate(extract(marc_filepath)):\n bf_rdf = transform(marc_xml)\n load(bf_rdf)\n if not i%100 and i > 0:\n click.echo(\".\", nl=False)\n if not i%1000:\n click.echo(i, nl=False)\n end = datetime.datetime.utcnow()\n click.echo(\"Finished ETL for {} at {}, total time={} minutes\".format(\n marc_file,\n end.isoformat(),\n (end-start).seconds / 60.0))","def parse_ensembl_transcripts(lines):\n header = []\n LOG.info(\"Parsing ensembl transcripts from file\")\n for index, line in enumerate(lines):\n # File allways start with a header line\n if index == 0:\n header = line.rstrip().split(\"\\t\")\n # After that each line represents a transcript\n else:\n yield parse_ensembl_line(line, header)","def parseGFF3(filename):\n\n # Parse with transparent decompression\n openFunc = gzip.open if filename.endswith(\".gz\") else open\n with openFunc(filename) as infile:\n for line in infile:\n if line.startswith(\"#\"):\n continue\n parts = line.strip().split(\"\\t\")\n # If this fails, the file format is not standard-compatible\n assert len(parts) == len(gffInfoFields)\n # Normalize data\n normalizedInfo = {\n \"seqid\": None if parts[0] == \".\" else urllib.unquote(parts[0]),\n \"source\": None if parts[1] == \".\" else urllib.unquote(parts[1]),\n \"type\": None if parts[2] == \".\" else urllib.unquote(parts[2]),\n \"start\": None if parts[3] == \".\" else int(parts[3]),\n \"end\": None if parts[4] == \".\" else int(parts[4]),\n \"score\": None if parts[5] == \".\" else float(parts[5]),\n \"strand\": None if parts[6] == \".\" else urllib.unquote(parts[6]),\n \"phase\": None if parts[7] == \".\" else urllib.unquote(parts[7]),\n \"attributes\": parseGFFAttributes(parts[8])\n }\n # Alternatively, you can emit the dictionary here, if you need\n # mutability:\n # yield normalizedInfo\n yield GFFRecord(**normalizedInfo)","def _GetSubFileEntries(self):\n if self._directory is None:\n self._directory = self._GetDirectory()\n\n if self._directory:\n tar_file = self._file_system.GetTARFile()\n if tar_file:\n for path_spec in self._directory.entries:\n location = getattr(path_spec, 'location', None)\n if location is None:\n continue\n\n kwargs = {}\n try:\n kwargs['tar_info'] = tar_file.getmember(location[1:])\n except KeyError:\n kwargs['is_virtual'] = True\n\n yield TARFileEntry(\n self._resolver_context, self._file_system, path_spec, **kwargs)","def parseGerber(self, fullname, layername, updateExtents = 0):\n\n GAT = config.GAT\n GAMT = config.GAMT\n # First construct reverse GAT/GAMT, mapping definition to code\n RevGAT = config.buildRevDict(GAT) # RevGAT[hash] = aperturename\n RevGAMT = config.buildRevDict(GAMT) # RevGAMT[hash] = aperturemacroname\n\n #print 'Reading data from %s ...' % fullname\n\n fid = file(fullname, 'rt')\n currtool = None\n\n self.apxlat[layername] = {}\n self.apmxlat[layername] = {}\n self.commands[layername] = []\n self.apertures[layername] = []\n\n # These divisors are used to scale (X,Y) co-ordinates. We store\n # everything as integers in hundred-thousandths of an inch (i.e., M.5\n # format). If we get something in M.4 format, we must multiply by\n # 10. If we get something in M.6 format we must divide by 10, etc.\n x_div = 1.0\n y_div = 1.0\n\n # Drawing commands can be repeated with X or Y omitted if they are\n # the same as before. These variables store the last X/Y value as\n # integers in hundred-thousandths of an inch.\n last_x = last_y = 0\n\n # Last modal G-code. Some G-codes introduce \"modes\", such as circular interpolation\n # mode, and we want to remember what mode we're in. We're interested in:\n # G01 -- linear interpolation, cancels all circular interpolation modes\n # G36 -- Turn on polygon area fill\n # G37 -- Turn off polygon area fill\n last_gmode = 1 # G01 by default, linear interpolation\n\n # We want to know whether to do signed (G75) or unsigned (G74) I/J offsets. These\n # modes are independent of G01/G02/G03, e.g., Protel will issue multiple G03/G01\n # codes all in G75 mode.\n # G74 -- Single-quadrant circular interpolation (disables multi-quadrant interpolation)\n # G02/G03 codes set clockwise/counterclockwise arcs in a single quadrant only\n # using X/Y/I/J commands with UNSIGNED (I,J).\n # G75 -- Multi-quadrant circular interpolation --> X/Y/I/J with signed (I,J)\n # G02/G03 codes set clockwise/counterclockwise arcs in all 4 quadrants\n # using X/Y/I/J commands with SIGNED (I,J).\n circ_signed = True # Assume G75...make sure this matches canned header we write out\n\n # If the very first flash/draw is a shorthand command (i.e., without an Xxxxx or Yxxxx)\n # component then we don't really \"see\" the first point X00000Y00000. To account for this\n # we use the following Boolean flag as well as the isLastShorthand flag during parsing\n # to manually insert the point X000000Y00000 into the command stream.\n firstFlash = True\n\n for line in fid:\n # Get rid of CR characters (0x0D) and leading/trailing blanks\n line = string.replace(line, '\\x0D', '').strip()\n\n # Old location of format_pat search. Now moved down into the sub-line parse loop below.\n\n # RS-274X statement? If so, echo it. Currently, only the \"LP\" statement is expected\n # (from Protel, of course). These will be distinguished from D-code and G-code\n # commands by the fact that the first character of the string is '%'.\n match = layerpol_pat.match(line)\n if match:\n self.commands[layername].append(line)\n continue\n \n # See if this is an aperture definition, and if so, map it.\n match = apdef_pat.match(line)\n if match:\n if currtool:\n raise RuntimeError, \"File %s has an aperture definition that comes after drawing commands.\" % fullname\n\n A = aptable.parseAperture(line, self.apmxlat[layername])\n if not A:\n raise RuntimeError, \"Unknown aperture definition in file %s\" % fullname\n\n hash = A.hash()\n if not RevGAT.has_key(hash):\n #print line\n #print self.apmxlat\n #print RevGAT\n raise RuntimeError, 'File %s has aperture definition \"%s\" not in global aperture table.' % (fullname, hash)\n\n # This says that all draw commands with this aperture code will\n # be replaced by aperture self.apxlat[layername][code].\n self.apxlat[layername][A.code] = RevGAT[hash]\n continue\n\n # Ignore %AMOC8* from Eagle for now as it uses a macro parameter, which\n # is not yet supported in GerbMerge.\n if line[:7]=='%AMOC8*':\n continue\n\n # See if this is an aperture macro definition, and if so, map it.\n M = amacro.parseApertureMacro(line,fid)\n if M:\n if currtool:\n raise RuntimeError, \"File %s has an aperture macro definition that comes after drawing commands.\" % fullname\n\n hash = M.hash()\n if not RevGAMT.has_key(hash):\n raise RuntimeError, 'File %s has aperture macro definition not in global aperture macro table:\\n%s' % (fullname, hash)\n\n # This says that all aperture definition commands that reference this macro name\n # will be replaced by aperture macro name self.apmxlat[layername][macroname].\n self.apmxlat[layername][M.name] = RevGAMT[hash]\n continue\n\n # From this point on we may have more than one match on this line, e.g.:\n # G54D11*X22400Y22300D02*X22500Y22200D01*\n sub_line = line\n while sub_line:\n # Handle \"comment\" G-codes first\n match = comment_pat.match(sub_line)\n if match:\n sub_line = sub_line[match.end():]\n continue\n\n # See if this is a format statement, and if so, map it. In version 1.3 this was moved down\n # from the line-only parse checks above (see comment) to handle OrCAD lines like\n # G74*%FSLAN2X34Y34*%\n match = format_pat.match(sub_line) # Used to be format_pat.search\n if match:\n sub_line = sub_line[match.end():]\n for item in match.groups():\n if item is None: continue # Optional group didn't match\n\n if item[0] in \"LA\": # omit leading zeroes and absolute co-ordinates\n continue\n\n if item[0]=='T': # omit trailing zeroes\n raise RuntimeError, \"Trailing zeroes not supported in RS274X files\"\n if item[0]=='I': # incremental co-ordinates\n raise RuntimeError, \"Incremental co-ordinates not supported in RS274X files\"\n\n if item[0]=='N': # Maximum digits for N* commands...ignore it\n continue\n\n if item[0]=='X': # M.N specification for X-axis.\n fracpart = int(item[2])\n x_div = 10.0**(5-fracpart)\n if item[0]=='Y': # M.N specification for Y-axis.\n fracpart = int(item[2])\n y_div = 10.0**(5-fracpart)\n continue\n\n # Parse and interpret G-codes\n match = gcode_pat.match(sub_line)\n if match:\n sub_line = sub_line[match.end():]\n gcode = int(match.group(1))\n\n # Determine if this is a G-Code that should be ignored because it has no effect\n # (e.g., G70 specifies \"inches\" which is already in effect).\n if gcode in [54, 70, 90]:\n continue\n\n # Determine if this is a G-Code that we have to emit because it matters.\n if gcode in [1, 2, 3, 36, 37, 74, 75]:\n self.commands[layername].append(\"G%02d\" % gcode)\n\n # Determine if this is a G-code that sets a new mode\n if gcode in [1, 36, 37]:\n last_gmode = gcode\n\n # Remember last G74/G75 code so we know whether to do signed or unsigned I/J\n # offsets.\n if gcode==74:\n circ_signed = False\n elif gcode==75:\n circ_signed = True\n \n continue\n\n raise RuntimeError, \"G-Code 'G%02d' is not supported\" % gcode\n\n # See if this is a tool change (aperture change) command\n match = tool_pat.match(sub_line)\n if match:\n currtool = match.group(1)\n\n # Protel likes to issue random D01, D02, and D03 commands instead of aperture\n # codes. We can ignore D01 because it simply means to move to the current location\n # while drawing. Well, that's drawing a point. We can ignore D02 because it means\n # to move to the current location without drawing. Truly pointless. We do NOT want\n # to ignore D03 because it implies a flash. Protel very inefficiently issues a D02\n # move to a location without drawing, then a single-line D03 to flash. However, a D02\n # terminates a polygon in G36 mode, so keep D02's in this case.\n if currtool=='D01' or (currtool=='D02' and (last_gmode != 36)):\n sub_line = sub_line[match.end():]\n continue\n\n if (currtool == 'D03') or (currtool=='D02' and (last_gmode == 36)):\n self.commands[layername].append(currtool)\n sub_line = sub_line[match.end():]\n continue\n\n # Map it using our translation table\n if not self.apxlat[layername].has_key(currtool):\n raise RuntimeError, 'File %s has tool change command \"%s\" with no corresponding translation' % (fullname, currtool)\n\n currtool = self.apxlat[layername][currtool]\n\n # Add it to the list of things to write out\n self.commands[layername].append(currtool)\n\n # Add it to the list of all apertures needed by this layer\n self.apertures[layername].append(currtool)\n\n # Move on to next match, if any\n sub_line = sub_line[match.end():]\n continue\n\n # Is it a simple draw command?\n I = J = None # For circular interpolation drawing commands\n match = drawXY_pat.match(sub_line)\n isLastShorthand = False # By default assume we don't make use of last_x and last_y\n if match:\n x, y, d = map(__builtin__.int, match.groups())\n else:\n match = drawX_pat.match(sub_line)\n if match:\n x, d = map(__builtin__.int, match.groups())\n y = last_y\n isLastShorthand = True # Indicate we're making use of last_x/last_y\n else:\n match = drawY_pat.match(sub_line)\n if match:\n y, d = map(__builtin__.int, match.groups())\n x = last_x\n isLastShorthand = True # Indicate we're making use of last_x/last_y\n\n # Maybe it's a circular interpolation draw command with IJ components\n if match is None:\n match = cdrawXY_pat.match(sub_line)\n if match:\n x, y, I, J, d = map(__builtin__.int, match.groups())\n else:\n match = cdrawX_pat.match(sub_line)\n if match:\n x, I, J, d = map(__builtin__.int, match.groups())\n y = last_y\n isLastShorthand = True # Indicate we're making use of last_x/last_y\n else:\n match = cdrawY_pat.match(sub_line)\n if match:\n y, I, J, d = map(__builtin__.int, match.groups())\n x = last_x\n isLastShorthand = True # Indicate we're making use of last_x/last_y\n\n if match:\n if currtool is None:\n # It's OK if this is an exposure-off movement command (specified with D02).\n # It's also OK if we're in the middle of a G36 polygon fill as we're only defining\n # the polygon extents.\n if (d != 2) and (last_gmode != 36):\n raise RuntimeError, 'File %s has draw command %s with no aperture chosen' % (fullname, sub_line)\n\n # Save last_x/y BEFORE scaling to 2.5 format else subsequent single-ordinate\n # flashes (e.g., Y with no X) will be scaled twice!\n last_x = x\n last_y = y\n\n # Corner case: if this is the first flash/draw and we are using shorthand (i.e., missing Xxxx\n # or Yxxxxx) then prepend the point X0000Y0000 into the commands as it is actually the starting\n # point of our layer. We prepend the command X0000Y0000D02, i.e., a move to (0,0) without drawing.\n if (isLastShorthand and firstFlash):\n self.commands[layername].append((0,0,2))\n if updateExtents:\n self.minx = min(self.minx,0)\n self.maxx = max(self.maxx,0)\n self.miny = min(self.miny,0)\n self.maxy = max(self.maxy,0)\n\n x = int(round(x*x_div))\n y = int(round(y*y_div))\n if I is not None:\n I = int(round(I*x_div))\n J = int(round(J*y_div))\n self.commands[layername].append((x,y,I,J,d,circ_signed))\n else:\n self.commands[layername].append((x,y,d))\n firstFlash = False\n\n # Update dimensions...this is complicated for circular interpolation commands\n # that span more than one quadrant. For now, we ignore this problem since users\n # should be using a border layer to indicate extents.\n if updateExtents:\n if x < self.minx: self.minx = x\n if x > self.maxx: self.maxx = x\n if y < self.miny: self.miny = y\n if y > self.maxy: self.maxy = y\n\n # Move on to next match, if any\n sub_line = sub_line[match.end():]\n continue\n\n # If it's none of the above, it had better be on our ignore list.\n for pat in IgnoreList:\n match = pat.match(sub_line)\n if match:\n break\n else:\n raise RuntimeError, 'File %s has uninterpretable line:\\n %s' % (fullname, line)\n\n sub_line = sub_line[match.end():]\n # end while still things to match on this line\n # end of for each line in file\n\n fid.close()\n if 0:\n print layername\n print self.commands[layername]","def get_tag_batch(self, tag, filenames):\n data = self.get_tags_batch([tag], filenames)\n result = []\n for d in data:\n d.pop(\"SourceFile\")\n result.append(next(iter(d.values()), None))\n return result"],"string":"[\n \"def extract_bz2(tar_bz_f, calc_type):\\n \\n # we give the gaussian calculator a label that includes the directory the\\n # log file is contained in, this does not affect the parsing process but\\n # generate a warning as it is not an expected form for the label. To avoid\\n # the profusion of warning messages in stdout we suppress warnings here.\\n warnings.filterwarnings(\\\"ignore\\\")\\n\\n extended_xyzs = []\\n\\n with tarfile.open(tar_bz_f,'r:bz2') as data_tar:\\n calc_logs = (log_tar for log_tar in data_tar \\n if calc_type in log_tar.name and '.log' in log_tar.name)\\n \\n for calc_log in calc_logs:\\n try:\\n # extract log file (and relevant directory)\\n data_tar.extract(calc_log)\\n\\n # convert to ASE/Gaussian format\\n mol = read(calc_log.name)\\n mol.set_calculator(\\n Gaussian(\\n label=calc_log.name.replace('.log','')\\n )\\n )\\n\\n # parse into ML readable format\\n parsed_mol = ase_mol_parse(mol)\\n extended_xyzs.append(parsed_mol)\\n except AttributeError:\\n # if the calculation didn't complete we get an empty dictionary \\n # so we we keep track of these failed calculations with a blank \\n # entry other than mol_id\\n blank_entry = {'mol_id':calc_log.name.replace('.log','')}\\n extended_xyzs.append(blank_entry)\\n finally:\\n # delete extracted log file\\n os.remove(calc_log.name)\\n\\n # solves memory problem\\n # http://blogs.it.ox.ac.uk/inapickle/2011/06/20/high-memory-usage-when-using-pythons-tarfile-module/ # noqa\\n data_tar.members=[]\\n \\n dir_name = tar_bz_f.replace('.tar.bz2','')\\n\\n # delete extracted directory\\n os.rmdir(dir_name)\\n\\n # search key function\\n # assumes files are named xxx_frame_{frame}_mol_{no}\\n def mol_no_frame(mol):\\n mol_no = int(mol['mol_id'].split('_')[-1].replace('.log',''))\\n mol_frame = int(mol['mol_id'].split('_')[-3])\\n return mol_no,mol_frame\\n\\n extended_xyzs = sorted(extended_xyzs,key=mol_no_frame)\\n\\n with open(dir_name + '_' + calc_type + '_data.pkl', 'w') as data_f:\\n dill.dump(extended_xyzs, data_f)\",\n \"def _read_recs(basedir):\\n for borotag in boro_tags:\\n datafile = \\\"%s/%s.csv\\\" % (basedir,borotag)\\n print(\\\"slurp '%s' ..\\\" % datafile)\\n recs = read_recs(datafile)\\n yield from (pluto.parse.normalize(r) for r in recs)\",\n \"def parse_gzipped_directory(input_dir, start_date, end_date, infos, backup_stamps):\\n try:\\n file_names = sorted(os.listdir(input_dir)) \\n for file_name in file_names:\\n if file_name.endswith(\\\".manifest.gz\\\") or file_name.endswith(\\\".manifest\\\"):\\n tmp = parse_file(input_dir + \\\"/\\\" + file_name, start_date, end_date, backup_stamps)\\n backup_stamps[tmp[\\\"backup_label\\\"]] = tmp[\\\"backup_timestamp_stop_ts\\\"]\\n if tmp:\\n infos.append(tmp)\\n except OSError as e:\\n logging.error(\\\"Failed to open directory\\\", exc_info=True)\\n exit(1)\\n except:\\n raise\",\n \"def debianize( strFilename ):\\n \\n #~ data = gzip.GzipFile( strFilename ).read();\\n #~ print data;\\n #~ return;\\n \\n #~ data = gzip.open( strFilename ).read();\\n #~ print data;\\n #~ return; \\n \\n #~ uncompressedData = bz2.BZ2File(strFilename).read()\\n #~ print str(uncompressedData)\\n #~ return;\\n \\n #~ file = open( strFilename, 'rb' );\\n #~ data = file.read();\\n #~ file.close();\\n #~ print debug.dumpHexa( data );\\n \\n #~ ar = tarfile.open(strFilename, 'r:*')\\n #~ for item in ar:\\n #~ print( str(item) );\\n #~ print( \\\"%s:\\\" % item.name );\\n #~ #print debug.dumpHexa(item.buf);\\n #~ #print zlib.decompress(item.buf)\\n #~ #print zlib.decompress(ar.extractfile(item).read())\\n #~ data = ar.extractfile(item.name).read()\\n #~ print data # works !\\n #~ ar.close() \\n #~ return;\\n \\n fileLists = [];\\n file = open( strFilename );\\n data = file.read();\\n file.close();\\n \\n print( \\\"data len: %d\\\" % len( data ) );\\n\\n nDataCompressedOffset = 0; # 132\\n\\n # works fine on toto.gz\\n #~ f = gzip.open(strFilename, 'rb')\\n #~ file_content = f.read()\\n #~ print file_content\\n #~ f.close() \\n \\n #~ decompressor = bz2.BZ2Decompressor();\\n #~ uncompressed = decompressor.decompress(data[nDataCompressedOffset:]);\\n \\n #~ uncompressed = zlib.decompress(data[nDataCompressedOffset:]);\\n \\n uncompressed = decompress( data );\\n print( \\\"uncompressed: %s\\\" % str( uncompressed ) );\",\n \"def _decompress_tarball(*, in_fileobj, out_fileobj):\\n with tarfile.open(fileobj=in_fileobj, mode=\\\"r\\\") as it, tarfile.open(\\n fileobj=out_fileobj, mode=\\\"w|\\\"\\n ) as ot:\\n for member in it.getmembers():\\n extracted = it.extractfile(member)\\n ot.addfile(member, extracted)\",\n \"def create_tarballs_from_xml_files_in_folder(xml_dir, download_date=\\\"2017.11.02\\\"):\\n\\n xml_list = glob.glob(os.path.join(xml_dir, \\\"*.xml\\\"))\\n\\n for xml in xml_list:\\n xml_renamed = xml[:-4] + \\\".BLAST.xml\\\"\\n xml_tar_gz = xml[:-4] + \\\".BLAST.xml.tar.gz\\\"\\n xml_txt = xml[:-4] + \\\"_details.txt\\\"\\n # xml_txt = xml[:-4] + \\\".BLAST_details.txt\\\"\\n\\n if not os.path.isfile(xml_tar_gz):\\n copyfile(xml, xml_renamed)\\n acc = os.path.basename(xml).split(\\\".\\\")[0]\\n sys.stdout.write(\\\"{}, \\\".format(acc))\\n sys.stdout.flush()\\n # create an empty text file with the download date\\n date = strftime(\\\"%Y%m%d\\\")\\n with open(xml_txt, \\\"w\\\") as f:\\n f.write(\\\"acc\\\\t{}\\\\ndownload_date\\\\t{}\\\\ndatabase\\\\tncbi_nr\\\\ne_value\\\\t1\\\\n\\\".format(acc, download_date))\\n\\n with tarfile.open(xml_tar_gz, mode='w:gz') as tar:\\n # add the files to the compressed tarfile\\n tar.add(xml_renamed, arcname=os.path.basename(xml_renamed))\\n tar.add(xml_txt, arcname=os.path.basename(xml_txt))\\n\\n # delete the original files\\n try:\\n os.remove(xml_renamed)\\n os.remove(xml_txt)\\n except:\\n sys.stdout.write(\\\"{} could not be deleted\\\".format(xml_renamed))\",\n \"def ParserTeil2():\\r\\n Bags = {}\\r\\n for Line in Lines:\\r\\n Words = Line.split()\\r\\n Farbe = Words[0]+\\\" \\\"+Words[1]\\r\\n Bags[Farbe] = re.findall(r\\\"(\\\\d+?) (.+?) bags?\\\", Line)\\r\\n return Bags\",\n \"def _unpack_tar(self, dir, filters):\\n try:\\n unpackArchive = gbpc.UnpackTarArchive(self.path, dir, filters)\\n unpackArchive()\\n except gbpc.CommandExecFailed:\\n # unpackArchive already printed an error message\\n raise GbpError\",\n \"def main(args):\\n # Extract keys\\n logger.info(\\\"Extracting brass bedpe file key from tarfile...\\\")\\n bedpe, bedpe_index = extract_tar_keys(args.results_archive)\\n # process bedpe\\n logger.info(\\\"Processing brass bedpe {0}...\\\".format(bedpe))\\n process_bedpe(args.results_archive, bedpe, bedpe_index, args.output_prefix)\",\n \"def bags(fondz_dir):\\n fondz_dir = os.path.abspath(fondz_dir)\\n results = {\\n 'bags': [],\\n 'num_files': 0,\\n 'bytes': 0\\n }\\n originals_dir = os.path.join(fondz_dir, \\\"originals\\\")\\n\\n for bag in os.listdir(originals_dir):\\n # TODO: look for other manifest types?\\n bag_dir = os.path.join(originals_dir, bag)\\n manifest = os.path.join(bag_dir, \\\"manifest-md5.txt\\\")\\n b = {\\n \\\"files\\\": [],\\n \\\"bytes\\\": 0,\\n }\\n for line in open(manifest):\\n line = line.strip()\\n cols = re.split(r' +', line)\\n path = os.path.join(bag_dir, cols[1])\\n st = os.stat(path)\\n rel_path = os.path.join(\\\"originals\\\", bag, path)\\n b['bytes'] += st.st_size\\n b['files'].append({\\n \\\"path\\\": rel_path,\\n \\\"bytes\\\": st.st_size,\\n \\\"created\\\": st.st_ctime,\\n \\\"modified\\\": st.st_mtime,\\n \\\"md5\\\": cols[0]\\n })\\n results['bytes'] += b['bytes']\\n results['num_files'] += len(b['files'])\\n results['bags'].append(b)\\n\\n bags_json = os.path.join(fondz_dir, \\\"js\\\", \\\"bags.json\\\")\\n write_json(results, bags_json)\\n return results\",\n \"def parse(path):\\n data = gzip.open(path, 'rb')\\n for byte_line in data:\\n yield eval(byte_line) # return generator instance to save memory\",\n \"def gbk_parse(fname):\\n fhand = _open_file(gbkfname)\\n unk = 1 \\n\\n for record in SeqIO.parse(fhand, \\\"genbank\\\"):\\n\\n gene_tags = dict()\\n tx_tags = collections.defaultdict(list) \\n exon = collections.defaultdict(list) \\n cds = collections.defaultdict(list) \\n mol_type, chr_id = None, None \\n\\n for rec in record.features:\\n\\n if rec.type == 'source':\\n mol_type = rec.qualifiers['mol_type'][0]\\n try:\\n chr_id = rec.qualifiers['chromosome'][0]\\n except:\\n chr_id = record.name \\n continue \\n\\n strand='-'\\n strand='+' if rec.strand>0 else strand\\n \\n fid = None \\n try:\\n fid = rec.qualifiers['gene'][0]\\n except:\\n pass\\n\\n transcript_id = None\\n try:\\n transcript_id = rec.qualifiers['transcript_id'][0]\\n except:\\n pass \\n\\n if re.search(r'gene', rec.type):\\n gene_tags[fid] = (rec.location._start.position+1, \\n rec.location._end.position, \\n strand,\\n rec.type,\\n rec.qualifiers['note'][0])\\n elif rec.type == 'exon':\\n exon[fid].append((rec.location._start.position+1, \\n rec.location._end.position))\\n elif rec.type=='CDS':\\n cds[fid].append((rec.location._start.position+1, \\n rec.location._end.position))\\n else: \\n # get all transcripts \\n if transcript_id: \\n tx_tags[fid].append((rec.location._start.position+1,\\n rec.location._end.position, \\n transcript_id,\\n rec.type))\\n # record extracted, generate feature table\\n unk = feature_table(chr_id, mol_type, strand, gene_tags, tx_tags, cds, exon, unk)\\n \\n #break\\n fhand.close()\",\n \"def _extract_data(inputs):\\n filename, split = inputs\\n for name, fobj in tfds.download.iter_archive(\\n filename, tfds.download.ExtractMethod.TAR_STREAM\\n ):\\n split_name = name.split(\\\"_\\\")\\n if len(split_name) > 2 and split_name[2] == split:\\n yield [name, fobj.read()]\",\n \"def parse_file(path):\\n if sys.platform.startswith('linux') or sys.platform.startswith('cygwin'):\\n # Assume Linux has GNU objdump. This has the options:\\n # -t (list symbols), -C (de-mangle symbol names)\\n objdump_args = ['objdump', '-t', '-C']\\n elif sys.platform.startswith('darwin'):\\n # Assume OSX has LLVM objdump. This has the options:\\n # -t (list symbols)\\n objdump_args = ['objdump', '-t']\\n objdump_args.append(path)\\n with StreamingProcess(objdump_args) as proc:\\n # Find the first non-blank line.\\n first_line = proc.peek()\\n while not first_line:\\n try:\\n proc.next()\\n first_line = proc.peek()\\n except StopIteration:\\n return []\\n # Is this an archive?\\n match = re.match(r'^.*[Aa]rchive\\\\s+(.+):$', first_line)\\n if match:\\n # In this format we have to skip this descriptive line.\\n proc.next()\\n return parse_archive(match.group(1), proc)\\n # Some objdumps format archives differently.\\n match = re.match(r'^(.+)\\\\((.+)\\\\):\\\\s+file format', first_line)\\n if match:\\n return parse_archive(match.group(1), proc)\\n # Otherwise maybe it's an object file?\\n match = re.match(r'^(.+):\\\\s+file format', first_line)\\n if match:\\n return [parse_object_file(match.group(1), proc)]\\n # Otherwise it's not an archive or object file.\\n return []\",\n \"def tar_file_and_group(data):\\n for sample in data:\\n assert \\\"stream\\\" in sample\\n stream = tarfile.open(fileobj=sample[\\\"stream\\\"], mode=\\\"r|*\\\")\\n prev_prefix = None\\n example = {}\\n valid = True\\n for tarinfo in stream:\\n name = tarinfo.name\\n pos = name.rfind(\\\".\\\")\\n assert pos > 0\\n prefix, postfix = name[:pos], name[pos + 1 :]\\n if prev_prefix is not None and prefix != prev_prefix:\\n example[\\\"key\\\"] = prev_prefix\\n if valid:\\n yield example\\n example = {}\\n valid = True\\n with stream.extractfile(tarinfo) as file_obj:\\n try:\\n if postfix == \\\"txt\\\":\\n example[\\\"txt\\\"] = file_obj.read().decode(\\\"utf8\\\").strip()\\n elif postfix in AUDIO_FORMAT_SETS:\\n waveform, sample_rate = torchaudio.load(file_obj)\\n example[\\\"wav\\\"] = waveform\\n example[\\\"sample_rate\\\"] = sample_rate\\n else:\\n example[postfix] = file_obj.read()\\n except Exception as ex:\\n valid = False\\n logging.warning(\\\"error to parse {}\\\".format(name))\\n prev_prefix = prefix\\n if prev_prefix is not None:\\n example[\\\"key\\\"] = prev_prefix\\n yield example\\n stream.close()\\n if \\\"process\\\" in sample:\\n sample[\\\"process\\\"].communicate()\\n sample[\\\"stream\\\"].close()\",\n \"def process_lines(self):\\n\\n for line in self.all_lines:\\n container_re = re.compile(r'(.*?) bags')\\n bags_re = re.compile(r'(?:(\\\\d+)|no other) (.*?) bags*')\\n container_name = re.match(container_re, line).group(1)\\n bags = re.findall(bags_re, line)\\n self.all_bags[container_name] = bags\",\n \"def parse_input():\\n with open(\\\"input_07.txt\\\", \\\"r\\\") as f:\\n for line in f:\\n Bag(line)\",\n \"def unpack_landsat(inpath, outpath, bands=None, clouds=None):\\r\\n tfile = tarfile.open(inpath,'r:gz')\\r\\n if bands is None:\\r\\n #Extract all of the bands.\\r\\n tfile.extractall(outpath);\\r\\n else:\\r\\n #Extract just the bands specified.\\r\\n\\r\\n #Get the names of the members of the archive\\r\\n names = tfile.getnames()\\r\\n\\r\\n #Make sure the bands are given as a list\\r\\n bands = list(bands)\\r\\n\\r\\n #Find those elements of the archive that match the bands specified\\r\\n #\\t(plus metadata file)\\r\\n members = tfile.getmembers()\\r\\n elements = []\\r\\n blist = ''.join(str(i) for i in bands)\\r\\n if clouds:\\r\\n patternStr = '.*_B[' + blist + ']\\\\.TIF|.*_MTL.txt|.*_band[' + blist + \\\\\\r\\n ']\\\\.tif|.*_cfmask.*\\\\.tif|.*\\\\.xml|.*cloud.*\\\\.tif'\\r\\n else:\\r\\n patternStr = '.*_B[' + blist + ']\\\\.TIF|.*_MTL.txt|.*_band[' + blist + \\\\\\r\\n ']\\\\.tif|.*_cfmask.*\\\\.tif|.*\\\\.xml'\\r\\n\\r\\n pattern = re.compile(patternStr)\\r\\n for i, name in enumerate(names):\\r\\n if pattern.match(name):\\r\\n elements.append(members[i])\\r\\n tfile.extractall(outpath,members = elements)\\r\\n\\r\\n '''\\r\\n Note: the below section was written with the intention of\\r\\n adding valuable metadata info to the .TIF files themselves.\\r\\n This theoretically allows easy retreival of key metadata info,\\r\\n but the method to set new metadata seems unreliable. Appears to\\r\\n be an open issue, but there may be a solution. For now, assume\\r\\n this does not work.\\r\\n\\r\\n #Now we loop through each output, adding important metadata.\\r\\n #Fetch metadata and make sure there is only one file.\\r\\n meta = glob.glob(outpath + '/*_MTL.txt')\\r\\n if len(meta) > 1:\\r\\n raise('MORE THAN ONE METADATA FILE FOUND!')\\r\\n\\r\\n metadata = read_metadata(meta[0])\\r\\n\\r\\n #Add the metadata.\\r\\n for tif in glob.glob(outpath + '*.TIF'):\\r\\n #Open the tif file\\r\\n ras = gdal.Open(tif)\\r\\n\\r\\n #Preserve any existing metadata & add important metadata from file\\r\\n meta = ras.GetMetadata()\\r\\n meta['SCENE_CENTER_TIME'] = metadata['SCENE_CENTER_TIME']\\r\\n meta['DATE_ACQUIRED'] = metadata['DATE_ACQUIRED']\\r\\n meta['LANDSAT_SCENE_ID'] = metadata['LANDSAT_SCENE_ID']\\r\\n\\r\\n #Now write the new metadata back to the tif.\\r\\n ras.SetMetadata(meta)\\r\\n ras.FlushCache()\\r\\n ras = None\\r\\n '''\",\n \"def parse_blast_XML(blast_xml):\\n\\tblast_xml_op = open (blast_xml, 'r')\\n\\tfor record in NCBIXML.parse(blast_xml_op):\\n\\t\\tfor align in record.alignments:\\n\\t\\t\\thit_id = align.hit_id.split(\\\"|\\\")\\n\\t\\t\\tprev_eval = 1\\n\\t\\t\\tcoverage = align.length / 390 ######arreglar per posar longitud sequencia\\n\\t\\t\\tfor hsp in align.hsps:\\n\\t\\t\\t\\tif hsp.expect < prev_eval:\\n\\t\\t\\t\\t\\tprev_eval = hsp.expect\\n\\t\\t\\tefetch = Entrez.efetch(db=\\\"protein\\\", id=hit_id, rettype=\\\"fasta\\\")\\n\\t\\t\\tfor line in efetch:\\n\\t\\t\\t\\tline = line.rstrip()\\n\\t\\t\\t\\tif line.startswith(\\\">\\\"):\\n\\t\\t\\t\\t\\tid_info = line\\n\\t\\t\\t\\t\\tsequence = \\\"\\\"\\n\\t\\t\\t\\telse:\\n\\t\\t\\t\\t\\tsequence += line\\n\\t\\t\\tsequence += line\\n\\n\\t\\t\\torganism = id_info[id_info.find(\\\"[\\\") + 1:id_info.find(\\\"]\\\")]\\n\\t\\t\\torganism = organism.split()\\n\\t\\t\\tif len(organism) != 1:\\n\\t\\t\\t\\tspecies = str(organism[0] + \\\"_\\\" + organism[1])\\n\\n\\t\\t\\tyield BlastResult(hit_id[1], species, sequence, prev_eval, coverage)\",\n \"def _unpack_archive(self, dir, filters):\\n ext = os.path.splitext(self.path)[1]\\n if ext in [\\\".zip\\\", \\\".xpi\\\"]:\\n if filters:\\n raise GbpError(\\\"Can only filter tar archives: %s\\\", (ext, self.path))\\n self._unpack_zip(dir)\\n else:\\n self._unpack_tar(dir, filters)\",\n \"def iterator(dataset_fn, sections=None, lang=None, field_indices=None):\\n files = filelist(lang=lang, sections=sections)\\n\\n with TarFile.open(dataset_fn, 'r:gz') as f:\\n for member in f:\\n if member.isfile() and os.path.basename(member.name) in files:\\n logging.info('parsing %s ...' % member.name)\\n m_f = f.extractfile(member)\\n\\n for sentence in parse_conll(m_f, field_indices=field_indices):\\n yield sentence\\n\\n m_f.close()\",\n \"def parse(self, recursive=True):\\n # Read and process the file header\\n self.fh.seek(0x0, 0)\\n header = struct.unpack(\\\"=10I\\\", self.fh.read(0x28))\\n\\n data_start_block = header[0x1]\\n\\n idx_table_entry_count = header[0x4]\\n\\n off_table_offset = header[0x5]\\n off_table_addr = self.IDX_TABLE_ADDR + off_table_offset\\n\\n self.fh.seek(self.IDX_TABLE_ADDR, 0)\\n\\n # Read and populate the index table\\n idx_table = []\\n for idx in range(idx_table_entry_count):\\n typ, num1, num2, num3, num4 = Image.parse_idx_entry(\\n self.fh.read(self.IDX_TABLE_ENTRY_SIZE)\\n )\\n idx_table.append([typ, num1, num2, num3, num4])\\n\\n self.fh.seek(off_table_addr, 0)\\n\\n # FIXME: Not sure what 'unk' is.\\n off_table_entry_count, unk = struct.unpack(\\\"=4x2I\\\", self.fh.read(0xC))\\n\\n # Read and populate the offset table\\n off_table = {}\\n for i in range(off_table_entry_count):\\n idx, blk_num = Image.parse_off_entry(\\n self.fh.read(self.OFF_TABLE_ENTRY_SIZE)\\n )\\n off_table[idx] = blk_num\\n\\n # Populate entries\\n self.entries = []\\n for idx, idx_entry in enumerate(idx_table):\\n if idx not in off_table:\\n self.entries.append(None)\\n continue\\n\\n blk_num = off_table[idx]\\n off = self.fh.tell()\\n\\n # We need to grab the actual (compressed) size from the PACKage header\\n res = None\\n addr = self.BLOCK_NUM_ADDR(blk_num)\\n if idx_entry[0x0] == b\\\"PAK \\\":\\n self.fh.seek(addr)\\n (\\n typ,\\n cnt,\\n ptr_off,\\n str_table_off,\\n dec_data_off,\\n dec_len,\\n cmp_len,\\n pad_len,\\n ) = Package.parse_header(self.fh.read(Package.ENTRY_SIZE))\\n res = Package(FileWindow(self.filename, addr, cmp_len), idx_entry[0x3])\\n else:\\n res = Resource(\\n idx_entry[0x0], FileWindow(self.filename, addr, idx_entry[0x1])\\n )\\n\\n if recursive:\\n res.parse(recursive)\\n self.entries.append(res)\\n self.fh.seek(off, 0)\",\n \"def bgzip_tabix(bedbz2):\\n bed = bedbz2.replace(\\\".bz2\\\", \\\"\\\")\\n bedgz = bed + \\\".gz\\\"\\n tbi = bedgz + \\\".tbi\\\"\\n if os.path.exists(bedgz) and os.path.exists(tbi):\\n print bedgz, tbi, \\\"has beed generated.\\\"\\n return\\n c1 = \\\"bzip2 -d %s\\\" % bedbz2\\n c2 = \\\"bgzip %s\\\" % bed\\n c3 = \\\"tabix -s 1 -b 2 -e 3 %s\\\" % bedgz\\n call_sys([c1, c2, c3])\",\n \"def readArff(filename):\\n \\n data = []\\n labels = []\\n\\n def parseLine(line): # csv.reader could not do this.\\n isopen = False\\n current = ''\\n for c in line:\\n if c == \\\"'\\\":\\n if isopen:\\n yield current\\n current = ''\\n isopen = not isopen\\n elif isopen:\\n current += c\\n\\n #with filename.open() as f:\\n with bz2.open(str(filename)+'.bz2', 'r') as f:\\n \\n line = ''\\n while line != '@data':\\n line = f.readline().decode().strip()\\n if line.startswith(\\\"@attribute 'classification'\\\"):\\n line = line[line.find('{') + 1:line.find('}')]\\n classes = {i:n for n,i in enumerate(parseLine(line))}\\n\\n for line in f.read().decode().splitlines():\\n record = list(parseLine(line))\\n labels.append(classes[record[-1]])\\n data.append([int(x) for x in record[:-1]])\\n return numpy.array(data, dtype=float), numpy.array(labels), classes\",\n \"def bz2_file_reader(path):\\n return bz2.open(path, 'rt')\",\n \"def decompress_bz2(filename):\\n basename = os.path.basename(filename)\\n newfilepath = os.path.dirname(filename) + '/' + '.'.join(basename.split('.')[0:-1]) # all but bz2\\n\\n with open(newfilepath, 'wb') as new_file, bz2.BZ2File(filename, 'rb') as bz2_file:\\n for data in iter(lambda : bz2_file.read(100 * 1024), b''):\\n new_file.write(data)\\n\\n return newfilepath\",\n \"def decompress_bz2(filename):\\n basename = os.path.basename(filename)\\n newfilepath = os.path.dirname(filename) + '/' + '.'.join(basename.split('.')[0:-1]) # all but bz2\\n\\n with open(newfilepath, 'wb') as new_file, bz2.BZ2File(filename, 'rb') as bz2_file:\\n for data in iter(lambda : bz2_file.read(100 * 1024), b''):\\n new_file.write(data)\\n\\n return newfilepath\",\n \"def convert(self, tag=\\\"Data\\\", delimiter=\\\",\\\", noheader=False,\\n limit=-1, buffer_size=1000):\\n\\n\\n file_ctr = 0\\n item_ctr = 0\\n for dirName, subdirList, fileList in os.walk(self.input_directory):\\n print('Found directory: %s' % dirName)\\n for fname in fileList:\\n print('\\\\t%s' % fname)\\n # open the xml file for iteration\\n if not fname.endswith(\\\".xml\\\"):\\n continue\\n #pdb.set_trace()\\n \\n input_file = dirName + \\\"/\\\" + fname\\n self.context = ETree.iterparse(input_file, events=(\\\"start\\\", \\\"end\\\"))\\n\\n # iterate through the xml\\n items = [{}]\\n\\n depth = 0\\n min_depth = 0\\n row_depth = -1\\n n = 0\\n for event, elem in self.context:\\n if event == \\\"start\\\":\\n depth += 1\\n continue\\n else:\\n depth -= 1\\n if depth < min_depth:\\n min_depth = depth\\n\\n if depth < row_depth and items:\\n if noheader:\\n noheader = False\\n else:\\n # new line\\n self.output_buffer.append(items)\\n items = []\\n # flush buffer to disk\\n if len(self.output_buffer) > buffer_size:\\n self._write_buffer(delimiter)\\n\\n plain_tag = elem.tag\\n last_delim = max(elem.tag.rfind('}'), elem.tag.rfind(':'))\\n if 0 < last_delim < len(elem.tag) - 1:\\n plain_tag = elem.tag[last_delim + 1:]\\n if tag == plain_tag:\\n if n == 0:\\n min_depth = depth\\n elif n == 1:\\n row_depth = min_depth\\n n += 1\\n if 0 < limit < n:\\n break\\n elem_name = elem.get(\\\"name\\\")\\n if elem_name in self.output_dict[0].keys():\\n if elem_name == 'SamS.ArchivedURL':\\n if hash(elem.text) in self.item_titles.keys() and self.item_titles[hash(elem.text)] == elem.text:\\n #item is repetative\\n self.output_dict[item_ctr]={}\\n #item_ctr-=1\\n break\\n else:\\n self.item_titles[hash(elem.text)] = elem.text\\n self.output_dict[item_ctr][elem_name]= elem.text and elem.text.encode('utf8') or ''\\n\\n #if (len(self.output_dict[item_ctr]) > 0 ) :\\n if ('SamS.ArchivedURL' in self.output_dict[item_ctr]):\\n item_ctr+=1\\n self.output_dict.append({})\\n else:\\n self.output_dict[item_ctr] = {}\\n \\n file_ctr+=1 #next row in the dictionary array\\n print \\\"processing file no \\\", file_ctr, \\\" item no\\\", item_ctr\\n\\n #pdb.set_trace()\\n self._write_buffer(delimiter) # write rest of the buffer to file\\n\\n return n\",\n \"def parse(self):\\n gen = self.v6_gen() # read from workers\\n gen = self.tuple_gen(gen) # convert v6->tuple\\n gen = self.batch_gen(gen) # assemble into batches\\n for b in gen:\\n yield b\",\n \"def parse(self, filename: str, input_format='csv', **kwargs):\\n if 'delimiter' not in kwargs:\\n kwargs['delimiter'] = self._extention_types[input_format]\\n if filename.endswith('.tar'):\\n with tarfile.open(filename) as tar:\\n for member in tar.getmembers():\\n f = tar.extractfile(member)\\n df = pd.read_csv(f, comment='#', **kwargs) # type: pd.DataFrame\\n if member.name == 'nodes.csv':\\n self.load_nodes(df)\\n elif member.name == 'edges.csv':\\n self.load_edges(df)\\n else:\\n raise Exception('Tar file contains unrecognized member {}'.format(member.name))\\n else:\\n df = pd.read_csv(filename, comment='#', **kwargs) # type: pd.DataFrame\\n self.load(df)\",\n \"def fromgroups(args):\\n from jcvi.formats.bed import Bed\\n\\n p = OptionParser(fromgroups.__doc__)\\n opts, args = p.parse_args(args)\\n\\n if len(args) < 2:\\n sys.exit(not p.print_help())\\n\\n groupsfile = args[0]\\n bedfiles = args[1:]\\n beds = [Bed(x) for x in bedfiles]\\n fp = open(groupsfile)\\n groups = [row.strip().split(\\\",\\\") for row in fp]\\n for b1, b2 in product(beds, repeat=2):\\n extract_pairs(b1, b2, groups)\",\n \"def parse(self, *args, **kwargs):\\n if self.is_gzipped:\\n fin = gzip.open(self.path, 'rb')\\n else:\\n fin = open(self.path, 'r')\\n line_num = 0\\n expect_header = True\\n for line in fin:\\n line_num += 1\\n line = line.strip()\\n if not line: # skip empty lines\\n continue\\n if expect_header:\\n if self._is_header(line):\\n logger.debug(\\n f\\\"Detected header at line {line_num}: {line!r}\\\")\\n continue\\n else:\\n expect_header = False\\n try:\\n chrom, pos = self._parse_line(line, *args, **kwargs)\\n if chrom is not None:\\n yield chrom, pos\\n except (IndexError, ValueError, TypeError):\\n fin.close()\\n raise FileFormatError(format=self.format, line_num=line_num,\\n line=line)\\n fin.close()\",\n \"def parse(fcontents, utf16=False): # TODO where does this conversion take place??\\n if utf16:\\n # Handle a bunch of Unicode nonsense; files appear to be in UTF-16LE\\n quant_results = fcontents.split(BLOCK_DIVIDER_UTF16)[3]\\\\\\n .decode(AWKWARD_ENCODING).encode('ascii', 'ignore').split(\\\"\\\\r\\\\n\\\")\\n else:\\n quant_results = fcontents.split(BLOCK_DIVIDER)[3].split(\\\"\\\\r\\\\n\\\")\\n\\n for res in quant_results:\\n items = res.split(\\\"\\\\t\\\")\\n if re.search(\\\"\\\\d+\\\", items[0]): # ignore non-digit rows\\n amt = items[9]\\n if amt == OUTSIDE_LADDER:\\n amt = 100\\n yield (int(items[0]), items[1], float(amt))\",\n \"def _add_tag_files(\\n zip_file, dir_name, payload_info_list, payload_byte_count, payload_file_count\\n):\\n tag_info_list = []\\n _add_tag_file(zip_file, dir_name, tag_info_list, _gen_bagit_text_file_tup())\\n _add_tag_file(\\n zip_file,\\n dir_name,\\n tag_info_list,\\n _gen_bag_info_file_tup(payload_byte_count, payload_file_count),\\n )\\n _add_tag_file(\\n zip_file, dir_name, tag_info_list, _gen_pid_mapping_file_tup(payload_info_list)\\n )\\n return tag_info_list\",\n \"def tarball(request):\\n\\n patches = (models.Patch\\n .query(ancestor=request.patchset.key)\\n .order(models.Patch.filename)\\n .fetch(1000))\\n\\n temp = tempfile.TemporaryFile()\\n tar = tarfile.open(mode=\\\"w|bz2\\\", fileobj=temp)\\n\\n def add_entry(prefix, content, patch):\\n data = content.data\\n if data is None:\\n data = content.text\\n if isinstance(data, unicode):\\n data = data.encode(\\\"utf-8\\\", \\\"replace\\\")\\n if data is None:\\n return\\n info = tarfile.TarInfo(prefix + patch.filename)\\n info.size = len(data)\\n # TODO(adonovan): set SYMTYPE/0755 when Rietveld supports symlinks.\\n info.type = tarfile.REGTYPE\\n info.mode = 0644\\n # datetime->time_t\\n delta = request.patchset.modified - datetime.datetime(1970, 1, 1)\\n info.mtime = int(delta.days * 86400 + delta.seconds)\\n tar.addfile(info, fileobj=StringIO(data))\\n\\n for patch in patches:\\n if not patch.no_base_file:\\n try:\\n add_entry('a/', patch.get_content(), patch) # before\\n except FetchError: # I/O problem?\\n logging.exception('tarball: patch(%s, %s).get_content failed' %\\n (patch.key.id(), patch.filename))\\n try:\\n add_entry('b/', patch.get_patched_content(), patch) # after\\n except FetchError: # file deletion? I/O problem?\\n logging.exception('tarball: patch(%s, %s).get_patched_content failed' %\\n (patch.key.id(), patch.filename))\\n\\n tar.close()\\n temp.flush()\\n\\n wrapper = FileWrapper(temp)\\n response = HttpResponse(wrapper, mimetype='application/x-gtar')\\n response['Content-Disposition'] = (\\n 'attachment; filename=patch%s_%s.tar.bz2' % (request.issue.key.id(),\\n request.patchset.key.id()))\\n response['Content-Length'] = temp.tell()\\n temp.seek(0)\\n return response\",\n \"def unpack(file, path='.'):\\n assert isfile(file)\\n assert isdir(path)\\n\\n for implementor in [GzipTarredFile, ZippedFile, Bzip2TarredFile]:\\n if implementor.is_valid(file):\\n with console.cd(path):\\n return [implementor(file).extract(), implementor]\\n else:\\n raise InvalidFile, 'compressed file format unknown: %s' % file\",\n \"def tarball(request):\\n\\n patches = (models.Patch\\n .query(models.Patch.patchset_key == request.patchset.key)\\n .order(models.Patch.filename)\\n .fetch(1000))\\n\\n temp = tempfile.TemporaryFile()\\n tar = tarfile.open(mode=\\\"w|bz2\\\", fileobj=temp)\\n\\n def add_entry(prefix, content):\\n data = content.data\\n if data is None:\\n data = content.text\\n if isinstance(data, unicode):\\n data = data.encode(\\\"utf-8\\\", \\\"replace\\\")\\n if data is None:\\n return\\n info = tarfile.TarInfo(prefix + patch.filename)\\n info.size = len(data)\\n # TODO(adonovan): set SYMTYPE/0755 when Rietveld supports symlinks.\\n info.type = tarfile.REGTYPE\\n info.mode = 0644\\n # datetime->time_t\\n delta = request.patchset.modified - datetime.datetime(1970, 1, 1)\\n info.mtime = int(delta.days * 86400 + delta.seconds)\\n tar.addfile(info, fileobj=StringIO(data))\\n\\n for patch in patches:\\n if not patch.no_base_file:\\n try:\\n add_entry('a/', patch.get_content()) # before\\n except FetchError: # I/O problem?\\n logging.exception('tarball: patch(%s, %s).get_content failed' %\\n (patch.key.id(), patch.filename))\\n try:\\n add_entry('b/', patch.get_patched_content()) # after\\n except FetchError: # file deletion? I/O problem?\\n logging.exception('tarball: patch(%s, %s).get_patched_content failed' %\\n (patch.key.id(), patch.filename))\\n\\n tar.close()\\n temp.flush()\\n\\n wrapper = FileWrapper(temp)\\n response = HttpResponse(wrapper, mimetype='application/x-gtar')\\n response['Content-Disposition'] = (\\n 'attachment; filename=patch%s_%s.tar.bz2' % (request.issue.key.id(),\\n request.patchset.key.id()))\\n response['Content-Length'] = temp.tell()\\n temp.seek(0)\\n return response\",\n \"def parse(self, ergFilePath):\\n infoFilePath = ergFilePath + '.info'\\n quantityList = self.getQuantityList(infoFilePath)\\n\\n # get block size\\n blockSize = sum(quantity.bytes for quantity in quantityList)\\n\\n with open(ergFilePath, 'rb') as ergFile:\\n\\n # read the first 16 bytes, as they are not needed now\\n ergFile.read(16)\\n\\n # now read the rest of the file block wise\\n block = ergFile.read(blockSize)\\n while len(block) == blockSize:\\n for q in quantityList:\\n q.values.append(np.fromstring(block[:q.bytes], q.dataType)[0])\\n block = block[q.bytes:]\\n block = ergFile.read(blockSize)\\n\\n self.quantityList = quantityList\\n return quantityList\",\n \"def extract_tars(file_pattern, path_in, path_out):\\n for f in glob.glob(os.path.join(path_in, file_pattern)):\\n shutil.unpack_archive(f, path_out)\",\n \"def gzip_files(topDir, afni_file,localizerfile):\\n\\n print 'GZIPPING FILES...'\\n\\n command1 = \\\"gzip %s*BRIK\\\" % (topDir)\\n command2 = \\\"gzip %s*HEAD\\\" % (topDir)\\n command3 = \\\"gzip %s%s/pb00*\\\" % (topDir,afni_file)\\n command4 = \\\"gzip %s%s/errts*\\\" % (topDir,afni_file)\\n command5 = \\\"gzip %s%s/fitts*\\\" % (topDir,afni_file)\\n command6 = \\\"gzip %s%s/*al*\\\" % (topDir,afni_file)\\n command7 = \\\"gzip %s%s/*ns*\\\" % (topDir,afni_file)\\n command8 = \\\"gzip %s%s/all_runs*\\\" % (topDir,afni_file)\\n command9 = \\\"gzip %s%s/*mask*\\\" % (topDir,afni_file)\\n command10 = \\\"gzip %s*nii\\\" % (topDir)\\n command11 = \\\"gzip %s%s/pb01*\\\" % (topDir,afni_file)\\n command12 = \\\"gzip %s%s/pb03*\\\" % (topDir,afni_file)\\n command13 = \\\"gzip %s%s/pb02*\\\" % (topDir,afni_file)\\n\\n os.system(command1)\\n os.system(command2)\\n os.system(command3)\\n os.system(command4)\\n os.system(command5)\\n os.system(command6)\\n os.system(command7)\\n os.system(command8)\\n #os.system(command9)\\n os.system(command10)\\n os.system(command11)\\n try:\\n os.system(command12)\\n except:\\n print 'Could not gzip pb03 files'\\n\\n if localizerfile == 'facescene_loc':\\n os.system(command13)\",\n \"def main():\\r\\n parser = CommonArgParser(__file__)\\r\\n parser.add_argument('src_dir', help='Source directory')\\r\\n parser.add_argument(\\r\\n 'out_dir',\\r\\n default='.',\\r\\n help=\\\"\\\"\\\"The directory the files to be extracted.\\r\\n (Default: Current directoty\\\"\\\"\\\")\\r\\n args = parser.parse_all()\\r\\n for f in next_file(args.src_dir, ['*.tgz', '*.tar.gz']):\\r\\n untgz(f, args.out_dir)\",\n \"def parse(all_blobs, all_angles):\",\n \"def boldExtract(genera):\\r\\n # Prepare Web Service Endpoint for BOLD's Public Data Portal API\\r\\n # Appending BOLD's base URL to each genera from the NSR list\\r\\n base_url = 'http://v4.boldsystems.org/index.php/API_Public/combined?taxon='\\r\\n source_urls = list(map(lambda x: \\\"{}{}{}\\\".\\r\\n format(base_url, x, '&format=tsv'), genera))\\r\\n\\r\\n # Download sequence data from BOLD using list of url's\\r\\n print('Beginning sequence data retrieval...')\\r\\n counter = 0\\r\\n for url in source_urls:\\r\\n r = http.request('GET', url)\\r\\n name = genera[counter]\\r\\n counter += 1\\r\\n with open(args.outdir1+\\\"/\\\"+name+\\\".tsv\\\", \\\"wb\\\") as fcont:\\r\\n fcont.write(r.data)\",\n \"def iter_libsvm(filepath_or_buffer, target_type=float, compression='infer'):\\n\\n # If a file is not opened, then we open it\\n if not hasattr(filepath_or_buffer, 'read'):\\n filepath_or_buffer = open_filepath(filepath_or_buffer, compression)\\n\\n def split_pair(pair):\\n name, value = pair.split(':')\\n value = float(value)\\n return name, value\\n\\n for line in filepath_or_buffer:\\n\\n # Remove carriage return and whitespace\\n line = line.rstrip()\\n # Remove potential end of line comments\\n line = line.split('#')[0]\\n\\n y, x = line.split(' ', maxsplit=1)\\n y = target_type(y)\\n x = dict([split_pair(pair) for pair in x.split(' ')])\\n yield x, y\",\n \"def yield_publications_metadata(tf):\\n logger.info('Start yielding...')\\n with gzip.GzipFile(fileobj=tf, mode='r') as json_file:\\n for index, line in enumerate(json_file):\\n yield build_es_bulk(line.decode('utf-8'))\",\n \"def parse_archive(path, objdump):\\n object_files = []\\n current_file = None\\n for line in objdump:\\n if not line:\\n continue\\n match = re.match(r'^(.*[^\\\\)])(\\\\((.+)\\\\))?:\\\\s+file format', line)\\n if match:\\n filename = match.group(3) if match.group(3) else match.group(1)\\n current_file = ObjectFile(filename, path)\\n object_files.append(current_file)\\n continue\\n if not current_file:\\n raise Exception('Archive does not specify object to attribute '\\n 'symbols to ' + path)\\n sym = parse_symbol(line)\\n if not sym:\\n if current_file.symbols:\\n current_file = None\\n continue\\n current_file.symbols.append(sym)\\n return object_files\",\n \"def bz2_file_bytes_reader(path):\\n return bz2.open(path, 'rb')\",\n \"def LoadBatch(filename):\",\n \"def parse_ensembl_genes(lines):\\n LOG.info(\\\"Parsing ensembl genes from file\\\")\\n header = []\\n for index, line in enumerate(lines):\\n # File allways start with a header line\\n if index == 0:\\n header = line.rstrip().split(\\\"\\\\t\\\")\\n continue\\n # After that each line represents a gene\\n\\n yield parse_ensembl_line(line, header)\",\n \"def __init__(self, fpath, prefix, suffix, globar_year=None):\\n self.fpath = fpath\\n prefix_len = len(prefix)\\n suffix_len = len(suffix)\\n self.year = globar_year\\n self.year_str = str(globar_year)\\n\\n # filename example : good_2005_0.pgz\\n files = [f for f in listdir(fpath) if isfile(join(fpath, f)) and\\n (f[-suffix_len:] == suffix and f[:prefix_len] == prefix)]\\n\\n pat = '{0}_{1}'.format(prefix, self.year_str)\\n last_batch = \\\\\\n list(sorted(filter(lambda f: pat in f, files)))\\n first_batch = \\\\\\n list(sorted(filter(lambda f: pat not in f, files)))\\n\\n logging.info('in ChunkReader.__init__() : '\\n '(last_batch) {0} files : {1}'.format(len(last_batch), ' '.join(last_batch)))\\n logging.info('in ChunkReader.__init__() : '\\n '(first_batch) {0} files : {1}'.format(len(first_batch), ' '.join(first_batch)))\\n\\n first_batch.extend(last_batch)\\n # queue-like usage\\n self.files = first_batch[::-1]\\n logging.info('in ChunkReader.__init__ : '\\n 'all files {0} files : {1}'.format(len(self.files), ' '.join(self.files)))\",\n \"def parseDec_GZIPLoader(self, data): # Once gziploader is decrypted, parse the 0xA9 byte config\\n hardcoded_val = data[0:1]\\n flag = data[1:2]\\n datfile_size = int.from_bytes(data[2:6], byteorder=\\\"little\\\")\\n print(\\\"[+] datfile size: \\\", datfile_size)\\n dllfile_size = int.from_bytes(data[6:10], byteorder=\\\"little\\\")\\n print(\\\"[+] dllfile size: \\\", dllfile_size)\\n dirname = self.extractStrFromBuff(data[10:])\\n print(\\\"[+] Directory Name:\\\", dirname)\\n\\n count = self.incNulls(data[10 + len(dirname):])\\n datname = self.extractStrFromBuff(data[count + 10 + len(dirname):])\\n print(\\\"[+] Dat Name :\\\", datname)\\n\\n count = count + 10 + len(dirname) + len(datname)\\n datname = datname[1:]\\n count2 = self.incNulls(data[count:])\\n count = count + count2\\n dllname = self.extractStrFromBuff(data[count:])\\n print(\\\"[+] Dll Name: \\\", dllname)\\n count += len(dllname)\\n count2 = self.incNulls(data[count:])\\n count += count2\\n # datfile offset is now 710 bytes in\\n datfile_data = data[710:710 + datfile_size]\\n dllfile_start = 710 + datfile_size\\n dllfile_data = data[dllfile_start:dllfile_start + dllfile_size]\\n datfile_b64 = base64.b64encode(datfile_data).decode()\\n dllfile_b64 = base64.b64encode(dllfile_data).decode()\\n ParsedDict = {\\\"Directory_Name\\\": dirname.decode(),\\n \\\"DatFile_Name\\\": datname.decode(),\\n \\\"DllFile_Name\\\": dllname.decode(),\\n \\\"DatFile\\\": datfile_b64,\\n \\\"DllFile\\\": dllfile_b64}\\n\\n return ParsedDict\",\n \"def untgz(tgz_filename, out_dir):\\r\\n logging.info(\\\"Source: %s\\\" % tgz_filename)\\r\\n tgz = TgzHelper(tgz_filename, out_dir)\\r\\n tgz.extract()\",\n \"def _process_fileobj(self,\\n tar_file_obj: IO[bytes],\\n object_node: graph.COSObject) -> None:\\n with tarfile.open(fileobj=tar_file_obj) as tar_file:\\n gz_file_names = [f.name for f in tar_file.getmembers()\\n if f.name.endswith('.gz')]\\n for gz_file_name in gz_file_names:\\n gz_file_obj = tar_file.extractfile(gz_file_name)\\n if gz_file_obj:\\n oem_data = self._parse_oem_data(gz_file_obj)\\n aso_id = self._get_aso_id_from_file_name(gz_file_name)\\n self._save_oem(oem_data, aso_id, object_node)\",\n \"def archive_bag_api_messages(bags, bucket):\\n for bag in bags:\\n yield {\\n 'type': 'Ingest',\\n 'ingestType': {\\n 'id': 'create',\\n 'type': 'IngestType'\\n },\\n 'uploadUrl': f's3://{bucket}/{bag}'\\n }\",\n \"def read_data_with_preprocess(filename):\\n\\n with bz2.BZ2File(filename) as f:\\n\\n data = []\\n file_size = os.stat(filename).st_size\\n chunk_size = 1024 * 1024 # reading 1 MB at a time as the dataset is moderately large\\n print('Reading data...')\\n for i in range(ceil(file_size//chunk_size)+1):\\n bytes_to_read = min(chunk_size,file_size-(i*chunk_size))\\n file_string = f.read(bytes_to_read).decode('utf-8')\\n file_string = file_string.lower()\\n # tokenizes a string to words residing in a list\\n file_string = nltk.word_tokenize(file_string)\\n data.extend(file_string)\\n return data\",\n \"def parse_records(self):\\n for record in sp.parse(gzip.open(\\n \\\"./human_uniprot_04_07_20.gz\\\", 'rt')):\\n # print(record.taxonomy_id)\\n # if record.organism != \\\"Homo sapiens\\\":\\n # continue\\n # print(record.features[0])\\n # for comment in record.comments:\\n # if comment.startswith(\\\"SUBCELLULAR LOCATION\\\"):\\n # print(comment)\\n self.extract_features_to_dict(record)\\n self.extract_localization(record)\",\n \"def extract_tarball(fileobj, path, callback=None):\\n tar_cmd = [\\\"tar\\\", \\\"-zx\\\", \\\"--directory=%s\\\" % path]\\n tar_proc = make_subprocess(tar_cmd, stderr=True, stdin=True)\\n\\n try:\\n while True:\\n chunk = fileobj.read(CHUNK_SIZE)\\n if chunk == '':\\n break\\n\\n if callback:\\n callback(chunk)\\n\\n tar_proc.stdin.write(chunk)\\n except Exception:\\n try_kill_process(tar_proc)\\n raise\\n\\n finish_subprocess(tar_proc, tar_cmd)\",\n \"def read_and_parse(path_pattern, parser, **kwargs):\\n for filename in glob.glob(path_pattern):\\n with open(filename, 'r') as file:\\n yield filename, parser.parse(file.read(), **kwargs)\",\n \"def decompress(self, chunk):\\n # print(self.decompressor.eof)\\n data = self.data_rem + self.decompressor.decompress(chunk)\\n if data != 0: # 0 is common -- waiting for a bzip2 block\\n # process dat here\\n\\n chunk_decoded, self.data_rem = self.decodeBytesUtf8Safe(data)\\n try:\\n ### A chunk might contain an incomplete game, which is difficult\\n ### to produce later. Therefore incomplete strings are saved in\\n ### remainder_string and concacated in the next run\\n chunk_decoded = self.games_rem + chunk_decoded\\n except:\\n chunk_decoded = chunk_decoded\\n\\n ### Split chunks at the \\\"Event\\\" key as it is the indicator\\n ### for a new game\\n games = re.sub(\\\"\\\\n\\\\n\\\\[Event\\\", \\\"\\\\n\\\\n;[Event\\\", chunk_decoded).split(\\\"\\\\n\\\\n;\\\")\\n\\n ### Extract the last chunk as it is typically incomplete and can be\\n ### concacated in the next run. Additionally, it removes the last\\n ### match from chunk and leaves chunk = [], in case no further data\\n ### can be extracted from the archive.\\n\\n self.games_rem = games.pop()\\n\\n self.extract_keys(games)\",\n \"def parse_blast_XML(blast_xml, config_file):\\n\\tblast_xml_op = open (blast_xml, 'r')\\n\\tEntrez.email = parse_config(config_file, \\\"email\\\")\\n\\tdb, evalue = parse_config(config_file, \\\"blast\\\")\\n\\n\\tfor record in NCBIXML.parse(blast_xml_op):\\n\\t\\tfor align in record.alignments:\\n\\t\\t\\thit_id = align.hit_id.split(\\\"|\\\")\\n\\t\\t\\tprev_eval = 1\\n\\t\\t\\tfor hsp in align.hsps:\\n\\t\\t\\t\\tif hsp.expect < prev_eval:\\n\\t\\t\\t\\t\\tprev_eval = hsp.expect\\n\\t\\t\\tefetch = Entrez.efetch(db=\\\"protein\\\", id=hit_id, rettype=\\\"fasta\\\")\\n\\t\\t\\tfor line in efetch:\\n\\t\\t\\t\\tline = line.rstrip()\\n\\t\\t\\t\\tif line.startswith(\\\">\\\"):\\n\\t\\t\\t\\t\\tid_info = line\\n\\t\\t\\t\\t\\tsequence = \\\"\\\"\\n\\t\\t\\t\\telse:\\n\\t\\t\\t\\t\\tsequence += line\\n\\t\\t\\tsequence += line\\n\\n\\t\\t\\torganism = id_info[id_info.find(\\\"[\\\") + 1:id_info.find(\\\"]\\\")]\\n\\t\\t\\torganism = organism.split()\\n\\t\\t\\tif len(organism) != 1:\\n\\t\\t\\t\\tspecies = str(organism[0] + \\\"_\\\" + organism[1])\\n\\n\\t\\t\\tif prev_eval <= float(evalue):\\n\\t\\t\\t\\tyield BlastResult(hit_id[1], species, sequence, prev_eval)\",\n \"def parse(self, limit=None):\\n if limit is not None:\\n logger.info(\\\"Only parsing first %d rows of each file\\\", limit)\\n logger.info(\\\"Parsing files...\\\")\\n\\n if self.testOnly:\\n self.testMode = True\\n\\n # the following will provide us the hash-lookups\\n self._process_dbxref()\\n self._process_cvterm()\\n self._process_genotypes(limit)\\n self._process_pubs(limit)\\n # do this before environments to get the external ids\\n self._process_environment_cvterm()\\n self._process_environments()\\n self._process_organisms(limit) # must be done before features\\n self._process_organism_dbxref(limit)\\n self._process_features(limit)\\n self._process_phenotype(limit)\\n self._process_phenotype_cvterm()\\n # gets external mappings for features (genes, variants, etc)\\n self._process_feature_dbxref(limit)\\n # do this after organisms to get the right taxonomy\\n self._process_stocks(limit)\\n # figures out types of some of the features\\n self._get_derived_feature_types(limit)\\n\\n # These are the associations amongst the objects above\\n self._process_stockprop(limit)\\n self._process_pub_dbxref(limit)\\n self._process_phendesc(limit)\\n self._process_feature_genotype(limit)\\n self._process_feature_pub(limit)\\n self._process_stock_genotype(limit)\\n self._process_phenstatement(limit) # these are G2P associations\\n\\n self._process_feature_relationship(limit)\\n\\n self._process_disease_models(limit)\\n # TODO add version info from file somehow\\n # (in parser rather than during fetching)\\n\\n logger.info(\\\"Finished parsing.\\\")\\n logger.info(\\\"Loaded %d nodes\\\", len(self.graph))\\n return\",\n \"def bzpull(request, target):\\n if target.startswith(\\\"sha1:\\\"):\\n target = target[5:]\\n url = \\\"http://bitzi.com/lookup/%s?v=tventtxt\\\" % target\\n tventtxt = urllib.urlopen(url)\\n tventdict = {}\\n targets_to_update = set()\\n count = 0\\n text = \\\"\\\"\\n try:\\n for line in tventtxt:\\n text += '\\\\n'\\n line = line.strip()\\n text += line\\n if not line:\\n if 'user' in tventdict and 'target_id' in tventdict and 'when' in tventdict:\\n tvent = Tvent()\\n tvent.when = tventdict['when']\\n tvent.user = tventdict['user']\\n target, created = Target.objects.get_or_create(id=tventdict['target_id'])\\n tvent.target = target\\n targets_to_update.add(target.id)\\n tvent.tagtext = tventdict['tagtext']\\n tvent.save()\\n count += 1\\n else:\\n # error; required field not present\\n text += '\\\\nERROR: incomplete tvent ' + str(tventdict)\\n tventdict = {}\\n continue\\n if line.startswith(\\\"=\\\"):\\n tventdict['when'] = line[1:]\\n continue\\n if line.startswith(\\\"~\\\"):\\n tventdict['user'] = line[1:]\\n continue\\n if line.startswith(\\\"@\\\"):\\n tventdict['target_id'] = line[1:]\\n continue\\n tventdict['tagtext'] = tventdict.get('tagtext','') + line + '\\\\n'\\n if 'user' in tventdict and 'target_id' in tventdict and 'when' in tventdict:\\n # TODO: reduce duplication with above\\n tvent = Tvent()\\n tvent.when = tventdict['when']\\n tvent.user = tventdict['user']\\n target = Target.objects.get_or_create(id=tventdict['target_id'])\\n tvent.target = target\\n targets_to_update.add(target.id)\\n # TODO: cleanup tags here? \\n tvent.save()\\n count += 1\\n else:\\n # error; required field not present\\n text += '\\\\nERROR: incomplete tvent ' + str(tventdict)\\n finally:\\n tventtxt.close()\\n # trigger update of any possibly-changed Target summaries\\n for id in targets_to_update:\\n Target.objects.get(id=id).updateFromTvents()\\n return HttpResponse('Pulled %d tvents from: %s\\\\n %s' % (count, url, text), mimetype='text/plain')\",\n \"def decompress_chunks(bstrm):\\n decompressor = zlib.decompressobj()\\n for chunk in iter(lambda: bstrm.read(BUFSIZE), b\\\"\\\"):\\n yield decompressor.decompress(chunk)\\n yield decompressor.flush()\",\n \"def process_file(self, filename, order=2):\\n fp = open(filename)\\n self.skip_gutenberg_header(fp)\\n\\n for line in fp:\\n for word in line.rstrip().split():\\n self.process_word(word, order)\\n\\n #print(\\\">>>DEBUG the suffix map\\\")\\n #i = 0\\n #for k,v in self.suffix_map.items():\\n # print(\\\"key is {}, value is {}\\\".format(k, v))\\n # i += 1\\n # if i > 10:\\n # break\",\n \"def parse(cls, bstr=None, filename=None, bytes_input=None, file_input=None,\\n offset_bytes=0, headers_only=False, recursive=True):\\n\\n if filename:\\n bstr = bs.ConstBitStream(filename=filename, offset=offset_bytes * 8)\\n elif bytes_input:\\n bstr = bs.ConstBitStream(bytes=bytes_input, offset=offset_bytes * 8)\\n elif file_input:\\n bstr = bs.ConstBitStream(auto=file_input, offset=offset_bytes * 8)\\n\\n log.debug(\\\"Starting parse\\\")\\n log.debug(\\\"Size is %d bits\\\", bstr.len)\\n\\n while bstr.pos < bstr.len:\\n log.debug(\\\"Byte pos before header: %d relative to (%d)\\\", bstr.bytepos, offset_bytes)\\n log.debug(\\\"Reading header\\\")\\n header = cls.parse_header(bstr)\\n log.debug(\\\"Header type: %s\\\", header.box_type)\\n log.debug(\\\"Byte pos after header: %d relative to (%d)\\\", bstr.bytepos, offset_bytes)\\n\\n if headers_only:\\n yield header\\n\\n # move pointer to next header if possible\\n try:\\n bstr.bytepos = header.start_pos + header.box_size\\n except ValueError:\\n log.warning(\\\"Premature end of data\\\")\\n raise\\n else:\\n yield cls.parse_box(bstr, header, recursive=recursive)\",\n \"def main(input_file=None, decoy_tag=None, output_file=None):\\n NEW_HEADERS = [\\n \\\"Raw data location\\\",\\n \\\"Spectrum ID\\\",\\n \\\"Spectrum Title\\\",\\n \\\"Retention Time (s)\\\",\\n \\\"Rank\\\",\\n \\\"Calc m/z\\\",\\n \\\"Exp m/z\\\",\\n \\\"Charge\\\",\\n \\\"Sequence\\\",\\n \\\"Modifications\\\",\\n \\\"X\\\\!Tandem:expect\\\",\\n \\\"X\\\\!Tandem:hyperscore\\\",\\n \\\"proteinacc_start_stop_pre_post_;\\\",\\n \\\"Is decoy\\\",\\n ]\\n PROTON = 1.00727646677\\n protein = None\\n group = None\\n group_counter = 0\\n protein_groups = []\\n\\n if input_file.endswith(\\\".gz\\\"):\\n compressed = True\\n # Gzipped files are not seekable\\n import gzip\\n\\n # file_object = codecs.getreader(\\\"utf-8\\\")(\\n # gzip.open(path)\\n # )\\n file_object = codecs.getreader(\\\"utf-8\\\")(gzip.open(input_file))\\n else:\\n file_object = codecs.open(input_file, mode=\\\"r\\\", encoding=\\\"utf-8\\\")\\n\\n csvOut = csv.DictWriter(open(output_file, \\\"w\\\", newline=\\\"\\\"), NEW_HEADERS)\\n csvOut.writeheader()\\n\\n print(\\\"Converting XTandem XML into CSV: {0}\\\".format(input_file))\\n tandemXML = iter(cElementTree.iterparse(file_object, events=(b\\\"start\\\", b\\\"end\\\")))\\n\\n for pos, (event, element) in enumerate(tandemXML):\\n if event == b\\\"start\\\":\\n if element.tag.endswith(\\\"bioml\\\"):\\n raw_data_location = element.attrib[\\\"label\\\"].split(\\\"'\\\")[1]\\n if element.tag.endswith(\\\"group\\\"):\\n if \\\"mh\\\" in element.attrib.keys():\\n group_counter = 0\\n notes = ddict(set)\\n notes_key = None\\n group = {} # reset group\\n group[\\\"Raw data location\\\"] = raw_data_location\\n group[\\\"Charge\\\"] = element.attrib[\\\"z\\\"]\\n group[\\\"Exp m/z\\\"] = (\\n float(element.attrib[\\\"mh\\\"]) / float(group[\\\"Charge\\\"])\\n ) + PROTON\\n group[\\\"X\\\\!Tandem:expect\\\"] = element.attrib[\\\"expect\\\"]\\n protein_groups = []\\n domain_groups = []\\n if element.attrib[\\\"label\\\"] == \\\"fragment ion mass spectrum\\\":\\n notes_key = \\\"spectrum\\\"\\n if element.attrib[\\\"label\\\"] == \\\"input parameters\\\":\\n notes_key = \\\"parameters\\\"\\n group_counter += 1\\n\\n elif element.tag.endswith(\\\"protein\\\"):\\n protein = {} # reset protein\\n notes_key = \\\"protein\\\"\\n\\n elif element.tag.endswith(\\\"domain\\\"):\\n if \\\"seq\\\" in element.attrib.keys():\\n domain = {header: \\\"\\\" for header in NEW_HEADERS} # reset domain\\n domain[\\\"Sequence\\\"] = element.attrib[\\\"seq\\\"]\\n domain[\\\"X\\\\!Tandem:hyperscore\\\"] = element.attrib[\\\"hyperscore\\\"]\\n domain[\\\"Calc m/z\\\"] = (\\n float(element.attrib[\\\"mh\\\"]) / float(group[\\\"Charge\\\"])\\n ) + PROTON\\n protein[\\\"Start\\\"] = element.attrib[\\\"start\\\"]\\n protein[\\\"Stop\\\"] = element.attrib[\\\"end\\\"]\\n protein[\\\"pre\\\"] = element.attrib[\\\"pre\\\"][-1]\\n protein[\\\"post\\\"] = element.attrib[\\\"post\\\"][0]\\n if protein[\\\"Start\\\"] == \\\"1\\\":\\n protein[\\\"pre\\\"] = \\\"-\\\"\\n if protein[\\\"post\\\"] == \\\"]\\\":\\n protein[\\\"post\\\"] = \\\"-\\\"\\n domain[\\n \\\"proteinacc_start_stop_pre_post_;\\\"\\n ] = \\\"{0}_{1}_{2}_{3}_{4};\\\".format(\\n protein[\\\"Defline\\\"],\\n protein[\\\"Start\\\"],\\n protein[\\\"Stop\\\"],\\n protein[\\\"pre\\\"],\\n protein[\\\"post\\\"],\\n )\\n if protein[\\\"Defline\\\"].startswith(decoy_tag):\\n domain[\\\"Is decoy\\\"] = True\\n else:\\n domain[\\\"Is decoy\\\"] = False\\n domain[\\\"Rank\\\"] = 1\\n\\n elif element.tag.endswith(\\\"aa\\\"):\\n if \\\"modified\\\" not in element.attrib.keys():\\n continue\\n mod = \\\"{0}:{1}\\\".format(\\n element.attrib[\\\"modified\\\"],\\n int(element.attrib[\\\"at\\\"]) - int(protein[\\\"Start\\\"]) + 1,\\n )\\n try:\\n domain[\\\"Modifications\\\"].append(mod)\\n except:\\n domain[\\\"Modifications\\\"] = [mod]\\n else:\\n if element.tag.endswith(\\\"protein\\\"):\\n protein_groups.append(protein)\\n if element.tag.endswith(\\\"domain\\\"):\\n for k, v in domain.items():\\n if k not in protein.keys():\\n protein[k] = v\\n # domain_groups.append( domain )\\n elif element.tag.endswith(\\\"note\\\"):\\n if notes_key == \\\"spectrum\\\":\\n group[\\\"Spectrum Title\\\"] = element.text.strip()\\n elif notes_key == \\\"protein\\\":\\n protein[\\\"Defline\\\"] = element.text.strip()\\n elif element.tag.endswith(\\\"group\\\"):\\n group_counter -= 1\\n if group_counter == 0:\\n dict2write = {}\\n # proteins = []\\n for protein_group in protein_groups:\\n for key in NEW_HEADERS:\\n # if key == 'proteinacc_start_stop_pre_post_;':\\n # proteins.append(protein_group[key])\\n # continue\\n if key == \\\"Modifications\\\" and protein_group[key] != \\\"\\\":\\n dict2write[key] = \\\";\\\".join(protein_group[key])\\n continue\\n try:\\n dict2write[key] = group[key]\\n except:\\n dict2write[key] = protein_group[key]\\n # dict2write['proteinacc_start_stop_pre_post_;'] = ''.join(proteins)\\n csvOut.writerow(dict2write)\\n protein_groups = []\\n return\",\n \"def uncompress_bzip2(location, target_dir):\\n return uncompress(location, target_dir, decompressor=bz2.BZ2File)\",\n \"def run(self):\\n lineage_csv_gz = self.input_files_local[0][0]\\n output_db = self.output_files_local()[0]\\n log.write(f\\\"input: {lineage_csv_gz} output: {output_db}\\\")\\n\\n with IdSeqDictForUpdate(output_db, IdSeqDictValue.VALUE_TYPE_ARRAY) as lineage_dict:\\n batch_list = {}\\n with gzip.open(lineage_csv_gz, \\\"rt\\\") as gzf:\\n for line in gzf:\\n fields = line.rstrip().split(\\\",\\\")\\n taxid = fields[0]\\n species, genus, family = fields[-1:-4:-1]\\n batch_list[taxid] = [species, genus, family]\\n if len(batch_list) >= BATCH_INSERT_SIZE:\\n lineage_dict.batch_inserts(batch_list.items())\\n batch_list = {}\\n lineage_dict.batch_inserts(batch_list.items())\",\n \"def _parse_tx_infos(self, gtf_path):\\n if os.path.exists('_tx_cache.bin'):\\n with open('_tx_cache.bin', 'rb') as f:\\n return pickle.load(f)\\n result = []\\n with gzip.open(gtf_path, 'rt') as f:\\n for i, line in enumerate(f):\\n if i % 1000 == 0:\\n print('processed {}'.format(i), file=sys.stderr)\\n if line.startswith('#'):\\n continue\\n if line.split('\\\\t', 3)[2] != 'transcript':\\n continue\\n record = GTFFeature.parse(line)\\n if record.feature != 'transcript':\\n continue\\n result.append(\\n TranscriptInfo(record.attrs['gene_id'],\\n record.attrs['transcript_id'],\\n record.attrs['transcript_type'],\\n record.seqname,\\n record.start,\\n record.end))\\n with open('_tx_cache.bin', 'wb') as g:\\n pickle.dump(result, g)\\n print(len(result), file=sys.stderr)\\n return result\",\n \"def batch_tadbit(directory, parser=None, **kwargs):\\n\\n matrix = []\\n for f_name in listdir(directory):\\n if f_name.startswith('.'):\\n continue\\n f_name = path.join(directory, f_name)\\n if parser:\\n matrix.append(parser(f_name))\\n continue\\n elif not path.isfile(f_name):\\n continue\\n matrix.append(f_name)\\n return tadbit(matrix, **kwargs)\",\n \"def extract_and_tag_test():\\n test_untagged_path = os.getcwd() + \\\"/data/test/test_untagged/\\\"\\n test_untagged_directory = os.fsencode(test_untagged_path)\\n\\n print(\\\"Tagging text. Please wait...\\\")\\n for file in os.listdir(test_untagged_directory):\\n filename = os.fsdecode(file)\\n try:\\n if filename.endswith(\\\".txt\\\"):\\n text = entity_process.read_data(test_untagged_path, file)\\n text = text.lower()\\n header,body = entity_process.split_text(text)\\n header_array = header.splitlines()\\n\\n\\n start_time, end_time = entity_process.extract_time(header)\\n location = entity_process.extract_location(header_array, body)\\n speaker = entity_process.extract_speaker(header_array, body)\\n\\n entity_tagger.tag_all(filename, text, start_time, end_time, location, speaker)\\n except Exception as e:\\n raise e\\n return \\\"No files found here!\\\"\\n print(\\\"Tagging complete! Text saved to\\\" + os.getcwd() + \\\"/out\\\")\",\n \"def unzipdir(path):\\n filenames = fullpathlist(path)\\n for filename in filenames:\\n if filename.endswith(\\\"bz2\\\"):\\n print \\\"doing\\\", filename\\n os.system('bunzip2 \\\"%s\\\"' % filename)\\n else:\\n print \\\"skipping\\\", filename\",\n \"def read_ptbtagged(ptbtagged_path: str) -> Iterator[Tuple[TokenSeq, PosSeq]]:\\n #do this immediately (first)\\n #start generating feature matrices\\n \\n #read file into an array \\n with open(ptbtagged_path) as f:\\n file_array = f.readlines()\\n file_array.append(\\\"\\\\n\\\")\\n array_of_tuples = create_tuples(file_array)\\n\\n return generator(array_of_tuples)\",\n \"def main():\\n parse_file(sys.argv[1])\",\n \"def extract_betti( fname, betti_file ):\\n # open and read chomp-produced data file\\n with open( fname + '.cbetti', 'r' ) as fh:\\n lines = fh.readlines()\\n # grab the line with the Betti numbers\\n if len( lines ) > 1:\\n for line in lines:\\n if line.startswith( 'Betti' ):\\n # keep only the numbers\\n betti_numbers = line.strip().split()[2:]\\n # chomp output single line of betti number (the \\\"other\\\" chomp\\n # version...)\\n else:\\n betti_numbers = lines[0].strip().split()\\n max_dim = len( betti_numbers )\\n # open betti file and save generators. write the same format for\\n # both chomp outputs to keep things consistent\\n with open( betti_file + '.betti', 'w' ) as fh:\\n for i, b in enumerate( betti_numbers ):\\n line = str(i) + ' ' + betti_numbers[i] +'\\\\n'\\n fh.write( line )\",\n \"def read_gz(images,labels):\\n\\t# Open the images with gzip in read binary mode\\n\\t# images = gzip.open('../MNIST-data/train-images-idx3-ubyte.gz', 'rb')\\n\\t# labels = gzip.open('../MNIST-data/train-labels-idx1-ubyte.gz', 'rb')\\n\\n\\t# Read the binary data\\n\\n\\t# We have to get big endian unsigned int. So we need '>I'\\n\\n\\t# Get metadata for images\\n\\timages.read(4) # skip the magic_number\\n\\tnumber_of_images = images.read(4)\\n\\tnumber_of_images = unpack('>I', number_of_images)[0]\\n\\trows = images.read(4)\\n\\trows = unpack('>I', rows)[0]#28\\n\\tcols = images.read(4)\\n\\tcols = unpack('>I', cols)[0]#28\\n\\n\\t# Get metadata for labels\\n\\tlabels.read(4) # skip the magic_number\\n\\tN = labels.read(4)\\n\\tN = unpack('>I', N)[0] #60000\\n\\t# print(number_of_images);\\n\\n\\tif number_of_images != N:\\n\\t raise Exception('number of labels did not match the number of images')\\n\\n\\t# Get the data\\n\\tx = zeros((N, rows, cols), dtype=float32) # Initialize numpy array #60000X28X28\\n\\ty = zeros((N, 1), dtype=uint8) # Initialize numpy array\\n\\tfor i in range(N):\\n\\t if i % 1000 == 0:\\n\\t print(\\\"i: %i\\\" % i)\\n\\t for row in range(rows):\\n\\t for col in range(cols):\\n\\t tmp_pixel = images.read(1) # Just a single byte\\n\\t tmp_pixel = unpack('>B', tmp_pixel)[0]\\n\\t x[i][row][col] = tmp_pixel\\n\\t tmp_label = labels.read(1)\\n\\t y[i] = unpack('>B', tmp_label)[0]\\n\\t # print(y.shape)#60000X1\\n\\treturn (x, y)\",\n \"def parse_region_data(self, region):\\r\\n \\r\\n self.download_data()\\r\\n region_filename = self.__get_region_filename(region)\\r\\n list_str = [\\\"region\\\", \\\"p1\\\", \\\"p36\\\", \\\"p37\\\", \\\"p2a\\\", \\\"weekday(p2a)\\\", \\\"p2b\\\", \\\"p6\\\", \\\"p7\\\", \\\"p8\\\", \\\"p9\\\", \\\"p10\\\", \\r\\n \\\"p11\\\", \\\"p12\\\", \\\"p13a\\\", \\\"p13b\\\", \\\"p13c\\\", \\\"p14\\\", \\\"p15\\\", \\\"p16\\\", \\\"p17\\\", \\\"p18\\\",\\\"p19\\\", \\\"p20\\\", \\\"p21\\\", \\r\\n \\\"p22\\\", \\\"p23\\\", \\\"p24\\\", \\\"p27\\\", \\\"p28\\\", \\\"p34\\\", \\\"p35\\\", \\\"p39\\\", \\\"p44\\\", \\\"p45a\\\", \\\"p47\\\", \\\"p48a\\\", \\\"p49\\\", \\r\\n \\\"p50a\\\", \\\"p50b\\\", \\\"p51\\\", \\\"p52\\\", \\\"p53\\\", \\\"p55a\\\", \\\"p57\\\", \\\"p58\\\", \\\"a\\\", \\\"b\\\", \\\"d\\\", \\\"e\\\", \\\"f\\\", \\\"g\\\", \\\"h\\\", \\r\\n \\\"i\\\", \\\"j\\\", \\\"k\\\", \\\"l\\\", \\\"m\\\", \\\"n\\\", \\\"o\\\", \\\"p\\\", \\\"q\\\", \\\"r\\\", \\\"s\\\", \\\"t\\\", \\\"p5a\\\"]\\r\\n \\r\\n row_count = self.__get_files_row_count(region)\\r\\n list_arrays = [np.zeros(row_count, dtype=dt) for dt in self.__types]\\r\\n row_index = 0\\r\\n for file in self.__files:\\r\\n file_to_parse = os.path.join(self.__folder, os.path.basename(file))\\r\\n with zipfile.ZipFile(file_to_parse, \\\"r\\\") as zf:\\r\\n with zf.open(region_filename, 'r') as csv_file:\\r\\n reader = csv.reader(TextIOWrapper(csv_file, 'windows-1250'), delimiter=';', quotechar='\\\"')\\r\\n for row in reader:\\r\\n list_arrays[0][row_index] = region\\r\\n for col_index, col in enumerate(row):\\r\\n try:\\r\\n list_arrays[col_index + 1][row_index] = col\\r\\n except ValueError:\\r\\n if list_arrays[col_index + 1][row_index].dtype == np.int64:\\r\\n list_arrays[col_index + 1][row_index] = -1\\r\\n elif list_arrays[col_index + 1][row_index].dtype == 'datetime64[D]':\\r\\n print('Error2:', col)\\r\\n elif list_arrays[col_index + 1][row_index].dtype == np.float64:\\r\\n if type(col) != str:\\r\\n list_arrays[col_index + 1][row_index] = col.replace(',', '.')\\r\\n else:\\r\\n list_arrays[col_index + 1][row_index] = float(\\\"nan\\\")\\r\\n row_index += 1\\r\\n \\r\\n return (list_str, list_arrays)\",\n \"def parse_file(file_name: str, delims='\\\\n', encoding='utf-8', zip_type=None):\\n try:\\n decoder = codecs.getincrementaldecoder(encoding)()\\n except LookupError as e:\\n print(str(e))\\n return\\n\\n read_buffer_size = 10*1024\\n max_line_size = 100*1024\\n\\n if not zip_type:\\n open_f = open\\n elif zip_type == 'gz':\\n open_f = gzip.open\\n else:\\n raise NotImplementedError()\\n\\n with open_f(file_name, 'rb') as fp:\\n buffered_str = ''\\n for bs in iter(partial(fp.read, read_buffer_size), b''):\\n decoded_str = decoder.decode(bs)\\n # FIXME: i don't think current implementation is efficient enough...\\n for c in decoded_str:\\n if c in delims:\\n if len(buffered_str) > 0:\\n yield buffered_str\\n buffered_str = ''\\n else:\\n buffered_str += c\\n if len(buffered_str) >= max_line_size:\\n yield buffered_str\\n buffered_str = ''\\n if len(buffered_str) > 0:\\n yield buffered_str\",\n \"def processfile(args, fh):\\n if args.quick:\\n scanner = quickScanZip(args, fh)\\n else:\\n scanner = findPKHeaders(args, fh)\\n\\n def checkarg(arg, ent):\\n if not arg:\\n return False\\n return '*' in arg or ent.name in arg\\n def checkname(a, b):\\n if a and '*' in a: return True\\n if b and '*' in b: return True\\n l = 0\\n if a: l += len(a)\\n if b: l += len(b)\\n return l > 1\\n\\n if args.verbose and not (args.cat or args.raw or args.save):\\n print(\\\" 0304 need flgs mth stamp --crc-- compsize fullsize nlen xlen namofs xofs datofs endofs\\\")\\n print(\\\" 0102 crea need flgs mth stamp --crc-- compsize fullsize nlen xlen clen dsk0 attr osattr datptr namofs xofs cmtofs endofs\\\")\\n for ent in scanner:\\n if args.cat or args.raw or args.save:\\n if args.quick and isinstance(ent, CentralDirEntry) or \\\\\\n not args.quick and isinstance(ent, LocalFileHeader):\\n ent.loaditems(fh)\\n do_cat = checkarg(args.cat, ent)\\n do_raw = checkarg(args.raw, ent)\\n do_save= checkarg(args.save, ent)\\n\\n do_name= checkname(args.cat, args.raw)\\n\\n if do_name:\\n print(\\\"\\\\n===> \\\" + ent.name + \\\" <===\\\\n\\\")\\n\\n sys.stdout.flush()\\n blks = zipraw(fh, ent)\\n\\n if args.password and ent.flags&1:\\n blks = zip_decrypt(blks, args.password)\\n if do_cat or do_save:\\n blks = skipbytes(blks, 12, args)\\n\\n if do_cat:\\n sys.stdout.buffer.writelines(zipcat(blks, ent))\\n if do_raw:\\n sys.stdout.buffer.writelines(blks)\\n if do_save:\\n savefile(args.outputdir, ent.name, zipcat(blks, ent))\\n else:\\n ent.loaditems(fh)\\n if args.verbose or not args.quick:\\n print(\\\"%08x: %s\\\" % (ent.pkOffset, ent))\\n else:\\n print(ent.summary())\\n if hasattr(ent, \\\"comment\\\") and ent.comment and not args.dumpraw:\\n print(ent.comment)\\n if args.dumpraw and hasattr(ent, \\\"extraLength\\\") and ent.extraLength:\\n print(\\\"%08x: XTRA: %s\\\" % (ent.extraOffset, binascii.b2a_hex(getbytes(fh, ent.extraOffset, ent.extraLength))))\\n if args.dumpraw and hasattr(ent, \\\"comment\\\") and ent.comment:\\n print(\\\"%08x: CMT: %s\\\" % (ent.commentOffset, binascii.b2a_hex(getbytes(fh, ent.commentOffset, ent.commentLength))))\\n if args.dumpraw and isinstance(ent, LocalFileHeader):\\n blks = zipraw(fh, ent)\\n if args.password and ent.flags&1:\\n blks = zip_decrypt(blks, args.password)\\n\\n blockdump(ent.dataOffset, blks)\",\n \"def reagent_parser(self, filename, initial_dictlist = dict()):\\n results = initial_dictlist\\n\\n filepath = os.path.join(self.base_dir, filename)\\n\\n with open(filepath, 'r') as fileobj:\\n xml = fileobj.read()\\n parsed = BeautifulSoup(xml, \\\"lxml-xml\\\")\\n\\n substances = parsed.find_all(\\\"substance\\\")\\n\\n # iterates for every substance in file\\n for substance in substances:\\n\\n # pulls the Beilstein Registry number\\n rn = substance.find(\\\"IDE.XRN\\\").text\\n\\n # finds all molfiles, indicated by \\\"YY.STR\\\"\\n molfiles = substance.find_all(\\\"YY.STR\\\")\\n\\n # V2000 files always follow V3000 files if V3000 files are available\\n # if V3000 files are not available, V2000 files are the first and only file\\n # we are only using V2000 files\\n try:\\n\\n # if possible, converts the second file (the V2000 file) to SMILES\\n mymol = readstring(\\\"mol\\\", molfiles[1].text)\\n smi = mymol.write(str(\\\"smi\\\")).split()[0]\\n\\n results[rn] = smi\\n except:\\n\\n # occurs when only zero or one file listed for specific registry number\\n try:\\n\\n # if possible, converts the first file (the V2000 file) to SMILES\\n mymol = readstring(\\\"mol\\\", molfiles[0].text)\\n smi = mymol.write(str(\\\"smi\\\")).split()[0]\\n\\n results[rn] = smi\\n except:\\n\\n # if not file is listed for the registry number, skips that number\\n continue\\n\\n return results\",\n \"def parse(self, f):\\n \\n for line in f:\\n self.parse_line(line)\",\n \"def load_ineraction_files(file_prefix):\\n\\tbinintfile=file_prefix+'.binint.log'\\n\\tcollfile=file_prefix+'.collision.log'\\n\\tmergefile=file_prefix+'.semergedisrupt.log'\\n\\tunitsfile=file_prefix+'.conv.sh'\\n\\n\\twith open(binintfile, 'r') as f:\\n\\t\\tnum_int = sum([1 for line in f if '****' in line])\\n\\t\\tf.seek(0) #need to count the encounters then reset the file handle\\n\\t\\tbinints = [binint(f) for __ in range(num_int)]\\n\\n\\twith open(mergefile,'r') as f:\\n\\t\\tnext(f) #skip the header\\n\\t\\tmergers = [se_merger(line) for line in f]\\n\\t\\t\\n\\twith open(collfile,'r') as f:\\n\\t\\tnext(f) #skip the header\\n\\t\\tcollisions = [collision(line) for line in f]\\n\\n\\tunits = conversion_file(unitsfile) \\n\\n\\treturn (units,binints,mergers,collisions)\",\n \"def process_file(filename):\\n print \\\"Reading and Parsing File: {}\\\".format(filename)\\n parsed_entries = file_parser(filename)\\n print \\\"Starting to Process Entries\\\"\\n chunked_entires = chunk_entries(parsed_entries)\\n return [process_entries(entry) for entry in chunked_entires]\",\n \"def __parsePackages__(self, f):\\n\\n\\t\\tp = apt_pkg.ParseTagFile(f)\\n\\n\\t\\t# Just load into memory the fields that are going to be useful\\n\\t\\twhile p.Step() == 1:\\n\\t\\t\\tpkg = p.Section['Package']\\n\\n\\t\\t\\tself.packages[pkg] = {}\\n\\n\\t\\t\\tfor field in p.Section.keys():\\n\\t\\t\\t\\tif field == 'Package':\\n\\t\\t\\t\\t\\tpass \\n\\t\\t\\t\\telif ['Depends', 'Recommends', 'Suggests', 'Enhances', 'Pre-Depends', 'Conflicts', 'Provides'].count(field):\\n\\t\\t\\t\\t\\tvalue = p.Section.get(field, \\\"\\\")\\n\\t\\t\\t\\t\\tself.packages[pkg][field] = apt_pkg.ParseDepends(value)\\n\\t\\t\\t\\telif ['Size', 'Installed-Size'].count(field):\\n\\t\\t\\t \\t\\tvalue = p.Section.get(field, \\\"0\\\")\\n\\t\\t\\t \\t\\tself.packages[pkg][field] = int(value)\\n\\t\\t\\t\\telif field == 'Source':\\n\\t\\t\\t\\t\\tsrc = p.Section.get(field, pkg)\\n\\t\\t\\t\\t\\tidx = src.find('(')\\n\\t\\t\\t\\t\\tif idx != -1:\\n\\t\\t\\t\\t\\t\\tsrc = src[:idx].strip()\\n\\t\\t\\t\\t\\tself.packages[pkg][field] = src\\n\\t\\t\\t\\telif field == 'Provides':\\n\\t\\t\\t\\t\\tself.packages[pkg][\\\"Provides\\\"] = apt_pkg.ParseDepends(p.Section.get(\\\"Provides\\\", \\\"\\\"))\\n\\t\\t\\t\\telse:\\n\\t\\t\\t\\t\\tself.packages[pkg][field] = p.Section.get(field, '')\\n\\n\\t f.close()\",\n \"def _bam_extract_impl(config: BamExtractConfig, sites: typing.List[vcf.Site]) -> None:\\n for path in config.input_files:\\n _bam_extract_impl_for_file(config, sites, path)\",\n \"def testTarBundling(self):\\n try:\\n tP = os.path.join(self.__workPath, \\\"t0.tar.gz\\\")\\n dirPath = os.path.join(self.__inpDirPath, \\\"topdir\\\")\\n\\n ok = self.__fileU.bundleTarfile(tP, [dirPath], mode=\\\"w:gz\\\", recursive=True)\\n self.assertTrue(ok)\\n\\n numBytes = self.__fileU.size(tP)\\n self.assertGreaterEqual(numBytes, 250)\\n #\\n md5 = self.__fileU.hash(tP, hashType=\\\"md5\\\")\\n self.assertTrue(md5 is not None)\\n #\\n ok = self.__fileU.unbundleTarfile(tP, dirPath=self.__workPath)\\n self.assertTrue(ok)\\n #\\n tP = os.path.join(self.__workPath, \\\"t1.tar.gz\\\")\\n dirPathList = [os.path.join(self.__inpDirPath, \\\"topdir\\\", \\\"subdirA\\\"), os.path.join(self.__inpDirPath, \\\"topdir\\\", \\\"subdirB\\\")]\\n\\n ok = self.__fileU.bundleTarfile(tP, dirPathList, mode=\\\"w:gz\\\", recursive=True)\\n self.assertTrue(ok)\\n #\\n ok = self.__fileU.unbundleTarfile(tP, dirPath=self.__workPath)\\n self.assertTrue(ok)\\n\\n tP = os.path.join(self.__workPath, \\\"t2.tar\\\")\\n dirPathList = [os.path.join(self.__inpDirPath, \\\"topdir\\\", \\\"subdirA\\\"), os.path.join(self.__inpDirPath, \\\"topdir\\\", \\\"subdirB\\\")]\\n\\n ok = self.__fileU.bundleTarfile(tP, dirPathList, mode=\\\"w\\\", recursive=True)\\n self.assertTrue(ok)\\n #\\n ok = self.__fileU.unbundleTarfile(tP, dirPath=self.__workPath)\\n self.assertTrue(ok)\\n\\n except Exception as e:\\n logger.exception(\\\"Failing with %s\\\", str(e))\\n self.fail()\",\n \"def compress_bz2(filename):\\n bz2_filename = filename + '.bz2'\\n\\n with open(filename, 'rb') as og_file, bz2.BZ2File(bz2_filename, 'wb') as bz2_file:\\n for data in iter(lambda : og_file.read(100 * 1024), b''):\\n bz2_file.write(data)\\n\\n return bz2_filename\",\n \"def compress_bz2(filename):\\n bz2_filename = filename + '.bz2'\\n\\n with open(filename, 'rb') as og_file, bz2.BZ2File(bz2_filename, 'wb') as bz2_file:\\n for data in iter(lambda : og_file.read(100 * 1024), b''):\\n bz2_file.write(data)\\n\\n return bz2_filename\",\n \"def process_bedpe(archive, bedpe, bedpe_index, output_prefix):\\n out_raw_bedpe = '{0}.tmp.bedpe.gz'.format(output_prefix)\\n logger.info(\\\"Extracting raw bedpe to tmp file {0}\\\".format(out_raw_bedpe))\\n extract_file(archive, bedpe, out_raw_bedpe)\\n\\n out_raw_bedpe_index = '{0}.tmp.bedpe.gz.tbi'.format(output_prefix)\\n logger.info(\\\"Extracting raw bedpe index to tmp file {0}\\\".format(out_raw_bedpe_index))\\n extract_file(archive, bedpe_index, out_raw_bedpe_index)\\n\\n out_formatted_bedpe = '{0}.bedpe.gz'.format(output_prefix)\\n logger.info(\\\"Creating final bedpe {0}\\\".format(out_formatted_bedpe))\\n writer = pysam.BGZFile(out_formatted_bedpe, mode='wb')\\n reader = pysam.BGZFile(out_raw_bedpe, mode='rb')\\n try:\\n meta_line = None\\n process_header = False\\n hdr = []\\n for line in reader:\\n line = line.decode('utf-8')\\n if line.startswith('#'):\\n meta_line = line\\n else:\\n if not process_header:\\n hdr = format_header(meta_line)\\n assert len(hdr) == len(set(hdr)), \\\\\\n \\\"Duplicate header keys {0}\\\".format(','.join(hdr))\\n writer.write(('#' + '\\\\t'.join(hdr) + '\\\\n').encode('utf-8'))\\n process_header = True\\n\\n dat = dict(zip(hdr, line.rstrip('\\\\r\\\\n').split('\\\\t')))\\n dat['brass_notation'] = dat['brass_notation'].replace('Chr.chr', 'chr')\\n new_line = \\\"\\\\t\\\".join([dat[i] for i in hdr]) + '\\\\n'\\n writer.write(new_line.encode('utf-8'))\\n finally:\\n writer.close()\\n reader.close()\\n\\n # tabix index\\n logger.info(\\\"Creating final bedpe index {0}\\\".format(out_formatted_bedpe + '.tbi'))\\n pysam.tabix_index( out_formatted_bedpe, preset='bed', force=True )\\n\\n # clean up\\n logger.info(\\\"Cleaning up tmp files...\\\")\\n os.remove(out_raw_bedpe)\\n os.remove(out_raw_bedpe_index)\",\n \"def split_batches(filenames):\\n by_time = {}\\n for path_name in filenames:\\n file_name = path.basename(path_name)\\n parsed_fn = parse_agdc_fn(file_name)\\n dt = parsed_fn['datetime']\\n by_time.setdefault(dt, []).append((path_name, parsed_fn))\\n\\n rv = list(by_time.values())\\n\\n for group in rv:\\n # Will raise exception if group is non-homogeneous\\n check_sane(parsed for _, parsed in group)\\n\\n return rv\",\n \"def _parse_ach_file(self, contents):\\n file_length = len(contents)\\n\\n for index in range(0, file_length, self.LINE_LENGTH):\\n line = contents[index:index + self.LINE_LENGTH]\\n\\n if line.startswith('1'):\\n self._read_header(line)\\n elif line.startswith('5'):\\n self._read_batch_header(line)\\n elif line.startswith('6'):\\n self._read_entry_detail(line)\\n elif line.startswith('7'):\\n self._read_addenda_record(line)\\n elif line.startswith('8'):\\n self._read_batch_control_record(line)\\n elif line.startswith('9'):\\n if line == '9' * 94:\\n continue\\n self._read_file_control_record(line)\",\n \"def parseGRO(filename):\\n\\tprint(\\\"Cannot parse .gro files yet.\\\")\\n\\texit()\",\n \"def parse(self, infile):\\r\\n raise NotImplementedError()\",\n \"def parse_tle_bytes(f):\\n lines=f.splitlines()\\n\\n tles=[]\\n ctle=None\\n state=\\\"none\\\"\\n for l in lines:\\n m_name=re.fullmatch(b\\\"^\\\\s*((\\\\S.*)?\\\\S)\\\\s*$\\\",l)\\n m_line1=re.fullmatch(\\\"^\\\\s*(1)\\\\s+(\\\\d{1,5})(\\\\w)\\\\s+\\\"\\\\\\n \\\"(\\\\d{2})(\\\\d{3})(\\\\w{0,3})\\\\s+(\\\\d{2})(\\\\s{0,2}\\\\d{1,3}\\\\.\\\\d{8})\\\\s+\\\"\\\\\\n \\\"([-+ 0]\\\\.\\\\d{8})\\\\s+([-+ ]\\\\d{5}[-+]\\\\d)\\\\s+([-+ ]\\\\d{5}[-+]\\\\d)\\\\s+\\\"\\\\\\n \\\"(0)\\\\s+(\\\\d{1,4})(\\\\d)\\\\s*$\\\",l.decode(\\\"ascii\\\"))\\n m_line2=re.fullmatch(\\\"^\\\\s*(2)\\\\s+(\\\\d{1,5})\\\\s+\\\"\\\\\\n \\\"(\\\\d{1,3}\\\\.\\\\d{4})\\\\s+(\\\\d{1,3}\\\\.\\\\d{4})\\\\s+(\\\\d{1,7})\\\\s+\\\"\\\\\\n \\\"(\\\\d{1,3}\\\\.\\\\d{4})\\\\s+(\\\\d{1,3}\\\\.\\\\d{4})\\\\s+\\\"\\\\\\n \\\"(\\\\d{1,2}\\\\.\\\\d{8})(\\\\s*\\\\d{1,5})(\\\\d)\\\\s*$\\\",l.decode(\\\"ascii\\\"))\\n if (state==\\\"name\\\" and m_line1 is None) or (state==\\\"line1\\\" and m_line2 is None):\\n if not _quiet:\\n print(\\\"WARNING: Non consecutive TLE line (\\\"+str(l)+\\\\\\n \\\"), discards partial TLE (\\\\\\\"\\\"+str(ctle.name)+\\\"\\\\\\\":\\\"+\\\\\\n str(ctle.id)+\\\")\\\",file=sys.stderr)\\n ctle=None\\n state=\\\"none\\\"\\n\\n if state==\\\"line1\\\" and m_line2 is not None:\\n cksum=int(m_line2.group(10))\\n nsum=0\\n for c in l.strip(b\\\" \\\\r\\\\n\\\\t\\\")[:-1].decode(\\\"ascii\\\"):\\n if c.isdigit():\\n nsum+=int(c)\\n elif c==\\\"-\\\":\\n nsum+=1\\n nsum%=10\\n ctle.line2valid=cksum==nsum\\n if ((not _quiet) and (cksum!=nsum)):\\n print(\\\"WARNING: checksum did not match [check(\\\\\\\"\\\"+\\\\\\n l.strip(b\\\" \\\\r\\\\n\\\\t\\\").decode(\\\"ascii\\\")+\\\"\\\\\\\")=\\\"+\\\\\\n str(nsum)+\\\"!=\\\"+str(cksum)+\\\"]\\\",file=sys.stderr)\\n newid=int(m_line2.group(2))\\n if newid!=ctle.id:\\n if not _quiet:\\n print(\\\"ERROR: unexpeced id in second line, skipping!\\\",\\n file=sys.stderr)\\n ctle=None\\n state=\\\"none\\\"\\n continue\\n ctle.inc=float(m_line2.group(3))\\n ctle.raan=float(m_line2.group(4))\\n ctle.ecc=float(\\\"0.\\\"+m_line2.group(5))\\n ctle.aop=float(m_line2.group(6))\\n ctle.ma=float(m_line2.group(7))\\n ctle.mm=float(m_line2.group(8))\\n ctle.revol=int(m_line2.group(9))\\n tles.append(copy.deepcopy(ctle))\\n if _verbose:\\n print(\\\"Successfully read in TLE for \\\\\\\"\\\"+ctle.name+\\\"\\\\\\\": \\\"+str(ctle.id),\\n file=sys.stderr)\\n ctle=None\\n state=\\\"none\\\"\\n elif state==\\\"name\\\" and m_line1 is not None:\\n cksum=int(m_line1.group(14))\\n nsum=0\\n for c in l.strip(b\\\" \\\\r\\\\n\\\\t\\\")[:-1].decode(\\\"ascii\\\"):\\n if c.isdigit():\\n nsum+=int(c)\\n elif c==\\\"-\\\":\\n nsum+=1\\n nsum%=10\\n ctle.line1valid=cksum==nsum\\n if ((not _quiet) and (cksum!=nsum)):\\n print(\\\"WARNING: checksum did not match [check(\\\\\\\"\\\"+\\\\\\n l.strip(b\\\" \\\\r\\\\n\\\\t\\\").decode(\\\"ascii\\\")+\\\"\\\\\\\")=\\\"+\\\\\\n str(nsum)+\\\"!=\\\"+str(cksum)+\\\"]\\\",file=sys.stderr)\\n ctle.id=int(m_line1.group(2))\\n ctle.desig[\\\"year\\\"]=int(m_line1.group(4))\\n ctle.desig[\\\"launch\\\"]=int(m_line1.group(5))\\n ctle.desig[\\\"object\\\"]=m_line1.group(6)\\n ctle.epoch[\\\"year\\\"]=int(m_line1.group(7))\\n ctle.epoch[\\\"day\\\"]=float(m_line1.group(8))\\n fdmm_str=m_line1.group(9)\\n ctle.fdmm=float(fdmm_str[0]+\\\"0\\\"+fdmm_str[1:])\\n sdmm_str=m_line1.group(10)\\n ctle.sdmm=float(sdmm_str[0]+\\\"0.\\\"+sdmm_str[1:6]+\\\"e\\\"+sdmm_str[6:])\\n bstar_str=m_line1.group(11)\\n ctle.bstar=float(bstar_str[0]+\\\"0.\\\"+bstar_str[1:6]+\\\"e\\\"+bstar_str[6:])\\n ctle.nr=int(m_line1.group(13))\\n state=\\\"line1\\\"\\n elif state==\\\"none\\\" and m_name is not None:\\n ctle=tle()\\n ctle.name=m_name.group(1).decode(\\\"ascii\\\")\\n state=\\\"name\\\"\\n return tles\",\n \"def parse_shard(shard_path):\\n with tf.io.gfile.GFile(shard_path, 'rb') as f:\\n with gzip.GzipFile(fileobj=f, mode='rb') as f_gz:\\n for line in f_gz: # Line-by-line.\\n yield deserialize_inference_result(line)\",\n \"def process(marc_filepath):\\n start = datetime.datetime.utcnow()\\n click.echo(\\\"Started transforming MARC to BF at {} for {}\\\".format(\\n start.isoformat(),\\n marc_filepath))\\n for i, marc_xml in enumerate(extract(marc_filepath)):\\n bf_rdf = transform(marc_xml)\\n load(bf_rdf)\\n if not i%100 and i > 0:\\n click.echo(\\\".\\\", nl=False)\\n if not i%1000:\\n click.echo(i, nl=False)\\n end = datetime.datetime.utcnow()\\n click.echo(\\\"Finished ETL for {} at {}, total time={} minutes\\\".format(\\n marc_file,\\n end.isoformat(),\\n (end-start).seconds / 60.0))\",\n \"def parse_ensembl_transcripts(lines):\\n header = []\\n LOG.info(\\\"Parsing ensembl transcripts from file\\\")\\n for index, line in enumerate(lines):\\n # File allways start with a header line\\n if index == 0:\\n header = line.rstrip().split(\\\"\\\\t\\\")\\n # After that each line represents a transcript\\n else:\\n yield parse_ensembl_line(line, header)\",\n \"def parseGFF3(filename):\\n\\n # Parse with transparent decompression\\n openFunc = gzip.open if filename.endswith(\\\".gz\\\") else open\\n with openFunc(filename) as infile:\\n for line in infile:\\n if line.startswith(\\\"#\\\"):\\n continue\\n parts = line.strip().split(\\\"\\\\t\\\")\\n # If this fails, the file format is not standard-compatible\\n assert len(parts) == len(gffInfoFields)\\n # Normalize data\\n normalizedInfo = {\\n \\\"seqid\\\": None if parts[0] == \\\".\\\" else urllib.unquote(parts[0]),\\n \\\"source\\\": None if parts[1] == \\\".\\\" else urllib.unquote(parts[1]),\\n \\\"type\\\": None if parts[2] == \\\".\\\" else urllib.unquote(parts[2]),\\n \\\"start\\\": None if parts[3] == \\\".\\\" else int(parts[3]),\\n \\\"end\\\": None if parts[4] == \\\".\\\" else int(parts[4]),\\n \\\"score\\\": None if parts[5] == \\\".\\\" else float(parts[5]),\\n \\\"strand\\\": None if parts[6] == \\\".\\\" else urllib.unquote(parts[6]),\\n \\\"phase\\\": None if parts[7] == \\\".\\\" else urllib.unquote(parts[7]),\\n \\\"attributes\\\": parseGFFAttributes(parts[8])\\n }\\n # Alternatively, you can emit the dictionary here, if you need\\n # mutability:\\n # yield normalizedInfo\\n yield GFFRecord(**normalizedInfo)\",\n \"def _GetSubFileEntries(self):\\n if self._directory is None:\\n self._directory = self._GetDirectory()\\n\\n if self._directory:\\n tar_file = self._file_system.GetTARFile()\\n if tar_file:\\n for path_spec in self._directory.entries:\\n location = getattr(path_spec, 'location', None)\\n if location is None:\\n continue\\n\\n kwargs = {}\\n try:\\n kwargs['tar_info'] = tar_file.getmember(location[1:])\\n except KeyError:\\n kwargs['is_virtual'] = True\\n\\n yield TARFileEntry(\\n self._resolver_context, self._file_system, path_spec, **kwargs)\",\n \"def parseGerber(self, fullname, layername, updateExtents = 0):\\n\\n GAT = config.GAT\\n GAMT = config.GAMT\\n # First construct reverse GAT/GAMT, mapping definition to code\\n RevGAT = config.buildRevDict(GAT) # RevGAT[hash] = aperturename\\n RevGAMT = config.buildRevDict(GAMT) # RevGAMT[hash] = aperturemacroname\\n\\n #print 'Reading data from %s ...' % fullname\\n\\n fid = file(fullname, 'rt')\\n currtool = None\\n\\n self.apxlat[layername] = {}\\n self.apmxlat[layername] = {}\\n self.commands[layername] = []\\n self.apertures[layername] = []\\n\\n # These divisors are used to scale (X,Y) co-ordinates. We store\\n # everything as integers in hundred-thousandths of an inch (i.e., M.5\\n # format). If we get something in M.4 format, we must multiply by\\n # 10. If we get something in M.6 format we must divide by 10, etc.\\n x_div = 1.0\\n y_div = 1.0\\n\\n # Drawing commands can be repeated with X or Y omitted if they are\\n # the same as before. These variables store the last X/Y value as\\n # integers in hundred-thousandths of an inch.\\n last_x = last_y = 0\\n\\n # Last modal G-code. Some G-codes introduce \\\"modes\\\", such as circular interpolation\\n # mode, and we want to remember what mode we're in. We're interested in:\\n # G01 -- linear interpolation, cancels all circular interpolation modes\\n # G36 -- Turn on polygon area fill\\n # G37 -- Turn off polygon area fill\\n last_gmode = 1 # G01 by default, linear interpolation\\n\\n # We want to know whether to do signed (G75) or unsigned (G74) I/J offsets. These\\n # modes are independent of G01/G02/G03, e.g., Protel will issue multiple G03/G01\\n # codes all in G75 mode.\\n # G74 -- Single-quadrant circular interpolation (disables multi-quadrant interpolation)\\n # G02/G03 codes set clockwise/counterclockwise arcs in a single quadrant only\\n # using X/Y/I/J commands with UNSIGNED (I,J).\\n # G75 -- Multi-quadrant circular interpolation --> X/Y/I/J with signed (I,J)\\n # G02/G03 codes set clockwise/counterclockwise arcs in all 4 quadrants\\n # using X/Y/I/J commands with SIGNED (I,J).\\n circ_signed = True # Assume G75...make sure this matches canned header we write out\\n\\n # If the very first flash/draw is a shorthand command (i.e., without an Xxxxx or Yxxxx)\\n # component then we don't really \\\"see\\\" the first point X00000Y00000. To account for this\\n # we use the following Boolean flag as well as the isLastShorthand flag during parsing\\n # to manually insert the point X000000Y00000 into the command stream.\\n firstFlash = True\\n\\n for line in fid:\\n # Get rid of CR characters (0x0D) and leading/trailing blanks\\n line = string.replace(line, '\\\\x0D', '').strip()\\n\\n # Old location of format_pat search. Now moved down into the sub-line parse loop below.\\n\\n # RS-274X statement? If so, echo it. Currently, only the \\\"LP\\\" statement is expected\\n # (from Protel, of course). These will be distinguished from D-code and G-code\\n # commands by the fact that the first character of the string is '%'.\\n match = layerpol_pat.match(line)\\n if match:\\n self.commands[layername].append(line)\\n continue\\n \\n # See if this is an aperture definition, and if so, map it.\\n match = apdef_pat.match(line)\\n if match:\\n if currtool:\\n raise RuntimeError, \\\"File %s has an aperture definition that comes after drawing commands.\\\" % fullname\\n\\n A = aptable.parseAperture(line, self.apmxlat[layername])\\n if not A:\\n raise RuntimeError, \\\"Unknown aperture definition in file %s\\\" % fullname\\n\\n hash = A.hash()\\n if not RevGAT.has_key(hash):\\n #print line\\n #print self.apmxlat\\n #print RevGAT\\n raise RuntimeError, 'File %s has aperture definition \\\"%s\\\" not in global aperture table.' % (fullname, hash)\\n\\n # This says that all draw commands with this aperture code will\\n # be replaced by aperture self.apxlat[layername][code].\\n self.apxlat[layername][A.code] = RevGAT[hash]\\n continue\\n\\n # Ignore %AMOC8* from Eagle for now as it uses a macro parameter, which\\n # is not yet supported in GerbMerge.\\n if line[:7]=='%AMOC8*':\\n continue\\n\\n # See if this is an aperture macro definition, and if so, map it.\\n M = amacro.parseApertureMacro(line,fid)\\n if M:\\n if currtool:\\n raise RuntimeError, \\\"File %s has an aperture macro definition that comes after drawing commands.\\\" % fullname\\n\\n hash = M.hash()\\n if not RevGAMT.has_key(hash):\\n raise RuntimeError, 'File %s has aperture macro definition not in global aperture macro table:\\\\n%s' % (fullname, hash)\\n\\n # This says that all aperture definition commands that reference this macro name\\n # will be replaced by aperture macro name self.apmxlat[layername][macroname].\\n self.apmxlat[layername][M.name] = RevGAMT[hash]\\n continue\\n\\n # From this point on we may have more than one match on this line, e.g.:\\n # G54D11*X22400Y22300D02*X22500Y22200D01*\\n sub_line = line\\n while sub_line:\\n # Handle \\\"comment\\\" G-codes first\\n match = comment_pat.match(sub_line)\\n if match:\\n sub_line = sub_line[match.end():]\\n continue\\n\\n # See if this is a format statement, and if so, map it. In version 1.3 this was moved down\\n # from the line-only parse checks above (see comment) to handle OrCAD lines like\\n # G74*%FSLAN2X34Y34*%\\n match = format_pat.match(sub_line) # Used to be format_pat.search\\n if match:\\n sub_line = sub_line[match.end():]\\n for item in match.groups():\\n if item is None: continue # Optional group didn't match\\n\\n if item[0] in \\\"LA\\\": # omit leading zeroes and absolute co-ordinates\\n continue\\n\\n if item[0]=='T': # omit trailing zeroes\\n raise RuntimeError, \\\"Trailing zeroes not supported in RS274X files\\\"\\n if item[0]=='I': # incremental co-ordinates\\n raise RuntimeError, \\\"Incremental co-ordinates not supported in RS274X files\\\"\\n\\n if item[0]=='N': # Maximum digits for N* commands...ignore it\\n continue\\n\\n if item[0]=='X': # M.N specification for X-axis.\\n fracpart = int(item[2])\\n x_div = 10.0**(5-fracpart)\\n if item[0]=='Y': # M.N specification for Y-axis.\\n fracpart = int(item[2])\\n y_div = 10.0**(5-fracpart)\\n continue\\n\\n # Parse and interpret G-codes\\n match = gcode_pat.match(sub_line)\\n if match:\\n sub_line = sub_line[match.end():]\\n gcode = int(match.group(1))\\n\\n # Determine if this is a G-Code that should be ignored because it has no effect\\n # (e.g., G70 specifies \\\"inches\\\" which is already in effect).\\n if gcode in [54, 70, 90]:\\n continue\\n\\n # Determine if this is a G-Code that we have to emit because it matters.\\n if gcode in [1, 2, 3, 36, 37, 74, 75]:\\n self.commands[layername].append(\\\"G%02d\\\" % gcode)\\n\\n # Determine if this is a G-code that sets a new mode\\n if gcode in [1, 36, 37]:\\n last_gmode = gcode\\n\\n # Remember last G74/G75 code so we know whether to do signed or unsigned I/J\\n # offsets.\\n if gcode==74:\\n circ_signed = False\\n elif gcode==75:\\n circ_signed = True\\n \\n continue\\n\\n raise RuntimeError, \\\"G-Code 'G%02d' is not supported\\\" % gcode\\n\\n # See if this is a tool change (aperture change) command\\n match = tool_pat.match(sub_line)\\n if match:\\n currtool = match.group(1)\\n\\n # Protel likes to issue random D01, D02, and D03 commands instead of aperture\\n # codes. We can ignore D01 because it simply means to move to the current location\\n # while drawing. Well, that's drawing a point. We can ignore D02 because it means\\n # to move to the current location without drawing. Truly pointless. We do NOT want\\n # to ignore D03 because it implies a flash. Protel very inefficiently issues a D02\\n # move to a location without drawing, then a single-line D03 to flash. However, a D02\\n # terminates a polygon in G36 mode, so keep D02's in this case.\\n if currtool=='D01' or (currtool=='D02' and (last_gmode != 36)):\\n sub_line = sub_line[match.end():]\\n continue\\n\\n if (currtool == 'D03') or (currtool=='D02' and (last_gmode == 36)):\\n self.commands[layername].append(currtool)\\n sub_line = sub_line[match.end():]\\n continue\\n\\n # Map it using our translation table\\n if not self.apxlat[layername].has_key(currtool):\\n raise RuntimeError, 'File %s has tool change command \\\"%s\\\" with no corresponding translation' % (fullname, currtool)\\n\\n currtool = self.apxlat[layername][currtool]\\n\\n # Add it to the list of things to write out\\n self.commands[layername].append(currtool)\\n\\n # Add it to the list of all apertures needed by this layer\\n self.apertures[layername].append(currtool)\\n\\n # Move on to next match, if any\\n sub_line = sub_line[match.end():]\\n continue\\n\\n # Is it a simple draw command?\\n I = J = None # For circular interpolation drawing commands\\n match = drawXY_pat.match(sub_line)\\n isLastShorthand = False # By default assume we don't make use of last_x and last_y\\n if match:\\n x, y, d = map(__builtin__.int, match.groups())\\n else:\\n match = drawX_pat.match(sub_line)\\n if match:\\n x, d = map(__builtin__.int, match.groups())\\n y = last_y\\n isLastShorthand = True # Indicate we're making use of last_x/last_y\\n else:\\n match = drawY_pat.match(sub_line)\\n if match:\\n y, d = map(__builtin__.int, match.groups())\\n x = last_x\\n isLastShorthand = True # Indicate we're making use of last_x/last_y\\n\\n # Maybe it's a circular interpolation draw command with IJ components\\n if match is None:\\n match = cdrawXY_pat.match(sub_line)\\n if match:\\n x, y, I, J, d = map(__builtin__.int, match.groups())\\n else:\\n match = cdrawX_pat.match(sub_line)\\n if match:\\n x, I, J, d = map(__builtin__.int, match.groups())\\n y = last_y\\n isLastShorthand = True # Indicate we're making use of last_x/last_y\\n else:\\n match = cdrawY_pat.match(sub_line)\\n if match:\\n y, I, J, d = map(__builtin__.int, match.groups())\\n x = last_x\\n isLastShorthand = True # Indicate we're making use of last_x/last_y\\n\\n if match:\\n if currtool is None:\\n # It's OK if this is an exposure-off movement command (specified with D02).\\n # It's also OK if we're in the middle of a G36 polygon fill as we're only defining\\n # the polygon extents.\\n if (d != 2) and (last_gmode != 36):\\n raise RuntimeError, 'File %s has draw command %s with no aperture chosen' % (fullname, sub_line)\\n\\n # Save last_x/y BEFORE scaling to 2.5 format else subsequent single-ordinate\\n # flashes (e.g., Y with no X) will be scaled twice!\\n last_x = x\\n last_y = y\\n\\n # Corner case: if this is the first flash/draw and we are using shorthand (i.e., missing Xxxx\\n # or Yxxxxx) then prepend the point X0000Y0000 into the commands as it is actually the starting\\n # point of our layer. We prepend the command X0000Y0000D02, i.e., a move to (0,0) without drawing.\\n if (isLastShorthand and firstFlash):\\n self.commands[layername].append((0,0,2))\\n if updateExtents:\\n self.minx = min(self.minx,0)\\n self.maxx = max(self.maxx,0)\\n self.miny = min(self.miny,0)\\n self.maxy = max(self.maxy,0)\\n\\n x = int(round(x*x_div))\\n y = int(round(y*y_div))\\n if I is not None:\\n I = int(round(I*x_div))\\n J = int(round(J*y_div))\\n self.commands[layername].append((x,y,I,J,d,circ_signed))\\n else:\\n self.commands[layername].append((x,y,d))\\n firstFlash = False\\n\\n # Update dimensions...this is complicated for circular interpolation commands\\n # that span more than one quadrant. For now, we ignore this problem since users\\n # should be using a border layer to indicate extents.\\n if updateExtents:\\n if x < self.minx: self.minx = x\\n if x > self.maxx: self.maxx = x\\n if y < self.miny: self.miny = y\\n if y > self.maxy: self.maxy = y\\n\\n # Move on to next match, if any\\n sub_line = sub_line[match.end():]\\n continue\\n\\n # If it's none of the above, it had better be on our ignore list.\\n for pat in IgnoreList:\\n match = pat.match(sub_line)\\n if match:\\n break\\n else:\\n raise RuntimeError, 'File %s has uninterpretable line:\\\\n %s' % (fullname, line)\\n\\n sub_line = sub_line[match.end():]\\n # end while still things to match on this line\\n # end of for each line in file\\n\\n fid.close()\\n if 0:\\n print layername\\n print self.commands[layername]\",\n \"def get_tag_batch(self, tag, filenames):\\n data = self.get_tags_batch([tag], filenames)\\n result = []\\n for d in data:\\n d.pop(\\\"SourceFile\\\")\\n result.append(next(iter(d.values()), None))\\n return result\"\n]","isConversational":false},"negative_scores":{"kind":"list like","value":["0.62602454","0.57246566","0.56907696","0.56726176","0.550637","0.5499982","0.54376435","0.542693","0.54081875","0.5403217","0.53807425","0.5374287","0.53654516","0.53579986","0.53536445","0.5324675","0.53113073","0.5298232","0.52399564","0.5238451","0.5226689","0.5225485","0.5222681","0.52178156","0.5207596","0.51027244","0.51027244","0.5101415","0.5097889","0.5075146","0.5061422","0.50535256","0.5037416","0.5037133","0.5022858","0.50089455","0.49830857","0.49778566","0.4975492","0.49716341","0.49629128","0.49601254","0.4943105","0.49096364","0.4903206","0.49012795","0.48983356","0.48931092","0.4892857","0.4890902","0.4873297","0.48678732","0.4867703","0.4867321","0.48558682","0.48503676","0.48416185","0.48268658","0.48171896","0.4815758","0.48034275","0.48016477","0.47980997","0.4793105","0.47781262","0.47776434","0.4774869","0.47669694","0.47641668","0.4758115","0.4748523","0.47420335","0.4741893","0.47410733","0.47338173","0.47310063","0.47259364","0.47185212","0.47157553","0.4711726","0.4706579","0.47039947","0.47007442","0.46962056","0.4690964","0.46851158","0.46786055","0.46786055","0.46711308","0.46650806","0.46606243","0.46595407","0.46571597","0.46541637","0.46486548","0.46475205","0.46438617","0.46420944","0.46381333","0.46350697","0.463408"],"string":"[\n \"0.62602454\",\n \"0.57246566\",\n \"0.56907696\",\n \"0.56726176\",\n \"0.550637\",\n \"0.5499982\",\n \"0.54376435\",\n \"0.542693\",\n \"0.54081875\",\n \"0.5403217\",\n \"0.53807425\",\n \"0.5374287\",\n \"0.53654516\",\n \"0.53579986\",\n \"0.53536445\",\n \"0.5324675\",\n \"0.53113073\",\n \"0.5298232\",\n \"0.52399564\",\n \"0.5238451\",\n \"0.5226689\",\n \"0.5225485\",\n \"0.5222681\",\n \"0.52178156\",\n \"0.5207596\",\n \"0.51027244\",\n \"0.51027244\",\n \"0.5101415\",\n \"0.5097889\",\n \"0.5075146\",\n \"0.5061422\",\n \"0.50535256\",\n \"0.5037416\",\n \"0.5037133\",\n \"0.5022858\",\n \"0.50089455\",\n \"0.49830857\",\n \"0.49778566\",\n \"0.4975492\",\n \"0.49716341\",\n \"0.49629128\",\n \"0.49601254\",\n \"0.4943105\",\n \"0.49096364\",\n \"0.4903206\",\n \"0.49012795\",\n \"0.48983356\",\n \"0.48931092\",\n \"0.4892857\",\n \"0.4890902\",\n \"0.4873297\",\n \"0.48678732\",\n \"0.4867703\",\n \"0.4867321\",\n \"0.48558682\",\n \"0.48503676\",\n \"0.48416185\",\n \"0.48268658\",\n \"0.48171896\",\n \"0.4815758\",\n \"0.48034275\",\n \"0.48016477\",\n \"0.47980997\",\n \"0.4793105\",\n \"0.47781262\",\n \"0.47776434\",\n \"0.4774869\",\n \"0.47669694\",\n \"0.47641668\",\n \"0.4758115\",\n \"0.4748523\",\n \"0.47420335\",\n \"0.4741893\",\n \"0.47410733\",\n \"0.47338173\",\n \"0.47310063\",\n \"0.47259364\",\n \"0.47185212\",\n \"0.47157553\",\n \"0.4711726\",\n \"0.4706579\",\n \"0.47039947\",\n \"0.47007442\",\n \"0.46962056\",\n \"0.4690964\",\n \"0.46851158\",\n \"0.46786055\",\n \"0.46786055\",\n \"0.46711308\",\n \"0.46650806\",\n \"0.46606243\",\n \"0.46595407\",\n \"0.46571597\",\n \"0.46541637\",\n \"0.46486548\",\n \"0.46475205\",\n \"0.46438617\",\n \"0.46420944\",\n \"0.46381333\",\n \"0.46350697\",\n \"0.463408\"\n]","isConversational":false},"document_score":{"kind":"string","value":"0.0"},"document_rank":{"kind":"string","value":"-1"}}},{"rowIdx":16586,"cells":{"query":{"kind":"string","value":"Parse a batch of gerber files in a gz tarball."},"document":{"kind":"string","value":"def test_gz_batch(self):\n assert self.design.layout.layers[0].name == 'top'"},"metadata":{"kind":"string","value":"{\n \"objective\": {\n \"self\": [],\n \"paired\": [],\n \"triplet\": [\n [\n \"query\",\n \"document\",\n \"negatives\"\n ]\n ]\n }\n}"},"negatives":{"kind":"list like","value":["def parse_gzipped_directory(input_dir, start_date, end_date, infos, backup_stamps):\n try:\n file_names = sorted(os.listdir(input_dir)) \n for file_name in file_names:\n if file_name.endswith(\".manifest.gz\") or file_name.endswith(\".manifest\"):\n tmp = parse_file(input_dir + \"/\" + file_name, start_date, end_date, backup_stamps)\n backup_stamps[tmp[\"backup_label\"]] = tmp[\"backup_timestamp_stop_ts\"]\n if tmp:\n infos.append(tmp)\n except OSError as e:\n logging.error(\"Failed to open directory\", exc_info=True)\n exit(1)\n except:\n raise","def parse(path):\n data = gzip.open(path, 'rb')\n for byte_line in data:\n yield eval(byte_line) # return generator instance to save memory","def tar_file_and_group(data):\n for sample in data:\n assert \"stream\" in sample\n stream = tarfile.open(fileobj=sample[\"stream\"], mode=\"r|*\")\n prev_prefix = None\n example = {}\n valid = True\n for tarinfo in stream:\n name = tarinfo.name\n pos = name.rfind(\".\")\n assert pos > 0\n prefix, postfix = name[:pos], name[pos + 1 :]\n if prev_prefix is not None and prefix != prev_prefix:\n example[\"key\"] = prev_prefix\n if valid:\n yield example\n example = {}\n valid = True\n with stream.extractfile(tarinfo) as file_obj:\n try:\n if postfix == \"txt\":\n example[\"txt\"] = file_obj.read().decode(\"utf8\").strip()\n elif postfix in AUDIO_FORMAT_SETS:\n waveform, sample_rate = torchaudio.load(file_obj)\n example[\"wav\"] = waveform\n example[\"sample_rate\"] = sample_rate\n else:\n example[postfix] = file_obj.read()\n except Exception as ex:\n valid = False\n logging.warning(\"error to parse {}\".format(name))\n prev_prefix = prefix\n if prev_prefix is not None:\n example[\"key\"] = prev_prefix\n yield example\n stream.close()\n if \"process\" in sample:\n sample[\"process\"].communicate()\n sample[\"stream\"].close()","def _extract_all_gz_in_dir(directory):\n for file in os.listdir(directory):\n if file.endswith(\".gz\"):\n gz_fname = os.path.join(directory, file)\n _extract_gz(gz_fname, os.path.dirname(gz_fname))\n os.remove(gz_fname)","def extract_bz2(tar_bz_f, calc_type):\n \n # we give the gaussian calculator a label that includes the directory the\n # log file is contained in, this does not affect the parsing process but\n # generate a warning as it is not an expected form for the label. To avoid\n # the profusion of warning messages in stdout we suppress warnings here.\n warnings.filterwarnings(\"ignore\")\n\n extended_xyzs = []\n\n with tarfile.open(tar_bz_f,'r:bz2') as data_tar:\n calc_logs = (log_tar for log_tar in data_tar \n if calc_type in log_tar.name and '.log' in log_tar.name)\n \n for calc_log in calc_logs:\n try:\n # extract log file (and relevant directory)\n data_tar.extract(calc_log)\n\n # convert to ASE/Gaussian format\n mol = read(calc_log.name)\n mol.set_calculator(\n Gaussian(\n label=calc_log.name.replace('.log','')\n )\n )\n\n # parse into ML readable format\n parsed_mol = ase_mol_parse(mol)\n extended_xyzs.append(parsed_mol)\n except AttributeError:\n # if the calculation didn't complete we get an empty dictionary \n # so we we keep track of these failed calculations with a blank \n # entry other than mol_id\n blank_entry = {'mol_id':calc_log.name.replace('.log','')}\n extended_xyzs.append(blank_entry)\n finally:\n # delete extracted log file\n os.remove(calc_log.name)\n\n # solves memory problem\n # http://blogs.it.ox.ac.uk/inapickle/2011/06/20/high-memory-usage-when-using-pythons-tarfile-module/ # noqa\n data_tar.members=[]\n \n dir_name = tar_bz_f.replace('.tar.bz2','')\n\n # delete extracted directory\n os.rmdir(dir_name)\n\n # search key function\n # assumes files are named xxx_frame_{frame}_mol_{no}\n def mol_no_frame(mol):\n mol_no = int(mol['mol_id'].split('_')[-1].replace('.log',''))\n mol_frame = int(mol['mol_id'].split('_')[-3])\n return mol_no,mol_frame\n\n extended_xyzs = sorted(extended_xyzs,key=mol_no_frame)\n\n with open(dir_name + '_' + calc_type + '_data.pkl', 'w') as data_f:\n dill.dump(extended_xyzs, data_f)","def debianize( strFilename ):\n \n #~ data = gzip.GzipFile( strFilename ).read();\n #~ print data;\n #~ return;\n \n #~ data = gzip.open( strFilename ).read();\n #~ print data;\n #~ return; \n \n #~ uncompressedData = bz2.BZ2File(strFilename).read()\n #~ print str(uncompressedData)\n #~ return;\n \n #~ file = open( strFilename, 'rb' );\n #~ data = file.read();\n #~ file.close();\n #~ print debug.dumpHexa( data );\n \n #~ ar = tarfile.open(strFilename, 'r:*')\n #~ for item in ar:\n #~ print( str(item) );\n #~ print( \"%s:\" % item.name );\n #~ #print debug.dumpHexa(item.buf);\n #~ #print zlib.decompress(item.buf)\n #~ #print zlib.decompress(ar.extractfile(item).read())\n #~ data = ar.extractfile(item.name).read()\n #~ print data # works !\n #~ ar.close() \n #~ return;\n \n fileLists = [];\n file = open( strFilename );\n data = file.read();\n file.close();\n \n print( \"data len: %d\" % len( data ) );\n\n nDataCompressedOffset = 0; # 132\n\n # works fine on toto.gz\n #~ f = gzip.open(strFilename, 'rb')\n #~ file_content = f.read()\n #~ print file_content\n #~ f.close() \n \n #~ decompressor = bz2.BZ2Decompressor();\n #~ uncompressed = decompressor.decompress(data[nDataCompressedOffset:]);\n \n #~ uncompressed = zlib.decompress(data[nDataCompressedOffset:]);\n \n uncompressed = decompress( data );\n print( \"uncompressed: %s\" % str( uncompressed ) );","def unpack_landsat(inpath, outpath, bands=None, clouds=None):\r\n tfile = tarfile.open(inpath,'r:gz')\r\n if bands is None:\r\n #Extract all of the bands.\r\n tfile.extractall(outpath);\r\n else:\r\n #Extract just the bands specified.\r\n\r\n #Get the names of the members of the archive\r\n names = tfile.getnames()\r\n\r\n #Make sure the bands are given as a list\r\n bands = list(bands)\r\n\r\n #Find those elements of the archive that match the bands specified\r\n #\t(plus metadata file)\r\n members = tfile.getmembers()\r\n elements = []\r\n blist = ''.join(str(i) for i in bands)\r\n if clouds:\r\n patternStr = '.*_B[' + blist + ']\\.TIF|.*_MTL.txt|.*_band[' + blist + \\\r\n ']\\.tif|.*_cfmask.*\\.tif|.*\\.xml|.*cloud.*\\.tif'\r\n else:\r\n patternStr = '.*_B[' + blist + ']\\.TIF|.*_MTL.txt|.*_band[' + blist + \\\r\n ']\\.tif|.*_cfmask.*\\.tif|.*\\.xml'\r\n\r\n pattern = re.compile(patternStr)\r\n for i, name in enumerate(names):\r\n if pattern.match(name):\r\n elements.append(members[i])\r\n tfile.extractall(outpath,members = elements)\r\n\r\n '''\r\n Note: the below section was written with the intention of\r\n adding valuable metadata info to the .TIF files themselves.\r\n This theoretically allows easy retreival of key metadata info,\r\n but the method to set new metadata seems unreliable. Appears to\r\n be an open issue, but there may be a solution. For now, assume\r\n this does not work.\r\n\r\n #Now we loop through each output, adding important metadata.\r\n #Fetch metadata and make sure there is only one file.\r\n meta = glob.glob(outpath + '/*_MTL.txt')\r\n if len(meta) > 1:\r\n raise('MORE THAN ONE METADATA FILE FOUND!')\r\n\r\n metadata = read_metadata(meta[0])\r\n\r\n #Add the metadata.\r\n for tif in glob.glob(outpath + '*.TIF'):\r\n #Open the tif file\r\n ras = gdal.Open(tif)\r\n\r\n #Preserve any existing metadata & add important metadata from file\r\n meta = ras.GetMetadata()\r\n meta['SCENE_CENTER_TIME'] = metadata['SCENE_CENTER_TIME']\r\n meta['DATE_ACQUIRED'] = metadata['DATE_ACQUIRED']\r\n meta['LANDSAT_SCENE_ID'] = metadata['LANDSAT_SCENE_ID']\r\n\r\n #Now write the new metadata back to the tif.\r\n ras.SetMetadata(meta)\r\n ras.FlushCache()\r\n ras = None\r\n '''","def iterator(dataset_fn, sections=None, lang=None, field_indices=None):\n files = filelist(lang=lang, sections=sections)\n\n with TarFile.open(dataset_fn, 'r:gz') as f:\n for member in f:\n if member.isfile() and os.path.basename(member.name) in files:\n logging.info('parsing %s ...' % member.name)\n m_f = f.extractfile(member)\n\n for sentence in parse_conll(m_f, field_indices=field_indices):\n yield sentence\n\n m_f.close()","def _unpack_tar(self, dir, filters):\n try:\n unpackArchive = gbpc.UnpackTarArchive(self.path, dir, filters)\n unpackArchive()\n except gbpc.CommandExecFailed:\n # unpackArchive already printed an error message\n raise GbpError","def yield_publications_metadata(tf):\n logger.info('Start yielding...')\n with gzip.GzipFile(fileobj=tf, mode='r') as json_file:\n for index, line in enumerate(json_file):\n yield build_es_bulk(line.decode('utf-8'))","def create_tarballs_from_xml_files_in_folder(xml_dir, download_date=\"2017.11.02\"):\n\n xml_list = glob.glob(os.path.join(xml_dir, \"*.xml\"))\n\n for xml in xml_list:\n xml_renamed = xml[:-4] + \".BLAST.xml\"\n xml_tar_gz = xml[:-4] + \".BLAST.xml.tar.gz\"\n xml_txt = xml[:-4] + \"_details.txt\"\n # xml_txt = xml[:-4] + \".BLAST_details.txt\"\n\n if not os.path.isfile(xml_tar_gz):\n copyfile(xml, xml_renamed)\n acc = os.path.basename(xml).split(\".\")[0]\n sys.stdout.write(\"{}, \".format(acc))\n sys.stdout.flush()\n # create an empty text file with the download date\n date = strftime(\"%Y%m%d\")\n with open(xml_txt, \"w\") as f:\n f.write(\"acc\\t{}\\ndownload_date\\t{}\\ndatabase\\tncbi_nr\\ne_value\\t1\\n\".format(acc, download_date))\n\n with tarfile.open(xml_tar_gz, mode='w:gz') as tar:\n # add the files to the compressed tarfile\n tar.add(xml_renamed, arcname=os.path.basename(xml_renamed))\n tar.add(xml_txt, arcname=os.path.basename(xml_txt))\n\n # delete the original files\n try:\n os.remove(xml_renamed)\n os.remove(xml_txt)\n except:\n sys.stdout.write(\"{} could not be deleted\".format(xml_renamed))","def _extract_data(inputs):\n filename, split = inputs\n for name, fobj in tfds.download.iter_archive(\n filename, tfds.download.ExtractMethod.TAR_STREAM\n ):\n split_name = name.split(\"_\")\n if len(split_name) > 2 and split_name[2] == split:\n yield [name, fobj.read()]","def untgz(tgz_filename, out_dir):\r\n logging.info(\"Source: %s\" % tgz_filename)\r\n tgz = TgzHelper(tgz_filename, out_dir)\r\n tgz.extract()","def _read_recs(basedir):\n for borotag in boro_tags:\n datafile = \"%s/%s.csv\" % (basedir,borotag)\n print(\"slurp '%s' ..\" % datafile)\n recs = read_recs(datafile)\n yield from (pluto.parse.normalize(r) for r in recs)","def gzip_files(topDir, afni_file,localizerfile):\n\n print 'GZIPPING FILES...'\n\n command1 = \"gzip %s*BRIK\" % (topDir)\n command2 = \"gzip %s*HEAD\" % (topDir)\n command3 = \"gzip %s%s/pb00*\" % (topDir,afni_file)\n command4 = \"gzip %s%s/errts*\" % (topDir,afni_file)\n command5 = \"gzip %s%s/fitts*\" % (topDir,afni_file)\n command6 = \"gzip %s%s/*al*\" % (topDir,afni_file)\n command7 = \"gzip %s%s/*ns*\" % (topDir,afni_file)\n command8 = \"gzip %s%s/all_runs*\" % (topDir,afni_file)\n command9 = \"gzip %s%s/*mask*\" % (topDir,afni_file)\n command10 = \"gzip %s*nii\" % (topDir)\n command11 = \"gzip %s%s/pb01*\" % (topDir,afni_file)\n command12 = \"gzip %s%s/pb03*\" % (topDir,afni_file)\n command13 = \"gzip %s%s/pb02*\" % (topDir,afni_file)\n\n os.system(command1)\n os.system(command2)\n os.system(command3)\n os.system(command4)\n os.system(command5)\n os.system(command6)\n os.system(command7)\n os.system(command8)\n #os.system(command9)\n os.system(command10)\n os.system(command11)\n try:\n os.system(command12)\n except:\n print 'Could not gzip pb03 files'\n\n if localizerfile == 'facescene_loc':\n os.system(command13)","def bags(fondz_dir):\n fondz_dir = os.path.abspath(fondz_dir)\n results = {\n 'bags': [],\n 'num_files': 0,\n 'bytes': 0\n }\n originals_dir = os.path.join(fondz_dir, \"originals\")\n\n for bag in os.listdir(originals_dir):\n # TODO: look for other manifest types?\n bag_dir = os.path.join(originals_dir, bag)\n manifest = os.path.join(bag_dir, \"manifest-md5.txt\")\n b = {\n \"files\": [],\n \"bytes\": 0,\n }\n for line in open(manifest):\n line = line.strip()\n cols = re.split(r' +', line)\n path = os.path.join(bag_dir, cols[1])\n st = os.stat(path)\n rel_path = os.path.join(\"originals\", bag, path)\n b['bytes'] += st.st_size\n b['files'].append({\n \"path\": rel_path,\n \"bytes\": st.st_size,\n \"created\": st.st_ctime,\n \"modified\": st.st_mtime,\n \"md5\": cols[0]\n })\n results['bytes'] += b['bytes']\n results['num_files'] += len(b['files'])\n results['bags'].append(b)\n\n bags_json = os.path.join(fondz_dir, \"js\", \"bags.json\")\n write_json(results, bags_json)\n return results","def clean_gzip():\n this_dir = os.getcwd()\n os.chdir(\"/data/COHERENT2/data/CrystalChar/raw\")\n all_files = glob.glob(\"./**\", recursive=True)\n for f in all_files:\n if \".gz\" in f and \"tar\" not in f:\n print(f)\n sh(\"gunzip \" + f)\n os.chdir(this_dir)","def main(args):\n # Extract keys\n logger.info(\"Extracting brass bedpe file key from tarfile...\")\n bedpe, bedpe_index = extract_tar_keys(args.results_archive)\n # process bedpe\n logger.info(\"Processing brass bedpe {0}...\".format(bedpe))\n process_bedpe(args.results_archive, bedpe, bedpe_index, args.output_prefix)","def _decompress_tarball(*, in_fileobj, out_fileobj):\n with tarfile.open(fileobj=in_fileobj, mode=\"r\") as it, tarfile.open(\n fileobj=out_fileobj, mode=\"w|\"\n ) as ot:\n for member in it.getmembers():\n extracted = it.extractfile(member)\n ot.addfile(member, extracted)","def parse(self, filename: str, input_format='csv', **kwargs):\n if 'delimiter' not in kwargs:\n kwargs['delimiter'] = self._extention_types[input_format]\n if filename.endswith('.tar'):\n with tarfile.open(filename) as tar:\n for member in tar.getmembers():\n f = tar.extractfile(member)\n df = pd.read_csv(f, comment='#', **kwargs) # type: pd.DataFrame\n if member.name == 'nodes.csv':\n self.load_nodes(df)\n elif member.name == 'edges.csv':\n self.load_edges(df)\n else:\n raise Exception('Tar file contains unrecognized member {}'.format(member.name))\n else:\n df = pd.read_csv(filename, comment='#', **kwargs) # type: pd.DataFrame\n self.load(df)","def gbk_parse(fname):\n fhand = _open_file(gbkfname)\n unk = 1 \n\n for record in SeqIO.parse(fhand, \"genbank\"):\n\n gene_tags = dict()\n tx_tags = collections.defaultdict(list) \n exon = collections.defaultdict(list) \n cds = collections.defaultdict(list) \n mol_type, chr_id = None, None \n\n for rec in record.features:\n\n if rec.type == 'source':\n mol_type = rec.qualifiers['mol_type'][0]\n try:\n chr_id = rec.qualifiers['chromosome'][0]\n except:\n chr_id = record.name \n continue \n\n strand='-'\n strand='+' if rec.strand>0 else strand\n \n fid = None \n try:\n fid = rec.qualifiers['gene'][0]\n except:\n pass\n\n transcript_id = None\n try:\n transcript_id = rec.qualifiers['transcript_id'][0]\n except:\n pass \n\n if re.search(r'gene', rec.type):\n gene_tags[fid] = (rec.location._start.position+1, \n rec.location._end.position, \n strand,\n rec.type,\n rec.qualifiers['note'][0])\n elif rec.type == 'exon':\n exon[fid].append((rec.location._start.position+1, \n rec.location._end.position))\n elif rec.type=='CDS':\n cds[fid].append((rec.location._start.position+1, \n rec.location._end.position))\n else: \n # get all transcripts \n if transcript_id: \n tx_tags[fid].append((rec.location._start.position+1,\n rec.location._end.position, \n transcript_id,\n rec.type))\n # record extracted, generate feature table\n unk = feature_table(chr_id, mol_type, strand, gene_tags, tx_tags, cds, exon, unk)\n \n #break\n fhand.close()","def _unpack_archive(self, dir, filters):\n ext = os.path.splitext(self.path)[1]\n if ext in [\".zip\", \".xpi\"]:\n if filters:\n raise GbpError(\"Can only filter tar archives: %s\", (ext, self.path))\n self._unpack_zip(dir)\n else:\n self._unpack_tar(dir, filters)","def main():\r\n parser = CommonArgParser(__file__)\r\n parser.add_argument('src_dir', help='Source directory')\r\n parser.add_argument(\r\n 'out_dir',\r\n default='.',\r\n help=\"\"\"The directory the files to be extracted.\r\n (Default: Current directoty\"\"\")\r\n args = parser.parse_all()\r\n for f in next_file(args.src_dir, ['*.tgz', '*.tar.gz']):\r\n untgz(f, args.out_dir)","def read_gz(images,labels):\n\t# Open the images with gzip in read binary mode\n\t# images = gzip.open('../MNIST-data/train-images-idx3-ubyte.gz', 'rb')\n\t# labels = gzip.open('../MNIST-data/train-labels-idx1-ubyte.gz', 'rb')\n\n\t# Read the binary data\n\n\t# We have to get big endian unsigned int. So we need '>I'\n\n\t# Get metadata for images\n\timages.read(4) # skip the magic_number\n\tnumber_of_images = images.read(4)\n\tnumber_of_images = unpack('>I', number_of_images)[0]\n\trows = images.read(4)\n\trows = unpack('>I', rows)[0]#28\n\tcols = images.read(4)\n\tcols = unpack('>I', cols)[0]#28\n\n\t# Get metadata for labels\n\tlabels.read(4) # skip the magic_number\n\tN = labels.read(4)\n\tN = unpack('>I', N)[0] #60000\n\t# print(number_of_images);\n\n\tif number_of_images != N:\n\t raise Exception('number of labels did not match the number of images')\n\n\t# Get the data\n\tx = zeros((N, rows, cols), dtype=float32) # Initialize numpy array #60000X28X28\n\ty = zeros((N, 1), dtype=uint8) # Initialize numpy array\n\tfor i in range(N):\n\t if i % 1000 == 0:\n\t print(\"i: %i\" % i)\n\t for row in range(rows):\n\t for col in range(cols):\n\t tmp_pixel = images.read(1) # Just a single byte\n\t tmp_pixel = unpack('>B', tmp_pixel)[0]\n\t x[i][row][col] = tmp_pixel\n\t tmp_label = labels.read(1)\n\t y[i] = unpack('>B', tmp_label)[0]\n\t # print(y.shape)#60000X1\n\treturn (x, y)","def parse(self, *args, **kwargs):\n if self.is_gzipped:\n fin = gzip.open(self.path, 'rb')\n else:\n fin = open(self.path, 'r')\n line_num = 0\n expect_header = True\n for line in fin:\n line_num += 1\n line = line.strip()\n if not line: # skip empty lines\n continue\n if expect_header:\n if self._is_header(line):\n logger.debug(\n f\"Detected header at line {line_num}: {line!r}\")\n continue\n else:\n expect_header = False\n try:\n chrom, pos = self._parse_line(line, *args, **kwargs)\n if chrom is not None:\n yield chrom, pos\n except (IndexError, ValueError, TypeError):\n fin.close()\n raise FileFormatError(format=self.format, line_num=line_num,\n line=line)\n fin.close()","def extract_tars(file_pattern, path_in, path_out):\n for f in glob.glob(os.path.join(path_in, file_pattern)):\n shutil.unpack_archive(f, path_out)","def parse_records(self):\n for record in sp.parse(gzip.open(\n \"./human_uniprot_04_07_20.gz\", 'rt')):\n # print(record.taxonomy_id)\n # if record.organism != \"Homo sapiens\":\n # continue\n # print(record.features[0])\n # for comment in record.comments:\n # if comment.startswith(\"SUBCELLULAR LOCATION\"):\n # print(comment)\n self.extract_features_to_dict(record)\n self.extract_localization(record)","def parse_file(path):\n if sys.platform.startswith('linux') or sys.platform.startswith('cygwin'):\n # Assume Linux has GNU objdump. This has the options:\n # -t (list symbols), -C (de-mangle symbol names)\n objdump_args = ['objdump', '-t', '-C']\n elif sys.platform.startswith('darwin'):\n # Assume OSX has LLVM objdump. This has the options:\n # -t (list symbols)\n objdump_args = ['objdump', '-t']\n objdump_args.append(path)\n with StreamingProcess(objdump_args) as proc:\n # Find the first non-blank line.\n first_line = proc.peek()\n while not first_line:\n try:\n proc.next()\n first_line = proc.peek()\n except StopIteration:\n return []\n # Is this an archive?\n match = re.match(r'^.*[Aa]rchive\\s+(.+):$', first_line)\n if match:\n # In this format we have to skip this descriptive line.\n proc.next()\n return parse_archive(match.group(1), proc)\n # Some objdumps format archives differently.\n match = re.match(r'^(.+)\\((.+)\\):\\s+file format', first_line)\n if match:\n return parse_archive(match.group(1), proc)\n # Otherwise maybe it's an object file?\n match = re.match(r'^(.+):\\s+file format', first_line)\n if match:\n return [parse_object_file(match.group(1), proc)]\n # Otherwise it's not an archive or object file.\n return []","def extract_and_tag_test():\n test_untagged_path = os.getcwd() + \"/data/test/test_untagged/\"\n test_untagged_directory = os.fsencode(test_untagged_path)\n\n print(\"Tagging text. Please wait...\")\n for file in os.listdir(test_untagged_directory):\n filename = os.fsdecode(file)\n try:\n if filename.endswith(\".txt\"):\n text = entity_process.read_data(test_untagged_path, file)\n text = text.lower()\n header,body = entity_process.split_text(text)\n header_array = header.splitlines()\n\n\n start_time, end_time = entity_process.extract_time(header)\n location = entity_process.extract_location(header_array, body)\n speaker = entity_process.extract_speaker(header_array, body)\n\n entity_tagger.tag_all(filename, text, start_time, end_time, location, speaker)\n except Exception as e:\n raise e\n return \"No files found here!\"\n print(\"Tagging complete! Text saved to\" + os.getcwd() + \"/out\")","def parse_ensembl_genes(lines):\n LOG.info(\"Parsing ensembl genes from file\")\n header = []\n for index, line in enumerate(lines):\n # File allways start with a header line\n if index == 0:\n header = line.rstrip().split(\"\\t\")\n continue\n # After that each line represents a gene\n\n yield parse_ensembl_line(line, header)","def parse(fcontents, utf16=False): # TODO where does this conversion take place??\n if utf16:\n # Handle a bunch of Unicode nonsense; files appear to be in UTF-16LE\n quant_results = fcontents.split(BLOCK_DIVIDER_UTF16)[3]\\\n .decode(AWKWARD_ENCODING).encode('ascii', 'ignore').split(\"\\r\\n\")\n else:\n quant_results = fcontents.split(BLOCK_DIVIDER)[3].split(\"\\r\\n\")\n\n for res in quant_results:\n items = res.split(\"\\t\")\n if re.search(\"\\d+\", items[0]): # ignore non-digit rows\n amt = items[9]\n if amt == OUTSIDE_LADDER:\n amt = 100\n yield (int(items[0]), items[1], float(amt))","def parse_shard(shard_path):\n with tf.io.gfile.GFile(shard_path, 'rb') as f:\n with gzip.GzipFile(fileobj=f, mode='rb') as f_gz:\n for line in f_gz: # Line-by-line.\n yield deserialize_inference_result(line)","def read_and_parse(path_pattern, parser, **kwargs):\n for filename in glob.glob(path_pattern):\n with open(filename, 'r') as file:\n yield filename, parser.parse(file.read(), **kwargs)","def run(self):\n lineage_csv_gz = self.input_files_local[0][0]\n output_db = self.output_files_local()[0]\n log.write(f\"input: {lineage_csv_gz} output: {output_db}\")\n\n with IdSeqDictForUpdate(output_db, IdSeqDictValue.VALUE_TYPE_ARRAY) as lineage_dict:\n batch_list = {}\n with gzip.open(lineage_csv_gz, \"rt\") as gzf:\n for line in gzf:\n fields = line.rstrip().split(\",\")\n taxid = fields[0]\n species, genus, family = fields[-1:-4:-1]\n batch_list[taxid] = [species, genus, family]\n if len(batch_list) >= BATCH_INSERT_SIZE:\n lineage_dict.batch_inserts(batch_list.items())\n batch_list = {}\n lineage_dict.batch_inserts(batch_list.items())","def process_lines(self):\n\n for line in self.all_lines:\n container_re = re.compile(r'(.*?) bags')\n bags_re = re.compile(r'(?:(\\d+)|no other) (.*?) bags*')\n container_name = re.match(container_re, line).group(1)\n bags = re.findall(bags_re, line)\n self.all_bags[container_name] = bags","def parse_ensembl_transcripts(lines):\n header = []\n LOG.info(\"Parsing ensembl transcripts from file\")\n for index, line in enumerate(lines):\n # File allways start with a header line\n if index == 0:\n header = line.rstrip().split(\"\\t\")\n # After that each line represents a transcript\n else:\n yield parse_ensembl_line(line, header)","def gunzip_file(gz_path, new_path):\n print(\"Unpacking %s to %s\" % (gz_path, new_path))\n with gzip.open(gz_path, \"rb\") as gz_file:\n with open(new_path, \"wb\") as new_file:\n for line in gz_file:\n new_file.write(line)","def czgenerator(cols, db):\n\n\tcfh = []\n\tif not cols:\n\t\tcols = czcols(db)\n\tfor col in cols:\n\t\tcolfile = db + \"/\" + col + \".gz\"\n\t\tcfh.append(gzip.GzipFile(colfile))\n\tfor line in cfh[0]:\n\t\tv = [line.strip()] + [c.readline().strip() for c in cfh[1:]]\n\t\tyield v","def _add_tag_files(\n zip_file, dir_name, payload_info_list, payload_byte_count, payload_file_count\n):\n tag_info_list = []\n _add_tag_file(zip_file, dir_name, tag_info_list, _gen_bagit_text_file_tup())\n _add_tag_file(\n zip_file,\n dir_name,\n tag_info_list,\n _gen_bag_info_file_tup(payload_byte_count, payload_file_count),\n )\n _add_tag_file(\n zip_file, dir_name, tag_info_list, _gen_pid_mapping_file_tup(payload_info_list)\n )\n return tag_info_list","def parse_input():\n with open(\"input_07.txt\", \"r\") as f:\n for line in f:\n Bag(line)","def gunzip_file(gz_path, new_path):\n print(\"Unpacking %s to %s\" % (gz_path, new_path))\n with gzip.open(gz_path, \"rb\") as gz_file:\n with open(new_path, \"wb\") as new_file:\n for line in gz_file:\n new_file.write(line)","def parse(self):\n gen = self.v6_gen() # read from workers\n gen = self.tuple_gen(gen) # convert v6->tuple\n gen = self.batch_gen(gen) # assemble into batches\n for b in gen:\n yield b","def parseDec_GZIPLoader(self, data): # Once gziploader is decrypted, parse the 0xA9 byte config\n hardcoded_val = data[0:1]\n flag = data[1:2]\n datfile_size = int.from_bytes(data[2:6], byteorder=\"little\")\n print(\"[+] datfile size: \", datfile_size)\n dllfile_size = int.from_bytes(data[6:10], byteorder=\"little\")\n print(\"[+] dllfile size: \", dllfile_size)\n dirname = self.extractStrFromBuff(data[10:])\n print(\"[+] Directory Name:\", dirname)\n\n count = self.incNulls(data[10 + len(dirname):])\n datname = self.extractStrFromBuff(data[count + 10 + len(dirname):])\n print(\"[+] Dat Name :\", datname)\n\n count = count + 10 + len(dirname) + len(datname)\n datname = datname[1:]\n count2 = self.incNulls(data[count:])\n count = count + count2\n dllname = self.extractStrFromBuff(data[count:])\n print(\"[+] Dll Name: \", dllname)\n count += len(dllname)\n count2 = self.incNulls(data[count:])\n count += count2\n # datfile offset is now 710 bytes in\n datfile_data = data[710:710 + datfile_size]\n dllfile_start = 710 + datfile_size\n dllfile_data = data[dllfile_start:dllfile_start + dllfile_size]\n datfile_b64 = base64.b64encode(datfile_data).decode()\n dllfile_b64 = base64.b64encode(dllfile_data).decode()\n ParsedDict = {\"Directory_Name\": dirname.decode(),\n \"DatFile_Name\": datname.decode(),\n \"DllFile_Name\": dllname.decode(),\n \"DatFile\": datfile_b64,\n \"DllFile\": dllfile_b64}\n\n return ParsedDict","def gunzip_file(gz_path, new_path):\n print(\"Unpacking %s to %s\" % (gz_path, new_path))\n with gzip.open(gz_path, \"rb\") as gz_file:\n with open(new_path, \"wb\") as new_file:\n for line in gz_file:\n new_file.write(line)","def parse_directory(input_dir, start_date = datetime(1970,1,1), end_date = datetime(9999,12,31,23,59,59)):\n logging.debug(\"Beginning parse_directory {}\".format(input_dir))\n\n def parse_gzipped_directory(input_dir, start_date, end_date, infos, backup_stamps):\n \"\"\" Scans a gzipped directory. This one in different situation \"\"\"\n try:\n file_names = sorted(os.listdir(input_dir)) \n for file_name in file_names:\n if file_name.endswith(\".manifest.gz\") or file_name.endswith(\".manifest\"):\n tmp = parse_file(input_dir + \"/\" + file_name, start_date, end_date, backup_stamps)\n backup_stamps[tmp[\"backup_label\"]] = tmp[\"backup_timestamp_stop_ts\"]\n if tmp:\n infos.append(tmp)\n except OSError as e:\n logging.error(\"Failed to open directory\", exc_info=True)\n exit(1)\n except:\n raise\n \n if not path.isdir(input_dir):\n logging.error(\"The specified path is not a directory\")\n exit(1)\n\n infos = []\n backup_stamps = {}\n if path.exists(input_dir + \"/backup.info\"):\n\n dir_names = sorted(os.listdir(input_dir + \"/backup.history\"))\n for dir_name in dir_names:\n parse_gzipped_directory(input_dir + \"/backup.history/\" + dir_name, start_date, end_date, infos, backup_stamps)\n\n else:\n parse_gzipped_directory(input_dir, start_date, end_date, infos, backup_stamps)\n \n logging.debug(\"End parse_directory\")\n return infos","def unpack(file, path='.'):\n assert isfile(file)\n assert isdir(path)\n\n for implementor in [GzipTarredFile, ZippedFile, Bzip2TarredFile]:\n if implementor.is_valid(file):\n with console.cd(path):\n return [implementor(file).extract(), implementor]\n else:\n raise InvalidFile, 'compressed file format unknown: %s' % file","def gunzip_file(gz_path, new_path):\n logging.info(\"Unpacking %s to %s\" % (gz_path, new_path))\n with gzip.open(gz_path, \"rb\") as gz_file:\n with open(new_path, \"wb\") as new_file:\n for line in gz_file:\n new_file.write(line)","def convert(src: str, tag: str, size: int = 0, unzip=unzip):\n t1 = glob.glob(f'{src}/*GG/*/*t1.nii.gz')\n t2 = glob.glob(f'{src}/*GG/*/*t2.nii.gz')\n flair = glob.glob(f'{src}/*GG/*/*flair.nii.gz')\n t1ce = glob.glob(f'{src}/*GG/*/*t1ce.nii.gz')\n seg = glob.glob(f'{src}/*GG/*/*seg.nii.gz') # Ground Truth\n pat = re.compile('.*_(\\w*)\\.nii\\.gz')\n\n data_paths = [{\n pat.findall(item)[0]: item\n for item in items\n }\n for items in list(zip(t1, t2, t1ce, flair, seg))]\n\n if not size:\n size = len(data_paths)\n total = len(data_paths[:size])\n step = 25 / total\n\n for i, imgs in enumerate(data_paths[:size]):\n try:\n [unzip(imgs[m], tag) for m in ['t1', 't2', 't1ce', 'flair', 'seg']]\n print('\\r\\n' + f'Progress: '\n f\"[{'=' * int((i + 1) * step) + ' ' * (24 - int((i + 1) * step))}]\"\n f\"({math.ceil((i + 1) * 100 / (total))} %)\" + '\\r\\n',\n end=''\n )\n except Exception as e:\n print(f'Something went wrong with {imgs[\"t1\"]}, skipping...\\n Exception:\\n{str(e)}')\n continue","def parseGRO(filename):\n\tprint(\"Cannot parse .gro files yet.\")\n\texit()","def read_files(filenames, gram_size=1):\n assert isinstance(filenames, list), \"filenames argument must be a list\"\n parser = MorParser()\n for fn in filenames:\n for uid, speaker, ngram in generate_chunks(parser.parse(fn), gram_size):\n yield fn, uid, speaker, ngram","def parse_file(self, domain_filename,\n gzip=False,\n fixed=True, pdf=False, output_path=None, **kargs):\n valid_file_formats = set(['fasta_style', 'dfam'])\n assert format in valid_file_formats, '{0} not in {1} valid_file_formats'.format(format, valid_file_formats)\n\n if output_path:\n if not os.path.exists(output_path):\n os.mkdir(output_path)\n self.output_path = output_path\n\n self.fixed = fixed\n self.pdf = pdf\n\n self.data = []\n\n if format == 'fasta_style':\n self.data = self.__load_fasta_style(filename, gzip)\n elif format == 'dfam':\n self.data = self.__load_dfam_style(filename, gzip)","def __init__(self, fpath, prefix, suffix, globar_year=None):\n self.fpath = fpath\n prefix_len = len(prefix)\n suffix_len = len(suffix)\n self.year = globar_year\n self.year_str = str(globar_year)\n\n # filename example : good_2005_0.pgz\n files = [f for f in listdir(fpath) if isfile(join(fpath, f)) and\n (f[-suffix_len:] == suffix and f[:prefix_len] == prefix)]\n\n pat = '{0}_{1}'.format(prefix, self.year_str)\n last_batch = \\\n list(sorted(filter(lambda f: pat in f, files)))\n first_batch = \\\n list(sorted(filter(lambda f: pat not in f, files)))\n\n logging.info('in ChunkReader.__init__() : '\n '(last_batch) {0} files : {1}'.format(len(last_batch), ' '.join(last_batch)))\n logging.info('in ChunkReader.__init__() : '\n '(first_batch) {0} files : {1}'.format(len(first_batch), ' '.join(first_batch)))\n\n first_batch.extend(last_batch)\n # queue-like usage\n self.files = first_batch[::-1]\n logging.info('in ChunkReader.__init__ : '\n 'all files {0} files : {1}'.format(len(self.files), ' '.join(self.files)))","def parse(all_blobs, all_angles):","def scan_corpus(training_corpus_loc):\n for block_fname in iglob( os.path.join( training_corpus_loc, '*.gz' ) ):\n print >> sys.stderr, 'processing dir: ' + block_fname\n with gzip.open( block_fname ) as f:\n num_lines = 0\n for line in f:\n # remember to remove the trailing \\n\n line = line.rstrip()\n num_lines += 1\n print >> sys.stderr, 'Number of lines in ' + block_fname + ' is ' + str(num_lines)","def parse_gazette(self, response):\n json_response = response.json()\n if not json_response:\n self.logger.warning(f\"Document not found in {response.url}\")\n return\n\n json_dir = json_response[\"dir\"]\n\n date = re.search(self.DATE_REGEX, json_dir).group()\n date = parse(date, settings={\"DATE_ORDER\": \"DMY\"}).date()\n is_extra_edition = self.EXTRA_EDITION_TEXT in json_dir\n path = json_dir.replace(\"/\", \"|\")\n\n json_data = json_response[\"data\"]\n file_urls = [self.PDF_URL.format(path, url.split(\"/\")[-1]) for url in json_data]\n\n yield Gazette(\n date=date,\n file_urls=file_urls,\n is_extra_edition=is_extra_edition,\n power=\"executive_legislative\",\n )","def parse(self, limit=None):\n if limit is not None:\n logger.info(\"Only parsing first %d rows of each file\", limit)\n logger.info(\"Parsing files...\")\n\n if self.testOnly:\n self.testMode = True\n\n # the following will provide us the hash-lookups\n self._process_dbxref()\n self._process_cvterm()\n self._process_genotypes(limit)\n self._process_pubs(limit)\n # do this before environments to get the external ids\n self._process_environment_cvterm()\n self._process_environments()\n self._process_organisms(limit) # must be done before features\n self._process_organism_dbxref(limit)\n self._process_features(limit)\n self._process_phenotype(limit)\n self._process_phenotype_cvterm()\n # gets external mappings for features (genes, variants, etc)\n self._process_feature_dbxref(limit)\n # do this after organisms to get the right taxonomy\n self._process_stocks(limit)\n # figures out types of some of the features\n self._get_derived_feature_types(limit)\n\n # These are the associations amongst the objects above\n self._process_stockprop(limit)\n self._process_pub_dbxref(limit)\n self._process_phendesc(limit)\n self._process_feature_genotype(limit)\n self._process_feature_pub(limit)\n self._process_stock_genotype(limit)\n self._process_phenstatement(limit) # these are G2P associations\n\n self._process_feature_relationship(limit)\n\n self._process_disease_models(limit)\n # TODO add version info from file somehow\n # (in parser rather than during fetching)\n\n logger.info(\"Finished parsing.\")\n logger.info(\"Loaded %d nodes\", len(self.graph))\n return","def parse(self, recursive=True):\n # Read and process the file header\n self.fh.seek(0x0, 0)\n header = struct.unpack(\"=10I\", self.fh.read(0x28))\n\n data_start_block = header[0x1]\n\n idx_table_entry_count = header[0x4]\n\n off_table_offset = header[0x5]\n off_table_addr = self.IDX_TABLE_ADDR + off_table_offset\n\n self.fh.seek(self.IDX_TABLE_ADDR, 0)\n\n # Read and populate the index table\n idx_table = []\n for idx in range(idx_table_entry_count):\n typ, num1, num2, num3, num4 = Image.parse_idx_entry(\n self.fh.read(self.IDX_TABLE_ENTRY_SIZE)\n )\n idx_table.append([typ, num1, num2, num3, num4])\n\n self.fh.seek(off_table_addr, 0)\n\n # FIXME: Not sure what 'unk' is.\n off_table_entry_count, unk = struct.unpack(\"=4x2I\", self.fh.read(0xC))\n\n # Read and populate the offset table\n off_table = {}\n for i in range(off_table_entry_count):\n idx, blk_num = Image.parse_off_entry(\n self.fh.read(self.OFF_TABLE_ENTRY_SIZE)\n )\n off_table[idx] = blk_num\n\n # Populate entries\n self.entries = []\n for idx, idx_entry in enumerate(idx_table):\n if idx not in off_table:\n self.entries.append(None)\n continue\n\n blk_num = off_table[idx]\n off = self.fh.tell()\n\n # We need to grab the actual (compressed) size from the PACKage header\n res = None\n addr = self.BLOCK_NUM_ADDR(blk_num)\n if idx_entry[0x0] == b\"PAK \":\n self.fh.seek(addr)\n (\n typ,\n cnt,\n ptr_off,\n str_table_off,\n dec_data_off,\n dec_len,\n cmp_len,\n pad_len,\n ) = Package.parse_header(self.fh.read(Package.ENTRY_SIZE))\n res = Package(FileWindow(self.filename, addr, cmp_len), idx_entry[0x3])\n else:\n res = Resource(\n idx_entry[0x0], FileWindow(self.filename, addr, idx_entry[0x1])\n )\n\n if recursive:\n res.parse(recursive)\n self.entries.append(res)\n self.fh.seek(off, 0)","def _parse_tx_infos(self, gtf_path):\n if os.path.exists('_tx_cache.bin'):\n with open('_tx_cache.bin', 'rb') as f:\n return pickle.load(f)\n result = []\n with gzip.open(gtf_path, 'rt') as f:\n for i, line in enumerate(f):\n if i % 1000 == 0:\n print('processed {}'.format(i), file=sys.stderr)\n if line.startswith('#'):\n continue\n if line.split('\\t', 3)[2] != 'transcript':\n continue\n record = GTFFeature.parse(line)\n if record.feature != 'transcript':\n continue\n result.append(\n TranscriptInfo(record.attrs['gene_id'],\n record.attrs['transcript_id'],\n record.attrs['transcript_type'],\n record.seqname,\n record.start,\n record.end))\n with open('_tx_cache.bin', 'wb') as g:\n pickle.dump(result, g)\n print(len(result), file=sys.stderr)\n return result","def batch_tadbit(directory, parser=None, **kwargs):\n\n matrix = []\n for f_name in listdir(directory):\n if f_name.startswith('.'):\n continue\n f_name = path.join(directory, f_name)\n if parser:\n matrix.append(parser(f_name))\n continue\n elif not path.isfile(f_name):\n continue\n matrix.append(f_name)\n return tadbit(matrix, **kwargs)","def untar(conn, tarball, path):\n conn.run(f\"tar xf {tarball} -C {path}\")","def parse(root_path, output_path, batch_file_paths):\n for file_path in batch_file_paths:\n d, f = split_path(file_path, root_path)\n print(time.ctime(), \"d =\", d, \"; f =\", f)\n if not os.path.exists(os.path.join(OUTPUT_PATH, d)):\n os.makedirs(os.path.join(OUTPUT_PATH, d))\n parsed_files = get_parsed_files(output_path, d)\n if f not in parsed_files:\n with open(file_path) as json_file:\n OUTPUT_FILE_PATH = os.path.join(OUTPUT_PATH, d, f)\n with open(OUTPUT_FILE_PATH, 'w') as writer:\n for num, line in enumerate(json_file):\n json_data = json.loads(line)\n title = json_data['title']\n if json_data['text']:\n definition = json_data['text'][0]['line']\n writer.write(f'{title}\\t{definition}\\n')\n else:\n writer.write(f'{title}\\tNone.\\n')","def create_tar(self):\n with tarfile.open(self.tgzfile, \"w:gz\") as tar_handle:\n for root, _, files in os.walk(self.dirname):\n for file in files:\n tar_handle.add(os.path.join(root, file))","def tarball(request):\n\n patches = (models.Patch\n .query(ancestor=request.patchset.key)\n .order(models.Patch.filename)\n .fetch(1000))\n\n temp = tempfile.TemporaryFile()\n tar = tarfile.open(mode=\"w|bz2\", fileobj=temp)\n\n def add_entry(prefix, content, patch):\n data = content.data\n if data is None:\n data = content.text\n if isinstance(data, unicode):\n data = data.encode(\"utf-8\", \"replace\")\n if data is None:\n return\n info = tarfile.TarInfo(prefix + patch.filename)\n info.size = len(data)\n # TODO(adonovan): set SYMTYPE/0755 when Rietveld supports symlinks.\n info.type = tarfile.REGTYPE\n info.mode = 0644\n # datetime->time_t\n delta = request.patchset.modified - datetime.datetime(1970, 1, 1)\n info.mtime = int(delta.days * 86400 + delta.seconds)\n tar.addfile(info, fileobj=StringIO(data))\n\n for patch in patches:\n if not patch.no_base_file:\n try:\n add_entry('a/', patch.get_content(), patch) # before\n except FetchError: # I/O problem?\n logging.exception('tarball: patch(%s, %s).get_content failed' %\n (patch.key.id(), patch.filename))\n try:\n add_entry('b/', patch.get_patched_content(), patch) # after\n except FetchError: # file deletion? I/O problem?\n logging.exception('tarball: patch(%s, %s).get_patched_content failed' %\n (patch.key.id(), patch.filename))\n\n tar.close()\n temp.flush()\n\n wrapper = FileWrapper(temp)\n response = HttpResponse(wrapper, mimetype='application/x-gtar')\n response['Content-Disposition'] = (\n 'attachment; filename=patch%s_%s.tar.bz2' % (request.issue.key.id(),\n request.patchset.key.id()))\n response['Content-Length'] = temp.tell()\n temp.seek(0)\n return response","def convert(self, tag=\"Data\", delimiter=\",\", noheader=False,\n limit=-1, buffer_size=1000):\n\n\n file_ctr = 0\n item_ctr = 0\n for dirName, subdirList, fileList in os.walk(self.input_directory):\n print('Found directory: %s' % dirName)\n for fname in fileList:\n print('\\t%s' % fname)\n # open the xml file for iteration\n if not fname.endswith(\".xml\"):\n continue\n #pdb.set_trace()\n \n input_file = dirName + \"/\" + fname\n self.context = ETree.iterparse(input_file, events=(\"start\", \"end\"))\n\n # iterate through the xml\n items = [{}]\n\n depth = 0\n min_depth = 0\n row_depth = -1\n n = 0\n for event, elem in self.context:\n if event == \"start\":\n depth += 1\n continue\n else:\n depth -= 1\n if depth < min_depth:\n min_depth = depth\n\n if depth < row_depth and items:\n if noheader:\n noheader = False\n else:\n # new line\n self.output_buffer.append(items)\n items = []\n # flush buffer to disk\n if len(self.output_buffer) > buffer_size:\n self._write_buffer(delimiter)\n\n plain_tag = elem.tag\n last_delim = max(elem.tag.rfind('}'), elem.tag.rfind(':'))\n if 0 < last_delim < len(elem.tag) - 1:\n plain_tag = elem.tag[last_delim + 1:]\n if tag == plain_tag:\n if n == 0:\n min_depth = depth\n elif n == 1:\n row_depth = min_depth\n n += 1\n if 0 < limit < n:\n break\n elem_name = elem.get(\"name\")\n if elem_name in self.output_dict[0].keys():\n if elem_name == 'SamS.ArchivedURL':\n if hash(elem.text) in self.item_titles.keys() and self.item_titles[hash(elem.text)] == elem.text:\n #item is repetative\n self.output_dict[item_ctr]={}\n #item_ctr-=1\n break\n else:\n self.item_titles[hash(elem.text)] = elem.text\n self.output_dict[item_ctr][elem_name]= elem.text and elem.text.encode('utf8') or ''\n\n #if (len(self.output_dict[item_ctr]) > 0 ) :\n if ('SamS.ArchivedURL' in self.output_dict[item_ctr]):\n item_ctr+=1\n self.output_dict.append({})\n else:\n self.output_dict[item_ctr] = {}\n \n file_ctr+=1 #next row in the dictionary array\n print \"processing file no \", file_ctr, \" item no\", item_ctr\n\n #pdb.set_trace()\n self._write_buffer(delimiter) # write rest of the buffer to file\n\n return n","def parse_fasta_file(filename):\n if filename.endswith('.gz'):\n opener = lambda filename: gzip.open(filename, 'rt')\n else:\n opener = lambda filename: open(filename, 'r')\n\n with opener(filename) as f:\n fasta_iter = (it[1] for it in itertools.groupby(f, is_header))\n for name in fasta_iter:\n name = name.__next__()[1:].strip()\n sequences = ''.join(seq.strip() for seq in fasta_iter.__next__())\n yield name, sequences","def processfile(args, fh):\n if args.quick:\n scanner = quickScanZip(args, fh)\n else:\n scanner = findPKHeaders(args, fh)\n\n def checkarg(arg, ent):\n if not arg:\n return False\n return '*' in arg or ent.name in arg\n def checkname(a, b):\n if a and '*' in a: return True\n if b and '*' in b: return True\n l = 0\n if a: l += len(a)\n if b: l += len(b)\n return l > 1\n\n if args.verbose and not (args.cat or args.raw or args.save):\n print(\" 0304 need flgs mth stamp --crc-- compsize fullsize nlen xlen namofs xofs datofs endofs\")\n print(\" 0102 crea need flgs mth stamp --crc-- compsize fullsize nlen xlen clen dsk0 attr osattr datptr namofs xofs cmtofs endofs\")\n for ent in scanner:\n if args.cat or args.raw or args.save:\n if args.quick and isinstance(ent, CentralDirEntry) or \\\n not args.quick and isinstance(ent, LocalFileHeader):\n ent.loaditems(fh)\n do_cat = checkarg(args.cat, ent)\n do_raw = checkarg(args.raw, ent)\n do_save= checkarg(args.save, ent)\n\n do_name= checkname(args.cat, args.raw)\n\n if do_name:\n print(\"\\n===> \" + ent.name + \" <===\\n\")\n\n sys.stdout.flush()\n blks = zipraw(fh, ent)\n\n if args.password and ent.flags&1:\n blks = zip_decrypt(blks, args.password)\n if do_cat or do_save:\n blks = skipbytes(blks, 12, args)\n\n if do_cat:\n sys.stdout.buffer.writelines(zipcat(blks, ent))\n if do_raw:\n sys.stdout.buffer.writelines(blks)\n if do_save:\n savefile(args.outputdir, ent.name, zipcat(blks, ent))\n else:\n ent.loaditems(fh)\n if args.verbose or not args.quick:\n print(\"%08x: %s\" % (ent.pkOffset, ent))\n else:\n print(ent.summary())\n if hasattr(ent, \"comment\") and ent.comment and not args.dumpraw:\n print(ent.comment)\n if args.dumpraw and hasattr(ent, \"extraLength\") and ent.extraLength:\n print(\"%08x: XTRA: %s\" % (ent.extraOffset, binascii.b2a_hex(getbytes(fh, ent.extraOffset, ent.extraLength))))\n if args.dumpraw and hasattr(ent, \"comment\") and ent.comment:\n print(\"%08x: CMT: %s\" % (ent.commentOffset, binascii.b2a_hex(getbytes(fh, ent.commentOffset, ent.commentLength))))\n if args.dumpraw and isinstance(ent, LocalFileHeader):\n blks = zipraw(fh, ent)\n if args.password and ent.flags&1:\n blks = zip_decrypt(blks, args.password)\n\n blockdump(ent.dataOffset, blks)","def extract_tarball(fileobj, path, callback=None):\n tar_cmd = [\"tar\", \"-zx\", \"--directory=%s\" % path]\n tar_proc = make_subprocess(tar_cmd, stderr=True, stdin=True)\n\n try:\n while True:\n chunk = fileobj.read(CHUNK_SIZE)\n if chunk == '':\n break\n\n if callback:\n callback(chunk)\n\n tar_proc.stdin.write(chunk)\n except Exception:\n try_kill_process(tar_proc)\n raise\n\n finish_subprocess(tar_proc, tar_cmd)","def tarball(request):\n\n patches = (models.Patch\n .query(models.Patch.patchset_key == request.patchset.key)\n .order(models.Patch.filename)\n .fetch(1000))\n\n temp = tempfile.TemporaryFile()\n tar = tarfile.open(mode=\"w|bz2\", fileobj=temp)\n\n def add_entry(prefix, content):\n data = content.data\n if data is None:\n data = content.text\n if isinstance(data, unicode):\n data = data.encode(\"utf-8\", \"replace\")\n if data is None:\n return\n info = tarfile.TarInfo(prefix + patch.filename)\n info.size = len(data)\n # TODO(adonovan): set SYMTYPE/0755 when Rietveld supports symlinks.\n info.type = tarfile.REGTYPE\n info.mode = 0644\n # datetime->time_t\n delta = request.patchset.modified - datetime.datetime(1970, 1, 1)\n info.mtime = int(delta.days * 86400 + delta.seconds)\n tar.addfile(info, fileobj=StringIO(data))\n\n for patch in patches:\n if not patch.no_base_file:\n try:\n add_entry('a/', patch.get_content()) # before\n except FetchError: # I/O problem?\n logging.exception('tarball: patch(%s, %s).get_content failed' %\n (patch.key.id(), patch.filename))\n try:\n add_entry('b/', patch.get_patched_content()) # after\n except FetchError: # file deletion? I/O problem?\n logging.exception('tarball: patch(%s, %s).get_patched_content failed' %\n (patch.key.id(), patch.filename))\n\n tar.close()\n temp.flush()\n\n wrapper = FileWrapper(temp)\n response = HttpResponse(wrapper, mimetype='application/x-gtar')\n response['Content-Disposition'] = (\n 'attachment; filename=patch%s_%s.tar.bz2' % (request.issue.key.id(),\n request.patchset.key.id()))\n response['Content-Length'] = temp.tell()\n temp.seek(0)\n return response","def open_files(filenames):\n for filename in filenames:\n if filename.endswith('.gz') or filename.endswith('.zip'):\n yield gzip.open(filename, 'r')\n else:\n yield open(filename, 'rb')","def _compress_meds_file(self, ucfilename, fzfilename):\n from os.path import basename\n\n tup=(basename(ucfilename),basename(fzfilename))\n print('compressing file: %s -> %s' % tup)\n tpath=files.expandpath(fzfilename)\n if os.path.exists(tpath):\n os.remove(tpath)\n\n tmpdir = os.path.dirname(ucfilename)\n with StagedOutFile(fzfilename,tmpdir=tmpdir) as sf:\n cmd = self['fpack_command']\n cmd = cmd.format(fname=ucfilename)\n ret=os.system(cmd)\n\n if ret != 0:\n raise RuntimeError(\"failed to compress file\")\n\n print('output is in:',fzfilename)","def parseGerber(self, fullname, layername, updateExtents = 0):\n\n GAT = config.GAT\n GAMT = config.GAMT\n # First construct reverse GAT/GAMT, mapping definition to code\n RevGAT = config.buildRevDict(GAT) # RevGAT[hash] = aperturename\n RevGAMT = config.buildRevDict(GAMT) # RevGAMT[hash] = aperturemacroname\n\n #print 'Reading data from %s ...' % fullname\n\n fid = file(fullname, 'rt')\n currtool = None\n\n self.apxlat[layername] = {}\n self.apmxlat[layername] = {}\n self.commands[layername] = []\n self.apertures[layername] = []\n\n # These divisors are used to scale (X,Y) co-ordinates. We store\n # everything as integers in hundred-thousandths of an inch (i.e., M.5\n # format). If we get something in M.4 format, we must multiply by\n # 10. If we get something in M.6 format we must divide by 10, etc.\n x_div = 1.0\n y_div = 1.0\n\n # Drawing commands can be repeated with X or Y omitted if they are\n # the same as before. These variables store the last X/Y value as\n # integers in hundred-thousandths of an inch.\n last_x = last_y = 0\n\n # Last modal G-code. Some G-codes introduce \"modes\", such as circular interpolation\n # mode, and we want to remember what mode we're in. We're interested in:\n # G01 -- linear interpolation, cancels all circular interpolation modes\n # G36 -- Turn on polygon area fill\n # G37 -- Turn off polygon area fill\n last_gmode = 1 # G01 by default, linear interpolation\n\n # We want to know whether to do signed (G75) or unsigned (G74) I/J offsets. These\n # modes are independent of G01/G02/G03, e.g., Protel will issue multiple G03/G01\n # codes all in G75 mode.\n # G74 -- Single-quadrant circular interpolation (disables multi-quadrant interpolation)\n # G02/G03 codes set clockwise/counterclockwise arcs in a single quadrant only\n # using X/Y/I/J commands with UNSIGNED (I,J).\n # G75 -- Multi-quadrant circular interpolation --> X/Y/I/J with signed (I,J)\n # G02/G03 codes set clockwise/counterclockwise arcs in all 4 quadrants\n # using X/Y/I/J commands with SIGNED (I,J).\n circ_signed = True # Assume G75...make sure this matches canned header we write out\n\n # If the very first flash/draw is a shorthand command (i.e., without an Xxxxx or Yxxxx)\n # component then we don't really \"see\" the first point X00000Y00000. To account for this\n # we use the following Boolean flag as well as the isLastShorthand flag during parsing\n # to manually insert the point X000000Y00000 into the command stream.\n firstFlash = True\n\n for line in fid:\n # Get rid of CR characters (0x0D) and leading/trailing blanks\n line = string.replace(line, '\\x0D', '').strip()\n\n # Old location of format_pat search. Now moved down into the sub-line parse loop below.\n\n # RS-274X statement? If so, echo it. Currently, only the \"LP\" statement is expected\n # (from Protel, of course). These will be distinguished from D-code and G-code\n # commands by the fact that the first character of the string is '%'.\n match = layerpol_pat.match(line)\n if match:\n self.commands[layername].append(line)\n continue\n \n # See if this is an aperture definition, and if so, map it.\n match = apdef_pat.match(line)\n if match:\n if currtool:\n raise RuntimeError, \"File %s has an aperture definition that comes after drawing commands.\" % fullname\n\n A = aptable.parseAperture(line, self.apmxlat[layername])\n if not A:\n raise RuntimeError, \"Unknown aperture definition in file %s\" % fullname\n\n hash = A.hash()\n if not RevGAT.has_key(hash):\n #print line\n #print self.apmxlat\n #print RevGAT\n raise RuntimeError, 'File %s has aperture definition \"%s\" not in global aperture table.' % (fullname, hash)\n\n # This says that all draw commands with this aperture code will\n # be replaced by aperture self.apxlat[layername][code].\n self.apxlat[layername][A.code] = RevGAT[hash]\n continue\n\n # Ignore %AMOC8* from Eagle for now as it uses a macro parameter, which\n # is not yet supported in GerbMerge.\n if line[:7]=='%AMOC8*':\n continue\n\n # See if this is an aperture macro definition, and if so, map it.\n M = amacro.parseApertureMacro(line,fid)\n if M:\n if currtool:\n raise RuntimeError, \"File %s has an aperture macro definition that comes after drawing commands.\" % fullname\n\n hash = M.hash()\n if not RevGAMT.has_key(hash):\n raise RuntimeError, 'File %s has aperture macro definition not in global aperture macro table:\\n%s' % (fullname, hash)\n\n # This says that all aperture definition commands that reference this macro name\n # will be replaced by aperture macro name self.apmxlat[layername][macroname].\n self.apmxlat[layername][M.name] = RevGAMT[hash]\n continue\n\n # From this point on we may have more than one match on this line, e.g.:\n # G54D11*X22400Y22300D02*X22500Y22200D01*\n sub_line = line\n while sub_line:\n # Handle \"comment\" G-codes first\n match = comment_pat.match(sub_line)\n if match:\n sub_line = sub_line[match.end():]\n continue\n\n # See if this is a format statement, and if so, map it. In version 1.3 this was moved down\n # from the line-only parse checks above (see comment) to handle OrCAD lines like\n # G74*%FSLAN2X34Y34*%\n match = format_pat.match(sub_line) # Used to be format_pat.search\n if match:\n sub_line = sub_line[match.end():]\n for item in match.groups():\n if item is None: continue # Optional group didn't match\n\n if item[0] in \"LA\": # omit leading zeroes and absolute co-ordinates\n continue\n\n if item[0]=='T': # omit trailing zeroes\n raise RuntimeError, \"Trailing zeroes not supported in RS274X files\"\n if item[0]=='I': # incremental co-ordinates\n raise RuntimeError, \"Incremental co-ordinates not supported in RS274X files\"\n\n if item[0]=='N': # Maximum digits for N* commands...ignore it\n continue\n\n if item[0]=='X': # M.N specification for X-axis.\n fracpart = int(item[2])\n x_div = 10.0**(5-fracpart)\n if item[0]=='Y': # M.N specification for Y-axis.\n fracpart = int(item[2])\n y_div = 10.0**(5-fracpart)\n continue\n\n # Parse and interpret G-codes\n match = gcode_pat.match(sub_line)\n if match:\n sub_line = sub_line[match.end():]\n gcode = int(match.group(1))\n\n # Determine if this is a G-Code that should be ignored because it has no effect\n # (e.g., G70 specifies \"inches\" which is already in effect).\n if gcode in [54, 70, 90]:\n continue\n\n # Determine if this is a G-Code that we have to emit because it matters.\n if gcode in [1, 2, 3, 36, 37, 74, 75]:\n self.commands[layername].append(\"G%02d\" % gcode)\n\n # Determine if this is a G-code that sets a new mode\n if gcode in [1, 36, 37]:\n last_gmode = gcode\n\n # Remember last G74/G75 code so we know whether to do signed or unsigned I/J\n # offsets.\n if gcode==74:\n circ_signed = False\n elif gcode==75:\n circ_signed = True\n \n continue\n\n raise RuntimeError, \"G-Code 'G%02d' is not supported\" % gcode\n\n # See if this is a tool change (aperture change) command\n match = tool_pat.match(sub_line)\n if match:\n currtool = match.group(1)\n\n # Protel likes to issue random D01, D02, and D03 commands instead of aperture\n # codes. We can ignore D01 because it simply means to move to the current location\n # while drawing. Well, that's drawing a point. We can ignore D02 because it means\n # to move to the current location without drawing. Truly pointless. We do NOT want\n # to ignore D03 because it implies a flash. Protel very inefficiently issues a D02\n # move to a location without drawing, then a single-line D03 to flash. However, a D02\n # terminates a polygon in G36 mode, so keep D02's in this case.\n if currtool=='D01' or (currtool=='D02' and (last_gmode != 36)):\n sub_line = sub_line[match.end():]\n continue\n\n if (currtool == 'D03') or (currtool=='D02' and (last_gmode == 36)):\n self.commands[layername].append(currtool)\n sub_line = sub_line[match.end():]\n continue\n\n # Map it using our translation table\n if not self.apxlat[layername].has_key(currtool):\n raise RuntimeError, 'File %s has tool change command \"%s\" with no corresponding translation' % (fullname, currtool)\n\n currtool = self.apxlat[layername][currtool]\n\n # Add it to the list of things to write out\n self.commands[layername].append(currtool)\n\n # Add it to the list of all apertures needed by this layer\n self.apertures[layername].append(currtool)\n\n # Move on to next match, if any\n sub_line = sub_line[match.end():]\n continue\n\n # Is it a simple draw command?\n I = J = None # For circular interpolation drawing commands\n match = drawXY_pat.match(sub_line)\n isLastShorthand = False # By default assume we don't make use of last_x and last_y\n if match:\n x, y, d = map(__builtin__.int, match.groups())\n else:\n match = drawX_pat.match(sub_line)\n if match:\n x, d = map(__builtin__.int, match.groups())\n y = last_y\n isLastShorthand = True # Indicate we're making use of last_x/last_y\n else:\n match = drawY_pat.match(sub_line)\n if match:\n y, d = map(__builtin__.int, match.groups())\n x = last_x\n isLastShorthand = True # Indicate we're making use of last_x/last_y\n\n # Maybe it's a circular interpolation draw command with IJ components\n if match is None:\n match = cdrawXY_pat.match(sub_line)\n if match:\n x, y, I, J, d = map(__builtin__.int, match.groups())\n else:\n match = cdrawX_pat.match(sub_line)\n if match:\n x, I, J, d = map(__builtin__.int, match.groups())\n y = last_y\n isLastShorthand = True # Indicate we're making use of last_x/last_y\n else:\n match = cdrawY_pat.match(sub_line)\n if match:\n y, I, J, d = map(__builtin__.int, match.groups())\n x = last_x\n isLastShorthand = True # Indicate we're making use of last_x/last_y\n\n if match:\n if currtool is None:\n # It's OK if this is an exposure-off movement command (specified with D02).\n # It's also OK if we're in the middle of a G36 polygon fill as we're only defining\n # the polygon extents.\n if (d != 2) and (last_gmode != 36):\n raise RuntimeError, 'File %s has draw command %s with no aperture chosen' % (fullname, sub_line)\n\n # Save last_x/y BEFORE scaling to 2.5 format else subsequent single-ordinate\n # flashes (e.g., Y with no X) will be scaled twice!\n last_x = x\n last_y = y\n\n # Corner case: if this is the first flash/draw and we are using shorthand (i.e., missing Xxxx\n # or Yxxxxx) then prepend the point X0000Y0000 into the commands as it is actually the starting\n # point of our layer. We prepend the command X0000Y0000D02, i.e., a move to (0,0) without drawing.\n if (isLastShorthand and firstFlash):\n self.commands[layername].append((0,0,2))\n if updateExtents:\n self.minx = min(self.minx,0)\n self.maxx = max(self.maxx,0)\n self.miny = min(self.miny,0)\n self.maxy = max(self.maxy,0)\n\n x = int(round(x*x_div))\n y = int(round(y*y_div))\n if I is not None:\n I = int(round(I*x_div))\n J = int(round(J*y_div))\n self.commands[layername].append((x,y,I,J,d,circ_signed))\n else:\n self.commands[layername].append((x,y,d))\n firstFlash = False\n\n # Update dimensions...this is complicated for circular interpolation commands\n # that span more than one quadrant. For now, we ignore this problem since users\n # should be using a border layer to indicate extents.\n if updateExtents:\n if x < self.minx: self.minx = x\n if x > self.maxx: self.maxx = x\n if y < self.miny: self.miny = y\n if y > self.maxy: self.maxy = y\n\n # Move on to next match, if any\n sub_line = sub_line[match.end():]\n continue\n\n # If it's none of the above, it had better be on our ignore list.\n for pat in IgnoreList:\n match = pat.match(sub_line)\n if match:\n break\n else:\n raise RuntimeError, 'File %s has uninterpretable line:\\n %s' % (fullname, line)\n\n sub_line = sub_line[match.end():]\n # end while still things to match on this line\n # end of for each line in file\n\n fid.close()\n if 0:\n print layername\n print self.commands[layername]","def parse(self, f):\n \n for line in f:\n self.parse_line(line)","def parse_file(file_name: str, delims='\\n', encoding='utf-8', zip_type=None):\n try:\n decoder = codecs.getincrementaldecoder(encoding)()\n except LookupError as e:\n print(str(e))\n return\n\n read_buffer_size = 10*1024\n max_line_size = 100*1024\n\n if not zip_type:\n open_f = open\n elif zip_type == 'gz':\n open_f = gzip.open\n else:\n raise NotImplementedError()\n\n with open_f(file_name, 'rb') as fp:\n buffered_str = ''\n for bs in iter(partial(fp.read, read_buffer_size), b''):\n decoded_str = decoder.decode(bs)\n # FIXME: i don't think current implementation is efficient enough...\n for c in decoded_str:\n if c in delims:\n if len(buffered_str) > 0:\n yield buffered_str\n buffered_str = ''\n else:\n buffered_str += c\n if len(buffered_str) >= max_line_size:\n yield buffered_str\n buffered_str = ''\n if len(buffered_str) > 0:\n yield buffered_str","def extractTar(tar_file):\r\n\r\n tfile = tarfile.open(tar_file, 'r')\r\n tar_members = tfile.getmembers()\r\n for tar_member in tar_members:\r\n tar_member.name = os.path.basename(tar_member.name) # Strip out the path and keep just the file name\r\n tfile.extract(tar_member, path=\"tempdata/\")\r\n tfile.close()\r\n print \"Finished extracting tar file\"\r\n return","def fromgroups(args):\n from jcvi.formats.bed import Bed\n\n p = OptionParser(fromgroups.__doc__)\n opts, args = p.parse_args(args)\n\n if len(args) < 2:\n sys.exit(not p.print_help())\n\n groupsfile = args[0]\n bedfiles = args[1:]\n beds = [Bed(x) for x in bedfiles]\n fp = open(groupsfile)\n groups = [row.strip().split(\",\") for row in fp]\n for b1, b2 in product(beds, repeat=2):\n extract_pairs(b1, b2, groups)","def parse_region_data(self, region):\r\n \r\n self.download_data()\r\n region_filename = self.__get_region_filename(region)\r\n list_str = [\"region\", \"p1\", \"p36\", \"p37\", \"p2a\", \"weekday(p2a)\", \"p2b\", \"p6\", \"p7\", \"p8\", \"p9\", \"p10\", \r\n \"p11\", \"p12\", \"p13a\", \"p13b\", \"p13c\", \"p14\", \"p15\", \"p16\", \"p17\", \"p18\",\"p19\", \"p20\", \"p21\", \r\n \"p22\", \"p23\", \"p24\", \"p27\", \"p28\", \"p34\", \"p35\", \"p39\", \"p44\", \"p45a\", \"p47\", \"p48a\", \"p49\", \r\n \"p50a\", \"p50b\", \"p51\", \"p52\", \"p53\", \"p55a\", \"p57\", \"p58\", \"a\", \"b\", \"d\", \"e\", \"f\", \"g\", \"h\", \r\n \"i\", \"j\", \"k\", \"l\", \"m\", \"n\", \"o\", \"p\", \"q\", \"r\", \"s\", \"t\", \"p5a\"]\r\n \r\n row_count = self.__get_files_row_count(region)\r\n list_arrays = [np.zeros(row_count, dtype=dt) for dt in self.__types]\r\n row_index = 0\r\n for file in self.__files:\r\n file_to_parse = os.path.join(self.__folder, os.path.basename(file))\r\n with zipfile.ZipFile(file_to_parse, \"r\") as zf:\r\n with zf.open(region_filename, 'r') as csv_file:\r\n reader = csv.reader(TextIOWrapper(csv_file, 'windows-1250'), delimiter=';', quotechar='\"')\r\n for row in reader:\r\n list_arrays[0][row_index] = region\r\n for col_index, col in enumerate(row):\r\n try:\r\n list_arrays[col_index + 1][row_index] = col\r\n except ValueError:\r\n if list_arrays[col_index + 1][row_index].dtype == np.int64:\r\n list_arrays[col_index + 1][row_index] = -1\r\n elif list_arrays[col_index + 1][row_index].dtype == 'datetime64[D]':\r\n print('Error2:', col)\r\n elif list_arrays[col_index + 1][row_index].dtype == np.float64:\r\n if type(col) != str:\r\n list_arrays[col_index + 1][row_index] = col.replace(',', '.')\r\n else:\r\n list_arrays[col_index + 1][row_index] = float(\"nan\")\r\n row_index += 1\r\n \r\n return (list_str, list_arrays)","def parse_fastq(filepath):\n if REGEX_GZIPPED.match(filepath):\n logging.debug('Opening \"%s\" as gzipped file', filepath)\n # using os.popen with zcat since it is much faster than gzip.open or gzip.open(io.BufferedReader)\n # http://aripollak.com/pythongzipbenchmarks/\n # assumes Linux os with zcat installed\n import os\n with os.popen('zcat < {}'.format(filepath)) as f:\n yield from _parse_fastq(f)\n else:\n with open(filepath, 'r') as f:\n yield from _parse_fastq(f)","def test_tarballs_pre_extracted(self) -> None:\n import hammer_config\n\n tech_dir, tech_dir_base = HammerToolTestHelpers.create_tech_dir(\"dummy28\")\n tech_json_filename = os.path.join(tech_dir, \"dummy28.tech.json\")\n\n # Add defaults to specify tarball_dir.\n with open(os.path.join(tech_dir, \"defaults.json\"), \"w\") as f:\n f.write(json.dumps({\n \"technology.dummy28.tarball_dir\": tech_dir,\n \"vlsi.technology.extracted_tarballs_dir\": tech_dir_base\n }, cls=HammerJSONEncoder))\n\n HammerToolTestHelpers.write_tech_json(tech_json_filename, self.add_tarballs)\n sys.path.append(tech_dir_base)\n tech = self.get_tech(hammer_tech.HammerTechnology.load_from_dir(\"dummy28\", tech_dir))\n tech.cache_dir = tech_dir\n\n database = hammer_config.HammerDatabase()\n database.update_technology(tech.get_config())\n HammerVLSISettings.load_builtins_and_core(database)\n tech.set_database(database)\n outputs = tech.process_library_filter(pre_filts=[], filt=hammer_tech.filters.gds_filter,\n must_exist=False,\n output_func=lambda str, _: [str])\n\n self.assertEqual(outputs, [\"{0}/foobar.tar.gz/test.gds\".format(tech_dir_base)])\n\n # Cleanup\n shutil.rmtree(tech_dir_base)","def ParserTeil2():\r\n Bags = {}\r\n for Line in Lines:\r\n Words = Line.split()\r\n Farbe = Words[0]+\" \"+Words[1]\r\n Bags[Farbe] = re.findall(r\"(\\d+?) (.+?) bags?\", Line)\r\n return Bags","def archive_bag_api_messages(bags, bucket):\n for bag in bags:\n yield {\n 'type': 'Ingest',\n 'ingestType': {\n 'id': 'create',\n 'type': 'IngestType'\n },\n 'uploadUrl': f's3://{bucket}/{bag}'\n }","def processSetOfCerFiles(files):\n printHeader()\n \n k = 0\n for f in files:\n k = k + 1\n sz = get_file_size(f)\n with open(f, 'rb') as fb:\n processCerFile(k, fb, sz=sz)","def split_batches(filenames):\n by_time = {}\n for path_name in filenames:\n file_name = path.basename(path_name)\n parsed_fn = parse_agdc_fn(file_name)\n dt = parsed_fn['datetime']\n by_time.setdefault(dt, []).append((path_name, parsed_fn))\n\n rv = list(by_time.values())\n\n for group in rv:\n # Will raise exception if group is non-homogeneous\n check_sane(parsed for _, parsed in group)\n\n return rv","def process_bedpe(archive, bedpe, bedpe_index, output_prefix):\n out_raw_bedpe = '{0}.tmp.bedpe.gz'.format(output_prefix)\n logger.info(\"Extracting raw bedpe to tmp file {0}\".format(out_raw_bedpe))\n extract_file(archive, bedpe, out_raw_bedpe)\n\n out_raw_bedpe_index = '{0}.tmp.bedpe.gz.tbi'.format(output_prefix)\n logger.info(\"Extracting raw bedpe index to tmp file {0}\".format(out_raw_bedpe_index))\n extract_file(archive, bedpe_index, out_raw_bedpe_index)\n\n out_formatted_bedpe = '{0}.bedpe.gz'.format(output_prefix)\n logger.info(\"Creating final bedpe {0}\".format(out_formatted_bedpe))\n writer = pysam.BGZFile(out_formatted_bedpe, mode='wb')\n reader = pysam.BGZFile(out_raw_bedpe, mode='rb')\n try:\n meta_line = None\n process_header = False\n hdr = []\n for line in reader:\n line = line.decode('utf-8')\n if line.startswith('#'):\n meta_line = line\n else:\n if not process_header:\n hdr = format_header(meta_line)\n assert len(hdr) == len(set(hdr)), \\\n \"Duplicate header keys {0}\".format(','.join(hdr))\n writer.write(('#' + '\\t'.join(hdr) + '\\n').encode('utf-8'))\n process_header = True\n\n dat = dict(zip(hdr, line.rstrip('\\r\\n').split('\\t')))\n dat['brass_notation'] = dat['brass_notation'].replace('Chr.chr', 'chr')\n new_line = \"\\t\".join([dat[i] for i in hdr]) + '\\n'\n writer.write(new_line.encode('utf-8'))\n finally:\n writer.close()\n reader.close()\n\n # tabix index\n logger.info(\"Creating final bedpe index {0}\".format(out_formatted_bedpe + '.tbi'))\n pysam.tabix_index( out_formatted_bedpe, preset='bed', force=True )\n\n # clean up\n logger.info(\"Cleaning up tmp files...\")\n os.remove(out_raw_bedpe)\n os.remove(out_raw_bedpe_index)","def unpack_tarfile(self, tarfile_path: str, target_directory: str) -> None:\n with tarfile.open(tarfile_path) as tar:\n tar.extractall(path=target_directory)\n\n found = True\n\n while found:\n\n found = False\n\n for root_directory, _, files in os.walk(target_directory):\n for file in files:\n if re.search('.*.tar.gz', file):\n found = True\n sub_filepath_ref = os.path.join(root_directory, file)\n with tarfile.open(sub_filepath_ref) as tar:\n tar.extractall(path=root_directory)\n os.remove(sub_filepath_ref)","def readDirectory():\n tagdir = \"tagreplacements\"\n data = os.listdir(tagdir)\n for d in data:\n processFile(os.path.join(tagdir,d))\n \n #print(repd)","def try7():\n path = '/Users/mayankkejriwal/datasets/memex-evaluation-november/nyu-text/'\n total = 1\n count = 1\n with gzip.open(path + 'output1.gz', 'rb') as f:\n for line in f:\n print 'line : ',\n print line\n count += 1\n if count > total:\n break","def _process_fileobj(self,\n tar_file_obj: IO[bytes],\n object_node: graph.COSObject) -> None:\n with tarfile.open(fileobj=tar_file_obj) as tar_file:\n gz_file_names = [f.name for f in tar_file.getmembers()\n if f.name.endswith('.gz')]\n for gz_file_name in gz_file_names:\n gz_file_obj = tar_file.extractfile(gz_file_name)\n if gz_file_obj:\n oem_data = self._parse_oem_data(gz_file_obj)\n aso_id = self._get_aso_id_from_file_name(gz_file_name)\n self._save_oem(oem_data, aso_id, object_node)","def parse(self, ergFilePath):\n infoFilePath = ergFilePath + '.info'\n quantityList = self.getQuantityList(infoFilePath)\n\n # get block size\n blockSize = sum(quantity.bytes for quantity in quantityList)\n\n with open(ergFilePath, 'rb') as ergFile:\n\n # read the first 16 bytes, as they are not needed now\n ergFile.read(16)\n\n # now read the rest of the file block wise\n block = ergFile.read(blockSize)\n while len(block) == blockSize:\n for q in quantityList:\n q.values.append(np.fromstring(block[:q.bytes], q.dataType)[0])\n block = block[q.bytes:]\n block = ergFile.read(blockSize)\n\n self.quantityList = quantityList\n return quantityList","def glob_upload_gz(pattern, egnyte_path, log=True, dryrun=False):\n\timport glob\n\tfor filename in glob.glob(pattern):\n\t\tif log:\n\t\t\telog(f\"found file for upload:{filename}\")\n\t\tif not dryrun:\n\t\t\tupload_file_gz(filename, egnyte_path, progress_callbacks=ProgressCallbacks() if log else None)","def process_raw_data(data_dir='/home/data/nbc/athena/athena-data/'):\n\n # Calls the process_corpus function, defined below\n # process_corpus reads in the text, performs abbreviation, spelling,\n # translation, and overall text Processing\n # process_corpus outputs the processed text for each file and the stemmed file\n for feature_source in ['abstract', 'full']:\n process_corpus(data_dir, feature_source)\n\n # Calls the label_data function, defined below\n # label_data reads in the metadata csv files, concatenates them, then\n # reads in the processed text files\n # label_data outputs a binary pmid by label metadata matrix\n label_data(data_dir)\n generate_gazetteer(data_dir)","def parse_archive(path, objdump):\n object_files = []\n current_file = None\n for line in objdump:\n if not line:\n continue\n match = re.match(r'^(.*[^\\)])(\\((.+)\\))?:\\s+file format', line)\n if match:\n filename = match.group(3) if match.group(3) else match.group(1)\n current_file = ObjectFile(filename, path)\n object_files.append(current_file)\n continue\n if not current_file:\n raise Exception('Archive does not specify object to attribute '\n 'symbols to ' + path)\n sym = parse_symbol(line)\n if not sym:\n if current_file.symbols:\n current_file = None\n continue\n current_file.symbols.append(sym)\n return object_files","def parseGFF3(filename):\n\n # Parse with transparent decompression\n openFunc = gzip.open if filename.endswith(\".gz\") else open\n with openFunc(filename) as infile:\n for line in infile:\n if line.startswith(\"#\"):\n continue\n parts = line.strip().split(\"\\t\")\n # If this fails, the file format is not standard-compatible\n assert len(parts) == len(gffInfoFields)\n # Normalize data\n normalizedInfo = {\n \"seqid\": None if parts[0] == \".\" else urllib.unquote(parts[0]),\n \"source\": None if parts[1] == \".\" else urllib.unquote(parts[1]),\n \"type\": None if parts[2] == \".\" else urllib.unquote(parts[2]),\n \"start\": None if parts[3] == \".\" else int(parts[3]),\n \"end\": None if parts[4] == \".\" else int(parts[4]),\n \"score\": None if parts[5] == \".\" else float(parts[5]),\n \"strand\": None if parts[6] == \".\" else urllib.unquote(parts[6]),\n \"phase\": None if parts[7] == \".\" else urllib.unquote(parts[7]),\n \"attributes\": parseGFFAttributes(parts[8])\n }\n # Alternatively, you can emit the dictionary here, if you need\n # mutability:\n # yield normalizedInfo\n yield GFFRecord(**normalizedInfo)","def parse(self, infile):\r\n raise NotImplementedError()","def process_file(filename):\n print \"Reading and Parsing File: {}\".format(filename)\n parsed_entries = file_parser(filename)\n print \"Starting to Process Entries\"\n chunked_entires = chunk_entries(parsed_entries)\n return [process_entries(entry) for entry in chunked_entires]","def main(input_file=None, decoy_tag=None, output_file=None):\n NEW_HEADERS = [\n \"Raw data location\",\n \"Spectrum ID\",\n \"Spectrum Title\",\n \"Retention Time (s)\",\n \"Rank\",\n \"Calc m/z\",\n \"Exp m/z\",\n \"Charge\",\n \"Sequence\",\n \"Modifications\",\n \"X\\!Tandem:expect\",\n \"X\\!Tandem:hyperscore\",\n \"proteinacc_start_stop_pre_post_;\",\n \"Is decoy\",\n ]\n PROTON = 1.00727646677\n protein = None\n group = None\n group_counter = 0\n protein_groups = []\n\n if input_file.endswith(\".gz\"):\n compressed = True\n # Gzipped files are not seekable\n import gzip\n\n # file_object = codecs.getreader(\"utf-8\")(\n # gzip.open(path)\n # )\n file_object = codecs.getreader(\"utf-8\")(gzip.open(input_file))\n else:\n file_object = codecs.open(input_file, mode=\"r\", encoding=\"utf-8\")\n\n csvOut = csv.DictWriter(open(output_file, \"w\", newline=\"\"), NEW_HEADERS)\n csvOut.writeheader()\n\n print(\"Converting XTandem XML into CSV: {0}\".format(input_file))\n tandemXML = iter(cElementTree.iterparse(file_object, events=(b\"start\", b\"end\")))\n\n for pos, (event, element) in enumerate(tandemXML):\n if event == b\"start\":\n if element.tag.endswith(\"bioml\"):\n raw_data_location = element.attrib[\"label\"].split(\"'\")[1]\n if element.tag.endswith(\"group\"):\n if \"mh\" in element.attrib.keys():\n group_counter = 0\n notes = ddict(set)\n notes_key = None\n group = {} # reset group\n group[\"Raw data location\"] = raw_data_location\n group[\"Charge\"] = element.attrib[\"z\"]\n group[\"Exp m/z\"] = (\n float(element.attrib[\"mh\"]) / float(group[\"Charge\"])\n ) + PROTON\n group[\"X\\!Tandem:expect\"] = element.attrib[\"expect\"]\n protein_groups = []\n domain_groups = []\n if element.attrib[\"label\"] == \"fragment ion mass spectrum\":\n notes_key = \"spectrum\"\n if element.attrib[\"label\"] == \"input parameters\":\n notes_key = \"parameters\"\n group_counter += 1\n\n elif element.tag.endswith(\"protein\"):\n protein = {} # reset protein\n notes_key = \"protein\"\n\n elif element.tag.endswith(\"domain\"):\n if \"seq\" in element.attrib.keys():\n domain = {header: \"\" for header in NEW_HEADERS} # reset domain\n domain[\"Sequence\"] = element.attrib[\"seq\"]\n domain[\"X\\!Tandem:hyperscore\"] = element.attrib[\"hyperscore\"]\n domain[\"Calc m/z\"] = (\n float(element.attrib[\"mh\"]) / float(group[\"Charge\"])\n ) + PROTON\n protein[\"Start\"] = element.attrib[\"start\"]\n protein[\"Stop\"] = element.attrib[\"end\"]\n protein[\"pre\"] = element.attrib[\"pre\"][-1]\n protein[\"post\"] = element.attrib[\"post\"][0]\n if protein[\"Start\"] == \"1\":\n protein[\"pre\"] = \"-\"\n if protein[\"post\"] == \"]\":\n protein[\"post\"] = \"-\"\n domain[\n \"proteinacc_start_stop_pre_post_;\"\n ] = \"{0}_{1}_{2}_{3}_{4};\".format(\n protein[\"Defline\"],\n protein[\"Start\"],\n protein[\"Stop\"],\n protein[\"pre\"],\n protein[\"post\"],\n )\n if protein[\"Defline\"].startswith(decoy_tag):\n domain[\"Is decoy\"] = True\n else:\n domain[\"Is decoy\"] = False\n domain[\"Rank\"] = 1\n\n elif element.tag.endswith(\"aa\"):\n if \"modified\" not in element.attrib.keys():\n continue\n mod = \"{0}:{1}\".format(\n element.attrib[\"modified\"],\n int(element.attrib[\"at\"]) - int(protein[\"Start\"]) + 1,\n )\n try:\n domain[\"Modifications\"].append(mod)\n except:\n domain[\"Modifications\"] = [mod]\n else:\n if element.tag.endswith(\"protein\"):\n protein_groups.append(protein)\n if element.tag.endswith(\"domain\"):\n for k, v in domain.items():\n if k not in protein.keys():\n protein[k] = v\n # domain_groups.append( domain )\n elif element.tag.endswith(\"note\"):\n if notes_key == \"spectrum\":\n group[\"Spectrum Title\"] = element.text.strip()\n elif notes_key == \"protein\":\n protein[\"Defline\"] = element.text.strip()\n elif element.tag.endswith(\"group\"):\n group_counter -= 1\n if group_counter == 0:\n dict2write = {}\n # proteins = []\n for protein_group in protein_groups:\n for key in NEW_HEADERS:\n # if key == 'proteinacc_start_stop_pre_post_;':\n # proteins.append(protein_group[key])\n # continue\n if key == \"Modifications\" and protein_group[key] != \"\":\n dict2write[key] = \";\".join(protein_group[key])\n continue\n try:\n dict2write[key] = group[key]\n except:\n dict2write[key] = protein_group[key]\n # dict2write['proteinacc_start_stop_pre_post_;'] = ''.join(proteins)\n csvOut.writerow(dict2write)\n protein_groups = []\n return","def _all_xonsh_parser(**kwargs):\n data_dir = builtins.__xonsh_env__.get('XONSH_DATA_DIR')\n data_dir = expanduser_abs_path(data_dir)\n\n files = [os.path.join(data_dir, f) for f in os.listdir(data_dir)\n if f.startswith('xonsh-') and f.endswith('.json')]\n ind = 0\n for f in files:\n try:\n json_file = LazyJSON(f, reopen=False)\n except ValueError:\n # Invalid json file\n pass\n commands = json_file.load()['cmds']\n for c in commands:\n yield (c['inp'].rstrip(), c['ts'][0], ind)\n ind += 1","def read_ptbtagged(ptbtagged_path: str) -> Iterator[Tuple[TokenSeq, PosSeq]]:\n #do this immediately (first)\n #start generating feature matrices\n \n #read file into an array \n with open(ptbtagged_path) as f:\n file_array = f.readlines()\n file_array.append(\"\\n\")\n array_of_tuples = create_tuples(file_array)\n\n return generator(array_of_tuples)","def extract_from_tgz(tgz_file, output_path):\n try:\n t = tarfile.open(name = tgz_file, mode = 'r')\n except tarfile.ReadError:\n raise ValueError, ERROR_MSG\n else:\n names_list = t.getnames()\n # if the tgz_file only has one file is not necessary to generate an\n # output directory\n if len(names_list) == 1:\n t.extractall()\n move(names_list[0], output_path)\n else:\n t.extractall(path=output_path)\n t.close()","def get_tag_batch(self, tag, filenames):\n data = self.get_tags_batch([tag], filenames)\n result = []\n for d in data:\n d.pop(\"SourceFile\")\n result.append(next(iter(d.values()), None))\n return result","async def create_tarball(output_path: str) -> bytes:\n file_paths = []\n for root, _, filenames in os.walk(output_path):\n for filename in filenames:\n file_path = os.path.join(root, filename)\n log.info(f'Adding {file_path} to tarball.')\n file_paths.append(file_path)\n\n with ByteStream() as stream:\n with tarfile.TarFile.open(fileobj=stream, mode='w:gz',\n compresslevel=1) as tar:\n for file_path in file_paths:\n tar_info = tar.gettarinfo(name=file_path)\n tar.addfile(tar_info)\n # Yield the header for the tarinfo file.\n yield stream.pop()\n\n with open(file_path, 'rb') as in_fp:\n # Read the input file in chunks of stream.block_size bytes.\n while True:\n data = in_fp.read(stream.block_size)\n if len(data) > 0:\n # Write the data to the buffer.\n tar.fileobj.write(data)\n # Yield a compressed file chunk so the client can receive it.\n yield stream.pop()\n # Write padding if necessary.\n if len(data) < stream.block_size:\n blocks, remainder = divmod(tar_info.size, tarfile.BLOCKSIZE)\n if remainder > 0:\n tar.fileobj.write(tarfile.NUL * (tarfile.BLOCKSIZE - remainder))\n yield stream.pop()\n blocks += 1\n tar.offset += blocks * tarfile.BLOCKSIZE\n break\n\n # Yield end-of-archive marker.\n yield stream.pop()","def decompress_chunks(bstrm):\n decompressor = zlib.decompressobj()\n for chunk in iter(lambda: bstrm.read(BUFSIZE), b\"\"):\n yield decompressor.decompress(chunk)\n yield decompressor.flush()"],"string":"[\n \"def parse_gzipped_directory(input_dir, start_date, end_date, infos, backup_stamps):\\n try:\\n file_names = sorted(os.listdir(input_dir)) \\n for file_name in file_names:\\n if file_name.endswith(\\\".manifest.gz\\\") or file_name.endswith(\\\".manifest\\\"):\\n tmp = parse_file(input_dir + \\\"/\\\" + file_name, start_date, end_date, backup_stamps)\\n backup_stamps[tmp[\\\"backup_label\\\"]] = tmp[\\\"backup_timestamp_stop_ts\\\"]\\n if tmp:\\n infos.append(tmp)\\n except OSError as e:\\n logging.error(\\\"Failed to open directory\\\", exc_info=True)\\n exit(1)\\n except:\\n raise\",\n \"def parse(path):\\n data = gzip.open(path, 'rb')\\n for byte_line in data:\\n yield eval(byte_line) # return generator instance to save memory\",\n \"def tar_file_and_group(data):\\n for sample in data:\\n assert \\\"stream\\\" in sample\\n stream = tarfile.open(fileobj=sample[\\\"stream\\\"], mode=\\\"r|*\\\")\\n prev_prefix = None\\n example = {}\\n valid = True\\n for tarinfo in stream:\\n name = tarinfo.name\\n pos = name.rfind(\\\".\\\")\\n assert pos > 0\\n prefix, postfix = name[:pos], name[pos + 1 :]\\n if prev_prefix is not None and prefix != prev_prefix:\\n example[\\\"key\\\"] = prev_prefix\\n if valid:\\n yield example\\n example = {}\\n valid = True\\n with stream.extractfile(tarinfo) as file_obj:\\n try:\\n if postfix == \\\"txt\\\":\\n example[\\\"txt\\\"] = file_obj.read().decode(\\\"utf8\\\").strip()\\n elif postfix in AUDIO_FORMAT_SETS:\\n waveform, sample_rate = torchaudio.load(file_obj)\\n example[\\\"wav\\\"] = waveform\\n example[\\\"sample_rate\\\"] = sample_rate\\n else:\\n example[postfix] = file_obj.read()\\n except Exception as ex:\\n valid = False\\n logging.warning(\\\"error to parse {}\\\".format(name))\\n prev_prefix = prefix\\n if prev_prefix is not None:\\n example[\\\"key\\\"] = prev_prefix\\n yield example\\n stream.close()\\n if \\\"process\\\" in sample:\\n sample[\\\"process\\\"].communicate()\\n sample[\\\"stream\\\"].close()\",\n \"def _extract_all_gz_in_dir(directory):\\n for file in os.listdir(directory):\\n if file.endswith(\\\".gz\\\"):\\n gz_fname = os.path.join(directory, file)\\n _extract_gz(gz_fname, os.path.dirname(gz_fname))\\n os.remove(gz_fname)\",\n \"def extract_bz2(tar_bz_f, calc_type):\\n \\n # we give the gaussian calculator a label that includes the directory the\\n # log file is contained in, this does not affect the parsing process but\\n # generate a warning as it is not an expected form for the label. To avoid\\n # the profusion of warning messages in stdout we suppress warnings here.\\n warnings.filterwarnings(\\\"ignore\\\")\\n\\n extended_xyzs = []\\n\\n with tarfile.open(tar_bz_f,'r:bz2') as data_tar:\\n calc_logs = (log_tar for log_tar in data_tar \\n if calc_type in log_tar.name and '.log' in log_tar.name)\\n \\n for calc_log in calc_logs:\\n try:\\n # extract log file (and relevant directory)\\n data_tar.extract(calc_log)\\n\\n # convert to ASE/Gaussian format\\n mol = read(calc_log.name)\\n mol.set_calculator(\\n Gaussian(\\n label=calc_log.name.replace('.log','')\\n )\\n )\\n\\n # parse into ML readable format\\n parsed_mol = ase_mol_parse(mol)\\n extended_xyzs.append(parsed_mol)\\n except AttributeError:\\n # if the calculation didn't complete we get an empty dictionary \\n # so we we keep track of these failed calculations with a blank \\n # entry other than mol_id\\n blank_entry = {'mol_id':calc_log.name.replace('.log','')}\\n extended_xyzs.append(blank_entry)\\n finally:\\n # delete extracted log file\\n os.remove(calc_log.name)\\n\\n # solves memory problem\\n # http://blogs.it.ox.ac.uk/inapickle/2011/06/20/high-memory-usage-when-using-pythons-tarfile-module/ # noqa\\n data_tar.members=[]\\n \\n dir_name = tar_bz_f.replace('.tar.bz2','')\\n\\n # delete extracted directory\\n os.rmdir(dir_name)\\n\\n # search key function\\n # assumes files are named xxx_frame_{frame}_mol_{no}\\n def mol_no_frame(mol):\\n mol_no = int(mol['mol_id'].split('_')[-1].replace('.log',''))\\n mol_frame = int(mol['mol_id'].split('_')[-3])\\n return mol_no,mol_frame\\n\\n extended_xyzs = sorted(extended_xyzs,key=mol_no_frame)\\n\\n with open(dir_name + '_' + calc_type + '_data.pkl', 'w') as data_f:\\n dill.dump(extended_xyzs, data_f)\",\n \"def debianize( strFilename ):\\n \\n #~ data = gzip.GzipFile( strFilename ).read();\\n #~ print data;\\n #~ return;\\n \\n #~ data = gzip.open( strFilename ).read();\\n #~ print data;\\n #~ return; \\n \\n #~ uncompressedData = bz2.BZ2File(strFilename).read()\\n #~ print str(uncompressedData)\\n #~ return;\\n \\n #~ file = open( strFilename, 'rb' );\\n #~ data = file.read();\\n #~ file.close();\\n #~ print debug.dumpHexa( data );\\n \\n #~ ar = tarfile.open(strFilename, 'r:*')\\n #~ for item in ar:\\n #~ print( str(item) );\\n #~ print( \\\"%s:\\\" % item.name );\\n #~ #print debug.dumpHexa(item.buf);\\n #~ #print zlib.decompress(item.buf)\\n #~ #print zlib.decompress(ar.extractfile(item).read())\\n #~ data = ar.extractfile(item.name).read()\\n #~ print data # works !\\n #~ ar.close() \\n #~ return;\\n \\n fileLists = [];\\n file = open( strFilename );\\n data = file.read();\\n file.close();\\n \\n print( \\\"data len: %d\\\" % len( data ) );\\n\\n nDataCompressedOffset = 0; # 132\\n\\n # works fine on toto.gz\\n #~ f = gzip.open(strFilename, 'rb')\\n #~ file_content = f.read()\\n #~ print file_content\\n #~ f.close() \\n \\n #~ decompressor = bz2.BZ2Decompressor();\\n #~ uncompressed = decompressor.decompress(data[nDataCompressedOffset:]);\\n \\n #~ uncompressed = zlib.decompress(data[nDataCompressedOffset:]);\\n \\n uncompressed = decompress( data );\\n print( \\\"uncompressed: %s\\\" % str( uncompressed ) );\",\n \"def unpack_landsat(inpath, outpath, bands=None, clouds=None):\\r\\n tfile = tarfile.open(inpath,'r:gz')\\r\\n if bands is None:\\r\\n #Extract all of the bands.\\r\\n tfile.extractall(outpath);\\r\\n else:\\r\\n #Extract just the bands specified.\\r\\n\\r\\n #Get the names of the members of the archive\\r\\n names = tfile.getnames()\\r\\n\\r\\n #Make sure the bands are given as a list\\r\\n bands = list(bands)\\r\\n\\r\\n #Find those elements of the archive that match the bands specified\\r\\n #\\t(plus metadata file)\\r\\n members = tfile.getmembers()\\r\\n elements = []\\r\\n blist = ''.join(str(i) for i in bands)\\r\\n if clouds:\\r\\n patternStr = '.*_B[' + blist + ']\\\\.TIF|.*_MTL.txt|.*_band[' + blist + \\\\\\r\\n ']\\\\.tif|.*_cfmask.*\\\\.tif|.*\\\\.xml|.*cloud.*\\\\.tif'\\r\\n else:\\r\\n patternStr = '.*_B[' + blist + ']\\\\.TIF|.*_MTL.txt|.*_band[' + blist + \\\\\\r\\n ']\\\\.tif|.*_cfmask.*\\\\.tif|.*\\\\.xml'\\r\\n\\r\\n pattern = re.compile(patternStr)\\r\\n for i, name in enumerate(names):\\r\\n if pattern.match(name):\\r\\n elements.append(members[i])\\r\\n tfile.extractall(outpath,members = elements)\\r\\n\\r\\n '''\\r\\n Note: the below section was written with the intention of\\r\\n adding valuable metadata info to the .TIF files themselves.\\r\\n This theoretically allows easy retreival of key metadata info,\\r\\n but the method to set new metadata seems unreliable. Appears to\\r\\n be an open issue, but there may be a solution. For now, assume\\r\\n this does not work.\\r\\n\\r\\n #Now we loop through each output, adding important metadata.\\r\\n #Fetch metadata and make sure there is only one file.\\r\\n meta = glob.glob(outpath + '/*_MTL.txt')\\r\\n if len(meta) > 1:\\r\\n raise('MORE THAN ONE METADATA FILE FOUND!')\\r\\n\\r\\n metadata = read_metadata(meta[0])\\r\\n\\r\\n #Add the metadata.\\r\\n for tif in glob.glob(outpath + '*.TIF'):\\r\\n #Open the tif file\\r\\n ras = gdal.Open(tif)\\r\\n\\r\\n #Preserve any existing metadata & add important metadata from file\\r\\n meta = ras.GetMetadata()\\r\\n meta['SCENE_CENTER_TIME'] = metadata['SCENE_CENTER_TIME']\\r\\n meta['DATE_ACQUIRED'] = metadata['DATE_ACQUIRED']\\r\\n meta['LANDSAT_SCENE_ID'] = metadata['LANDSAT_SCENE_ID']\\r\\n\\r\\n #Now write the new metadata back to the tif.\\r\\n ras.SetMetadata(meta)\\r\\n ras.FlushCache()\\r\\n ras = None\\r\\n '''\",\n \"def iterator(dataset_fn, sections=None, lang=None, field_indices=None):\\n files = filelist(lang=lang, sections=sections)\\n\\n with TarFile.open(dataset_fn, 'r:gz') as f:\\n for member in f:\\n if member.isfile() and os.path.basename(member.name) in files:\\n logging.info('parsing %s ...' % member.name)\\n m_f = f.extractfile(member)\\n\\n for sentence in parse_conll(m_f, field_indices=field_indices):\\n yield sentence\\n\\n m_f.close()\",\n \"def _unpack_tar(self, dir, filters):\\n try:\\n unpackArchive = gbpc.UnpackTarArchive(self.path, dir, filters)\\n unpackArchive()\\n except gbpc.CommandExecFailed:\\n # unpackArchive already printed an error message\\n raise GbpError\",\n \"def yield_publications_metadata(tf):\\n logger.info('Start yielding...')\\n with gzip.GzipFile(fileobj=tf, mode='r') as json_file:\\n for index, line in enumerate(json_file):\\n yield build_es_bulk(line.decode('utf-8'))\",\n \"def create_tarballs_from_xml_files_in_folder(xml_dir, download_date=\\\"2017.11.02\\\"):\\n\\n xml_list = glob.glob(os.path.join(xml_dir, \\\"*.xml\\\"))\\n\\n for xml in xml_list:\\n xml_renamed = xml[:-4] + \\\".BLAST.xml\\\"\\n xml_tar_gz = xml[:-4] + \\\".BLAST.xml.tar.gz\\\"\\n xml_txt = xml[:-4] + \\\"_details.txt\\\"\\n # xml_txt = xml[:-4] + \\\".BLAST_details.txt\\\"\\n\\n if not os.path.isfile(xml_tar_gz):\\n copyfile(xml, xml_renamed)\\n acc = os.path.basename(xml).split(\\\".\\\")[0]\\n sys.stdout.write(\\\"{}, \\\".format(acc))\\n sys.stdout.flush()\\n # create an empty text file with the download date\\n date = strftime(\\\"%Y%m%d\\\")\\n with open(xml_txt, \\\"w\\\") as f:\\n f.write(\\\"acc\\\\t{}\\\\ndownload_date\\\\t{}\\\\ndatabase\\\\tncbi_nr\\\\ne_value\\\\t1\\\\n\\\".format(acc, download_date))\\n\\n with tarfile.open(xml_tar_gz, mode='w:gz') as tar:\\n # add the files to the compressed tarfile\\n tar.add(xml_renamed, arcname=os.path.basename(xml_renamed))\\n tar.add(xml_txt, arcname=os.path.basename(xml_txt))\\n\\n # delete the original files\\n try:\\n os.remove(xml_renamed)\\n os.remove(xml_txt)\\n except:\\n sys.stdout.write(\\\"{} could not be deleted\\\".format(xml_renamed))\",\n \"def _extract_data(inputs):\\n filename, split = inputs\\n for name, fobj in tfds.download.iter_archive(\\n filename, tfds.download.ExtractMethod.TAR_STREAM\\n ):\\n split_name = name.split(\\\"_\\\")\\n if len(split_name) > 2 and split_name[2] == split:\\n yield [name, fobj.read()]\",\n \"def untgz(tgz_filename, out_dir):\\r\\n logging.info(\\\"Source: %s\\\" % tgz_filename)\\r\\n tgz = TgzHelper(tgz_filename, out_dir)\\r\\n tgz.extract()\",\n \"def _read_recs(basedir):\\n for borotag in boro_tags:\\n datafile = \\\"%s/%s.csv\\\" % (basedir,borotag)\\n print(\\\"slurp '%s' ..\\\" % datafile)\\n recs = read_recs(datafile)\\n yield from (pluto.parse.normalize(r) for r in recs)\",\n \"def gzip_files(topDir, afni_file,localizerfile):\\n\\n print 'GZIPPING FILES...'\\n\\n command1 = \\\"gzip %s*BRIK\\\" % (topDir)\\n command2 = \\\"gzip %s*HEAD\\\" % (topDir)\\n command3 = \\\"gzip %s%s/pb00*\\\" % (topDir,afni_file)\\n command4 = \\\"gzip %s%s/errts*\\\" % (topDir,afni_file)\\n command5 = \\\"gzip %s%s/fitts*\\\" % (topDir,afni_file)\\n command6 = \\\"gzip %s%s/*al*\\\" % (topDir,afni_file)\\n command7 = \\\"gzip %s%s/*ns*\\\" % (topDir,afni_file)\\n command8 = \\\"gzip %s%s/all_runs*\\\" % (topDir,afni_file)\\n command9 = \\\"gzip %s%s/*mask*\\\" % (topDir,afni_file)\\n command10 = \\\"gzip %s*nii\\\" % (topDir)\\n command11 = \\\"gzip %s%s/pb01*\\\" % (topDir,afni_file)\\n command12 = \\\"gzip %s%s/pb03*\\\" % (topDir,afni_file)\\n command13 = \\\"gzip %s%s/pb02*\\\" % (topDir,afni_file)\\n\\n os.system(command1)\\n os.system(command2)\\n os.system(command3)\\n os.system(command4)\\n os.system(command5)\\n os.system(command6)\\n os.system(command7)\\n os.system(command8)\\n #os.system(command9)\\n os.system(command10)\\n os.system(command11)\\n try:\\n os.system(command12)\\n except:\\n print 'Could not gzip pb03 files'\\n\\n if localizerfile == 'facescene_loc':\\n os.system(command13)\",\n \"def bags(fondz_dir):\\n fondz_dir = os.path.abspath(fondz_dir)\\n results = {\\n 'bags': [],\\n 'num_files': 0,\\n 'bytes': 0\\n }\\n originals_dir = os.path.join(fondz_dir, \\\"originals\\\")\\n\\n for bag in os.listdir(originals_dir):\\n # TODO: look for other manifest types?\\n bag_dir = os.path.join(originals_dir, bag)\\n manifest = os.path.join(bag_dir, \\\"manifest-md5.txt\\\")\\n b = {\\n \\\"files\\\": [],\\n \\\"bytes\\\": 0,\\n }\\n for line in open(manifest):\\n line = line.strip()\\n cols = re.split(r' +', line)\\n path = os.path.join(bag_dir, cols[1])\\n st = os.stat(path)\\n rel_path = os.path.join(\\\"originals\\\", bag, path)\\n b['bytes'] += st.st_size\\n b['files'].append({\\n \\\"path\\\": rel_path,\\n \\\"bytes\\\": st.st_size,\\n \\\"created\\\": st.st_ctime,\\n \\\"modified\\\": st.st_mtime,\\n \\\"md5\\\": cols[0]\\n })\\n results['bytes'] += b['bytes']\\n results['num_files'] += len(b['files'])\\n results['bags'].append(b)\\n\\n bags_json = os.path.join(fondz_dir, \\\"js\\\", \\\"bags.json\\\")\\n write_json(results, bags_json)\\n return results\",\n \"def clean_gzip():\\n this_dir = os.getcwd()\\n os.chdir(\\\"/data/COHERENT2/data/CrystalChar/raw\\\")\\n all_files = glob.glob(\\\"./**\\\", recursive=True)\\n for f in all_files:\\n if \\\".gz\\\" in f and \\\"tar\\\" not in f:\\n print(f)\\n sh(\\\"gunzip \\\" + f)\\n os.chdir(this_dir)\",\n \"def main(args):\\n # Extract keys\\n logger.info(\\\"Extracting brass bedpe file key from tarfile...\\\")\\n bedpe, bedpe_index = extract_tar_keys(args.results_archive)\\n # process bedpe\\n logger.info(\\\"Processing brass bedpe {0}...\\\".format(bedpe))\\n process_bedpe(args.results_archive, bedpe, bedpe_index, args.output_prefix)\",\n \"def _decompress_tarball(*, in_fileobj, out_fileobj):\\n with tarfile.open(fileobj=in_fileobj, mode=\\\"r\\\") as it, tarfile.open(\\n fileobj=out_fileobj, mode=\\\"w|\\\"\\n ) as ot:\\n for member in it.getmembers():\\n extracted = it.extractfile(member)\\n ot.addfile(member, extracted)\",\n \"def parse(self, filename: str, input_format='csv', **kwargs):\\n if 'delimiter' not in kwargs:\\n kwargs['delimiter'] = self._extention_types[input_format]\\n if filename.endswith('.tar'):\\n with tarfile.open(filename) as tar:\\n for member in tar.getmembers():\\n f = tar.extractfile(member)\\n df = pd.read_csv(f, comment='#', **kwargs) # type: pd.DataFrame\\n if member.name == 'nodes.csv':\\n self.load_nodes(df)\\n elif member.name == 'edges.csv':\\n self.load_edges(df)\\n else:\\n raise Exception('Tar file contains unrecognized member {}'.format(member.name))\\n else:\\n df = pd.read_csv(filename, comment='#', **kwargs) # type: pd.DataFrame\\n self.load(df)\",\n \"def gbk_parse(fname):\\n fhand = _open_file(gbkfname)\\n unk = 1 \\n\\n for record in SeqIO.parse(fhand, \\\"genbank\\\"):\\n\\n gene_tags = dict()\\n tx_tags = collections.defaultdict(list) \\n exon = collections.defaultdict(list) \\n cds = collections.defaultdict(list) \\n mol_type, chr_id = None, None \\n\\n for rec in record.features:\\n\\n if rec.type == 'source':\\n mol_type = rec.qualifiers['mol_type'][0]\\n try:\\n chr_id = rec.qualifiers['chromosome'][0]\\n except:\\n chr_id = record.name \\n continue \\n\\n strand='-'\\n strand='+' if rec.strand>0 else strand\\n \\n fid = None \\n try:\\n fid = rec.qualifiers['gene'][0]\\n except:\\n pass\\n\\n transcript_id = None\\n try:\\n transcript_id = rec.qualifiers['transcript_id'][0]\\n except:\\n pass \\n\\n if re.search(r'gene', rec.type):\\n gene_tags[fid] = (rec.location._start.position+1, \\n rec.location._end.position, \\n strand,\\n rec.type,\\n rec.qualifiers['note'][0])\\n elif rec.type == 'exon':\\n exon[fid].append((rec.location._start.position+1, \\n rec.location._end.position))\\n elif rec.type=='CDS':\\n cds[fid].append((rec.location._start.position+1, \\n rec.location._end.position))\\n else: \\n # get all transcripts \\n if transcript_id: \\n tx_tags[fid].append((rec.location._start.position+1,\\n rec.location._end.position, \\n transcript_id,\\n rec.type))\\n # record extracted, generate feature table\\n unk = feature_table(chr_id, mol_type, strand, gene_tags, tx_tags, cds, exon, unk)\\n \\n #break\\n fhand.close()\",\n \"def _unpack_archive(self, dir, filters):\\n ext = os.path.splitext(self.path)[1]\\n if ext in [\\\".zip\\\", \\\".xpi\\\"]:\\n if filters:\\n raise GbpError(\\\"Can only filter tar archives: %s\\\", (ext, self.path))\\n self._unpack_zip(dir)\\n else:\\n self._unpack_tar(dir, filters)\",\n \"def main():\\r\\n parser = CommonArgParser(__file__)\\r\\n parser.add_argument('src_dir', help='Source directory')\\r\\n parser.add_argument(\\r\\n 'out_dir',\\r\\n default='.',\\r\\n help=\\\"\\\"\\\"The directory the files to be extracted.\\r\\n (Default: Current directoty\\\"\\\"\\\")\\r\\n args = parser.parse_all()\\r\\n for f in next_file(args.src_dir, ['*.tgz', '*.tar.gz']):\\r\\n untgz(f, args.out_dir)\",\n \"def read_gz(images,labels):\\n\\t# Open the images with gzip in read binary mode\\n\\t# images = gzip.open('../MNIST-data/train-images-idx3-ubyte.gz', 'rb')\\n\\t# labels = gzip.open('../MNIST-data/train-labels-idx1-ubyte.gz', 'rb')\\n\\n\\t# Read the binary data\\n\\n\\t# We have to get big endian unsigned int. So we need '>I'\\n\\n\\t# Get metadata for images\\n\\timages.read(4) # skip the magic_number\\n\\tnumber_of_images = images.read(4)\\n\\tnumber_of_images = unpack('>I', number_of_images)[0]\\n\\trows = images.read(4)\\n\\trows = unpack('>I', rows)[0]#28\\n\\tcols = images.read(4)\\n\\tcols = unpack('>I', cols)[0]#28\\n\\n\\t# Get metadata for labels\\n\\tlabels.read(4) # skip the magic_number\\n\\tN = labels.read(4)\\n\\tN = unpack('>I', N)[0] #60000\\n\\t# print(number_of_images);\\n\\n\\tif number_of_images != N:\\n\\t raise Exception('number of labels did not match the number of images')\\n\\n\\t# Get the data\\n\\tx = zeros((N, rows, cols), dtype=float32) # Initialize numpy array #60000X28X28\\n\\ty = zeros((N, 1), dtype=uint8) # Initialize numpy array\\n\\tfor i in range(N):\\n\\t if i % 1000 == 0:\\n\\t print(\\\"i: %i\\\" % i)\\n\\t for row in range(rows):\\n\\t for col in range(cols):\\n\\t tmp_pixel = images.read(1) # Just a single byte\\n\\t tmp_pixel = unpack('>B', tmp_pixel)[0]\\n\\t x[i][row][col] = tmp_pixel\\n\\t tmp_label = labels.read(1)\\n\\t y[i] = unpack('>B', tmp_label)[0]\\n\\t # print(y.shape)#60000X1\\n\\treturn (x, y)\",\n \"def parse(self, *args, **kwargs):\\n if self.is_gzipped:\\n fin = gzip.open(self.path, 'rb')\\n else:\\n fin = open(self.path, 'r')\\n line_num = 0\\n expect_header = True\\n for line in fin:\\n line_num += 1\\n line = line.strip()\\n if not line: # skip empty lines\\n continue\\n if expect_header:\\n if self._is_header(line):\\n logger.debug(\\n f\\\"Detected header at line {line_num}: {line!r}\\\")\\n continue\\n else:\\n expect_header = False\\n try:\\n chrom, pos = self._parse_line(line, *args, **kwargs)\\n if chrom is not None:\\n yield chrom, pos\\n except (IndexError, ValueError, TypeError):\\n fin.close()\\n raise FileFormatError(format=self.format, line_num=line_num,\\n line=line)\\n fin.close()\",\n \"def extract_tars(file_pattern, path_in, path_out):\\n for f in glob.glob(os.path.join(path_in, file_pattern)):\\n shutil.unpack_archive(f, path_out)\",\n \"def parse_records(self):\\n for record in sp.parse(gzip.open(\\n \\\"./human_uniprot_04_07_20.gz\\\", 'rt')):\\n # print(record.taxonomy_id)\\n # if record.organism != \\\"Homo sapiens\\\":\\n # continue\\n # print(record.features[0])\\n # for comment in record.comments:\\n # if comment.startswith(\\\"SUBCELLULAR LOCATION\\\"):\\n # print(comment)\\n self.extract_features_to_dict(record)\\n self.extract_localization(record)\",\n \"def parse_file(path):\\n if sys.platform.startswith('linux') or sys.platform.startswith('cygwin'):\\n # Assume Linux has GNU objdump. This has the options:\\n # -t (list symbols), -C (de-mangle symbol names)\\n objdump_args = ['objdump', '-t', '-C']\\n elif sys.platform.startswith('darwin'):\\n # Assume OSX has LLVM objdump. This has the options:\\n # -t (list symbols)\\n objdump_args = ['objdump', '-t']\\n objdump_args.append(path)\\n with StreamingProcess(objdump_args) as proc:\\n # Find the first non-blank line.\\n first_line = proc.peek()\\n while not first_line:\\n try:\\n proc.next()\\n first_line = proc.peek()\\n except StopIteration:\\n return []\\n # Is this an archive?\\n match = re.match(r'^.*[Aa]rchive\\\\s+(.+):$', first_line)\\n if match:\\n # In this format we have to skip this descriptive line.\\n proc.next()\\n return parse_archive(match.group(1), proc)\\n # Some objdumps format archives differently.\\n match = re.match(r'^(.+)\\\\((.+)\\\\):\\\\s+file format', first_line)\\n if match:\\n return parse_archive(match.group(1), proc)\\n # Otherwise maybe it's an object file?\\n match = re.match(r'^(.+):\\\\s+file format', first_line)\\n if match:\\n return [parse_object_file(match.group(1), proc)]\\n # Otherwise it's not an archive or object file.\\n return []\",\n \"def extract_and_tag_test():\\n test_untagged_path = os.getcwd() + \\\"/data/test/test_untagged/\\\"\\n test_untagged_directory = os.fsencode(test_untagged_path)\\n\\n print(\\\"Tagging text. Please wait...\\\")\\n for file in os.listdir(test_untagged_directory):\\n filename = os.fsdecode(file)\\n try:\\n if filename.endswith(\\\".txt\\\"):\\n text = entity_process.read_data(test_untagged_path, file)\\n text = text.lower()\\n header,body = entity_process.split_text(text)\\n header_array = header.splitlines()\\n\\n\\n start_time, end_time = entity_process.extract_time(header)\\n location = entity_process.extract_location(header_array, body)\\n speaker = entity_process.extract_speaker(header_array, body)\\n\\n entity_tagger.tag_all(filename, text, start_time, end_time, location, speaker)\\n except Exception as e:\\n raise e\\n return \\\"No files found here!\\\"\\n print(\\\"Tagging complete! Text saved to\\\" + os.getcwd() + \\\"/out\\\")\",\n \"def parse_ensembl_genes(lines):\\n LOG.info(\\\"Parsing ensembl genes from file\\\")\\n header = []\\n for index, line in enumerate(lines):\\n # File allways start with a header line\\n if index == 0:\\n header = line.rstrip().split(\\\"\\\\t\\\")\\n continue\\n # After that each line represents a gene\\n\\n yield parse_ensembl_line(line, header)\",\n \"def parse(fcontents, utf16=False): # TODO where does this conversion take place??\\n if utf16:\\n # Handle a bunch of Unicode nonsense; files appear to be in UTF-16LE\\n quant_results = fcontents.split(BLOCK_DIVIDER_UTF16)[3]\\\\\\n .decode(AWKWARD_ENCODING).encode('ascii', 'ignore').split(\\\"\\\\r\\\\n\\\")\\n else:\\n quant_results = fcontents.split(BLOCK_DIVIDER)[3].split(\\\"\\\\r\\\\n\\\")\\n\\n for res in quant_results:\\n items = res.split(\\\"\\\\t\\\")\\n if re.search(\\\"\\\\d+\\\", items[0]): # ignore non-digit rows\\n amt = items[9]\\n if amt == OUTSIDE_LADDER:\\n amt = 100\\n yield (int(items[0]), items[1], float(amt))\",\n \"def parse_shard(shard_path):\\n with tf.io.gfile.GFile(shard_path, 'rb') as f:\\n with gzip.GzipFile(fileobj=f, mode='rb') as f_gz:\\n for line in f_gz: # Line-by-line.\\n yield deserialize_inference_result(line)\",\n \"def read_and_parse(path_pattern, parser, **kwargs):\\n for filename in glob.glob(path_pattern):\\n with open(filename, 'r') as file:\\n yield filename, parser.parse(file.read(), **kwargs)\",\n \"def run(self):\\n lineage_csv_gz = self.input_files_local[0][0]\\n output_db = self.output_files_local()[0]\\n log.write(f\\\"input: {lineage_csv_gz} output: {output_db}\\\")\\n\\n with IdSeqDictForUpdate(output_db, IdSeqDictValue.VALUE_TYPE_ARRAY) as lineage_dict:\\n batch_list = {}\\n with gzip.open(lineage_csv_gz, \\\"rt\\\") as gzf:\\n for line in gzf:\\n fields = line.rstrip().split(\\\",\\\")\\n taxid = fields[0]\\n species, genus, family = fields[-1:-4:-1]\\n batch_list[taxid] = [species, genus, family]\\n if len(batch_list) >= BATCH_INSERT_SIZE:\\n lineage_dict.batch_inserts(batch_list.items())\\n batch_list = {}\\n lineage_dict.batch_inserts(batch_list.items())\",\n \"def process_lines(self):\\n\\n for line in self.all_lines:\\n container_re = re.compile(r'(.*?) bags')\\n bags_re = re.compile(r'(?:(\\\\d+)|no other) (.*?) bags*')\\n container_name = re.match(container_re, line).group(1)\\n bags = re.findall(bags_re, line)\\n self.all_bags[container_name] = bags\",\n \"def parse_ensembl_transcripts(lines):\\n header = []\\n LOG.info(\\\"Parsing ensembl transcripts from file\\\")\\n for index, line in enumerate(lines):\\n # File allways start with a header line\\n if index == 0:\\n header = line.rstrip().split(\\\"\\\\t\\\")\\n # After that each line represents a transcript\\n else:\\n yield parse_ensembl_line(line, header)\",\n \"def gunzip_file(gz_path, new_path):\\n print(\\\"Unpacking %s to %s\\\" % (gz_path, new_path))\\n with gzip.open(gz_path, \\\"rb\\\") as gz_file:\\n with open(new_path, \\\"wb\\\") as new_file:\\n for line in gz_file:\\n new_file.write(line)\",\n \"def czgenerator(cols, db):\\n\\n\\tcfh = []\\n\\tif not cols:\\n\\t\\tcols = czcols(db)\\n\\tfor col in cols:\\n\\t\\tcolfile = db + \\\"/\\\" + col + \\\".gz\\\"\\n\\t\\tcfh.append(gzip.GzipFile(colfile))\\n\\tfor line in cfh[0]:\\n\\t\\tv = [line.strip()] + [c.readline().strip() for c in cfh[1:]]\\n\\t\\tyield v\",\n \"def _add_tag_files(\\n zip_file, dir_name, payload_info_list, payload_byte_count, payload_file_count\\n):\\n tag_info_list = []\\n _add_tag_file(zip_file, dir_name, tag_info_list, _gen_bagit_text_file_tup())\\n _add_tag_file(\\n zip_file,\\n dir_name,\\n tag_info_list,\\n _gen_bag_info_file_tup(payload_byte_count, payload_file_count),\\n )\\n _add_tag_file(\\n zip_file, dir_name, tag_info_list, _gen_pid_mapping_file_tup(payload_info_list)\\n )\\n return tag_info_list\",\n \"def parse_input():\\n with open(\\\"input_07.txt\\\", \\\"r\\\") as f:\\n for line in f:\\n Bag(line)\",\n \"def gunzip_file(gz_path, new_path):\\n print(\\\"Unpacking %s to %s\\\" % (gz_path, new_path))\\n with gzip.open(gz_path, \\\"rb\\\") as gz_file:\\n with open(new_path, \\\"wb\\\") as new_file:\\n for line in gz_file:\\n new_file.write(line)\",\n \"def parse(self):\\n gen = self.v6_gen() # read from workers\\n gen = self.tuple_gen(gen) # convert v6->tuple\\n gen = self.batch_gen(gen) # assemble into batches\\n for b in gen:\\n yield b\",\n \"def parseDec_GZIPLoader(self, data): # Once gziploader is decrypted, parse the 0xA9 byte config\\n hardcoded_val = data[0:1]\\n flag = data[1:2]\\n datfile_size = int.from_bytes(data[2:6], byteorder=\\\"little\\\")\\n print(\\\"[+] datfile size: \\\", datfile_size)\\n dllfile_size = int.from_bytes(data[6:10], byteorder=\\\"little\\\")\\n print(\\\"[+] dllfile size: \\\", dllfile_size)\\n dirname = self.extractStrFromBuff(data[10:])\\n print(\\\"[+] Directory Name:\\\", dirname)\\n\\n count = self.incNulls(data[10 + len(dirname):])\\n datname = self.extractStrFromBuff(data[count + 10 + len(dirname):])\\n print(\\\"[+] Dat Name :\\\", datname)\\n\\n count = count + 10 + len(dirname) + len(datname)\\n datname = datname[1:]\\n count2 = self.incNulls(data[count:])\\n count = count + count2\\n dllname = self.extractStrFromBuff(data[count:])\\n print(\\\"[+] Dll Name: \\\", dllname)\\n count += len(dllname)\\n count2 = self.incNulls(data[count:])\\n count += count2\\n # datfile offset is now 710 bytes in\\n datfile_data = data[710:710 + datfile_size]\\n dllfile_start = 710 + datfile_size\\n dllfile_data = data[dllfile_start:dllfile_start + dllfile_size]\\n datfile_b64 = base64.b64encode(datfile_data).decode()\\n dllfile_b64 = base64.b64encode(dllfile_data).decode()\\n ParsedDict = {\\\"Directory_Name\\\": dirname.decode(),\\n \\\"DatFile_Name\\\": datname.decode(),\\n \\\"DllFile_Name\\\": dllname.decode(),\\n \\\"DatFile\\\": datfile_b64,\\n \\\"DllFile\\\": dllfile_b64}\\n\\n return ParsedDict\",\n \"def gunzip_file(gz_path, new_path):\\n print(\\\"Unpacking %s to %s\\\" % (gz_path, new_path))\\n with gzip.open(gz_path, \\\"rb\\\") as gz_file:\\n with open(new_path, \\\"wb\\\") as new_file:\\n for line in gz_file:\\n new_file.write(line)\",\n \"def parse_directory(input_dir, start_date = datetime(1970,1,1), end_date = datetime(9999,12,31,23,59,59)):\\n logging.debug(\\\"Beginning parse_directory {}\\\".format(input_dir))\\n\\n def parse_gzipped_directory(input_dir, start_date, end_date, infos, backup_stamps):\\n \\\"\\\"\\\" Scans a gzipped directory. This one in different situation \\\"\\\"\\\"\\n try:\\n file_names = sorted(os.listdir(input_dir)) \\n for file_name in file_names:\\n if file_name.endswith(\\\".manifest.gz\\\") or file_name.endswith(\\\".manifest\\\"):\\n tmp = parse_file(input_dir + \\\"/\\\" + file_name, start_date, end_date, backup_stamps)\\n backup_stamps[tmp[\\\"backup_label\\\"]] = tmp[\\\"backup_timestamp_stop_ts\\\"]\\n if tmp:\\n infos.append(tmp)\\n except OSError as e:\\n logging.error(\\\"Failed to open directory\\\", exc_info=True)\\n exit(1)\\n except:\\n raise\\n \\n if not path.isdir(input_dir):\\n logging.error(\\\"The specified path is not a directory\\\")\\n exit(1)\\n\\n infos = []\\n backup_stamps = {}\\n if path.exists(input_dir + \\\"/backup.info\\\"):\\n\\n dir_names = sorted(os.listdir(input_dir + \\\"/backup.history\\\"))\\n for dir_name in dir_names:\\n parse_gzipped_directory(input_dir + \\\"/backup.history/\\\" + dir_name, start_date, end_date, infos, backup_stamps)\\n\\n else:\\n parse_gzipped_directory(input_dir, start_date, end_date, infos, backup_stamps)\\n \\n logging.debug(\\\"End parse_directory\\\")\\n return infos\",\n \"def unpack(file, path='.'):\\n assert isfile(file)\\n assert isdir(path)\\n\\n for implementor in [GzipTarredFile, ZippedFile, Bzip2TarredFile]:\\n if implementor.is_valid(file):\\n with console.cd(path):\\n return [implementor(file).extract(), implementor]\\n else:\\n raise InvalidFile, 'compressed file format unknown: %s' % file\",\n \"def gunzip_file(gz_path, new_path):\\n logging.info(\\\"Unpacking %s to %s\\\" % (gz_path, new_path))\\n with gzip.open(gz_path, \\\"rb\\\") as gz_file:\\n with open(new_path, \\\"wb\\\") as new_file:\\n for line in gz_file:\\n new_file.write(line)\",\n \"def convert(src: str, tag: str, size: int = 0, unzip=unzip):\\n t1 = glob.glob(f'{src}/*GG/*/*t1.nii.gz')\\n t2 = glob.glob(f'{src}/*GG/*/*t2.nii.gz')\\n flair = glob.glob(f'{src}/*GG/*/*flair.nii.gz')\\n t1ce = glob.glob(f'{src}/*GG/*/*t1ce.nii.gz')\\n seg = glob.glob(f'{src}/*GG/*/*seg.nii.gz') # Ground Truth\\n pat = re.compile('.*_(\\\\w*)\\\\.nii\\\\.gz')\\n\\n data_paths = [{\\n pat.findall(item)[0]: item\\n for item in items\\n }\\n for items in list(zip(t1, t2, t1ce, flair, seg))]\\n\\n if not size:\\n size = len(data_paths)\\n total = len(data_paths[:size])\\n step = 25 / total\\n\\n for i, imgs in enumerate(data_paths[:size]):\\n try:\\n [unzip(imgs[m], tag) for m in ['t1', 't2', 't1ce', 'flair', 'seg']]\\n print('\\\\r\\\\n' + f'Progress: '\\n f\\\"[{'=' * int((i + 1) * step) + ' ' * (24 - int((i + 1) * step))}]\\\"\\n f\\\"({math.ceil((i + 1) * 100 / (total))} %)\\\" + '\\\\r\\\\n',\\n end=''\\n )\\n except Exception as e:\\n print(f'Something went wrong with {imgs[\\\"t1\\\"]}, skipping...\\\\n Exception:\\\\n{str(e)}')\\n continue\",\n \"def parseGRO(filename):\\n\\tprint(\\\"Cannot parse .gro files yet.\\\")\\n\\texit()\",\n \"def read_files(filenames, gram_size=1):\\n assert isinstance(filenames, list), \\\"filenames argument must be a list\\\"\\n parser = MorParser()\\n for fn in filenames:\\n for uid, speaker, ngram in generate_chunks(parser.parse(fn), gram_size):\\n yield fn, uid, speaker, ngram\",\n \"def parse_file(self, domain_filename,\\n gzip=False,\\n fixed=True, pdf=False, output_path=None, **kargs):\\n valid_file_formats = set(['fasta_style', 'dfam'])\\n assert format in valid_file_formats, '{0} not in {1} valid_file_formats'.format(format, valid_file_formats)\\n\\n if output_path:\\n if not os.path.exists(output_path):\\n os.mkdir(output_path)\\n self.output_path = output_path\\n\\n self.fixed = fixed\\n self.pdf = pdf\\n\\n self.data = []\\n\\n if format == 'fasta_style':\\n self.data = self.__load_fasta_style(filename, gzip)\\n elif format == 'dfam':\\n self.data = self.__load_dfam_style(filename, gzip)\",\n \"def __init__(self, fpath, prefix, suffix, globar_year=None):\\n self.fpath = fpath\\n prefix_len = len(prefix)\\n suffix_len = len(suffix)\\n self.year = globar_year\\n self.year_str = str(globar_year)\\n\\n # filename example : good_2005_0.pgz\\n files = [f for f in listdir(fpath) if isfile(join(fpath, f)) and\\n (f[-suffix_len:] == suffix and f[:prefix_len] == prefix)]\\n\\n pat = '{0}_{1}'.format(prefix, self.year_str)\\n last_batch = \\\\\\n list(sorted(filter(lambda f: pat in f, files)))\\n first_batch = \\\\\\n list(sorted(filter(lambda f: pat not in f, files)))\\n\\n logging.info('in ChunkReader.__init__() : '\\n '(last_batch) {0} files : {1}'.format(len(last_batch), ' '.join(last_batch)))\\n logging.info('in ChunkReader.__init__() : '\\n '(first_batch) {0} files : {1}'.format(len(first_batch), ' '.join(first_batch)))\\n\\n first_batch.extend(last_batch)\\n # queue-like usage\\n self.files = first_batch[::-1]\\n logging.info('in ChunkReader.__init__ : '\\n 'all files {0} files : {1}'.format(len(self.files), ' '.join(self.files)))\",\n \"def parse(all_blobs, all_angles):\",\n \"def scan_corpus(training_corpus_loc):\\n for block_fname in iglob( os.path.join( training_corpus_loc, '*.gz' ) ):\\n print >> sys.stderr, 'processing dir: ' + block_fname\\n with gzip.open( block_fname ) as f:\\n num_lines = 0\\n for line in f:\\n # remember to remove the trailing \\\\n\\n line = line.rstrip()\\n num_lines += 1\\n print >> sys.stderr, 'Number of lines in ' + block_fname + ' is ' + str(num_lines)\",\n \"def parse_gazette(self, response):\\n json_response = response.json()\\n if not json_response:\\n self.logger.warning(f\\\"Document not found in {response.url}\\\")\\n return\\n\\n json_dir = json_response[\\\"dir\\\"]\\n\\n date = re.search(self.DATE_REGEX, json_dir).group()\\n date = parse(date, settings={\\\"DATE_ORDER\\\": \\\"DMY\\\"}).date()\\n is_extra_edition = self.EXTRA_EDITION_TEXT in json_dir\\n path = json_dir.replace(\\\"/\\\", \\\"|\\\")\\n\\n json_data = json_response[\\\"data\\\"]\\n file_urls = [self.PDF_URL.format(path, url.split(\\\"/\\\")[-1]) for url in json_data]\\n\\n yield Gazette(\\n date=date,\\n file_urls=file_urls,\\n is_extra_edition=is_extra_edition,\\n power=\\\"executive_legislative\\\",\\n )\",\n \"def parse(self, limit=None):\\n if limit is not None:\\n logger.info(\\\"Only parsing first %d rows of each file\\\", limit)\\n logger.info(\\\"Parsing files...\\\")\\n\\n if self.testOnly:\\n self.testMode = True\\n\\n # the following will provide us the hash-lookups\\n self._process_dbxref()\\n self._process_cvterm()\\n self._process_genotypes(limit)\\n self._process_pubs(limit)\\n # do this before environments to get the external ids\\n self._process_environment_cvterm()\\n self._process_environments()\\n self._process_organisms(limit) # must be done before features\\n self._process_organism_dbxref(limit)\\n self._process_features(limit)\\n self._process_phenotype(limit)\\n self._process_phenotype_cvterm()\\n # gets external mappings for features (genes, variants, etc)\\n self._process_feature_dbxref(limit)\\n # do this after organisms to get the right taxonomy\\n self._process_stocks(limit)\\n # figures out types of some of the features\\n self._get_derived_feature_types(limit)\\n\\n # These are the associations amongst the objects above\\n self._process_stockprop(limit)\\n self._process_pub_dbxref(limit)\\n self._process_phendesc(limit)\\n self._process_feature_genotype(limit)\\n self._process_feature_pub(limit)\\n self._process_stock_genotype(limit)\\n self._process_phenstatement(limit) # these are G2P associations\\n\\n self._process_feature_relationship(limit)\\n\\n self._process_disease_models(limit)\\n # TODO add version info from file somehow\\n # (in parser rather than during fetching)\\n\\n logger.info(\\\"Finished parsing.\\\")\\n logger.info(\\\"Loaded %d nodes\\\", len(self.graph))\\n return\",\n \"def parse(self, recursive=True):\\n # Read and process the file header\\n self.fh.seek(0x0, 0)\\n header = struct.unpack(\\\"=10I\\\", self.fh.read(0x28))\\n\\n data_start_block = header[0x1]\\n\\n idx_table_entry_count = header[0x4]\\n\\n off_table_offset = header[0x5]\\n off_table_addr = self.IDX_TABLE_ADDR + off_table_offset\\n\\n self.fh.seek(self.IDX_TABLE_ADDR, 0)\\n\\n # Read and populate the index table\\n idx_table = []\\n for idx in range(idx_table_entry_count):\\n typ, num1, num2, num3, num4 = Image.parse_idx_entry(\\n self.fh.read(self.IDX_TABLE_ENTRY_SIZE)\\n )\\n idx_table.append([typ, num1, num2, num3, num4])\\n\\n self.fh.seek(off_table_addr, 0)\\n\\n # FIXME: Not sure what 'unk' is.\\n off_table_entry_count, unk = struct.unpack(\\\"=4x2I\\\", self.fh.read(0xC))\\n\\n # Read and populate the offset table\\n off_table = {}\\n for i in range(off_table_entry_count):\\n idx, blk_num = Image.parse_off_entry(\\n self.fh.read(self.OFF_TABLE_ENTRY_SIZE)\\n )\\n off_table[idx] = blk_num\\n\\n # Populate entries\\n self.entries = []\\n for idx, idx_entry in enumerate(idx_table):\\n if idx not in off_table:\\n self.entries.append(None)\\n continue\\n\\n blk_num = off_table[idx]\\n off = self.fh.tell()\\n\\n # We need to grab the actual (compressed) size from the PACKage header\\n res = None\\n addr = self.BLOCK_NUM_ADDR(blk_num)\\n if idx_entry[0x0] == b\\\"PAK \\\":\\n self.fh.seek(addr)\\n (\\n typ,\\n cnt,\\n ptr_off,\\n str_table_off,\\n dec_data_off,\\n dec_len,\\n cmp_len,\\n pad_len,\\n ) = Package.parse_header(self.fh.read(Package.ENTRY_SIZE))\\n res = Package(FileWindow(self.filename, addr, cmp_len), idx_entry[0x3])\\n else:\\n res = Resource(\\n idx_entry[0x0], FileWindow(self.filename, addr, idx_entry[0x1])\\n )\\n\\n if recursive:\\n res.parse(recursive)\\n self.entries.append(res)\\n self.fh.seek(off, 0)\",\n \"def _parse_tx_infos(self, gtf_path):\\n if os.path.exists('_tx_cache.bin'):\\n with open('_tx_cache.bin', 'rb') as f:\\n return pickle.load(f)\\n result = []\\n with gzip.open(gtf_path, 'rt') as f:\\n for i, line in enumerate(f):\\n if i % 1000 == 0:\\n print('processed {}'.format(i), file=sys.stderr)\\n if line.startswith('#'):\\n continue\\n if line.split('\\\\t', 3)[2] != 'transcript':\\n continue\\n record = GTFFeature.parse(line)\\n if record.feature != 'transcript':\\n continue\\n result.append(\\n TranscriptInfo(record.attrs['gene_id'],\\n record.attrs['transcript_id'],\\n record.attrs['transcript_type'],\\n record.seqname,\\n record.start,\\n record.end))\\n with open('_tx_cache.bin', 'wb') as g:\\n pickle.dump(result, g)\\n print(len(result), file=sys.stderr)\\n return result\",\n \"def batch_tadbit(directory, parser=None, **kwargs):\\n\\n matrix = []\\n for f_name in listdir(directory):\\n if f_name.startswith('.'):\\n continue\\n f_name = path.join(directory, f_name)\\n if parser:\\n matrix.append(parser(f_name))\\n continue\\n elif not path.isfile(f_name):\\n continue\\n matrix.append(f_name)\\n return tadbit(matrix, **kwargs)\",\n \"def untar(conn, tarball, path):\\n conn.run(f\\\"tar xf {tarball} -C {path}\\\")\",\n \"def parse(root_path, output_path, batch_file_paths):\\n for file_path in batch_file_paths:\\n d, f = split_path(file_path, root_path)\\n print(time.ctime(), \\\"d =\\\", d, \\\"; f =\\\", f)\\n if not os.path.exists(os.path.join(OUTPUT_PATH, d)):\\n os.makedirs(os.path.join(OUTPUT_PATH, d))\\n parsed_files = get_parsed_files(output_path, d)\\n if f not in parsed_files:\\n with open(file_path) as json_file:\\n OUTPUT_FILE_PATH = os.path.join(OUTPUT_PATH, d, f)\\n with open(OUTPUT_FILE_PATH, 'w') as writer:\\n for num, line in enumerate(json_file):\\n json_data = json.loads(line)\\n title = json_data['title']\\n if json_data['text']:\\n definition = json_data['text'][0]['line']\\n writer.write(f'{title}\\\\t{definition}\\\\n')\\n else:\\n writer.write(f'{title}\\\\tNone.\\\\n')\",\n \"def create_tar(self):\\n with tarfile.open(self.tgzfile, \\\"w:gz\\\") as tar_handle:\\n for root, _, files in os.walk(self.dirname):\\n for file in files:\\n tar_handle.add(os.path.join(root, file))\",\n \"def tarball(request):\\n\\n patches = (models.Patch\\n .query(ancestor=request.patchset.key)\\n .order(models.Patch.filename)\\n .fetch(1000))\\n\\n temp = tempfile.TemporaryFile()\\n tar = tarfile.open(mode=\\\"w|bz2\\\", fileobj=temp)\\n\\n def add_entry(prefix, content, patch):\\n data = content.data\\n if data is None:\\n data = content.text\\n if isinstance(data, unicode):\\n data = data.encode(\\\"utf-8\\\", \\\"replace\\\")\\n if data is None:\\n return\\n info = tarfile.TarInfo(prefix + patch.filename)\\n info.size = len(data)\\n # TODO(adonovan): set SYMTYPE/0755 when Rietveld supports symlinks.\\n info.type = tarfile.REGTYPE\\n info.mode = 0644\\n # datetime->time_t\\n delta = request.patchset.modified - datetime.datetime(1970, 1, 1)\\n info.mtime = int(delta.days * 86400 + delta.seconds)\\n tar.addfile(info, fileobj=StringIO(data))\\n\\n for patch in patches:\\n if not patch.no_base_file:\\n try:\\n add_entry('a/', patch.get_content(), patch) # before\\n except FetchError: # I/O problem?\\n logging.exception('tarball: patch(%s, %s).get_content failed' %\\n (patch.key.id(), patch.filename))\\n try:\\n add_entry('b/', patch.get_patched_content(), patch) # after\\n except FetchError: # file deletion? I/O problem?\\n logging.exception('tarball: patch(%s, %s).get_patched_content failed' %\\n (patch.key.id(), patch.filename))\\n\\n tar.close()\\n temp.flush()\\n\\n wrapper = FileWrapper(temp)\\n response = HttpResponse(wrapper, mimetype='application/x-gtar')\\n response['Content-Disposition'] = (\\n 'attachment; filename=patch%s_%s.tar.bz2' % (request.issue.key.id(),\\n request.patchset.key.id()))\\n response['Content-Length'] = temp.tell()\\n temp.seek(0)\\n return response\",\n \"def convert(self, tag=\\\"Data\\\", delimiter=\\\",\\\", noheader=False,\\n limit=-1, buffer_size=1000):\\n\\n\\n file_ctr = 0\\n item_ctr = 0\\n for dirName, subdirList, fileList in os.walk(self.input_directory):\\n print('Found directory: %s' % dirName)\\n for fname in fileList:\\n print('\\\\t%s' % fname)\\n # open the xml file for iteration\\n if not fname.endswith(\\\".xml\\\"):\\n continue\\n #pdb.set_trace()\\n \\n input_file = dirName + \\\"/\\\" + fname\\n self.context = ETree.iterparse(input_file, events=(\\\"start\\\", \\\"end\\\"))\\n\\n # iterate through the xml\\n items = [{}]\\n\\n depth = 0\\n min_depth = 0\\n row_depth = -1\\n n = 0\\n for event, elem in self.context:\\n if event == \\\"start\\\":\\n depth += 1\\n continue\\n else:\\n depth -= 1\\n if depth < min_depth:\\n min_depth = depth\\n\\n if depth < row_depth and items:\\n if noheader:\\n noheader = False\\n else:\\n # new line\\n self.output_buffer.append(items)\\n items = []\\n # flush buffer to disk\\n if len(self.output_buffer) > buffer_size:\\n self._write_buffer(delimiter)\\n\\n plain_tag = elem.tag\\n last_delim = max(elem.tag.rfind('}'), elem.tag.rfind(':'))\\n if 0 < last_delim < len(elem.tag) - 1:\\n plain_tag = elem.tag[last_delim + 1:]\\n if tag == plain_tag:\\n if n == 0:\\n min_depth = depth\\n elif n == 1:\\n row_depth = min_depth\\n n += 1\\n if 0 < limit < n:\\n break\\n elem_name = elem.get(\\\"name\\\")\\n if elem_name in self.output_dict[0].keys():\\n if elem_name == 'SamS.ArchivedURL':\\n if hash(elem.text) in self.item_titles.keys() and self.item_titles[hash(elem.text)] == elem.text:\\n #item is repetative\\n self.output_dict[item_ctr]={}\\n #item_ctr-=1\\n break\\n else:\\n self.item_titles[hash(elem.text)] = elem.text\\n self.output_dict[item_ctr][elem_name]= elem.text and elem.text.encode('utf8') or ''\\n\\n #if (len(self.output_dict[item_ctr]) > 0 ) :\\n if ('SamS.ArchivedURL' in self.output_dict[item_ctr]):\\n item_ctr+=1\\n self.output_dict.append({})\\n else:\\n self.output_dict[item_ctr] = {}\\n \\n file_ctr+=1 #next row in the dictionary array\\n print \\\"processing file no \\\", file_ctr, \\\" item no\\\", item_ctr\\n\\n #pdb.set_trace()\\n self._write_buffer(delimiter) # write rest of the buffer to file\\n\\n return n\",\n \"def parse_fasta_file(filename):\\n if filename.endswith('.gz'):\\n opener = lambda filename: gzip.open(filename, 'rt')\\n else:\\n opener = lambda filename: open(filename, 'r')\\n\\n with opener(filename) as f:\\n fasta_iter = (it[1] for it in itertools.groupby(f, is_header))\\n for name in fasta_iter:\\n name = name.__next__()[1:].strip()\\n sequences = ''.join(seq.strip() for seq in fasta_iter.__next__())\\n yield name, sequences\",\n \"def processfile(args, fh):\\n if args.quick:\\n scanner = quickScanZip(args, fh)\\n else:\\n scanner = findPKHeaders(args, fh)\\n\\n def checkarg(arg, ent):\\n if not arg:\\n return False\\n return '*' in arg or ent.name in arg\\n def checkname(a, b):\\n if a and '*' in a: return True\\n if b and '*' in b: return True\\n l = 0\\n if a: l += len(a)\\n if b: l += len(b)\\n return l > 1\\n\\n if args.verbose and not (args.cat or args.raw or args.save):\\n print(\\\" 0304 need flgs mth stamp --crc-- compsize fullsize nlen xlen namofs xofs datofs endofs\\\")\\n print(\\\" 0102 crea need flgs mth stamp --crc-- compsize fullsize nlen xlen clen dsk0 attr osattr datptr namofs xofs cmtofs endofs\\\")\\n for ent in scanner:\\n if args.cat or args.raw or args.save:\\n if args.quick and isinstance(ent, CentralDirEntry) or \\\\\\n not args.quick and isinstance(ent, LocalFileHeader):\\n ent.loaditems(fh)\\n do_cat = checkarg(args.cat, ent)\\n do_raw = checkarg(args.raw, ent)\\n do_save= checkarg(args.save, ent)\\n\\n do_name= checkname(args.cat, args.raw)\\n\\n if do_name:\\n print(\\\"\\\\n===> \\\" + ent.name + \\\" <===\\\\n\\\")\\n\\n sys.stdout.flush()\\n blks = zipraw(fh, ent)\\n\\n if args.password and ent.flags&1:\\n blks = zip_decrypt(blks, args.password)\\n if do_cat or do_save:\\n blks = skipbytes(blks, 12, args)\\n\\n if do_cat:\\n sys.stdout.buffer.writelines(zipcat(blks, ent))\\n if do_raw:\\n sys.stdout.buffer.writelines(blks)\\n if do_save:\\n savefile(args.outputdir, ent.name, zipcat(blks, ent))\\n else:\\n ent.loaditems(fh)\\n if args.verbose or not args.quick:\\n print(\\\"%08x: %s\\\" % (ent.pkOffset, ent))\\n else:\\n print(ent.summary())\\n if hasattr(ent, \\\"comment\\\") and ent.comment and not args.dumpraw:\\n print(ent.comment)\\n if args.dumpraw and hasattr(ent, \\\"extraLength\\\") and ent.extraLength:\\n print(\\\"%08x: XTRA: %s\\\" % (ent.extraOffset, binascii.b2a_hex(getbytes(fh, ent.extraOffset, ent.extraLength))))\\n if args.dumpraw and hasattr(ent, \\\"comment\\\") and ent.comment:\\n print(\\\"%08x: CMT: %s\\\" % (ent.commentOffset, binascii.b2a_hex(getbytes(fh, ent.commentOffset, ent.commentLength))))\\n if args.dumpraw and isinstance(ent, LocalFileHeader):\\n blks = zipraw(fh, ent)\\n if args.password and ent.flags&1:\\n blks = zip_decrypt(blks, args.password)\\n\\n blockdump(ent.dataOffset, blks)\",\n \"def extract_tarball(fileobj, path, callback=None):\\n tar_cmd = [\\\"tar\\\", \\\"-zx\\\", \\\"--directory=%s\\\" % path]\\n tar_proc = make_subprocess(tar_cmd, stderr=True, stdin=True)\\n\\n try:\\n while True:\\n chunk = fileobj.read(CHUNK_SIZE)\\n if chunk == '':\\n break\\n\\n if callback:\\n callback(chunk)\\n\\n tar_proc.stdin.write(chunk)\\n except Exception:\\n try_kill_process(tar_proc)\\n raise\\n\\n finish_subprocess(tar_proc, tar_cmd)\",\n \"def tarball(request):\\n\\n patches = (models.Patch\\n .query(models.Patch.patchset_key == request.patchset.key)\\n .order(models.Patch.filename)\\n .fetch(1000))\\n\\n temp = tempfile.TemporaryFile()\\n tar = tarfile.open(mode=\\\"w|bz2\\\", fileobj=temp)\\n\\n def add_entry(prefix, content):\\n data = content.data\\n if data is None:\\n data = content.text\\n if isinstance(data, unicode):\\n data = data.encode(\\\"utf-8\\\", \\\"replace\\\")\\n if data is None:\\n return\\n info = tarfile.TarInfo(prefix + patch.filename)\\n info.size = len(data)\\n # TODO(adonovan): set SYMTYPE/0755 when Rietveld supports symlinks.\\n info.type = tarfile.REGTYPE\\n info.mode = 0644\\n # datetime->time_t\\n delta = request.patchset.modified - datetime.datetime(1970, 1, 1)\\n info.mtime = int(delta.days * 86400 + delta.seconds)\\n tar.addfile(info, fileobj=StringIO(data))\\n\\n for patch in patches:\\n if not patch.no_base_file:\\n try:\\n add_entry('a/', patch.get_content()) # before\\n except FetchError: # I/O problem?\\n logging.exception('tarball: patch(%s, %s).get_content failed' %\\n (patch.key.id(), patch.filename))\\n try:\\n add_entry('b/', patch.get_patched_content()) # after\\n except FetchError: # file deletion? I/O problem?\\n logging.exception('tarball: patch(%s, %s).get_patched_content failed' %\\n (patch.key.id(), patch.filename))\\n\\n tar.close()\\n temp.flush()\\n\\n wrapper = FileWrapper(temp)\\n response = HttpResponse(wrapper, mimetype='application/x-gtar')\\n response['Content-Disposition'] = (\\n 'attachment; filename=patch%s_%s.tar.bz2' % (request.issue.key.id(),\\n request.patchset.key.id()))\\n response['Content-Length'] = temp.tell()\\n temp.seek(0)\\n return response\",\n \"def open_files(filenames):\\n for filename in filenames:\\n if filename.endswith('.gz') or filename.endswith('.zip'):\\n yield gzip.open(filename, 'r')\\n else:\\n yield open(filename, 'rb')\",\n \"def _compress_meds_file(self, ucfilename, fzfilename):\\n from os.path import basename\\n\\n tup=(basename(ucfilename),basename(fzfilename))\\n print('compressing file: %s -> %s' % tup)\\n tpath=files.expandpath(fzfilename)\\n if os.path.exists(tpath):\\n os.remove(tpath)\\n\\n tmpdir = os.path.dirname(ucfilename)\\n with StagedOutFile(fzfilename,tmpdir=tmpdir) as sf:\\n cmd = self['fpack_command']\\n cmd = cmd.format(fname=ucfilename)\\n ret=os.system(cmd)\\n\\n if ret != 0:\\n raise RuntimeError(\\\"failed to compress file\\\")\\n\\n print('output is in:',fzfilename)\",\n \"def parseGerber(self, fullname, layername, updateExtents = 0):\\n\\n GAT = config.GAT\\n GAMT = config.GAMT\\n # First construct reverse GAT/GAMT, mapping definition to code\\n RevGAT = config.buildRevDict(GAT) # RevGAT[hash] = aperturename\\n RevGAMT = config.buildRevDict(GAMT) # RevGAMT[hash] = aperturemacroname\\n\\n #print 'Reading data from %s ...' % fullname\\n\\n fid = file(fullname, 'rt')\\n currtool = None\\n\\n self.apxlat[layername] = {}\\n self.apmxlat[layername] = {}\\n self.commands[layername] = []\\n self.apertures[layername] = []\\n\\n # These divisors are used to scale (X,Y) co-ordinates. We store\\n # everything as integers in hundred-thousandths of an inch (i.e., M.5\\n # format). If we get something in M.4 format, we must multiply by\\n # 10. If we get something in M.6 format we must divide by 10, etc.\\n x_div = 1.0\\n y_div = 1.0\\n\\n # Drawing commands can be repeated with X or Y omitted if they are\\n # the same as before. These variables store the last X/Y value as\\n # integers in hundred-thousandths of an inch.\\n last_x = last_y = 0\\n\\n # Last modal G-code. Some G-codes introduce \\\"modes\\\", such as circular interpolation\\n # mode, and we want to remember what mode we're in. We're interested in:\\n # G01 -- linear interpolation, cancels all circular interpolation modes\\n # G36 -- Turn on polygon area fill\\n # G37 -- Turn off polygon area fill\\n last_gmode = 1 # G01 by default, linear interpolation\\n\\n # We want to know whether to do signed (G75) or unsigned (G74) I/J offsets. These\\n # modes are independent of G01/G02/G03, e.g., Protel will issue multiple G03/G01\\n # codes all in G75 mode.\\n # G74 -- Single-quadrant circular interpolation (disables multi-quadrant interpolation)\\n # G02/G03 codes set clockwise/counterclockwise arcs in a single quadrant only\\n # using X/Y/I/J commands with UNSIGNED (I,J).\\n # G75 -- Multi-quadrant circular interpolation --> X/Y/I/J with signed (I,J)\\n # G02/G03 codes set clockwise/counterclockwise arcs in all 4 quadrants\\n # using X/Y/I/J commands with SIGNED (I,J).\\n circ_signed = True # Assume G75...make sure this matches canned header we write out\\n\\n # If the very first flash/draw is a shorthand command (i.e., without an Xxxxx or Yxxxx)\\n # component then we don't really \\\"see\\\" the first point X00000Y00000. To account for this\\n # we use the following Boolean flag as well as the isLastShorthand flag during parsing\\n # to manually insert the point X000000Y00000 into the command stream.\\n firstFlash = True\\n\\n for line in fid:\\n # Get rid of CR characters (0x0D) and leading/trailing blanks\\n line = string.replace(line, '\\\\x0D', '').strip()\\n\\n # Old location of format_pat search. Now moved down into the sub-line parse loop below.\\n\\n # RS-274X statement? If so, echo it. Currently, only the \\\"LP\\\" statement is expected\\n # (from Protel, of course). These will be distinguished from D-code and G-code\\n # commands by the fact that the first character of the string is '%'.\\n match = layerpol_pat.match(line)\\n if match:\\n self.commands[layername].append(line)\\n continue\\n \\n # See if this is an aperture definition, and if so, map it.\\n match = apdef_pat.match(line)\\n if match:\\n if currtool:\\n raise RuntimeError, \\\"File %s has an aperture definition that comes after drawing commands.\\\" % fullname\\n\\n A = aptable.parseAperture(line, self.apmxlat[layername])\\n if not A:\\n raise RuntimeError, \\\"Unknown aperture definition in file %s\\\" % fullname\\n\\n hash = A.hash()\\n if not RevGAT.has_key(hash):\\n #print line\\n #print self.apmxlat\\n #print RevGAT\\n raise RuntimeError, 'File %s has aperture definition \\\"%s\\\" not in global aperture table.' % (fullname, hash)\\n\\n # This says that all draw commands with this aperture code will\\n # be replaced by aperture self.apxlat[layername][code].\\n self.apxlat[layername][A.code] = RevGAT[hash]\\n continue\\n\\n # Ignore %AMOC8* from Eagle for now as it uses a macro parameter, which\\n # is not yet supported in GerbMerge.\\n if line[:7]=='%AMOC8*':\\n continue\\n\\n # See if this is an aperture macro definition, and if so, map it.\\n M = amacro.parseApertureMacro(line,fid)\\n if M:\\n if currtool:\\n raise RuntimeError, \\\"File %s has an aperture macro definition that comes after drawing commands.\\\" % fullname\\n\\n hash = M.hash()\\n if not RevGAMT.has_key(hash):\\n raise RuntimeError, 'File %s has aperture macro definition not in global aperture macro table:\\\\n%s' % (fullname, hash)\\n\\n # This says that all aperture definition commands that reference this macro name\\n # will be replaced by aperture macro name self.apmxlat[layername][macroname].\\n self.apmxlat[layername][M.name] = RevGAMT[hash]\\n continue\\n\\n # From this point on we may have more than one match on this line, e.g.:\\n # G54D11*X22400Y22300D02*X22500Y22200D01*\\n sub_line = line\\n while sub_line:\\n # Handle \\\"comment\\\" G-codes first\\n match = comment_pat.match(sub_line)\\n if match:\\n sub_line = sub_line[match.end():]\\n continue\\n\\n # See if this is a format statement, and if so, map it. In version 1.3 this was moved down\\n # from the line-only parse checks above (see comment) to handle OrCAD lines like\\n # G74*%FSLAN2X34Y34*%\\n match = format_pat.match(sub_line) # Used to be format_pat.search\\n if match:\\n sub_line = sub_line[match.end():]\\n for item in match.groups():\\n if item is None: continue # Optional group didn't match\\n\\n if item[0] in \\\"LA\\\": # omit leading zeroes and absolute co-ordinates\\n continue\\n\\n if item[0]=='T': # omit trailing zeroes\\n raise RuntimeError, \\\"Trailing zeroes not supported in RS274X files\\\"\\n if item[0]=='I': # incremental co-ordinates\\n raise RuntimeError, \\\"Incremental co-ordinates not supported in RS274X files\\\"\\n\\n if item[0]=='N': # Maximum digits for N* commands...ignore it\\n continue\\n\\n if item[0]=='X': # M.N specification for X-axis.\\n fracpart = int(item[2])\\n x_div = 10.0**(5-fracpart)\\n if item[0]=='Y': # M.N specification for Y-axis.\\n fracpart = int(item[2])\\n y_div = 10.0**(5-fracpart)\\n continue\\n\\n # Parse and interpret G-codes\\n match = gcode_pat.match(sub_line)\\n if match:\\n sub_line = sub_line[match.end():]\\n gcode = int(match.group(1))\\n\\n # Determine if this is a G-Code that should be ignored because it has no effect\\n # (e.g., G70 specifies \\\"inches\\\" which is already in effect).\\n if gcode in [54, 70, 90]:\\n continue\\n\\n # Determine if this is a G-Code that we have to emit because it matters.\\n if gcode in [1, 2, 3, 36, 37, 74, 75]:\\n self.commands[layername].append(\\\"G%02d\\\" % gcode)\\n\\n # Determine if this is a G-code that sets a new mode\\n if gcode in [1, 36, 37]:\\n last_gmode = gcode\\n\\n # Remember last G74/G75 code so we know whether to do signed or unsigned I/J\\n # offsets.\\n if gcode==74:\\n circ_signed = False\\n elif gcode==75:\\n circ_signed = True\\n \\n continue\\n\\n raise RuntimeError, \\\"G-Code 'G%02d' is not supported\\\" % gcode\\n\\n # See if this is a tool change (aperture change) command\\n match = tool_pat.match(sub_line)\\n if match:\\n currtool = match.group(1)\\n\\n # Protel likes to issue random D01, D02, and D03 commands instead of aperture\\n # codes. We can ignore D01 because it simply means to move to the current location\\n # while drawing. Well, that's drawing a point. We can ignore D02 because it means\\n # to move to the current location without drawing. Truly pointless. We do NOT want\\n # to ignore D03 because it implies a flash. Protel very inefficiently issues a D02\\n # move to a location without drawing, then a single-line D03 to flash. However, a D02\\n # terminates a polygon in G36 mode, so keep D02's in this case.\\n if currtool=='D01' or (currtool=='D02' and (last_gmode != 36)):\\n sub_line = sub_line[match.end():]\\n continue\\n\\n if (currtool == 'D03') or (currtool=='D02' and (last_gmode == 36)):\\n self.commands[layername].append(currtool)\\n sub_line = sub_line[match.end():]\\n continue\\n\\n # Map it using our translation table\\n if not self.apxlat[layername].has_key(currtool):\\n raise RuntimeError, 'File %s has tool change command \\\"%s\\\" with no corresponding translation' % (fullname, currtool)\\n\\n currtool = self.apxlat[layername][currtool]\\n\\n # Add it to the list of things to write out\\n self.commands[layername].append(currtool)\\n\\n # Add it to the list of all apertures needed by this layer\\n self.apertures[layername].append(currtool)\\n\\n # Move on to next match, if any\\n sub_line = sub_line[match.end():]\\n continue\\n\\n # Is it a simple draw command?\\n I = J = None # For circular interpolation drawing commands\\n match = drawXY_pat.match(sub_line)\\n isLastShorthand = False # By default assume we don't make use of last_x and last_y\\n if match:\\n x, y, d = map(__builtin__.int, match.groups())\\n else:\\n match = drawX_pat.match(sub_line)\\n if match:\\n x, d = map(__builtin__.int, match.groups())\\n y = last_y\\n isLastShorthand = True # Indicate we're making use of last_x/last_y\\n else:\\n match = drawY_pat.match(sub_line)\\n if match:\\n y, d = map(__builtin__.int, match.groups())\\n x = last_x\\n isLastShorthand = True # Indicate we're making use of last_x/last_y\\n\\n # Maybe it's a circular interpolation draw command with IJ components\\n if match is None:\\n match = cdrawXY_pat.match(sub_line)\\n if match:\\n x, y, I, J, d = map(__builtin__.int, match.groups())\\n else:\\n match = cdrawX_pat.match(sub_line)\\n if match:\\n x, I, J, d = map(__builtin__.int, match.groups())\\n y = last_y\\n isLastShorthand = True # Indicate we're making use of last_x/last_y\\n else:\\n match = cdrawY_pat.match(sub_line)\\n if match:\\n y, I, J, d = map(__builtin__.int, match.groups())\\n x = last_x\\n isLastShorthand = True # Indicate we're making use of last_x/last_y\\n\\n if match:\\n if currtool is None:\\n # It's OK if this is an exposure-off movement command (specified with D02).\\n # It's also OK if we're in the middle of a G36 polygon fill as we're only defining\\n # the polygon extents.\\n if (d != 2) and (last_gmode != 36):\\n raise RuntimeError, 'File %s has draw command %s with no aperture chosen' % (fullname, sub_line)\\n\\n # Save last_x/y BEFORE scaling to 2.5 format else subsequent single-ordinate\\n # flashes (e.g., Y with no X) will be scaled twice!\\n last_x = x\\n last_y = y\\n\\n # Corner case: if this is the first flash/draw and we are using shorthand (i.e., missing Xxxx\\n # or Yxxxxx) then prepend the point X0000Y0000 into the commands as it is actually the starting\\n # point of our layer. We prepend the command X0000Y0000D02, i.e., a move to (0,0) without drawing.\\n if (isLastShorthand and firstFlash):\\n self.commands[layername].append((0,0,2))\\n if updateExtents:\\n self.minx = min(self.minx,0)\\n self.maxx = max(self.maxx,0)\\n self.miny = min(self.miny,0)\\n self.maxy = max(self.maxy,0)\\n\\n x = int(round(x*x_div))\\n y = int(round(y*y_div))\\n if I is not None:\\n I = int(round(I*x_div))\\n J = int(round(J*y_div))\\n self.commands[layername].append((x,y,I,J,d,circ_signed))\\n else:\\n self.commands[layername].append((x,y,d))\\n firstFlash = False\\n\\n # Update dimensions...this is complicated for circular interpolation commands\\n # that span more than one quadrant. For now, we ignore this problem since users\\n # should be using a border layer to indicate extents.\\n if updateExtents:\\n if x < self.minx: self.minx = x\\n if x > self.maxx: self.maxx = x\\n if y < self.miny: self.miny = y\\n if y > self.maxy: self.maxy = y\\n\\n # Move on to next match, if any\\n sub_line = sub_line[match.end():]\\n continue\\n\\n # If it's none of the above, it had better be on our ignore list.\\n for pat in IgnoreList:\\n match = pat.match(sub_line)\\n if match:\\n break\\n else:\\n raise RuntimeError, 'File %s has uninterpretable line:\\\\n %s' % (fullname, line)\\n\\n sub_line = sub_line[match.end():]\\n # end while still things to match on this line\\n # end of for each line in file\\n\\n fid.close()\\n if 0:\\n print layername\\n print self.commands[layername]\",\n \"def parse(self, f):\\n \\n for line in f:\\n self.parse_line(line)\",\n \"def parse_file(file_name: str, delims='\\\\n', encoding='utf-8', zip_type=None):\\n try:\\n decoder = codecs.getincrementaldecoder(encoding)()\\n except LookupError as e:\\n print(str(e))\\n return\\n\\n read_buffer_size = 10*1024\\n max_line_size = 100*1024\\n\\n if not zip_type:\\n open_f = open\\n elif zip_type == 'gz':\\n open_f = gzip.open\\n else:\\n raise NotImplementedError()\\n\\n with open_f(file_name, 'rb') as fp:\\n buffered_str = ''\\n for bs in iter(partial(fp.read, read_buffer_size), b''):\\n decoded_str = decoder.decode(bs)\\n # FIXME: i don't think current implementation is efficient enough...\\n for c in decoded_str:\\n if c in delims:\\n if len(buffered_str) > 0:\\n yield buffered_str\\n buffered_str = ''\\n else:\\n buffered_str += c\\n if len(buffered_str) >= max_line_size:\\n yield buffered_str\\n buffered_str = ''\\n if len(buffered_str) > 0:\\n yield buffered_str\",\n \"def extractTar(tar_file):\\r\\n\\r\\n tfile = tarfile.open(tar_file, 'r')\\r\\n tar_members = tfile.getmembers()\\r\\n for tar_member in tar_members:\\r\\n tar_member.name = os.path.basename(tar_member.name) # Strip out the path and keep just the file name\\r\\n tfile.extract(tar_member, path=\\\"tempdata/\\\")\\r\\n tfile.close()\\r\\n print \\\"Finished extracting tar file\\\"\\r\\n return\",\n \"def fromgroups(args):\\n from jcvi.formats.bed import Bed\\n\\n p = OptionParser(fromgroups.__doc__)\\n opts, args = p.parse_args(args)\\n\\n if len(args) < 2:\\n sys.exit(not p.print_help())\\n\\n groupsfile = args[0]\\n bedfiles = args[1:]\\n beds = [Bed(x) for x in bedfiles]\\n fp = open(groupsfile)\\n groups = [row.strip().split(\\\",\\\") for row in fp]\\n for b1, b2 in product(beds, repeat=2):\\n extract_pairs(b1, b2, groups)\",\n \"def parse_region_data(self, region):\\r\\n \\r\\n self.download_data()\\r\\n region_filename = self.__get_region_filename(region)\\r\\n list_str = [\\\"region\\\", \\\"p1\\\", \\\"p36\\\", \\\"p37\\\", \\\"p2a\\\", \\\"weekday(p2a)\\\", \\\"p2b\\\", \\\"p6\\\", \\\"p7\\\", \\\"p8\\\", \\\"p9\\\", \\\"p10\\\", \\r\\n \\\"p11\\\", \\\"p12\\\", \\\"p13a\\\", \\\"p13b\\\", \\\"p13c\\\", \\\"p14\\\", \\\"p15\\\", \\\"p16\\\", \\\"p17\\\", \\\"p18\\\",\\\"p19\\\", \\\"p20\\\", \\\"p21\\\", \\r\\n \\\"p22\\\", \\\"p23\\\", \\\"p24\\\", \\\"p27\\\", \\\"p28\\\", \\\"p34\\\", \\\"p35\\\", \\\"p39\\\", \\\"p44\\\", \\\"p45a\\\", \\\"p47\\\", \\\"p48a\\\", \\\"p49\\\", \\r\\n \\\"p50a\\\", \\\"p50b\\\", \\\"p51\\\", \\\"p52\\\", \\\"p53\\\", \\\"p55a\\\", \\\"p57\\\", \\\"p58\\\", \\\"a\\\", \\\"b\\\", \\\"d\\\", \\\"e\\\", \\\"f\\\", \\\"g\\\", \\\"h\\\", \\r\\n \\\"i\\\", \\\"j\\\", \\\"k\\\", \\\"l\\\", \\\"m\\\", \\\"n\\\", \\\"o\\\", \\\"p\\\", \\\"q\\\", \\\"r\\\", \\\"s\\\", \\\"t\\\", \\\"p5a\\\"]\\r\\n \\r\\n row_count = self.__get_files_row_count(region)\\r\\n list_arrays = [np.zeros(row_count, dtype=dt) for dt in self.__types]\\r\\n row_index = 0\\r\\n for file in self.__files:\\r\\n file_to_parse = os.path.join(self.__folder, os.path.basename(file))\\r\\n with zipfile.ZipFile(file_to_parse, \\\"r\\\") as zf:\\r\\n with zf.open(region_filename, 'r') as csv_file:\\r\\n reader = csv.reader(TextIOWrapper(csv_file, 'windows-1250'), delimiter=';', quotechar='\\\"')\\r\\n for row in reader:\\r\\n list_arrays[0][row_index] = region\\r\\n for col_index, col in enumerate(row):\\r\\n try:\\r\\n list_arrays[col_index + 1][row_index] = col\\r\\n except ValueError:\\r\\n if list_arrays[col_index + 1][row_index].dtype == np.int64:\\r\\n list_arrays[col_index + 1][row_index] = -1\\r\\n elif list_arrays[col_index + 1][row_index].dtype == 'datetime64[D]':\\r\\n print('Error2:', col)\\r\\n elif list_arrays[col_index + 1][row_index].dtype == np.float64:\\r\\n if type(col) != str:\\r\\n list_arrays[col_index + 1][row_index] = col.replace(',', '.')\\r\\n else:\\r\\n list_arrays[col_index + 1][row_index] = float(\\\"nan\\\")\\r\\n row_index += 1\\r\\n \\r\\n return (list_str, list_arrays)\",\n \"def parse_fastq(filepath):\\n if REGEX_GZIPPED.match(filepath):\\n logging.debug('Opening \\\"%s\\\" as gzipped file', filepath)\\n # using os.popen with zcat since it is much faster than gzip.open or gzip.open(io.BufferedReader)\\n # http://aripollak.com/pythongzipbenchmarks/\\n # assumes Linux os with zcat installed\\n import os\\n with os.popen('zcat < {}'.format(filepath)) as f:\\n yield from _parse_fastq(f)\\n else:\\n with open(filepath, 'r') as f:\\n yield from _parse_fastq(f)\",\n \"def test_tarballs_pre_extracted(self) -> None:\\n import hammer_config\\n\\n tech_dir, tech_dir_base = HammerToolTestHelpers.create_tech_dir(\\\"dummy28\\\")\\n tech_json_filename = os.path.join(tech_dir, \\\"dummy28.tech.json\\\")\\n\\n # Add defaults to specify tarball_dir.\\n with open(os.path.join(tech_dir, \\\"defaults.json\\\"), \\\"w\\\") as f:\\n f.write(json.dumps({\\n \\\"technology.dummy28.tarball_dir\\\": tech_dir,\\n \\\"vlsi.technology.extracted_tarballs_dir\\\": tech_dir_base\\n }, cls=HammerJSONEncoder))\\n\\n HammerToolTestHelpers.write_tech_json(tech_json_filename, self.add_tarballs)\\n sys.path.append(tech_dir_base)\\n tech = self.get_tech(hammer_tech.HammerTechnology.load_from_dir(\\\"dummy28\\\", tech_dir))\\n tech.cache_dir = tech_dir\\n\\n database = hammer_config.HammerDatabase()\\n database.update_technology(tech.get_config())\\n HammerVLSISettings.load_builtins_and_core(database)\\n tech.set_database(database)\\n outputs = tech.process_library_filter(pre_filts=[], filt=hammer_tech.filters.gds_filter,\\n must_exist=False,\\n output_func=lambda str, _: [str])\\n\\n self.assertEqual(outputs, [\\\"{0}/foobar.tar.gz/test.gds\\\".format(tech_dir_base)])\\n\\n # Cleanup\\n shutil.rmtree(tech_dir_base)\",\n \"def ParserTeil2():\\r\\n Bags = {}\\r\\n for Line in Lines:\\r\\n Words = Line.split()\\r\\n Farbe = Words[0]+\\\" \\\"+Words[1]\\r\\n Bags[Farbe] = re.findall(r\\\"(\\\\d+?) (.+?) bags?\\\", Line)\\r\\n return Bags\",\n \"def archive_bag_api_messages(bags, bucket):\\n for bag in bags:\\n yield {\\n 'type': 'Ingest',\\n 'ingestType': {\\n 'id': 'create',\\n 'type': 'IngestType'\\n },\\n 'uploadUrl': f's3://{bucket}/{bag}'\\n }\",\n \"def processSetOfCerFiles(files):\\n printHeader()\\n \\n k = 0\\n for f in files:\\n k = k + 1\\n sz = get_file_size(f)\\n with open(f, 'rb') as fb:\\n processCerFile(k, fb, sz=sz)\",\n \"def split_batches(filenames):\\n by_time = {}\\n for path_name in filenames:\\n file_name = path.basename(path_name)\\n parsed_fn = parse_agdc_fn(file_name)\\n dt = parsed_fn['datetime']\\n by_time.setdefault(dt, []).append((path_name, parsed_fn))\\n\\n rv = list(by_time.values())\\n\\n for group in rv:\\n # Will raise exception if group is non-homogeneous\\n check_sane(parsed for _, parsed in group)\\n\\n return rv\",\n \"def process_bedpe(archive, bedpe, bedpe_index, output_prefix):\\n out_raw_bedpe = '{0}.tmp.bedpe.gz'.format(output_prefix)\\n logger.info(\\\"Extracting raw bedpe to tmp file {0}\\\".format(out_raw_bedpe))\\n extract_file(archive, bedpe, out_raw_bedpe)\\n\\n out_raw_bedpe_index = '{0}.tmp.bedpe.gz.tbi'.format(output_prefix)\\n logger.info(\\\"Extracting raw bedpe index to tmp file {0}\\\".format(out_raw_bedpe_index))\\n extract_file(archive, bedpe_index, out_raw_bedpe_index)\\n\\n out_formatted_bedpe = '{0}.bedpe.gz'.format(output_prefix)\\n logger.info(\\\"Creating final bedpe {0}\\\".format(out_formatted_bedpe))\\n writer = pysam.BGZFile(out_formatted_bedpe, mode='wb')\\n reader = pysam.BGZFile(out_raw_bedpe, mode='rb')\\n try:\\n meta_line = None\\n process_header = False\\n hdr = []\\n for line in reader:\\n line = line.decode('utf-8')\\n if line.startswith('#'):\\n meta_line = line\\n else:\\n if not process_header:\\n hdr = format_header(meta_line)\\n assert len(hdr) == len(set(hdr)), \\\\\\n \\\"Duplicate header keys {0}\\\".format(','.join(hdr))\\n writer.write(('#' + '\\\\t'.join(hdr) + '\\\\n').encode('utf-8'))\\n process_header = True\\n\\n dat = dict(zip(hdr, line.rstrip('\\\\r\\\\n').split('\\\\t')))\\n dat['brass_notation'] = dat['brass_notation'].replace('Chr.chr', 'chr')\\n new_line = \\\"\\\\t\\\".join([dat[i] for i in hdr]) + '\\\\n'\\n writer.write(new_line.encode('utf-8'))\\n finally:\\n writer.close()\\n reader.close()\\n\\n # tabix index\\n logger.info(\\\"Creating final bedpe index {0}\\\".format(out_formatted_bedpe + '.tbi'))\\n pysam.tabix_index( out_formatted_bedpe, preset='bed', force=True )\\n\\n # clean up\\n logger.info(\\\"Cleaning up tmp files...\\\")\\n os.remove(out_raw_bedpe)\\n os.remove(out_raw_bedpe_index)\",\n \"def unpack_tarfile(self, tarfile_path: str, target_directory: str) -> None:\\n with tarfile.open(tarfile_path) as tar:\\n tar.extractall(path=target_directory)\\n\\n found = True\\n\\n while found:\\n\\n found = False\\n\\n for root_directory, _, files in os.walk(target_directory):\\n for file in files:\\n if re.search('.*.tar.gz', file):\\n found = True\\n sub_filepath_ref = os.path.join(root_directory, file)\\n with tarfile.open(sub_filepath_ref) as tar:\\n tar.extractall(path=root_directory)\\n os.remove(sub_filepath_ref)\",\n \"def readDirectory():\\n tagdir = \\\"tagreplacements\\\"\\n data = os.listdir(tagdir)\\n for d in data:\\n processFile(os.path.join(tagdir,d))\\n \\n #print(repd)\",\n \"def try7():\\n path = '/Users/mayankkejriwal/datasets/memex-evaluation-november/nyu-text/'\\n total = 1\\n count = 1\\n with gzip.open(path + 'output1.gz', 'rb') as f:\\n for line in f:\\n print 'line : ',\\n print line\\n count += 1\\n if count > total:\\n break\",\n \"def _process_fileobj(self,\\n tar_file_obj: IO[bytes],\\n object_node: graph.COSObject) -> None:\\n with tarfile.open(fileobj=tar_file_obj) as tar_file:\\n gz_file_names = [f.name for f in tar_file.getmembers()\\n if f.name.endswith('.gz')]\\n for gz_file_name in gz_file_names:\\n gz_file_obj = tar_file.extractfile(gz_file_name)\\n if gz_file_obj:\\n oem_data = self._parse_oem_data(gz_file_obj)\\n aso_id = self._get_aso_id_from_file_name(gz_file_name)\\n self._save_oem(oem_data, aso_id, object_node)\",\n \"def parse(self, ergFilePath):\\n infoFilePath = ergFilePath + '.info'\\n quantityList = self.getQuantityList(infoFilePath)\\n\\n # get block size\\n blockSize = sum(quantity.bytes for quantity in quantityList)\\n\\n with open(ergFilePath, 'rb') as ergFile:\\n\\n # read the first 16 bytes, as they are not needed now\\n ergFile.read(16)\\n\\n # now read the rest of the file block wise\\n block = ergFile.read(blockSize)\\n while len(block) == blockSize:\\n for q in quantityList:\\n q.values.append(np.fromstring(block[:q.bytes], q.dataType)[0])\\n block = block[q.bytes:]\\n block = ergFile.read(blockSize)\\n\\n self.quantityList = quantityList\\n return quantityList\",\n \"def glob_upload_gz(pattern, egnyte_path, log=True, dryrun=False):\\n\\timport glob\\n\\tfor filename in glob.glob(pattern):\\n\\t\\tif log:\\n\\t\\t\\telog(f\\\"found file for upload:{filename}\\\")\\n\\t\\tif not dryrun:\\n\\t\\t\\tupload_file_gz(filename, egnyte_path, progress_callbacks=ProgressCallbacks() if log else None)\",\n \"def process_raw_data(data_dir='/home/data/nbc/athena/athena-data/'):\\n\\n # Calls the process_corpus function, defined below\\n # process_corpus reads in the text, performs abbreviation, spelling,\\n # translation, and overall text Processing\\n # process_corpus outputs the processed text for each file and the stemmed file\\n for feature_source in ['abstract', 'full']:\\n process_corpus(data_dir, feature_source)\\n\\n # Calls the label_data function, defined below\\n # label_data reads in the metadata csv files, concatenates them, then\\n # reads in the processed text files\\n # label_data outputs a binary pmid by label metadata matrix\\n label_data(data_dir)\\n generate_gazetteer(data_dir)\",\n \"def parse_archive(path, objdump):\\n object_files = []\\n current_file = None\\n for line in objdump:\\n if not line:\\n continue\\n match = re.match(r'^(.*[^\\\\)])(\\\\((.+)\\\\))?:\\\\s+file format', line)\\n if match:\\n filename = match.group(3) if match.group(3) else match.group(1)\\n current_file = ObjectFile(filename, path)\\n object_files.append(current_file)\\n continue\\n if not current_file:\\n raise Exception('Archive does not specify object to attribute '\\n 'symbols to ' + path)\\n sym = parse_symbol(line)\\n if not sym:\\n if current_file.symbols:\\n current_file = None\\n continue\\n current_file.symbols.append(sym)\\n return object_files\",\n \"def parseGFF3(filename):\\n\\n # Parse with transparent decompression\\n openFunc = gzip.open if filename.endswith(\\\".gz\\\") else open\\n with openFunc(filename) as infile:\\n for line in infile:\\n if line.startswith(\\\"#\\\"):\\n continue\\n parts = line.strip().split(\\\"\\\\t\\\")\\n # If this fails, the file format is not standard-compatible\\n assert len(parts) == len(gffInfoFields)\\n # Normalize data\\n normalizedInfo = {\\n \\\"seqid\\\": None if parts[0] == \\\".\\\" else urllib.unquote(parts[0]),\\n \\\"source\\\": None if parts[1] == \\\".\\\" else urllib.unquote(parts[1]),\\n \\\"type\\\": None if parts[2] == \\\".\\\" else urllib.unquote(parts[2]),\\n \\\"start\\\": None if parts[3] == \\\".\\\" else int(parts[3]),\\n \\\"end\\\": None if parts[4] == \\\".\\\" else int(parts[4]),\\n \\\"score\\\": None if parts[5] == \\\".\\\" else float(parts[5]),\\n \\\"strand\\\": None if parts[6] == \\\".\\\" else urllib.unquote(parts[6]),\\n \\\"phase\\\": None if parts[7] == \\\".\\\" else urllib.unquote(parts[7]),\\n \\\"attributes\\\": parseGFFAttributes(parts[8])\\n }\\n # Alternatively, you can emit the dictionary here, if you need\\n # mutability:\\n # yield normalizedInfo\\n yield GFFRecord(**normalizedInfo)\",\n \"def parse(self, infile):\\r\\n raise NotImplementedError()\",\n \"def process_file(filename):\\n print \\\"Reading and Parsing File: {}\\\".format(filename)\\n parsed_entries = file_parser(filename)\\n print \\\"Starting to Process Entries\\\"\\n chunked_entires = chunk_entries(parsed_entries)\\n return [process_entries(entry) for entry in chunked_entires]\",\n \"def main(input_file=None, decoy_tag=None, output_file=None):\\n NEW_HEADERS = [\\n \\\"Raw data location\\\",\\n \\\"Spectrum ID\\\",\\n \\\"Spectrum Title\\\",\\n \\\"Retention Time (s)\\\",\\n \\\"Rank\\\",\\n \\\"Calc m/z\\\",\\n \\\"Exp m/z\\\",\\n \\\"Charge\\\",\\n \\\"Sequence\\\",\\n \\\"Modifications\\\",\\n \\\"X\\\\!Tandem:expect\\\",\\n \\\"X\\\\!Tandem:hyperscore\\\",\\n \\\"proteinacc_start_stop_pre_post_;\\\",\\n \\\"Is decoy\\\",\\n ]\\n PROTON = 1.00727646677\\n protein = None\\n group = None\\n group_counter = 0\\n protein_groups = []\\n\\n if input_file.endswith(\\\".gz\\\"):\\n compressed = True\\n # Gzipped files are not seekable\\n import gzip\\n\\n # file_object = codecs.getreader(\\\"utf-8\\\")(\\n # gzip.open(path)\\n # )\\n file_object = codecs.getreader(\\\"utf-8\\\")(gzip.open(input_file))\\n else:\\n file_object = codecs.open(input_file, mode=\\\"r\\\", encoding=\\\"utf-8\\\")\\n\\n csvOut = csv.DictWriter(open(output_file, \\\"w\\\", newline=\\\"\\\"), NEW_HEADERS)\\n csvOut.writeheader()\\n\\n print(\\\"Converting XTandem XML into CSV: {0}\\\".format(input_file))\\n tandemXML = iter(cElementTree.iterparse(file_object, events=(b\\\"start\\\", b\\\"end\\\")))\\n\\n for pos, (event, element) in enumerate(tandemXML):\\n if event == b\\\"start\\\":\\n if element.tag.endswith(\\\"bioml\\\"):\\n raw_data_location = element.attrib[\\\"label\\\"].split(\\\"'\\\")[1]\\n if element.tag.endswith(\\\"group\\\"):\\n if \\\"mh\\\" in element.attrib.keys():\\n group_counter = 0\\n notes = ddict(set)\\n notes_key = None\\n group = {} # reset group\\n group[\\\"Raw data location\\\"] = raw_data_location\\n group[\\\"Charge\\\"] = element.attrib[\\\"z\\\"]\\n group[\\\"Exp m/z\\\"] = (\\n float(element.attrib[\\\"mh\\\"]) / float(group[\\\"Charge\\\"])\\n ) + PROTON\\n group[\\\"X\\\\!Tandem:expect\\\"] = element.attrib[\\\"expect\\\"]\\n protein_groups = []\\n domain_groups = []\\n if element.attrib[\\\"label\\\"] == \\\"fragment ion mass spectrum\\\":\\n notes_key = \\\"spectrum\\\"\\n if element.attrib[\\\"label\\\"] == \\\"input parameters\\\":\\n notes_key = \\\"parameters\\\"\\n group_counter += 1\\n\\n elif element.tag.endswith(\\\"protein\\\"):\\n protein = {} # reset protein\\n notes_key = \\\"protein\\\"\\n\\n elif element.tag.endswith(\\\"domain\\\"):\\n if \\\"seq\\\" in element.attrib.keys():\\n domain = {header: \\\"\\\" for header in NEW_HEADERS} # reset domain\\n domain[\\\"Sequence\\\"] = element.attrib[\\\"seq\\\"]\\n domain[\\\"X\\\\!Tandem:hyperscore\\\"] = element.attrib[\\\"hyperscore\\\"]\\n domain[\\\"Calc m/z\\\"] = (\\n float(element.attrib[\\\"mh\\\"]) / float(group[\\\"Charge\\\"])\\n ) + PROTON\\n protein[\\\"Start\\\"] = element.attrib[\\\"start\\\"]\\n protein[\\\"Stop\\\"] = element.attrib[\\\"end\\\"]\\n protein[\\\"pre\\\"] = element.attrib[\\\"pre\\\"][-1]\\n protein[\\\"post\\\"] = element.attrib[\\\"post\\\"][0]\\n if protein[\\\"Start\\\"] == \\\"1\\\":\\n protein[\\\"pre\\\"] = \\\"-\\\"\\n if protein[\\\"post\\\"] == \\\"]\\\":\\n protein[\\\"post\\\"] = \\\"-\\\"\\n domain[\\n \\\"proteinacc_start_stop_pre_post_;\\\"\\n ] = \\\"{0}_{1}_{2}_{3}_{4};\\\".format(\\n protein[\\\"Defline\\\"],\\n protein[\\\"Start\\\"],\\n protein[\\\"Stop\\\"],\\n protein[\\\"pre\\\"],\\n protein[\\\"post\\\"],\\n )\\n if protein[\\\"Defline\\\"].startswith(decoy_tag):\\n domain[\\\"Is decoy\\\"] = True\\n else:\\n domain[\\\"Is decoy\\\"] = False\\n domain[\\\"Rank\\\"] = 1\\n\\n elif element.tag.endswith(\\\"aa\\\"):\\n if \\\"modified\\\" not in element.attrib.keys():\\n continue\\n mod = \\\"{0}:{1}\\\".format(\\n element.attrib[\\\"modified\\\"],\\n int(element.attrib[\\\"at\\\"]) - int(protein[\\\"Start\\\"]) + 1,\\n )\\n try:\\n domain[\\\"Modifications\\\"].append(mod)\\n except:\\n domain[\\\"Modifications\\\"] = [mod]\\n else:\\n if element.tag.endswith(\\\"protein\\\"):\\n protein_groups.append(protein)\\n if element.tag.endswith(\\\"domain\\\"):\\n for k, v in domain.items():\\n if k not in protein.keys():\\n protein[k] = v\\n # domain_groups.append( domain )\\n elif element.tag.endswith(\\\"note\\\"):\\n if notes_key == \\\"spectrum\\\":\\n group[\\\"Spectrum Title\\\"] = element.text.strip()\\n elif notes_key == \\\"protein\\\":\\n protein[\\\"Defline\\\"] = element.text.strip()\\n elif element.tag.endswith(\\\"group\\\"):\\n group_counter -= 1\\n if group_counter == 0:\\n dict2write = {}\\n # proteins = []\\n for protein_group in protein_groups:\\n for key in NEW_HEADERS:\\n # if key == 'proteinacc_start_stop_pre_post_;':\\n # proteins.append(protein_group[key])\\n # continue\\n if key == \\\"Modifications\\\" and protein_group[key] != \\\"\\\":\\n dict2write[key] = \\\";\\\".join(protein_group[key])\\n continue\\n try:\\n dict2write[key] = group[key]\\n except:\\n dict2write[key] = protein_group[key]\\n # dict2write['proteinacc_start_stop_pre_post_;'] = ''.join(proteins)\\n csvOut.writerow(dict2write)\\n protein_groups = []\\n return\",\n \"def _all_xonsh_parser(**kwargs):\\n data_dir = builtins.__xonsh_env__.get('XONSH_DATA_DIR')\\n data_dir = expanduser_abs_path(data_dir)\\n\\n files = [os.path.join(data_dir, f) for f in os.listdir(data_dir)\\n if f.startswith('xonsh-') and f.endswith('.json')]\\n ind = 0\\n for f in files:\\n try:\\n json_file = LazyJSON(f, reopen=False)\\n except ValueError:\\n # Invalid json file\\n pass\\n commands = json_file.load()['cmds']\\n for c in commands:\\n yield (c['inp'].rstrip(), c['ts'][0], ind)\\n ind += 1\",\n \"def read_ptbtagged(ptbtagged_path: str) -> Iterator[Tuple[TokenSeq, PosSeq]]:\\n #do this immediately (first)\\n #start generating feature matrices\\n \\n #read file into an array \\n with open(ptbtagged_path) as f:\\n file_array = f.readlines()\\n file_array.append(\\\"\\\\n\\\")\\n array_of_tuples = create_tuples(file_array)\\n\\n return generator(array_of_tuples)\",\n \"def extract_from_tgz(tgz_file, output_path):\\n try:\\n t = tarfile.open(name = tgz_file, mode = 'r')\\n except tarfile.ReadError:\\n raise ValueError, ERROR_MSG\\n else:\\n names_list = t.getnames()\\n # if the tgz_file only has one file is not necessary to generate an\\n # output directory\\n if len(names_list) == 1:\\n t.extractall()\\n move(names_list[0], output_path)\\n else:\\n t.extractall(path=output_path)\\n t.close()\",\n \"def get_tag_batch(self, tag, filenames):\\n data = self.get_tags_batch([tag], filenames)\\n result = []\\n for d in data:\\n d.pop(\\\"SourceFile\\\")\\n result.append(next(iter(d.values()), None))\\n return result\",\n \"async def create_tarball(output_path: str) -> bytes:\\n file_paths = []\\n for root, _, filenames in os.walk(output_path):\\n for filename in filenames:\\n file_path = os.path.join(root, filename)\\n log.info(f'Adding {file_path} to tarball.')\\n file_paths.append(file_path)\\n\\n with ByteStream() as stream:\\n with tarfile.TarFile.open(fileobj=stream, mode='w:gz',\\n compresslevel=1) as tar:\\n for file_path in file_paths:\\n tar_info = tar.gettarinfo(name=file_path)\\n tar.addfile(tar_info)\\n # Yield the header for the tarinfo file.\\n yield stream.pop()\\n\\n with open(file_path, 'rb') as in_fp:\\n # Read the input file in chunks of stream.block_size bytes.\\n while True:\\n data = in_fp.read(stream.block_size)\\n if len(data) > 0:\\n # Write the data to the buffer.\\n tar.fileobj.write(data)\\n # Yield a compressed file chunk so the client can receive it.\\n yield stream.pop()\\n # Write padding if necessary.\\n if len(data) < stream.block_size:\\n blocks, remainder = divmod(tar_info.size, tarfile.BLOCKSIZE)\\n if remainder > 0:\\n tar.fileobj.write(tarfile.NUL * (tarfile.BLOCKSIZE - remainder))\\n yield stream.pop()\\n blocks += 1\\n tar.offset += blocks * tarfile.BLOCKSIZE\\n break\\n\\n # Yield end-of-archive marker.\\n yield stream.pop()\",\n \"def decompress_chunks(bstrm):\\n decompressor = zlib.decompressobj()\\n for chunk in iter(lambda: bstrm.read(BUFSIZE), b\\\"\\\"):\\n yield decompressor.decompress(chunk)\\n yield decompressor.flush()\"\n]","isConversational":false},"negative_scores":{"kind":"list like","value":["0.62771606","0.5906162","0.580242","0.57709885","0.567405","0.5659064","0.56499046","0.5587792","0.5565765","0.55654675","0.5555699","0.5538824","0.5521462","0.548998","0.54764485","0.54678583","0.54415685","0.5418712","0.5413513","0.54120094","0.54090226","0.53498405","0.5349773","0.53226805","0.5305671","0.52688885","0.5262013","0.52614504","0.51705647","0.5139825","0.5123269","0.5113661","0.51099485","0.5097275","0.5096686","0.5090791","0.5086269","0.5070068","0.50684416","0.50610065","0.50532424","0.5033683","0.502673","0.5015979","0.50108933","0.50041586","0.4981543","0.4971301","0.49684438","0.4957856","0.49571645","0.49570966","0.49399942","0.49377057","0.4937558","0.49338245","0.49239948","0.49209252","0.49171707","0.49103168","0.49075875","0.49017975","0.4899262","0.48976088","0.488743","0.48854205","0.48648733","0.4864631","0.4861221","0.48508838","0.4849085","0.484406","0.48425424","0.48406425","0.4839994","0.48395464","0.48322597","0.48271742","0.4824915","0.4814281","0.48083812","0.48050687","0.4797544","0.4795961","0.47926384","0.47874603","0.47792467","0.4777281","0.47772774","0.4775924","0.47749805","0.47666517","0.47644043","0.4763087","0.47598702","0.4751736","0.47494292","0.47314554","0.47299036","0.4727382","0.47236273"],"string":"[\n \"0.62771606\",\n \"0.5906162\",\n \"0.580242\",\n \"0.57709885\",\n \"0.567405\",\n \"0.5659064\",\n \"0.56499046\",\n \"0.5587792\",\n \"0.5565765\",\n \"0.55654675\",\n \"0.5555699\",\n \"0.5538824\",\n \"0.5521462\",\n \"0.548998\",\n \"0.54764485\",\n \"0.54678583\",\n \"0.54415685\",\n \"0.5418712\",\n \"0.5413513\",\n \"0.54120094\",\n \"0.54090226\",\n \"0.53498405\",\n \"0.5349773\",\n \"0.53226805\",\n \"0.5305671\",\n \"0.52688885\",\n \"0.5262013\",\n \"0.52614504\",\n \"0.51705647\",\n \"0.5139825\",\n \"0.5123269\",\n \"0.5113661\",\n \"0.51099485\",\n \"0.5097275\",\n \"0.5096686\",\n \"0.5090791\",\n \"0.5086269\",\n \"0.5070068\",\n \"0.50684416\",\n \"0.50610065\",\n \"0.50532424\",\n \"0.5033683\",\n \"0.502673\",\n \"0.5015979\",\n \"0.50108933\",\n \"0.50041586\",\n \"0.4981543\",\n \"0.4971301\",\n \"0.49684438\",\n \"0.4957856\",\n \"0.49571645\",\n \"0.49570966\",\n \"0.49399942\",\n \"0.49377057\",\n \"0.4937558\",\n \"0.49338245\",\n \"0.49239948\",\n \"0.49209252\",\n \"0.49171707\",\n \"0.49103168\",\n \"0.49075875\",\n \"0.49017975\",\n \"0.4899262\",\n \"0.48976088\",\n \"0.488743\",\n \"0.48854205\",\n \"0.48648733\",\n \"0.4864631\",\n \"0.4861221\",\n \"0.48508838\",\n \"0.4849085\",\n \"0.484406\",\n \"0.48425424\",\n \"0.48406425\",\n \"0.4839994\",\n \"0.48395464\",\n \"0.48322597\",\n \"0.48271742\",\n \"0.4824915\",\n \"0.4814281\",\n \"0.48083812\",\n \"0.48050687\",\n \"0.4797544\",\n \"0.4795961\",\n \"0.47926384\",\n \"0.47874603\",\n \"0.47792467\",\n \"0.4777281\",\n \"0.47772774\",\n \"0.4775924\",\n \"0.47749805\",\n \"0.47666517\",\n \"0.47644043\",\n \"0.4763087\",\n \"0.47598702\",\n \"0.4751736\",\n \"0.47494292\",\n \"0.47314554\",\n \"0.47299036\",\n \"0.4727382\",\n \"0.47236273\"\n]","isConversational":false},"document_score":{"kind":"string","value":"0.0"},"document_rank":{"kind":"string","value":"-1"}}},{"rowIdx":16587,"cells":{"query":{"kind":"string","value":"The Modifier can evaluate expressions correctly."},"document":{"kind":"string","value":"def test_modifier(self):\n modif = Modifier('1.2')\n self.assertEqual(modif.evaluate({}), 1.2)\n modif = Modifier('$1')\n self.assertEqual(modif.evaluate({1:3.2}), 3.2)\n modif = Modifier('1+1')\n self.assertEqual(modif.evaluate({}), 2)\n modif = Modifier('3-1.5')\n self.assertEqual(modif.evaluate({}), 1.5)\n modif = Modifier('2.2X3')\n self.assertAlmostEqual(modif.evaluate({}), 6.6, 3)\n modif = Modifier('4.4/2.2')\n self.assertAlmostEqual(modif.evaluate({}), 2, 2)\n modif = Modifier('1+4.4/2.2')\n self.assertAlmostEqual(modif.evaluate({}), 3, 2)\n modif = Modifier('$1+$2')\n self.assertAlmostEqual(modif.evaluate({1:1, 2:2.2}), 3.2, 2)\n modif = Modifier('$3=$1+$2')\n values = {1:1, 2:2}\n self.assertEqual(modif.evaluate(values), 3)\n self.assertEqual(values, {1:1, 2:2, 3:3.0})"},"metadata":{"kind":"string","value":"{\n \"objective\": {\n \"self\": [],\n \"paired\": [],\n \"triplet\": [\n [\n \"query\",\n \"document\",\n \"negatives\"\n ]\n ]\n }\n}"},"negatives":{"kind":"list like","value":["def _should_eval(self):\n return False","def evaluate(compiled_expression):","def evaluate(self):\n pass","def evaluate(self):\n pass","def eval(self):\n pass","def eval(self):\n pass","def eval(self):\n pass","def evaluate(self) :\n pass","def test(self):\n self.eval()","def test_expression_sanitizer(self):\n\n self.assertFalse(_is_math_expr_safe('INSERT INTO students VALUES (?,?)'))\n self.assertFalse(_is_math_expr_safe('import math'))\n self.assertFalse(_is_math_expr_safe('complex'))\n self.assertFalse(_is_math_expr_safe('__import__(\"os\").system(\"clear\")'))\n self.assertFalse(_is_math_expr_safe('eval(\"()._\" + \"_class_\" + \"_._\" +'\n ' \"_bases_\" + \"_[0]\")'))\n self.assertFalse(_is_math_expr_safe('2***2'))\n self.assertFalse(_is_math_expr_safe('avdfd*3'))\n self.assertFalse(_is_math_expr_safe('Cos(1+2)'))\n self.assertFalse(_is_math_expr_safe('hello'))\n self.assertFalse(_is_math_expr_safe('hello_world'))\n self.assertFalse(_is_math_expr_safe('1_2'))\n self.assertFalse(_is_math_expr_safe('2+-2'))\n self.assertFalse(_is_math_expr_safe('print(1.0)'))\n self.assertFalse(_is_math_expr_safe('1.1.1.1'))\n self.assertFalse(_is_math_expr_safe('abc.1'))\n\n self.assertTrue(_is_math_expr_safe('1+1*2*3.2+8*cos(1)**2'))\n self.assertTrue(_is_math_expr_safe('pi*2'))\n self.assertTrue(_is_math_expr_safe('-P1*cos(P2)'))\n self.assertTrue(_is_math_expr_safe('-P1*P2*P3'))\n self.assertTrue(_is_math_expr_safe('-P1'))\n self.assertTrue(_is_math_expr_safe('-1.*P1'))\n self.assertTrue(_is_math_expr_safe('-1.*P1*P2'))\n self.assertTrue(_is_math_expr_safe('-(P1)'))","def eval(self) -> typing.Any:\n return self.expr()","def evaluate(self):\r\n raise Exception(\"Not implemented.\")","def evaluator_side_effect(_, __, math_string):\r\n if math_string != '4':\r\n raise err","def eval(self):\n raise NotImplemented()","def expression(self) -> Expression:\n ...","def evaluate(self):\n raise Exception(\"Not implemented.\")","def eval(self):\n raise NotImplementedError","def evaluateBoolean(compiled_expression):","def expression(self):\n assert not self._handle_used\n self._expression_used = True\n return self._expression","def evaluate(self):\n raise NotImplementedError()","def evaluateValue(compiled_expression):","def test_expr(self):\n self.common_test_expr(True)","def evaluator_side_effect(_, __, math_string):\r\n return mapping[math_string]","def evaluate(self, tree):\n\t\tpass","def evaluate_raw(self):\n raise NotImplementedError","def _evaluate(self, x):\n raise NotImplementedError()","def _evalAndDer(self, x):\n raise NotImplementedError()","def test_RestrictingNodeTransformer__visit_LtE__1():\n assert restricted_eval('1 <= 3') is True","def is_equation(self): \n return False","def test_RestrictingNodeTransformer__visit_GtE__1():\n assert restricted_eval('1 >= 3') is False","def evaluateText(compiled_expression):","def evaluate(self, operand: object) -> bool:\n pass","def evaluate(self, edict):\n pass","def _evalContext(self):\n def xor(*args):\n return sum(args) == 1\n def neg(result):\n return not result\n context = {\n 'xor': xor,\n 'neg': neg\n }\n return context","def evaluate(self, X):\n\n\t\tpass","def test_RestrictingNodeTransformer__visit_Lt__1():\n assert restricted_eval('1 < 3') is True","def mutate(self):\n if self.mutator.evaluate(self):\n self.evaluated = 0\n return 1\n return 0","def evaluate(self):\n raise NotImplementedError(\"Abstract method\")","def eval(self, *args, **kwargs):\n raise NotImplementedError","def test_RestrictingNodeTransformer__visit_Eq__1():\n assert restricted_eval('1 == int(\"1\")') is True","def test00(self):\n a = 3\n cr = bcolz.eval(\"2 * a\", rootdir=self.rootdir)\n # print \"bcolz.eval ->\", cr\n self.assertTrue(cr == 6, \"eval does not work correctly\")","def evaluate(self) -> int:","def test_compiler_expression(patch, compiler, lines, tree):\n patch.object(Objects, 'expression')\n compiler.expression(tree, '1')\n Objects.expression.assert_called_with(tree.expression)\n args = [Objects.expression()]\n lines.append.assert_called_with('expression', tree.line(), args=args,\n parent='1')","def eval(self, expr, locals):\r\n sav = self.locals_ptr\r\n self.locals_ptr = locals\r\n x = eval(self.compile(expr), {\"__builtins__\":self.eval_allowed_globals}, locals)\r\n self.locals_ptr = sav\r\n return x","def test_RestrictingNodeTransformer__visit_Gt__1():\n assert restricted_eval('1 > 3') is False","def is_equation(self):\n return True","def is_equation(self):\n return True","def test_power_simple(self):\r\n self.assertEquals(preview.latex_preview('2^3^4'), '2^{3^{4}}')","def on_true(self) -> global___Expression:","def mineval(expr, ctx):\n for k, v in ctx.items():\n if k in expr:\n expr = re.sub(k, str(v), expr)\n return evaluateRPN(expr)","def eval(self):\n return self.with_transforms(\"eval\")","def __evaluate(self, var_x):\n # pylint: disable=W0612,C0103\n x = var_x\n # pylint: enable=W0612,C0103\n return eval(self.expr)","def expr(self):\n return self._express","def eval(self):\n raise NotImplementedError('Must define eval function to use this base class')","def result(self) -> global___Expression:","def evaluate(self, state):\n abstract","def fix_evaluator(self):\n with self.override_evaluator(self._get_evaluators()):\n yield","def evaluate(self):\n try:\n test_val = self.expression()\n return test_val != 0\n except ValueError:\n raise ParseError(\"Could not evaluate expression.\")","def evaluateStructure(compiled_expression):","def is_equation(self):\n return False","def evaluateMacro(compiled_expression):","def test_expression_regex(self):\n\n # Checks on a specified attribute with operators \"==\" and \"!=\" with integers\n expression = BooleanExpression(\"NORMAL\", models.Network.label.op(\"REGEXP\")(\"network_3\"))\n value = expression.evaluate(KeyedTuple([{\"label\": \"network_3\"}], [\"networks\"]))\n self.assertTrue(value, \"\"\"models.Network.label REGEXP /pattern/ with models.Network.label=\"network_3\" (1)\"\"\")\n\n expression = BooleanExpression(\"NORMAL\", models.Network.label.op(\"REGEXP\")(\"(network_3|network_2)\"))\n value = expression.evaluate(KeyedTuple([{\"label\": \"network_3\"}], [\"networks\"]))\n self.assertTrue(value, \"\"\"models.Network.label REGEXP /pattern/ with models.Network.label=\"network_3\" (2)\"\"\")\n\n expression = BooleanExpression(\"NORMAL\", models.Network.label.op(\"REGEXP\")(\"(network_1|network_2)\"))\n value = expression.evaluate(KeyedTuple([{\"label\": \"network_3\"}], [\"networks\"]))\n self.assertFalse(value, \"\"\"models.Network.label REGEXP /pattern/ with models.Network.label=\"network_3\" (3)\"\"\")","def test_power_parens(self):\r\n self.assertEquals(preview.latex_preview('2^3^(4+5)'), '2^{3^{4+5}}')","def evaluateExpression(self, expression):\n # remove spaces\n expression = expression.replace(\" \", \"\")\n # perform lazy initialization\n if not self.hasInitializedStringSubstitution:\n\n # The groups of substitution rules it contains will loop until there\n # is no more changes, thus only the relative order between the\n # groups matter: make sure groups appear earlier contain expansions\n # that should be done before groups appear later.\n # Note that all the substitution strings contain no spaces\n self.useStringSubstitution_normalization = (\n\n # 0th priorities: standardize notations\n StringSubstitution((\n\n # common\n (\"\\(e\\)\", \"(ed)\"), # ed -> e\n (\"\\(s\\)\", \"(sd)\"), # sd -> s\n\n # add {} to subscript to enable expansion of [2] and [4]\n (\"_([\\d]+)\", \"_{{{0[0]}}}\"), # add { } to subscripts\n\n # eccentricities\n (\"Eccentricity_\", \"Ecc_\"), # Eccentricity_ -> Ecc_\n (\"E_\", \"Ecc_\"), # E_ -> Ecc_\n (\"eccentricity_\", \"ecc_\"), # eccentricity_ -> ecc_\n (\"e_\", \"ecc_\"), # e_ -> ecc_\n # latex style support\n (\"Epsilon_\", \"Ecc_\"),\n (\"epsilon_\", \"ecc_\"),\n\n # eccentricity:\n # Ecc_{m,n}(ed) := {r^m e^{i n phi}}_e\n (\"Ecc_{([\\d]+)}\", \"Ecc_{{{0[0]},{0[0]}}}\"), # Ecc_{n} -> Ecc_{n,n}\n\n # r-averages\n # {r^m}(ed) := int(r^m*ed)/int(ed)\n (\"{R\\^\", \"{{r^\"),\n\n # r-integrals\n # [r^m](ed) := int(r^m*ed)\n (\"\\[R\\^\", \"[r^\"),\n\n # multiplicity:\n # dN/dy(pion) := pion multiplicity\n (\"[^d]N\\(\", \"dN/dy(\"),\n (\"dN\\(\", \"dN/dy(\"),\n\n # spectra:\n # dN/(dydpT)(pTs)(pion) := pion spectra at pTs values\n (\"dN/dpT\", \"dN/(dydpT)\"),\n (\"dN/dydpT\", \"dN/(dydpT)\"),\n )),\n\n # 1st priorities: expanding [2] [4]\n StringSubstitution((\n\n # support for xxx_{ooo}[2](oxox)\n (\"([\\w_]+)_{([\\d,]+)}\\[2\\]\\(([\\w_]+)\\)\", 'sqrt(<{0[0]}_{{{0[1]}}}({0[2]})**2>)'), # without (pTs)\n (\"([\\w_]+)_{([\\d,]+)}\\[2\\](\\(.*?\\))\\(([\\w_]+)\\)\", 'sqrt(<{0[0]}_{{{0[1]}}}{0[2]}({0[3]})**2>)'), # with (pTs)\n\n # support for xxx_{ooo}[4](oxox)\n (\"([\\w_]+)_{([\\d,]+)}\\[4\\]\\(([\\w_]+)\\)\", '((2*<{0[0]}_{{{0[1]}}}({0[2]})**2>**2-<{0[0]}_{{{0[1]}}}({0[2]})**4>)**0.25)'), # without (pTs)\n (\"([\\w_]+)_{([\\d,]+)}\\[4\\](\\(.*?\\))\\(([\\w_]+)\\)\", '((2*<{0[0]}_{{{0[1]}}}{0[2]}({0[3]})**2>**2-<{0[0]}_{{{0[1]}}}{0[2]}({0[3]})**4>)**0.25)'), # with (pTs)\n )),\n\n # 2nd priorities: expand special functions || <> $$ (related: ecc, v, Phi, Psi)\n StringSubstitution((\n\n # ecc = |Ecc|\n (\"ecc_\", \"|Ecc|_\"),\n # v = |V|\n (\"v_\", \"|V|_\"),\n\n # || = abs\n (\"\\|([\\w_]+)\\|(.*?)\\(([\\w_]+)\\)\", \"|{0[0]}{0[1]}({0[2]})|\"), # |ooo|xxx(oxox) -> |oooxxx(oxox)|; oxox is a word\n\n # <> = mean\n (\"<([\\w_]+)>(.*?)\\(([\\w_]+)\\)\", \"<{0[0]}{0[1]}({0[2]})>\"), # <ooo>xxx(oxox) -> <oooxxx(oxox)>; oxox is a word\n\n # Phi = $Ecc$\n (\"Phi_\", \"$Ecc$_\"),\n # Psi = $V$\n (\"Psi_\", '$V$_'),\n\n # $$ = get plane angles; only applies to Ecc and V\n (\"\\$([\\w_]+)\\$(.*?)\\(([\\w_]+)\\)\", \"${0[0]}{0[1]}({0[2]})$\"), # <ooo>xxx(oxox) -> <oooxxx(oxox)>; oxox is a word\n )),\n\n )\n\n # convert standardized notations to functions\n self.useStringSubstitution_functionization = StringSubstitution((\n\n # ||: absolute value\n (\"\\|(.*?)\\|\", 'abs({0[0]})'),\n\n # <>: mean value\n (\"<(.*?)>\", 'mean({0[0]},0)'),\n\n # $$: get plane angles; only applies to Ecc (angle(-Ecc_n)/n) and V (angle(V_n)/n)\n (\"\\$Ecc_{([\\d\\w+]),([\\d\\w+])}(.*?)\\$\", 'angle(Ecc_{{{0[0]},{0[1]}}}{0[2]})/{0[1]}'),\n (\"\\$V_{([\\d\\w+])}(.*?)\\$\", 'angle(V_{{{0[0]}}}{0[1]})/{0[0]}'),\n\n # eccentricity:\n # ecc_{m,n}(ed) := {-r^m e^{i n phi}}_e\n (\"Ecc_{([\\d]+),([\\d]+)}\\((\\w\\w)\\)\", 'self.get_Ecc_n(eccType=\"{0[2]}\", r_power={0[0]}, order={0[1]})'), # to functions\n\n # r-averages\n # {r^m}(ed) := int(r^m*ed)/int(ed)\n (\"{r\\^([\\d]+)}\\((\\w\\w)\\)\", 'self.getRIntegrals(eccType=\"{0[1]}\", r_power={0[0]}) / self.getRIntegrals(eccType=\"{0[1]}\", r_power=0)'),\n\n # r-integrals\n # [r^m](ed) := int(r^m*ed)\n (\"\\[r\\^([\\d]+)\\]\\((\\w\\w)\\)\", 'self.getRIntegrals(eccType=\"{0[1]}\", r_power={0[0]})'),\n\n # lifetimes\n (\"lifetime\", 'self.getLifetimes()'),\n\n # integrated flow:\n # V_{n}(pion) := pion complex flow vector of order n\n (\"V_{([\\d]+)}\\(([\\w_]+)\\)\", 'self.get_V_n(particleName=\"{0[1]}\", order={0[0]})'),\n\n # multiplicity:\n # dN/dy(pion) := pion multiplicity\n (\"dN/dy\\(([\\w_]+)\\)\", 'self.get_dNdy(particleName=\"{0[0]}\")'),\n\n # differential flows\n # V_{n}(pTs)(pion) := complex differential flow vector of order n for pion at pTs values\n (\"V_{([\\d]+)}\\((.*?)\\)\\(([\\w_]+)\\)\", 'self.get_diff_V_n(particleName=\"{0[2]}\", order={0[0]}, pTs={0[1]}, verbose=True)'),\n\n # spectra:\n # dN/(dydpT)(pTs)(pion) := pion spectra at pTs values\n (\"dN/\\(dydpT\\)\\((.*?)\\)\\(([\\w_]+)\\)\", 'self.get_dNdydpT(particleName=\"{0[1]}\", pTs={0[0]}, verbose=True)'),\n\n ))\n\n\n # perform normalization, should repeat until there is no more changes\n exprAfterNormalization = expression\n needMoreChanges = True\n while needMoreChanges:\n needMoreChanges = False\n for stringSubstitution in self.useStringSubstitution_normalization:\n exprAfterNormalization, numberOfScans = stringSubstitution.applyAllRules(exprAfterNormalization)\n if numberOfScans>0: needMoreChanges = True\n # perform functionization, should do only once\n exprAfterFunctionization, numberOfScans = self.useStringSubstitution_functionization.applyAllRules(exprAfterNormalization)\n # try to evaluate it\n try:\n value = eval(exprAfterFunctionization)\n return (value, exprAfterNormalization, exprAfterFunctionization)\n except:\n print(\"Error encounterred evaluating {}:\".format(expression))\n print(\"-> {}\\n-> {}\".format(exprAfterNormalization, exprAfterFunctionization))\n raise","def evaluate(self, g):\n pass","def test_lazy_evaluation(self):\n pass","def test_product_mult_only(self):\r\n self.assertEquals(preview.latex_preview('2*3'), r'2\\cdot 3')","def compile_expressions(self):\n if getattr(self, \"_attrs\", None):\n for k, v in self._attrs.items():\n try:\n Expression.compile_cache(v)\n except:\n pass\n if \"${\" in v and \"}\" in v:\n Expression.extract(v)\n if getattr(self, \"_let\", None):\n for k, v in self._let.items():\n try:\n Expression.compile_cache(v)\n except:\n pass\n if getattr(self, \"text\", None):\n Expression.extract(self.text)","def test_evaluate_mod_expression(self):\n value = self.evaluate_common(\"5.5M mod 2M\")\n self.assertTrue(\n value.type_code == edm.SimpleType.Decimal, \"Expected Decimal\")\n self.assertTrue(value.value == decimal.Decimal('1.5'),\n \"Expected 1.5; found %s\" % repr(value.value))\n value = self.evaluate_common(\"5.5D mod 2M\")\n self.assertTrue(\n value.type_code == edm.SimpleType.Double, \"Expected Double\")\n self.assertTrue(value.value == 1.5, \"Expected 1.5\")\n try:\n value = self.evaluate_common(\"5.5D mod 0\")\n self.fail(\"Division by zero\")\n except odata.EvaluationError:\n pass\n value = self.evaluate_common(\"5.5F mod 2D\")\n self.assertTrue(\n value.type_code == edm.SimpleType.Double, \"Expected Double\")\n self.assertTrue(value.value == 1.5, \"Expected 1.5\")\n value = self.evaluate_common(\"5 mod 2L\")\n self.assertTrue(\n value.type_code == edm.SimpleType.Int64, \"Expected Int64\")\n self.assertTrue(value.value == 1, \"Expected 1L\")\n value = self.evaluate_common(\"-5 mod 2L\")\n self.assertTrue(\n value.type_code == edm.SimpleType.Int64, \"Expected Int64\")\n self.assertTrue(value.value == -1, \"Expected -1L\")\n try:\n value = self.evaluate_common(\"5 mod '2'\")\n self.fail(\"String promotion to int\")\n except odata.EvaluationError:\n pass\n value = self.evaluate_common(\"5 mod null\")\n self.assertTrue(\n value.type_code == edm.SimpleType.Int32, \"Expected Int32\")\n self.assertTrue(value.value is None, \"Expected None\")","def expression_used(self):\n return self._expression_used","def eval(cls, *args):\n raise NotImplementedError(\"subclasses need to override this method\")","def user_expressions(self, expressions):\n compiled_expressions = {}\n for key, expr in expressions.items():\n try:\n compiled_expressions[key] = COMPILER.parse_eval(expr)\n except CoconutException:\n compiled_expressions[key] = expr\n return super(CoconutShell, self).user_expressions(compiled_expressions)","def test_staff_inputs_expressions_legacy(self):\r\n problem = self.build_problem(answer=\"1+1j\", tolerance=1e-3)\r\n self.assert_grade(problem, '1+j', 'correct')","def expression(self, expr):\n self.set(expression=expr)","def multiplier(self) -> global___Expression:","def calc(bot, sender, sendmsg, label, args):\n\n expr = \" \".join(args)\n banned = dir() + dir(builtins)\n for word in banned:\n if word in expr:\n sendmsg(\"Illegal word found: \" + word)\n return\n try:\n sendmsg(eval(expr))\n except Exception as e:\n sendmsg(str(e))","def expression(*args, alwaysEvaluate: Union[int, bool]=0, animated: Union[int, bool]=0,\n attribute: Union[AnyStr, bool]=\"\", name: Union[AnyStr, bool]=\"\", object:\n Union[AnyStr, bool]=\"\", safe: bool=True, shortNames: bool=True, string:\n Union[AnyStr, bool]=\"\", timeDependent: bool=True, unitConversion: Union[AnyStr,\n bool]=\"all.\", q=True, query=True, e=True, edit=True, **kwargs)->Union[AnyStr,\n Any]:\n pass","def test_expr(self):\n x = t.Action(\"returnStuff()\")\n self.assertEqual(writePython(x),\n dd(\"\"\"\n _G_python_1, lastError = eval('returnStuff()', self.globals, _locals), None\n self.considerError(lastError, None)\n _G_python_1\n \"\"\"))","def evaluate(self, *args, **kwargs) -> Union[str, int, float, bool]:\n return True","def has_expression(self):\n return self._expression is not None","def evaluateExpression(expr):\n\toperators = {ast.Add: op.add, ast.Sub: op.sub, ast.Mult: op.mul,\n\t\t\t\t ast.Div: op.truediv, ast.USub: op.neg, ast.Pow: myPow}\n\tnode = ast.parse(expr.strip(), mode='eval')\n\treturn evaluate(node.body,operators)","def is_expression(self):\r\n return conf.lib.clang_isExpression(self)","def expression(self, item):\n a = item.get(\"assertion\", item.get(\"expression\"))\n\n values = item[\"values\"]\n\n left = self.resolve(values[0])\n\n if a == \"equals\" or a == \"equal\":\n right = self.resolve(values[1])\n return left == right\n elif a == \"less\":\n right = self.resolve(values[1])\n return left < right\n elif a == \"less_equal\":\n right = self.resolve(values[1])\n return left <= right\n elif a == \"not\":\n return not left\n elif a == \"or\":\n if left is True:\n return True\n\n for i in range(1, len(values)):\n result = self.resolve(values[i])\n if result is True:\n return True\n\n return False\n elif a == \"and\":\n if left is False:\n return False\n\n for i in range(1, len(values)):\n result = self.resolve(values[i])\n if result is False:\n return False\n\n return True\n elif a == \"sum\":\n result = left\n\n assert type(left) in (int, float, str, list)\n # Sum supports flattened values since this only occurs when\n # a string like \"{a} {b} {c}\" is compiled. Everything else,\n # including arithmetic is compiled as a nested expression.\n for i in range(1, len(values)):\n r = self.resolve(values[i])\n\n if type(r) in (int, float, list) and type(result) in (\n int,\n float,\n list,\n ):\n result += r\n else:\n result = f\"{str(result)}{str(r)}\"\n\n return result\n elif a == \"subtraction\":\n right = self.resolve(values[1])\n assert type(left) in (int, float)\n assert type(right) in (int, float)\n return left - right\n elif a == \"multiplication\":\n right = self.resolve(values[1])\n assert type(left) in (int, float, str)\n assert type(right) in (int, float, str)\n return left * right\n elif a == \"modulus\":\n right = self.resolve(values[1])\n assert type(left) in (int, float)\n assert type(right) in (int, float)\n return left % right\n elif a == \"division\":\n right = self.resolve(values[1])\n assert type(left) in (int, float, str)\n assert type(right) in (int, float, str)\n return left / right\n elif a == \"exponential\":\n right = self.resolve(values[1])\n assert type(left) in (int, float)\n assert type(right) in (int, float)\n return left ** right\n else:\n assert False, f\"Unsupported operation: {a}\"","def reinit_exprs(self):\n command = reduce(lambda acc, e: acc | e[1], self.commands, NoMatch())\n self.dm_expr = self.dm_expr_head + command\n self.expr = self.expr_head + command","def eval(self, A):\n\t\tpass","def treat_as_expression(self):\n special_chars = '{}()[]=<>.\"\\'/'\n return any(special_char in self.key for special_char in special_chars)","def test_unary_op_support():\n check_peval_expression(\"+(2)\", {}, \"2\", fully_evaluated=True, expected_value=2)\n check_peval_expression(\"-(-3)\", {}, \"3\", fully_evaluated=True, expected_value=3)\n check_peval_expression_bool(\"not 0\", {}, True)\n check_peval_expression(\"~(-4)\", {}, \"3\", fully_evaluated=True, expected_value=3)","def __bool__(self):\n return bool(self.exp)","def with_continual_eval(self):\n return self._with_continual_eval","def test_RestrictingNodeTransformer__visit_NotEq__1():\n assert restricted_eval('1 != int(\"1\")') is False","def evaluator(self, candidates, args):\n\t\traise NotImplementedError","def usesEvaluationManager(self):\n \n pass","def testCalculate(self):\r\n for i in range(len(self.__testExpressions)):\r\n self.__Calculator.setExpression(self.__testExpressions[i])\r\n self.__Calculator.calculateResult()\r\n self.assertEqual(self.__Calculator.getResult(), self.__testResult[i])","def evaluator(self, candidates, args):\r\n raise NotImplementedError","def __call__(self, expression):\n self.set_expression(expression)","def static_call(self, *args):\n return self.expression","def test_bin_op_support():\n check_peval_expression(\"1 + 2\", {}, \"3\", fully_evaluated=True, expected_value=3)\n check_peval_expression(\"2 - 1\", {}, \"1\", fully_evaluated=True, expected_value=1)\n check_peval_expression(\"2 * 3\", {}, \"6\", fully_evaluated=True, expected_value=6)\n check_peval_expression(\"9 / 2\", {}, \"4.5\", fully_evaluated=True, expected_value=4.5)\n check_peval_expression(\"9 // 2\", {}, \"4\", fully_evaluated=True, expected_value=4)\n check_peval_expression(\"9 % 2\", {}, \"1\", fully_evaluated=True, expected_value=1)\n check_peval_expression(\"2 ** 4\", {}, \"16\", fully_evaluated=True, expected_value=16)\n check_peval_expression(\"3 << 2\", {}, \"12\", fully_evaluated=True, expected_value=12)\n check_peval_expression(\"64 >> 3\", {}, \"8\", fully_evaluated=True, expected_value=8)\n check_peval_expression(\"17 | 3\", {}, \"19\", fully_evaluated=True, expected_value=19)\n check_peval_expression(\"17 ^ 3\", {}, \"18\", fully_evaluated=True, expected_value=18)\n check_peval_expression(\"17 & 3\", {}, \"1\", fully_evaluated=True, expected_value=1)","def value(self) -> global___Expression:","def value(self) -> global___Expression:","def parsable_as_expression(self):\n return self.parsable and self.expression_ast_node is not None"],"string":"[\n \"def _should_eval(self):\\n return False\",\n \"def evaluate(compiled_expression):\",\n \"def evaluate(self):\\n pass\",\n \"def evaluate(self):\\n pass\",\n \"def eval(self):\\n pass\",\n \"def eval(self):\\n pass\",\n \"def eval(self):\\n pass\",\n \"def evaluate(self) :\\n pass\",\n \"def test(self):\\n self.eval()\",\n \"def test_expression_sanitizer(self):\\n\\n self.assertFalse(_is_math_expr_safe('INSERT INTO students VALUES (?,?)'))\\n self.assertFalse(_is_math_expr_safe('import math'))\\n self.assertFalse(_is_math_expr_safe('complex'))\\n self.assertFalse(_is_math_expr_safe('__import__(\\\"os\\\").system(\\\"clear\\\")'))\\n self.assertFalse(_is_math_expr_safe('eval(\\\"()._\\\" + \\\"_class_\\\" + \\\"_._\\\" +'\\n ' \\\"_bases_\\\" + \\\"_[0]\\\")'))\\n self.assertFalse(_is_math_expr_safe('2***2'))\\n self.assertFalse(_is_math_expr_safe('avdfd*3'))\\n self.assertFalse(_is_math_expr_safe('Cos(1+2)'))\\n self.assertFalse(_is_math_expr_safe('hello'))\\n self.assertFalse(_is_math_expr_safe('hello_world'))\\n self.assertFalse(_is_math_expr_safe('1_2'))\\n self.assertFalse(_is_math_expr_safe('2+-2'))\\n self.assertFalse(_is_math_expr_safe('print(1.0)'))\\n self.assertFalse(_is_math_expr_safe('1.1.1.1'))\\n self.assertFalse(_is_math_expr_safe('abc.1'))\\n\\n self.assertTrue(_is_math_expr_safe('1+1*2*3.2+8*cos(1)**2'))\\n self.assertTrue(_is_math_expr_safe('pi*2'))\\n self.assertTrue(_is_math_expr_safe('-P1*cos(P2)'))\\n self.assertTrue(_is_math_expr_safe('-P1*P2*P3'))\\n self.assertTrue(_is_math_expr_safe('-P1'))\\n self.assertTrue(_is_math_expr_safe('-1.*P1'))\\n self.assertTrue(_is_math_expr_safe('-1.*P1*P2'))\\n self.assertTrue(_is_math_expr_safe('-(P1)'))\",\n \"def eval(self) -> typing.Any:\\n return self.expr()\",\n \"def evaluate(self):\\r\\n raise Exception(\\\"Not implemented.\\\")\",\n \"def evaluator_side_effect(_, __, math_string):\\r\\n if math_string != '4':\\r\\n raise err\",\n \"def eval(self):\\n raise NotImplemented()\",\n \"def expression(self) -> Expression:\\n ...\",\n \"def evaluate(self):\\n raise Exception(\\\"Not implemented.\\\")\",\n \"def eval(self):\\n raise NotImplementedError\",\n \"def evaluateBoolean(compiled_expression):\",\n \"def expression(self):\\n assert not self._handle_used\\n self._expression_used = True\\n return self._expression\",\n \"def evaluate(self):\\n raise NotImplementedError()\",\n \"def evaluateValue(compiled_expression):\",\n \"def test_expr(self):\\n self.common_test_expr(True)\",\n \"def evaluator_side_effect(_, __, math_string):\\r\\n return mapping[math_string]\",\n \"def evaluate(self, tree):\\n\\t\\tpass\",\n \"def evaluate_raw(self):\\n raise NotImplementedError\",\n \"def _evaluate(self, x):\\n raise NotImplementedError()\",\n \"def _evalAndDer(self, x):\\n raise NotImplementedError()\",\n \"def test_RestrictingNodeTransformer__visit_LtE__1():\\n assert restricted_eval('1 <= 3') is True\",\n \"def is_equation(self): \\n return False\",\n \"def test_RestrictingNodeTransformer__visit_GtE__1():\\n assert restricted_eval('1 >= 3') is False\",\n \"def evaluateText(compiled_expression):\",\n \"def evaluate(self, operand: object) -> bool:\\n pass\",\n \"def evaluate(self, edict):\\n pass\",\n \"def _evalContext(self):\\n def xor(*args):\\n return sum(args) == 1\\n def neg(result):\\n return not result\\n context = {\\n 'xor': xor,\\n 'neg': neg\\n }\\n return context\",\n \"def evaluate(self, X):\\n\\n\\t\\tpass\",\n \"def test_RestrictingNodeTransformer__visit_Lt__1():\\n assert restricted_eval('1 < 3') is True\",\n \"def mutate(self):\\n if self.mutator.evaluate(self):\\n self.evaluated = 0\\n return 1\\n return 0\",\n \"def evaluate(self):\\n raise NotImplementedError(\\\"Abstract method\\\")\",\n \"def eval(self, *args, **kwargs):\\n raise NotImplementedError\",\n \"def test_RestrictingNodeTransformer__visit_Eq__1():\\n assert restricted_eval('1 == int(\\\"1\\\")') is True\",\n \"def test00(self):\\n a = 3\\n cr = bcolz.eval(\\\"2 * a\\\", rootdir=self.rootdir)\\n # print \\\"bcolz.eval ->\\\", cr\\n self.assertTrue(cr == 6, \\\"eval does not work correctly\\\")\",\n \"def evaluate(self) -> int:\",\n \"def test_compiler_expression(patch, compiler, lines, tree):\\n patch.object(Objects, 'expression')\\n compiler.expression(tree, '1')\\n Objects.expression.assert_called_with(tree.expression)\\n args = [Objects.expression()]\\n lines.append.assert_called_with('expression', tree.line(), args=args,\\n parent='1')\",\n \"def eval(self, expr, locals):\\r\\n sav = self.locals_ptr\\r\\n self.locals_ptr = locals\\r\\n x = eval(self.compile(expr), {\\\"__builtins__\\\":self.eval_allowed_globals}, locals)\\r\\n self.locals_ptr = sav\\r\\n return x\",\n \"def test_RestrictingNodeTransformer__visit_Gt__1():\\n assert restricted_eval('1 > 3') is False\",\n \"def is_equation(self):\\n return True\",\n \"def is_equation(self):\\n return True\",\n \"def test_power_simple(self):\\r\\n self.assertEquals(preview.latex_preview('2^3^4'), '2^{3^{4}}')\",\n \"def on_true(self) -> global___Expression:\",\n \"def mineval(expr, ctx):\\n for k, v in ctx.items():\\n if k in expr:\\n expr = re.sub(k, str(v), expr)\\n return evaluateRPN(expr)\",\n \"def eval(self):\\n return self.with_transforms(\\\"eval\\\")\",\n \"def __evaluate(self, var_x):\\n # pylint: disable=W0612,C0103\\n x = var_x\\n # pylint: enable=W0612,C0103\\n return eval(self.expr)\",\n \"def expr(self):\\n return self._express\",\n \"def eval(self):\\n raise NotImplementedError('Must define eval function to use this base class')\",\n \"def result(self) -> global___Expression:\",\n \"def evaluate(self, state):\\n abstract\",\n \"def fix_evaluator(self):\\n with self.override_evaluator(self._get_evaluators()):\\n yield\",\n \"def evaluate(self):\\n try:\\n test_val = self.expression()\\n return test_val != 0\\n except ValueError:\\n raise ParseError(\\\"Could not evaluate expression.\\\")\",\n \"def evaluateStructure(compiled_expression):\",\n \"def is_equation(self):\\n return False\",\n \"def evaluateMacro(compiled_expression):\",\n \"def test_expression_regex(self):\\n\\n # Checks on a specified attribute with operators \\\"==\\\" and \\\"!=\\\" with integers\\n expression = BooleanExpression(\\\"NORMAL\\\", models.Network.label.op(\\\"REGEXP\\\")(\\\"network_3\\\"))\\n value = expression.evaluate(KeyedTuple([{\\\"label\\\": \\\"network_3\\\"}], [\\\"networks\\\"]))\\n self.assertTrue(value, \\\"\\\"\\\"models.Network.label REGEXP /pattern/ with models.Network.label=\\\"network_3\\\" (1)\\\"\\\"\\\")\\n\\n expression = BooleanExpression(\\\"NORMAL\\\", models.Network.label.op(\\\"REGEXP\\\")(\\\"(network_3|network_2)\\\"))\\n value = expression.evaluate(KeyedTuple([{\\\"label\\\": \\\"network_3\\\"}], [\\\"networks\\\"]))\\n self.assertTrue(value, \\\"\\\"\\\"models.Network.label REGEXP /pattern/ with models.Network.label=\\\"network_3\\\" (2)\\\"\\\"\\\")\\n\\n expression = BooleanExpression(\\\"NORMAL\\\", models.Network.label.op(\\\"REGEXP\\\")(\\\"(network_1|network_2)\\\"))\\n value = expression.evaluate(KeyedTuple([{\\\"label\\\": \\\"network_3\\\"}], [\\\"networks\\\"]))\\n self.assertFalse(value, \\\"\\\"\\\"models.Network.label REGEXP /pattern/ with models.Network.label=\\\"network_3\\\" (3)\\\"\\\"\\\")\",\n \"def test_power_parens(self):\\r\\n self.assertEquals(preview.latex_preview('2^3^(4+5)'), '2^{3^{4+5}}')\",\n \"def evaluateExpression(self, expression):\\n # remove spaces\\n expression = expression.replace(\\\" \\\", \\\"\\\")\\n # perform lazy initialization\\n if not self.hasInitializedStringSubstitution:\\n\\n # The groups of substitution rules it contains will loop until there\\n # is no more changes, thus only the relative order between the\\n # groups matter: make sure groups appear earlier contain expansions\\n # that should be done before groups appear later.\\n # Note that all the substitution strings contain no spaces\\n self.useStringSubstitution_normalization = (\\n\\n # 0th priorities: standardize notations\\n StringSubstitution((\\n\\n # common\\n (\\\"\\\\(e\\\\)\\\", \\\"(ed)\\\"), # ed -> e\\n (\\\"\\\\(s\\\\)\\\", \\\"(sd)\\\"), # sd -> s\\n\\n # add {} to subscript to enable expansion of [2] and [4]\\n (\\\"_([\\\\d]+)\\\", \\\"_{{{0[0]}}}\\\"), # add { } to subscripts\\n\\n # eccentricities\\n (\\\"Eccentricity_\\\", \\\"Ecc_\\\"), # Eccentricity_ -> Ecc_\\n (\\\"E_\\\", \\\"Ecc_\\\"), # E_ -> Ecc_\\n (\\\"eccentricity_\\\", \\\"ecc_\\\"), # eccentricity_ -> ecc_\\n (\\\"e_\\\", \\\"ecc_\\\"), # e_ -> ecc_\\n # latex style support\\n (\\\"Epsilon_\\\", \\\"Ecc_\\\"),\\n (\\\"epsilon_\\\", \\\"ecc_\\\"),\\n\\n # eccentricity:\\n # Ecc_{m,n}(ed) := {r^m e^{i n phi}}_e\\n (\\\"Ecc_{([\\\\d]+)}\\\", \\\"Ecc_{{{0[0]},{0[0]}}}\\\"), # Ecc_{n} -> Ecc_{n,n}\\n\\n # r-averages\\n # {r^m}(ed) := int(r^m*ed)/int(ed)\\n (\\\"{R\\\\^\\\", \\\"{{r^\\\"),\\n\\n # r-integrals\\n # [r^m](ed) := int(r^m*ed)\\n (\\\"\\\\[R\\\\^\\\", \\\"[r^\\\"),\\n\\n # multiplicity:\\n # dN/dy(pion) := pion multiplicity\\n (\\\"[^d]N\\\\(\\\", \\\"dN/dy(\\\"),\\n (\\\"dN\\\\(\\\", \\\"dN/dy(\\\"),\\n\\n # spectra:\\n # dN/(dydpT)(pTs)(pion) := pion spectra at pTs values\\n (\\\"dN/dpT\\\", \\\"dN/(dydpT)\\\"),\\n (\\\"dN/dydpT\\\", \\\"dN/(dydpT)\\\"),\\n )),\\n\\n # 1st priorities: expanding [2] [4]\\n StringSubstitution((\\n\\n # support for xxx_{ooo}[2](oxox)\\n (\\\"([\\\\w_]+)_{([\\\\d,]+)}\\\\[2\\\\]\\\\(([\\\\w_]+)\\\\)\\\", 'sqrt(<{0[0]}_{{{0[1]}}}({0[2]})**2>)'), # without (pTs)\\n (\\\"([\\\\w_]+)_{([\\\\d,]+)}\\\\[2\\\\](\\\\(.*?\\\\))\\\\(([\\\\w_]+)\\\\)\\\", 'sqrt(<{0[0]}_{{{0[1]}}}{0[2]}({0[3]})**2>)'), # with (pTs)\\n\\n # support for xxx_{ooo}[4](oxox)\\n (\\\"([\\\\w_]+)_{([\\\\d,]+)}\\\\[4\\\\]\\\\(([\\\\w_]+)\\\\)\\\", '((2*<{0[0]}_{{{0[1]}}}({0[2]})**2>**2-<{0[0]}_{{{0[1]}}}({0[2]})**4>)**0.25)'), # without (pTs)\\n (\\\"([\\\\w_]+)_{([\\\\d,]+)}\\\\[4\\\\](\\\\(.*?\\\\))\\\\(([\\\\w_]+)\\\\)\\\", '((2*<{0[0]}_{{{0[1]}}}{0[2]}({0[3]})**2>**2-<{0[0]}_{{{0[1]}}}{0[2]}({0[3]})**4>)**0.25)'), # with (pTs)\\n )),\\n\\n # 2nd priorities: expand special functions || <> $$ (related: ecc, v, Phi, Psi)\\n StringSubstitution((\\n\\n # ecc = |Ecc|\\n (\\\"ecc_\\\", \\\"|Ecc|_\\\"),\\n # v = |V|\\n (\\\"v_\\\", \\\"|V|_\\\"),\\n\\n # || = abs\\n (\\\"\\\\|([\\\\w_]+)\\\\|(.*?)\\\\(([\\\\w_]+)\\\\)\\\", \\\"|{0[0]}{0[1]}({0[2]})|\\\"), # |ooo|xxx(oxox) -> |oooxxx(oxox)|; oxox is a word\\n\\n # <> = mean\\n (\\\"<([\\\\w_]+)>(.*?)\\\\(([\\\\w_]+)\\\\)\\\", \\\"<{0[0]}{0[1]}({0[2]})>\\\"), # <ooo>xxx(oxox) -> <oooxxx(oxox)>; oxox is a word\\n\\n # Phi = $Ecc$\\n (\\\"Phi_\\\", \\\"$Ecc$_\\\"),\\n # Psi = $V$\\n (\\\"Psi_\\\", '$V$_'),\\n\\n # $$ = get plane angles; only applies to Ecc and V\\n (\\\"\\\\$([\\\\w_]+)\\\\$(.*?)\\\\(([\\\\w_]+)\\\\)\\\", \\\"${0[0]}{0[1]}({0[2]})$\\\"), # <ooo>xxx(oxox) -> <oooxxx(oxox)>; oxox is a word\\n )),\\n\\n )\\n\\n # convert standardized notations to functions\\n self.useStringSubstitution_functionization = StringSubstitution((\\n\\n # ||: absolute value\\n (\\\"\\\\|(.*?)\\\\|\\\", 'abs({0[0]})'),\\n\\n # <>: mean value\\n (\\\"<(.*?)>\\\", 'mean({0[0]},0)'),\\n\\n # $$: get plane angles; only applies to Ecc (angle(-Ecc_n)/n) and V (angle(V_n)/n)\\n (\\\"\\\\$Ecc_{([\\\\d\\\\w+]),([\\\\d\\\\w+])}(.*?)\\\\$\\\", 'angle(Ecc_{{{0[0]},{0[1]}}}{0[2]})/{0[1]}'),\\n (\\\"\\\\$V_{([\\\\d\\\\w+])}(.*?)\\\\$\\\", 'angle(V_{{{0[0]}}}{0[1]})/{0[0]}'),\\n\\n # eccentricity:\\n # ecc_{m,n}(ed) := {-r^m e^{i n phi}}_e\\n (\\\"Ecc_{([\\\\d]+),([\\\\d]+)}\\\\((\\\\w\\\\w)\\\\)\\\", 'self.get_Ecc_n(eccType=\\\"{0[2]}\\\", r_power={0[0]}, order={0[1]})'), # to functions\\n\\n # r-averages\\n # {r^m}(ed) := int(r^m*ed)/int(ed)\\n (\\\"{r\\\\^([\\\\d]+)}\\\\((\\\\w\\\\w)\\\\)\\\", 'self.getRIntegrals(eccType=\\\"{0[1]}\\\", r_power={0[0]}) / self.getRIntegrals(eccType=\\\"{0[1]}\\\", r_power=0)'),\\n\\n # r-integrals\\n # [r^m](ed) := int(r^m*ed)\\n (\\\"\\\\[r\\\\^([\\\\d]+)\\\\]\\\\((\\\\w\\\\w)\\\\)\\\", 'self.getRIntegrals(eccType=\\\"{0[1]}\\\", r_power={0[0]})'),\\n\\n # lifetimes\\n (\\\"lifetime\\\", 'self.getLifetimes()'),\\n\\n # integrated flow:\\n # V_{n}(pion) := pion complex flow vector of order n\\n (\\\"V_{([\\\\d]+)}\\\\(([\\\\w_]+)\\\\)\\\", 'self.get_V_n(particleName=\\\"{0[1]}\\\", order={0[0]})'),\\n\\n # multiplicity:\\n # dN/dy(pion) := pion multiplicity\\n (\\\"dN/dy\\\\(([\\\\w_]+)\\\\)\\\", 'self.get_dNdy(particleName=\\\"{0[0]}\\\")'),\\n\\n # differential flows\\n # V_{n}(pTs)(pion) := complex differential flow vector of order n for pion at pTs values\\n (\\\"V_{([\\\\d]+)}\\\\((.*?)\\\\)\\\\(([\\\\w_]+)\\\\)\\\", 'self.get_diff_V_n(particleName=\\\"{0[2]}\\\", order={0[0]}, pTs={0[1]}, verbose=True)'),\\n\\n # spectra:\\n # dN/(dydpT)(pTs)(pion) := pion spectra at pTs values\\n (\\\"dN/\\\\(dydpT\\\\)\\\\((.*?)\\\\)\\\\(([\\\\w_]+)\\\\)\\\", 'self.get_dNdydpT(particleName=\\\"{0[1]}\\\", pTs={0[0]}, verbose=True)'),\\n\\n ))\\n\\n\\n # perform normalization, should repeat until there is no more changes\\n exprAfterNormalization = expression\\n needMoreChanges = True\\n while needMoreChanges:\\n needMoreChanges = False\\n for stringSubstitution in self.useStringSubstitution_normalization:\\n exprAfterNormalization, numberOfScans = stringSubstitution.applyAllRules(exprAfterNormalization)\\n if numberOfScans>0: needMoreChanges = True\\n # perform functionization, should do only once\\n exprAfterFunctionization, numberOfScans = self.useStringSubstitution_functionization.applyAllRules(exprAfterNormalization)\\n # try to evaluate it\\n try:\\n value = eval(exprAfterFunctionization)\\n return (value, exprAfterNormalization, exprAfterFunctionization)\\n except:\\n print(\\\"Error encounterred evaluating {}:\\\".format(expression))\\n print(\\\"-> {}\\\\n-> {}\\\".format(exprAfterNormalization, exprAfterFunctionization))\\n raise\",\n \"def evaluate(self, g):\\n pass\",\n \"def test_lazy_evaluation(self):\\n pass\",\n \"def test_product_mult_only(self):\\r\\n self.assertEquals(preview.latex_preview('2*3'), r'2\\\\cdot 3')\",\n \"def compile_expressions(self):\\n if getattr(self, \\\"_attrs\\\", None):\\n for k, v in self._attrs.items():\\n try:\\n Expression.compile_cache(v)\\n except:\\n pass\\n if \\\"${\\\" in v and \\\"}\\\" in v:\\n Expression.extract(v)\\n if getattr(self, \\\"_let\\\", None):\\n for k, v in self._let.items():\\n try:\\n Expression.compile_cache(v)\\n except:\\n pass\\n if getattr(self, \\\"text\\\", None):\\n Expression.extract(self.text)\",\n \"def test_evaluate_mod_expression(self):\\n value = self.evaluate_common(\\\"5.5M mod 2M\\\")\\n self.assertTrue(\\n value.type_code == edm.SimpleType.Decimal, \\\"Expected Decimal\\\")\\n self.assertTrue(value.value == decimal.Decimal('1.5'),\\n \\\"Expected 1.5; found %s\\\" % repr(value.value))\\n value = self.evaluate_common(\\\"5.5D mod 2M\\\")\\n self.assertTrue(\\n value.type_code == edm.SimpleType.Double, \\\"Expected Double\\\")\\n self.assertTrue(value.value == 1.5, \\\"Expected 1.5\\\")\\n try:\\n value = self.evaluate_common(\\\"5.5D mod 0\\\")\\n self.fail(\\\"Division by zero\\\")\\n except odata.EvaluationError:\\n pass\\n value = self.evaluate_common(\\\"5.5F mod 2D\\\")\\n self.assertTrue(\\n value.type_code == edm.SimpleType.Double, \\\"Expected Double\\\")\\n self.assertTrue(value.value == 1.5, \\\"Expected 1.5\\\")\\n value = self.evaluate_common(\\\"5 mod 2L\\\")\\n self.assertTrue(\\n value.type_code == edm.SimpleType.Int64, \\\"Expected Int64\\\")\\n self.assertTrue(value.value == 1, \\\"Expected 1L\\\")\\n value = self.evaluate_common(\\\"-5 mod 2L\\\")\\n self.assertTrue(\\n value.type_code == edm.SimpleType.Int64, \\\"Expected Int64\\\")\\n self.assertTrue(value.value == -1, \\\"Expected -1L\\\")\\n try:\\n value = self.evaluate_common(\\\"5 mod '2'\\\")\\n self.fail(\\\"String promotion to int\\\")\\n except odata.EvaluationError:\\n pass\\n value = self.evaluate_common(\\\"5 mod null\\\")\\n self.assertTrue(\\n value.type_code == edm.SimpleType.Int32, \\\"Expected Int32\\\")\\n self.assertTrue(value.value is None, \\\"Expected None\\\")\",\n \"def expression_used(self):\\n return self._expression_used\",\n \"def eval(cls, *args):\\n raise NotImplementedError(\\\"subclasses need to override this method\\\")\",\n \"def user_expressions(self, expressions):\\n compiled_expressions = {}\\n for key, expr in expressions.items():\\n try:\\n compiled_expressions[key] = COMPILER.parse_eval(expr)\\n except CoconutException:\\n compiled_expressions[key] = expr\\n return super(CoconutShell, self).user_expressions(compiled_expressions)\",\n \"def test_staff_inputs_expressions_legacy(self):\\r\\n problem = self.build_problem(answer=\\\"1+1j\\\", tolerance=1e-3)\\r\\n self.assert_grade(problem, '1+j', 'correct')\",\n \"def expression(self, expr):\\n self.set(expression=expr)\",\n \"def multiplier(self) -> global___Expression:\",\n \"def calc(bot, sender, sendmsg, label, args):\\n\\n expr = \\\" \\\".join(args)\\n banned = dir() + dir(builtins)\\n for word in banned:\\n if word in expr:\\n sendmsg(\\\"Illegal word found: \\\" + word)\\n return\\n try:\\n sendmsg(eval(expr))\\n except Exception as e:\\n sendmsg(str(e))\",\n \"def expression(*args, alwaysEvaluate: Union[int, bool]=0, animated: Union[int, bool]=0,\\n attribute: Union[AnyStr, bool]=\\\"\\\", name: Union[AnyStr, bool]=\\\"\\\", object:\\n Union[AnyStr, bool]=\\\"\\\", safe: bool=True, shortNames: bool=True, string:\\n Union[AnyStr, bool]=\\\"\\\", timeDependent: bool=True, unitConversion: Union[AnyStr,\\n bool]=\\\"all.\\\", q=True, query=True, e=True, edit=True, **kwargs)->Union[AnyStr,\\n Any]:\\n pass\",\n \"def test_expr(self):\\n x = t.Action(\\\"returnStuff()\\\")\\n self.assertEqual(writePython(x),\\n dd(\\\"\\\"\\\"\\n _G_python_1, lastError = eval('returnStuff()', self.globals, _locals), None\\n self.considerError(lastError, None)\\n _G_python_1\\n \\\"\\\"\\\"))\",\n \"def evaluate(self, *args, **kwargs) -> Union[str, int, float, bool]:\\n return True\",\n \"def has_expression(self):\\n return self._expression is not None\",\n \"def evaluateExpression(expr):\\n\\toperators = {ast.Add: op.add, ast.Sub: op.sub, ast.Mult: op.mul,\\n\\t\\t\\t\\t ast.Div: op.truediv, ast.USub: op.neg, ast.Pow: myPow}\\n\\tnode = ast.parse(expr.strip(), mode='eval')\\n\\treturn evaluate(node.body,operators)\",\n \"def is_expression(self):\\r\\n return conf.lib.clang_isExpression(self)\",\n \"def expression(self, item):\\n a = item.get(\\\"assertion\\\", item.get(\\\"expression\\\"))\\n\\n values = item[\\\"values\\\"]\\n\\n left = self.resolve(values[0])\\n\\n if a == \\\"equals\\\" or a == \\\"equal\\\":\\n right = self.resolve(values[1])\\n return left == right\\n elif a == \\\"less\\\":\\n right = self.resolve(values[1])\\n return left < right\\n elif a == \\\"less_equal\\\":\\n right = self.resolve(values[1])\\n return left <= right\\n elif a == \\\"not\\\":\\n return not left\\n elif a == \\\"or\\\":\\n if left is True:\\n return True\\n\\n for i in range(1, len(values)):\\n result = self.resolve(values[i])\\n if result is True:\\n return True\\n\\n return False\\n elif a == \\\"and\\\":\\n if left is False:\\n return False\\n\\n for i in range(1, len(values)):\\n result = self.resolve(values[i])\\n if result is False:\\n return False\\n\\n return True\\n elif a == \\\"sum\\\":\\n result = left\\n\\n assert type(left) in (int, float, str, list)\\n # Sum supports flattened values since this only occurs when\\n # a string like \\\"{a} {b} {c}\\\" is compiled. Everything else,\\n # including arithmetic is compiled as a nested expression.\\n for i in range(1, len(values)):\\n r = self.resolve(values[i])\\n\\n if type(r) in (int, float, list) and type(result) in (\\n int,\\n float,\\n list,\\n ):\\n result += r\\n else:\\n result = f\\\"{str(result)}{str(r)}\\\"\\n\\n return result\\n elif a == \\\"subtraction\\\":\\n right = self.resolve(values[1])\\n assert type(left) in (int, float)\\n assert type(right) in (int, float)\\n return left - right\\n elif a == \\\"multiplication\\\":\\n right = self.resolve(values[1])\\n assert type(left) in (int, float, str)\\n assert type(right) in (int, float, str)\\n return left * right\\n elif a == \\\"modulus\\\":\\n right = self.resolve(values[1])\\n assert type(left) in (int, float)\\n assert type(right) in (int, float)\\n return left % right\\n elif a == \\\"division\\\":\\n right = self.resolve(values[1])\\n assert type(left) in (int, float, str)\\n assert type(right) in (int, float, str)\\n return left / right\\n elif a == \\\"exponential\\\":\\n right = self.resolve(values[1])\\n assert type(left) in (int, float)\\n assert type(right) in (int, float)\\n return left ** right\\n else:\\n assert False, f\\\"Unsupported operation: {a}\\\"\",\n \"def reinit_exprs(self):\\n command = reduce(lambda acc, e: acc | e[1], self.commands, NoMatch())\\n self.dm_expr = self.dm_expr_head + command\\n self.expr = self.expr_head + command\",\n \"def eval(self, A):\\n\\t\\tpass\",\n \"def treat_as_expression(self):\\n special_chars = '{}()[]=<>.\\\"\\\\'/'\\n return any(special_char in self.key for special_char in special_chars)\",\n \"def test_unary_op_support():\\n check_peval_expression(\\\"+(2)\\\", {}, \\\"2\\\", fully_evaluated=True, expected_value=2)\\n check_peval_expression(\\\"-(-3)\\\", {}, \\\"3\\\", fully_evaluated=True, expected_value=3)\\n check_peval_expression_bool(\\\"not 0\\\", {}, True)\\n check_peval_expression(\\\"~(-4)\\\", {}, \\\"3\\\", fully_evaluated=True, expected_value=3)\",\n \"def __bool__(self):\\n return bool(self.exp)\",\n \"def with_continual_eval(self):\\n return self._with_continual_eval\",\n \"def test_RestrictingNodeTransformer__visit_NotEq__1():\\n assert restricted_eval('1 != int(\\\"1\\\")') is False\",\n \"def evaluator(self, candidates, args):\\n\\t\\traise NotImplementedError\",\n \"def usesEvaluationManager(self):\\n \\n pass\",\n \"def testCalculate(self):\\r\\n for i in range(len(self.__testExpressions)):\\r\\n self.__Calculator.setExpression(self.__testExpressions[i])\\r\\n self.__Calculator.calculateResult()\\r\\n self.assertEqual(self.__Calculator.getResult(), self.__testResult[i])\",\n \"def evaluator(self, candidates, args):\\r\\n raise NotImplementedError\",\n \"def __call__(self, expression):\\n self.set_expression(expression)\",\n \"def static_call(self, *args):\\n return self.expression\",\n \"def test_bin_op_support():\\n check_peval_expression(\\\"1 + 2\\\", {}, \\\"3\\\", fully_evaluated=True, expected_value=3)\\n check_peval_expression(\\\"2 - 1\\\", {}, \\\"1\\\", fully_evaluated=True, expected_value=1)\\n check_peval_expression(\\\"2 * 3\\\", {}, \\\"6\\\", fully_evaluated=True, expected_value=6)\\n check_peval_expression(\\\"9 / 2\\\", {}, \\\"4.5\\\", fully_evaluated=True, expected_value=4.5)\\n check_peval_expression(\\\"9 // 2\\\", {}, \\\"4\\\", fully_evaluated=True, expected_value=4)\\n check_peval_expression(\\\"9 % 2\\\", {}, \\\"1\\\", fully_evaluated=True, expected_value=1)\\n check_peval_expression(\\\"2 ** 4\\\", {}, \\\"16\\\", fully_evaluated=True, expected_value=16)\\n check_peval_expression(\\\"3 << 2\\\", {}, \\\"12\\\", fully_evaluated=True, expected_value=12)\\n check_peval_expression(\\\"64 >> 3\\\", {}, \\\"8\\\", fully_evaluated=True, expected_value=8)\\n check_peval_expression(\\\"17 | 3\\\", {}, \\\"19\\\", fully_evaluated=True, expected_value=19)\\n check_peval_expression(\\\"17 ^ 3\\\", {}, \\\"18\\\", fully_evaluated=True, expected_value=18)\\n check_peval_expression(\\\"17 & 3\\\", {}, \\\"1\\\", fully_evaluated=True, expected_value=1)\",\n \"def value(self) -> global___Expression:\",\n \"def value(self) -> global___Expression:\",\n \"def parsable_as_expression(self):\\n return self.parsable and self.expression_ast_node is not None\"\n]","isConversational":false},"negative_scores":{"kind":"list like","value":["0.6572281","0.6568479","0.65574527","0.65574527","0.64303815","0.64303815","0.64303815","0.6407245","0.6345367","0.62577146","0.6183484","0.61799407","0.61565596","0.6149802","0.61396885","0.6117585","0.6077628","0.60701233","0.6039489","0.60292995","0.60206705","0.60191786","0.59915483","0.59470314","0.5879327","0.585465","0.5849977","0.584972","0.58419895","0.5833385","0.5829656","0.5815401","0.58123887","0.58111537","0.5806883","0.5785931","0.5764871","0.5734846","0.56907314","0.5680855","0.5664111","0.5661119","0.56469285","0.56336975","0.5624941","0.5598784","0.5598784","0.5598413","0.5597431","0.5594371","0.55929285","0.5590202","0.5588007","0.55842125","0.557657","0.55494124","0.55101854","0.55056965","0.55051863","0.5486196","0.5482433","0.54780906","0.5476766","0.5473439","0.54724216","0.547194","0.5469833","0.54655933","0.5454055","0.5450637","0.54475904","0.54409444","0.5435357","0.5434681","0.5433786","0.54245347","0.5420258","0.5394213","0.5393372","0.5388947","0.5385896","0.53611714","0.53567904","0.53541565","0.5349882","0.5347199","0.53446764","0.5344267","0.53403664","0.53399515","0.53327066","0.5320873","0.53151983","0.5309388","0.5300123","0.5299554","0.5298743","0.52981323","0.52981323","0.5290363"],"string":"[\n \"0.6572281\",\n \"0.6568479\",\n \"0.65574527\",\n \"0.65574527\",\n \"0.64303815\",\n \"0.64303815\",\n \"0.64303815\",\n \"0.6407245\",\n \"0.6345367\",\n \"0.62577146\",\n \"0.6183484\",\n \"0.61799407\",\n \"0.61565596\",\n \"0.6149802\",\n \"0.61396885\",\n \"0.6117585\",\n \"0.6077628\",\n \"0.60701233\",\n \"0.6039489\",\n \"0.60292995\",\n \"0.60206705\",\n \"0.60191786\",\n \"0.59915483\",\n \"0.59470314\",\n \"0.5879327\",\n \"0.585465\",\n \"0.5849977\",\n \"0.584972\",\n \"0.58419895\",\n \"0.5833385\",\n \"0.5829656\",\n \"0.5815401\",\n \"0.58123887\",\n \"0.58111537\",\n \"0.5806883\",\n \"0.5785931\",\n \"0.5764871\",\n \"0.5734846\",\n \"0.56907314\",\n \"0.5680855\",\n \"0.5664111\",\n \"0.5661119\",\n \"0.56469285\",\n \"0.56336975\",\n \"0.5624941\",\n \"0.5598784\",\n \"0.5598784\",\n \"0.5598413\",\n \"0.5597431\",\n \"0.5594371\",\n \"0.55929285\",\n \"0.5590202\",\n \"0.5588007\",\n \"0.55842125\",\n \"0.557657\",\n \"0.55494124\",\n \"0.55101854\",\n \"0.55056965\",\n \"0.55051863\",\n \"0.5486196\",\n \"0.5482433\",\n \"0.54780906\",\n \"0.5476766\",\n \"0.5473439\",\n \"0.54724216\",\n \"0.547194\",\n \"0.5469833\",\n \"0.54655933\",\n \"0.5454055\",\n \"0.5450637\",\n \"0.54475904\",\n \"0.54409444\",\n \"0.5435357\",\n \"0.5434681\",\n \"0.5433786\",\n \"0.54245347\",\n \"0.5420258\",\n \"0.5394213\",\n \"0.5393372\",\n \"0.5388947\",\n \"0.5385896\",\n \"0.53611714\",\n \"0.53567904\",\n \"0.53541565\",\n \"0.5349882\",\n \"0.5347199\",\n \"0.53446764\",\n \"0.5344267\",\n \"0.53403664\",\n \"0.53399515\",\n \"0.53327066\",\n \"0.5320873\",\n \"0.53151983\",\n \"0.5309388\",\n \"0.5300123\",\n \"0.5299554\",\n \"0.5298743\",\n \"0.52981323\",\n \"0.52981323\",\n \"0.5290363\"\n]","isConversational":false},"document_score":{"kind":"string","value":"0.71497124"},"document_rank":{"kind":"string","value":"0"}}},{"rowIdx":16588,"cells":{"query":{"kind":"string","value":"Trap param outside of gerber param block."},"document":{"kind":"string","value":"def test_missing_delim(self):"},"metadata":{"kind":"string","value":"{\n \"objective\": {\n \"self\": [],\n \"paired\": [],\n \"triplet\": [\n [\n \"query\",\n \"document\",\n \"negatives\"\n ]\n ]\n }\n}"},"negatives":{"kind":"list like","value":["def prepost_hook_too_many_parameters(self, param) -> None:\n pass","def _handleInput(self, paramInput):\n pass","def paramValueChanged(self, param):\n if self._printSWAP == True:\n print param.name + \" in address \" + str(param.getRegAddress()) + \" changed to \" + param.getValueInAscii()","def _arg(self, t):\n self.RaiseError(t, \"Arguments should already have been processed\")","def log_param(key, value):\n mlflow.log_param(key, value)","def _load_parameter(self):","def set_params(self, *arg):\n pass","def init_params(self):\n blah","def _setup_params(self,**params):\n ### a parameter might be passed in for one of the extra_pos;\n ### if a key in the params dict is not a *parameter* of this\n ### PO, then try it on the extra_pos\n for n,p in params.items():\n if n not in self.params():\n self.set_parameter_value(n,p)\n del params[n]\n\n Parameterized._setup_params(self,**params)","def passer(self, value=None):\n pass","def _check_params(self):\n pass","def setParam(self,param,value):\n if param in self.params.keys():\n self.params[param] = value","def change_general_param(self, param, val):\n assert param in self.params, '%s is not recognized as a valid parameter' % param\n self.params[param].change_value(val)","def log_param(self, name: str, value):\n self.params[name] = value\n\n self._sync_log_event()","def __call__(self, param, xyz=False):\n pass","def inner_test(param: int):\n pass","def inner_test(param: int):\n pass","def inner_test(param: int):\n pass","def _pyro_param(self, msg):\n name = msg[\"name\"]\n param_name = params.user_param_name(name)\n if isinstance(self.prior, dict):\n # prior is a dict of distributions\n if param_name in self.prior.keys():\n msg[\"fn\"] = self.prior[param_name]\n if isinstance(msg['fn'], Distribution):\n msg[\"args\"] = ()\n msg[\"kwargs\"] = {}\n msg[\"baseline\"] = {}\n else:\n return super(LiftPoutine, self)._pyro_param(msg)\n elif isinstance(self.prior, Distribution):\n # prior is a distribution\n msg[\"fn\"] = self.prior\n msg[\"args\"] = ()\n msg[\"kwargs\"] = {}\n msg[\"baseline\"] = {}\n elif callable(self.prior):\n if not isinstance(self.prior, Distribution):\n # prior is a stochastic fn. block sample\n msg[\"stop\"] = True\n msg[\"fn\"] = self.prior\n else:\n # otherwise leave as is\n return super(LiftPoutine, self)._pyro_param(msg)\n msg[\"type\"] = \"sample\"\n msg[\"done\"] = False\n msg[\"is_observed\"] = False\n return self._pyro_sample(msg)","def override__args(self,arg,value):\n self.__args[arg] = value","def exc_to_catch(request):\n return request.param","def process_parameter(self, resources, resource, api, operation, parameter,\n context):\n pass","def _update_param_from_tkvar(self,param_name,force=False):\n self.debug(\"TkPO._update_param_from_tkvar(%s)\"%param_name)\n\n param_obj = self.get_parameter_object(param_name)\n\n if not lookup_by_class(self.param_immediately_apply_change,\n type(param_obj)) and not force:\n return\n else:\n super(TkParameterized,self)._update_param_from_tkvar(param_name)","def HandleMissingParameterDoc(self, token, param_name):\n raise TypeError('Abstract method HandleMissingParameterDoc not implemented')","def set_params(self):\r\n pass","def setParameter(self, name, value):","def params(self):\n pass","def Junk(val):\n print 'val is:', val","def set_params(self, params):","def inner_test(param: dict):\n pass","def _handleInput(self, paramInput):\n super()._handleInput(paramInput)\n lambdaFind = paramInput.findFirst('lambda')\n if lambdaFind != None:\n self.lambdaVar = lambdaFind.value\n else:\n self.raiseAnError(IOError,'lambda value needed for Exponential distribution')\n low = paramInput.findFirst('low')\n if low != None:\n self.low = low.value\n else:\n self.low = 0.0\n # check if lower bound is set, otherwise default\n if not self.lowerBoundUsed:\n self.lowerBoundUsed = True\n self.lowerBound = self.low\n self.initializeDistribution()","def resetParam(key, value):\n \n if globalParams == {}:\n warning(\"WARNING: runtime parameters not yet initialized\")\n LoadParams(\"_defaults\")\n \n if key in globalParams.keys():\n globalParams[key] = value\n else:\n raise ValueError()","def patience_param(x):\n # -- TODO: make this do something!\n return x","def check_params(self):\n raise NotImplementedError","def define_parameters(self):","def putintparam(self,param_,parvalue_): # 3\n if not isinstance(param_,iparam): raise TypeError(\"Argument param has wrong type\")\n res = self.__obj.putintparam(param_,parvalue_)\n if res != 0:\n result,msg = self.__getlasterror(res)\n raise Error(rescode(res),msg)","def __set_callback(self, req):\n recv_val = _retrieve_rtparam_value(req.param)\n\n if recv_val is None:\n rospy.logerr('Unknown parameter type: %d', req.param.type)\n return None\n\n if not isinstance(recv_val, self._type):\n rospy.logerr('Parameter %s is type %s but got %s',\n self._name, str(self._type), str(recv_val))\n\n self.__set_value(recv_val)\n return _generate_rtparam_msg(self._value)","def _handleInput(self, paramInput):\n super()._handleInput(paramInput)\n lambdaFind = paramInput.findFirst('lambda')\n if lambdaFind != None:\n self.lambdaVar = lambdaFind.value\n else:\n self.raiseAnError(IOError,'lambda (scale) value needed for Weibull distribution')\n kFind = paramInput.findFirst('k')\n if kFind != None:\n self.k = kFind.value\n else:\n self.raiseAnError(IOError,'k (shape) value needed for Weibull distribution')\n lowFind = paramInput.findFirst('low')\n if lowFind != None:\n self.low = lowFind.value\n else:\n self.low = 0.0\n self.initializeDistribution()","def handleParameterRequest(self,data):\n req = RequestParamRequest()\n req.deserialize(data)\n resp = RequestParamResponse()\n param = rospy.get_param(req.name)\n if param == None:\n rospy.logerr(\"Parameter %s does not exist\"%req.name)\n return\n if (type(param) == dict):\n rospy.logerr(\"Cannot send param %s because it is a dictionary\"%req.name)\n return\n if (type(param) != list):\n param = [param]\n #check to make sure that all parameters in list are same type\n t = type(param[0])\n for p in param:\n if t!= type(p):\n rospy.logerr('All Paramers in the list %s must be of the same type'%req.name)\n return \n if (t == int):\n resp.ints= param\n if (t == float):\n resp.floats=param\n if (t == str):\n resp.strings = param\n print resp\n data_buffer = StringIO.StringIO()\n resp.serialize(data_buffer)\n self.send(TopicInfo.ID_PARAMETER_REQUEST, data_buffer.getvalue())","def __init__(self, param):","def set_params(self, **kwargs):\n ...","def handle_context_missing(self):","def initialize_params(self, params):\n pass","def getParameter(self, name):","def putparam(self,parname_,parvalue_): # 3\n res = self.__obj.putparam(parname_,parvalue_)\n if res != 0:\n result,msg = self.__getlasterror(res)\n raise Error(rescode(res),msg)","def _handleInput(self, paramInput):\n super()._handleInput(paramInput)\n locationFind = paramInput.findFirst('location')\n if locationFind != None:\n self.location = locationFind.value\n else:\n self.raiseAnError(IOError,'location value needed for Laplace distribution')\n scaleFind = paramInput.findFirst('scale')\n if scaleFind != None:\n self.scale = scaleFind.value\n else:\n self.raiseAnError(IOError,'scale value needed for Laplace distribution')\n self.initializeDistribution()","def set_param(self, param, value):\n self._set_param_client(param, value)","def inner_test(param: str):\n pass","def __breakpointhook__(*args, **kwargs): # real signature unknown\n pass","def test_wrong_parameters(self):\n with self.assertWarns(RuntimeWarning):\n Parameters(1, mu=3, lambda_=2)","def _get_raw_params(self, node):","def _handleInput(self, paramInput):\n super()._handleInput(paramInput)\n pFind = paramInput.findFirst('p')\n if pFind != None:\n self.p = pFind.value\n else: self.raiseAnError(IOError,'p value needed for Geometric distribution')\n self.initializeDistribution()","def log_params(self, params=None):\n if params is not None:\n dump_obj = params.__dict__\n else:\n dump_obj = self.params.__dict__\n self.logger.log_params(dump_obj)","def param(self, *args, **kwargs):\n return self.options.param(*args,**kwargs)","def handleInput(self, paramInput):\n MCMC.handleInput(self, paramInput)","def postparse_hook_undeclared_parameter_annotation(self, data) -> cmd2.plugin.PostparsingData:\n pass","def __init__(self, *args: Any, **kwargs: Any) -> None:\n kwargs[\"aux_params\"] = None\n super().__init__(*args, **kwargs)","def set_parameter(self, param, value, stripe = 0, location = 3):\n if param in self.fpga.cabac_top[0].params:\n self.fpga.set_cabac_value(param, value, stripe)\n time.sleep(0.1)\n self.fpga.send_cabac_config(stripe)\n\n elif param in [\"V_SL\", \"V_SH\", \"V_RGL\", \"V_RGH\", \"V_PL\", \"V_PH\"]:\n self.fpga.set_clock_voltages({param: value})\n\n elif param == \"I_OS\":\n self.fpga.set_current_source(value, stripe)\n\n else:\n print(\"Warning: unidentified parameter for the REB: %s\" % param)","def _arguments(self, t):\n self.RaiseError(t, \"Arguments should already have been processed\")","def _sanitize_param(self, param):\n if param:\n # Can't send unicode.\n param = str(param)\n return param","def set_parameter_value(self, parameter, value):\n pass","def set_parameter(self, params, name, val):\n raise NotImplementedError()","def transclusion_param(self, **kw):\n return self._open('param',\n allowed_attrs=['name', 'type', 'value', 'valuetype', ],\n **kw)","def set_params(self, **kwargs) -> NoReturn:\n pass","def gui_set_param(self,param_name,val):\n self._tkvar_set(param_name,val) # ERROR: presumably calls trace stuff twice\n self._handle_gui_set(param_name,force=True)","def monkey_set_f_params(self):\n self._monkey_set_f_params_counter += 1","def monkey_set_f_params(self):\n self._monkey_set_f_params_counter += 1","def as_param(self):\n self._clean()\n return self.param","def _getParam(self, callerId, key):\n if key not in self.FilterParameters:\n self.__docWriter.addParam(callerId, key)","def set_param_raw(param, value, verbose=False):\n if type(value) == dict:\n # #1098 changing dictionary behavior to be an update, rather\n # than replace behavior.\n for k, v in value.items():\n # dictionary keys must be non-unicode strings\n if isinstance(k, str):\n set_param_raw(ns_join(param, k), v, verbose=verbose)\n else:\n raise RosParamException(\"YAML dictionaries must have string keys. Invalid dictionary is:\\n%s\"%value)\n else:\n try:\n expected_type = long\n except NameError :\n expected_type = int\n \n if type(value) == expected_type:\n if value > sys.maxsize:\n raise RosParamException(\"Overflow: Parameter Server integers must be 32-bit signed integers:\\n\\t-%s <= value <= %s\"%(maxint - 1, maxint))\n \n try:\n get_param_server().setParam(param, value)\n except socket.error:\n raise RosParamIOException(\"Unable to communicate with master!\")\n if verbose:\n print(\"set parameter [%s] to [%s]\"%(param, value))","def edit_parameter(request, parameter, **_kwargs):\n pass","def set_param(self, name, value, *, distrib=None, ref=None):\n raise NotImplementedError","def _handleInput(self, paramInput):\n super()._handleInput(paramInput)\n lowFind = paramInput.findFirst('low')\n if lowFind != None:\n self.low = lowFind.value\n alphaFind = paramInput.findFirst('alpha')\n if alphaFind != None:\n self.alpha = alphaFind.value\n else:\n self.raiseAnError(IOError,'alpha value needed for Gamma distribution')\n betaFind = paramInput.findFirst('beta')\n if betaFind != None:\n self.beta = betaFind.value\n # check if lower bound are set, otherwise default\n if not self.lowerBoundUsed:\n self.lowerBoundUsed = True\n self.lowerBound = self.low\n self.initializeDistribution() #TODO this exists in a couple classes; does it really need to be here and not in Simulation? - No. - Andrea","def handle_arguments(self, args):\n debug(\"BloomGenerator.handle_arguments: got args -> \" + str(args))","def _prepare_site(self, msg):\n name = msg[\"name\"]\n param_name = params.user_param_name(name)\n if isinstance(self.prior, dict) and param_name in self.prior.keys() \\\n or callable(self.prior):\n if msg[\"type\"] == \"param\":\n msg[\"done\"] = True\n return msg","def _add_setup_param(self, name, fmt, **kwargs):\n self._param_dict.add(name, '', None, fmt,\n startup_param=False,\n direct_access=True,\n visibility=ParameterDictVisibility.READ_ONLY,\n **kwargs)","def _pre_argument_parsing(self):\n pass","def set_params(self, *, params: Params) -> None: # pragma: no cover\n\t\tsuper().set_params(params=params)","def _update_param_from_tkvar(self,param_name):\n self.debug(\"TkPOb._update_param_from_tkvar(%s)\"%param_name)\n\n parameter,sourcePO=self.get_parameter_object(param_name,with_source=True)\n\n ### can only edit constant parameters for class objects\n if parameter.constant is True and not isinstance(sourcePO,type):\n return ### HIDDEN\n\n tkvar = self._tkvars[param_name]\n\n if self._tkvar_changed(param_name):\n # don't attempt to set if there was a string-to-object translation error\n if self.translators[param_name].last_string2object_failed:\n return ### HIDDEN\n\n # (use _original_get() because we don't want the tkvar to be reset to\n # the parameter's current value!)\n val = self._string2object(param_name,tkvar._original_get())\n\n try:\n self._set_parameter(param_name,val)\n except: # everything\n tkvar.set(tkvar._last_good_val)\n raise # whatever the parameter-setting error was\n\n self.debug(\"set %s to %s\"%(param_name,val))\n\n if hasattr(tkvar,'_on_modify'):\n tkvar._on_modify()\n\n ### call any function associated with GUI set()\n if hasattr(tkvar,'_on_set'):\n\n # CEBALERT: provide a way of allowing other gui components\n # to figure out where a callback error might have come\n # from. Callback instances (the Callback class is defined\n # in Tkinter.py) store a widget, but often it appears to\n # be the Tk instance - which is of no use in later\n # determining where an error might have originated.\n global _last_one_set\n if hasattr(self,'master'):\n _last_one_set = self.master\n\n tkvar._on_set()","def monkey_set_params(self, **args):\n self._monkey_set_params_counter += 1\n assert self._args == (args,), 'unexpected additional arguments. Keep the type in mind'","def update_parameter(self, param, val, force=False):\n self._update_dict[param] = val\n if force:\n self._cur_val[param] = None","def set_params(self, **params):\n return super().set_params(**params)","def set_reg_param(self,reg_param):\n \n type_name = type(reg_param).__name__\n if re.search('float',type_name) != None:\n if reg_param < 0:\n raise KINSOL_Exception(\"Value sent to set_reg_param must be equal to or larger than zero.\")\n else:\n self.reg_param = reg_param\n else:\n raise KINSOL_Exception(\"The variable sent to 'set_reg_param' must be a float.\")","def __init__(self):\n self._params = None","def _post_argument_parsing(self):\n pass","def _check_param(in_params, req_param, opt_param=list()):\n for param in req_param:\n if param not in in_params:\n raise ValueError('{} parameter is required'.format(param))\n defined_param = set(req_param + opt_param)\n for param in in_params:\n if param not in defined_param:\n print(\n \"WARNING: received unexpected parameter {}\".format(param))","def parameters_changed(self):\n pass","def test_deregister_parameter_handler(self, to_deregister):\n ff = ForceField(xml_simple_ff)\n # Make sure the handler is present in the test force field\n handler_found = False\n for handler in ff._parameter_handlers.values():\n if isinstance(handler, ToolkitAM1BCCHandler):\n handler_found = True\n assert handler_found\n ff.deregister_parameter_handler(to_deregister)\n # Make sure the handler is absent after deletion\n handler_found = False\n for handler in ff._parameter_handlers.values():\n if isinstance(handler, ToolkitAM1BCCHandler):\n handler_found = True\n assert not (handler_found)\n\n with pytest.raises(KeyError):\n ff.deregister_parameter_handler(to_deregister)","def set_params(self, *argv, **kwargs):\n pass","def set_params(self, *argv, **kwargs):\n pass","def set_params(self, *argv, **kwargs):\n pass","def set_params(self, *argv, **kwargs):\n pass","def set_params(self, *argv, **kwargs):\n pass","def inv_patience_param(x):\n # -- TODO: make this do something!\n return x","def handle_argument(self, bit):\n if self.current_argument is None:\n try:\n self.current_argument = self.arguments.pop(0)\n except IndexError:\n raise TooManyArguments(self.tagname, self.todo)\n handled = self.current_argument.parse(self.parser, bit, self.tagname, self.kwargs)\n while not handled:\n try:\n self.current_argument = self.arguments.pop(0)\n except IndexError:\n if self.options.breakpoints:\n raise BreakpointExpected(self.tagname, self.options.breakpoints, bit)\n elif self.options.next_breakpoint:\n raise BreakpointExpected(self.tagname, [self.options.next_breakpoint], bit)\n else:\n raise TooManyArguments(self.tagname, self.todo)\n handled = self.current_argument.parse(self.parser, bit, self.tagname, self.kwargs)","def test_validate_late_contextual_fparam_raises(self):\n fsig = FSignature(\n [forge.arg('a'), forge.ctx('self')],\n __validate_parameters__=False,\n )\n with pytest.raises(TypeError) as excinfo:\n fsig.validate()\n assert excinfo.value.args[0] == \\\n 'Only the first parameter can be contextual'","def putintparam(self,param_,parvalue_):\n res = __library__.MSK_XX_putintparam(self.__nativep,param_,parvalue_)\n if res != 0:\n _,msg = self.__getlasterror(res)\n raise Error(rescode(res),msg)","def triggered(self, *args, **kwargs): # real signature unknown\n pass","def _get_parameters(self):\n return None","def _paramUpdate(self):\n\n # Update the database attributes accordingly.\n dt.utilities.DB_attrs_save(self.Database, self.newParam)","def getintparam(self,param_): # 3\n if not isinstance(param_,iparam): raise TypeError(\"Argument param has wrong type\")\n res,resargs = self.__obj.getintparam(param_)\n if res != 0:\n result,msg = self.__getlasterror(res)\n raise Error(rescode(res),msg)\n _parvalue_return_value = resargs\n return _parvalue_return_value"],"string":"[\n \"def prepost_hook_too_many_parameters(self, param) -> None:\\n pass\",\n \"def _handleInput(self, paramInput):\\n pass\",\n \"def paramValueChanged(self, param):\\n if self._printSWAP == True:\\n print param.name + \\\" in address \\\" + str(param.getRegAddress()) + \\\" changed to \\\" + param.getValueInAscii()\",\n \"def _arg(self, t):\\n self.RaiseError(t, \\\"Arguments should already have been processed\\\")\",\n \"def log_param(key, value):\\n mlflow.log_param(key, value)\",\n \"def _load_parameter(self):\",\n \"def set_params(self, *arg):\\n pass\",\n \"def init_params(self):\\n blah\",\n \"def _setup_params(self,**params):\\n ### a parameter might be passed in for one of the extra_pos;\\n ### if a key in the params dict is not a *parameter* of this\\n ### PO, then try it on the extra_pos\\n for n,p in params.items():\\n if n not in self.params():\\n self.set_parameter_value(n,p)\\n del params[n]\\n\\n Parameterized._setup_params(self,**params)\",\n \"def passer(self, value=None):\\n pass\",\n \"def _check_params(self):\\n pass\",\n \"def setParam(self,param,value):\\n if param in self.params.keys():\\n self.params[param] = value\",\n \"def change_general_param(self, param, val):\\n assert param in self.params, '%s is not recognized as a valid parameter' % param\\n self.params[param].change_value(val)\",\n \"def log_param(self, name: str, value):\\n self.params[name] = value\\n\\n self._sync_log_event()\",\n \"def __call__(self, param, xyz=False):\\n pass\",\n \"def inner_test(param: int):\\n pass\",\n \"def inner_test(param: int):\\n pass\",\n \"def inner_test(param: int):\\n pass\",\n \"def _pyro_param(self, msg):\\n name = msg[\\\"name\\\"]\\n param_name = params.user_param_name(name)\\n if isinstance(self.prior, dict):\\n # prior is a dict of distributions\\n if param_name in self.prior.keys():\\n msg[\\\"fn\\\"] = self.prior[param_name]\\n if isinstance(msg['fn'], Distribution):\\n msg[\\\"args\\\"] = ()\\n msg[\\\"kwargs\\\"] = {}\\n msg[\\\"baseline\\\"] = {}\\n else:\\n return super(LiftPoutine, self)._pyro_param(msg)\\n elif isinstance(self.prior, Distribution):\\n # prior is a distribution\\n msg[\\\"fn\\\"] = self.prior\\n msg[\\\"args\\\"] = ()\\n msg[\\\"kwargs\\\"] = {}\\n msg[\\\"baseline\\\"] = {}\\n elif callable(self.prior):\\n if not isinstance(self.prior, Distribution):\\n # prior is a stochastic fn. block sample\\n msg[\\\"stop\\\"] = True\\n msg[\\\"fn\\\"] = self.prior\\n else:\\n # otherwise leave as is\\n return super(LiftPoutine, self)._pyro_param(msg)\\n msg[\\\"type\\\"] = \\\"sample\\\"\\n msg[\\\"done\\\"] = False\\n msg[\\\"is_observed\\\"] = False\\n return self._pyro_sample(msg)\",\n \"def override__args(self,arg,value):\\n self.__args[arg] = value\",\n \"def exc_to_catch(request):\\n return request.param\",\n \"def process_parameter(self, resources, resource, api, operation, parameter,\\n context):\\n pass\",\n \"def _update_param_from_tkvar(self,param_name,force=False):\\n self.debug(\\\"TkPO._update_param_from_tkvar(%s)\\\"%param_name)\\n\\n param_obj = self.get_parameter_object(param_name)\\n\\n if not lookup_by_class(self.param_immediately_apply_change,\\n type(param_obj)) and not force:\\n return\\n else:\\n super(TkParameterized,self)._update_param_from_tkvar(param_name)\",\n \"def HandleMissingParameterDoc(self, token, param_name):\\n raise TypeError('Abstract method HandleMissingParameterDoc not implemented')\",\n \"def set_params(self):\\r\\n pass\",\n \"def setParameter(self, name, value):\",\n \"def params(self):\\n pass\",\n \"def Junk(val):\\n print 'val is:', val\",\n \"def set_params(self, params):\",\n \"def inner_test(param: dict):\\n pass\",\n \"def _handleInput(self, paramInput):\\n super()._handleInput(paramInput)\\n lambdaFind = paramInput.findFirst('lambda')\\n if lambdaFind != None:\\n self.lambdaVar = lambdaFind.value\\n else:\\n self.raiseAnError(IOError,'lambda value needed for Exponential distribution')\\n low = paramInput.findFirst('low')\\n if low != None:\\n self.low = low.value\\n else:\\n self.low = 0.0\\n # check if lower bound is set, otherwise default\\n if not self.lowerBoundUsed:\\n self.lowerBoundUsed = True\\n self.lowerBound = self.low\\n self.initializeDistribution()\",\n \"def resetParam(key, value):\\n \\n if globalParams == {}:\\n warning(\\\"WARNING: runtime parameters not yet initialized\\\")\\n LoadParams(\\\"_defaults\\\")\\n \\n if key in globalParams.keys():\\n globalParams[key] = value\\n else:\\n raise ValueError()\",\n \"def patience_param(x):\\n # -- TODO: make this do something!\\n return x\",\n \"def check_params(self):\\n raise NotImplementedError\",\n \"def define_parameters(self):\",\n \"def putintparam(self,param_,parvalue_): # 3\\n if not isinstance(param_,iparam): raise TypeError(\\\"Argument param has wrong type\\\")\\n res = self.__obj.putintparam(param_,parvalue_)\\n if res != 0:\\n result,msg = self.__getlasterror(res)\\n raise Error(rescode(res),msg)\",\n \"def __set_callback(self, req):\\n recv_val = _retrieve_rtparam_value(req.param)\\n\\n if recv_val is None:\\n rospy.logerr('Unknown parameter type: %d', req.param.type)\\n return None\\n\\n if not isinstance(recv_val, self._type):\\n rospy.logerr('Parameter %s is type %s but got %s',\\n self._name, str(self._type), str(recv_val))\\n\\n self.__set_value(recv_val)\\n return _generate_rtparam_msg(self._value)\",\n \"def _handleInput(self, paramInput):\\n super()._handleInput(paramInput)\\n lambdaFind = paramInput.findFirst('lambda')\\n if lambdaFind != None:\\n self.lambdaVar = lambdaFind.value\\n else:\\n self.raiseAnError(IOError,'lambda (scale) value needed for Weibull distribution')\\n kFind = paramInput.findFirst('k')\\n if kFind != None:\\n self.k = kFind.value\\n else:\\n self.raiseAnError(IOError,'k (shape) value needed for Weibull distribution')\\n lowFind = paramInput.findFirst('low')\\n if lowFind != None:\\n self.low = lowFind.value\\n else:\\n self.low = 0.0\\n self.initializeDistribution()\",\n \"def handleParameterRequest(self,data):\\n req = RequestParamRequest()\\n req.deserialize(data)\\n resp = RequestParamResponse()\\n param = rospy.get_param(req.name)\\n if param == None:\\n rospy.logerr(\\\"Parameter %s does not exist\\\"%req.name)\\n return\\n if (type(param) == dict):\\n rospy.logerr(\\\"Cannot send param %s because it is a dictionary\\\"%req.name)\\n return\\n if (type(param) != list):\\n param = [param]\\n #check to make sure that all parameters in list are same type\\n t = type(param[0])\\n for p in param:\\n if t!= type(p):\\n rospy.logerr('All Paramers in the list %s must be of the same type'%req.name)\\n return \\n if (t == int):\\n resp.ints= param\\n if (t == float):\\n resp.floats=param\\n if (t == str):\\n resp.strings = param\\n print resp\\n data_buffer = StringIO.StringIO()\\n resp.serialize(data_buffer)\\n self.send(TopicInfo.ID_PARAMETER_REQUEST, data_buffer.getvalue())\",\n \"def __init__(self, param):\",\n \"def set_params(self, **kwargs):\\n ...\",\n \"def handle_context_missing(self):\",\n \"def initialize_params(self, params):\\n pass\",\n \"def getParameter(self, name):\",\n \"def putparam(self,parname_,parvalue_): # 3\\n res = self.__obj.putparam(parname_,parvalue_)\\n if res != 0:\\n result,msg = self.__getlasterror(res)\\n raise Error(rescode(res),msg)\",\n \"def _handleInput(self, paramInput):\\n super()._handleInput(paramInput)\\n locationFind = paramInput.findFirst('location')\\n if locationFind != None:\\n self.location = locationFind.value\\n else:\\n self.raiseAnError(IOError,'location value needed for Laplace distribution')\\n scaleFind = paramInput.findFirst('scale')\\n if scaleFind != None:\\n self.scale = scaleFind.value\\n else:\\n self.raiseAnError(IOError,'scale value needed for Laplace distribution')\\n self.initializeDistribution()\",\n \"def set_param(self, param, value):\\n self._set_param_client(param, value)\",\n \"def inner_test(param: str):\\n pass\",\n \"def __breakpointhook__(*args, **kwargs): # real signature unknown\\n pass\",\n \"def test_wrong_parameters(self):\\n with self.assertWarns(RuntimeWarning):\\n Parameters(1, mu=3, lambda_=2)\",\n \"def _get_raw_params(self, node):\",\n \"def _handleInput(self, paramInput):\\n super()._handleInput(paramInput)\\n pFind = paramInput.findFirst('p')\\n if pFind != None:\\n self.p = pFind.value\\n else: self.raiseAnError(IOError,'p value needed for Geometric distribution')\\n self.initializeDistribution()\",\n \"def log_params(self, params=None):\\n if params is not None:\\n dump_obj = params.__dict__\\n else:\\n dump_obj = self.params.__dict__\\n self.logger.log_params(dump_obj)\",\n \"def param(self, *args, **kwargs):\\n return self.options.param(*args,**kwargs)\",\n \"def handleInput(self, paramInput):\\n MCMC.handleInput(self, paramInput)\",\n \"def postparse_hook_undeclared_parameter_annotation(self, data) -> cmd2.plugin.PostparsingData:\\n pass\",\n \"def __init__(self, *args: Any, **kwargs: Any) -> None:\\n kwargs[\\\"aux_params\\\"] = None\\n super().__init__(*args, **kwargs)\",\n \"def set_parameter(self, param, value, stripe = 0, location = 3):\\n if param in self.fpga.cabac_top[0].params:\\n self.fpga.set_cabac_value(param, value, stripe)\\n time.sleep(0.1)\\n self.fpga.send_cabac_config(stripe)\\n\\n elif param in [\\\"V_SL\\\", \\\"V_SH\\\", \\\"V_RGL\\\", \\\"V_RGH\\\", \\\"V_PL\\\", \\\"V_PH\\\"]:\\n self.fpga.set_clock_voltages({param: value})\\n\\n elif param == \\\"I_OS\\\":\\n self.fpga.set_current_source(value, stripe)\\n\\n else:\\n print(\\\"Warning: unidentified parameter for the REB: %s\\\" % param)\",\n \"def _arguments(self, t):\\n self.RaiseError(t, \\\"Arguments should already have been processed\\\")\",\n \"def _sanitize_param(self, param):\\n if param:\\n # Can't send unicode.\\n param = str(param)\\n return param\",\n \"def set_parameter_value(self, parameter, value):\\n pass\",\n \"def set_parameter(self, params, name, val):\\n raise NotImplementedError()\",\n \"def transclusion_param(self, **kw):\\n return self._open('param',\\n allowed_attrs=['name', 'type', 'value', 'valuetype', ],\\n **kw)\",\n \"def set_params(self, **kwargs) -> NoReturn:\\n pass\",\n \"def gui_set_param(self,param_name,val):\\n self._tkvar_set(param_name,val) # ERROR: presumably calls trace stuff twice\\n self._handle_gui_set(param_name,force=True)\",\n \"def monkey_set_f_params(self):\\n self._monkey_set_f_params_counter += 1\",\n \"def monkey_set_f_params(self):\\n self._monkey_set_f_params_counter += 1\",\n \"def as_param(self):\\n self._clean()\\n return self.param\",\n \"def _getParam(self, callerId, key):\\n if key not in self.FilterParameters:\\n self.__docWriter.addParam(callerId, key)\",\n \"def set_param_raw(param, value, verbose=False):\\n if type(value) == dict:\\n # #1098 changing dictionary behavior to be an update, rather\\n # than replace behavior.\\n for k, v in value.items():\\n # dictionary keys must be non-unicode strings\\n if isinstance(k, str):\\n set_param_raw(ns_join(param, k), v, verbose=verbose)\\n else:\\n raise RosParamException(\\\"YAML dictionaries must have string keys. Invalid dictionary is:\\\\n%s\\\"%value)\\n else:\\n try:\\n expected_type = long\\n except NameError :\\n expected_type = int\\n \\n if type(value) == expected_type:\\n if value > sys.maxsize:\\n raise RosParamException(\\\"Overflow: Parameter Server integers must be 32-bit signed integers:\\\\n\\\\t-%s <= value <= %s\\\"%(maxint - 1, maxint))\\n \\n try:\\n get_param_server().setParam(param, value)\\n except socket.error:\\n raise RosParamIOException(\\\"Unable to communicate with master!\\\")\\n if verbose:\\n print(\\\"set parameter [%s] to [%s]\\\"%(param, value))\",\n \"def edit_parameter(request, parameter, **_kwargs):\\n pass\",\n \"def set_param(self, name, value, *, distrib=None, ref=None):\\n raise NotImplementedError\",\n \"def _handleInput(self, paramInput):\\n super()._handleInput(paramInput)\\n lowFind = paramInput.findFirst('low')\\n if lowFind != None:\\n self.low = lowFind.value\\n alphaFind = paramInput.findFirst('alpha')\\n if alphaFind != None:\\n self.alpha = alphaFind.value\\n else:\\n self.raiseAnError(IOError,'alpha value needed for Gamma distribution')\\n betaFind = paramInput.findFirst('beta')\\n if betaFind != None:\\n self.beta = betaFind.value\\n # check if lower bound are set, otherwise default\\n if not self.lowerBoundUsed:\\n self.lowerBoundUsed = True\\n self.lowerBound = self.low\\n self.initializeDistribution() #TODO this exists in a couple classes; does it really need to be here and not in Simulation? - No. - Andrea\",\n \"def handle_arguments(self, args):\\n debug(\\\"BloomGenerator.handle_arguments: got args -> \\\" + str(args))\",\n \"def _prepare_site(self, msg):\\n name = msg[\\\"name\\\"]\\n param_name = params.user_param_name(name)\\n if isinstance(self.prior, dict) and param_name in self.prior.keys() \\\\\\n or callable(self.prior):\\n if msg[\\\"type\\\"] == \\\"param\\\":\\n msg[\\\"done\\\"] = True\\n return msg\",\n \"def _add_setup_param(self, name, fmt, **kwargs):\\n self._param_dict.add(name, '', None, fmt,\\n startup_param=False,\\n direct_access=True,\\n visibility=ParameterDictVisibility.READ_ONLY,\\n **kwargs)\",\n \"def _pre_argument_parsing(self):\\n pass\",\n \"def set_params(self, *, params: Params) -> None: # pragma: no cover\\n\\t\\tsuper().set_params(params=params)\",\n \"def _update_param_from_tkvar(self,param_name):\\n self.debug(\\\"TkPOb._update_param_from_tkvar(%s)\\\"%param_name)\\n\\n parameter,sourcePO=self.get_parameter_object(param_name,with_source=True)\\n\\n ### can only edit constant parameters for class objects\\n if parameter.constant is True and not isinstance(sourcePO,type):\\n return ### HIDDEN\\n\\n tkvar = self._tkvars[param_name]\\n\\n if self._tkvar_changed(param_name):\\n # don't attempt to set if there was a string-to-object translation error\\n if self.translators[param_name].last_string2object_failed:\\n return ### HIDDEN\\n\\n # (use _original_get() because we don't want the tkvar to be reset to\\n # the parameter's current value!)\\n val = self._string2object(param_name,tkvar._original_get())\\n\\n try:\\n self._set_parameter(param_name,val)\\n except: # everything\\n tkvar.set(tkvar._last_good_val)\\n raise # whatever the parameter-setting error was\\n\\n self.debug(\\\"set %s to %s\\\"%(param_name,val))\\n\\n if hasattr(tkvar,'_on_modify'):\\n tkvar._on_modify()\\n\\n ### call any function associated with GUI set()\\n if hasattr(tkvar,'_on_set'):\\n\\n # CEBALERT: provide a way of allowing other gui components\\n # to figure out where a callback error might have come\\n # from. Callback instances (the Callback class is defined\\n # in Tkinter.py) store a widget, but often it appears to\\n # be the Tk instance - which is of no use in later\\n # determining where an error might have originated.\\n global _last_one_set\\n if hasattr(self,'master'):\\n _last_one_set = self.master\\n\\n tkvar._on_set()\",\n \"def monkey_set_params(self, **args):\\n self._monkey_set_params_counter += 1\\n assert self._args == (args,), 'unexpected additional arguments. Keep the type in mind'\",\n \"def update_parameter(self, param, val, force=False):\\n self._update_dict[param] = val\\n if force:\\n self._cur_val[param] = None\",\n \"def set_params(self, **params):\\n return super().set_params(**params)\",\n \"def set_reg_param(self,reg_param):\\n \\n type_name = type(reg_param).__name__\\n if re.search('float',type_name) != None:\\n if reg_param < 0:\\n raise KINSOL_Exception(\\\"Value sent to set_reg_param must be equal to or larger than zero.\\\")\\n else:\\n self.reg_param = reg_param\\n else:\\n raise KINSOL_Exception(\\\"The variable sent to 'set_reg_param' must be a float.\\\")\",\n \"def __init__(self):\\n self._params = None\",\n \"def _post_argument_parsing(self):\\n pass\",\n \"def _check_param(in_params, req_param, opt_param=list()):\\n for param in req_param:\\n if param not in in_params:\\n raise ValueError('{} parameter is required'.format(param))\\n defined_param = set(req_param + opt_param)\\n for param in in_params:\\n if param not in defined_param:\\n print(\\n \\\"WARNING: received unexpected parameter {}\\\".format(param))\",\n \"def parameters_changed(self):\\n pass\",\n \"def test_deregister_parameter_handler(self, to_deregister):\\n ff = ForceField(xml_simple_ff)\\n # Make sure the handler is present in the test force field\\n handler_found = False\\n for handler in ff._parameter_handlers.values():\\n if isinstance(handler, ToolkitAM1BCCHandler):\\n handler_found = True\\n assert handler_found\\n ff.deregister_parameter_handler(to_deregister)\\n # Make sure the handler is absent after deletion\\n handler_found = False\\n for handler in ff._parameter_handlers.values():\\n if isinstance(handler, ToolkitAM1BCCHandler):\\n handler_found = True\\n assert not (handler_found)\\n\\n with pytest.raises(KeyError):\\n ff.deregister_parameter_handler(to_deregister)\",\n \"def set_params(self, *argv, **kwargs):\\n pass\",\n \"def set_params(self, *argv, **kwargs):\\n pass\",\n \"def set_params(self, *argv, **kwargs):\\n pass\",\n \"def set_params(self, *argv, **kwargs):\\n pass\",\n \"def set_params(self, *argv, **kwargs):\\n pass\",\n \"def inv_patience_param(x):\\n # -- TODO: make this do something!\\n return x\",\n \"def handle_argument(self, bit):\\n if self.current_argument is None:\\n try:\\n self.current_argument = self.arguments.pop(0)\\n except IndexError:\\n raise TooManyArguments(self.tagname, self.todo)\\n handled = self.current_argument.parse(self.parser, bit, self.tagname, self.kwargs)\\n while not handled:\\n try:\\n self.current_argument = self.arguments.pop(0)\\n except IndexError:\\n if self.options.breakpoints:\\n raise BreakpointExpected(self.tagname, self.options.breakpoints, bit)\\n elif self.options.next_breakpoint:\\n raise BreakpointExpected(self.tagname, [self.options.next_breakpoint], bit)\\n else:\\n raise TooManyArguments(self.tagname, self.todo)\\n handled = self.current_argument.parse(self.parser, bit, self.tagname, self.kwargs)\",\n \"def test_validate_late_contextual_fparam_raises(self):\\n fsig = FSignature(\\n [forge.arg('a'), forge.ctx('self')],\\n __validate_parameters__=False,\\n )\\n with pytest.raises(TypeError) as excinfo:\\n fsig.validate()\\n assert excinfo.value.args[0] == \\\\\\n 'Only the first parameter can be contextual'\",\n \"def putintparam(self,param_,parvalue_):\\n res = __library__.MSK_XX_putintparam(self.__nativep,param_,parvalue_)\\n if res != 0:\\n _,msg = self.__getlasterror(res)\\n raise Error(rescode(res),msg)\",\n \"def triggered(self, *args, **kwargs): # real signature unknown\\n pass\",\n \"def _get_parameters(self):\\n return None\",\n \"def _paramUpdate(self):\\n\\n # Update the database attributes accordingly.\\n dt.utilities.DB_attrs_save(self.Database, self.newParam)\",\n \"def getintparam(self,param_): # 3\\n if not isinstance(param_,iparam): raise TypeError(\\\"Argument param has wrong type\\\")\\n res,resargs = self.__obj.getintparam(param_)\\n if res != 0:\\n result,msg = self.__getlasterror(res)\\n raise Error(rescode(res),msg)\\n _parvalue_return_value = resargs\\n return _parvalue_return_value\"\n]","isConversational":false},"negative_scores":{"kind":"list like","value":["0.6485111","0.6299571","0.5991846","0.590375","0.58012176","0.5784556","0.5730866","0.5685745","0.5592114","0.5574099","0.5539806","0.55120116","0.55019736","0.54560244","0.5417562","0.5411254","0.5411254","0.5411254","0.5406385","0.537721","0.53710365","0.53664345","0.5366124","0.5335561","0.53344244","0.533248","0.5332294","0.5324557","0.52898926","0.52828324","0.527533","0.5264441","0.522333","0.5212794","0.5207419","0.5199028","0.51973","0.51940644","0.5183911","0.5181848","0.5176354","0.5169352","0.5167642","0.5153724","0.5146635","0.51278996","0.512777","0.51223403","0.511629","0.5115245","0.5107706","0.51046735","0.509498","0.50944275","0.50854313","0.50848925","0.5081074","0.50808233","0.50797653","0.50532174","0.50531226","0.5050972","0.5047617","0.50474936","0.50428474","0.50378495","0.50378495","0.5036627","0.5034467","0.503405","0.5021827","0.5021492","0.5019418","0.5018055","0.5015424","0.50150585","0.5008875","0.50088227","0.50019944","0.49925423","0.49860513","0.49778318","0.49778187","0.49745384","0.49653828","0.49589846","0.4955387","0.4951987","0.49513522","0.49513522","0.49513522","0.49513522","0.49513522","0.4951201","0.49478194","0.4944901","0.49431193","0.49408633","0.49387255","0.49378785","0.4937145"],"string":"[\n \"0.6485111\",\n \"0.6299571\",\n \"0.5991846\",\n \"0.590375\",\n \"0.58012176\",\n \"0.5784556\",\n \"0.5730866\",\n \"0.5685745\",\n \"0.5592114\",\n \"0.5574099\",\n \"0.5539806\",\n \"0.55120116\",\n \"0.55019736\",\n \"0.54560244\",\n \"0.5417562\",\n \"0.5411254\",\n \"0.5411254\",\n \"0.5411254\",\n \"0.5406385\",\n \"0.537721\",\n \"0.53710365\",\n \"0.53664345\",\n \"0.5366124\",\n \"0.5335561\",\n \"0.53344244\",\n \"0.533248\",\n \"0.5332294\",\n \"0.5324557\",\n \"0.52898926\",\n \"0.52828324\",\n \"0.527533\",\n \"0.5264441\",\n \"0.522333\",\n \"0.5212794\",\n \"0.5207419\",\n \"0.5199028\",\n \"0.51973\",\n \"0.51940644\",\n \"0.5183911\",\n \"0.5181848\",\n \"0.5176354\",\n \"0.5169352\",\n \"0.5167642\",\n \"0.5153724\",\n \"0.5146635\",\n \"0.51278996\",\n \"0.512777\",\n \"0.51223403\",\n \"0.511629\",\n \"0.5115245\",\n \"0.5107706\",\n \"0.51046735\",\n \"0.509498\",\n \"0.50944275\",\n \"0.50854313\",\n \"0.50848925\",\n \"0.5081074\",\n \"0.50808233\",\n \"0.50797653\",\n \"0.50532174\",\n \"0.50531226\",\n \"0.5050972\",\n \"0.5047617\",\n \"0.50474936\",\n \"0.50428474\",\n \"0.50378495\",\n \"0.50378495\",\n \"0.5036627\",\n \"0.5034467\",\n \"0.503405\",\n \"0.5021827\",\n \"0.5021492\",\n \"0.5019418\",\n \"0.5018055\",\n \"0.5015424\",\n \"0.50150585\",\n \"0.5008875\",\n \"0.50088227\",\n \"0.50019944\",\n \"0.49925423\",\n \"0.49860513\",\n \"0.49778318\",\n \"0.49778187\",\n \"0.49745384\",\n \"0.49653828\",\n \"0.49589846\",\n \"0.4955387\",\n \"0.4951987\",\n \"0.49513522\",\n \"0.49513522\",\n \"0.49513522\",\n \"0.49513522\",\n \"0.49513522\",\n \"0.4951201\",\n \"0.49478194\",\n \"0.4944901\",\n \"0.49431193\",\n \"0.49408633\",\n \"0.49387255\",\n \"0.49378785\",\n \"0.4937145\"\n]","isConversational":false},"document_score":{"kind":"string","value":"0.0"},"document_rank":{"kind":"string","value":"-1"}}},{"rowIdx":16589,"cells":{"query":{"kind":"string","value":"Trap coord preceding gerber format spec."},"document":{"kind":"string","value":"def test_coord_preceding_fs(self):"},"metadata":{"kind":"string","value":"{\n \"objective\": {\n \"self\": [],\n \"paired\": [],\n \"triplet\": [\n [\n \"query\",\n \"document\",\n \"negatives\"\n ]\n ]\n }\n}"},"negatives":{"kind":"list like","value":["def trace(self, coord01: np.ndarray) -> np.ndarray:\n rect = self.clip_rect()\n return (rect.position + coord01 * rect.size).astype(np.int)","def frac11(self,lx,ly,lz):\n return str(self.coord[0]/lx*2)+'\\t'+str(self.coord[1]/ly*2)+'\\t'+str(self.coord[2]/lz*2)","def _format_point(self, point):\n return (point + self.draw_offset).intify()","def frac01(self,lx,ly,lz):\n return str(self.coord[0]/lx)+'\\t'+str(self.coord[1]/ly)+'\\t'+str(self.coord[2]/lz)","def xy(self):\n ...","def extra_coords(self) -> ExtraCoordsABC:","def convertdirection(self, frame):\n return _coordsys.coordsys_convertdirection(self, frame)","def setup(self):\r\n m = re.match(r'\\[([0-9]+),([0-9]+)]',\r\n self.value.strip().replace(' ', ''))\r\n if m:\r\n # Note: we subtract 15 to compensate for the size of the dot on the screen.\r\n # (is a 30x30 image--lms/static/green-pointer.png).\r\n (self.gx, self.gy) = [int(x) - 15 for x in m.groups()]\r\n else:\r\n (self.gx, self.gy) = (0, 0)","def coordinates(self):","def calcPos(self,newpol):\n\n\t\tdetlatoff=(self.offset9()-self.offset10())*cosd(newpol)+self.offset10()\n\t\tnewoffcry = (self.offset2()-self.offset3())*cosd(newpol)+self.offset3()\n\t\tnewdetoff = (self.offset4()-self.offset8())*cosd(newpol)+self.offset8() +self.offset5()\n\n\t\twl = BLi.getWavelength()\n\t\tself.thbragg = 180/pi*asin(wl/(2*self.dspace))\n\t\tnewthp=self.sign()*self.thbragg+newoffcry\n\t\tnewtthp=2*self.sign()*self.thbragg+newdetoff\n\t\tprint \"stokes=%1.2f thp=%1.2f tthp=%1.2f detlatoff=%1.2f\"%(newpol,newthp,newtthp,detlatoff)","def coords_format(format):\n if format == 'galactic':\n return 'galactic'\n elif format in ['fk5','icrs']:\n return 'celestial'","def parse_telemetry(self):\n telemetry = self.buffer\n self.buffer = \"\"\n if telemetry[0] == '<':\n if telemetry[len(telemetry) - 1] == '>':\n values = telemetry[1:len(telemetry)-1].split(',')\n coord = Coordinate(int(values[0]), int(values[1]))\n return coord\n return None","def set_coord(self, l, sign, b):\n if l is not None:\n self.l = float(l)\n if b is not None:\n self.b = float(b)\n if sign == '-':\n self.b *= -1.","def get_stig_xy(self):\n raise NotImplementedError","def _fixupPosition(self, position):\n if \"latitudeI\" in position:\n position[\"latitude\"] = position[\"latitudeI\"] * 1e-7\n if \"longitudeI\" in position:\n position[\"longitude\"] = position[\"longitudeI\"] * 1e-7","def deg_locations_writer(cell,width,(x,y)):\n if np.any(np.isnan(cell)):\n sys.stdout.write(' ' * width)\n else:\n sys.stdout.write(\n \"{0:^{width}s}\".format(\n \"{0:.2f},{1:.2f}\".format(cell[0],cell[1]),\n width=width\n )\n )","def __coding_coordinate(self):\n region1 = self.long_side_len\n region2 = self.short_side_len\n length = len(self.seq)\n if self.direction == '+':\n a_s = 0\n a_e = region2\n b_s = self.length - region1\n b_e = self.length - 1\n elif self.direction == '-':\n a_s = 0\n a_e = region1\n b_s = self.length - region2\n b_e = self.length - 1\n return (a_s, a_e, b_s, b_e)","def setGxLocation(self):\n if self.xyz is None:\n gxobs = self.obs.get(None, {}).get(\"GX\")\n if gxobs is not None:\n gxyz = np.array((0.0, 0.0, 0.0))\n for gx in gxobs:\n gxyz += gx.obsvalue.value\n self.xyz = gxyz / len(gxobs)\n self.locator.write(\n \"Fixing station {0} using GNSS coordinate observations\\n\".format(\n self.code\n )\n )","def update_coords(self, l, b):\n self.l = l\n self.b = b\n self.ra, self.dec = astLib.astCoords.convertCoords(\n \"GALACTIC\", \"J2000\", self.l, self.b, epoch=2000.)","def hex_from_oddr(newsystem, coord):\n x = coord.x + (coord.y + (coord.y&1)) // 2\n z = -coord.y\n y = -x-z\n newcoord = newsystem.coord(x=x, y=y, z=z)\n #logger.debug(\"OldCoord:%s NewCoord:%s\", coord, newcoord)\n return newcoord","def _cte_postformat(self):\n# if type(self.idxs) == list:\n# self.idxs = np.array(self.idxs)\n if self.sp_relative_pos is not None:\n if type(self.sp_relative_pos) == list:\n self.sp_relative_pos = np.array(self.sp_relative_pos)","def set_robot_pos(self):\n\t\tx,y,z = self.geo2desiredENU(self.curr_lat, self.curr_lon, self.gpsAlt)\n\t\tself.robot_msg.point.x = x\n\t\tself.robot_msg.point.y = y\n\t\tself.robot_msg.point.z = z","def pfs_format_coord(x, y, detectorMap=detectorMap):\n if detectorMap is None:\n return \"\"\n else:\n fid = detectorMap.findFiberId(geom.PointD(x, y))\n fidStr = f\"{fid:3}\"\n if pfsConfig:\n try:\n mtpInfo = fiberIds.fiberIdToMTP([fid], pfsConfig)[0]\n fidStr += f\" {', '.join([str(i) for i, l in zip(mtpInfo, mtpDetails) if l])}\"\n except RuntimeError:\n pass # fiber isn't in pfsConfig\n\n return f\"FiberId {fidStr} {detectorMap.findWavelength(fid, y):8.3f}nm\"","def aligne_grille(self,x,y,t):\r\n [xmin,ymin,xmax,ymax] = self.can.coords(self.hitbox[t])\r\n tx,ty=xmax-xmin,ymax-ymin\r\n a,b=23,23\r\n if tx==92 or ty==92 or tx==184 or ty==184:\r\n if tx==92 or tx==184:a,b=0,23\r\n if ty==92 or ty==184:a,b=23,0\r\n if 142<y<602 and 66<x<528:\r\n x=(x-66)//46*46+66+a\r\n y=(y-142)//46*46+142+b\r\n return x,y","def return_zeropoint():\n return 22.5","def _coord(self, x, y):\n gridEdge = 7 # originally 5\n y = gridEdge - y\n cx = 100 * (x - 1) + 50\n cy = 100 * (y - 1) + 50\n r = 20\n return (cx - r, cy - r, cx + r, cy + r)","def coord(self, coord):\n\n self._coord = coord","def configure_location(self):\n # Set floor correctly\n self.floor.set(\"pos\", array_to_string(self.bottom_pos))","def __getxy(x1, y1, x2, y2):\n\t\treturn x1*27+y1*9+x2*3+y2","def GetLoCorner(self):\n ...","def handlelocationevent(self, event, platform, nem, component, data):\n event = emaneeventlocation.EventLocation(data)\n entries = event.entries()\n for e in entries.values():\n # yaw,pitch,roll,azimuth,elevation,velocity are unhandled\n (nemid, lat, long, alt) = e[:4]\n self.handlelocationeventtoxyz(nemid, lat, long, alt)","def translateLoc(loc):\n\tif(loc[0].isalpha()):\t\n\t\treturn [int(loc[1:])-1,colDict[loc[0]],'V']\n\telse:\n\t\treturn [int(loc[:-1])-1, colDict[loc[-1]],'H']","def northing(self):\r\n x, y = self.lonlat2xy(self.longitude, self.latitude)\r\n return y","def _UTMLetterDesignator(Lat):\n if Lat >= 0: return 'N'\n else: return 'S'","def position(self, name, tdb):\n if name == 'earth':\n return self._interpolate_earth(tdb, differentiate=False)\n else:\n return self._interpolate(name, tdb, differentiate=False)","def formatCoordinates(string):\n if string == 'N/A':\n return 0\n else:\n return float(string)","def initialCoordinates():\r\n return (-250,-250)","def fix_coord_units(cat, RA, DEC):\n cat[RA].info.unit = u.deg\n cat[DEC].info.unit = u.deg\n return cat","def format_coord(self, xd, yd):\n\n if self.M is None:\n return ''\n\n if self.button_pressed in self._rotate_btn:\n return 'azimuth=%d deg, elevation=%d deg ' % (self.azim, self.elev)\n # ignore xd and yd and display angles instead\n\n p = (xd, yd)\n edges = self.tunit_edges()\n #lines = [proj3d.line2d(p0,p1) for (p0,p1) in edges]\n ldists = [(proj3d.line2d_seg_dist(p0, p1, p), i) for \\\n i, (p0, p1) in enumerate(edges)]\n ldists.sort()\n # nearest edge\n edgei = ldists[0][1]\n\n p0, p1 = edges[edgei]\n\n # scale the z value to match\n x0, y0, z0 = p0\n x1, y1, z1 = p1\n d0 = np.hypot(x0-xd, y0-yd)\n d1 = np.hypot(x1-xd, y1-yd)\n dt = d0+d1\n z = d1/dt * z0 + d0/dt * z1\n\n x, y, z = proj3d.inv_transform(xd, yd, z, self.M)\n\n xs = self.format_xdata(x)\n ys = self.format_ydata(y)\n zs = self.format_ydata(z)\n return 'x=%s, y=%s, z=%s' % (xs, ys, zs)","def test_conversion_to_xyz_with_negatives(self):\r\n\r\n self.color.spec_530nm = -0.0736\r\n # TODO: Convert here.\r","def getCoords(self): # real signature unknown; restored from __doc__\r\n pass","def _extract_location_xyz(self, log):\n\n if \"location\" in log:\n x = log[\"location\"][\"latitude\"]\n y = log[\"location\"][\"longitude\"]\n z = log[\"location\"][\"altitude\"]\n else:\n self.logger.debug(\"NaN case\")\n x = \"NaN\" # matlab Nan?\n y = \"NaN\"\n z = \"NaN\"\n pass\n return str(x) + \",\" + str(y) + \",\" + str(z)","def _coord_byval(coord: COORD) -> c_long:\n return c_long(coord.Y * 0x10000 | coord.X & 0xFFFF)","def placeCrate (self, crates_char, row, column):","def test_RNA_position_placement(self):\n \n \n tool = pybedtools.create_interval_from_list(\"chr1 50 60 ENSMUSG1_1_83;ENSMUSG1_6_83 0 + 60 60\".split())\n location_dict = {\"ENSMUSG1\" : {\"strand\" : \"+\", \"regions\" : [(0,100),\n ] \n }\n }\n \n self.assertEqual(RNA_position(tool, location_dict), (.60, .60))\n \n tool = pybedtools.create_interval_from_list(\"chr1 50 60 ENSMUSG1_1_83;ENSMUSG1_6_83 0 - 60 60\".split())\n location_dict = {\"ENSMUSG1\" : {\"strand\" : \"-\", \"regions\" : [(0,100),\n ] \n }\n }\n \n #individual_fraction, total_fraction\n self.assertEqual(RNA_position(tool, location_dict), (.4, .4))","def integrate(coords,data,fault_pts,dshape_hex8,gll_weights,elmt):\n norm=0.0\n normx=0.0\n normy=0.0\n normz=0.0\n div=0.0 #normalizing factor to divide by\n divx=0.\n divy=0.\n divz=0.\n\n eps=1.0*g.mesh_spacing/(g.ngllx-1.)\n print 'eps=', eps\n f=open('eliminated_coords.vtk','w')\n\n #create integer versions of arrays to use in pulling out gll pts for each element\n data_round=np.rint(data)\n dati=data_round.astype(int)\n coord_round=np.rint(coords)\n coordi=coord_round.astype(int)\n\n #remove duplicates from data array\n dat_struc=np.ascontiguousarray(dati).view(np.dtype((np.void,dati.dtype.itemsize *dati.shape[1])))\n _,idx=np.unique(dat_struc,return_index=True)\n datu=dati[idx]\n data_unique=data[idx]\n\n for i_elmt in range(g.nelmt):\n #pull out geometric coordinates for this element\n elmt_coord_id=[j-1 for j in elmt[i_elmt]]\n elmt_coord=coordi[elmt_coord_id]\n\n #find corresponding gll pts for this element\n xmin=min(elmt_coord[:,0]);xmax=max(elmt_coord[:,0])\n ymin=min(elmt_coord[:,1]);ymax=max(elmt_coord[:,1])\n zmin=min(elmt_coord[:,2]);zmax=max(elmt_coord[:,2])\n gll_coord_id=np.nonzero((datu[:,0]>=xmin) & (datu[:,0]<=xmax) & (datu[:,1]>=ymin) & (datu[:,1]<=ymax) & (datu[:,2]>=zmin) & (datu[:,2]<=zmax))\n elmt_data=data_unique[gll_coord_id]\n if len(gll_coord_id[0]) != g.ngll:\n print \"elmt=\", elmt_coord_id\n print xmin,xmax,ymin,ymax,zmin,zmax\n print 'elmt_data=', elmt_data\n print \"gll pts found=\", len(gll_coord_id[0])\n raise ValueError(\"incorrect number of gll points found in element!\")\n exit\n\n #sort the gll coords so they correspond the order of the arrays giving the weights and shape function\n dat_sorted=elmt_data[npi.argsort((elmt_data[:,0], elmt_data[:,1],elmt_data[:,2]))]\n func=dat_sorted[:,3:]\n\n #if any gll pt is too close to fault, remove the element from the integration\n dist=distance.cdist(fault_pts,dat_sorted[:,0:3],'euclidean')\n if (dist<eps).any():\n print \"eliminated element #\", i_elmt\n np.savetxt(f,dat_sorted[:,0:3],fmt='%3.3f')\n continue\n\n for i_gll in range(g.ngll):\n\n #compute jacobian, its derivative and inverse\n jac=np.matmul(dshape_hex8[:,:,i_gll],elmt_coord)\n det_jac=np.linalg.det(jac)\n\n #perform the integration\n norm=norm+det_jac*gll_weights[i_gll]*np.dot((func[i_gll,3:6]-func[i_gll,0:3]),(func[i_gll,3:6]-func[i_gll,0:3]))\n div=div+det_jac*gll_weights[i_gll]*np.dot(func[i_gll,3:6],func[i_gll,3:6])\n normx=normx+det_jac*gll_weights[i_gll]*(func[i_gll,3]-func[i_gll,0])**2\n divx=divx+det_jac*gll_weights[i_gll]*(func[i_gll,3])**2\n normy=normy+det_jac*gll_weights[i_gll]*(func[i_gll,4]-func[i_gll,1])**2\n divy=divy+det_jac*gll_weights[i_gll]*(func[i_gll,4])**2\n normz=normz+det_jac*gll_weights[i_gll]*(func[i_gll,5]-func[i_gll,2])**2\n divz=divz+det_jac*gll_weights[i_gll]*(func[i_gll,5])**2\n\n norm_finalx=sqrt(normx/divx)\n norm_finaly=sqrt(normy/divy)\n norm_finalz=sqrt(normz/divz)\n norm_final=sqrt(norm/div)\n\n f.close()\n\n return norm_finalx, norm_finaly, norm_finalz,norm_final","def coord(self):\n fmt = \"{min_col}{min_row}:{max_col}{max_row}\"\n if (self.min_col == self.max_col\n and self.min_row == self.max_row):\n fmt = \"{min_col}{min_row}\"\n\n return fmt.format(\n min_col=get_column_letter(self.min_col),\n min_row=self.min_row,\n max_col=get_column_letter(self.max_col),\n max_row=self.max_row\n )","def cell_value(self, x, y):\n if x == 8 and y == 0:\n return \"--\"\n (r, g) = self[(x, y)]\n return \"%s%s\" % (r, g)","def spot_coords(self,spot):\n if spot == '1':\n return (330 - 60 ,335 - 15)\n if spot == '2':\n return (419 - 60, 335 - 15)\n if spot == '3':\n return (591 - 60, 159 - 15)\n if spot == '4':\n return (588 - 60, 248 - 15)","def extract_raw_simple_coordinates (raw_location):\n pattern = re.compile('(\\d+).(\\d+)?')\n x_result = pattern.match(str(raw_location[0]))\n y_result = pattern.match(str(raw_location[1]))\n return int(x_result[1]), int(y_result[1])","def readable(self):\n return \"(x: %.1f, y:%.1f)\" % (self.x, self.y)","def __getxyB(x, y):\n\t\treturn x*3+y","def _set_real_format(self, fmt):\n # try to use the _nomax variant if available\n if not self._max and fmt + '_nomax' in self.formats:\n self._format = self.formats[fmt + '_nomax']\n elif fmt in self.formats:\n self._format = self.formats[fmt]\n else:\n self._format = fmt\n\n self._format_line_count = self._format.count('\\n')","def edwin_location(self, res):\n if res.data[0:5] == \"WHERE\":\n #gets edwin's location\n where = res.data[5:]\n\n #massive string formatting - takes the string, splits by a formatter, then takes the array index that holds the XYZ,\n #then strips that string and splits it by spacing, and then takes the XYZ\n #reason for this massive formatting is b/c sent data format is not consistent\n where = where.split(\"\\r\\n\")[2].strip().split(' ')\n\n #gets rid of empty strings that result from formatting\n where = filter(None, where)[0:3]\n\n #makes everything numbers that can be used as coordinates for Edwin\n where = [int(float(coord) * 10) for coord in where]\n\n self.edwinx = where[0]\n self.edwiny = where[1]\n self.edwinz = where[2]","def __post_init__(self) -> None:\n self.annotate = self.x_y[0] == 0 or self.x_y[1] == 0","def log_robot_location(self):\n trans, rot = self.get_robot_location()\n if trans != None and rot != None:\n degrees = (rot.yaw * 180./math.pi)\n message = {\n 'x':'{0:.3f}'.format(trans.x),\n 'y':'{0:.3f}'.format(trans.y),\n 'rotation':'{0:.3f}'.format(degrees)}\n\n self.logger.log('ROS_XYR', 'ROS_XYR', message, 'state')","def _fix_iris_bug_derived_coord(cube):\n air_pressure_coord = cube.coord('air_pressure')\n try:\n altitude_coord = cube.coord('altitude')\n except iris.exceptions.CoordinateNotFoundError:\n altitude_coord = None\n for aux_factory in cube.aux_factories:\n cube.remove_aux_factory(aux_factory)\n try:\n cube.coord('air_pressure')\n except iris.exceptions.CoordinateNotFoundError:\n cube.add_aux_coord(air_pressure_coord, np.arange(cube.ndim))\n if altitude_coord is not None:\n cube.add_aux_coord(altitude_coord, (1, 2, 3))","def get_cell_coords(self, pt):\n\n\t return int(pt[0] // self.a), int(pt[1] // self.a)","def location_to_pos(self,row, col):\r\n\r\n pos_row = str(row + 1)\r\n pos_col = chr(col + 97)\r\n return pos_col + pos_row","def _correct_indel_coords(chrom, pos, ref, alt, pysamtxeff):\n lref = len(ref)\n lalt = len(alt)\n if lref == 1 and lalt == 1:\n # Substitution case\n change = '>'.join([ref, alt])\n new_pos = str(pos) + change\n return new_pos\n elif lalt == 1 and lref > lalt:\n dels = RptHandler(pysamtxeff, chrom, pos, ref)\n # Deletion case\n if dels.check_rpt_status():\n new_start, new_end = dels.find_rpt_coords()\n if len(dels.allele) == 1:\n new_pos = '_'.join([str(new_start)]) + 'del'\n else:\n new_pos = '_'.join([str(new_start), str(new_end)]) + 'del'\n else:\n shift = lref - lalt\n if shift == 1:\n new_pos = str(int(pos) + 1) + 'del'\n else:\n new_start = str(int(pos) + 1)\n new_end = str(int(pos) + shift)\n new_pos = '_'.join([new_start, new_end]) + 'del'\n return new_pos\n elif lref == 1 and lalt > lref:\n dups = RptHandler(pysamtxeff, chrom, pos, alt)\n # Duplication case\n if dups.check_rpt_status():\n new_start, new_end = dups.find_rpt_coords()\n # Check if there is a padding base, then adjust accordingly.\n if alt[0] == ref[0]:\n new_start += 1\n new_end += 1\n if len(dups.allele) == 1:\n new_pos = '_'.join([str(new_start)]) + 'dup'\n else:\n new_pos = '_'.join([str(new_start), str(new_end)]) + 'dup'\n # Insertion case\n else:\n new_start = str(pos)\n new_end = str(int(pos) + 1)\n new_pos = '_'.join([new_start, new_end]) + 'ins' + alt[1:]\n return new_pos\n elif lref > 1 and lalt > 1:\n # Multi-nucleotide substitution case\n # NG_012232.1: g.12_13delinsTG\n new_start = pos\n new_end = str(int(pos) + lref - 1)\n # If there is a common padding base, like ATG>ACC, make sure we are taking this in to account.\n if alt[0] == ref[0]:\n new_start += 1\n alt = alt[1:]\n new_pos = '_'.join([str(new_start), new_end]) + 'delins' + alt\n return new_pos\n else:\n raise Exception(\"Unknown change type: \" + pos + ':' + ref + '>' + alt)","def _callback_compass(self, msg):\n\n\t\tself.heading = self.north2east( msg.heading )","def _get_xy_coords(self, exterior, coord_type):\n if coord_type == 'x':\n return exterior.coords.xy[0]\n elif coord_type == 'y':\n return exterior.coords.xy[1]","def get_coord(self):\n return self.coord","def dump_coords(geom): # -> Any | list[Unknown]:\n ...","def test_location_to_coord():\n result_a = wwiki.location_to_coord(location)\n result_b = wwiki.location_to_coord(location)\n\n assert isinstance(result_a, str)\n assert result_b == \"48.76569917989272|2.392394129892722\"","def handle_position(data: bytes) -> Tuple[bytes, str]:\n x, y, z = struct.unpack('fff', data[0:3 * 4])\n return data[20:], f'Current Position (x,y,z): {x} {y} {z}'","def mousePositionRaw(self):","def mousePositionRaw(self):","def xy(event):\n return map(int, event.get_coords())","def set_marker(self, packet):\n if self.file_type == 'csv':\n self.write_data(packet=packet)\n elif self.file_type == 'edf':\n timestamp, code = packet.get_data()\n if self._rectime_offset is None:\n self._rectime_offset = timestamp[0]\n timestamp = timestamp-np.float64(self._rectime_offset)\n self._file_obj.writeAnnotation(timestamp[0], 0.001, str(int(code[0])))","def floatize(self):\n self.x = float(self.x)\n self.y = float(self.y)","def floatize(self):\n self.x = float(self.x)\n self.y = float(self.y)","def fixture_coord():\n\tEXAMPLE_FILE_FOLDER = str(MODULE_DIR) + \"/data/nail1/\"\n\tcoord_x, coord_y, coord = read.load_coord(EXAMPLE_FILE_FOLDER)\n\treturn coord","def test_lng_preserved(self):\n response = get_recent_point(None)\n fields = json.loads(response.content.decode('utf-8'))[0]['fields']\n self.assertAlmostEqual(fields['lng'], self.pt.lng)","def test_adjust_offsets_short(self):\n tool = pybedtools.BedTool(\"chr15 91512755 91512836 ENSG00000198901_1_147 0 -\", from_string=True)\n offsets = {\"ENSG00000198901_1_147\" : 10}\n results = adjust_offsets(tool, offsets)","def getChrNum(self):\n chrLookup = {\"X\":23,\"x\":23,\"Y\":24,\"y\":24}\n if self.chr.startswith(\"chr\"):\n num = self.chr[3:]\n if num in (\"X\",\"x\",\"Y\",\"y\"):\n num = chrLookup[num]\n return int(num)\n else: return self.chr","def test_lat_preserved(self):\n response = get_recent_point(None)\n fields = json.loads(response.content.decode('utf-8'))[0]['fields']\n self.assertAlmostEqual(fields['lat'], self.pt.lat)","def __str__(self):\n\t\treturn '<' + str(self._coords)[1:-1] + '>'","def coordPlt(grid, buffer=10, step=5):\n plt.cla()\n\n plt.plot(grid[1][0::step, 0::step],\n grid[0][0::step, 0::step],\n '.-b' )\n\n plt.plot(grid[1][0::step, 0::step].T,\n grid[0][0::step, 0::step].T,\n '.-b' )\n\n plt.axis( [ grid[1].max() + buffer,\n grid[1].min() - buffer,\n grid[0].max() + buffer,\n grid[0].min() - buffer],\n )\n plt.axis('off')\n plt.grid()","def putCoordInfo(self, hdu):\n\n hdu.header.update(\"CDELT1\", self.cdelt, \"pixel size, degrees\")\n hdu.header.update(\"CDELT2\", self.cdelt, \"pixel size, degrees\")\n shape = hdu.data.shape\n crpix1 = (shape[0] + 1) // 2 + 1\n crpix2 = (shape[1] + 1) // 2 + 1\n hdu.header.update(\"CRPIX1\", float(crpix1), \"reference pixel\")\n hdu.header.update(\"CRPIX2\", float(crpix2), \"reference pixel\")","def __calculateOffset(self):\n #if len(self.__XValue) > 0:\n # print(\"GPSBearing: \"+str(round(self.__GPSBearing[-1]))+\", heading: \"+str(round(self.value))+\n # \", x: \"+str(round(self.__XValue[-1]))+\", stdev: \"+str(round(np.std(self.__GPSBearing),5))+\n # \", offset: \"+str(self.__offset))\n if len(self.__GPSBearing) == self.__GPSBearing.maxlen and np.std(self.__GPSBearing) < 0.2 and self.speed > 7:\n self.__offset = (np.mean(self.__GPSBearing) + 360 - np.mean(self.__XValue)) % 360\n #print(\"new offset: \"+str(self.__offset)) ","def __get_x__(self):\n return self.Direction['x']","def offset_point(self,base, offset):\r\n return (base[0] + offset[0], base[1] + offset[1])","def setup_fmt(self, ctx):\n ctx.implicit_errors = False","def coord (i, j):\r\n return j, i","def init_atom_coords(self) -> None:\n ...","def wellname_to_coordinates(wellname):\n rowname, colname = re.match(\"([a-zA-Z]+)([0-9]+)\", wellname).groups()\n return rowname_to_number(rowname), int(colname)","def get_text_loc_axis_coord(xArr, yArr, xr, yr, delta):\n\tdff = N.abs(yArr - yr[1])\n\tii = N.where(dff == N.min(dff))[0]\n\tif xArr[ii] < xr[1]:\n\t\tyloc = 1. + delta[1]\n\t\txloc = N.abs(N.log10(xArr[ii]/xr[0]))/N.abs(N.log10(xr[1]/xr[0]))\n\telse:\n\t\txloc = 1. + delta[0]\n\t\tdff = N.abs(xArr - xr[1])\n\t\tjj = N.where(dff == N.min(dff))[0]\n\t\tyloc = N.abs(N.log10(yArr[jj]/yr[0]))/N.abs(N.log10(yr[1]/yr[0]))\n\treturn [xloc, yloc]","def __str__(self):\r\n if self.y == 1:\r\n return \"{}\".format(self.x)\r\n else:\r\n return \"{}/{}\".format(self.x, self.y)","def atom_to_internal_coordinates(self, verbose: bool = ...) -> None:\n ...","def atom_to_internal_coordinates(self, verbose: bool = ...) -> None:\n ...","def atm241(coord: numpy.array) -> numpy.array:\n ...","def test_RNA_position_fail(self):\n \n tool = pybedtools.create_interval_from_list(\"chr1 50 60 ENSMUSG1_1_83;ENSMUSG1_6_83 0 - 10 10\".split())\n location_dict = {\"ENSMUSG1\" : {\"strand\" : \"-\", \"regions\" : [(100, 150),\n (25,50),\n ] \n }\n }\n \n self.assertEqual(RNA_position(tool, location_dict), (None, None))\n \n tool = pybedtools.create_interval_from_list(\"chr1 50 60 ENSMUSG1_1_83;ENSMUSG1_6_83 0 - 175 175\".split())\n \n self.assertEqual(RNA_position(tool, location_dict), (None, None))","def get_real_leg(self):\n if self.invert_y:\n inv = -1\n else:\n inv = 1\n\n c = self.C[-1]\n\n c = Coordinate(\n x=c.x + self.structure_offset.x,\n y=c.y * inv + self.structure_offset.y,\n z=c.z + self.structure_offset.z\n )\n return c","def get_starting_coordinate(self):\n if type(self._starting_coordinate) != tuple:\n self._logger.write(\"Error! starting_coordinate should be a tupple\")\n elif self._starting_coordinate == None:\n #this is dead code\n self._logger.write(\"Error! starting_coordinate does not contain a value\")\n else:\n try:\n return self._starting_coordinate\n except Exception as e:\n self._logger.write(\"Error! could not get starting_coordinate: %s\" % e)","def __init__(self, *args, **kwargs):\n # Impose default formatter\n super().__init__(*args, **kwargs)\n formatter = axistools.Formatter('auto')\n self.xaxis.set_major_formatter(formatter)\n self.yaxis.set_major_formatter(formatter)\n self.xaxis.isDefault_majfmt = True\n self.yaxis.isDefault_majfmt = True\n # Custom attributes\n self._datex_rotated = False # whether manual rotation has been applied\n self._dualy_arg = None # for scaling units on opposite side of ax\n self._dualx_arg = None\n self._dualy_cache = None # prevent excess _dualy_overrides calls\n self._dualx_cache = None","def geo_transform(self):\n pass","def _get_origin_ted(self):\n return self.__origin_ted","def position_region(reg):\n x,y = reg.coord_list[:2]\n posn = coords.Position([x,y],system=coords_format(reg.coord_format))\n return posn","def _origin(self):\n return 1"],"string":"[\n \"def trace(self, coord01: np.ndarray) -> np.ndarray:\\n rect = self.clip_rect()\\n return (rect.position + coord01 * rect.size).astype(np.int)\",\n \"def frac11(self,lx,ly,lz):\\n return str(self.coord[0]/lx*2)+'\\\\t'+str(self.coord[1]/ly*2)+'\\\\t'+str(self.coord[2]/lz*2)\",\n \"def _format_point(self, point):\\n return (point + self.draw_offset).intify()\",\n \"def frac01(self,lx,ly,lz):\\n return str(self.coord[0]/lx)+'\\\\t'+str(self.coord[1]/ly)+'\\\\t'+str(self.coord[2]/lz)\",\n \"def xy(self):\\n ...\",\n \"def extra_coords(self) -> ExtraCoordsABC:\",\n \"def convertdirection(self, frame):\\n return _coordsys.coordsys_convertdirection(self, frame)\",\n \"def setup(self):\\r\\n m = re.match(r'\\\\[([0-9]+),([0-9]+)]',\\r\\n self.value.strip().replace(' ', ''))\\r\\n if m:\\r\\n # Note: we subtract 15 to compensate for the size of the dot on the screen.\\r\\n # (is a 30x30 image--lms/static/green-pointer.png).\\r\\n (self.gx, self.gy) = [int(x) - 15 for x in m.groups()]\\r\\n else:\\r\\n (self.gx, self.gy) = (0, 0)\",\n \"def coordinates(self):\",\n \"def calcPos(self,newpol):\\n\\n\\t\\tdetlatoff=(self.offset9()-self.offset10())*cosd(newpol)+self.offset10()\\n\\t\\tnewoffcry = (self.offset2()-self.offset3())*cosd(newpol)+self.offset3()\\n\\t\\tnewdetoff = (self.offset4()-self.offset8())*cosd(newpol)+self.offset8() +self.offset5()\\n\\n\\t\\twl = BLi.getWavelength()\\n\\t\\tself.thbragg = 180/pi*asin(wl/(2*self.dspace))\\n\\t\\tnewthp=self.sign()*self.thbragg+newoffcry\\n\\t\\tnewtthp=2*self.sign()*self.thbragg+newdetoff\\n\\t\\tprint \\\"stokes=%1.2f thp=%1.2f tthp=%1.2f detlatoff=%1.2f\\\"%(newpol,newthp,newtthp,detlatoff)\",\n \"def coords_format(format):\\n if format == 'galactic':\\n return 'galactic'\\n elif format in ['fk5','icrs']:\\n return 'celestial'\",\n \"def parse_telemetry(self):\\n telemetry = self.buffer\\n self.buffer = \\\"\\\"\\n if telemetry[0] == '<':\\n if telemetry[len(telemetry) - 1] == '>':\\n values = telemetry[1:len(telemetry)-1].split(',')\\n coord = Coordinate(int(values[0]), int(values[1]))\\n return coord\\n return None\",\n \"def set_coord(self, l, sign, b):\\n if l is not None:\\n self.l = float(l)\\n if b is not None:\\n self.b = float(b)\\n if sign == '-':\\n self.b *= -1.\",\n \"def get_stig_xy(self):\\n raise NotImplementedError\",\n \"def _fixupPosition(self, position):\\n if \\\"latitudeI\\\" in position:\\n position[\\\"latitude\\\"] = position[\\\"latitudeI\\\"] * 1e-7\\n if \\\"longitudeI\\\" in position:\\n position[\\\"longitude\\\"] = position[\\\"longitudeI\\\"] * 1e-7\",\n \"def deg_locations_writer(cell,width,(x,y)):\\n if np.any(np.isnan(cell)):\\n sys.stdout.write(' ' * width)\\n else:\\n sys.stdout.write(\\n \\\"{0:^{width}s}\\\".format(\\n \\\"{0:.2f},{1:.2f}\\\".format(cell[0],cell[1]),\\n width=width\\n )\\n )\",\n \"def __coding_coordinate(self):\\n region1 = self.long_side_len\\n region2 = self.short_side_len\\n length = len(self.seq)\\n if self.direction == '+':\\n a_s = 0\\n a_e = region2\\n b_s = self.length - region1\\n b_e = self.length - 1\\n elif self.direction == '-':\\n a_s = 0\\n a_e = region1\\n b_s = self.length - region2\\n b_e = self.length - 1\\n return (a_s, a_e, b_s, b_e)\",\n \"def setGxLocation(self):\\n if self.xyz is None:\\n gxobs = self.obs.get(None, {}).get(\\\"GX\\\")\\n if gxobs is not None:\\n gxyz = np.array((0.0, 0.0, 0.0))\\n for gx in gxobs:\\n gxyz += gx.obsvalue.value\\n self.xyz = gxyz / len(gxobs)\\n self.locator.write(\\n \\\"Fixing station {0} using GNSS coordinate observations\\\\n\\\".format(\\n self.code\\n )\\n )\",\n \"def update_coords(self, l, b):\\n self.l = l\\n self.b = b\\n self.ra, self.dec = astLib.astCoords.convertCoords(\\n \\\"GALACTIC\\\", \\\"J2000\\\", self.l, self.b, epoch=2000.)\",\n \"def hex_from_oddr(newsystem, coord):\\n x = coord.x + (coord.y + (coord.y&1)) // 2\\n z = -coord.y\\n y = -x-z\\n newcoord = newsystem.coord(x=x, y=y, z=z)\\n #logger.debug(\\\"OldCoord:%s NewCoord:%s\\\", coord, newcoord)\\n return newcoord\",\n \"def _cte_postformat(self):\\n# if type(self.idxs) == list:\\n# self.idxs = np.array(self.idxs)\\n if self.sp_relative_pos is not None:\\n if type(self.sp_relative_pos) == list:\\n self.sp_relative_pos = np.array(self.sp_relative_pos)\",\n \"def set_robot_pos(self):\\n\\t\\tx,y,z = self.geo2desiredENU(self.curr_lat, self.curr_lon, self.gpsAlt)\\n\\t\\tself.robot_msg.point.x = x\\n\\t\\tself.robot_msg.point.y = y\\n\\t\\tself.robot_msg.point.z = z\",\n \"def pfs_format_coord(x, y, detectorMap=detectorMap):\\n if detectorMap is None:\\n return \\\"\\\"\\n else:\\n fid = detectorMap.findFiberId(geom.PointD(x, y))\\n fidStr = f\\\"{fid:3}\\\"\\n if pfsConfig:\\n try:\\n mtpInfo = fiberIds.fiberIdToMTP([fid], pfsConfig)[0]\\n fidStr += f\\\" {', '.join([str(i) for i, l in zip(mtpInfo, mtpDetails) if l])}\\\"\\n except RuntimeError:\\n pass # fiber isn't in pfsConfig\\n\\n return f\\\"FiberId {fidStr} {detectorMap.findWavelength(fid, y):8.3f}nm\\\"\",\n \"def aligne_grille(self,x,y,t):\\r\\n [xmin,ymin,xmax,ymax] = self.can.coords(self.hitbox[t])\\r\\n tx,ty=xmax-xmin,ymax-ymin\\r\\n a,b=23,23\\r\\n if tx==92 or ty==92 or tx==184 or ty==184:\\r\\n if tx==92 or tx==184:a,b=0,23\\r\\n if ty==92 or ty==184:a,b=23,0\\r\\n if 142<y<602 and 66<x<528:\\r\\n x=(x-66)//46*46+66+a\\r\\n y=(y-142)//46*46+142+b\\r\\n return x,y\",\n \"def return_zeropoint():\\n return 22.5\",\n \"def _coord(self, x, y):\\n gridEdge = 7 # originally 5\\n y = gridEdge - y\\n cx = 100 * (x - 1) + 50\\n cy = 100 * (y - 1) + 50\\n r = 20\\n return (cx - r, cy - r, cx + r, cy + r)\",\n \"def coord(self, coord):\\n\\n self._coord = coord\",\n \"def configure_location(self):\\n # Set floor correctly\\n self.floor.set(\\\"pos\\\", array_to_string(self.bottom_pos))\",\n \"def __getxy(x1, y1, x2, y2):\\n\\t\\treturn x1*27+y1*9+x2*3+y2\",\n \"def GetLoCorner(self):\\n ...\",\n \"def handlelocationevent(self, event, platform, nem, component, data):\\n event = emaneeventlocation.EventLocation(data)\\n entries = event.entries()\\n for e in entries.values():\\n # yaw,pitch,roll,azimuth,elevation,velocity are unhandled\\n (nemid, lat, long, alt) = e[:4]\\n self.handlelocationeventtoxyz(nemid, lat, long, alt)\",\n \"def translateLoc(loc):\\n\\tif(loc[0].isalpha()):\\t\\n\\t\\treturn [int(loc[1:])-1,colDict[loc[0]],'V']\\n\\telse:\\n\\t\\treturn [int(loc[:-1])-1, colDict[loc[-1]],'H']\",\n \"def northing(self):\\r\\n x, y = self.lonlat2xy(self.longitude, self.latitude)\\r\\n return y\",\n \"def _UTMLetterDesignator(Lat):\\n if Lat >= 0: return 'N'\\n else: return 'S'\",\n \"def position(self, name, tdb):\\n if name == 'earth':\\n return self._interpolate_earth(tdb, differentiate=False)\\n else:\\n return self._interpolate(name, tdb, differentiate=False)\",\n \"def formatCoordinates(string):\\n if string == 'N/A':\\n return 0\\n else:\\n return float(string)\",\n \"def initialCoordinates():\\r\\n return (-250,-250)\",\n \"def fix_coord_units(cat, RA, DEC):\\n cat[RA].info.unit = u.deg\\n cat[DEC].info.unit = u.deg\\n return cat\",\n \"def format_coord(self, xd, yd):\\n\\n if self.M is None:\\n return ''\\n\\n if self.button_pressed in self._rotate_btn:\\n return 'azimuth=%d deg, elevation=%d deg ' % (self.azim, self.elev)\\n # ignore xd and yd and display angles instead\\n\\n p = (xd, yd)\\n edges = self.tunit_edges()\\n #lines = [proj3d.line2d(p0,p1) for (p0,p1) in edges]\\n ldists = [(proj3d.line2d_seg_dist(p0, p1, p), i) for \\\\\\n i, (p0, p1) in enumerate(edges)]\\n ldists.sort()\\n # nearest edge\\n edgei = ldists[0][1]\\n\\n p0, p1 = edges[edgei]\\n\\n # scale the z value to match\\n x0, y0, z0 = p0\\n x1, y1, z1 = p1\\n d0 = np.hypot(x0-xd, y0-yd)\\n d1 = np.hypot(x1-xd, y1-yd)\\n dt = d0+d1\\n z = d1/dt * z0 + d0/dt * z1\\n\\n x, y, z = proj3d.inv_transform(xd, yd, z, self.M)\\n\\n xs = self.format_xdata(x)\\n ys = self.format_ydata(y)\\n zs = self.format_ydata(z)\\n return 'x=%s, y=%s, z=%s' % (xs, ys, zs)\",\n \"def test_conversion_to_xyz_with_negatives(self):\\r\\n\\r\\n self.color.spec_530nm = -0.0736\\r\\n # TODO: Convert here.\\r\",\n \"def getCoords(self): # real signature unknown; restored from __doc__\\r\\n pass\",\n \"def _extract_location_xyz(self, log):\\n\\n if \\\"location\\\" in log:\\n x = log[\\\"location\\\"][\\\"latitude\\\"]\\n y = log[\\\"location\\\"][\\\"longitude\\\"]\\n z = log[\\\"location\\\"][\\\"altitude\\\"]\\n else:\\n self.logger.debug(\\\"NaN case\\\")\\n x = \\\"NaN\\\" # matlab Nan?\\n y = \\\"NaN\\\"\\n z = \\\"NaN\\\"\\n pass\\n return str(x) + \\\",\\\" + str(y) + \\\",\\\" + str(z)\",\n \"def _coord_byval(coord: COORD) -> c_long:\\n return c_long(coord.Y * 0x10000 | coord.X & 0xFFFF)\",\n \"def placeCrate (self, crates_char, row, column):\",\n \"def test_RNA_position_placement(self):\\n \\n \\n tool = pybedtools.create_interval_from_list(\\\"chr1 50 60 ENSMUSG1_1_83;ENSMUSG1_6_83 0 + 60 60\\\".split())\\n location_dict = {\\\"ENSMUSG1\\\" : {\\\"strand\\\" : \\\"+\\\", \\\"regions\\\" : [(0,100),\\n ] \\n }\\n }\\n \\n self.assertEqual(RNA_position(tool, location_dict), (.60, .60))\\n \\n tool = pybedtools.create_interval_from_list(\\\"chr1 50 60 ENSMUSG1_1_83;ENSMUSG1_6_83 0 - 60 60\\\".split())\\n location_dict = {\\\"ENSMUSG1\\\" : {\\\"strand\\\" : \\\"-\\\", \\\"regions\\\" : [(0,100),\\n ] \\n }\\n }\\n \\n #individual_fraction, total_fraction\\n self.assertEqual(RNA_position(tool, location_dict), (.4, .4))\",\n \"def integrate(coords,data,fault_pts,dshape_hex8,gll_weights,elmt):\\n norm=0.0\\n normx=0.0\\n normy=0.0\\n normz=0.0\\n div=0.0 #normalizing factor to divide by\\n divx=0.\\n divy=0.\\n divz=0.\\n\\n eps=1.0*g.mesh_spacing/(g.ngllx-1.)\\n print 'eps=', eps\\n f=open('eliminated_coords.vtk','w')\\n\\n #create integer versions of arrays to use in pulling out gll pts for each element\\n data_round=np.rint(data)\\n dati=data_round.astype(int)\\n coord_round=np.rint(coords)\\n coordi=coord_round.astype(int)\\n\\n #remove duplicates from data array\\n dat_struc=np.ascontiguousarray(dati).view(np.dtype((np.void,dati.dtype.itemsize *dati.shape[1])))\\n _,idx=np.unique(dat_struc,return_index=True)\\n datu=dati[idx]\\n data_unique=data[idx]\\n\\n for i_elmt in range(g.nelmt):\\n #pull out geometric coordinates for this element\\n elmt_coord_id=[j-1 for j in elmt[i_elmt]]\\n elmt_coord=coordi[elmt_coord_id]\\n\\n #find corresponding gll pts for this element\\n xmin=min(elmt_coord[:,0]);xmax=max(elmt_coord[:,0])\\n ymin=min(elmt_coord[:,1]);ymax=max(elmt_coord[:,1])\\n zmin=min(elmt_coord[:,2]);zmax=max(elmt_coord[:,2])\\n gll_coord_id=np.nonzero((datu[:,0]>=xmin) & (datu[:,0]<=xmax) & (datu[:,1]>=ymin) & (datu[:,1]<=ymax) & (datu[:,2]>=zmin) & (datu[:,2]<=zmax))\\n elmt_data=data_unique[gll_coord_id]\\n if len(gll_coord_id[0]) != g.ngll:\\n print \\\"elmt=\\\", elmt_coord_id\\n print xmin,xmax,ymin,ymax,zmin,zmax\\n print 'elmt_data=', elmt_data\\n print \\\"gll pts found=\\\", len(gll_coord_id[0])\\n raise ValueError(\\\"incorrect number of gll points found in element!\\\")\\n exit\\n\\n #sort the gll coords so they correspond the order of the arrays giving the weights and shape function\\n dat_sorted=elmt_data[npi.argsort((elmt_data[:,0], elmt_data[:,1],elmt_data[:,2]))]\\n func=dat_sorted[:,3:]\\n\\n #if any gll pt is too close to fault, remove the element from the integration\\n dist=distance.cdist(fault_pts,dat_sorted[:,0:3],'euclidean')\\n if (dist<eps).any():\\n print \\\"eliminated element #\\\", i_elmt\\n np.savetxt(f,dat_sorted[:,0:3],fmt='%3.3f')\\n continue\\n\\n for i_gll in range(g.ngll):\\n\\n #compute jacobian, its derivative and inverse\\n jac=np.matmul(dshape_hex8[:,:,i_gll],elmt_coord)\\n det_jac=np.linalg.det(jac)\\n\\n #perform the integration\\n norm=norm+det_jac*gll_weights[i_gll]*np.dot((func[i_gll,3:6]-func[i_gll,0:3]),(func[i_gll,3:6]-func[i_gll,0:3]))\\n div=div+det_jac*gll_weights[i_gll]*np.dot(func[i_gll,3:6],func[i_gll,3:6])\\n normx=normx+det_jac*gll_weights[i_gll]*(func[i_gll,3]-func[i_gll,0])**2\\n divx=divx+det_jac*gll_weights[i_gll]*(func[i_gll,3])**2\\n normy=normy+det_jac*gll_weights[i_gll]*(func[i_gll,4]-func[i_gll,1])**2\\n divy=divy+det_jac*gll_weights[i_gll]*(func[i_gll,4])**2\\n normz=normz+det_jac*gll_weights[i_gll]*(func[i_gll,5]-func[i_gll,2])**2\\n divz=divz+det_jac*gll_weights[i_gll]*(func[i_gll,5])**2\\n\\n norm_finalx=sqrt(normx/divx)\\n norm_finaly=sqrt(normy/divy)\\n norm_finalz=sqrt(normz/divz)\\n norm_final=sqrt(norm/div)\\n\\n f.close()\\n\\n return norm_finalx, norm_finaly, norm_finalz,norm_final\",\n \"def coord(self):\\n fmt = \\\"{min_col}{min_row}:{max_col}{max_row}\\\"\\n if (self.min_col == self.max_col\\n and self.min_row == self.max_row):\\n fmt = \\\"{min_col}{min_row}\\\"\\n\\n return fmt.format(\\n min_col=get_column_letter(self.min_col),\\n min_row=self.min_row,\\n max_col=get_column_letter(self.max_col),\\n max_row=self.max_row\\n )\",\n \"def cell_value(self, x, y):\\n if x == 8 and y == 0:\\n return \\\"--\\\"\\n (r, g) = self[(x, y)]\\n return \\\"%s%s\\\" % (r, g)\",\n \"def spot_coords(self,spot):\\n if spot == '1':\\n return (330 - 60 ,335 - 15)\\n if spot == '2':\\n return (419 - 60, 335 - 15)\\n if spot == '3':\\n return (591 - 60, 159 - 15)\\n if spot == '4':\\n return (588 - 60, 248 - 15)\",\n \"def extract_raw_simple_coordinates (raw_location):\\n pattern = re.compile('(\\\\d+).(\\\\d+)?')\\n x_result = pattern.match(str(raw_location[0]))\\n y_result = pattern.match(str(raw_location[1]))\\n return int(x_result[1]), int(y_result[1])\",\n \"def readable(self):\\n return \\\"(x: %.1f, y:%.1f)\\\" % (self.x, self.y)\",\n \"def __getxyB(x, y):\\n\\t\\treturn x*3+y\",\n \"def _set_real_format(self, fmt):\\n # try to use the _nomax variant if available\\n if not self._max and fmt + '_nomax' in self.formats:\\n self._format = self.formats[fmt + '_nomax']\\n elif fmt in self.formats:\\n self._format = self.formats[fmt]\\n else:\\n self._format = fmt\\n\\n self._format_line_count = self._format.count('\\\\n')\",\n \"def edwin_location(self, res):\\n if res.data[0:5] == \\\"WHERE\\\":\\n #gets edwin's location\\n where = res.data[5:]\\n\\n #massive string formatting - takes the string, splits by a formatter, then takes the array index that holds the XYZ,\\n #then strips that string and splits it by spacing, and then takes the XYZ\\n #reason for this massive formatting is b/c sent data format is not consistent\\n where = where.split(\\\"\\\\r\\\\n\\\")[2].strip().split(' ')\\n\\n #gets rid of empty strings that result from formatting\\n where = filter(None, where)[0:3]\\n\\n #makes everything numbers that can be used as coordinates for Edwin\\n where = [int(float(coord) * 10) for coord in where]\\n\\n self.edwinx = where[0]\\n self.edwiny = where[1]\\n self.edwinz = where[2]\",\n \"def __post_init__(self) -> None:\\n self.annotate = self.x_y[0] == 0 or self.x_y[1] == 0\",\n \"def log_robot_location(self):\\n trans, rot = self.get_robot_location()\\n if trans != None and rot != None:\\n degrees = (rot.yaw * 180./math.pi)\\n message = {\\n 'x':'{0:.3f}'.format(trans.x),\\n 'y':'{0:.3f}'.format(trans.y),\\n 'rotation':'{0:.3f}'.format(degrees)}\\n\\n self.logger.log('ROS_XYR', 'ROS_XYR', message, 'state')\",\n \"def _fix_iris_bug_derived_coord(cube):\\n air_pressure_coord = cube.coord('air_pressure')\\n try:\\n altitude_coord = cube.coord('altitude')\\n except iris.exceptions.CoordinateNotFoundError:\\n altitude_coord = None\\n for aux_factory in cube.aux_factories:\\n cube.remove_aux_factory(aux_factory)\\n try:\\n cube.coord('air_pressure')\\n except iris.exceptions.CoordinateNotFoundError:\\n cube.add_aux_coord(air_pressure_coord, np.arange(cube.ndim))\\n if altitude_coord is not None:\\n cube.add_aux_coord(altitude_coord, (1, 2, 3))\",\n \"def get_cell_coords(self, pt):\\n\\n\\t return int(pt[0] // self.a), int(pt[1] // self.a)\",\n \"def location_to_pos(self,row, col):\\r\\n\\r\\n pos_row = str(row + 1)\\r\\n pos_col = chr(col + 97)\\r\\n return pos_col + pos_row\",\n \"def _correct_indel_coords(chrom, pos, ref, alt, pysamtxeff):\\n lref = len(ref)\\n lalt = len(alt)\\n if lref == 1 and lalt == 1:\\n # Substitution case\\n change = '>'.join([ref, alt])\\n new_pos = str(pos) + change\\n return new_pos\\n elif lalt == 1 and lref > lalt:\\n dels = RptHandler(pysamtxeff, chrom, pos, ref)\\n # Deletion case\\n if dels.check_rpt_status():\\n new_start, new_end = dels.find_rpt_coords()\\n if len(dels.allele) == 1:\\n new_pos = '_'.join([str(new_start)]) + 'del'\\n else:\\n new_pos = '_'.join([str(new_start), str(new_end)]) + 'del'\\n else:\\n shift = lref - lalt\\n if shift == 1:\\n new_pos = str(int(pos) + 1) + 'del'\\n else:\\n new_start = str(int(pos) + 1)\\n new_end = str(int(pos) + shift)\\n new_pos = '_'.join([new_start, new_end]) + 'del'\\n return new_pos\\n elif lref == 1 and lalt > lref:\\n dups = RptHandler(pysamtxeff, chrom, pos, alt)\\n # Duplication case\\n if dups.check_rpt_status():\\n new_start, new_end = dups.find_rpt_coords()\\n # Check if there is a padding base, then adjust accordingly.\\n if alt[0] == ref[0]:\\n new_start += 1\\n new_end += 1\\n if len(dups.allele) == 1:\\n new_pos = '_'.join([str(new_start)]) + 'dup'\\n else:\\n new_pos = '_'.join([str(new_start), str(new_end)]) + 'dup'\\n # Insertion case\\n else:\\n new_start = str(pos)\\n new_end = str(int(pos) + 1)\\n new_pos = '_'.join([new_start, new_end]) + 'ins' + alt[1:]\\n return new_pos\\n elif lref > 1 and lalt > 1:\\n # Multi-nucleotide substitution case\\n # NG_012232.1: g.12_13delinsTG\\n new_start = pos\\n new_end = str(int(pos) + lref - 1)\\n # If there is a common padding base, like ATG>ACC, make sure we are taking this in to account.\\n if alt[0] == ref[0]:\\n new_start += 1\\n alt = alt[1:]\\n new_pos = '_'.join([str(new_start), new_end]) + 'delins' + alt\\n return new_pos\\n else:\\n raise Exception(\\\"Unknown change type: \\\" + pos + ':' + ref + '>' + alt)\",\n \"def _callback_compass(self, msg):\\n\\n\\t\\tself.heading = self.north2east( msg.heading )\",\n \"def _get_xy_coords(self, exterior, coord_type):\\n if coord_type == 'x':\\n return exterior.coords.xy[0]\\n elif coord_type == 'y':\\n return exterior.coords.xy[1]\",\n \"def get_coord(self):\\n return self.coord\",\n \"def dump_coords(geom): # -> Any | list[Unknown]:\\n ...\",\n \"def test_location_to_coord():\\n result_a = wwiki.location_to_coord(location)\\n result_b = wwiki.location_to_coord(location)\\n\\n assert isinstance(result_a, str)\\n assert result_b == \\\"48.76569917989272|2.392394129892722\\\"\",\n \"def handle_position(data: bytes) -> Tuple[bytes, str]:\\n x, y, z = struct.unpack('fff', data[0:3 * 4])\\n return data[20:], f'Current Position (x,y,z): {x} {y} {z}'\",\n \"def mousePositionRaw(self):\",\n \"def mousePositionRaw(self):\",\n \"def xy(event):\\n return map(int, event.get_coords())\",\n \"def set_marker(self, packet):\\n if self.file_type == 'csv':\\n self.write_data(packet=packet)\\n elif self.file_type == 'edf':\\n timestamp, code = packet.get_data()\\n if self._rectime_offset is None:\\n self._rectime_offset = timestamp[0]\\n timestamp = timestamp-np.float64(self._rectime_offset)\\n self._file_obj.writeAnnotation(timestamp[0], 0.001, str(int(code[0])))\",\n \"def floatize(self):\\n self.x = float(self.x)\\n self.y = float(self.y)\",\n \"def floatize(self):\\n self.x = float(self.x)\\n self.y = float(self.y)\",\n \"def fixture_coord():\\n\\tEXAMPLE_FILE_FOLDER = str(MODULE_DIR) + \\\"/data/nail1/\\\"\\n\\tcoord_x, coord_y, coord = read.load_coord(EXAMPLE_FILE_FOLDER)\\n\\treturn coord\",\n \"def test_lng_preserved(self):\\n response = get_recent_point(None)\\n fields = json.loads(response.content.decode('utf-8'))[0]['fields']\\n self.assertAlmostEqual(fields['lng'], self.pt.lng)\",\n \"def test_adjust_offsets_short(self):\\n tool = pybedtools.BedTool(\\\"chr15 91512755 91512836 ENSG00000198901_1_147 0 -\\\", from_string=True)\\n offsets = {\\\"ENSG00000198901_1_147\\\" : 10}\\n results = adjust_offsets(tool, offsets)\",\n \"def getChrNum(self):\\n chrLookup = {\\\"X\\\":23,\\\"x\\\":23,\\\"Y\\\":24,\\\"y\\\":24}\\n if self.chr.startswith(\\\"chr\\\"):\\n num = self.chr[3:]\\n if num in (\\\"X\\\",\\\"x\\\",\\\"Y\\\",\\\"y\\\"):\\n num = chrLookup[num]\\n return int(num)\\n else: return self.chr\",\n \"def test_lat_preserved(self):\\n response = get_recent_point(None)\\n fields = json.loads(response.content.decode('utf-8'))[0]['fields']\\n self.assertAlmostEqual(fields['lat'], self.pt.lat)\",\n \"def __str__(self):\\n\\t\\treturn '<' + str(self._coords)[1:-1] + '>'\",\n \"def coordPlt(grid, buffer=10, step=5):\\n plt.cla()\\n\\n plt.plot(grid[1][0::step, 0::step],\\n grid[0][0::step, 0::step],\\n '.-b' )\\n\\n plt.plot(grid[1][0::step, 0::step].T,\\n grid[0][0::step, 0::step].T,\\n '.-b' )\\n\\n plt.axis( [ grid[1].max() + buffer,\\n grid[1].min() - buffer,\\n grid[0].max() + buffer,\\n grid[0].min() - buffer],\\n )\\n plt.axis('off')\\n plt.grid()\",\n \"def putCoordInfo(self, hdu):\\n\\n hdu.header.update(\\\"CDELT1\\\", self.cdelt, \\\"pixel size, degrees\\\")\\n hdu.header.update(\\\"CDELT2\\\", self.cdelt, \\\"pixel size, degrees\\\")\\n shape = hdu.data.shape\\n crpix1 = (shape[0] + 1) // 2 + 1\\n crpix2 = (shape[1] + 1) // 2 + 1\\n hdu.header.update(\\\"CRPIX1\\\", float(crpix1), \\\"reference pixel\\\")\\n hdu.header.update(\\\"CRPIX2\\\", float(crpix2), \\\"reference pixel\\\")\",\n \"def __calculateOffset(self):\\n #if len(self.__XValue) > 0:\\n # print(\\\"GPSBearing: \\\"+str(round(self.__GPSBearing[-1]))+\\\", heading: \\\"+str(round(self.value))+\\n # \\\", x: \\\"+str(round(self.__XValue[-1]))+\\\", stdev: \\\"+str(round(np.std(self.__GPSBearing),5))+\\n # \\\", offset: \\\"+str(self.__offset))\\n if len(self.__GPSBearing) == self.__GPSBearing.maxlen and np.std(self.__GPSBearing) < 0.2 and self.speed > 7:\\n self.__offset = (np.mean(self.__GPSBearing) + 360 - np.mean(self.__XValue)) % 360\\n #print(\\\"new offset: \\\"+str(self.__offset)) \",\n \"def __get_x__(self):\\n return self.Direction['x']\",\n \"def offset_point(self,base, offset):\\r\\n return (base[0] + offset[0], base[1] + offset[1])\",\n \"def setup_fmt(self, ctx):\\n ctx.implicit_errors = False\",\n \"def coord (i, j):\\r\\n return j, i\",\n \"def init_atom_coords(self) -> None:\\n ...\",\n \"def wellname_to_coordinates(wellname):\\n rowname, colname = re.match(\\\"([a-zA-Z]+)([0-9]+)\\\", wellname).groups()\\n return rowname_to_number(rowname), int(colname)\",\n \"def get_text_loc_axis_coord(xArr, yArr, xr, yr, delta):\\n\\tdff = N.abs(yArr - yr[1])\\n\\tii = N.where(dff == N.min(dff))[0]\\n\\tif xArr[ii] < xr[1]:\\n\\t\\tyloc = 1. + delta[1]\\n\\t\\txloc = N.abs(N.log10(xArr[ii]/xr[0]))/N.abs(N.log10(xr[1]/xr[0]))\\n\\telse:\\n\\t\\txloc = 1. + delta[0]\\n\\t\\tdff = N.abs(xArr - xr[1])\\n\\t\\tjj = N.where(dff == N.min(dff))[0]\\n\\t\\tyloc = N.abs(N.log10(yArr[jj]/yr[0]))/N.abs(N.log10(yr[1]/yr[0]))\\n\\treturn [xloc, yloc]\",\n \"def __str__(self):\\r\\n if self.y == 1:\\r\\n return \\\"{}\\\".format(self.x)\\r\\n else:\\r\\n return \\\"{}/{}\\\".format(self.x, self.y)\",\n \"def atom_to_internal_coordinates(self, verbose: bool = ...) -> None:\\n ...\",\n \"def atom_to_internal_coordinates(self, verbose: bool = ...) -> None:\\n ...\",\n \"def atm241(coord: numpy.array) -> numpy.array:\\n ...\",\n \"def test_RNA_position_fail(self):\\n \\n tool = pybedtools.create_interval_from_list(\\\"chr1 50 60 ENSMUSG1_1_83;ENSMUSG1_6_83 0 - 10 10\\\".split())\\n location_dict = {\\\"ENSMUSG1\\\" : {\\\"strand\\\" : \\\"-\\\", \\\"regions\\\" : [(100, 150),\\n (25,50),\\n ] \\n }\\n }\\n \\n self.assertEqual(RNA_position(tool, location_dict), (None, None))\\n \\n tool = pybedtools.create_interval_from_list(\\\"chr1 50 60 ENSMUSG1_1_83;ENSMUSG1_6_83 0 - 175 175\\\".split())\\n \\n self.assertEqual(RNA_position(tool, location_dict), (None, None))\",\n \"def get_real_leg(self):\\n if self.invert_y:\\n inv = -1\\n else:\\n inv = 1\\n\\n c = self.C[-1]\\n\\n c = Coordinate(\\n x=c.x + self.structure_offset.x,\\n y=c.y * inv + self.structure_offset.y,\\n z=c.z + self.structure_offset.z\\n )\\n return c\",\n \"def get_starting_coordinate(self):\\n if type(self._starting_coordinate) != tuple:\\n self._logger.write(\\\"Error! starting_coordinate should be a tupple\\\")\\n elif self._starting_coordinate == None:\\n #this is dead code\\n self._logger.write(\\\"Error! starting_coordinate does not contain a value\\\")\\n else:\\n try:\\n return self._starting_coordinate\\n except Exception as e:\\n self._logger.write(\\\"Error! could not get starting_coordinate: %s\\\" % e)\",\n \"def __init__(self, *args, **kwargs):\\n # Impose default formatter\\n super().__init__(*args, **kwargs)\\n formatter = axistools.Formatter('auto')\\n self.xaxis.set_major_formatter(formatter)\\n self.yaxis.set_major_formatter(formatter)\\n self.xaxis.isDefault_majfmt = True\\n self.yaxis.isDefault_majfmt = True\\n # Custom attributes\\n self._datex_rotated = False # whether manual rotation has been applied\\n self._dualy_arg = None # for scaling units on opposite side of ax\\n self._dualx_arg = None\\n self._dualy_cache = None # prevent excess _dualy_overrides calls\\n self._dualx_cache = None\",\n \"def geo_transform(self):\\n pass\",\n \"def _get_origin_ted(self):\\n return self.__origin_ted\",\n \"def position_region(reg):\\n x,y = reg.coord_list[:2]\\n posn = coords.Position([x,y],system=coords_format(reg.coord_format))\\n return posn\",\n \"def _origin(self):\\n return 1\"\n]","isConversational":false},"negative_scores":{"kind":"list like","value":["0.52641153","0.5259147","0.5174216","0.5166887","0.5154606","0.514098","0.51310825","0.51202244","0.51102793","0.5103446","0.50844723","0.5079553","0.507823","0.50599504","0.5053271","0.5025921","0.5018617","0.4984303","0.49542806","0.4949716","0.49197924","0.49083477","0.49048135","0.4904781","0.48888385","0.48834026","0.48808634","0.48483774","0.48334146","0.4830994","0.48307422","0.48299617","0.48293793","0.48175246","0.48064935","0.48055935","0.47877857","0.47801015","0.47757772","0.47742087","0.4764549","0.47458404","0.47446752","0.47415462","0.47364852","0.4735368","0.47336447","0.47204825","0.47184494","0.47107625","0.47054034","0.4702515","0.46985954","0.46966335","0.46800566","0.46773484","0.46738243","0.4669964","0.4666686","0.46622336","0.4660443","0.4658784","0.4655283","0.46512347","0.4638116","0.4636769","0.46322072","0.46322072","0.4621601","0.46168977","0.4613658","0.4613658","0.46103746","0.46077472","0.46072283","0.46049178","0.46023437","0.46014908","0.46010262","0.46000618","0.45984623","0.4596039","0.45956898","0.45825964","0.45770395","0.4571577","0.45652825","0.45612568","0.45571256","0.4555774","0.4555774","0.45542857","0.454674","0.45451874","0.45450845","0.45425707","0.45401055","0.4534757","0.45347303","0.45302448"],"string":"[\n \"0.52641153\",\n \"0.5259147\",\n \"0.5174216\",\n \"0.5166887\",\n \"0.5154606\",\n \"0.514098\",\n \"0.51310825\",\n \"0.51202244\",\n \"0.51102793\",\n \"0.5103446\",\n \"0.50844723\",\n \"0.5079553\",\n \"0.507823\",\n \"0.50599504\",\n \"0.5053271\",\n \"0.5025921\",\n \"0.5018617\",\n \"0.4984303\",\n \"0.49542806\",\n \"0.4949716\",\n \"0.49197924\",\n \"0.49083477\",\n \"0.49048135\",\n \"0.4904781\",\n \"0.48888385\",\n \"0.48834026\",\n \"0.48808634\",\n \"0.48483774\",\n \"0.48334146\",\n \"0.4830994\",\n \"0.48307422\",\n \"0.48299617\",\n \"0.48293793\",\n \"0.48175246\",\n \"0.48064935\",\n \"0.48055935\",\n \"0.47877857\",\n \"0.47801015\",\n \"0.47757772\",\n \"0.47742087\",\n \"0.4764549\",\n \"0.47458404\",\n \"0.47446752\",\n \"0.47415462\",\n \"0.47364852\",\n \"0.4735368\",\n \"0.47336447\",\n \"0.47204825\",\n \"0.47184494\",\n \"0.47107625\",\n \"0.47054034\",\n \"0.4702515\",\n \"0.46985954\",\n \"0.46966335\",\n \"0.46800566\",\n \"0.46773484\",\n \"0.46738243\",\n \"0.4669964\",\n \"0.4666686\",\n \"0.46622336\",\n \"0.4660443\",\n \"0.4658784\",\n \"0.4655283\",\n \"0.46512347\",\n \"0.4638116\",\n \"0.4636769\",\n \"0.46322072\",\n \"0.46322072\",\n \"0.4621601\",\n \"0.46168977\",\n \"0.4613658\",\n \"0.4613658\",\n \"0.46103746\",\n \"0.46077472\",\n \"0.46072283\",\n \"0.46049178\",\n \"0.46023437\",\n \"0.46014908\",\n \"0.46010262\",\n \"0.46000618\",\n \"0.45984623\",\n \"0.4596039\",\n \"0.45956898\",\n \"0.45825964\",\n \"0.45770395\",\n \"0.4571577\",\n \"0.45652825\",\n \"0.45612568\",\n \"0.45571256\",\n \"0.4555774\",\n \"0.4555774\",\n \"0.45542857\",\n \"0.454674\",\n \"0.45451874\",\n \"0.45450845\",\n \"0.45425707\",\n \"0.45401055\",\n \"0.4534757\",\n \"0.45347303\",\n \"0.45302448\"\n]","isConversational":false},"document_score":{"kind":"string","value":"0.61945975"},"document_rank":{"kind":"string","value":"0"}}},{"rowIdx":16590,"cells":{"query":{"kind":"string","value":"Trap coord inside gerber param block."},"document":{"kind":"string","value":"def test_data_in_param(self):"},"metadata":{"kind":"string","value":"{\n \"objective\": {\n \"self\": [],\n \"paired\": [],\n \"triplet\": [\n [\n \"query\",\n \"document\",\n \"negatives\"\n ]\n ]\n }\n}"},"negatives":{"kind":"list like","value":["def xy(self):\n ...","def paramValueChanged(self, param):\n if self._printSWAP == True:\n print param.name + \" in address \" + str(param.getRegAddress()) + \" changed to \" + param.getValueInAscii()","def modifyPoint(self, *args, **kwargs):\n ...","def set_coord(self, l, sign, b):\n if l is not None:\n self.l = float(l)\n if b is not None:\n self.b = float(b)\n if sign == '-':\n self.b *= -1.","def set_xy(self, x, y, val):\r\n\t\tself.grid[y, x] = val","def set_robot_pos(self):\n\t\tx,y,z = self.geo2desiredENU(self.curr_lat, self.curr_lon, self.gpsAlt)\n\t\tself.robot_msg.point.x = x\n\t\tself.robot_msg.point.y = y\n\t\tself.robot_msg.point.z = z","def setPos(self,x,y):\n for i in self.itemType.find('parameters'):\n paramType = i.find('type').text.strip()\n if paramType.startswith('position-x'):\n self.params[i.find('name').text] = x\n if paramType.startswith('position-y'):\n self.params[i.find('name').text] = y","def setCoords(self, p_float, p_float_1, p_float_2, p_float_3): # real signature unknown; restored from __doc__\r\n pass","def coordinates(self):","def setPosition(*args):","def setPosition(*args):","def setPosition(*args):","def setPosition(*args):","def setPosition(*args):","def setPosition(*args):","def setPosition(*args):","def setPosition(*args):","def setPosition(*args):","def setPosition(*args):","def setPosition(*args):","def _set_params(self,x):\r\n self.k._set_params(x)","def set_parameter(self, param, value, stripe = 0, location = 3):\n if param in self.fpga.cabac_top[0].params:\n self.fpga.set_cabac_value(param, value, stripe)\n time.sleep(0.1)\n self.fpga.send_cabac_config(stripe)\n\n elif param in [\"V_SL\", \"V_SH\", \"V_RGL\", \"V_RGH\", \"V_PL\", \"V_PH\"]:\n self.fpga.set_clock_voltages({param: value})\n\n elif param == \"I_OS\":\n self.fpga.set_current_source(value, stripe)\n\n else:\n print(\"Warning: unidentified parameter for the REB: %s\" % param)","def coord(self, coord):\n\n self._coord = coord","def prep_latlng_params(self, lat, lng):\n self._api_params['latlng'] = '{},{}'.format(lat, lng)","def set_new_location(self, xPos, yPos):","def test_coord_preceding_fs(self):","def _handleInput(self, paramInput):\n super()._handleInput(paramInput)\n locationFind = paramInput.findFirst('location')\n if locationFind != None:\n self.location = locationFind.value\n else:\n self.raiseAnError(IOError,'location value needed for Laplace distribution')\n scaleFind = paramInput.findFirst('scale')\n if scaleFind != None:\n self.scale = scaleFind.value\n else:\n self.raiseAnError(IOError,'scale value needed for Laplace distribution')\n self.initializeDistribution()","def mousePositionRaw(self):","def mousePositionRaw(self):","def _setup_params(self,**params):\n ### a parameter might be passed in for one of the extra_pos;\n ### if a key in the params dict is not a *parameter* of this\n ### PO, then try it on the extra_pos\n for n,p in params.items():\n if n not in self.params():\n self.set_parameter_value(n,p)\n del params[n]\n\n Parameterized._setup_params(self,**params)","def __init__(self, x, y, elevation):\n super(GridPoint, self).__init__(x, y)\n self.elevation = elevation","def get_location(self):\n self.location = self.func(0)","def EvaluateLocation(self, p_int, , p_float=..., p_float=..., p_float=..., *args, **kwargs):\n ...","def _get_raw_params(self, node):","def param2pos( param, stickguy ):\n\n hip_pos = np.array([0.0, param[0]])\n spine_vec = np.array([0.0, 1.0])\n spine_vec = rotate(spine_vec, param[1])\n neck_pos = hip_pos + spine_vec\n basic_arm_vec = -0.6*spine_vec\n arm_vec = rotate(basic_arm_vec, param[2])\n left_elbow_pos = neck_pos + arm_vec\n arm_vec = rotate(arm_vec, param[3])\n left_hand_pos = left_elbow_pos + arm_vec\n lad = np.array([neck_pos,left_elbow_pos,left_hand_pos])\n stickguy.left_arm.set_data(lad[:,0],lad[:,1])\n\n arm_vec = rotate(basic_arm_vec, param[4])\n right_elbow_pos = neck_pos + arm_vec\n arm_vec = rotate(arm_vec, param[5])\n right_hand_pos = right_elbow_pos + arm_vec\n rad = np.array([neck_pos,right_elbow_pos,right_hand_pos])\n stickguy.right_arm.set_data(rad[:,0],rad[:,1])\n\n neck_vec = 0.3*spine_vec\n neck_vec = rotate( neck_vec, param[6])\n head_pos = neck_pos + neck_vec\n sd = np.array([hip_pos,neck_pos,head_pos])\n stickguy.spine.set_data(sd[:,0],sd[:,1])\n\n basic_leg_vec = (0.0,-0.7)\n leg_vec = rotate(basic_leg_vec, param[7])\n left_knee_pos = hip_pos + leg_vec\n leg_vec = rotate(leg_vec, param[8])\n left_foot_pos = left_knee_pos + leg_vec\n lld = np.array([hip_pos,left_knee_pos,left_foot_pos])\n stickguy.left_leg.set_data(lld[:,0],lld[:,1])\n\n leg_vec = rotate(basic_leg_vec, param[9])\n right_knee_pos = hip_pos + leg_vec\n leg_vec = rotate(leg_vec, param[10])\n right_foot_pos = right_knee_pos + leg_vec\n rld = np.array([hip_pos,right_knee_pos,right_foot_pos])\n stickguy.right_leg.set_data(rld[:,0],rld[:,1])\n\n return","def m_location_set(self, x: int, y: int):\n pass","def set_params(self, **kwargs):\n warnings.warn(\"'set_params()' not defined for locator of type \" +\n str(type(self)))","def mousePosition(self):","def initialCoordinates():\r\n return (-250,-250)","def flash_location(self,params):\n loc = params['location']\n if self.participant:\n if self.service.groupOfParticipant(self) and self.participant.status != AVOID:\n self.participant.changeStatus(LISTEN)\n #print loc\n (x,y) = self.service.grid.conformToGrid(loc)\n self.participant.setLocation((x,y))\n self.receiveDirectCommand(\"location\",{\"x\":x,\"y\":y})\n \n else:\n self.notLoggedIn()","def Modifier_UserGPS(self):","def global_coords(self) -> GlobalCoordsABC:","def grab_current_point(self):\n self.open_gripper(80)\n time.sleep(2.5)\n self.execute_action((0, 0, -10), self.GRAB_ORIENTATION)\n self.open_gripper(-30)\n time.sleep(2.5)\n self.execute_action((0, 0, 10), self.GRAB_ORIENTATION)\n time.sleep(2.5)\n self.initial_position = np.array(self.get_current_cartesian_position().position)\n print self.initial_position","def set_params(self, params):","def setLocation(self, p):\n super(PolygonTool, self).setLocation(p.point)\n _x, _y = self.getLocation().getCoords()\n _count = self.__nsides\n _inc = self.__increment\n if self.__external:\n _offset = _inc/2.0\n else:\n _offset = 0.0\n _cx, _cy = self.__center.point.getCoords()\n _xsep = _x - _cx\n _ysep = _y - _cy\n _angle = math.atan2(_ysep, _xsep) + _offset\n _rad = math.hypot(_xsep, _ysep)/math.cos(_offset)\n _xp = self.__xpts\n _yp = self.__ypts\n for _i in range(_count):\n _xp[_i] = _cx + (_rad * math.cos(_angle))\n _yp[_i] = _cy + (_rad * math.sin(_angle))\n _angle = _angle + _inc","def get_set_extended_position_args(self,comArgs):\n params, flags = self.get_params(comArgs)\n point = self.get_point(params)\n step_point = self.multiply_vector(point,self.spm)\n args = [step_point]\n self.current_point = point\n return args","def place(self,y,x):\n self.y = y\n self.x = x","def setGxLocation(self):\n if self.xyz is None:\n gxobs = self.obs.get(None, {}).get(\"GX\")\n if gxobs is not None:\n gxyz = np.array((0.0, 0.0, 0.0))\n for gx in gxobs:\n gxyz += gx.obsvalue.value\n self.xyz = gxyz / len(gxobs)\n self.locator.write(\n \"Fixing station {0} using GNSS coordinate observations\\n\".format(\n self.code\n )\n )","def set_2d_location(self, x, y):\r\n self.unif[42:44] = [x, y]","def set_params(self, *arg):\n pass","def setUp(self):\n self.location = [(0, 0), (0, 1)]\n self.hit = (0, 0)","def grab(self, event):\n self.ypos = event.y\n self.xpos = event.x\n self.config(cursor='fleur')","def set_parameters(self, params):\n self.kp = params.pgain","def _global_pose_cb(self, msg):\n self.global_pose = msg","def on_VI_XY_set_clicked(self):\n # TODO: not implemented yet\n disp_coord()\n if qmdz_const.Auto_Range == 0:\n xmin = int(read_config(qmdz_const.SYS_CONF_PATH, 'COORD', 'x_min'))\n xmax = int(read_config(qmdz_const.SYS_CONF_PATH, 'COORD', 'x_max'))\n ymin = int(read_config(qmdz_const.SYS_CONF_PATH, 'COORD', 'y_min'))\n ymax = int(read_config(qmdz_const.SYS_CONF_PATH, 'COORD', 'y_max'))\n self.VI_MPL.change_xy(xmin, xmax, ymin, ymax)","def location(self, value: 'Point'):\n self.geometry.location = value","def xy(self, xy_position):\n print(f\"xy: {xy_position}\")\n self.device_control.xy = xy_position\n yield","def _as_parameter_(self):\n return POINT(self.x, self.y)","def aligne_grille(self,x,y,t):\r\n [xmin,ymin,xmax,ymax] = self.can.coords(self.hitbox[t])\r\n tx,ty=xmax-xmin,ymax-ymin\r\n a,b=23,23\r\n if tx==92 or ty==92 or tx==184 or ty==184:\r\n if tx==92 or tx==184:a,b=0,23\r\n if ty==92 or ty==184:a,b=23,0\r\n if 142<y<602 and 66<x<528:\r\n x=(x-66)//46*46+66+a\r\n y=(y-142)//46*46+142+b\r\n return x,y","def _update_loc(self) -> None:\n self.state[:, :, Boids.Attr.LOC] += self.state[:, :, Boids.Attr.VEL]\n # wrap-around the simulated environment\n self.state[:, :, Boids.Attr.LOC] %= np.expand_dims(self.env_bounds, axis=1)","def coord (i, j):\r\n return j, i","def _update_param_from_tkvar(self,param_name,force=False):\n self.debug(\"TkPO._update_param_from_tkvar(%s)\"%param_name)\n\n param_obj = self.get_parameter_object(param_name)\n\n if not lookup_by_class(self.param_immediately_apply_change,\n type(param_obj)) and not force:\n return\n else:\n super(TkParameterized,self)._update_param_from_tkvar(param_name)","def getCoords(self): # real signature unknown; restored from __doc__\r\n pass","def set_scanner_position(self, axis):\n change = 'not'\n\n if axis == 'X':\n scanner_pos = self.gui.doubleSpinBox_scannerX.value()\n self.scanner_unitX = self.gui.comboBox_unitX.currentText()\n scanner_unit = self.scanner_unitX\n elif axis == 'Y':\n scanner_pos = self.gui.doubleSpinBox_scannerY.value()\n self.scanner_unitY = self.gui.comboBox_unitY.currentText()\n scanner_unit = self.scanner_unitY\n elif axis == 'Z':\n scanner_pos = self.gui.doubleSpinBox_scannerZ.value()\n self.scanner_unitZ = self.gui.comboBox_unitZ.currentText()\n scanner_unit = self.scanner_unitZ\n\n local_position = ur(str(scanner_pos)+scanner_unit)\n self.logger.debug('{} local scanner position value: {}'.format(axis, local_position))\n\n if local_position > self.max_dclevel_V:\n self.logger.debug('value too high')\n local_max = self.max_dclevel_V.to(scanner_unit)\n self.logger.debug(str(local_max))\n change = 'high'\n elif local_position > self.max_dcLevel_mV_300K:\n self.logger.warning('You are exceeding the 60V maximum for the piezo at room temperature')\n elif local_position < 0:\n self.logger.debug('value too low')\n change = 'low'\n\n if axis == 'X':\n if change == 'high':\n self.gui.doubleSpinBox_scannerX.setValue(local_max.m_as(scanner_unit))\n elif change == 'low':\n self.gui.doubleSpinBox_scannerX.setValue(0)\n scanner_pos = self.gui.doubleSpinBox_scannerX.value()\n local_position = ur(str(scanner_pos) + scanner_unit)\n self.dcX = local_position\n self.logger.debug('dictionary position {} changed to: {}'.format(axis, self.dcX))\n\n elif axis == 'Y':\n if change == 'high':\n self.gui.doubleSpinBox_scannerY.setValue(local_max.m_as(scanner_unit))\n elif change == 'low':\n self.gui.doubleSpinBox_scannerY.setValue(0)\n scanner_pos = self.gui.doubleSpinBox_scannerY.value()\n local_position = ur(str(scanner_pos) + scanner_unit)\n self.dcY = local_position\n self.logger.debug('dictionary position {} changed to: {}'.format(axis, self.dcY))\n\n elif axis == 'Z':\n if change == 'high':\n self.gui.doubleSpinBox_scannerZ.setValue(local_max.m_as(scanner_unit))\n elif change == 'low':\n self.gui.doubleSpinBox_scannerZ.setValue(0)\n scanner_pos = self.gui.doubleSpinBox_scannerZ.value()\n local_position = ur(str(scanner_pos) + scanner_unit)\n self.dcZ = local_position\n self.logger.debug('dictionary position {} changed to: {}'.format(axis, self.dcZ))\n\n self.move_scanner('dc'+axis)","def _set_params_transformed(self, x):\r\n self._set_params(self._untransform_params(x))","def __init__(self, location: Tuple[int, int]) -> None:\n self.loc = location\n self.can_pass = True\n self.up = None\n self.down = None\n self.left = None\n self.right = None","def set_params(self):\r\n pass","def onEnterTrap(self, entity, range_xz, range_y, controllerID, userarg):\n\t\tAI.onEnterTrap(self, entity, range_xz, range_y, controllerID, userarg)","def position(self):\r\n pass","def positioning(self):\n pass","def cell_params(x,y,**kwargs):\n\n GR = glo.global_results()\n\n p = copy.copy(params)\n for key,val in kwargs.items():\n setattr(p,key,val)\n\n cloudy_library = clo.library()\n lookup_table = cloudy_library._restore_lookup_table()\n lookup_table['logG0s'] = lookup_table['logFUVs']\n if x == 'NH': \n x_cloudy,R_NIR_FUV_cl = aux.get_NH_from_cloudy()\n else:\n x_cloudy = np.unique(lookup_table['log'+x+'s'])\n if y == 'NH': \n y_cloudy,R_NIR_FUV_cl = aux.get_NH_from_cloudy()\n else:\n y_cloudy = np.unique(lookup_table['log'+y+'s'])\n\n if not p.ylim:\n p.ylim = [1e-3,30]\n if not p.xlim:\n p.xlim = [1e-7,1e3]\n \n # SELECT GALAXIES\n rand_gal_index = np.random.randint(0, GR.N_gal, size=(p.bins))\n if p.bins == GR.N_gal: rand_gal_index = np.arange(GR.N_gal)\n if p.gal_index: \n rand_gal_index = [p.gal_index]\n print(rand_gal_index)\n xs = np.array([])\n ys = np.array([])\n m_tot,m_encomp,m_y0 = 0,0,0\n for gal_index in rand_gal_index:\n print(gal_index)\n gal_ob = gal.galaxy(gal_index)\n df = gal_ob.cell_data.get_dataframe()\n df['nSFR'] = df.nSFR.values#/(0.2**3)\n #df['nSFR'] = df['SFR_density']\n #df['NH'] = 10.**df['NH']\n x1 = df[x].values\n y1 = df[y].values\n x1[x1 <= p.xlim[0]] = p.xlim[0]\n y1[y1 <= p.ylim[0]] = p.ylim[0]\n m_tot += np.sum(df.m.values)\n m_encomp += np.sum(df.m[(x1>=p.xlim[0]) & (y1>=p.ylim[0])].values)\n m_y0 += np.sum(df.m[(y1 == 0)].values)\n #print(x,x1.min(),x1.max())\n #print(y,y1.min(),y1.max())\n ys = np.append(ys,y1[(x1>=p.xlim[0]) & (y1>=p.ylim[0])])\n xs = np.append(xs,x1[(x1>=p.xlim[0]) & (y1>=p.ylim[0])])\n print('Min max of %s:' % x)\n print(xs.min(),xs.max())\n print('Min max of %s:' % y)\n print(ys.min(),ys.max())\n fig,ax = plt.subplots(figsize=(10,8))\n hb = ax.hexbin(xs,ys,xscale='log',yscale='log',bins='log',mincnt=1,lw=None,gridsize=50,cmap='inferno')\n cb = fig.colorbar(hb, ax=ax)\n cb.set_label('Number of cells in %i galaxies' % len(rand_gal_index))\n ax.set_xlabel(getlabel(x))\n ax.set_ylabel(getlabel(y))\n print('Total gas mass fraction encompassed: %.4f%%' % (m_encomp/m_tot*100))\n print('Total gas mass fraction with y = 0: %.4f%%' % (m_y0/m_tot*100))\n ax.set_xlim(p.xlim)\n ax.set_ylim(p.ylim)\n # Overplot Cloudy grid params\n print(x,x_cloudy)\n print(y,y_cloudy)\n for x1 in x_cloudy:\n ax.plot([10**x1,10**x1],ax.get_ylim(),'-',color='white',alpha=0.7)\n ax.plot([10**x1,10**x1],ax.get_ylim(),'--k',alpha=0.7)\n for y1 in y_cloudy:\n ax.plot(ax.get_xlim(),[10.**y1,10.**y1],'-',color='white',alpha=0.7)\n ax.plot(ax.get_xlim(),[10.**y1,10.**y1],'--k',alpha=0.7)\n\n if not os.path.isdir(p.d_plot + 'cell_data/'): os.mkdir(p.d_plot + 'cell_data/') \n plt.savefig('plots/cell_data/%s%s_cell_params_%s_%s_%s.png' % (p.sim_name,p.sim_run,p.z1,x,y),dpi=250, facecolor='w')","def gui_set_param(self,param_name,val):\n self._tkvar_set(param_name,val) # ERROR: presumably calls trace stuff twice\n self._handle_gui_set(param_name,force=True)","def pan(self, parameter):\n self.tx += parameter[0] / self.sx\n self.ty += parameter[1] / self.sy","def setPoint(self,set_point):\n self.set_point = set_point\n self.Integrator=0\n self.Derivator=0","def setPoint(self,set_point):\n self.set_point = set_point\n self.Integrator=0\n self.Derivator=0","def setup(self):\r\n m = re.match(r'\\[([0-9]+),([0-9]+)]',\r\n self.value.strip().replace(' ', ''))\r\n if m:\r\n # Note: we subtract 15 to compensate for the size of the dot on the screen.\r\n # (is a 30x30 image--lms/static/green-pointer.png).\r\n (self.gx, self.gy) = [int(x) - 15 for x in m.groups()]\r\n else:\r\n (self.gx, self.gy) = (0, 0)","def pop_extra_coords(kwargs):\n if \"extra_coords\" in kwargs:\n warn(\"EQL gridder will ignore extra_coords: {}.\".format(kwargs[\"extra_coords\"]))\n kwargs.pop(\"extra_coords\")","def on_spinBox_valueChanged(self, p0):\n self.nbr_pts_caracterisation = self.spinBox.value()","def GetLoCorner(self):\n ...","def collocation_points(self, **kw):\n pass","def default_location(self, thing):\n if isinstance(thing, Agent):\n return (1, 1)\n else:\n get_rand = lambda arg: random.choice(range(1, arg-1))\n while True:\n xloc, yloc = (get_rand(self.width), get_rand(self.height))\n if (1, 1) == (xloc, yloc):\n continue\n break\n return (xloc, yloc)","def __init__(self, block):\n super(CraftFlowerPot, self).__init__(block)\n self.pot = (block.getWorld()).getTileEntityAt(getX(), getY(), getZ())","def _core_fix_params(self,bx,phase,eqnid) :\n\t\tif self.ss.exptype == 'fullinfo' :\n\t\t\treturn bx\n\t\telif self.ss.exptype in ('noinfo','partialinfo') :\n\t\t\treg_fix = self._regressors_fix[eqnid] \n\t\t\tif phase == 1 : \n\t\t\t\tprod_fix = reg_fix['prod']\n\t\t\t\tfor varid in prod_fix : \n\t\t\t\t\tbx[varid] = 0.0\n\t\t\telif phase == 2 : \t\t\t\n\t\t\t\tdegrad_fix = reg_fix['degrad']\n\t\t\t\tfor varid in degrad_fix :\n\t\t\t\t\tbx[varid] = 0.0 \n\t\t\telse : \n\t\t\t\tself.logger.error(\"Incorrect phase %r\"%(phase))\n\t\t\t\tsys.exit(1)\n\t\telse :\n\t\t\tself.logger.error(\"Unrecognized exptype %s quitting...\"%\\\n\t\t\t(self.ss.exptype))\n\n\t\treturn bx","def set_position(self, updated):\n self.buff_x = updated[0]\n self.buff_y = updated[1]","def setGravity(*argv):","def __init__(self):\n super().__init__()\n self.waypoint_vector = [-1, 10]","def __init__(self):\n super(SteklovBoundary, self).__init__()\n self.value = SteklovBoundary.value\n SteklovBoundary.value -= 1\n self.update(param=\"1\")","def get_coord(self):\n return self.coord","def init_params(self):\n blah","def setDesiredPosition(self, x, y):\n (self.setX, self.setY) = (x , y)","def GetParametricCoords(self):\n ...","def getPosition(*args):","def getPosition(*args):","def getPosition(*args):","def getPosition(*args):","def getPosition(*args):","def getPosition(*args):","def getPosition(*args):","def getPosition(*args):","def getPosition(*args):","def getPosition(*args):"],"string":"[\n \"def xy(self):\\n ...\",\n \"def paramValueChanged(self, param):\\n if self._printSWAP == True:\\n print param.name + \\\" in address \\\" + str(param.getRegAddress()) + \\\" changed to \\\" + param.getValueInAscii()\",\n \"def modifyPoint(self, *args, **kwargs):\\n ...\",\n \"def set_coord(self, l, sign, b):\\n if l is not None:\\n self.l = float(l)\\n if b is not None:\\n self.b = float(b)\\n if sign == '-':\\n self.b *= -1.\",\n \"def set_xy(self, x, y, val):\\r\\n\\t\\tself.grid[y, x] = val\",\n \"def set_robot_pos(self):\\n\\t\\tx,y,z = self.geo2desiredENU(self.curr_lat, self.curr_lon, self.gpsAlt)\\n\\t\\tself.robot_msg.point.x = x\\n\\t\\tself.robot_msg.point.y = y\\n\\t\\tself.robot_msg.point.z = z\",\n \"def setPos(self,x,y):\\n for i in self.itemType.find('parameters'):\\n paramType = i.find('type').text.strip()\\n if paramType.startswith('position-x'):\\n self.params[i.find('name').text] = x\\n if paramType.startswith('position-y'):\\n self.params[i.find('name').text] = y\",\n \"def setCoords(self, p_float, p_float_1, p_float_2, p_float_3): # real signature unknown; restored from __doc__\\r\\n pass\",\n \"def coordinates(self):\",\n \"def setPosition(*args):\",\n \"def setPosition(*args):\",\n \"def setPosition(*args):\",\n \"def setPosition(*args):\",\n \"def setPosition(*args):\",\n \"def setPosition(*args):\",\n \"def setPosition(*args):\",\n \"def setPosition(*args):\",\n \"def setPosition(*args):\",\n \"def setPosition(*args):\",\n \"def setPosition(*args):\",\n \"def _set_params(self,x):\\r\\n self.k._set_params(x)\",\n \"def set_parameter(self, param, value, stripe = 0, location = 3):\\n if param in self.fpga.cabac_top[0].params:\\n self.fpga.set_cabac_value(param, value, stripe)\\n time.sleep(0.1)\\n self.fpga.send_cabac_config(stripe)\\n\\n elif param in [\\\"V_SL\\\", \\\"V_SH\\\", \\\"V_RGL\\\", \\\"V_RGH\\\", \\\"V_PL\\\", \\\"V_PH\\\"]:\\n self.fpga.set_clock_voltages({param: value})\\n\\n elif param == \\\"I_OS\\\":\\n self.fpga.set_current_source(value, stripe)\\n\\n else:\\n print(\\\"Warning: unidentified parameter for the REB: %s\\\" % param)\",\n \"def coord(self, coord):\\n\\n self._coord = coord\",\n \"def prep_latlng_params(self, lat, lng):\\n self._api_params['latlng'] = '{},{}'.format(lat, lng)\",\n \"def set_new_location(self, xPos, yPos):\",\n \"def test_coord_preceding_fs(self):\",\n \"def _handleInput(self, paramInput):\\n super()._handleInput(paramInput)\\n locationFind = paramInput.findFirst('location')\\n if locationFind != None:\\n self.location = locationFind.value\\n else:\\n self.raiseAnError(IOError,'location value needed for Laplace distribution')\\n scaleFind = paramInput.findFirst('scale')\\n if scaleFind != None:\\n self.scale = scaleFind.value\\n else:\\n self.raiseAnError(IOError,'scale value needed for Laplace distribution')\\n self.initializeDistribution()\",\n \"def mousePositionRaw(self):\",\n \"def mousePositionRaw(self):\",\n \"def _setup_params(self,**params):\\n ### a parameter might be passed in for one of the extra_pos;\\n ### if a key in the params dict is not a *parameter* of this\\n ### PO, then try it on the extra_pos\\n for n,p in params.items():\\n if n not in self.params():\\n self.set_parameter_value(n,p)\\n del params[n]\\n\\n Parameterized._setup_params(self,**params)\",\n \"def __init__(self, x, y, elevation):\\n super(GridPoint, self).__init__(x, y)\\n self.elevation = elevation\",\n \"def get_location(self):\\n self.location = self.func(0)\",\n \"def EvaluateLocation(self, p_int, , p_float=..., p_float=..., p_float=..., *args, **kwargs):\\n ...\",\n \"def _get_raw_params(self, node):\",\n \"def param2pos( param, stickguy ):\\n\\n hip_pos = np.array([0.0, param[0]])\\n spine_vec = np.array([0.0, 1.0])\\n spine_vec = rotate(spine_vec, param[1])\\n neck_pos = hip_pos + spine_vec\\n basic_arm_vec = -0.6*spine_vec\\n arm_vec = rotate(basic_arm_vec, param[2])\\n left_elbow_pos = neck_pos + arm_vec\\n arm_vec = rotate(arm_vec, param[3])\\n left_hand_pos = left_elbow_pos + arm_vec\\n lad = np.array([neck_pos,left_elbow_pos,left_hand_pos])\\n stickguy.left_arm.set_data(lad[:,0],lad[:,1])\\n\\n arm_vec = rotate(basic_arm_vec, param[4])\\n right_elbow_pos = neck_pos + arm_vec\\n arm_vec = rotate(arm_vec, param[5])\\n right_hand_pos = right_elbow_pos + arm_vec\\n rad = np.array([neck_pos,right_elbow_pos,right_hand_pos])\\n stickguy.right_arm.set_data(rad[:,0],rad[:,1])\\n\\n neck_vec = 0.3*spine_vec\\n neck_vec = rotate( neck_vec, param[6])\\n head_pos = neck_pos + neck_vec\\n sd = np.array([hip_pos,neck_pos,head_pos])\\n stickguy.spine.set_data(sd[:,0],sd[:,1])\\n\\n basic_leg_vec = (0.0,-0.7)\\n leg_vec = rotate(basic_leg_vec, param[7])\\n left_knee_pos = hip_pos + leg_vec\\n leg_vec = rotate(leg_vec, param[8])\\n left_foot_pos = left_knee_pos + leg_vec\\n lld = np.array([hip_pos,left_knee_pos,left_foot_pos])\\n stickguy.left_leg.set_data(lld[:,0],lld[:,1])\\n\\n leg_vec = rotate(basic_leg_vec, param[9])\\n right_knee_pos = hip_pos + leg_vec\\n leg_vec = rotate(leg_vec, param[10])\\n right_foot_pos = right_knee_pos + leg_vec\\n rld = np.array([hip_pos,right_knee_pos,right_foot_pos])\\n stickguy.right_leg.set_data(rld[:,0],rld[:,1])\\n\\n return\",\n \"def m_location_set(self, x: int, y: int):\\n pass\",\n \"def set_params(self, **kwargs):\\n warnings.warn(\\\"'set_params()' not defined for locator of type \\\" +\\n str(type(self)))\",\n \"def mousePosition(self):\",\n \"def initialCoordinates():\\r\\n return (-250,-250)\",\n \"def flash_location(self,params):\\n loc = params['location']\\n if self.participant:\\n if self.service.groupOfParticipant(self) and self.participant.status != AVOID:\\n self.participant.changeStatus(LISTEN)\\n #print loc\\n (x,y) = self.service.grid.conformToGrid(loc)\\n self.participant.setLocation((x,y))\\n self.receiveDirectCommand(\\\"location\\\",{\\\"x\\\":x,\\\"y\\\":y})\\n \\n else:\\n self.notLoggedIn()\",\n \"def Modifier_UserGPS(self):\",\n \"def global_coords(self) -> GlobalCoordsABC:\",\n \"def grab_current_point(self):\\n self.open_gripper(80)\\n time.sleep(2.5)\\n self.execute_action((0, 0, -10), self.GRAB_ORIENTATION)\\n self.open_gripper(-30)\\n time.sleep(2.5)\\n self.execute_action((0, 0, 10), self.GRAB_ORIENTATION)\\n time.sleep(2.5)\\n self.initial_position = np.array(self.get_current_cartesian_position().position)\\n print self.initial_position\",\n \"def set_params(self, params):\",\n \"def setLocation(self, p):\\n super(PolygonTool, self).setLocation(p.point)\\n _x, _y = self.getLocation().getCoords()\\n _count = self.__nsides\\n _inc = self.__increment\\n if self.__external:\\n _offset = _inc/2.0\\n else:\\n _offset = 0.0\\n _cx, _cy = self.__center.point.getCoords()\\n _xsep = _x - _cx\\n _ysep = _y - _cy\\n _angle = math.atan2(_ysep, _xsep) + _offset\\n _rad = math.hypot(_xsep, _ysep)/math.cos(_offset)\\n _xp = self.__xpts\\n _yp = self.__ypts\\n for _i in range(_count):\\n _xp[_i] = _cx + (_rad * math.cos(_angle))\\n _yp[_i] = _cy + (_rad * math.sin(_angle))\\n _angle = _angle + _inc\",\n \"def get_set_extended_position_args(self,comArgs):\\n params, flags = self.get_params(comArgs)\\n point = self.get_point(params)\\n step_point = self.multiply_vector(point,self.spm)\\n args = [step_point]\\n self.current_point = point\\n return args\",\n \"def place(self,y,x):\\n self.y = y\\n self.x = x\",\n \"def setGxLocation(self):\\n if self.xyz is None:\\n gxobs = self.obs.get(None, {}).get(\\\"GX\\\")\\n if gxobs is not None:\\n gxyz = np.array((0.0, 0.0, 0.0))\\n for gx in gxobs:\\n gxyz += gx.obsvalue.value\\n self.xyz = gxyz / len(gxobs)\\n self.locator.write(\\n \\\"Fixing station {0} using GNSS coordinate observations\\\\n\\\".format(\\n self.code\\n )\\n )\",\n \"def set_2d_location(self, x, y):\\r\\n self.unif[42:44] = [x, y]\",\n \"def set_params(self, *arg):\\n pass\",\n \"def setUp(self):\\n self.location = [(0, 0), (0, 1)]\\n self.hit = (0, 0)\",\n \"def grab(self, event):\\n self.ypos = event.y\\n self.xpos = event.x\\n self.config(cursor='fleur')\",\n \"def set_parameters(self, params):\\n self.kp = params.pgain\",\n \"def _global_pose_cb(self, msg):\\n self.global_pose = msg\",\n \"def on_VI_XY_set_clicked(self):\\n # TODO: not implemented yet\\n disp_coord()\\n if qmdz_const.Auto_Range == 0:\\n xmin = int(read_config(qmdz_const.SYS_CONF_PATH, 'COORD', 'x_min'))\\n xmax = int(read_config(qmdz_const.SYS_CONF_PATH, 'COORD', 'x_max'))\\n ymin = int(read_config(qmdz_const.SYS_CONF_PATH, 'COORD', 'y_min'))\\n ymax = int(read_config(qmdz_const.SYS_CONF_PATH, 'COORD', 'y_max'))\\n self.VI_MPL.change_xy(xmin, xmax, ymin, ymax)\",\n \"def location(self, value: 'Point'):\\n self.geometry.location = value\",\n \"def xy(self, xy_position):\\n print(f\\\"xy: {xy_position}\\\")\\n self.device_control.xy = xy_position\\n yield\",\n \"def _as_parameter_(self):\\n return POINT(self.x, self.y)\",\n \"def aligne_grille(self,x,y,t):\\r\\n [xmin,ymin,xmax,ymax] = self.can.coords(self.hitbox[t])\\r\\n tx,ty=xmax-xmin,ymax-ymin\\r\\n a,b=23,23\\r\\n if tx==92 or ty==92 or tx==184 or ty==184:\\r\\n if tx==92 or tx==184:a,b=0,23\\r\\n if ty==92 or ty==184:a,b=23,0\\r\\n if 142<y<602 and 66<x<528:\\r\\n x=(x-66)//46*46+66+a\\r\\n y=(y-142)//46*46+142+b\\r\\n return x,y\",\n \"def _update_loc(self) -> None:\\n self.state[:, :, Boids.Attr.LOC] += self.state[:, :, Boids.Attr.VEL]\\n # wrap-around the simulated environment\\n self.state[:, :, Boids.Attr.LOC] %= np.expand_dims(self.env_bounds, axis=1)\",\n \"def coord (i, j):\\r\\n return j, i\",\n \"def _update_param_from_tkvar(self,param_name,force=False):\\n self.debug(\\\"TkPO._update_param_from_tkvar(%s)\\\"%param_name)\\n\\n param_obj = self.get_parameter_object(param_name)\\n\\n if not lookup_by_class(self.param_immediately_apply_change,\\n type(param_obj)) and not force:\\n return\\n else:\\n super(TkParameterized,self)._update_param_from_tkvar(param_name)\",\n \"def getCoords(self): # real signature unknown; restored from __doc__\\r\\n pass\",\n \"def set_scanner_position(self, axis):\\n change = 'not'\\n\\n if axis == 'X':\\n scanner_pos = self.gui.doubleSpinBox_scannerX.value()\\n self.scanner_unitX = self.gui.comboBox_unitX.currentText()\\n scanner_unit = self.scanner_unitX\\n elif axis == 'Y':\\n scanner_pos = self.gui.doubleSpinBox_scannerY.value()\\n self.scanner_unitY = self.gui.comboBox_unitY.currentText()\\n scanner_unit = self.scanner_unitY\\n elif axis == 'Z':\\n scanner_pos = self.gui.doubleSpinBox_scannerZ.value()\\n self.scanner_unitZ = self.gui.comboBox_unitZ.currentText()\\n scanner_unit = self.scanner_unitZ\\n\\n local_position = ur(str(scanner_pos)+scanner_unit)\\n self.logger.debug('{} local scanner position value: {}'.format(axis, local_position))\\n\\n if local_position > self.max_dclevel_V:\\n self.logger.debug('value too high')\\n local_max = self.max_dclevel_V.to(scanner_unit)\\n self.logger.debug(str(local_max))\\n change = 'high'\\n elif local_position > self.max_dcLevel_mV_300K:\\n self.logger.warning('You are exceeding the 60V maximum for the piezo at room temperature')\\n elif local_position < 0:\\n self.logger.debug('value too low')\\n change = 'low'\\n\\n if axis == 'X':\\n if change == 'high':\\n self.gui.doubleSpinBox_scannerX.setValue(local_max.m_as(scanner_unit))\\n elif change == 'low':\\n self.gui.doubleSpinBox_scannerX.setValue(0)\\n scanner_pos = self.gui.doubleSpinBox_scannerX.value()\\n local_position = ur(str(scanner_pos) + scanner_unit)\\n self.dcX = local_position\\n self.logger.debug('dictionary position {} changed to: {}'.format(axis, self.dcX))\\n\\n elif axis == 'Y':\\n if change == 'high':\\n self.gui.doubleSpinBox_scannerY.setValue(local_max.m_as(scanner_unit))\\n elif change == 'low':\\n self.gui.doubleSpinBox_scannerY.setValue(0)\\n scanner_pos = self.gui.doubleSpinBox_scannerY.value()\\n local_position = ur(str(scanner_pos) + scanner_unit)\\n self.dcY = local_position\\n self.logger.debug('dictionary position {} changed to: {}'.format(axis, self.dcY))\\n\\n elif axis == 'Z':\\n if change == 'high':\\n self.gui.doubleSpinBox_scannerZ.setValue(local_max.m_as(scanner_unit))\\n elif change == 'low':\\n self.gui.doubleSpinBox_scannerZ.setValue(0)\\n scanner_pos = self.gui.doubleSpinBox_scannerZ.value()\\n local_position = ur(str(scanner_pos) + scanner_unit)\\n self.dcZ = local_position\\n self.logger.debug('dictionary position {} changed to: {}'.format(axis, self.dcZ))\\n\\n self.move_scanner('dc'+axis)\",\n \"def _set_params_transformed(self, x):\\r\\n self._set_params(self._untransform_params(x))\",\n \"def __init__(self, location: Tuple[int, int]) -> None:\\n self.loc = location\\n self.can_pass = True\\n self.up = None\\n self.down = None\\n self.left = None\\n self.right = None\",\n \"def set_params(self):\\r\\n pass\",\n \"def onEnterTrap(self, entity, range_xz, range_y, controllerID, userarg):\\n\\t\\tAI.onEnterTrap(self, entity, range_xz, range_y, controllerID, userarg)\",\n \"def position(self):\\r\\n pass\",\n \"def positioning(self):\\n pass\",\n \"def cell_params(x,y,**kwargs):\\n\\n GR = glo.global_results()\\n\\n p = copy.copy(params)\\n for key,val in kwargs.items():\\n setattr(p,key,val)\\n\\n cloudy_library = clo.library()\\n lookup_table = cloudy_library._restore_lookup_table()\\n lookup_table['logG0s'] = lookup_table['logFUVs']\\n if x == 'NH': \\n x_cloudy,R_NIR_FUV_cl = aux.get_NH_from_cloudy()\\n else:\\n x_cloudy = np.unique(lookup_table['log'+x+'s'])\\n if y == 'NH': \\n y_cloudy,R_NIR_FUV_cl = aux.get_NH_from_cloudy()\\n else:\\n y_cloudy = np.unique(lookup_table['log'+y+'s'])\\n\\n if not p.ylim:\\n p.ylim = [1e-3,30]\\n if not p.xlim:\\n p.xlim = [1e-7,1e3]\\n \\n # SELECT GALAXIES\\n rand_gal_index = np.random.randint(0, GR.N_gal, size=(p.bins))\\n if p.bins == GR.N_gal: rand_gal_index = np.arange(GR.N_gal)\\n if p.gal_index: \\n rand_gal_index = [p.gal_index]\\n print(rand_gal_index)\\n xs = np.array([])\\n ys = np.array([])\\n m_tot,m_encomp,m_y0 = 0,0,0\\n for gal_index in rand_gal_index:\\n print(gal_index)\\n gal_ob = gal.galaxy(gal_index)\\n df = gal_ob.cell_data.get_dataframe()\\n df['nSFR'] = df.nSFR.values#/(0.2**3)\\n #df['nSFR'] = df['SFR_density']\\n #df['NH'] = 10.**df['NH']\\n x1 = df[x].values\\n y1 = df[y].values\\n x1[x1 <= p.xlim[0]] = p.xlim[0]\\n y1[y1 <= p.ylim[0]] = p.ylim[0]\\n m_tot += np.sum(df.m.values)\\n m_encomp += np.sum(df.m[(x1>=p.xlim[0]) & (y1>=p.ylim[0])].values)\\n m_y0 += np.sum(df.m[(y1 == 0)].values)\\n #print(x,x1.min(),x1.max())\\n #print(y,y1.min(),y1.max())\\n ys = np.append(ys,y1[(x1>=p.xlim[0]) & (y1>=p.ylim[0])])\\n xs = np.append(xs,x1[(x1>=p.xlim[0]) & (y1>=p.ylim[0])])\\n print('Min max of %s:' % x)\\n print(xs.min(),xs.max())\\n print('Min max of %s:' % y)\\n print(ys.min(),ys.max())\\n fig,ax = plt.subplots(figsize=(10,8))\\n hb = ax.hexbin(xs,ys,xscale='log',yscale='log',bins='log',mincnt=1,lw=None,gridsize=50,cmap='inferno')\\n cb = fig.colorbar(hb, ax=ax)\\n cb.set_label('Number of cells in %i galaxies' % len(rand_gal_index))\\n ax.set_xlabel(getlabel(x))\\n ax.set_ylabel(getlabel(y))\\n print('Total gas mass fraction encompassed: %.4f%%' % (m_encomp/m_tot*100))\\n print('Total gas mass fraction with y = 0: %.4f%%' % (m_y0/m_tot*100))\\n ax.set_xlim(p.xlim)\\n ax.set_ylim(p.ylim)\\n # Overplot Cloudy grid params\\n print(x,x_cloudy)\\n print(y,y_cloudy)\\n for x1 in x_cloudy:\\n ax.plot([10**x1,10**x1],ax.get_ylim(),'-',color='white',alpha=0.7)\\n ax.plot([10**x1,10**x1],ax.get_ylim(),'--k',alpha=0.7)\\n for y1 in y_cloudy:\\n ax.plot(ax.get_xlim(),[10.**y1,10.**y1],'-',color='white',alpha=0.7)\\n ax.plot(ax.get_xlim(),[10.**y1,10.**y1],'--k',alpha=0.7)\\n\\n if not os.path.isdir(p.d_plot + 'cell_data/'): os.mkdir(p.d_plot + 'cell_data/') \\n plt.savefig('plots/cell_data/%s%s_cell_params_%s_%s_%s.png' % (p.sim_name,p.sim_run,p.z1,x,y),dpi=250, facecolor='w')\",\n \"def gui_set_param(self,param_name,val):\\n self._tkvar_set(param_name,val) # ERROR: presumably calls trace stuff twice\\n self._handle_gui_set(param_name,force=True)\",\n \"def pan(self, parameter):\\n self.tx += parameter[0] / self.sx\\n self.ty += parameter[1] / self.sy\",\n \"def setPoint(self,set_point):\\n self.set_point = set_point\\n self.Integrator=0\\n self.Derivator=0\",\n \"def setPoint(self,set_point):\\n self.set_point = set_point\\n self.Integrator=0\\n self.Derivator=0\",\n \"def setup(self):\\r\\n m = re.match(r'\\\\[([0-9]+),([0-9]+)]',\\r\\n self.value.strip().replace(' ', ''))\\r\\n if m:\\r\\n # Note: we subtract 15 to compensate for the size of the dot on the screen.\\r\\n # (is a 30x30 image--lms/static/green-pointer.png).\\r\\n (self.gx, self.gy) = [int(x) - 15 for x in m.groups()]\\r\\n else:\\r\\n (self.gx, self.gy) = (0, 0)\",\n \"def pop_extra_coords(kwargs):\\n if \\\"extra_coords\\\" in kwargs:\\n warn(\\\"EQL gridder will ignore extra_coords: {}.\\\".format(kwargs[\\\"extra_coords\\\"]))\\n kwargs.pop(\\\"extra_coords\\\")\",\n \"def on_spinBox_valueChanged(self, p0):\\n self.nbr_pts_caracterisation = self.spinBox.value()\",\n \"def GetLoCorner(self):\\n ...\",\n \"def collocation_points(self, **kw):\\n pass\",\n \"def default_location(self, thing):\\n if isinstance(thing, Agent):\\n return (1, 1)\\n else:\\n get_rand = lambda arg: random.choice(range(1, arg-1))\\n while True:\\n xloc, yloc = (get_rand(self.width), get_rand(self.height))\\n if (1, 1) == (xloc, yloc):\\n continue\\n break\\n return (xloc, yloc)\",\n \"def __init__(self, block):\\n super(CraftFlowerPot, self).__init__(block)\\n self.pot = (block.getWorld()).getTileEntityAt(getX(), getY(), getZ())\",\n \"def _core_fix_params(self,bx,phase,eqnid) :\\n\\t\\tif self.ss.exptype == 'fullinfo' :\\n\\t\\t\\treturn bx\\n\\t\\telif self.ss.exptype in ('noinfo','partialinfo') :\\n\\t\\t\\treg_fix = self._regressors_fix[eqnid] \\n\\t\\t\\tif phase == 1 : \\n\\t\\t\\t\\tprod_fix = reg_fix['prod']\\n\\t\\t\\t\\tfor varid in prod_fix : \\n\\t\\t\\t\\t\\tbx[varid] = 0.0\\n\\t\\t\\telif phase == 2 : \\t\\t\\t\\n\\t\\t\\t\\tdegrad_fix = reg_fix['degrad']\\n\\t\\t\\t\\tfor varid in degrad_fix :\\n\\t\\t\\t\\t\\tbx[varid] = 0.0 \\n\\t\\t\\telse : \\n\\t\\t\\t\\tself.logger.error(\\\"Incorrect phase %r\\\"%(phase))\\n\\t\\t\\t\\tsys.exit(1)\\n\\t\\telse :\\n\\t\\t\\tself.logger.error(\\\"Unrecognized exptype %s quitting...\\\"%\\\\\\n\\t\\t\\t(self.ss.exptype))\\n\\n\\t\\treturn bx\",\n \"def set_position(self, updated):\\n self.buff_x = updated[0]\\n self.buff_y = updated[1]\",\n \"def setGravity(*argv):\",\n \"def __init__(self):\\n super().__init__()\\n self.waypoint_vector = [-1, 10]\",\n \"def __init__(self):\\n super(SteklovBoundary, self).__init__()\\n self.value = SteklovBoundary.value\\n SteklovBoundary.value -= 1\\n self.update(param=\\\"1\\\")\",\n \"def get_coord(self):\\n return self.coord\",\n \"def init_params(self):\\n blah\",\n \"def setDesiredPosition(self, x, y):\\n (self.setX, self.setY) = (x , y)\",\n \"def GetParametricCoords(self):\\n ...\",\n \"def getPosition(*args):\",\n \"def getPosition(*args):\",\n \"def getPosition(*args):\",\n \"def getPosition(*args):\",\n \"def getPosition(*args):\",\n \"def getPosition(*args):\",\n \"def getPosition(*args):\",\n \"def getPosition(*args):\",\n \"def getPosition(*args):\",\n \"def getPosition(*args):\"\n]","isConversational":false},"negative_scores":{"kind":"list like","value":["0.56467545","0.553417","0.53961","0.5391049","0.5386599","0.5367348","0.53164357","0.5312498","0.53037393","0.5255599","0.5255599","0.5255599","0.5255599","0.5255599","0.5255599","0.5255599","0.5255599","0.5255599","0.5255599","0.5255599","0.5238645","0.5231543","0.5185645","0.51544154","0.5120039","0.51175374","0.5115503","0.50951564","0.50951564","0.5091024","0.5074391","0.5061243","0.5058775","0.504241","0.502475","0.5014015","0.5004261","0.5001785","0.49950626","0.4982765","0.4979123","0.49679658","0.4934663","0.49298406","0.49121168","0.4910493","0.4908866","0.49031565","0.48949862","0.48939705","0.48883504","0.48880914","0.48723388","0.48704782","0.4867413","0.486675","0.48662874","0.4856601","0.48505515","0.48445818","0.4827636","0.48201326","0.48105255","0.4809926","0.48065582","0.48049223","0.47914782","0.47820726","0.47814733","0.4780654","0.4776435","0.4760723","0.4756163","0.47548833","0.47548833","0.4753183","0.47495922","0.4747916","0.47457874","0.47415626","0.4741403","0.47402906","0.47401708","0.4736566","0.47363174","0.47320506","0.4727151","0.4726087","0.47257137","0.4724759","0.47232804","0.47221893","0.47221893","0.47221893","0.47221893","0.47221893","0.47221893","0.47221893","0.47221893","0.47221893","0.47221893"],"string":"[\n \"0.56467545\",\n \"0.553417\",\n \"0.53961\",\n \"0.5391049\",\n \"0.5386599\",\n \"0.5367348\",\n \"0.53164357\",\n \"0.5312498\",\n \"0.53037393\",\n \"0.5255599\",\n \"0.5255599\",\n \"0.5255599\",\n \"0.5255599\",\n \"0.5255599\",\n \"0.5255599\",\n \"0.5255599\",\n \"0.5255599\",\n \"0.5255599\",\n \"0.5255599\",\n \"0.5255599\",\n \"0.5238645\",\n \"0.5231543\",\n \"0.5185645\",\n \"0.51544154\",\n \"0.5120039\",\n \"0.51175374\",\n \"0.5115503\",\n \"0.50951564\",\n \"0.50951564\",\n \"0.5091024\",\n \"0.5074391\",\n \"0.5061243\",\n \"0.5058775\",\n \"0.504241\",\n \"0.502475\",\n \"0.5014015\",\n \"0.5004261\",\n \"0.5001785\",\n \"0.49950626\",\n \"0.4982765\",\n \"0.4979123\",\n \"0.49679658\",\n \"0.4934663\",\n \"0.49298406\",\n \"0.49121168\",\n \"0.4910493\",\n \"0.4908866\",\n \"0.49031565\",\n \"0.48949862\",\n \"0.48939705\",\n \"0.48883504\",\n \"0.48880914\",\n \"0.48723388\",\n \"0.48704782\",\n \"0.4867413\",\n \"0.486675\",\n \"0.48662874\",\n \"0.4856601\",\n \"0.48505515\",\n \"0.48445818\",\n \"0.4827636\",\n \"0.48201326\",\n \"0.48105255\",\n \"0.4809926\",\n \"0.48065582\",\n \"0.48049223\",\n \"0.47914782\",\n \"0.47820726\",\n \"0.47814733\",\n \"0.4780654\",\n \"0.4776435\",\n \"0.4760723\",\n \"0.4756163\",\n \"0.47548833\",\n \"0.47548833\",\n \"0.4753183\",\n \"0.47495922\",\n \"0.4747916\",\n \"0.47457874\",\n \"0.47415626\",\n \"0.4741403\",\n \"0.47402906\",\n \"0.47401708\",\n \"0.4736566\",\n \"0.47363174\",\n \"0.47320506\",\n \"0.4727151\",\n \"0.4726087\",\n \"0.47257137\",\n \"0.4724759\",\n \"0.47232804\",\n \"0.47221893\",\n \"0.47221893\",\n \"0.47221893\",\n \"0.47221893\",\n \"0.47221893\",\n \"0.47221893\",\n \"0.47221893\",\n \"0.47221893\",\n \"0.47221893\",\n \"0.47221893\"\n]","isConversational":false},"document_score":{"kind":"string","value":"0.0"},"document_rank":{"kind":"string","value":"-1"}}},{"rowIdx":16591,"cells":{"query":{"kind":"string","value":"Trap coord with 'Y' before 'X' gerber."},"document":{"kind":"string","value":"def test_y_before_x(self):"},"metadata":{"kind":"string","value":"{\n \"objective\": {\n \"self\": [],\n \"paired\": [],\n \"triplet\": [\n [\n \"query\",\n \"document\",\n \"negatives\"\n ]\n ]\n }\n}"},"negatives":{"kind":"list like","value":["def _coord(self, x, y):\n gridEdge = 7 # originally 5\n y = gridEdge - y\n cx = 100 * (x - 1) + 50\n cy = 100 * (y - 1) + 50\n r = 20\n return (cx - r, cy - r, cx + r, cy + r)","def _transform_point(self, x, y):\n return (x, y)","def set_position(self, x, y):\n self.tx = -x\n self.ty = -y","def __getxy(x1, y1, x2, y2):\n\t\treturn x1*27+y1*9+x2*3+y2","def pixel2coord(self, x, y):\n # NEED TO CHANGE TO USE INVERSE TRANSFORM COEFFS\n # partly taken from Sean Gillies \"affine.py\"\n a,b,c,d,e,f = self.coordspace_transform\n det = a*e - b*d\n idet = 1 / float(det)\n ra = e * idet\n rb = -b * idet\n rd = -d * idet\n re = a * idet\n newx = (x*ra + y*rb + (-c*ra - f*rb) )\n newy = (x*rd + y*re + (-c*rd - f*re) )\n return newx,newy","def get_pos(x, y):\r\n return normalize(x) // 2, normalize(y) // 4","def XY(x, y):\n return ESC + str(y + 1) + ';' + str(x + 1) + 'H'","def _translate_coordinate(self, x1, y1, x2, y2):\n\n return (x1 + x2, y1 + y2)","def __getxyB(x, y):\n\t\treturn x*3+y","def relmoveto(self, x = 0, y = 0):\n self.cur_x += x\n self.cur_y += y\n if x < 0:\n self.out.write(self.csi + \"%sD\" % -x)\n elif x > 0:\n self.out.write(self.csi + \"%sC\" % x)\n if y < 0:\n self.out.write(self.csi + \"%sA\" % -y)\n elif y > 0:\n self.out.write(self.csi + \"%sB\" % y)","def toind(x, y):\n return x + 15 * y","def _increase_coordinates(coordinates, x, y):\n orig_x, orig_y = coordinates[\"x\"], coordinates[\"y\"]\n coordinates[\"x\"], coordinates[\"y\"] = orig_x + x, orig_y + y","def translateCoord(self,absX,absY):\n rawConvertedX=hex(absX*(16**4-1)/self.maxX).upper()[2:]\n rawConvertedY=hex(absY*(16**4-1)/self.maxY).upper()[2:]\n return {'x':rawConvertedX,'y':rawConvertedY}","def transform(self, X, y=None):\n return super().transform(X, y)","def transform(self, X, y=None):\n return super().transform(X, y)","def get_xy(self, x, y):\r\n\t\treturn self.grid[y, x]","def trace(self, coord01: np.ndarray) -> np.ndarray:\n rect = self.clip_rect()\n return (rect.position + coord01 * rect.size).astype(np.int)","def _fix_coords(x, y):\n if x.ndim != 1 or all(x < x[0]): # skip 2D arrays and monotonic backwards data\n return x, y\n lon1 = x[0]\n filter_ = x < lon1\n while filter_.sum():\n filter_ = x < lon1\n x[filter_] += 360\n return x, y","def xy(self):\n ...","def pos(self, x, y):\n\n if isinstance(x, float):\n x = int(x)\n\n self.screen.write(colorama.Cursor.POS(x, y), ansi=True)\n self.x = x\n self.y = y\n\n return x, y","def ED(X,Y):","def convertdirection(self, frame):\n return _coordsys.coordsys_convertdirection(self, frame)","def coord(self, x, y):\n origin_x = self._raster_meta['transform'][3]\n origin_y = self._raster_meta['transform'][0]\n pixel_x = self._raster_meta['transform'][5]\n pixel_y = self._raster_meta['transform'][1]\n\n x = int((x - origin_x) / pixel_x)\n y = int((y - origin_y) / pixel_y)\n return self[x, y]","def pos(self, x=-1, y=-1):\n self._p('[pos] {} {}'.format(x, y))","def xy2ind(self, x, y):\n return self.sub2ind(*self.xy2sub(x, y))","def Translate(X,Y,Xoffset=0,Yoffset=0):\n X1 = X + Xoffset\n Y1 = Y + Yoffset\n return X1,Y1","def place(self,y,x):\n self.y = y\n self.x = x","def setDesiredPosition(self, x, y):\n (self.setX, self.setY) = (x , y)","def coord2pixel(self, x, y):\n a,b,c,d,e,f = self.coordspace_transform\n newx,newy = (x*a + y*b + c, x*d + y*e + f)\n return int(newx),int(newy)","def __get_x__(self):\n return self.Direction['x']","def dest_xy(self) -> Tuple[int, int]:\n return self.entity.x + self.dx, self.entity.y + self.dy","def set_2d_location(self, x, y):\r\n self.unif[42:44] = [x, y]","def set_XY(self, X, Y):\n self.update_model(False)\n self.set_Y(Y)\n self.set_X(X)\n self.update_model(True)","def pixel_to_position(self, pixel):\n x, y = pixel\n return y // 60, x // 60","def move_origin(self, x, y):\n return Position(self.x - x, self.y - y)","def set_new_location(self, xPos, yPos):","def _get_xy_coords(self, exterior, coord_type):\n if coord_type == 'x':\n return exterior.coords.xy[0]\n elif coord_type == 'y':\n return exterior.coords.xy[1]","def m_location_set(self, x: int, y: int):\n pass","def shift(self, coord, y=None):\n assert isinstance(coord, Coordinate) or isinstance(y, AxisDistance), \"incorrect type of arg coord: should be Coordinate or AxisDistance, is {}\".format(type(coord))\n if y is not None: coord = Coordinate(coord, y)\n self.x += coord.x\n self.y += coord.y\n return self","def get_stig_xy(self):\n raise NotImplementedError","def eval_Dxy(self):\n\n return self.X - self.Y","def aligne_grille(self,x,y,t):\r\n [xmin,ymin,xmax,ymax] = self.can.coords(self.hitbox[t])\r\n tx,ty=xmax-xmin,ymax-ymin\r\n a,b=23,23\r\n if tx==92 or ty==92 or tx==184 or ty==184:\r\n if tx==92 or tx==184:a,b=0,23\r\n if ty==92 or ty==184:a,b=23,0\r\n if 142<y<602 and 66<x<528:\r\n x=(x-66)//46*46+66+a\r\n y=(y-142)//46*46+142+b\r\n return x,y","def to_position(self, x, y, i, j):\n return (x * self.SIZE + i, y * self.SIZE + j)","def xy(event):\n return map(int, event.get_coords())","def position(self, x, y):\n self.x = x \n self.y = y\n self.pos[0] = x \n self.pos[1] = y","def pixel2coords(self, x, y):\n xoff, a, b, yoff, d, e = self.geotransform()\n\n xp = a * x + b * y + xoff\n yp = d * x + e * y + yoff\n return (xp, yp)","def _get_x_y_from_pos(self, col,row): \r\n return (self.margin_left+(self.text_width*col),\r\n self.margin_top+(self.text_height*row))","def coord (i, j):\r\n return j, i","def set_xy(self, x, y, val):\r\n\t\tself.grid[y, x] = val","def getXY(self):\n return (self.X,self.Y)","def y(self):\r\n return self.position.y","def get_new_coordinate(x_y_coordinate: dict, move_direction: str) -> tuple:\n direction_dict = {'n': (0, -1), 's': (0, 1), 'w': (-1, 0), 'e': (1, 0)}\n x = x_y_coordinate['x'] + direction_dict[move_direction][0]\n y = x_y_coordinate['y'] + direction_dict[move_direction][1]\n return x, y","def translate_to_point_O(self):\n self.translate(-self.pcs.origin)","def new_x_y(self, patch, points, idx):\n raise NotImplementedError","def setzePosition(self, x, y):\n self.zielX = x\n self.zielY = y","def inverse_coord_shift(kalman_coord):\n x_c, y_c, aspect_ratio, height = kalman_coord[:4]\n width = height / aspect_ratio\n x_min = x_c - width / 2\n x_max = x_c + width / 2\n y_min = y_c - height / 2\n y_max = y_c + height / 2\n std_coord = np.array([x_min, y_min, x_max, y_max])\n return np.int_(np.round(std_coord))","def xy2ang(self, x, y=None, lonlat=False, direct=False):\n pass","def y(self):\n return self.coords[1]","def xy2sub(self, x, y):\n # ix = int(round(x/self.Lx*(self.Nx-1)))\n # iy = int(round(y/self.Ly*(self.Ny-1)))\n ix = (np.array(x) / self.Lx*(self.Nx-1)).round().astype(int)\n iy = (np.array(y) / self.Ly*(self.Ny-1)).round().astype(int)\n return ix, iy","def move_abs(self, y, x):\n max_y, max_x = self.stdscr.getmaxyx()\n delta_y, new_x = divmod(x, max_x)\n new_y = max(y + delta_y, 0)\n self.stdscr.move(new_y, new_x)","def _coord_byval(coord: COORD) -> c_long:\n return c_long(coord.Y * 0x10000 | coord.X & 0xFFFF)","def adjustCoordByBorders(self, x, y):\n (x_offset, y_offset) = (0, 0)\n if (127 < x < (255+4)):\n x_offset -= 4\n \n if (31 < y < (63+4*1)):\n y_offset -= 4\n elif ( (63+4*1) < y < (95+4*2) ):\n y_offset -= 4*2\n elif ( (95+4*2) < y < (127+4*3) ):\n y_offset -= 4*3\n elif ( (127+4*3) < y < (159+4*4) ):\n y_offset -= 4*4\n elif ( (159+4*4) < y < (191+4*5) ):\n y_offset -= 4*5\n elif ( (191+4*5) < y < (223+4*6) ):\n y_offset -= 4*6\n elif ( (223+4*6) < y < (255+4*7) ):\n y_offset -= 4*7\n return x_offset, y_offset","def get_xy_position(row, col):\n spacing_x = 86 + 11\n spacing_y = 98 + 8\n top_y = 50\n left_x = 50\n return left_x + col * spacing_x, top_y + row * spacing_y","def mouse_position_event(self, x: int, y: int):\n pass","def xy(self):\n return self.to_xyah()[0:2]","def location_to_pos(self,row, col):\r\n\r\n pos_row = str(row + 1)\r\n pos_col = chr(col + 97)\r\n return pos_col + pos_row","def correct_point(point: Tuple[int, int]) -> Tuple[int, int]:\n corrected_x = point[0] + WIDTH_START\n corrected_y = point[1] + HEIGHT_START\n return corrected_x, corrected_y","def initialCoordinates():\r\n return (-250,-250)","def track_point(self, flags, x, y):\n ret_val, x.value, y.value = self._track_point(flags, x.value, y.value)\n return ret_val","def _limit_coordinates(self, coord):\n coord[0] = min(coord[0], self.shape[0] - 1)\n coord[0] = max(coord[0], 0)\n coord[1] = min(coord[1], self.shape[1] - 1)\n coord[1] = max(coord[1], 0)\n return coord","def _limit_coordinates(self, coord):\n coord[0] = min(coord[0], self.shape[0] - 1)\n coord[0] = max(coord[0], 0)\n coord[1] = min(coord[1], self.shape[1] - 1)\n coord[1] = max(coord[1], 0)\n return coord","def convert_coords(x, y, conversion):\n if conversion == \"cartesian\" :\n # convert to cartesian plane coordinates \n x_new = x - (width/2)\n y_new = (height/2) + y \n\n elif conversion == \"pygame\":\n # only needed to place images in pygame\n x_new = x + (width/2)\n y_new = (height/2) - y\n \n return x_new, y_new","def __set_y__(self,y):\n\n # Input vaidation\n try:\n y = int(y)\n except:\n raise ValueError('H Bridge direction is not valid')\n \n if(y != 0 and y != 1 and y != -1):\n raise ValueError('H Bridge direction is not valid')\n \n self.direction['y'] = y\n self.HBridges['y'].SetDirection(y)","def get_xy_position(gcode_command):\n\tpattern = re.compile(r\"^G\\dX(\\d+(?:\\.\\d*)?|\\.\\d+)Y(\\d+(?:\\.\\d*)?|\\.\\d+)F(\\d+)$\") # using non-capturing groups\n\tm = pattern.match(gcode_command) # no need for re.search() because we have a complete pattern\n\t(x, y) = m.group(1,2)\n\ttry:\n\t\tx = float(x)\n\t\ty = float(y)\n\texcept:\n\t\traise Exception(\"Could not convert X and Y to floats. X={}, Y={}\".format(x,y))\n\tx_pixel = round(x/X_STEP) # round to nearest int\n\ty_pixel = round(y/Y_STEP*12)\n\treturn (x_pixel, y_pixel)","def offset_y(self, X, y):\n X, y = self.check_consistent_params(X, y)\n if len(y.shape) == 1:\n offset = len(y) - X.shape[0]\n return y[offset:]\n else:\n offset = len(y[0]) - X.shape[0]\n return y[0, offset:]","def update_before(self, x: int, y: float, w: float) -> None:\n old_value = 0\n if x < len(self.x):\n old_value = self.y[x]\n self.update(x + 1, y, w)\n while len(self.x) < x:\n self.x.append(len(self.x))\n self.y.append(y)\n self.w.append(w)\n if self.w[x] <= w:\n self.x[x] = x\n self.y[x] = y\n self.w[x] = w\n pl = x - 1\n while pl >= 0 and (self.y[pl] == 0 or (self.w[pl] <= w and self.y[pl] == old_value)):\n self.y[pl] = y\n self.w[pl] = w\n pl -= 1","def shift_negative_coordinates(self):\n X = self.contents['X']\n Y = self.contents['Y']\n Z = self.contents['Z']\n\n X_new = np.where(X > 0, X, 0)\n Y_new = np.where(Y > 0, Y, 0)\n Z_new = np.where(Z > 0, Z, 0)\n\n self.contents['X'] = X_new\n self.contents['Y'] = Y_new\n self.contents['Z'] = Z_new","def toggle_xy(self, x, y):\r\n\t\tself.grid[y, x] = False if self.grid[y,x] else True","def getY(self):\n return self.position[1]","def pixel_offset(self, x, y):\n return y * self.width + x","def upright(self):\n return Coord([self.x + 1, self.y - 1])","def le(self, x, y):","def mousePositionRaw(self):","def mousePositionRaw(self):","def transpose_coordinates(self, x, y):\n return (x, self.height - 1 - y)","def coordinates(self):","def invert_y(self):\n return Position(x_or_tuple=self.x, y=self.y * -1)","def backward_character():\r\n set_point(point().offset(-1))","def get_data_coordinates(self, x, y):\n return x/self.sx - self.tx, y/self.sy - self.ty","def offset_y(self, y: int):\n self.tk_ref.geometry(f'{self.width}x{self.height}+{self.offset_x}+{y}')","def origin_y(self):\n return self._origin[1]","def calibrate(self, x, y) -> None:\n pass","def position(self, x, y):\n assert 0 <= x < self.width, \"x must be between 0 and 83\"\n assert 0 <= y < self.height // 8, \"y must be between 0 and 5\"\n assert self.instr == self.INSTR_BASIC, \"Please switch to basic instruction set first.\"\n self.command([x + 0x80, y + 0x40])","def _apply_tore(y_coordinate, x_coordinate, game_data):\n\n board_x = game_data['variables']['board_size']['x']\n board_y = game_data['variables']['board_size']['y']\n\n if x_coordinate > board_x:\n x_coordinate -= board_x\n if y_coordinate > board_y:\n y_coordinate -= board_y\n\n if x_coordinate < 1:\n x_coordinate += board_x\n if y_coordinate < 1:\n y_coordinate += board_y\n\n return y_coordinate, x_coordinate","def positioning_ship(self):\n self.rect.midleft = self.screen_rect.midleft\n self.y = float(self.rect.y)","def set_position(self, x, y):\n self.geometry('%s%s' % (x, y))","def get_xy(self):\r\n return self.board.get_xy()","def y(self, x):\n return x","def set_ly(self):\r\n self._ly = self.dy * self.ny - self.oy","def YtoX2(x1, y):\n return 0.5 * y * (x1**2 + 1) - x1**2"],"string":"[\n \"def _coord(self, x, y):\\n gridEdge = 7 # originally 5\\n y = gridEdge - y\\n cx = 100 * (x - 1) + 50\\n cy = 100 * (y - 1) + 50\\n r = 20\\n return (cx - r, cy - r, cx + r, cy + r)\",\n \"def _transform_point(self, x, y):\\n return (x, y)\",\n \"def set_position(self, x, y):\\n self.tx = -x\\n self.ty = -y\",\n \"def __getxy(x1, y1, x2, y2):\\n\\t\\treturn x1*27+y1*9+x2*3+y2\",\n \"def pixel2coord(self, x, y):\\n # NEED TO CHANGE TO USE INVERSE TRANSFORM COEFFS\\n # partly taken from Sean Gillies \\\"affine.py\\\"\\n a,b,c,d,e,f = self.coordspace_transform\\n det = a*e - b*d\\n idet = 1 / float(det)\\n ra = e * idet\\n rb = -b * idet\\n rd = -d * idet\\n re = a * idet\\n newx = (x*ra + y*rb + (-c*ra - f*rb) )\\n newy = (x*rd + y*re + (-c*rd - f*re) )\\n return newx,newy\",\n \"def get_pos(x, y):\\r\\n return normalize(x) // 2, normalize(y) // 4\",\n \"def XY(x, y):\\n return ESC + str(y + 1) + ';' + str(x + 1) + 'H'\",\n \"def _translate_coordinate(self, x1, y1, x2, y2):\\n\\n return (x1 + x2, y1 + y2)\",\n \"def __getxyB(x, y):\\n\\t\\treturn x*3+y\",\n \"def relmoveto(self, x = 0, y = 0):\\n self.cur_x += x\\n self.cur_y += y\\n if x < 0:\\n self.out.write(self.csi + \\\"%sD\\\" % -x)\\n elif x > 0:\\n self.out.write(self.csi + \\\"%sC\\\" % x)\\n if y < 0:\\n self.out.write(self.csi + \\\"%sA\\\" % -y)\\n elif y > 0:\\n self.out.write(self.csi + \\\"%sB\\\" % y)\",\n \"def toind(x, y):\\n return x + 15 * y\",\n \"def _increase_coordinates(coordinates, x, y):\\n orig_x, orig_y = coordinates[\\\"x\\\"], coordinates[\\\"y\\\"]\\n coordinates[\\\"x\\\"], coordinates[\\\"y\\\"] = orig_x + x, orig_y + y\",\n \"def translateCoord(self,absX,absY):\\n rawConvertedX=hex(absX*(16**4-1)/self.maxX).upper()[2:]\\n rawConvertedY=hex(absY*(16**4-1)/self.maxY).upper()[2:]\\n return {'x':rawConvertedX,'y':rawConvertedY}\",\n \"def transform(self, X, y=None):\\n return super().transform(X, y)\",\n \"def transform(self, X, y=None):\\n return super().transform(X, y)\",\n \"def get_xy(self, x, y):\\r\\n\\t\\treturn self.grid[y, x]\",\n \"def trace(self, coord01: np.ndarray) -> np.ndarray:\\n rect = self.clip_rect()\\n return (rect.position + coord01 * rect.size).astype(np.int)\",\n \"def _fix_coords(x, y):\\n if x.ndim != 1 or all(x < x[0]): # skip 2D arrays and monotonic backwards data\\n return x, y\\n lon1 = x[0]\\n filter_ = x < lon1\\n while filter_.sum():\\n filter_ = x < lon1\\n x[filter_] += 360\\n return x, y\",\n \"def xy(self):\\n ...\",\n \"def pos(self, x, y):\\n\\n if isinstance(x, float):\\n x = int(x)\\n\\n self.screen.write(colorama.Cursor.POS(x, y), ansi=True)\\n self.x = x\\n self.y = y\\n\\n return x, y\",\n \"def ED(X,Y):\",\n \"def convertdirection(self, frame):\\n return _coordsys.coordsys_convertdirection(self, frame)\",\n \"def coord(self, x, y):\\n origin_x = self._raster_meta['transform'][3]\\n origin_y = self._raster_meta['transform'][0]\\n pixel_x = self._raster_meta['transform'][5]\\n pixel_y = self._raster_meta['transform'][1]\\n\\n x = int((x - origin_x) / pixel_x)\\n y = int((y - origin_y) / pixel_y)\\n return self[x, y]\",\n \"def pos(self, x=-1, y=-1):\\n self._p('[pos] {} {}'.format(x, y))\",\n \"def xy2ind(self, x, y):\\n return self.sub2ind(*self.xy2sub(x, y))\",\n \"def Translate(X,Y,Xoffset=0,Yoffset=0):\\n X1 = X + Xoffset\\n Y1 = Y + Yoffset\\n return X1,Y1\",\n \"def place(self,y,x):\\n self.y = y\\n self.x = x\",\n \"def setDesiredPosition(self, x, y):\\n (self.setX, self.setY) = (x , y)\",\n \"def coord2pixel(self, x, y):\\n a,b,c,d,e,f = self.coordspace_transform\\n newx,newy = (x*a + y*b + c, x*d + y*e + f)\\n return int(newx),int(newy)\",\n \"def __get_x__(self):\\n return self.Direction['x']\",\n \"def dest_xy(self) -> Tuple[int, int]:\\n return self.entity.x + self.dx, self.entity.y + self.dy\",\n \"def set_2d_location(self, x, y):\\r\\n self.unif[42:44] = [x, y]\",\n \"def set_XY(self, X, Y):\\n self.update_model(False)\\n self.set_Y(Y)\\n self.set_X(X)\\n self.update_model(True)\",\n \"def pixel_to_position(self, pixel):\\n x, y = pixel\\n return y // 60, x // 60\",\n \"def move_origin(self, x, y):\\n return Position(self.x - x, self.y - y)\",\n \"def set_new_location(self, xPos, yPos):\",\n \"def _get_xy_coords(self, exterior, coord_type):\\n if coord_type == 'x':\\n return exterior.coords.xy[0]\\n elif coord_type == 'y':\\n return exterior.coords.xy[1]\",\n \"def m_location_set(self, x: int, y: int):\\n pass\",\n \"def shift(self, coord, y=None):\\n assert isinstance(coord, Coordinate) or isinstance(y, AxisDistance), \\\"incorrect type of arg coord: should be Coordinate or AxisDistance, is {}\\\".format(type(coord))\\n if y is not None: coord = Coordinate(coord, y)\\n self.x += coord.x\\n self.y += coord.y\\n return self\",\n \"def get_stig_xy(self):\\n raise NotImplementedError\",\n \"def eval_Dxy(self):\\n\\n return self.X - self.Y\",\n \"def aligne_grille(self,x,y,t):\\r\\n [xmin,ymin,xmax,ymax] = self.can.coords(self.hitbox[t])\\r\\n tx,ty=xmax-xmin,ymax-ymin\\r\\n a,b=23,23\\r\\n if tx==92 or ty==92 or tx==184 or ty==184:\\r\\n if tx==92 or tx==184:a,b=0,23\\r\\n if ty==92 or ty==184:a,b=23,0\\r\\n if 142<y<602 and 66<x<528:\\r\\n x=(x-66)//46*46+66+a\\r\\n y=(y-142)//46*46+142+b\\r\\n return x,y\",\n \"def to_position(self, x, y, i, j):\\n return (x * self.SIZE + i, y * self.SIZE + j)\",\n \"def xy(event):\\n return map(int, event.get_coords())\",\n \"def position(self, x, y):\\n self.x = x \\n self.y = y\\n self.pos[0] = x \\n self.pos[1] = y\",\n \"def pixel2coords(self, x, y):\\n xoff, a, b, yoff, d, e = self.geotransform()\\n\\n xp = a * x + b * y + xoff\\n yp = d * x + e * y + yoff\\n return (xp, yp)\",\n \"def _get_x_y_from_pos(self, col,row): \\r\\n return (self.margin_left+(self.text_width*col),\\r\\n self.margin_top+(self.text_height*row))\",\n \"def coord (i, j):\\r\\n return j, i\",\n \"def set_xy(self, x, y, val):\\r\\n\\t\\tself.grid[y, x] = val\",\n \"def getXY(self):\\n return (self.X,self.Y)\",\n \"def y(self):\\r\\n return self.position.y\",\n \"def get_new_coordinate(x_y_coordinate: dict, move_direction: str) -> tuple:\\n direction_dict = {'n': (0, -1), 's': (0, 1), 'w': (-1, 0), 'e': (1, 0)}\\n x = x_y_coordinate['x'] + direction_dict[move_direction][0]\\n y = x_y_coordinate['y'] + direction_dict[move_direction][1]\\n return x, y\",\n \"def translate_to_point_O(self):\\n self.translate(-self.pcs.origin)\",\n \"def new_x_y(self, patch, points, idx):\\n raise NotImplementedError\",\n \"def setzePosition(self, x, y):\\n self.zielX = x\\n self.zielY = y\",\n \"def inverse_coord_shift(kalman_coord):\\n x_c, y_c, aspect_ratio, height = kalman_coord[:4]\\n width = height / aspect_ratio\\n x_min = x_c - width / 2\\n x_max = x_c + width / 2\\n y_min = y_c - height / 2\\n y_max = y_c + height / 2\\n std_coord = np.array([x_min, y_min, x_max, y_max])\\n return np.int_(np.round(std_coord))\",\n \"def xy2ang(self, x, y=None, lonlat=False, direct=False):\\n pass\",\n \"def y(self):\\n return self.coords[1]\",\n \"def xy2sub(self, x, y):\\n # ix = int(round(x/self.Lx*(self.Nx-1)))\\n # iy = int(round(y/self.Ly*(self.Ny-1)))\\n ix = (np.array(x) / self.Lx*(self.Nx-1)).round().astype(int)\\n iy = (np.array(y) / self.Ly*(self.Ny-1)).round().astype(int)\\n return ix, iy\",\n \"def move_abs(self, y, x):\\n max_y, max_x = self.stdscr.getmaxyx()\\n delta_y, new_x = divmod(x, max_x)\\n new_y = max(y + delta_y, 0)\\n self.stdscr.move(new_y, new_x)\",\n \"def _coord_byval(coord: COORD) -> c_long:\\n return c_long(coord.Y * 0x10000 | coord.X & 0xFFFF)\",\n \"def adjustCoordByBorders(self, x, y):\\n (x_offset, y_offset) = (0, 0)\\n if (127 < x < (255+4)):\\n x_offset -= 4\\n \\n if (31 < y < (63+4*1)):\\n y_offset -= 4\\n elif ( (63+4*1) < y < (95+4*2) ):\\n y_offset -= 4*2\\n elif ( (95+4*2) < y < (127+4*3) ):\\n y_offset -= 4*3\\n elif ( (127+4*3) < y < (159+4*4) ):\\n y_offset -= 4*4\\n elif ( (159+4*4) < y < (191+4*5) ):\\n y_offset -= 4*5\\n elif ( (191+4*5) < y < (223+4*6) ):\\n y_offset -= 4*6\\n elif ( (223+4*6) < y < (255+4*7) ):\\n y_offset -= 4*7\\n return x_offset, y_offset\",\n \"def get_xy_position(row, col):\\n spacing_x = 86 + 11\\n spacing_y = 98 + 8\\n top_y = 50\\n left_x = 50\\n return left_x + col * spacing_x, top_y + row * spacing_y\",\n \"def mouse_position_event(self, x: int, y: int):\\n pass\",\n \"def xy(self):\\n return self.to_xyah()[0:2]\",\n \"def location_to_pos(self,row, col):\\r\\n\\r\\n pos_row = str(row + 1)\\r\\n pos_col = chr(col + 97)\\r\\n return pos_col + pos_row\",\n \"def correct_point(point: Tuple[int, int]) -> Tuple[int, int]:\\n corrected_x = point[0] + WIDTH_START\\n corrected_y = point[1] + HEIGHT_START\\n return corrected_x, corrected_y\",\n \"def initialCoordinates():\\r\\n return (-250,-250)\",\n \"def track_point(self, flags, x, y):\\n ret_val, x.value, y.value = self._track_point(flags, x.value, y.value)\\n return ret_val\",\n \"def _limit_coordinates(self, coord):\\n coord[0] = min(coord[0], self.shape[0] - 1)\\n coord[0] = max(coord[0], 0)\\n coord[1] = min(coord[1], self.shape[1] - 1)\\n coord[1] = max(coord[1], 0)\\n return coord\",\n \"def _limit_coordinates(self, coord):\\n coord[0] = min(coord[0], self.shape[0] - 1)\\n coord[0] = max(coord[0], 0)\\n coord[1] = min(coord[1], self.shape[1] - 1)\\n coord[1] = max(coord[1], 0)\\n return coord\",\n \"def convert_coords(x, y, conversion):\\n if conversion == \\\"cartesian\\\" :\\n # convert to cartesian plane coordinates \\n x_new = x - (width/2)\\n y_new = (height/2) + y \\n\\n elif conversion == \\\"pygame\\\":\\n # only needed to place images in pygame\\n x_new = x + (width/2)\\n y_new = (height/2) - y\\n \\n return x_new, y_new\",\n \"def __set_y__(self,y):\\n\\n # Input vaidation\\n try:\\n y = int(y)\\n except:\\n raise ValueError('H Bridge direction is not valid')\\n \\n if(y != 0 and y != 1 and y != -1):\\n raise ValueError('H Bridge direction is not valid')\\n \\n self.direction['y'] = y\\n self.HBridges['y'].SetDirection(y)\",\n \"def get_xy_position(gcode_command):\\n\\tpattern = re.compile(r\\\"^G\\\\dX(\\\\d+(?:\\\\.\\\\d*)?|\\\\.\\\\d+)Y(\\\\d+(?:\\\\.\\\\d*)?|\\\\.\\\\d+)F(\\\\d+)$\\\") # using non-capturing groups\\n\\tm = pattern.match(gcode_command) # no need for re.search() because we have a complete pattern\\n\\t(x, y) = m.group(1,2)\\n\\ttry:\\n\\t\\tx = float(x)\\n\\t\\ty = float(y)\\n\\texcept:\\n\\t\\traise Exception(\\\"Could not convert X and Y to floats. X={}, Y={}\\\".format(x,y))\\n\\tx_pixel = round(x/X_STEP) # round to nearest int\\n\\ty_pixel = round(y/Y_STEP*12)\\n\\treturn (x_pixel, y_pixel)\",\n \"def offset_y(self, X, y):\\n X, y = self.check_consistent_params(X, y)\\n if len(y.shape) == 1:\\n offset = len(y) - X.shape[0]\\n return y[offset:]\\n else:\\n offset = len(y[0]) - X.shape[0]\\n return y[0, offset:]\",\n \"def update_before(self, x: int, y: float, w: float) -> None:\\n old_value = 0\\n if x < len(self.x):\\n old_value = self.y[x]\\n self.update(x + 1, y, w)\\n while len(self.x) < x:\\n self.x.append(len(self.x))\\n self.y.append(y)\\n self.w.append(w)\\n if self.w[x] <= w:\\n self.x[x] = x\\n self.y[x] = y\\n self.w[x] = w\\n pl = x - 1\\n while pl >= 0 and (self.y[pl] == 0 or (self.w[pl] <= w and self.y[pl] == old_value)):\\n self.y[pl] = y\\n self.w[pl] = w\\n pl -= 1\",\n \"def shift_negative_coordinates(self):\\n X = self.contents['X']\\n Y = self.contents['Y']\\n Z = self.contents['Z']\\n\\n X_new = np.where(X > 0, X, 0)\\n Y_new = np.where(Y > 0, Y, 0)\\n Z_new = np.where(Z > 0, Z, 0)\\n\\n self.contents['X'] = X_new\\n self.contents['Y'] = Y_new\\n self.contents['Z'] = Z_new\",\n \"def toggle_xy(self, x, y):\\r\\n\\t\\tself.grid[y, x] = False if self.grid[y,x] else True\",\n \"def getY(self):\\n return self.position[1]\",\n \"def pixel_offset(self, x, y):\\n return y * self.width + x\",\n \"def upright(self):\\n return Coord([self.x + 1, self.y - 1])\",\n \"def le(self, x, y):\",\n \"def mousePositionRaw(self):\",\n \"def mousePositionRaw(self):\",\n \"def transpose_coordinates(self, x, y):\\n return (x, self.height - 1 - y)\",\n \"def coordinates(self):\",\n \"def invert_y(self):\\n return Position(x_or_tuple=self.x, y=self.y * -1)\",\n \"def backward_character():\\r\\n set_point(point().offset(-1))\",\n \"def get_data_coordinates(self, x, y):\\n return x/self.sx - self.tx, y/self.sy - self.ty\",\n \"def offset_y(self, y: int):\\n self.tk_ref.geometry(f'{self.width}x{self.height}+{self.offset_x}+{y}')\",\n \"def origin_y(self):\\n return self._origin[1]\",\n \"def calibrate(self, x, y) -> None:\\n pass\",\n \"def position(self, x, y):\\n assert 0 <= x < self.width, \\\"x must be between 0 and 83\\\"\\n assert 0 <= y < self.height // 8, \\\"y must be between 0 and 5\\\"\\n assert self.instr == self.INSTR_BASIC, \\\"Please switch to basic instruction set first.\\\"\\n self.command([x + 0x80, y + 0x40])\",\n \"def _apply_tore(y_coordinate, x_coordinate, game_data):\\n\\n board_x = game_data['variables']['board_size']['x']\\n board_y = game_data['variables']['board_size']['y']\\n\\n if x_coordinate > board_x:\\n x_coordinate -= board_x\\n if y_coordinate > board_y:\\n y_coordinate -= board_y\\n\\n if x_coordinate < 1:\\n x_coordinate += board_x\\n if y_coordinate < 1:\\n y_coordinate += board_y\\n\\n return y_coordinate, x_coordinate\",\n \"def positioning_ship(self):\\n self.rect.midleft = self.screen_rect.midleft\\n self.y = float(self.rect.y)\",\n \"def set_position(self, x, y):\\n self.geometry('%s%s' % (x, y))\",\n \"def get_xy(self):\\r\\n return self.board.get_xy()\",\n \"def y(self, x):\\n return x\",\n \"def set_ly(self):\\r\\n self._ly = self.dy * self.ny - self.oy\",\n \"def YtoX2(x1, y):\\n return 0.5 * y * (x1**2 + 1) - x1**2\"\n]","isConversational":false},"negative_scores":{"kind":"list like","value":["0.6347154","0.615938","0.59551126","0.594736","0.5881816","0.5860635","0.5815088","0.57782364","0.5747512","0.57448643","0.57318264","0.57293063","0.57039654","0.5697053","0.5697053","0.56909347","0.5679062","0.5646204","0.5643103","0.5624204","0.561082","0.56082517","0.55979645","0.55878174","0.5580932","0.557102","0.55665857","0.5564508","0.555829","0.5556041","0.5546819","0.55466366","0.5540014","0.5536807","0.5536112","0.5524833","0.5507789","0.5505033","0.5504965","0.54985225","0.5487783","0.54842675","0.54812855","0.54707587","0.5451921","0.54503477","0.5446935","0.5441225","0.5439551","0.5434427","0.5429941","0.5424947","0.54224956","0.54190236","0.54161686","0.5415922","0.54147255","0.5414485","0.5413803","0.54080063","0.540784","0.54029125","0.53944385","0.5388243","0.5374664","0.5364227","0.5362007","0.5360032","0.5354534","0.5353378","0.5353378","0.5350478","0.5344976","0.5339992","0.5338767","0.53387237","0.5338138","0.53205395","0.53165954","0.5314249","0.53113824","0.5310912","0.5310757","0.5310757","0.5306137","0.53023267","0.5301439","0.5299495","0.5298444","0.528927","0.5286771","0.5286195","0.5285037","0.52833956","0.5281395","0.527837","0.5276841","0.52762645","0.52746636","0.5272801"],"string":"[\n \"0.6347154\",\n \"0.615938\",\n \"0.59551126\",\n \"0.594736\",\n \"0.5881816\",\n \"0.5860635\",\n \"0.5815088\",\n \"0.57782364\",\n \"0.5747512\",\n \"0.57448643\",\n \"0.57318264\",\n \"0.57293063\",\n \"0.57039654\",\n \"0.5697053\",\n \"0.5697053\",\n \"0.56909347\",\n \"0.5679062\",\n \"0.5646204\",\n \"0.5643103\",\n \"0.5624204\",\n \"0.561082\",\n \"0.56082517\",\n \"0.55979645\",\n \"0.55878174\",\n \"0.5580932\",\n \"0.557102\",\n \"0.55665857\",\n \"0.5564508\",\n \"0.555829\",\n \"0.5556041\",\n \"0.5546819\",\n \"0.55466366\",\n \"0.5540014\",\n \"0.5536807\",\n \"0.5536112\",\n \"0.5524833\",\n \"0.5507789\",\n \"0.5505033\",\n \"0.5504965\",\n \"0.54985225\",\n \"0.5487783\",\n \"0.54842675\",\n \"0.54812855\",\n \"0.54707587\",\n \"0.5451921\",\n \"0.54503477\",\n \"0.5446935\",\n \"0.5441225\",\n \"0.5439551\",\n \"0.5434427\",\n \"0.5429941\",\n \"0.5424947\",\n \"0.54224956\",\n \"0.54190236\",\n \"0.54161686\",\n \"0.5415922\",\n \"0.54147255\",\n \"0.5414485\",\n \"0.5413803\",\n \"0.54080063\",\n \"0.540784\",\n \"0.54029125\",\n \"0.53944385\",\n \"0.5388243\",\n \"0.5374664\",\n \"0.5364227\",\n \"0.5362007\",\n \"0.5360032\",\n \"0.5354534\",\n \"0.5353378\",\n \"0.5353378\",\n \"0.5350478\",\n \"0.5344976\",\n \"0.5339992\",\n \"0.5338767\",\n \"0.53387237\",\n \"0.5338138\",\n \"0.53205395\",\n \"0.53165954\",\n \"0.5314249\",\n \"0.53113824\",\n \"0.5310912\",\n \"0.5310757\",\n \"0.5310757\",\n \"0.5306137\",\n \"0.53023267\",\n \"0.5301439\",\n \"0.5299495\",\n \"0.5298444\",\n \"0.528927\",\n \"0.5286771\",\n \"0.5286195\",\n \"0.5285037\",\n \"0.52833956\",\n \"0.5281395\",\n \"0.527837\",\n \"0.5276841\",\n \"0.52762645\",\n \"0.52746636\",\n \"0.5272801\"\n]","isConversational":false},"document_score":{"kind":"string","value":"0.5459573"},"document_rank":{"kind":"string","value":"44"}}},{"rowIdx":16592,"cells":{"query":{"kind":"string","value":"Trap data following M02 block gerber."},"document":{"kind":"string","value":"def test_trailing_data(self):"},"metadata":{"kind":"string","value":"{\n \"objective\": {\n \"self\": [],\n \"paired\": [],\n \"triplet\": [\n [\n \"query\",\n \"document\",\n \"negatives\"\n ]\n ]\n }\n}"},"negatives":{"kind":"list like","value":["def _data_move_out_mc_on_h():\n\n pass","def onBlock(self, data) :\n pass","def readBumper(self, msg):\n #\n # if(msg.state==1):#the bumper is pressed\n self.executeTrajectory()","def _handle_MonitorData (self, event, packet, reverse):\n pass","def handleModuleMessage(self, data, datapathSendFcn):\n print (\"handler not implemented in silverline.\")","def callback(self, data):\n if not self.barcode_detected:\n rospy.loginfo(\"Started to dodge !\")\n self.angular_speed = 1.5\n self.barcode_detected = True\n self.t0 = time()","def step(self):\r\n cmd = struct.pack('>B', 54)\r\n self.send(cmd)","def on_data(data: dict):\n if 'symbol' in data and 'messageType' in data:\n if data['symbol'] == 'AAPL' and data['messageType'] == 'tradingstatus':\n print(\"APPL initial message received\")\n event1.set()\n if data['symbol'] == 'KPTI' and data['messageType'] == 'tradingstatus':\n print(\"KPTI initial message received\")\n event2.set()","def bumperCallback(self,data):\n if data.state == 1 :\n rospy.loginfo(\"Bumper enfonce\") \n self.soundPub.publish(0)","def abort_ber_meas(self):\r\r\n loggerCmw = logging.getLogger('abort_ber_meas')\r\r\n self.write('ABORt:WCDMa:SIGN:BER')\r\r\n loggerCmw.info(\"Aborting BER measurements\")\r\r\n time.sleep(1)","def test_back_fill(self):\n self.driver.start_sampling()\n\n # step 2 contains 2 blocks, start with this and get both since we used them\n # separately in other tests \n self.clear_async_data()\n self.create_sample_data_set_dir(\n \"node59p1_step2.dat\",\n TELEM_DIR,\n \"node59p1.dat\",\n copy_metadata=False\n )\n self.assert_data(\n (DostadParserTelemeteredDataParticle, DostadParserTelemeteredMetadataDataParticle),\n 'test_data_1-2.txt.result.yml',\n count=3\n )\n\n # This file has had a section of DO data replaced with 0s\n self.clear_async_data()\n self.create_sample_data_set_dir(\n 'node59p1_step3.dat',\n TELEM_DIR,\n \"node59p1.dat\",\n copy_metadata=False\n )\n self.assert_data(\n DostadParserTelemeteredDataParticle,\n 'test_data_3.txt.result.yml',\n count=3\n )\n\n # Now fill in the zeroed section from step3, this should just return the new\n # data\n self.clear_async_data()\n self.create_sample_data_set_dir(\n 'node59p1_step4.dat',\n TELEM_DIR,\n \"node59p1.dat\",\n copy_metadata=False\n )\n self.assert_data(\n DostadParserTelemeteredDataParticle,\n 'test_data_4.txt.result.yml',\n count=1\n )\n\n # start over now, using step 4\n self.driver.stop_sampling()\n\n # Reset the driver with no memento\n self.memento = None\n self.driver = MflmDOSTADDataSetDriver(\n self._driver_config()['startup_config'],\n self.memento,\n self.data_callback,\n self.state_callback,\n self.event_callback,\n self.exception_callback)\n self.driver.start_sampling()\n\n self.clear_async_data()\n self.create_sample_data_set_dir(\n 'node59p1_step4.dat',\n TELEM_DIR,\n \"node59p1.dat\",\n copy_metadata=False\n )\n self.assert_data(\n (DostadParserTelemeteredDataParticle, DostadParserTelemeteredMetadataDataParticle),\n 'test_data_1-4.txt.result.yml',\n count=7\n )","def __flight_data_handler(self, event, sender, data):\n self.battery = data.battery_percentage\n self.fly_mode = data.fly_mode\n self.throw_fly_timer = data.throw_fly_timer\n self.throw_ongoing = data.throw_fly_timer > 0\n\n if self.prev_flight_data != str(data):\n print(data)\n self.prev_flight_data = str(data)\n self.flight_data = data\n\n if self.is_flying != data.em_sky:\n self.is_flying = data.em_sky\n log.debug(f\"FLYING : {self.is_flying}\")\n if not self.is_flying:\n self.reset()\n else:\n if self.tracking_after_takeoff:\n log.info(\"Tracking on after takeoff\")\n self.toggle_tracking(True)\n\n # if self.write_header_log:\n # self.write_header_log = False\n # self.log_file_log.write(f\"{data.format_cvs_header()}\\n\")\n # self.log_file_log.write(f\"{data.format_cvs(0)}\\n\")","def modify_data(self, message):\n assert message.arbitration_id == self.can_id, \"You cannot modify the can identifier\"\n self.message = message\n self._tx_setup()","def _handle_block_data(self, block: Eth1Block) -> None:\n # Check timestamp.\n if len(self._block_timestamp_to_number) != 0:\n # Sanity check.\n if block.timestamp < self._largest_block_timestamp:\n raise Eth1MonitorValidationError(\n \"Later block with earlier timestamp: \"\n f\"largest_timestamp={self._largest_block_timestamp}, \"\n f\"block.timestamp={block.timestamp}\"\n )\n self._block_timestamp_to_number[block.timestamp] = block.number\n self._largest_block_timestamp = block.timestamp","def _hook_data(self, data):\n if self.data_hook is not None:\n self.data_hook(data)","def after_process(self, packet, ret_packet):\n pass","def parse_MTData2(self, data):\n # Functions to parse each type of packet\n def parse_orientation(data_id, content):\n o = struct.unpack('!'+3*self._ffmt, content)\n if self._coorSys == 'ENU':\n self._imu.orientation.x = o[0]\n self._imu.orientation.y = o[1]\n self._imu.orientation.z = o[2]\n elif self._coorSys == 'NED':\n self._imu.orientation.x = o[0]\n self._imu.orientation.y = -o[1]\n self._imu.orientation.z = -o[2]\n self._getAll = True\n\n def parse_acceleration(data_id, content):\n o = struct.unpack('!'+3*self._ffmt, content)\n if self._coorSys == 'ENU':\n self._imu.linear_acceleration.x = o[0]\n self._imu.linear_acceleration.y = o[1]\n self._imu.linear_acceleration.z = o[2]\n elif self._coorSys == 'NED':\n self._imu.linear_acceleration.x = o[0]\n self._imu.linear_acceleration.y = -o[1]\n self._imu.linear_acceleration.z = -o[2]\n\n def parse_angular_velocity(data_id, content):\n o = struct.unpack('!'+3*self._ffmt, content)\n if self._coorSys == 'ENU':\n self._imu.angular_velocity.x = o[0]\n self._imu.angular_velocity.y = o[1]\n self._imu.angular_velocity.z = o[2]\n if self._coorSys == 'NED':\n self._imu.angular_velocity.x = o[0]\n self._imu.angular_velocity.y = -o[1]\n self._imu.angular_velocity.z = -o[2]\n\n # data object\n while data:\n data_id, size = struct.unpack('!HB', data[:3])\n # determind a data format (double or float)\n\n content = data[3:3+size]\n data = data[3+size:]\n group = data_id & 0xFFF0\n\n if group == XDIGroup.OrientationData:\n parse_orientation(data_id, content)\n elif group == XDIGroup.Acceleration:\n parse_acceleration(data_id, content)\n elif group == XDIGroup.AngularVelocity:\n parse_angular_velocity(data_id, content)","def handle_data(self, line):\n\n # AorM - 0: M / 1: A\n feedback_AorM = ord(line[4])\n\n # Gear - 0: B / 1: N / 2: D\n feedback_gear = ord(line[5])\n\n # Speed\n feedback_KPH = (ord(line[6]) + ord(line[7]) * 256) / 10\n feedback_speed = self.kph2mps(value=feedback_KPH)\n\n # Steer\n feedback_DEG = ord(line[8]) + ord(line[9]) * 256\n\n if feedback_DEG >= 23768:\n feedback_DEG -= 65536\n\n if feedback_DEG != 0:\n feedback_DEG /= 71.0\n\n feedback_steer = m.radians(feedback_DEG)\n\n # Brake\n feedback_brake = ord(line[10])\n\n # Encoder\n self.feedback_encoder = (ord(line[11]) + ord(line[12]) * 256 + ord(\n line[13]) * 256 * 256 + ord(line[14]) * 256 * 256 * 256)\n\n if self.feedback_encoder >= 2147483648:\n self.feedback_encoder -= 4294967296\n\n # print(self.feedback_encoder)\n\n data = encoderMsg()\n\n data.speed = feedback_speed\n data.steer = feedback_steer\n data.steer = feedback_DEG\n data.brake = feedback_brake\n data.gear = feedback_gear\n data.AorM = feedback_AorM\n data.Encoder = self.feedback_encoder\n\n self.feedbackMsg = data\n encoder_pub.publish(data)","def process_bump_sensing(self, data):\n if data.state == BumperEvent.PRESSED:\n self.bump = True\n self.bumpDir = data.bumper\n rospy.loginfo(\"Bumper Event :)\")\n rospy.loginfo(data.bumper)","def handleModuleMessage(self, data):\n # print (\"got a message in silverline module.\")\n (messageType, content) = self.ofxAgent.unpackModuleMessage(data)\n # print \"\\tmessage type: %s\"%messageType\n if messageType == ENABLEDECLASSIFIER:\n self.enableDeclassifier()\n elif messageType == ADDFLOWPERMISSION:\n self.addFlowPermission(content)","def handle_sensor_data(data):\n \n #print dir( data )\n D.data = data\n\n #Check for a bump\n if data.bumpRight or data.bumpLeft:\n print \"Bumped!\"\n\n\n #Check if play button was pressed\t\n if data.play:\n\tprint \"Play button pressed!\"\n\tStateMachine.state_stop()\n\trospy.signal_shutdown(\"play button pressed\")","def bruno_mes(self):\n MI = -125\n MA = 125\n INCR = 19\n####################################################################\n ### CHANNEL 1\n self.write('CHN 1')\n self.write('CHN?')\n print 'Acting on channel:',self.read()\n self.write('WAVE ARB')\n self.write('ARBLOAD ARB1')\n self.write('FREQ 100')\n self.write('DCOFFS 0.05')\n self.write('AMPL 0.1')\n \n l =(125,-125,125)#arange(MI,MA,INCR) # the ramp\n# lll = copy(l)[::-1][1:-1]\n# l = concatenate((l,lll))\n self.write_array_to_byte(l,1)","def mv_step(self):\n # def mv_all(self):\n self.device_reg_data &= ~(0x1 << 3)\n bus.write_byte_data(self.device_address, self.device_reg_mode1, self.device_reg_data)","def event0():\n header(0, 0)\n\n if DEBUG.GET_CHTHONIC_SPARK:\n item.award_item_to_host_only(1600)\n if DEBUG.GET_DARKMOON_SEANCE_RING:\n item.award_item_to_host_only(1600310)\n if DEBUG.GWYNDOLIN_DEAD:\n flag.enable(EVENT.GwyndolinDead)\n item.award_item_to_host_only(2600)\n if DEBUG.ORNSTEIN_AND_SMOUGH_DEAD:\n flag.enable(EVENT.OrnsteinAndSmoughDead)\n if DEBUG.DARK_ANOR_LONDO:\n flag.enable(EVENT.OrnsteinAndSmoughDead)\n flag.enable(EVENT.GwyndolinDead)\n flag.enable(EVENT.DarkAnorLondo)\n if DEBUG.GET_LAUTREC_BLACK_EYE_ORB:\n item.award_item_to_host_only(2034)\n if DEBUG.CAPRICIOUS_THRALL_ACTIVE:\n flag.enable(EVENT.CapriciousThrallActive)\n if DEBUG.GET_BUTTERFLY_SOUL:\n item.award_item_to_host_only(2530)\n item.award_item_to_host_only(0)\n if DEBUG.DISABLE_FOG_ARCHER:\n chr.disable(CHR.SilverKnightArcherNearBossFog)\n if DEBUG.JAREEL_DEAD:\n flag.enable(EVENT.JareelDead)\n\n skip_if_event_flag_off(1, EVENT.OrnsteinAndSmoughDead)\n map.register_bonfire(11510920, 1511950)\n for bonfire_flag, bonfire_id, kindle_level in zip((11510992, 11510984, 11510976), (1511960, 1511961, 1511962),\n (10, 0, 0)):\n map.register_bonfire(bonfire_flag, bonfire_id, initial_kindle_level=kindle_level)\n map.register_ladder(11510010, 11510011, 1511140)\n map.register_ladder(11510012, 11510013, 1511141)\n\n # Make elevator work immediately (and skip cutscene).\n flag.enable(11510305)\n\n flag.disable(11510304)\n skip_if_client(2)\n obj.disable(1511994)\n sfx.delete_map_sfx(1511995, False)\n obj.disable(1511310)\n for hitbox_id in (1513301, 1513302, 1513303):\n hitbox.disable_hitbox(hitbox_id)\n skip_if_event_flag_off(1, 11510300)\n skip_if_event_flag_off(6, 11510303)\n flag.disable(11510301)\n flag.disable(11510302)\n flag.enable(11510303)\n anim.end_animation(1511300, 53)\n hitbox.enable_hitbox(1513303)\n skip(13)\n skip_if_event_flag_off(6, 11510302)\n flag.disable(11510301)\n flag.enable(11510302)\n flag.disable(11510303)\n anim.end_animation(1511300, 50)\n hitbox.enable_hitbox(1513302)\n skip(6)\n skip_if_event_flag_off(5, 11510301)\n flag.enable(11510301)\n flag.disable(11510302)\n flag.disable(11510303)\n anim.end_animation(1511300, 51)\n hitbox.enable_hitbox(1513301)\n\n obj.disable(1511450)\n flag.disable(11510460)\n run_event_with_slot(11510090, 0, (1511700, 1511701, 1512600, 1512601))\n run_event_with_slot(11510090, 1, (1511702, 1511703, 1512602, 1512603))\n\n for event_id in (11515040, 11515041, 11515042):\n run_event(event_id)\n\n run_event(11510200) # Rotating lever to open palace.\n run_event(11510205) # (New) Rotating lever to open palace in Dark Anor Londo (Jareel must be dead).\n run_event(11510201) # Palace locked from the outside.\n run_event(11510100) # Break chandelier.\n run_event(11510210) # Open one-way gate to blacksmith.\n run_event(11510211) # Blacksmith gate is locked.\n run_event(11510220) # First activation of gondola. (Now pre-enabled.)\n run_event(11510300) # Main gondola activation.\n run_event(11510319) # Gondola flags.\n run_event(11510340) # Gondola navimesh.\n run_event(11510350) # Gondola sync.\n run_event(11510310) # Gondola lever can't be pushed.\n run_event(11515250) # Painting Guardian ambush.\n run_event(11515251) # Provoke a Silver Knight.\n run_event(11510110) # Open door to Sun Chamber. (Now requires key.)\n run_event(11510111) # (New) Sun Chamber is locked.\n run_event(11510400) # Trigger Dark Anor Londo.\n run_event(11510401) # Disable Darkmoon Tomb statue.\n run_event(11510230) # Enter Painted World if you have the Painted Doll.\n run_event(11510240) # Return to Sen's Fortress.\n run_event(11515050) # Offend Pale Demon and cut off Fortress return.\n run_event(11510120) # Enable special effect 4501 in Darkmoon Tomb.\n run_event(11510130) # (Updated) Control Dark Anor Londo enemies.\n # (Gone) Player always respawns at 'Anor Londo' bonfire in Dark Anor Londo.\n run_event(11510460) # Kneel to Darkmoon Covenant.\n run_event(11510462) # Two-frame sync for above.\n run_event(11510461) # Kneel to Darkmoon Covenant, simple version.\n run_event(11510140) # Move your bloodstain out of endless Gwyndolin corridor when you win.\n run_event(11510150) # Trigger flag for quivering Black Eye Orb.\n run_event(11512008) # (New) Message that Thrall has fled higher again.\n\n run_event(11512043) # (NEW) Monitor resting at Sun Chamber bonfire for warping (11512045).\n run_event(11512044) # (NEW) Monitor resting at Gwyn's Altar bonfire for warping (11512046).\n\n run_event(151)\n run_event(11510215)\n\n # Sentinel shield parts.\n for slot, sentinel_id in zip(range(14), range(1510400, 1510414)):\n run_event_with_slot(11515060, slot, (sentinel_id,))\n\n # Gargoyle tails removed.\n\n # One-way shortcut doors.\n run_event_with_slot(11510260, 0, (11510251, 1512251, 1512250), 'iii')\n run_event_with_slot(11510260, 1, (11510257, 1512253, 1512252), 'iii')\n run_event_with_slot(11510260, 2, (11510258, 1512255, 1512254), 'iii')\n\n # ORNSTEIN AND SMOUGH / GWYN, LORD OF LIGHT\n\n sound.disable_map_sound(1513800) # Ornstein and Smough.\n sound.disable_map_sound(1513805) # Gwyn.\n\n # GWYN:\n run_event(11512200) # Gwyn trigger.\n run_event(11512201) # Gwyn death.\n skip_if_event_flag_on(22, EVENT.AnorLondoGwynWarp) # Skip O&S events (light and dark). Keep an eye on length.\n\n skip_if_event_flag_off(10, EVENT.OrnsteinAndSmoughDead)\n # Already dead:\n anim.force_animation(1511401, 0, loop=True) # Start elevators\n anim.force_animation(1511402, 0, loop=True)\n run_event(11515392)\n for fog_wall, fog_sfx in zip((1511990, 1511992, 1511988), (1511991, 1511993, 1511989)):\n obj.disable(fog_wall)\n sfx.delete_map_sfx(fog_sfx, False)\n skip(11)\n\n # Alive:\n for relative_id in (5390, 5391, 5393, 5392, 1, 5394, 5395, 5396, 5397, 5398, 5399):\n run_event(BASE_FLAG + relative_id)\n\n # FORSAKEN KNIGHT ORNSTEIN & SUN-EATER SMOUGH\n\n run_event(11515492) # Trigger. Handles all other events within.\n run_event(11512001) # Die.\n\n # DARK SUN GWYNDOLIN\n\n sound.disable_map_sound(1513802)\n skip_if_event_flag_off(6, EVENT.GwyndolinDead)\n # Already dead:\n run_event(11515382)\n obj.disable(1511890)\n sfx.delete_map_sfx(1511891, False)\n obj.disable(1511892)\n sfx.delete_map_sfx(1511893, False)\n skip(13)\n # Alive:\n # Disable Jareel fog (otherwise visible in boss start cutscene).\n obj.disable(1511970)\n sfx.delete_map_sfx(1511971, False)\n obj.disable(1511972)\n sfx.delete_map_sfx(1511973, False)\n for relative_id in (5380, 5381, 5383, 5382, 900, 5384, 5385, 5386, 450):\n run_event(BASE_FLAG + relative_id)\n\n # NEW: Abyssal King Jareel.\n sound.disable_map_sound(1513803)\n skip_if_event_flag_off(6, EVENT.JareelDead)\n # Already dead:\n run_event(11515372)\n obj.disable(1511970)\n sfx.delete_map_sfx(1511971, False)\n obj.disable(1511972)\n sfx.delete_map_sfx(1511973, False)\n skip(7)\n # Alive:\n run_event(11515370)\n run_event(11515371)\n run_event(11515373)\n run_event(11515372)\n run_event(11515374)\n run_event(11515375)\n run_event(11510901)\n\n # Open three doors for enemies (I think).\n for relative_door_id, base_slot in zip((251, 257, 258), (0, 20, 40)):\n run_event_with_slot(11510710, base_slot, (BASE_FLAG + relative_door_id, 6750,\n 1512000 + relative_door_id, 1512000 + relative_door_id - 1))\n for i, relative_enemy_id in enumerate((300, 301, 302, 305, 320, 321, 322, # Silver Knights\n 323, 324, 325, 326, 327, 328, 329, 500,\n 177, 178, 179, 180, 181, 181, 182, 183, # Darkwraiths\n 184, 185, 186, 187, 188, 189, 190)):\n run_event_with_slot(\n 11510710, base_slot + i + 1, (BASE_FLAG + relative_door_id, 1510000 + relative_enemy_id,\n 1512000 + relative_door_id, 1512000 + relative_door_id - 1))\n\n # Mimic triggers.\n for slot, relative_mimic_id in enumerate(range(4)):\n run_event_with_slot(11515200, slot, (1510200 + relative_mimic_id,))\n run_event_with_slot(11515210, slot, (1510200 + relative_mimic_id,))\n run_event_with_slot(11515220, slot, (1510200 + relative_mimic_id,))\n run_event_with_slot(11515230, slot, (1510200 + relative_mimic_id,))\n run_event_with_slot(11515240, slot, (1510200 + relative_mimic_id, 1512010 + relative_mimic_id))\n run_event_with_slot(11510850, slot, (1510200 + relative_mimic_id,))\n run_event_with_slot(11515190, slot, (1510200 + relative_mimic_id,))\n\n # Treasure chests.\n for i in range(1, 21):\n if i == 12 or i == 19:\n continue\n run_event_with_slot(11510600, i, (1511650 + i, 11510600 + i))\n anim.end_animation(1511662, 0) # Gwyn's chest already looted\n # Only activate chapel chest before Dark Anor Londo (replaced by Mimic).\n skip_if_event_flag_on(1, EVENT.DarkAnorLondo)\n run_event_with_slot(11510600, 19, (1511669, 11510619))\n\n # Non-respawning enemies.\n run_event_with_slot(11510860, 0, (1510250, 0)) # Haunting Semblance\n run_event_with_slot(11510860, 3, (6640, 0)) # Dark Anor Londo Knight 1\n run_event_with_slot(11510860, 4, (6650, 0)) # Dark Anor Londo Knight 2\n run_event_with_slot(11510870, 0, (CHR.DarkmoonGuardian,))\n\n # NEW: Allied Silver Knights and Sentinels stop respawning in Dark Anor Londo if killed (unless Jareel is dead).\n for slot, enemy_id in enumerate(DarkAnorLondoAllies):\n run_event_with_slot(11512050, slot, (enemy_id,))\n run_event_with_slot(11512150, slot, (enemy_id,)) # They also turn hostile again if attacked in Dark AL.\n\n # NEW: Darkwraiths stop respawning in Dark Anor Londo if killed (unless Jareel is alive).\n for slot, enemy_id in enumerate(Darkwraiths):\n run_event_with_slot(11512100, slot, (enemy_id,))\n\n # NEW: Scripted rampart battle between archers and Darkwraiths. Also disables gravity\n # for the high archer.\n run_event(11512040)\n\n # NEW: Scripted battle between Darkwraith and Pale Demons.\n run_event(11512041)\n\n # NEW: Angry Giant Blacksmith in Dark Anor Londo.\n run_event(11512042)\n\n # NEW: Capricious Thrall one-off attack on the rooftop.\n sound.disable_map_sound(1513804)\n obj.disable(1511974)\n sfx.delete_map_sfx(1511975, False)\n obj.disable(1511976)\n sfx.delete_map_sfx(1511977, False)\n obj.disable(1511978)\n sfx.delete_map_sfx(1511979, False)\n run_event(11512060) # Trigger and timer.\n run_event(11512061) # Death.","def dataPtoTB(self,u):\n n = self.ues[u].prbs\n [tbSbits,mod,bits,mcs__] = self.setMod(u,n)\n if self.schType[0:2]=='PF':\n if len(self.ues[u].pastTbsz)>self.promLen:\n self.ues[u].pastTbsz.popleft()\n self.ues[u].pastTbsz.append(self.ues[u].tbsz)\n\n self.ues[u].tbsz = tbSbits\n self.ues[u].MCS = mcs__\n self.setBLER(u)\n tbSize = int(float(tbSbits)/8) # TB size in bytes\n self.printDebDataDM('TBs: '+str(tbSize)+' nrb: '+str(n)+' FreeSp: '+str(self.queue.getFreeSpace())+'<br>')\n pks_s = 0\n list_p = []\n while pks_s<tbSize and len(self.ues[u].bearers[0].buffer.pckts)>0:\n pacD = self.ues[u].bearers[0].buffer.removePckt()\n pks_s = pks_s + pacD.size\n list_p.append(pacD.secNum)\n\n insrt = self.insertTB(self.ues[u].TBid,mod,u,'data',list_p,n,min(int(pks_s),tbSize))\n if (pks_s - tbSize)>0:\n pacD.size = pks_s - tbSize\n self.ues[u].bearers[0].buffer.insertPcktLeft(pacD)\n return self.ues[u].symb","def decode_faceshift_datastream(self, data):\n \n #block_id = struct.unpack_from('H', data)\n #print(\"Received block id \" + str(block_id)) ;\n\n offset = 0\n block_id, version, block_size = struct.unpack_from('HHI', data, offset)\n \n #print(\"ID, v, size = \" + str(block_id) + \",\" + str(version) + \",\" + str(block_size) )\n \n offset += 8\n\n if(block_id == BLOCK_ID_TRACKING_STATE):\n n_blocks, = struct.unpack_from('H', data, offset)\n #print(\"n_blocks = \" + str(n_blocks))\n offset += 2\n\n track_ok = 0 # Will be a byte: 1 if tracking ok, 0 otherwise.\n head_rotation_quat = None # Will be filled with the rotation using mathutils.Quaternion\n blend_shape_values = [] # Will be a list of float in the range 0-1\n #eyes_values = None # Will be a sequence of 4 angle values\n markers_position = [] # Will be a list of mathutils.Vector\n \n curr_block = 0\n while(curr_block < n_blocks):\n block_id, version, block_size = struct.unpack_from('HHI', data, offset)\n #print(\"ID, v, size = \" + str(block_id) + \",\" + str(version) + \",\" + str(block_size) )\n \n # put the offset at the beginning of the block\n offset += 8\n \n if(block_id == 101): # Frame Information blobk (timestamp and tracking status)\n ts, track_ok = struct.unpack_from('dB', data, offset)\n #print(\"timestamp, track_ok \" + str(ts) + \", \" + str(track_ok) )\n #offset += 9\n elif(block_id == 102): # Pose block (head rotation and position)\n x,y,z,w = struct.unpack_from('ffff', data, offset)\n #head_rotation_quat = mathutils.Quaternion((w,x,y,z))\n elif(block_id == 103): # Blendshapes block (blendshape values)\n n_coefficients, = struct.unpack_from('I', data, offset)\n #print(\"Blend shapes count=\"+ str(n_coefficients) )\n i = 0\n coeff_list = \"\"\n while(i < n_coefficients):\n # Offset of the block, plus the 4 bytes for int n_coefficients, plus 4 bytes per float\n val, = struct.unpack_from('f', data, offset + 4 + (i*4))\n blend_shape_values.append(val)\n coeff_list += repr(val) + \" \"\n i += 1\n print(\"Values: \" + coeff_list)\n elif(block_id == 104): # Eyes block (eyes gaze)\n leye_theta, leye_phi, reye_theta, reye_phi = struct.unpack_from('ffff', data, offset)\n elif(block_id == 105): # Markers block (absolute position of mark points)\n n_markers, = struct.unpack_from('H', data, offset)\n #print(\"n markers=\"+str(n_markers))\n i = 0\n while(i < n_markers):\n # Offset of the block, plus the 2 bytes for int n_markers, plus 4 bytes for each x,y,z floats\n x, y, z = struct.unpack_from('fff', data, offset + 2 + (i*4*3))\n #print(\"m\" + str(i) + \" \" + str(x) + \"\\t\" + str(y) + \"\\t\" + str(z))\n markers_position.append(mathutils.Vector((x,y,z)))\n i += 1\n \n curr_block += 1\n offset += block_size\n \n msg = fsMsgTrackingState()\n\n msg.m_timestamp = ts\n\n self.pub.publish(msg)\n\n # end -- while on blocks. Track State scan complete","def handle_data(self, data):\n if verbose(): print(\"TIParser.handle_data(self, '%s')\" % (data))\n pass","def packet_handler(pkt):\n if pkt[Ether].type == 0x800:\n if pkt[IP].dst == VICTIM_IP:\n if pkt[Ether].dst == HACKER_MAC:\n print(pkt.summary()) # print spoofed packet\n pkt[Ether].dst = VICTIM_MAC\n PACKET_QUEUE.insert(0, pkt)","def on_b(self):\r\n self.log()","def process_event(self, event):\n\n trap = v2c.TRAP()\n self._encoded_oids = []\n self._encoded_vals = []\n\n # Since this is a v2 trap, we must include sysUpTime as well\n # as sysTrapOID to indicate what the OID of this trap.\n self._add_varbind(SnmpTrapEventHandler.sysUpTime,\n SnmpTrapEventHandler.TIMETICKS.encode(int(time())))\n self._add_varbind(SnmpTrapEventHandler.sysTrapOID,\n self.trapoid)\n\n # We do late encoding of the value data because it may contain\n # positional parameters that need to be expanded on a per\n # event basis. \n for oid, type, value in self.varbinds:\n self._add_varbind(oid, self._encode_value(type, \n value, \n event.data.match))\n # Encode the trap and send it to all hosts.\n encoded_trap = trap.encode(encoded_oids=self._encoded_oids,\n encoded_vals=self._encoded_vals)\n for host in self.hosts:\n host.send(encoded_trap)\n\n return 1","def write_versa5(self,addr,data):\n time.sleep(0.002)\n data = data & 0x0ff\n addr = addr & 0x0ff\n ## i2caddr is 7 bits, no read write\n ## Bit 8 is set to indicate stop to HL2\n ## i2caddr = 0x80 | (0xd4 >> 1) ## ea\n cmd = bytes([0x06,0xea,addr,data])\n return self.command(0x3c,cmd)","def onAdaptorData(self, message):\n #logging.debug(\"%s onadaptorData, message: %s\", ModuleName, message)\n if message[\"characteristic\"] == \"acceleration\":\n for a in self.accel:\n if a.id == self.idToName[message[\"id\"]]: \n a.processAccel(message)\n break\n elif message[\"characteristic\"] == \"temperature\":\n for t in self.temp:\n if t.id == self.idToName[message[\"id\"]]:\n t.processTemp(message)\n break\n elif message[\"characteristic\"] == \"ir_temperature\":\n for t in self.irTemp:\n if t.id == self.idToName[message[\"id\"]]:\n t.processIrTemp(message)\n break\n elif message[\"characteristic\"] == \"gyro\":\n for g in self.gyro:\n if g.id == self.idToName[message[\"id\"]]:\n g.processGyro(message)\n break\n elif message[\"characteristic\"] == \"magnetometer\":\n for g in self.magnet:\n if g.id == self.idToName[message[\"id\"]]:\n g.processMagnet(message)\n break\n elif message[\"characteristic\"] == \"buttons\":\n for b in self.buttons:\n if b.id == self.idToName[message[\"id\"]]:\n b.processButtons(message)\n break\n elif message[\"characteristic\"] == \"humidity\":\n for b in self.humidity:\n if b.id == self.idToName[message[\"id\"]]:\n b.processHumidity(message)\n break\n elif message[\"characteristic\"] == \"binary_sensor\":\n for b in self.binary:\n if b.id == self.idToName[message[\"id\"]]:\n b.processBinary(message)\n break\n elif message[\"characteristic\"] == \"power\":\n for b in self.power:\n if b.id == self.idToName[message[\"id\"]]:\n b.processPower(message)\n break\n elif message[\"characteristic\"] == \"battery\":\n for b in self.battery:\n if b.id == self.idToName[message[\"id\"]]:\n b.processBattery(message)\n break\n elif message[\"characteristic\"] == \"connected\":\n for b in self.connected:\n if b.id == self.idToName[message[\"id\"]]:\n b.processConnected(message)\n break\n elif message[\"characteristic\"] == \"luminance\":\n for b in self.luminance:\n if b.id == self.idToName[message[\"id\"]]:\n b.processLuminance(message)\n break","def _do_some_logic(self, packet):\n\n\n pass","def handleSystemMessage(self,data):\n message = data.split()[0]\n if message == \"detectorError\":\n #handle dcs detector error\n message,detId = data.split()\n pcaId = self.detectorMapping[detId]\n partition = self.PCAs[pcaId]\n data = {\n \"id\": \"DCS\",\n \"detectorId\": detId,\n \"message\": message,\n }\n self.sendDCSMessage(data,partition)\n else:\n super().handleSystemMessage(message)","def process_MAM_data(self, spec):\n \n # Hack bucket if spec is loaded from the dataloader\n if len(spec.shape) == 4: # Bucketing should cause acoustic feature to have shape 1xBxTxD\n spec = spec.squeeze(0)\n # add arbitary batch axis B if input `spec` has shape of TxD\n elif len(spec.shape) == 2:\n spec = spec.unsqueeze(0)\n # input `spec` should have shape BxTxD\n elif len(spec.shape) != 3:\n raise ValueError('Input argument `spec` has invalid shape: {}'.format(spec.shape))\n\n # Down sample\n spec_stacked = self.down_sample_frames(spec) # (batch_size, seq_len, mel_dim * dr)\n\n # Record length for each uttr\n spec_len = np.sum(np.sum(spec_stacked.data.numpy(), axis=-1) != 0, axis=-1)\n spec_len = [int(sl) for sl in spec_len]\n\n batch_size = spec_stacked.shape[0]\n seq_len = spec_stacked.shape[1]\n\n pos_enc = self.position_encoding(seq_len, batch_size) # (batch_size, seq_len, hidden_size)\n attn_mask = np.ones((batch_size, seq_len)) # (batch_size, seq_len)\n\n # zero vectors for padding dimension\n for idx in range(len(spec_stacked)):\n pos_enc[idx][spec_len[idx]:] = 0 \n attn_mask[idx][spec_len[idx]:] = 0 \n\n spec_stacked = spec_stacked.to(device=self.device, dtype=torch.float32)\n pos_enc = torch.FloatTensor(pos_enc).to(device=self.device, dtype=torch.float32)\n attn_mask = torch.FloatTensor(attn_mask).to(device=self.device, dtype=torch.float32)\n return spec_stacked, pos_enc, attn_mask # (x, pos_enc, attention_mask)","def tell(self):\n ...","def receiver():\r\n global data\r\n DW1000.newReceive()\r\n DW1000.receivePermanently()\r\n DW1000.startReceive()","def bt_process():\n try:\n while(True):\n data = get_data()\n set_queue_data(data)\n broadcast(data[0])\n # Diagnostic\n grovepi.digitalWrite(LED, data[0])\n except IOError:\n if DEBUG:\n print 'IOError detected and excepted'\n pass","def event11510537():\n header(11510537, 0)\n npc, start_flag, end_flag, new_flag = define_args('iiii')\n if_event_flag_on(1, 1493) # Still stuck at the archers.\n if_event_flag_on(1, EVENT.DarkAnorLondo)\n if_condition_true(0, 1)\n flag.disable_chunk(start_flag, end_flag)\n flag.enable(new_flag)\n chr.disable(npc)","def _stop_capture_to_ram(self):\n self.regs.SDRAM_SINK_GO = 0","def __data_handler__(self, msg):\n print(msg)","def resetData(self):\n self.alive = 1\n self.fromSystem = self.toSystem\n self.systemGrid = 5\n mySystem = self.myGalaxy.systems[self.toSystem]\n mySystem.availSYC += self.repair","def got_data(self, data):\n if self.get_current_state() == SBE37ProtocolState.DIRECT_ACCESS:\n # direct access mode\n if len(data) > 0:\n mi_logger.debug(\"SBE37Protocol._got_data(): <\" + data + \">\") \n if self._driver_event:\n self._driver_event(DriverAsyncEvent.DIRECT_ACCESS, data)\n # TODO: what about logging this as an event?\n return\n \n if len(data)>0:\n # Call the superclass to update line and prompt buffers.\n CommandResponseInstrumentProtocol.got_data(self, data)\n \n # If in streaming mode, process the buffer for samples to publish.\n cur_state = self.get_current_state()\n if cur_state == SBE37ProtocolState.AUTOSAMPLE:\n if SBE37_NEWLINE in self._linebuf:\n lines = self._linebuf.split(SBE37_NEWLINE)\n self._linebuf = lines[-1]\n for line in lines:\n self._extract_sample(line)","def test_verify_clear_trace_mid_reassembly(self):\n\n self.pg_enable_capture()\n self.src_if.add_stream(self.fragments_400[0:-1])\n self.pg_start()\n\n self.logger.debug(self.vapi.cli(\"show trace\"))\n self.vapi.cli(\"clear trace\")\n\n self.src_if.add_stream(self.fragments_400[-1])\n self.pg_start()\n packets = self.dst_if.get_capture(len(self.pkt_infos))\n self.verify_capture(packets)","def syncloss(self):\n # expect a disassociation indication with a correct status\n assert(self.a.nxapi_disassociate_ind() == True)\n \n # generate a random frame\n msdu = self.host.tx_msdu(da=self.ap1.macaddr, length=1000, prio=1)\n \n # wait for data send confirmation (not in the air)\n self.a.host_send_data_cfm(msdu)","def data_received(self, data):\n pass","def test_post_voltage_maps(self):\n pass","def _process_msg(self, data):\n\n # print(data)\n\n tilt = data.linear.x\n pan = data.angular.z\n\n #self.controller.pantilt_magnitude(pan, tilt)\n self.controller.pantilt_increase_angle(pan * self.scale_pan, tilt * self.scale_tilt)","def receiver(): \n global data\n DW1000.newReceive()\n DW1000.receivePermanently()\n DW1000.startReceive()","def slot_recv(self, dummy_sender, data):\r\n (str_json) = data\r\n handler = None\r\n if type(str_json) == dict:\r\n msg = str_json # was already a dict\r\n else:\r\n msg = json.loads(str_json)\r\n self.msg = msg\r\n\r\n if \"stamp\" in msg:\r\n delay = time.time() * 1e6 - int(msg[\"stamp\"])\r\n self.socket_lag = (self.socket_lag * 29 + delay) / 30\r\n\r\n if \"op\" in msg:\r\n try:\r\n msg_op = msg[\"op\"]\r\n handler = getattr(self, \"_on_op_\" + msg_op)\r\n\r\n except AttributeError:\r\n self.debug(\"slot_recv() ignoring: op=%s\" % msg_op)\r\n else:\r\n self.debug(\"slot_recv() ignoring:\", msg)\r\n\r\n if handler:\r\n handler(msg)","def on_flip(self):\r\n self.next_data_has_pump = not self.next_data_has_pump\r\n self.probe_only_data, self.pump_probe_data = (\r\n self.pump_probe_data, self.probe_only_data)","def on_L2(self):\r\n self.log()","def callback(self, data):\n self.state = data.data\n #rospy.loginfo('HEARD')","def do_before_dump(self):\n self.checksummer.prepare_checksums()","def process(self, data):\n\n\t\t# Check if the 802.15.4 packet is valid\n\t\tif makeFCS(data[:-2]) != data[-2:]:\n\t\t\tprint(hue.bad(\"Received invalid packet\"))\n\t\t\treturn\n\n\t\tpacket = Dot15d4FCS(data)\n\n\t\tif packet.fcf_frametype == 2: # ACK\n\t\t\tself.last_ack = packet.seqnum","def initial(self, e):\r\n self._add_message(\"top-INIT;\")\r\n self.foo_ = 0\r\n self.INIT(HsmTst.d2)","def on_t_message(self, message: IncomingMessage) -> None:\n with message.process():\n log.debug(f\"received [x] {message.routing_key}:{message.body}\")","def data_received(self, data):\n\n data = self.remaining_data + data\n\n packetlength = data[0] + 1 if len(data) > 0 else 1\n while packetlength <= len(data):\n packettype = data[1]\n subtype = data[2]\n if (packettype == PACKETTYPE_DSMR and subtype == SUBTYPE_P1):\n dsmr_data = data[4:packetlength]\n super().data_received(dsmr_data)\n data = data[packetlength:]\n packetlength = data[0] + 1 if len(data) > 0 else 1\n\n self.remaining_data = data","def post_process_trap(): \n #################### 0) assign internal values #################### \n from project_parameters import trapType,debug,trapFile,name,driveAmplitude,driveFrequency,Omega,dcplot,weightElectrodes,coefs,ax,az,phi,save,scale\n #from all_functions import find_saddle,plot_potential,dc_potential,set_voltages,exact_saddle,spher_harm_bas,spher_harm_exp,pfit,plotN\n import pickle\n\n with open(trapFile,'rb') as f:\n trap = pickle.load(f)\n\n qe = trap.configuration.charge\n mass = trap.configuration.mass\n Zval = trap.configuration.position\n r0 = trap.configuration.r0\n RFampl = driveAmplitude \n V0 = mass*(2*np.pi*Omega)**2*(r0*10**-3)**2/qe\n X,Y,Z=trap.instance.X,trap.instance.Y,trap.instance.Z \n data = trap.configuration\n dcVoltages = set_voltages()\n ne = len(weightElectrodes)\n E = trap.instance.E\n out = trap.configuration\n if debug.post_process_trap:\n print dcVoltages,np.max(dcVoltages)#np.sum(abs(dcVoltages))\n plotN(dcVoltages,trap,'set DC voltages') \n Vdc = dc_potential(trap,dcVoltages,E)\n #[IDC,JDC,KDC] = find_saddle(Vdc,X,Y,Z,3,Zval) \n #[XDC,YDC,ZDC] = exact_saddle(Vdc,X,Y,Z,3,Zval)\n #XDC,YDC,ZDC = X[IDC],150/scale,Z[KDC]\n #print XDC,YDC,ZDC,IDC,JDC,KDC\n #dcbasis,dcscale= spher_harm_bas(XDC,YDC,ZDC,X,Y,Z,4)\n #QQ = spher_harm_exp(Vdc,dcbasis,dcscale) \n #print QQ[0:9].T\n #1) RF Analysis\n print('RF Analysis') \n Vrf = RFampl*data.EL_RF\n [Irf,Jrf,Krf] = find_saddle(Vrf,X,Y,Z,2,Zval)\n if debug.post_process_trap:\n plot_potential(Vrf,X,Y,Z,dcplot,'weighted RF potential','V_{rf} (eV)',[Irf,Jrf,Krf])\n #2) DC Analysis\n print('DC Analysis')\n trap = dc_potential(trap,dcVoltages,E,update=None)\n Vdc = trap.instance.DC\n [Idc,Jdc,Kdc] = find_saddle(Vdc,X,Y,Z,3,Zval) # only used to calculate error at end\n if debug.post_process_trap:\n plot_potential(Vdc,X,Y,Z,'1D plots','full DC potential')\n #3) determine the exact saddles of the RF and DC\n trap = dc_potential(trap,dcVoltages,E)\n Vdc = trap.instance.DC\n print('Determining exact RF saddle...')\n [Xrf,Yrf,Zrf] = exact_saddle(Vrf,X,Y,Z,2,Zval) \n print('Determining exact DC saddle...')\n [Xdc,Ydc,Zdc] = exact_saddle(Vdc,X,Y,Z,3,Zval)\n #4) determine stray field (beginning of justAnalyzeTrap)\n print('Determining compensation due to E field...')\n nx,ny,nz=X.shape[0],Y.shape[0],Z.shape[0]\n x,y,z = np.zeros((nx,ny,nz)),np.zeros((nx,ny,nz)),np.zeros((nx,ny,nz))\n for i in range(nx):\n for j in range(ny):\n for k in range(nz):\n x[i,j,k] = X[i]\n y[i,j,k] = Y[j]\n z[i,j,k] = Z[k]\n VlessE = Vdc-E[0]*x-E[1]*y-E[2]*z\n [Xdc,Ydc,Zdc] = exact_saddle(VlessE,X,Y,Z,3) \n dist = np.sqrt((Xrf-Xdc)**2+(Yrf-Ydc)**2+(Zrf-Zdc)**2) \n #5) call pfit to built teh total field and determine the trap characteristics\n [fx,fy,fz,theta,Depth,Xe,Ye,Ze] = pfit(Vrf,Vdc,X,Y,Z,Irf,Jrf,Krf)#pfit(trap,E,Freq,RFampl)\n print('Stray field is ({0},{1},{2}) V/m.'.format(scale*E[0],scale*E[1],scale*E[2]))\n print('With this field, the compensation is optimized to {} micron.'.format(scale*dist))\n print('RF saddle: ({0},{1},{2})\\nDC saddle ({3},{4},{5}).'.format(Xrf,Yrf,Zrf,Xdc,Ydc,Zdc)) \n if debug.trap_depth:\n print('The trap escape position is at ({0},{1},{2}) microns, for a trap depth of {3} mV'.format(Xe*scale,Ye*scale,Ze*scale,Depth*scale))\n print('The trap frequencies are fx = {0} MHz, fy = {1} MHz, and fz = {2} MHz'.format(fx*10**-6,fy*10**-6,fz*10**-6))\n #6) Sanity testing; quality check no longer used\n if debug.post_process_trap:\n rfbasis,rfscale= spher_harm_bas(Xrf,Yrf,Zrf,X,Y,Z,2)\n Qrf = spher_harm_exp(Vrf,rfbasis,rfscale) \n if np.sqrt((Xrf-Xdc)**2+(Yrf-Ydc)**2+(Zrf-Zdc)**2)>0.008: \n print('Expanding DC with RF for saniy checking.')\n Qdc = spher_harm_exp(Vdc,rfbasis,rfscale) \n else:\n print('Expanding DC without RF for sanity checking.')\n dcbasis,dcscale= spher_harm_bas(Xdc,Ydc,Zdc,X,Y,Z,2)\n Qdc = spher_harm_exp(Vdc,dcbasis,dcscale) \n Arf = 2*np.sqrt( (3*Qrf[7])**2+(3*Qrf[8])**2 )\n Thetarf = 45*(Qrf[8]/abs(Qrf[8]))-90*np.arctan((3*Qrf[7])/(3*Qrf[8]))/np.pi\n Adc = 2*np.sqrt( (3*Qdc[7])**2+(3*Qdc[8])**2 )\n Thetadc = 45*(Qrf[8]/abs(Qrf[8]))-90*np.arctan((3*Qdc[7])/(3*Qdc[8]))/np.pi\n out.E = E\n out.miscompensation = dist\n out.ionpos = [Xrf,Yrf,Zdc]\n out.ionposIndex = [Irf,Jrf,Krf]\n out.frequency = [fx,fy,fz]\n out.theta = theta\n out.trap_depth = Depth/qe \n out.escapepos = [Xe,Ye,Ze]\n out.Quadrf = 2*np.array([Qrf[7]*3,Qrf[4]/2,Qrf[8]*6,-Qrf[6]*3,-Qrf[5]*3])\n out.Quaddc = 2*np.array([Qdc[7]*3,Qdc[4]/2,Qdc[8]*6,-Qdc[6]*3,-Qdc[5]*3])\n out.Arf = Arf\n out.Thetarf = Thetarf\n out.Adc = Adc\n out.Thetadc = Thetadc\n T = np.array([[2,-2,0,0,0],[-2,-2,0,0,0],[0,4,0,0,0],[0,0,1,0,0],[0,0,0,1,0],[0, 0,0,0,1]])\n Qdrf = out.Quadrf.T\n Qddc = out.Quaddc.T\n out.q = (1/V0)*T*Qdrf\n out.alpha = (2/V0)*T*Qddc\n out.Error = [X[Idc]-Xdc,Y[Jdc]-Ydc,Z[Kdc]-Zdc]\n #7) update the trapping field data structure with instance attributes\n trap.configuration=out\n trap.instance.driveAmplitude = driveAmplitude\n trap.instance.driveFrequency = driveFrequency\n trap.instance.coefs = coefs\n trap.instance.ax = ax\n trap.instance.az = az\n trap.instance.phi = phi\n trap.instance.ppt = True\n trap.instance.out = out\n if save==True:\n print('Saving '+trapFile+' as a data structure...')\n with open(trapFile,'wb') as f:\n pickle.dump(trap,f)\n return 'post_proccess_trap complete' #out # no output needed really","def reset_10gbe():\n snap.write_int('valid_en',0)\n snap.write_int('rst',1)\n time.sleep(1)\n snap.write_int('rst',0)\n snap.write_int('valid_en',3)","def shift_balance(mp, standing_leg):\n pass","def test_back_fill(self):\n self.driver.start_sampling()\n\n # step 2 contains 3 blocks (4 records), start with this and get both since we used them\n # separately in other tests\n self.create_sample_data_set_dir(\"node59p1_step2.dat\", TELEM_DIR, \"node59p1.dat\",\n copy_metadata=False)\n self.assert_data((PhsenParserDataParticle,PhsenControlDataParticle),\n 'test_data_1-2.txt.result.yml', count=4)\n\n # This file has had a section of data replaced with 0s (14171-14675),\n # replacing PH1236501_01D6u51F11341_5D_E538\n self.create_sample_data_set_dir('node59p1_step3.dat', TELEM_DIR, \"node59p1.dat\",\n copy_metadata=False)\n self.assert_data(PhsenParserDataParticle, 'test_data_3.txt.result.yml',\n count=5)\n\n # Now fill in the zeroed section from step3, this should just return the new\n # data \n self.create_sample_data_set_dir('node59p1_step4.dat', TELEM_DIR, \"node59p1.dat\",\n copy_metadata=False)\n self.assert_data(PhsenParserDataParticle, 'test_data_4.txt.result.yml',\n count=1)\n\n # start over now using step 4\n self.driver.stop_sampling()\n # Reset the driver with no memento\n self.driver = self._get_driver_object(memento=None)\n self.driver.start_sampling()\n\n self.clear_async_data()\n self.create_sample_data_set_dir('node59p1_step4.dat', TELEM_DIR, \"node59p1.dat\",\n copy_metadata=False)\n self.assert_data((PhsenParserDataParticle,PhsenControlDataParticle),\n 'test_data_1-4.txt.result.yml', count=10)","def _get_dma(cls, data):\n\t\tdata['dma'] = data['close_10_sma'] - data['close_50_sma']","def sensorverarbeiten(self):\n self.Sensordata.justmw(self)","def recieveArbirator():\n\trospy.init_node('arbitrator') \n\trospy.Subscriber(\"arbitratorOutput\", trackbotMotors, serialTransmit)\n\trospy.Subscriber(\"rxtx/recieveMA\", UInt8MultiArray, recieveSerial)\n\trospy.spin()","def event11512500():\n header(11512500, 1)\n flag.disable(EVENT.CathedralStableFooting)\n\n if_event_flag_on(1, EVENT.OrnsteinAndSmoughDead)\n if_event_flag_off(1, EVENT.AnorLondoGwynWarp)\n if_condition_true(0, 1)\n\n flag.enable(EVENT.CathedralStableFooting)","def test_verify_clear_trace_mid_reassembly(self):\n\n self.pg_enable_capture()\n self.src_if.add_stream(self.fragments_200[0:-1])\n self.pg_start()\n\n self.logger.debug(self.vapi.cli(\"show trace\"))\n self.vapi.cli(\"clear trace\")\n\n self.src_if.add_stream(self.fragments_200[-1])\n self.pg_start()\n packets = self.dst_if.get_capture(len(self.pkt_infos))\n self.verify_capture(packets)","def passPacketToStreamMgr(self, _data, _opcode, _managerCode):\n if _opcode == MSG_SERVER_PACKET:\n \tself.client.streamMgr.handlePacket(_opcode, _managerCode, _data)\n\n else:\n print \"Client: BAD-opcode - %d\" % _opcode\n print \"Client: Opcode Data -\", _data\n \n return","def case():\r\n #ppc = {\"version\": '2'}\r\n ppc = {}\r\n ##----- Power Flow Data -----##\r\n ## system MVA base\r\n ppc[\"baseMVA\"] = 100.0\r\n\r\n ## bus data\r\n # bus_i type Pd Qd Gs Bs area Vm Va baseKV zone Vmax Vmin\r\n ppc[\"bus\"] = array([\r\n [1, 3, 0, 0, 0, 0, 1, 1, 0, 0.4, 1, 1.1, 0.9, 0,0, 0, 0],\r\n [2, 1, 0, 0, 0, 0, 1, 1, 0, 0.4, 1, 1.1, 0.9, 0,0, 0, 0],\r\n [3, 1, 0, 0, 0, 0, 1, 1, 0, 0.4, 1, 1.1, 0.9, 0,0, 0, 0],\r\n [4, 1, 0, 0, 0, 0, 1, 1, 0, 0.4, 1, 1.1, 0.9, 0,0, 0, 0],\r\n [5, 1, 0, 0, 0, 0, 1, 1, 0, 0.4, 1, 1.1, 0.9, 0,0, 0, 0],\r\n [6, 1, 0, 0, 0, 0, 1, 1, 0, 0.4, 1, 1.1, 0.9, 0,0, 0, 0],\r\n [7, 1, 0, 0, 0, 0, 1, 1, 0, 0.4, 1, 1.1, 0.9, 0,0, 0, 0],\r\n [8, 1, 0, 0, 0, 0, 1, 1, 0, 0.4, 1, 1.1, 0.9, 0,0, 0, 0],\r\n [9, 1, 0, 0, 0, 0, 1, 1, 0, 0.4, 1, 1.1, 0.9, 0,0, 0, 0],\r\n [10, 1, 0, 0, 0, 0, 1, 1, 0, 0.4, 1, 1.1, 0.9, 0,0, 0, 0],\r\n [11, 1, 0, 0, 0, 0, 1, 1, 0, 0.4, 1, 1.1, 0.9, 0,0, 0, 0],\r\n [12, 1, 0, 0, 0, 0, 1, 1, 0, 0.4, 1, 1.1, 0.9, 0,0, 0, 0],\r\n [13, 1, 0, 0, 0, 0, 1, 1, 0, 0.4, 1, 1.1, 0.9, 0,0, 0, 0],\r\n [14, 1, 0, 0, 0, 0, 1, 1, 0, 0.4, 1, 1.1, 0.9, 0,0, 0, 0],\r\n [15, 1, 0, 0, 0, 0, 1, 1, 0, 0.4, 1, 1.1, 0.9, 0,0, 0, 0],\r\n [16, 1, 0, 0, 0, 0, 1, 1, 0, 0.4, 1, 1.1, 0.9, 0,0, 0, 0]\r\n ])\r\n\r\n ## generator data\r\n # bus, Pg, Qg, Qmax, Qmin, Vg, mBase, status, Pmax, Pmin, Pc1, Pc2,\r\n # Qc1min, Qc1max, Qc2min, Qc2max, ramp_agc, ramp_10, ramp_30, ramp_q, apf\r\n ppc[\"gen\"] = array([\r\n [1,\t0,\t0,\t10,\t-10,\t1.0224,\t100,\t1,\t10,\t-10,\t0,\t0,\t0,\t0,\t0,\t0,\t0,\t0,\t0,\t0, 0, 0,0, 0, 0],\r\n [3 ,0, 0, 50e-3, -50e-3, 1, 100, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,0, 0, 0],\r\n [5 , 0, 0, 10e-3, -10e-3, 1, 100, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,0, 0, 0],\r\n [10 , 0, 0, 10e-3, -10e-3, 1, 100, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,0, 0, 0],\r\n [13 ,0, 0, 10e-3, -10e-3, 1, 100, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,0, 0, 0],\r\n [15 , 0, 0, 50e-3, -50e-3, 1, 100, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,0, 0, 0]\r\n ])\r\n load_b = array([2, 4, 9, 12, 14])\r\n ppc[\"bus\"][load_b, 2] = multiply(array([-2.1125, -0.2231, -0.1664, -0.0719, -1.4633]).T, 0.03)\r\n ppc[\"bus\"][load_b, 3] = multiply(array([1.6492, 0.4054, 0.8599, 0.8845, 0.6778]).T, 0.03)\r\n ## branch data\r\n # fbus, tbus, r, x, b, rateA, rateB, rateC, ratio, angle, status, angmin, angmax\r\n ppc[\"branch\"] = array([\r\n [1, 2, 0.0, 0.0, 0.0, 250, 250, 250, 0, 0, 1, -360, 360, 0,0, 0, 0, 0,0, 0, 0],\r\n [1, 8, 0.0, 0.0, 0.0, 250, 250, 250, 0, 0, 1, -360, 360, 0,0, 0, 0, 0,0, 0, 0],\r\n [1, 15, 0.0, 0.0, 0.0, 250, 250, 250, 0, 0, 1, -360, 360, 0,0, 0, 0, 0,0, 0, 0],\r\n [2, 3, 0.0, 0.0, 0.0, 250, 250, 250, 0, 0, 1, -360, 360, 0,0, 0, 0, 0,0, 0, 0],\r\n [2, 6, 0.0, 0.0, 0.0, 250, 250, 250, 0, 0, 1, -360, 360, 0,0, 0, 0, 0,0, 0, 0],\r\n [2, 7, 0.0, 0.0, 0.0, 250, 250, 250, 0, 0, 1, -360, 360, 0,0, 0, 0, 0,0, 0, 0],\r\n [3, 4, 0.0, 0.0, 0.0, 250, 250, 250, 0, 0, 1, -360, 360, 0,0, 0, 0, 0,0, 0, 0],\r\n [4, 5, 0.0, 0.0, 0.0, 250, 250, 250, 0, 0, 1, -360, 360, 0,0, 0, 0, 0,0, 0, 0],\r\n [8, 9, 0.0, 0.0, 0.0, 250, 250, 250, 0, 0, 1, -360, 360, 0,0, 0, 0, 0,0, 0, 0],\r\n [8, 12, 0.0, 0.0, 0.0, 250, 250, 250, 0, 0, 1, -360, 360, 0,0, 0, 0, 0,0, 0, 0],\r\n [8, 13, 0.0, 0.0, 0.0, 250, 250, 250, 0, 0, 1, -360, 360, 0,0, 0, 0, 0,0, 0, 0],\r\n [9, 10, 0.0, 0.0, 0.0, 250, 250, 250, 0, 0, 1, -360, 360, 0,0, 0, 0, 0,0, 0, 0],\r\n [9, 14, 0.0, 0.0, 0.0, 250, 250, 250, 0, 0, 1, -360, 360, 0,0, 0, 0, 0,0, 0, 0],\r\n [10, 11, 0.0, 0.0, 0.0, 250, 250, 250, 0, 0, 1, -360, 360, 0,0, 0, 0, 0,0, 0, 0],\r\n [15, 16, 0.0, 0.0, 0.0, 250, 250, 250, 0, 0, 1, -360, 360, 0,0, 0, 0, 0,0, 0, 0]\r\n ])\r\n R1 = 0.43\r\n L1 = 0.4e-3\r\n RS1 = 0.32\r\n LS1 = 0.39e-3\r\n Zbase = (0.4*0.4/100)\r\n branch_phase =array([\r\n [1, 1, 2, 188, R1, L1],\r\n [2, 1 ,8, 346, R1, L1],\r\n [3 ,1 ,15,501, R1 ,L1],\r\n [4, 2, 3, 130, RS1,LS1],\r\n [5, 2, 6, 145, RS1,LS1],\r\n [6, 2 ,7, 157, RS1,LS1],\r\n [7, 3, 4, 185, RS1,LS1],\r\n [8, 4, 5, 1000,RS1,LS1],\r\n [9, 8 ,9, 416, RS1,LS1],\r\n [10,8 ,12,130, RS1,LS1],\r\n [11,8 ,13,121, RS1,LS1],\r\n [12,9 ,10,130, RS1,LS1],\r\n [13,9 ,14,127, RS1,LS1],\r\n [14,10,11,251, RS1,LS1],\r\n [15,15,16,345, RS1,LS1]\r\n ])\r\n ppc[\"branch\"][:, [2,3]] = multiply(array([branch_phase[:, 4]*branch_phase[:, 3], branch_phase[:, 4]*branch_phase[:, 4]*100*pi]).T,0.001/Zbase)\r\n\r\n ##----- OPF Data -----##\r\n ## area data\r\n # area refbus\r\n\r\n\r\n ## generator cost data\r\n # 1 startup shutdown n x1 y1 ... xn yn\r\n # 2 startup shutdown n c(n-1) ... c0\r\n\r\n\r\n return ppc","def event_m20_11_4000000():\n \"\"\"State 0,2: [Lib] Character: Petrified: Key Guide_SubState\"\"\"\n assert event_m20_11_x37(z94=5300, z95=0, z96=15, z97=211000030, z98=0, z99=1600, z100=6, z101=4000010)\n \"\"\"State 1: Finish\"\"\"\n EndMachine()","def write_data(self, data):\n # send data\n for ptr, value in data:\n self._write_byte(ptr, value)\n # set 'data changed'\n self._write_byte(fixed_format['data_changed'][0], 0xAA)\n # wait for station to clear 'data changed'\n while True:\n ack = _decode(self._read_fixed_block(0x0020),\n fixed_format['data_changed'])\n if ack == 0:\n break\n log.debug('waiting for ack')\n time.sleep(6)","def data_received(self, data):\n # self.debug(\"received data=%r\", binascii.hexlify(data))\n self.dispatcher.add_data(data)","def handle_thrusters(self, data):\n self.thrs_current = np.roll(self.thrs_current, -1, axis=1) # roll the vector (shift)\n self.thrs_current[0:4, -1] = data.current[0:4] # selected thrusters only\n\n self.thrs_energy += THR_VNOM * np.trapz(self.thrs_current, dx=THR_FRAME, axis=1)\n self.energy_last = np.sum(self.thrs_energy)","def dataReceived(self, data):\n print \"received:\", data","def handleSystemMessage(self,data):\n message = data.split()[0]\n if message == \"QAError\":\n message,detID = data.split()\n pcaId = self.detectorMapping[detId]\n partition = self.PCAs[pcaId]\n data = {\n \"id\": \"DCS\",\n \"detectorId\": detId,\n \"message\": message,\n }\n self.sendQAMessage(data,partition)\n else:\n super().handleSystemMessage(message)","def test_back(self):\n self.protocol.back()\n expected = [\n \"AWAY :\",\n \"\",\n ]\n self.assertEqualBufferValue(self.transport.value().split(b\"\\r\\n\"), expected)","def __frame_tx(self,data):\n\n if self._spy_frame_tx is not None:\n self._spy_frame_tx(data)\n\n data=self.__pad(data)\n\n if len(data) < self.other_bufferlen:\n self.com.tx(data)\n else:\n chunks = (len(data)-1) // self.other_bufferlen\n #print(\"__frame_tx: %d full chunks + last\"%chunks,flush=True)\n for i in range(0,chunks):\n self.com.tx(data[i*self.other_bufferlen:(i+1)*self.other_bufferlen])\n self.com.rx_ack()\n self.com.tx(data[chunks*self.other_bufferlen:])\n #print(\"__frame_tx done\",flush=True)","def FL_2_mav_sensor(self, data):\n\n (data['velocities/phidot-rad_sec_bf'],\n data['velocities/thetadot-rad_sec_bf'],\n data['velocities/psidot-rad_sec_bf']) = self.convert_body_frame(\n data['attitude/phi-rad'],\n data['attitude/theta-rad'],\n data['velocities/phidot-rad_sec'],\n data['velocities/thetadot-rad_sec'],\n data['velocities/psidot-rad_sec']\n )\n\n #Data treatment\n messagedata = [\n int(data['simulation/sim-time-sec']*self._sec2usec), #time_usec boot time usec int\n data['accelerations/udot-ft_sec2'], #xacc m/s**2 float\n data['accelerations/vdot-ft_sec2'], #yacc m/s**2 float\n data['accelerations/wdot-ft_sec2'], #zacc m/s**2 float\n data['velocities/phidot-rad_sec'], #xgyro rad/s float\n data['velocities/thetadot-rad_sec'], #ygyro rad/s float\n data['velocities/psidot-rad_sec'], #zgyro rad/s float\n data['sensors/magnetometer/X/output'], #xmag Gauss float\n data['sensors/magnetometer/Y/output'], #ymag Gauss float\n data['sensors/magnetometer/Z/output'], #zmag Gauss float\n data['atmosphere/P-psf']*0.478802589, #abs_pr mbar float\n 0.0, #dif_pr mbar float\n data['atmosphere/pressure-altitude'], #pr_alt meter float\n 15.0, #temp C float\n int(8186) #fields_updated (ALL)\n ]\n\n return messagedata","def exittime10_message_received(msg):\n data = IndexIntData.from_msg(msg)\n if data is None:\n _LOGGER.error(\"Undable to parse MQTT message\")\n\n if data.value == 1:\n self._exittime10.add(data.index)\n else:\n self._exittime10.discard(data.index)\n\n _LOGGER.debug(\"Arming >10s: %s\", self._exittime10)\n self.async_write_ha_state()","def mv_all(self):\n # def mv_step(self):\n self.device_reg_data &= ~(0x1 << 2)\n bus.write_byte_data(self.device_address, self.device_reg_mode1, self.device_reg_data)","def event_m20_11_16010():\n \"\"\"State 0,2: [DC] [Preset] Lizard extinction judgment_3 bodies_SubState\"\"\"\n assert event_m20_11_x122(z1=211000016)\n \"\"\"State 1: Finish\"\"\"\n EndMachine()","def event_m20_11_x96(z34=802):\n \"\"\"State 0,1: Stop generator following sound\"\"\"\n StopSoundFollowingGenerator(z34)\n \"\"\"State 2: End state\"\"\"\n return 0","def fix_calldata(self) -> None:\n for step in self.steps:\n step.call_data = step.call_data.replace(\n \"deadbeefdeadbeefdeadbeefdeadbeefdeadbeef\", self.sender[2:]\n )","def __write_block(self, block, data):\n if nfc.nfc_device_set_property_bool(self.__device, nfc.NP_EASY_FRAMING, True) < 0:\n raise Exception(\"Error setting Easy Framing property\")\n if len(data) > 16:\n raise ValueError(\"Data value to be written cannot be more than 16 characters.\")\n abttx = (ctypes.c_uint8 * 18)()\n abttx[0] = self.MC_WRITE\n abttx[1] = block\n abtrx = (ctypes.c_uint8 * 250)()\n for i in range(16):\n abttx[i + 2] = ord((data + \"\\x00\" * (16 - len(data)))[i])\n return nfc.nfc_initiator_transceive_bytes(self.__device, ctypes.pointer(abttx), len(abttx),\n ctypes.pointer(abtrx), len(abtrx), 0)","def hatHandler(valLR, valUD):\n print(\"Digital Hat Changed: L/R:{} U/D:{}\".format(valLR,valUD) )","def event_m20_11_82000():\n \"\"\"State 0,2: [Lib] [Preset] Reproduction fire _SubState\"\"\"\n assert event_m20_11_x53(z73=2011200, z74=2011299)\n \"\"\"State 1: Finish\"\"\"\n EndMachine()","def run(self):\n try:\n self.listener.connect(self.b2bPeer)\n\n print('\\n<1. Version Message>')\n version = self.versionMsg()\n self.messageControl(version)\n\n print('\\n\\n<2. Verack Message>')\n verack = self.verackMsg()\n self.messageControl(verack)\n\n print('\\n\\n<3. GetBlocks Message> - Get Inventory #{}'.format(TARGET_BLOCK))\n target_block = self.getBlocks()\n\n print('\\n\\n<4. GetData Message>')\n get_data = self.getDataMsg(target_block)\n self.largeMessageControl(get_data, 'block')\n except Exception as e:\n print(e)","def climb(self):\n print(\"Inside WoodElf.climb\")","def outReceived(self, data):\n self.protocol.dataReceived(data)","def flight_data_handler(self, event, sender, data):\n self.battery = data.battery_percentage\n self.fly_mode = data.fly_mode\n self.throw_fly_timer = data.throw_fly_timer\n self.throw_ongoing = data.throw_fly_timer > 0\n\n # print(\"fly_mode\",data.fly_mode)\n # print(\"throw_fly_timer\",data.throw_fly_timer)\n # print(\"em_ground\",data.em_ground)\n # print(\"em_sky\",data.em_sky)\n # print(\"electrical_machinery_state\",data.electrical_machinery_state)\n #print(\"em_sky\",data.em_sky,\"em_ground\",data.em_ground,\"em_open\",data.em_open)\n #print(\"height\",data.height,\"imu_state\",data.imu_state,\"down_visual_state\",data.down_visual_state)\n if self.is_flying != data.em_sky: \n self.is_flying = data.em_sky\n log.debug(f\"FLYING : {self.is_flying}\")\n if not self.is_flying:\n self.reset()\n else:\n if self.tracking_after_takeoff:\n log.info(\"Tracking on after takeoff\")\n self.toggle_tracking(True)\n \n log.debug(f\"MODE: {self.fly_mode} - Throw fly timer: {self.throw_fly_timer}\")","def event_m20_11_3020():\n \"\"\"State 0,2: [Preset] Beautiful frog singing voice_flag_SubState\"\"\"\n assert event_m20_11_x110(z24=211000081, z25=802, z26=211020082)\n \"\"\"State 1: Finish\"\"\"\n EndMachine()","def dataReceived(self, data):\n\n def write(result):\n fauxResult = self._addPreIPBusHeader(result)\n print(\"Writing %r\" % fauxResult)\n self.transport.write(fauxResult)\n\n d = self.d()\n d.addCallback(write) # errors are silently ignored!\n d.callback(self._stripPreIPBusHeader(data))","def off(self):\n self.rs485.write_command('#{}bf'.format(self.address))\n time.sleep(1)","def on_R2(self):\r\n self.log()","def event11512008():\n header(11512008)\n end_if_this_event_on()\n if_event_flag_on(1, 11512060) # Ambush done.\n if_event_flag_on(1, EVENT.CapriciousThrallActive) # Thrall still active (e.g. Archive appearance not done).\n if_event_flag_off(1, EVENT.ThrallAmbushOngoing)\n if_player_inside_region(1, REGION.CapriciousThrallTrigger)\n if_condition_true(0, 1)\n message.status_explanation(TEXT.ThrallHasFled)","def dataReceived(self, data):","def slot_depth(self, dummy_sender, data):\r\n (typ, price, _voldiff, total_vol) = data\r\n if self._update_book(typ, price, total_vol):\r\n self.signal_changed(self, None)","def event_m20_11_5000():\n \"\"\"State 0,2: [Preset] Living Altar_SubState\"\"\"\n assert event_m20_11_x82()\n \"\"\"State 1: Rerun\"\"\"\n RestartMachine()","def handle_switch_give_up(self, message):\n # TODO: ADD timer and close\n if message.type == 11 and not self.giving_up:\n #print \"giving up control\"\n ########## Evaluation ######\n print \"Switch migrated: \", self.last_xid\n ########################\n if self.buffer:\n self.handle_write()\n if self.controller.buffer:\n self.controller.handle_write()\n self.giving_up = True\n # Keep processing replies, they are not sent to other controllers.\n if message.type in [3, 6, 8, 19, 21, 23, 25]:\n self.controller.buffer.append(message)","def slot_orderlag(self, dummy_sender, (usec, text)):\r\n self.order_lag = usec\r\n self.order_lag_txt = text\r\n self.do_paint()","def dummyF(self, arg, signal, sender):\n \n if self.isDead == True:\n return\n \n \n #print \"DUMMY\"\n if self.aborting:\n self.aborting = False\n self.isActive = False\n self.__orderQueue.popleft()\n del self.slaveTalk\n self.slaveTalk = None\n# self.__orderQueue.popleft()\n try:\n self.releaseLock()\n except:\n pass\n #print \"No lock, actually.\" \n dispatcher.send('SLAVE_PARSE_QUEUE', self, '')"],"string":"[\n \"def _data_move_out_mc_on_h():\\n\\n pass\",\n \"def onBlock(self, data) :\\n pass\",\n \"def readBumper(self, msg):\\n #\\n # if(msg.state==1):#the bumper is pressed\\n self.executeTrajectory()\",\n \"def _handle_MonitorData (self, event, packet, reverse):\\n pass\",\n \"def handleModuleMessage(self, data, datapathSendFcn):\\n print (\\\"handler not implemented in silverline.\\\")\",\n \"def callback(self, data):\\n if not self.barcode_detected:\\n rospy.loginfo(\\\"Started to dodge !\\\")\\n self.angular_speed = 1.5\\n self.barcode_detected = True\\n self.t0 = time()\",\n \"def step(self):\\r\\n cmd = struct.pack('>B', 54)\\r\\n self.send(cmd)\",\n \"def on_data(data: dict):\\n if 'symbol' in data and 'messageType' in data:\\n if data['symbol'] == 'AAPL' and data['messageType'] == 'tradingstatus':\\n print(\\\"APPL initial message received\\\")\\n event1.set()\\n if data['symbol'] == 'KPTI' and data['messageType'] == 'tradingstatus':\\n print(\\\"KPTI initial message received\\\")\\n event2.set()\",\n \"def bumperCallback(self,data):\\n if data.state == 1 :\\n rospy.loginfo(\\\"Bumper enfonce\\\") \\n self.soundPub.publish(0)\",\n \"def abort_ber_meas(self):\\r\\r\\n loggerCmw = logging.getLogger('abort_ber_meas')\\r\\r\\n self.write('ABORt:WCDMa:SIGN:BER')\\r\\r\\n loggerCmw.info(\\\"Aborting BER measurements\\\")\\r\\r\\n time.sleep(1)\",\n \"def test_back_fill(self):\\n self.driver.start_sampling()\\n\\n # step 2 contains 2 blocks, start with this and get both since we used them\\n # separately in other tests \\n self.clear_async_data()\\n self.create_sample_data_set_dir(\\n \\\"node59p1_step2.dat\\\",\\n TELEM_DIR,\\n \\\"node59p1.dat\\\",\\n copy_metadata=False\\n )\\n self.assert_data(\\n (DostadParserTelemeteredDataParticle, DostadParserTelemeteredMetadataDataParticle),\\n 'test_data_1-2.txt.result.yml',\\n count=3\\n )\\n\\n # This file has had a section of DO data replaced with 0s\\n self.clear_async_data()\\n self.create_sample_data_set_dir(\\n 'node59p1_step3.dat',\\n TELEM_DIR,\\n \\\"node59p1.dat\\\",\\n copy_metadata=False\\n )\\n self.assert_data(\\n DostadParserTelemeteredDataParticle,\\n 'test_data_3.txt.result.yml',\\n count=3\\n )\\n\\n # Now fill in the zeroed section from step3, this should just return the new\\n # data\\n self.clear_async_data()\\n self.create_sample_data_set_dir(\\n 'node59p1_step4.dat',\\n TELEM_DIR,\\n \\\"node59p1.dat\\\",\\n copy_metadata=False\\n )\\n self.assert_data(\\n DostadParserTelemeteredDataParticle,\\n 'test_data_4.txt.result.yml',\\n count=1\\n )\\n\\n # start over now, using step 4\\n self.driver.stop_sampling()\\n\\n # Reset the driver with no memento\\n self.memento = None\\n self.driver = MflmDOSTADDataSetDriver(\\n self._driver_config()['startup_config'],\\n self.memento,\\n self.data_callback,\\n self.state_callback,\\n self.event_callback,\\n self.exception_callback)\\n self.driver.start_sampling()\\n\\n self.clear_async_data()\\n self.create_sample_data_set_dir(\\n 'node59p1_step4.dat',\\n TELEM_DIR,\\n \\\"node59p1.dat\\\",\\n copy_metadata=False\\n )\\n self.assert_data(\\n (DostadParserTelemeteredDataParticle, DostadParserTelemeteredMetadataDataParticle),\\n 'test_data_1-4.txt.result.yml',\\n count=7\\n )\",\n \"def __flight_data_handler(self, event, sender, data):\\n self.battery = data.battery_percentage\\n self.fly_mode = data.fly_mode\\n self.throw_fly_timer = data.throw_fly_timer\\n self.throw_ongoing = data.throw_fly_timer > 0\\n\\n if self.prev_flight_data != str(data):\\n print(data)\\n self.prev_flight_data = str(data)\\n self.flight_data = data\\n\\n if self.is_flying != data.em_sky:\\n self.is_flying = data.em_sky\\n log.debug(f\\\"FLYING : {self.is_flying}\\\")\\n if not self.is_flying:\\n self.reset()\\n else:\\n if self.tracking_after_takeoff:\\n log.info(\\\"Tracking on after takeoff\\\")\\n self.toggle_tracking(True)\\n\\n # if self.write_header_log:\\n # self.write_header_log = False\\n # self.log_file_log.write(f\\\"{data.format_cvs_header()}\\\\n\\\")\\n # self.log_file_log.write(f\\\"{data.format_cvs(0)}\\\\n\\\")\",\n \"def modify_data(self, message):\\n assert message.arbitration_id == self.can_id, \\\"You cannot modify the can identifier\\\"\\n self.message = message\\n self._tx_setup()\",\n \"def _handle_block_data(self, block: Eth1Block) -> None:\\n # Check timestamp.\\n if len(self._block_timestamp_to_number) != 0:\\n # Sanity check.\\n if block.timestamp < self._largest_block_timestamp:\\n raise Eth1MonitorValidationError(\\n \\\"Later block with earlier timestamp: \\\"\\n f\\\"largest_timestamp={self._largest_block_timestamp}, \\\"\\n f\\\"block.timestamp={block.timestamp}\\\"\\n )\\n self._block_timestamp_to_number[block.timestamp] = block.number\\n self._largest_block_timestamp = block.timestamp\",\n \"def _hook_data(self, data):\\n if self.data_hook is not None:\\n self.data_hook(data)\",\n \"def after_process(self, packet, ret_packet):\\n pass\",\n \"def parse_MTData2(self, data):\\n # Functions to parse each type of packet\\n def parse_orientation(data_id, content):\\n o = struct.unpack('!'+3*self._ffmt, content)\\n if self._coorSys == 'ENU':\\n self._imu.orientation.x = o[0]\\n self._imu.orientation.y = o[1]\\n self._imu.orientation.z = o[2]\\n elif self._coorSys == 'NED':\\n self._imu.orientation.x = o[0]\\n self._imu.orientation.y = -o[1]\\n self._imu.orientation.z = -o[2]\\n self._getAll = True\\n\\n def parse_acceleration(data_id, content):\\n o = struct.unpack('!'+3*self._ffmt, content)\\n if self._coorSys == 'ENU':\\n self._imu.linear_acceleration.x = o[0]\\n self._imu.linear_acceleration.y = o[1]\\n self._imu.linear_acceleration.z = o[2]\\n elif self._coorSys == 'NED':\\n self._imu.linear_acceleration.x = o[0]\\n self._imu.linear_acceleration.y = -o[1]\\n self._imu.linear_acceleration.z = -o[2]\\n\\n def parse_angular_velocity(data_id, content):\\n o = struct.unpack('!'+3*self._ffmt, content)\\n if self._coorSys == 'ENU':\\n self._imu.angular_velocity.x = o[0]\\n self._imu.angular_velocity.y = o[1]\\n self._imu.angular_velocity.z = o[2]\\n if self._coorSys == 'NED':\\n self._imu.angular_velocity.x = o[0]\\n self._imu.angular_velocity.y = -o[1]\\n self._imu.angular_velocity.z = -o[2]\\n\\n # data object\\n while data:\\n data_id, size = struct.unpack('!HB', data[:3])\\n # determind a data format (double or float)\\n\\n content = data[3:3+size]\\n data = data[3+size:]\\n group = data_id & 0xFFF0\\n\\n if group == XDIGroup.OrientationData:\\n parse_orientation(data_id, content)\\n elif group == XDIGroup.Acceleration:\\n parse_acceleration(data_id, content)\\n elif group == XDIGroup.AngularVelocity:\\n parse_angular_velocity(data_id, content)\",\n \"def handle_data(self, line):\\n\\n # AorM - 0: M / 1: A\\n feedback_AorM = ord(line[4])\\n\\n # Gear - 0: B / 1: N / 2: D\\n feedback_gear = ord(line[5])\\n\\n # Speed\\n feedback_KPH = (ord(line[6]) + ord(line[7]) * 256) / 10\\n feedback_speed = self.kph2mps(value=feedback_KPH)\\n\\n # Steer\\n feedback_DEG = ord(line[8]) + ord(line[9]) * 256\\n\\n if feedback_DEG >= 23768:\\n feedback_DEG -= 65536\\n\\n if feedback_DEG != 0:\\n feedback_DEG /= 71.0\\n\\n feedback_steer = m.radians(feedback_DEG)\\n\\n # Brake\\n feedback_brake = ord(line[10])\\n\\n # Encoder\\n self.feedback_encoder = (ord(line[11]) + ord(line[12]) * 256 + ord(\\n line[13]) * 256 * 256 + ord(line[14]) * 256 * 256 * 256)\\n\\n if self.feedback_encoder >= 2147483648:\\n self.feedback_encoder -= 4294967296\\n\\n # print(self.feedback_encoder)\\n\\n data = encoderMsg()\\n\\n data.speed = feedback_speed\\n data.steer = feedback_steer\\n data.steer = feedback_DEG\\n data.brake = feedback_brake\\n data.gear = feedback_gear\\n data.AorM = feedback_AorM\\n data.Encoder = self.feedback_encoder\\n\\n self.feedbackMsg = data\\n encoder_pub.publish(data)\",\n \"def process_bump_sensing(self, data):\\n if data.state == BumperEvent.PRESSED:\\n self.bump = True\\n self.bumpDir = data.bumper\\n rospy.loginfo(\\\"Bumper Event :)\\\")\\n rospy.loginfo(data.bumper)\",\n \"def handleModuleMessage(self, data):\\n # print (\\\"got a message in silverline module.\\\")\\n (messageType, content) = self.ofxAgent.unpackModuleMessage(data)\\n # print \\\"\\\\tmessage type: %s\\\"%messageType\\n if messageType == ENABLEDECLASSIFIER:\\n self.enableDeclassifier()\\n elif messageType == ADDFLOWPERMISSION:\\n self.addFlowPermission(content)\",\n \"def handle_sensor_data(data):\\n \\n #print dir( data )\\n D.data = data\\n\\n #Check for a bump\\n if data.bumpRight or data.bumpLeft:\\n print \\\"Bumped!\\\"\\n\\n\\n #Check if play button was pressed\\t\\n if data.play:\\n\\tprint \\\"Play button pressed!\\\"\\n\\tStateMachine.state_stop()\\n\\trospy.signal_shutdown(\\\"play button pressed\\\")\",\n \"def bruno_mes(self):\\n MI = -125\\n MA = 125\\n INCR = 19\\n####################################################################\\n ### CHANNEL 1\\n self.write('CHN 1')\\n self.write('CHN?')\\n print 'Acting on channel:',self.read()\\n self.write('WAVE ARB')\\n self.write('ARBLOAD ARB1')\\n self.write('FREQ 100')\\n self.write('DCOFFS 0.05')\\n self.write('AMPL 0.1')\\n \\n l =(125,-125,125)#arange(MI,MA,INCR) # the ramp\\n# lll = copy(l)[::-1][1:-1]\\n# l = concatenate((l,lll))\\n self.write_array_to_byte(l,1)\",\n \"def mv_step(self):\\n # def mv_all(self):\\n self.device_reg_data &= ~(0x1 << 3)\\n bus.write_byte_data(self.device_address, self.device_reg_mode1, self.device_reg_data)\",\n \"def event0():\\n header(0, 0)\\n\\n if DEBUG.GET_CHTHONIC_SPARK:\\n item.award_item_to_host_only(1600)\\n if DEBUG.GET_DARKMOON_SEANCE_RING:\\n item.award_item_to_host_only(1600310)\\n if DEBUG.GWYNDOLIN_DEAD:\\n flag.enable(EVENT.GwyndolinDead)\\n item.award_item_to_host_only(2600)\\n if DEBUG.ORNSTEIN_AND_SMOUGH_DEAD:\\n flag.enable(EVENT.OrnsteinAndSmoughDead)\\n if DEBUG.DARK_ANOR_LONDO:\\n flag.enable(EVENT.OrnsteinAndSmoughDead)\\n flag.enable(EVENT.GwyndolinDead)\\n flag.enable(EVENT.DarkAnorLondo)\\n if DEBUG.GET_LAUTREC_BLACK_EYE_ORB:\\n item.award_item_to_host_only(2034)\\n if DEBUG.CAPRICIOUS_THRALL_ACTIVE:\\n flag.enable(EVENT.CapriciousThrallActive)\\n if DEBUG.GET_BUTTERFLY_SOUL:\\n item.award_item_to_host_only(2530)\\n item.award_item_to_host_only(0)\\n if DEBUG.DISABLE_FOG_ARCHER:\\n chr.disable(CHR.SilverKnightArcherNearBossFog)\\n if DEBUG.JAREEL_DEAD:\\n flag.enable(EVENT.JareelDead)\\n\\n skip_if_event_flag_off(1, EVENT.OrnsteinAndSmoughDead)\\n map.register_bonfire(11510920, 1511950)\\n for bonfire_flag, bonfire_id, kindle_level in zip((11510992, 11510984, 11510976), (1511960, 1511961, 1511962),\\n (10, 0, 0)):\\n map.register_bonfire(bonfire_flag, bonfire_id, initial_kindle_level=kindle_level)\\n map.register_ladder(11510010, 11510011, 1511140)\\n map.register_ladder(11510012, 11510013, 1511141)\\n\\n # Make elevator work immediately (and skip cutscene).\\n flag.enable(11510305)\\n\\n flag.disable(11510304)\\n skip_if_client(2)\\n obj.disable(1511994)\\n sfx.delete_map_sfx(1511995, False)\\n obj.disable(1511310)\\n for hitbox_id in (1513301, 1513302, 1513303):\\n hitbox.disable_hitbox(hitbox_id)\\n skip_if_event_flag_off(1, 11510300)\\n skip_if_event_flag_off(6, 11510303)\\n flag.disable(11510301)\\n flag.disable(11510302)\\n flag.enable(11510303)\\n anim.end_animation(1511300, 53)\\n hitbox.enable_hitbox(1513303)\\n skip(13)\\n skip_if_event_flag_off(6, 11510302)\\n flag.disable(11510301)\\n flag.enable(11510302)\\n flag.disable(11510303)\\n anim.end_animation(1511300, 50)\\n hitbox.enable_hitbox(1513302)\\n skip(6)\\n skip_if_event_flag_off(5, 11510301)\\n flag.enable(11510301)\\n flag.disable(11510302)\\n flag.disable(11510303)\\n anim.end_animation(1511300, 51)\\n hitbox.enable_hitbox(1513301)\\n\\n obj.disable(1511450)\\n flag.disable(11510460)\\n run_event_with_slot(11510090, 0, (1511700, 1511701, 1512600, 1512601))\\n run_event_with_slot(11510090, 1, (1511702, 1511703, 1512602, 1512603))\\n\\n for event_id in (11515040, 11515041, 11515042):\\n run_event(event_id)\\n\\n run_event(11510200) # Rotating lever to open palace.\\n run_event(11510205) # (New) Rotating lever to open palace in Dark Anor Londo (Jareel must be dead).\\n run_event(11510201) # Palace locked from the outside.\\n run_event(11510100) # Break chandelier.\\n run_event(11510210) # Open one-way gate to blacksmith.\\n run_event(11510211) # Blacksmith gate is locked.\\n run_event(11510220) # First activation of gondola. (Now pre-enabled.)\\n run_event(11510300) # Main gondola activation.\\n run_event(11510319) # Gondola flags.\\n run_event(11510340) # Gondola navimesh.\\n run_event(11510350) # Gondola sync.\\n run_event(11510310) # Gondola lever can't be pushed.\\n run_event(11515250) # Painting Guardian ambush.\\n run_event(11515251) # Provoke a Silver Knight.\\n run_event(11510110) # Open door to Sun Chamber. (Now requires key.)\\n run_event(11510111) # (New) Sun Chamber is locked.\\n run_event(11510400) # Trigger Dark Anor Londo.\\n run_event(11510401) # Disable Darkmoon Tomb statue.\\n run_event(11510230) # Enter Painted World if you have the Painted Doll.\\n run_event(11510240) # Return to Sen's Fortress.\\n run_event(11515050) # Offend Pale Demon and cut off Fortress return.\\n run_event(11510120) # Enable special effect 4501 in Darkmoon Tomb.\\n run_event(11510130) # (Updated) Control Dark Anor Londo enemies.\\n # (Gone) Player always respawns at 'Anor Londo' bonfire in Dark Anor Londo.\\n run_event(11510460) # Kneel to Darkmoon Covenant.\\n run_event(11510462) # Two-frame sync for above.\\n run_event(11510461) # Kneel to Darkmoon Covenant, simple version.\\n run_event(11510140) # Move your bloodstain out of endless Gwyndolin corridor when you win.\\n run_event(11510150) # Trigger flag for quivering Black Eye Orb.\\n run_event(11512008) # (New) Message that Thrall has fled higher again.\\n\\n run_event(11512043) # (NEW) Monitor resting at Sun Chamber bonfire for warping (11512045).\\n run_event(11512044) # (NEW) Monitor resting at Gwyn's Altar bonfire for warping (11512046).\\n\\n run_event(151)\\n run_event(11510215)\\n\\n # Sentinel shield parts.\\n for slot, sentinel_id in zip(range(14), range(1510400, 1510414)):\\n run_event_with_slot(11515060, slot, (sentinel_id,))\\n\\n # Gargoyle tails removed.\\n\\n # One-way shortcut doors.\\n run_event_with_slot(11510260, 0, (11510251, 1512251, 1512250), 'iii')\\n run_event_with_slot(11510260, 1, (11510257, 1512253, 1512252), 'iii')\\n run_event_with_slot(11510260, 2, (11510258, 1512255, 1512254), 'iii')\\n\\n # ORNSTEIN AND SMOUGH / GWYN, LORD OF LIGHT\\n\\n sound.disable_map_sound(1513800) # Ornstein and Smough.\\n sound.disable_map_sound(1513805) # Gwyn.\\n\\n # GWYN:\\n run_event(11512200) # Gwyn trigger.\\n run_event(11512201) # Gwyn death.\\n skip_if_event_flag_on(22, EVENT.AnorLondoGwynWarp) # Skip O&S events (light and dark). Keep an eye on length.\\n\\n skip_if_event_flag_off(10, EVENT.OrnsteinAndSmoughDead)\\n # Already dead:\\n anim.force_animation(1511401, 0, loop=True) # Start elevators\\n anim.force_animation(1511402, 0, loop=True)\\n run_event(11515392)\\n for fog_wall, fog_sfx in zip((1511990, 1511992, 1511988), (1511991, 1511993, 1511989)):\\n obj.disable(fog_wall)\\n sfx.delete_map_sfx(fog_sfx, False)\\n skip(11)\\n\\n # Alive:\\n for relative_id in (5390, 5391, 5393, 5392, 1, 5394, 5395, 5396, 5397, 5398, 5399):\\n run_event(BASE_FLAG + relative_id)\\n\\n # FORSAKEN KNIGHT ORNSTEIN & SUN-EATER SMOUGH\\n\\n run_event(11515492) # Trigger. Handles all other events within.\\n run_event(11512001) # Die.\\n\\n # DARK SUN GWYNDOLIN\\n\\n sound.disable_map_sound(1513802)\\n skip_if_event_flag_off(6, EVENT.GwyndolinDead)\\n # Already dead:\\n run_event(11515382)\\n obj.disable(1511890)\\n sfx.delete_map_sfx(1511891, False)\\n obj.disable(1511892)\\n sfx.delete_map_sfx(1511893, False)\\n skip(13)\\n # Alive:\\n # Disable Jareel fog (otherwise visible in boss start cutscene).\\n obj.disable(1511970)\\n sfx.delete_map_sfx(1511971, False)\\n obj.disable(1511972)\\n sfx.delete_map_sfx(1511973, False)\\n for relative_id in (5380, 5381, 5383, 5382, 900, 5384, 5385, 5386, 450):\\n run_event(BASE_FLAG + relative_id)\\n\\n # NEW: Abyssal King Jareel.\\n sound.disable_map_sound(1513803)\\n skip_if_event_flag_off(6, EVENT.JareelDead)\\n # Already dead:\\n run_event(11515372)\\n obj.disable(1511970)\\n sfx.delete_map_sfx(1511971, False)\\n obj.disable(1511972)\\n sfx.delete_map_sfx(1511973, False)\\n skip(7)\\n # Alive:\\n run_event(11515370)\\n run_event(11515371)\\n run_event(11515373)\\n run_event(11515372)\\n run_event(11515374)\\n run_event(11515375)\\n run_event(11510901)\\n\\n # Open three doors for enemies (I think).\\n for relative_door_id, base_slot in zip((251, 257, 258), (0, 20, 40)):\\n run_event_with_slot(11510710, base_slot, (BASE_FLAG + relative_door_id, 6750,\\n 1512000 + relative_door_id, 1512000 + relative_door_id - 1))\\n for i, relative_enemy_id in enumerate((300, 301, 302, 305, 320, 321, 322, # Silver Knights\\n 323, 324, 325, 326, 327, 328, 329, 500,\\n 177, 178, 179, 180, 181, 181, 182, 183, # Darkwraiths\\n 184, 185, 186, 187, 188, 189, 190)):\\n run_event_with_slot(\\n 11510710, base_slot + i + 1, (BASE_FLAG + relative_door_id, 1510000 + relative_enemy_id,\\n 1512000 + relative_door_id, 1512000 + relative_door_id - 1))\\n\\n # Mimic triggers.\\n for slot, relative_mimic_id in enumerate(range(4)):\\n run_event_with_slot(11515200, slot, (1510200 + relative_mimic_id,))\\n run_event_with_slot(11515210, slot, (1510200 + relative_mimic_id,))\\n run_event_with_slot(11515220, slot, (1510200 + relative_mimic_id,))\\n run_event_with_slot(11515230, slot, (1510200 + relative_mimic_id,))\\n run_event_with_slot(11515240, slot, (1510200 + relative_mimic_id, 1512010 + relative_mimic_id))\\n run_event_with_slot(11510850, slot, (1510200 + relative_mimic_id,))\\n run_event_with_slot(11515190, slot, (1510200 + relative_mimic_id,))\\n\\n # Treasure chests.\\n for i in range(1, 21):\\n if i == 12 or i == 19:\\n continue\\n run_event_with_slot(11510600, i, (1511650 + i, 11510600 + i))\\n anim.end_animation(1511662, 0) # Gwyn's chest already looted\\n # Only activate chapel chest before Dark Anor Londo (replaced by Mimic).\\n skip_if_event_flag_on(1, EVENT.DarkAnorLondo)\\n run_event_with_slot(11510600, 19, (1511669, 11510619))\\n\\n # Non-respawning enemies.\\n run_event_with_slot(11510860, 0, (1510250, 0)) # Haunting Semblance\\n run_event_with_slot(11510860, 3, (6640, 0)) # Dark Anor Londo Knight 1\\n run_event_with_slot(11510860, 4, (6650, 0)) # Dark Anor Londo Knight 2\\n run_event_with_slot(11510870, 0, (CHR.DarkmoonGuardian,))\\n\\n # NEW: Allied Silver Knights and Sentinels stop respawning in Dark Anor Londo if killed (unless Jareel is dead).\\n for slot, enemy_id in enumerate(DarkAnorLondoAllies):\\n run_event_with_slot(11512050, slot, (enemy_id,))\\n run_event_with_slot(11512150, slot, (enemy_id,)) # They also turn hostile again if attacked in Dark AL.\\n\\n # NEW: Darkwraiths stop respawning in Dark Anor Londo if killed (unless Jareel is alive).\\n for slot, enemy_id in enumerate(Darkwraiths):\\n run_event_with_slot(11512100, slot, (enemy_id,))\\n\\n # NEW: Scripted rampart battle between archers and Darkwraiths. Also disables gravity\\n # for the high archer.\\n run_event(11512040)\\n\\n # NEW: Scripted battle between Darkwraith and Pale Demons.\\n run_event(11512041)\\n\\n # NEW: Angry Giant Blacksmith in Dark Anor Londo.\\n run_event(11512042)\\n\\n # NEW: Capricious Thrall one-off attack on the rooftop.\\n sound.disable_map_sound(1513804)\\n obj.disable(1511974)\\n sfx.delete_map_sfx(1511975, False)\\n obj.disable(1511976)\\n sfx.delete_map_sfx(1511977, False)\\n obj.disable(1511978)\\n sfx.delete_map_sfx(1511979, False)\\n run_event(11512060) # Trigger and timer.\\n run_event(11512061) # Death.\",\n \"def dataPtoTB(self,u):\\n n = self.ues[u].prbs\\n [tbSbits,mod,bits,mcs__] = self.setMod(u,n)\\n if self.schType[0:2]=='PF':\\n if len(self.ues[u].pastTbsz)>self.promLen:\\n self.ues[u].pastTbsz.popleft()\\n self.ues[u].pastTbsz.append(self.ues[u].tbsz)\\n\\n self.ues[u].tbsz = tbSbits\\n self.ues[u].MCS = mcs__\\n self.setBLER(u)\\n tbSize = int(float(tbSbits)/8) # TB size in bytes\\n self.printDebDataDM('TBs: '+str(tbSize)+' nrb: '+str(n)+' FreeSp: '+str(self.queue.getFreeSpace())+'<br>')\\n pks_s = 0\\n list_p = []\\n while pks_s<tbSize and len(self.ues[u].bearers[0].buffer.pckts)>0:\\n pacD = self.ues[u].bearers[0].buffer.removePckt()\\n pks_s = pks_s + pacD.size\\n list_p.append(pacD.secNum)\\n\\n insrt = self.insertTB(self.ues[u].TBid,mod,u,'data',list_p,n,min(int(pks_s),tbSize))\\n if (pks_s - tbSize)>0:\\n pacD.size = pks_s - tbSize\\n self.ues[u].bearers[0].buffer.insertPcktLeft(pacD)\\n return self.ues[u].symb\",\n \"def decode_faceshift_datastream(self, data):\\n \\n #block_id = struct.unpack_from('H', data)\\n #print(\\\"Received block id \\\" + str(block_id)) ;\\n\\n offset = 0\\n block_id, version, block_size = struct.unpack_from('HHI', data, offset)\\n \\n #print(\\\"ID, v, size = \\\" + str(block_id) + \\\",\\\" + str(version) + \\\",\\\" + str(block_size) )\\n \\n offset += 8\\n\\n if(block_id == BLOCK_ID_TRACKING_STATE):\\n n_blocks, = struct.unpack_from('H', data, offset)\\n #print(\\\"n_blocks = \\\" + str(n_blocks))\\n offset += 2\\n\\n track_ok = 0 # Will be a byte: 1 if tracking ok, 0 otherwise.\\n head_rotation_quat = None # Will be filled with the rotation using mathutils.Quaternion\\n blend_shape_values = [] # Will be a list of float in the range 0-1\\n #eyes_values = None # Will be a sequence of 4 angle values\\n markers_position = [] # Will be a list of mathutils.Vector\\n \\n curr_block = 0\\n while(curr_block < n_blocks):\\n block_id, version, block_size = struct.unpack_from('HHI', data, offset)\\n #print(\\\"ID, v, size = \\\" + str(block_id) + \\\",\\\" + str(version) + \\\",\\\" + str(block_size) )\\n \\n # put the offset at the beginning of the block\\n offset += 8\\n \\n if(block_id == 101): # Frame Information blobk (timestamp and tracking status)\\n ts, track_ok = struct.unpack_from('dB', data, offset)\\n #print(\\\"timestamp, track_ok \\\" + str(ts) + \\\", \\\" + str(track_ok) )\\n #offset += 9\\n elif(block_id == 102): # Pose block (head rotation and position)\\n x,y,z,w = struct.unpack_from('ffff', data, offset)\\n #head_rotation_quat = mathutils.Quaternion((w,x,y,z))\\n elif(block_id == 103): # Blendshapes block (blendshape values)\\n n_coefficients, = struct.unpack_from('I', data, offset)\\n #print(\\\"Blend shapes count=\\\"+ str(n_coefficients) )\\n i = 0\\n coeff_list = \\\"\\\"\\n while(i < n_coefficients):\\n # Offset of the block, plus the 4 bytes for int n_coefficients, plus 4 bytes per float\\n val, = struct.unpack_from('f', data, offset + 4 + (i*4))\\n blend_shape_values.append(val)\\n coeff_list += repr(val) + \\\" \\\"\\n i += 1\\n print(\\\"Values: \\\" + coeff_list)\\n elif(block_id == 104): # Eyes block (eyes gaze)\\n leye_theta, leye_phi, reye_theta, reye_phi = struct.unpack_from('ffff', data, offset)\\n elif(block_id == 105): # Markers block (absolute position of mark points)\\n n_markers, = struct.unpack_from('H', data, offset)\\n #print(\\\"n markers=\\\"+str(n_markers))\\n i = 0\\n while(i < n_markers):\\n # Offset of the block, plus the 2 bytes for int n_markers, plus 4 bytes for each x,y,z floats\\n x, y, z = struct.unpack_from('fff', data, offset + 2 + (i*4*3))\\n #print(\\\"m\\\" + str(i) + \\\" \\\" + str(x) + \\\"\\\\t\\\" + str(y) + \\\"\\\\t\\\" + str(z))\\n markers_position.append(mathutils.Vector((x,y,z)))\\n i += 1\\n \\n curr_block += 1\\n offset += block_size\\n \\n msg = fsMsgTrackingState()\\n\\n msg.m_timestamp = ts\\n\\n self.pub.publish(msg)\\n\\n # end -- while on blocks. Track State scan complete\",\n \"def handle_data(self, data):\\n if verbose(): print(\\\"TIParser.handle_data(self, '%s')\\\" % (data))\\n pass\",\n \"def packet_handler(pkt):\\n if pkt[Ether].type == 0x800:\\n if pkt[IP].dst == VICTIM_IP:\\n if pkt[Ether].dst == HACKER_MAC:\\n print(pkt.summary()) # print spoofed packet\\n pkt[Ether].dst = VICTIM_MAC\\n PACKET_QUEUE.insert(0, pkt)\",\n \"def on_b(self):\\r\\n self.log()\",\n \"def process_event(self, event):\\n\\n trap = v2c.TRAP()\\n self._encoded_oids = []\\n self._encoded_vals = []\\n\\n # Since this is a v2 trap, we must include sysUpTime as well\\n # as sysTrapOID to indicate what the OID of this trap.\\n self._add_varbind(SnmpTrapEventHandler.sysUpTime,\\n SnmpTrapEventHandler.TIMETICKS.encode(int(time())))\\n self._add_varbind(SnmpTrapEventHandler.sysTrapOID,\\n self.trapoid)\\n\\n # We do late encoding of the value data because it may contain\\n # positional parameters that need to be expanded on a per\\n # event basis. \\n for oid, type, value in self.varbinds:\\n self._add_varbind(oid, self._encode_value(type, \\n value, \\n event.data.match))\\n # Encode the trap and send it to all hosts.\\n encoded_trap = trap.encode(encoded_oids=self._encoded_oids,\\n encoded_vals=self._encoded_vals)\\n for host in self.hosts:\\n host.send(encoded_trap)\\n\\n return 1\",\n \"def write_versa5(self,addr,data):\\n time.sleep(0.002)\\n data = data & 0x0ff\\n addr = addr & 0x0ff\\n ## i2caddr is 7 bits, no read write\\n ## Bit 8 is set to indicate stop to HL2\\n ## i2caddr = 0x80 | (0xd4 >> 1) ## ea\\n cmd = bytes([0x06,0xea,addr,data])\\n return self.command(0x3c,cmd)\",\n \"def onAdaptorData(self, message):\\n #logging.debug(\\\"%s onadaptorData, message: %s\\\", ModuleName, message)\\n if message[\\\"characteristic\\\"] == \\\"acceleration\\\":\\n for a in self.accel:\\n if a.id == self.idToName[message[\\\"id\\\"]]: \\n a.processAccel(message)\\n break\\n elif message[\\\"characteristic\\\"] == \\\"temperature\\\":\\n for t in self.temp:\\n if t.id == self.idToName[message[\\\"id\\\"]]:\\n t.processTemp(message)\\n break\\n elif message[\\\"characteristic\\\"] == \\\"ir_temperature\\\":\\n for t in self.irTemp:\\n if t.id == self.idToName[message[\\\"id\\\"]]:\\n t.processIrTemp(message)\\n break\\n elif message[\\\"characteristic\\\"] == \\\"gyro\\\":\\n for g in self.gyro:\\n if g.id == self.idToName[message[\\\"id\\\"]]:\\n g.processGyro(message)\\n break\\n elif message[\\\"characteristic\\\"] == \\\"magnetometer\\\":\\n for g in self.magnet:\\n if g.id == self.idToName[message[\\\"id\\\"]]:\\n g.processMagnet(message)\\n break\\n elif message[\\\"characteristic\\\"] == \\\"buttons\\\":\\n for b in self.buttons:\\n if b.id == self.idToName[message[\\\"id\\\"]]:\\n b.processButtons(message)\\n break\\n elif message[\\\"characteristic\\\"] == \\\"humidity\\\":\\n for b in self.humidity:\\n if b.id == self.idToName[message[\\\"id\\\"]]:\\n b.processHumidity(message)\\n break\\n elif message[\\\"characteristic\\\"] == \\\"binary_sensor\\\":\\n for b in self.binary:\\n if b.id == self.idToName[message[\\\"id\\\"]]:\\n b.processBinary(message)\\n break\\n elif message[\\\"characteristic\\\"] == \\\"power\\\":\\n for b in self.power:\\n if b.id == self.idToName[message[\\\"id\\\"]]:\\n b.processPower(message)\\n break\\n elif message[\\\"characteristic\\\"] == \\\"battery\\\":\\n for b in self.battery:\\n if b.id == self.idToName[message[\\\"id\\\"]]:\\n b.processBattery(message)\\n break\\n elif message[\\\"characteristic\\\"] == \\\"connected\\\":\\n for b in self.connected:\\n if b.id == self.idToName[message[\\\"id\\\"]]:\\n b.processConnected(message)\\n break\\n elif message[\\\"characteristic\\\"] == \\\"luminance\\\":\\n for b in self.luminance:\\n if b.id == self.idToName[message[\\\"id\\\"]]:\\n b.processLuminance(message)\\n break\",\n \"def _do_some_logic(self, packet):\\n\\n\\n pass\",\n \"def handleSystemMessage(self,data):\\n message = data.split()[0]\\n if message == \\\"detectorError\\\":\\n #handle dcs detector error\\n message,detId = data.split()\\n pcaId = self.detectorMapping[detId]\\n partition = self.PCAs[pcaId]\\n data = {\\n \\\"id\\\": \\\"DCS\\\",\\n \\\"detectorId\\\": detId,\\n \\\"message\\\": message,\\n }\\n self.sendDCSMessage(data,partition)\\n else:\\n super().handleSystemMessage(message)\",\n \"def process_MAM_data(self, spec):\\n \\n # Hack bucket if spec is loaded from the dataloader\\n if len(spec.shape) == 4: # Bucketing should cause acoustic feature to have shape 1xBxTxD\\n spec = spec.squeeze(0)\\n # add arbitary batch axis B if input `spec` has shape of TxD\\n elif len(spec.shape) == 2:\\n spec = spec.unsqueeze(0)\\n # input `spec` should have shape BxTxD\\n elif len(spec.shape) != 3:\\n raise ValueError('Input argument `spec` has invalid shape: {}'.format(spec.shape))\\n\\n # Down sample\\n spec_stacked = self.down_sample_frames(spec) # (batch_size, seq_len, mel_dim * dr)\\n\\n # Record length for each uttr\\n spec_len = np.sum(np.sum(spec_stacked.data.numpy(), axis=-1) != 0, axis=-1)\\n spec_len = [int(sl) for sl in spec_len]\\n\\n batch_size = spec_stacked.shape[0]\\n seq_len = spec_stacked.shape[1]\\n\\n pos_enc = self.position_encoding(seq_len, batch_size) # (batch_size, seq_len, hidden_size)\\n attn_mask = np.ones((batch_size, seq_len)) # (batch_size, seq_len)\\n\\n # zero vectors for padding dimension\\n for idx in range(len(spec_stacked)):\\n pos_enc[idx][spec_len[idx]:] = 0 \\n attn_mask[idx][spec_len[idx]:] = 0 \\n\\n spec_stacked = spec_stacked.to(device=self.device, dtype=torch.float32)\\n pos_enc = torch.FloatTensor(pos_enc).to(device=self.device, dtype=torch.float32)\\n attn_mask = torch.FloatTensor(attn_mask).to(device=self.device, dtype=torch.float32)\\n return spec_stacked, pos_enc, attn_mask # (x, pos_enc, attention_mask)\",\n \"def tell(self):\\n ...\",\n \"def receiver():\\r\\n global data\\r\\n DW1000.newReceive()\\r\\n DW1000.receivePermanently()\\r\\n DW1000.startReceive()\",\n \"def bt_process():\\n try:\\n while(True):\\n data = get_data()\\n set_queue_data(data)\\n broadcast(data[0])\\n # Diagnostic\\n grovepi.digitalWrite(LED, data[0])\\n except IOError:\\n if DEBUG:\\n print 'IOError detected and excepted'\\n pass\",\n \"def event11510537():\\n header(11510537, 0)\\n npc, start_flag, end_flag, new_flag = define_args('iiii')\\n if_event_flag_on(1, 1493) # Still stuck at the archers.\\n if_event_flag_on(1, EVENT.DarkAnorLondo)\\n if_condition_true(0, 1)\\n flag.disable_chunk(start_flag, end_flag)\\n flag.enable(new_flag)\\n chr.disable(npc)\",\n \"def _stop_capture_to_ram(self):\\n self.regs.SDRAM_SINK_GO = 0\",\n \"def __data_handler__(self, msg):\\n print(msg)\",\n \"def resetData(self):\\n self.alive = 1\\n self.fromSystem = self.toSystem\\n self.systemGrid = 5\\n mySystem = self.myGalaxy.systems[self.toSystem]\\n mySystem.availSYC += self.repair\",\n \"def got_data(self, data):\\n if self.get_current_state() == SBE37ProtocolState.DIRECT_ACCESS:\\n # direct access mode\\n if len(data) > 0:\\n mi_logger.debug(\\\"SBE37Protocol._got_data(): <\\\" + data + \\\">\\\") \\n if self._driver_event:\\n self._driver_event(DriverAsyncEvent.DIRECT_ACCESS, data)\\n # TODO: what about logging this as an event?\\n return\\n \\n if len(data)>0:\\n # Call the superclass to update line and prompt buffers.\\n CommandResponseInstrumentProtocol.got_data(self, data)\\n \\n # If in streaming mode, process the buffer for samples to publish.\\n cur_state = self.get_current_state()\\n if cur_state == SBE37ProtocolState.AUTOSAMPLE:\\n if SBE37_NEWLINE in self._linebuf:\\n lines = self._linebuf.split(SBE37_NEWLINE)\\n self._linebuf = lines[-1]\\n for line in lines:\\n self._extract_sample(line)\",\n \"def test_verify_clear_trace_mid_reassembly(self):\\n\\n self.pg_enable_capture()\\n self.src_if.add_stream(self.fragments_400[0:-1])\\n self.pg_start()\\n\\n self.logger.debug(self.vapi.cli(\\\"show trace\\\"))\\n self.vapi.cli(\\\"clear trace\\\")\\n\\n self.src_if.add_stream(self.fragments_400[-1])\\n self.pg_start()\\n packets = self.dst_if.get_capture(len(self.pkt_infos))\\n self.verify_capture(packets)\",\n \"def syncloss(self):\\n # expect a disassociation indication with a correct status\\n assert(self.a.nxapi_disassociate_ind() == True)\\n \\n # generate a random frame\\n msdu = self.host.tx_msdu(da=self.ap1.macaddr, length=1000, prio=1)\\n \\n # wait for data send confirmation (not in the air)\\n self.a.host_send_data_cfm(msdu)\",\n \"def data_received(self, data):\\n pass\",\n \"def test_post_voltage_maps(self):\\n pass\",\n \"def _process_msg(self, data):\\n\\n # print(data)\\n\\n tilt = data.linear.x\\n pan = data.angular.z\\n\\n #self.controller.pantilt_magnitude(pan, tilt)\\n self.controller.pantilt_increase_angle(pan * self.scale_pan, tilt * self.scale_tilt)\",\n \"def receiver(): \\n global data\\n DW1000.newReceive()\\n DW1000.receivePermanently()\\n DW1000.startReceive()\",\n \"def slot_recv(self, dummy_sender, data):\\r\\n (str_json) = data\\r\\n handler = None\\r\\n if type(str_json) == dict:\\r\\n msg = str_json # was already a dict\\r\\n else:\\r\\n msg = json.loads(str_json)\\r\\n self.msg = msg\\r\\n\\r\\n if \\\"stamp\\\" in msg:\\r\\n delay = time.time() * 1e6 - int(msg[\\\"stamp\\\"])\\r\\n self.socket_lag = (self.socket_lag * 29 + delay) / 30\\r\\n\\r\\n if \\\"op\\\" in msg:\\r\\n try:\\r\\n msg_op = msg[\\\"op\\\"]\\r\\n handler = getattr(self, \\\"_on_op_\\\" + msg_op)\\r\\n\\r\\n except AttributeError:\\r\\n self.debug(\\\"slot_recv() ignoring: op=%s\\\" % msg_op)\\r\\n else:\\r\\n self.debug(\\\"slot_recv() ignoring:\\\", msg)\\r\\n\\r\\n if handler:\\r\\n handler(msg)\",\n \"def on_flip(self):\\r\\n self.next_data_has_pump = not self.next_data_has_pump\\r\\n self.probe_only_data, self.pump_probe_data = (\\r\\n self.pump_probe_data, self.probe_only_data)\",\n \"def on_L2(self):\\r\\n self.log()\",\n \"def callback(self, data):\\n self.state = data.data\\n #rospy.loginfo('HEARD')\",\n \"def do_before_dump(self):\\n self.checksummer.prepare_checksums()\",\n \"def process(self, data):\\n\\n\\t\\t# Check if the 802.15.4 packet is valid\\n\\t\\tif makeFCS(data[:-2]) != data[-2:]:\\n\\t\\t\\tprint(hue.bad(\\\"Received invalid packet\\\"))\\n\\t\\t\\treturn\\n\\n\\t\\tpacket = Dot15d4FCS(data)\\n\\n\\t\\tif packet.fcf_frametype == 2: # ACK\\n\\t\\t\\tself.last_ack = packet.seqnum\",\n \"def initial(self, e):\\r\\n self._add_message(\\\"top-INIT;\\\")\\r\\n self.foo_ = 0\\r\\n self.INIT(HsmTst.d2)\",\n \"def on_t_message(self, message: IncomingMessage) -> None:\\n with message.process():\\n log.debug(f\\\"received [x] {message.routing_key}:{message.body}\\\")\",\n \"def data_received(self, data):\\n\\n data = self.remaining_data + data\\n\\n packetlength = data[0] + 1 if len(data) > 0 else 1\\n while packetlength <= len(data):\\n packettype = data[1]\\n subtype = data[2]\\n if (packettype == PACKETTYPE_DSMR and subtype == SUBTYPE_P1):\\n dsmr_data = data[4:packetlength]\\n super().data_received(dsmr_data)\\n data = data[packetlength:]\\n packetlength = data[0] + 1 if len(data) > 0 else 1\\n\\n self.remaining_data = data\",\n \"def post_process_trap(): \\n #################### 0) assign internal values #################### \\n from project_parameters import trapType,debug,trapFile,name,driveAmplitude,driveFrequency,Omega,dcplot,weightElectrodes,coefs,ax,az,phi,save,scale\\n #from all_functions import find_saddle,plot_potential,dc_potential,set_voltages,exact_saddle,spher_harm_bas,spher_harm_exp,pfit,plotN\\n import pickle\\n\\n with open(trapFile,'rb') as f:\\n trap = pickle.load(f)\\n\\n qe = trap.configuration.charge\\n mass = trap.configuration.mass\\n Zval = trap.configuration.position\\n r0 = trap.configuration.r0\\n RFampl = driveAmplitude \\n V0 = mass*(2*np.pi*Omega)**2*(r0*10**-3)**2/qe\\n X,Y,Z=trap.instance.X,trap.instance.Y,trap.instance.Z \\n data = trap.configuration\\n dcVoltages = set_voltages()\\n ne = len(weightElectrodes)\\n E = trap.instance.E\\n out = trap.configuration\\n if debug.post_process_trap:\\n print dcVoltages,np.max(dcVoltages)#np.sum(abs(dcVoltages))\\n plotN(dcVoltages,trap,'set DC voltages') \\n Vdc = dc_potential(trap,dcVoltages,E)\\n #[IDC,JDC,KDC] = find_saddle(Vdc,X,Y,Z,3,Zval) \\n #[XDC,YDC,ZDC] = exact_saddle(Vdc,X,Y,Z,3,Zval)\\n #XDC,YDC,ZDC = X[IDC],150/scale,Z[KDC]\\n #print XDC,YDC,ZDC,IDC,JDC,KDC\\n #dcbasis,dcscale= spher_harm_bas(XDC,YDC,ZDC,X,Y,Z,4)\\n #QQ = spher_harm_exp(Vdc,dcbasis,dcscale) \\n #print QQ[0:9].T\\n #1) RF Analysis\\n print('RF Analysis') \\n Vrf = RFampl*data.EL_RF\\n [Irf,Jrf,Krf] = find_saddle(Vrf,X,Y,Z,2,Zval)\\n if debug.post_process_trap:\\n plot_potential(Vrf,X,Y,Z,dcplot,'weighted RF potential','V_{rf} (eV)',[Irf,Jrf,Krf])\\n #2) DC Analysis\\n print('DC Analysis')\\n trap = dc_potential(trap,dcVoltages,E,update=None)\\n Vdc = trap.instance.DC\\n [Idc,Jdc,Kdc] = find_saddle(Vdc,X,Y,Z,3,Zval) # only used to calculate error at end\\n if debug.post_process_trap:\\n plot_potential(Vdc,X,Y,Z,'1D plots','full DC potential')\\n #3) determine the exact saddles of the RF and DC\\n trap = dc_potential(trap,dcVoltages,E)\\n Vdc = trap.instance.DC\\n print('Determining exact RF saddle...')\\n [Xrf,Yrf,Zrf] = exact_saddle(Vrf,X,Y,Z,2,Zval) \\n print('Determining exact DC saddle...')\\n [Xdc,Ydc,Zdc] = exact_saddle(Vdc,X,Y,Z,3,Zval)\\n #4) determine stray field (beginning of justAnalyzeTrap)\\n print('Determining compensation due to E field...')\\n nx,ny,nz=X.shape[0],Y.shape[0],Z.shape[0]\\n x,y,z = np.zeros((nx,ny,nz)),np.zeros((nx,ny,nz)),np.zeros((nx,ny,nz))\\n for i in range(nx):\\n for j in range(ny):\\n for k in range(nz):\\n x[i,j,k] = X[i]\\n y[i,j,k] = Y[j]\\n z[i,j,k] = Z[k]\\n VlessE = Vdc-E[0]*x-E[1]*y-E[2]*z\\n [Xdc,Ydc,Zdc] = exact_saddle(VlessE,X,Y,Z,3) \\n dist = np.sqrt((Xrf-Xdc)**2+(Yrf-Ydc)**2+(Zrf-Zdc)**2) \\n #5) call pfit to built teh total field and determine the trap characteristics\\n [fx,fy,fz,theta,Depth,Xe,Ye,Ze] = pfit(Vrf,Vdc,X,Y,Z,Irf,Jrf,Krf)#pfit(trap,E,Freq,RFampl)\\n print('Stray field is ({0},{1},{2}) V/m.'.format(scale*E[0],scale*E[1],scale*E[2]))\\n print('With this field, the compensation is optimized to {} micron.'.format(scale*dist))\\n print('RF saddle: ({0},{1},{2})\\\\nDC saddle ({3},{4},{5}).'.format(Xrf,Yrf,Zrf,Xdc,Ydc,Zdc)) \\n if debug.trap_depth:\\n print('The trap escape position is at ({0},{1},{2}) microns, for a trap depth of {3} mV'.format(Xe*scale,Ye*scale,Ze*scale,Depth*scale))\\n print('The trap frequencies are fx = {0} MHz, fy = {1} MHz, and fz = {2} MHz'.format(fx*10**-6,fy*10**-6,fz*10**-6))\\n #6) Sanity testing; quality check no longer used\\n if debug.post_process_trap:\\n rfbasis,rfscale= spher_harm_bas(Xrf,Yrf,Zrf,X,Y,Z,2)\\n Qrf = spher_harm_exp(Vrf,rfbasis,rfscale) \\n if np.sqrt((Xrf-Xdc)**2+(Yrf-Ydc)**2+(Zrf-Zdc)**2)>0.008: \\n print('Expanding DC with RF for saniy checking.')\\n Qdc = spher_harm_exp(Vdc,rfbasis,rfscale) \\n else:\\n print('Expanding DC without RF for sanity checking.')\\n dcbasis,dcscale= spher_harm_bas(Xdc,Ydc,Zdc,X,Y,Z,2)\\n Qdc = spher_harm_exp(Vdc,dcbasis,dcscale) \\n Arf = 2*np.sqrt( (3*Qrf[7])**2+(3*Qrf[8])**2 )\\n Thetarf = 45*(Qrf[8]/abs(Qrf[8]))-90*np.arctan((3*Qrf[7])/(3*Qrf[8]))/np.pi\\n Adc = 2*np.sqrt( (3*Qdc[7])**2+(3*Qdc[8])**2 )\\n Thetadc = 45*(Qrf[8]/abs(Qrf[8]))-90*np.arctan((3*Qdc[7])/(3*Qdc[8]))/np.pi\\n out.E = E\\n out.miscompensation = dist\\n out.ionpos = [Xrf,Yrf,Zdc]\\n out.ionposIndex = [Irf,Jrf,Krf]\\n out.frequency = [fx,fy,fz]\\n out.theta = theta\\n out.trap_depth = Depth/qe \\n out.escapepos = [Xe,Ye,Ze]\\n out.Quadrf = 2*np.array([Qrf[7]*3,Qrf[4]/2,Qrf[8]*6,-Qrf[6]*3,-Qrf[5]*3])\\n out.Quaddc = 2*np.array([Qdc[7]*3,Qdc[4]/2,Qdc[8]*6,-Qdc[6]*3,-Qdc[5]*3])\\n out.Arf = Arf\\n out.Thetarf = Thetarf\\n out.Adc = Adc\\n out.Thetadc = Thetadc\\n T = np.array([[2,-2,0,0,0],[-2,-2,0,0,0],[0,4,0,0,0],[0,0,1,0,0],[0,0,0,1,0],[0, 0,0,0,1]])\\n Qdrf = out.Quadrf.T\\n Qddc = out.Quaddc.T\\n out.q = (1/V0)*T*Qdrf\\n out.alpha = (2/V0)*T*Qddc\\n out.Error = [X[Idc]-Xdc,Y[Jdc]-Ydc,Z[Kdc]-Zdc]\\n #7) update the trapping field data structure with instance attributes\\n trap.configuration=out\\n trap.instance.driveAmplitude = driveAmplitude\\n trap.instance.driveFrequency = driveFrequency\\n trap.instance.coefs = coefs\\n trap.instance.ax = ax\\n trap.instance.az = az\\n trap.instance.phi = phi\\n trap.instance.ppt = True\\n trap.instance.out = out\\n if save==True:\\n print('Saving '+trapFile+' as a data structure...')\\n with open(trapFile,'wb') as f:\\n pickle.dump(trap,f)\\n return 'post_proccess_trap complete' #out # no output needed really\",\n \"def reset_10gbe():\\n snap.write_int('valid_en',0)\\n snap.write_int('rst',1)\\n time.sleep(1)\\n snap.write_int('rst',0)\\n snap.write_int('valid_en',3)\",\n \"def shift_balance(mp, standing_leg):\\n pass\",\n \"def test_back_fill(self):\\n self.driver.start_sampling()\\n\\n # step 2 contains 3 blocks (4 records), start with this and get both since we used them\\n # separately in other tests\\n self.create_sample_data_set_dir(\\\"node59p1_step2.dat\\\", TELEM_DIR, \\\"node59p1.dat\\\",\\n copy_metadata=False)\\n self.assert_data((PhsenParserDataParticle,PhsenControlDataParticle),\\n 'test_data_1-2.txt.result.yml', count=4)\\n\\n # This file has had a section of data replaced with 0s (14171-14675),\\n # replacing PH1236501_01D6u51F11341_5D_E538\\n self.create_sample_data_set_dir('node59p1_step3.dat', TELEM_DIR, \\\"node59p1.dat\\\",\\n copy_metadata=False)\\n self.assert_data(PhsenParserDataParticle, 'test_data_3.txt.result.yml',\\n count=5)\\n\\n # Now fill in the zeroed section from step3, this should just return the new\\n # data \\n self.create_sample_data_set_dir('node59p1_step4.dat', TELEM_DIR, \\\"node59p1.dat\\\",\\n copy_metadata=False)\\n self.assert_data(PhsenParserDataParticle, 'test_data_4.txt.result.yml',\\n count=1)\\n\\n # start over now using step 4\\n self.driver.stop_sampling()\\n # Reset the driver with no memento\\n self.driver = self._get_driver_object(memento=None)\\n self.driver.start_sampling()\\n\\n self.clear_async_data()\\n self.create_sample_data_set_dir('node59p1_step4.dat', TELEM_DIR, \\\"node59p1.dat\\\",\\n copy_metadata=False)\\n self.assert_data((PhsenParserDataParticle,PhsenControlDataParticle),\\n 'test_data_1-4.txt.result.yml', count=10)\",\n \"def _get_dma(cls, data):\\n\\t\\tdata['dma'] = data['close_10_sma'] - data['close_50_sma']\",\n \"def sensorverarbeiten(self):\\n self.Sensordata.justmw(self)\",\n \"def recieveArbirator():\\n\\trospy.init_node('arbitrator') \\n\\trospy.Subscriber(\\\"arbitratorOutput\\\", trackbotMotors, serialTransmit)\\n\\trospy.Subscriber(\\\"rxtx/recieveMA\\\", UInt8MultiArray, recieveSerial)\\n\\trospy.spin()\",\n \"def event11512500():\\n header(11512500, 1)\\n flag.disable(EVENT.CathedralStableFooting)\\n\\n if_event_flag_on(1, EVENT.OrnsteinAndSmoughDead)\\n if_event_flag_off(1, EVENT.AnorLondoGwynWarp)\\n if_condition_true(0, 1)\\n\\n flag.enable(EVENT.CathedralStableFooting)\",\n \"def test_verify_clear_trace_mid_reassembly(self):\\n\\n self.pg_enable_capture()\\n self.src_if.add_stream(self.fragments_200[0:-1])\\n self.pg_start()\\n\\n self.logger.debug(self.vapi.cli(\\\"show trace\\\"))\\n self.vapi.cli(\\\"clear trace\\\")\\n\\n self.src_if.add_stream(self.fragments_200[-1])\\n self.pg_start()\\n packets = self.dst_if.get_capture(len(self.pkt_infos))\\n self.verify_capture(packets)\",\n \"def passPacketToStreamMgr(self, _data, _opcode, _managerCode):\\n if _opcode == MSG_SERVER_PACKET:\\n \\tself.client.streamMgr.handlePacket(_opcode, _managerCode, _data)\\n\\n else:\\n print \\\"Client: BAD-opcode - %d\\\" % _opcode\\n print \\\"Client: Opcode Data -\\\", _data\\n \\n return\",\n \"def case():\\r\\n #ppc = {\\\"version\\\": '2'}\\r\\n ppc = {}\\r\\n ##----- Power Flow Data -----##\\r\\n ## system MVA base\\r\\n ppc[\\\"baseMVA\\\"] = 100.0\\r\\n\\r\\n ## bus data\\r\\n # bus_i type Pd Qd Gs Bs area Vm Va baseKV zone Vmax Vmin\\r\\n ppc[\\\"bus\\\"] = array([\\r\\n [1, 3, 0, 0, 0, 0, 1, 1, 0, 0.4, 1, 1.1, 0.9, 0,0, 0, 0],\\r\\n [2, 1, 0, 0, 0, 0, 1, 1, 0, 0.4, 1, 1.1, 0.9, 0,0, 0, 0],\\r\\n [3, 1, 0, 0, 0, 0, 1, 1, 0, 0.4, 1, 1.1, 0.9, 0,0, 0, 0],\\r\\n [4, 1, 0, 0, 0, 0, 1, 1, 0, 0.4, 1, 1.1, 0.9, 0,0, 0, 0],\\r\\n [5, 1, 0, 0, 0, 0, 1, 1, 0, 0.4, 1, 1.1, 0.9, 0,0, 0, 0],\\r\\n [6, 1, 0, 0, 0, 0, 1, 1, 0, 0.4, 1, 1.1, 0.9, 0,0, 0, 0],\\r\\n [7, 1, 0, 0, 0, 0, 1, 1, 0, 0.4, 1, 1.1, 0.9, 0,0, 0, 0],\\r\\n [8, 1, 0, 0, 0, 0, 1, 1, 0, 0.4, 1, 1.1, 0.9, 0,0, 0, 0],\\r\\n [9, 1, 0, 0, 0, 0, 1, 1, 0, 0.4, 1, 1.1, 0.9, 0,0, 0, 0],\\r\\n [10, 1, 0, 0, 0, 0, 1, 1, 0, 0.4, 1, 1.1, 0.9, 0,0, 0, 0],\\r\\n [11, 1, 0, 0, 0, 0, 1, 1, 0, 0.4, 1, 1.1, 0.9, 0,0, 0, 0],\\r\\n [12, 1, 0, 0, 0, 0, 1, 1, 0, 0.4, 1, 1.1, 0.9, 0,0, 0, 0],\\r\\n [13, 1, 0, 0, 0, 0, 1, 1, 0, 0.4, 1, 1.1, 0.9, 0,0, 0, 0],\\r\\n [14, 1, 0, 0, 0, 0, 1, 1, 0, 0.4, 1, 1.1, 0.9, 0,0, 0, 0],\\r\\n [15, 1, 0, 0, 0, 0, 1, 1, 0, 0.4, 1, 1.1, 0.9, 0,0, 0, 0],\\r\\n [16, 1, 0, 0, 0, 0, 1, 1, 0, 0.4, 1, 1.1, 0.9, 0,0, 0, 0]\\r\\n ])\\r\\n\\r\\n ## generator data\\r\\n # bus, Pg, Qg, Qmax, Qmin, Vg, mBase, status, Pmax, Pmin, Pc1, Pc2,\\r\\n # Qc1min, Qc1max, Qc2min, Qc2max, ramp_agc, ramp_10, ramp_30, ramp_q, apf\\r\\n ppc[\\\"gen\\\"] = array([\\r\\n [1,\\t0,\\t0,\\t10,\\t-10,\\t1.0224,\\t100,\\t1,\\t10,\\t-10,\\t0,\\t0,\\t0,\\t0,\\t0,\\t0,\\t0,\\t0,\\t0,\\t0, 0, 0,0, 0, 0],\\r\\n [3 ,0, 0, 50e-3, -50e-3, 1, 100, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,0, 0, 0],\\r\\n [5 , 0, 0, 10e-3, -10e-3, 1, 100, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,0, 0, 0],\\r\\n [10 , 0, 0, 10e-3, -10e-3, 1, 100, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,0, 0, 0],\\r\\n [13 ,0, 0, 10e-3, -10e-3, 1, 100, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,0, 0, 0],\\r\\n [15 , 0, 0, 50e-3, -50e-3, 1, 100, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,0, 0, 0]\\r\\n ])\\r\\n load_b = array([2, 4, 9, 12, 14])\\r\\n ppc[\\\"bus\\\"][load_b, 2] = multiply(array([-2.1125, -0.2231, -0.1664, -0.0719, -1.4633]).T, 0.03)\\r\\n ppc[\\\"bus\\\"][load_b, 3] = multiply(array([1.6492, 0.4054, 0.8599, 0.8845, 0.6778]).T, 0.03)\\r\\n ## branch data\\r\\n # fbus, tbus, r, x, b, rateA, rateB, rateC, ratio, angle, status, angmin, angmax\\r\\n ppc[\\\"branch\\\"] = array([\\r\\n [1, 2, 0.0, 0.0, 0.0, 250, 250, 250, 0, 0, 1, -360, 360, 0,0, 0, 0, 0,0, 0, 0],\\r\\n [1, 8, 0.0, 0.0, 0.0, 250, 250, 250, 0, 0, 1, -360, 360, 0,0, 0, 0, 0,0, 0, 0],\\r\\n [1, 15, 0.0, 0.0, 0.0, 250, 250, 250, 0, 0, 1, -360, 360, 0,0, 0, 0, 0,0, 0, 0],\\r\\n [2, 3, 0.0, 0.0, 0.0, 250, 250, 250, 0, 0, 1, -360, 360, 0,0, 0, 0, 0,0, 0, 0],\\r\\n [2, 6, 0.0, 0.0, 0.0, 250, 250, 250, 0, 0, 1, -360, 360, 0,0, 0, 0, 0,0, 0, 0],\\r\\n [2, 7, 0.0, 0.0, 0.0, 250, 250, 250, 0, 0, 1, -360, 360, 0,0, 0, 0, 0,0, 0, 0],\\r\\n [3, 4, 0.0, 0.0, 0.0, 250, 250, 250, 0, 0, 1, -360, 360, 0,0, 0, 0, 0,0, 0, 0],\\r\\n [4, 5, 0.0, 0.0, 0.0, 250, 250, 250, 0, 0, 1, -360, 360, 0,0, 0, 0, 0,0, 0, 0],\\r\\n [8, 9, 0.0, 0.0, 0.0, 250, 250, 250, 0, 0, 1, -360, 360, 0,0, 0, 0, 0,0, 0, 0],\\r\\n [8, 12, 0.0, 0.0, 0.0, 250, 250, 250, 0, 0, 1, -360, 360, 0,0, 0, 0, 0,0, 0, 0],\\r\\n [8, 13, 0.0, 0.0, 0.0, 250, 250, 250, 0, 0, 1, -360, 360, 0,0, 0, 0, 0,0, 0, 0],\\r\\n [9, 10, 0.0, 0.0, 0.0, 250, 250, 250, 0, 0, 1, -360, 360, 0,0, 0, 0, 0,0, 0, 0],\\r\\n [9, 14, 0.0, 0.0, 0.0, 250, 250, 250, 0, 0, 1, -360, 360, 0,0, 0, 0, 0,0, 0, 0],\\r\\n [10, 11, 0.0, 0.0, 0.0, 250, 250, 250, 0, 0, 1, -360, 360, 0,0, 0, 0, 0,0, 0, 0],\\r\\n [15, 16, 0.0, 0.0, 0.0, 250, 250, 250, 0, 0, 1, -360, 360, 0,0, 0, 0, 0,0, 0, 0]\\r\\n ])\\r\\n R1 = 0.43\\r\\n L1 = 0.4e-3\\r\\n RS1 = 0.32\\r\\n LS1 = 0.39e-3\\r\\n Zbase = (0.4*0.4/100)\\r\\n branch_phase =array([\\r\\n [1, 1, 2, 188, R1, L1],\\r\\n [2, 1 ,8, 346, R1, L1],\\r\\n [3 ,1 ,15,501, R1 ,L1],\\r\\n [4, 2, 3, 130, RS1,LS1],\\r\\n [5, 2, 6, 145, RS1,LS1],\\r\\n [6, 2 ,7, 157, RS1,LS1],\\r\\n [7, 3, 4, 185, RS1,LS1],\\r\\n [8, 4, 5, 1000,RS1,LS1],\\r\\n [9, 8 ,9, 416, RS1,LS1],\\r\\n [10,8 ,12,130, RS1,LS1],\\r\\n [11,8 ,13,121, RS1,LS1],\\r\\n [12,9 ,10,130, RS1,LS1],\\r\\n [13,9 ,14,127, RS1,LS1],\\r\\n [14,10,11,251, RS1,LS1],\\r\\n [15,15,16,345, RS1,LS1]\\r\\n ])\\r\\n ppc[\\\"branch\\\"][:, [2,3]] = multiply(array([branch_phase[:, 4]*branch_phase[:, 3], branch_phase[:, 4]*branch_phase[:, 4]*100*pi]).T,0.001/Zbase)\\r\\n\\r\\n ##----- OPF Data -----##\\r\\n ## area data\\r\\n # area refbus\\r\\n\\r\\n\\r\\n ## generator cost data\\r\\n # 1 startup shutdown n x1 y1 ... xn yn\\r\\n # 2 startup shutdown n c(n-1) ... c0\\r\\n\\r\\n\\r\\n return ppc\",\n \"def event_m20_11_4000000():\\n \\\"\\\"\\\"State 0,2: [Lib] Character: Petrified: Key Guide_SubState\\\"\\\"\\\"\\n assert event_m20_11_x37(z94=5300, z95=0, z96=15, z97=211000030, z98=0, z99=1600, z100=6, z101=4000010)\\n \\\"\\\"\\\"State 1: Finish\\\"\\\"\\\"\\n EndMachine()\",\n \"def write_data(self, data):\\n # send data\\n for ptr, value in data:\\n self._write_byte(ptr, value)\\n # set 'data changed'\\n self._write_byte(fixed_format['data_changed'][0], 0xAA)\\n # wait for station to clear 'data changed'\\n while True:\\n ack = _decode(self._read_fixed_block(0x0020),\\n fixed_format['data_changed'])\\n if ack == 0:\\n break\\n log.debug('waiting for ack')\\n time.sleep(6)\",\n \"def data_received(self, data):\\n # self.debug(\\\"received data=%r\\\", binascii.hexlify(data))\\n self.dispatcher.add_data(data)\",\n \"def handle_thrusters(self, data):\\n self.thrs_current = np.roll(self.thrs_current, -1, axis=1) # roll the vector (shift)\\n self.thrs_current[0:4, -1] = data.current[0:4] # selected thrusters only\\n\\n self.thrs_energy += THR_VNOM * np.trapz(self.thrs_current, dx=THR_FRAME, axis=1)\\n self.energy_last = np.sum(self.thrs_energy)\",\n \"def dataReceived(self, data):\\n print \\\"received:\\\", data\",\n \"def handleSystemMessage(self,data):\\n message = data.split()[0]\\n if message == \\\"QAError\\\":\\n message,detID = data.split()\\n pcaId = self.detectorMapping[detId]\\n partition = self.PCAs[pcaId]\\n data = {\\n \\\"id\\\": \\\"DCS\\\",\\n \\\"detectorId\\\": detId,\\n \\\"message\\\": message,\\n }\\n self.sendQAMessage(data,partition)\\n else:\\n super().handleSystemMessage(message)\",\n \"def test_back(self):\\n self.protocol.back()\\n expected = [\\n \\\"AWAY :\\\",\\n \\\"\\\",\\n ]\\n self.assertEqualBufferValue(self.transport.value().split(b\\\"\\\\r\\\\n\\\"), expected)\",\n \"def __frame_tx(self,data):\\n\\n if self._spy_frame_tx is not None:\\n self._spy_frame_tx(data)\\n\\n data=self.__pad(data)\\n\\n if len(data) < self.other_bufferlen:\\n self.com.tx(data)\\n else:\\n chunks = (len(data)-1) // self.other_bufferlen\\n #print(\\\"__frame_tx: %d full chunks + last\\\"%chunks,flush=True)\\n for i in range(0,chunks):\\n self.com.tx(data[i*self.other_bufferlen:(i+1)*self.other_bufferlen])\\n self.com.rx_ack()\\n self.com.tx(data[chunks*self.other_bufferlen:])\\n #print(\\\"__frame_tx done\\\",flush=True)\",\n \"def FL_2_mav_sensor(self, data):\\n\\n (data['velocities/phidot-rad_sec_bf'],\\n data['velocities/thetadot-rad_sec_bf'],\\n data['velocities/psidot-rad_sec_bf']) = self.convert_body_frame(\\n data['attitude/phi-rad'],\\n data['attitude/theta-rad'],\\n data['velocities/phidot-rad_sec'],\\n data['velocities/thetadot-rad_sec'],\\n data['velocities/psidot-rad_sec']\\n )\\n\\n #Data treatment\\n messagedata = [\\n int(data['simulation/sim-time-sec']*self._sec2usec), #time_usec boot time usec int\\n data['accelerations/udot-ft_sec2'], #xacc m/s**2 float\\n data['accelerations/vdot-ft_sec2'], #yacc m/s**2 float\\n data['accelerations/wdot-ft_sec2'], #zacc m/s**2 float\\n data['velocities/phidot-rad_sec'], #xgyro rad/s float\\n data['velocities/thetadot-rad_sec'], #ygyro rad/s float\\n data['velocities/psidot-rad_sec'], #zgyro rad/s float\\n data['sensors/magnetometer/X/output'], #xmag Gauss float\\n data['sensors/magnetometer/Y/output'], #ymag Gauss float\\n data['sensors/magnetometer/Z/output'], #zmag Gauss float\\n data['atmosphere/P-psf']*0.478802589, #abs_pr mbar float\\n 0.0, #dif_pr mbar float\\n data['atmosphere/pressure-altitude'], #pr_alt meter float\\n 15.0, #temp C float\\n int(8186) #fields_updated (ALL)\\n ]\\n\\n return messagedata\",\n \"def exittime10_message_received(msg):\\n data = IndexIntData.from_msg(msg)\\n if data is None:\\n _LOGGER.error(\\\"Undable to parse MQTT message\\\")\\n\\n if data.value == 1:\\n self._exittime10.add(data.index)\\n else:\\n self._exittime10.discard(data.index)\\n\\n _LOGGER.debug(\\\"Arming >10s: %s\\\", self._exittime10)\\n self.async_write_ha_state()\",\n \"def mv_all(self):\\n # def mv_step(self):\\n self.device_reg_data &= ~(0x1 << 2)\\n bus.write_byte_data(self.device_address, self.device_reg_mode1, self.device_reg_data)\",\n \"def event_m20_11_16010():\\n \\\"\\\"\\\"State 0,2: [DC] [Preset] Lizard extinction judgment_3 bodies_SubState\\\"\\\"\\\"\\n assert event_m20_11_x122(z1=211000016)\\n \\\"\\\"\\\"State 1: Finish\\\"\\\"\\\"\\n EndMachine()\",\n \"def event_m20_11_x96(z34=802):\\n \\\"\\\"\\\"State 0,1: Stop generator following sound\\\"\\\"\\\"\\n StopSoundFollowingGenerator(z34)\\n \\\"\\\"\\\"State 2: End state\\\"\\\"\\\"\\n return 0\",\n \"def fix_calldata(self) -> None:\\n for step in self.steps:\\n step.call_data = step.call_data.replace(\\n \\\"deadbeefdeadbeefdeadbeefdeadbeefdeadbeef\\\", self.sender[2:]\\n )\",\n \"def __write_block(self, block, data):\\n if nfc.nfc_device_set_property_bool(self.__device, nfc.NP_EASY_FRAMING, True) < 0:\\n raise Exception(\\\"Error setting Easy Framing property\\\")\\n if len(data) > 16:\\n raise ValueError(\\\"Data value to be written cannot be more than 16 characters.\\\")\\n abttx = (ctypes.c_uint8 * 18)()\\n abttx[0] = self.MC_WRITE\\n abttx[1] = block\\n abtrx = (ctypes.c_uint8 * 250)()\\n for i in range(16):\\n abttx[i + 2] = ord((data + \\\"\\\\x00\\\" * (16 - len(data)))[i])\\n return nfc.nfc_initiator_transceive_bytes(self.__device, ctypes.pointer(abttx), len(abttx),\\n ctypes.pointer(abtrx), len(abtrx), 0)\",\n \"def hatHandler(valLR, valUD):\\n print(\\\"Digital Hat Changed: L/R:{} U/D:{}\\\".format(valLR,valUD) )\",\n \"def event_m20_11_82000():\\n \\\"\\\"\\\"State 0,2: [Lib] [Preset] Reproduction fire _SubState\\\"\\\"\\\"\\n assert event_m20_11_x53(z73=2011200, z74=2011299)\\n \\\"\\\"\\\"State 1: Finish\\\"\\\"\\\"\\n EndMachine()\",\n \"def run(self):\\n try:\\n self.listener.connect(self.b2bPeer)\\n\\n print('\\\\n<1. Version Message>')\\n version = self.versionMsg()\\n self.messageControl(version)\\n\\n print('\\\\n\\\\n<2. Verack Message>')\\n verack = self.verackMsg()\\n self.messageControl(verack)\\n\\n print('\\\\n\\\\n<3. GetBlocks Message> - Get Inventory #{}'.format(TARGET_BLOCK))\\n target_block = self.getBlocks()\\n\\n print('\\\\n\\\\n<4. GetData Message>')\\n get_data = self.getDataMsg(target_block)\\n self.largeMessageControl(get_data, 'block')\\n except Exception as e:\\n print(e)\",\n \"def climb(self):\\n print(\\\"Inside WoodElf.climb\\\")\",\n \"def outReceived(self, data):\\n self.protocol.dataReceived(data)\",\n \"def flight_data_handler(self, event, sender, data):\\n self.battery = data.battery_percentage\\n self.fly_mode = data.fly_mode\\n self.throw_fly_timer = data.throw_fly_timer\\n self.throw_ongoing = data.throw_fly_timer > 0\\n\\n # print(\\\"fly_mode\\\",data.fly_mode)\\n # print(\\\"throw_fly_timer\\\",data.throw_fly_timer)\\n # print(\\\"em_ground\\\",data.em_ground)\\n # print(\\\"em_sky\\\",data.em_sky)\\n # print(\\\"electrical_machinery_state\\\",data.electrical_machinery_state)\\n #print(\\\"em_sky\\\",data.em_sky,\\\"em_ground\\\",data.em_ground,\\\"em_open\\\",data.em_open)\\n #print(\\\"height\\\",data.height,\\\"imu_state\\\",data.imu_state,\\\"down_visual_state\\\",data.down_visual_state)\\n if self.is_flying != data.em_sky: \\n self.is_flying = data.em_sky\\n log.debug(f\\\"FLYING : {self.is_flying}\\\")\\n if not self.is_flying:\\n self.reset()\\n else:\\n if self.tracking_after_takeoff:\\n log.info(\\\"Tracking on after takeoff\\\")\\n self.toggle_tracking(True)\\n \\n log.debug(f\\\"MODE: {self.fly_mode} - Throw fly timer: {self.throw_fly_timer}\\\")\",\n \"def event_m20_11_3020():\\n \\\"\\\"\\\"State 0,2: [Preset] Beautiful frog singing voice_flag_SubState\\\"\\\"\\\"\\n assert event_m20_11_x110(z24=211000081, z25=802, z26=211020082)\\n \\\"\\\"\\\"State 1: Finish\\\"\\\"\\\"\\n EndMachine()\",\n \"def dataReceived(self, data):\\n\\n def write(result):\\n fauxResult = self._addPreIPBusHeader(result)\\n print(\\\"Writing %r\\\" % fauxResult)\\n self.transport.write(fauxResult)\\n\\n d = self.d()\\n d.addCallback(write) # errors are silently ignored!\\n d.callback(self._stripPreIPBusHeader(data))\",\n \"def off(self):\\n self.rs485.write_command('#{}bf'.format(self.address))\\n time.sleep(1)\",\n \"def on_R2(self):\\r\\n self.log()\",\n \"def event11512008():\\n header(11512008)\\n end_if_this_event_on()\\n if_event_flag_on(1, 11512060) # Ambush done.\\n if_event_flag_on(1, EVENT.CapriciousThrallActive) # Thrall still active (e.g. Archive appearance not done).\\n if_event_flag_off(1, EVENT.ThrallAmbushOngoing)\\n if_player_inside_region(1, REGION.CapriciousThrallTrigger)\\n if_condition_true(0, 1)\\n message.status_explanation(TEXT.ThrallHasFled)\",\n \"def dataReceived(self, data):\",\n \"def slot_depth(self, dummy_sender, data):\\r\\n (typ, price, _voldiff, total_vol) = data\\r\\n if self._update_book(typ, price, total_vol):\\r\\n self.signal_changed(self, None)\",\n \"def event_m20_11_5000():\\n \\\"\\\"\\\"State 0,2: [Preset] Living Altar_SubState\\\"\\\"\\\"\\n assert event_m20_11_x82()\\n \\\"\\\"\\\"State 1: Rerun\\\"\\\"\\\"\\n RestartMachine()\",\n \"def handle_switch_give_up(self, message):\\n # TODO: ADD timer and close\\n if message.type == 11 and not self.giving_up:\\n #print \\\"giving up control\\\"\\n ########## Evaluation ######\\n print \\\"Switch migrated: \\\", self.last_xid\\n ########################\\n if self.buffer:\\n self.handle_write()\\n if self.controller.buffer:\\n self.controller.handle_write()\\n self.giving_up = True\\n # Keep processing replies, they are not sent to other controllers.\\n if message.type in [3, 6, 8, 19, 21, 23, 25]:\\n self.controller.buffer.append(message)\",\n \"def slot_orderlag(self, dummy_sender, (usec, text)):\\r\\n self.order_lag = usec\\r\\n self.order_lag_txt = text\\r\\n self.do_paint()\",\n \"def dummyF(self, arg, signal, sender):\\n \\n if self.isDead == True:\\n return\\n \\n \\n #print \\\"DUMMY\\\"\\n if self.aborting:\\n self.aborting = False\\n self.isActive = False\\n self.__orderQueue.popleft()\\n del self.slaveTalk\\n self.slaveTalk = None\\n# self.__orderQueue.popleft()\\n try:\\n self.releaseLock()\\n except:\\n pass\\n #print \\\"No lock, actually.\\\" \\n dispatcher.send('SLAVE_PARSE_QUEUE', self, '')\"\n]","isConversational":false},"negative_scores":{"kind":"list like","value":["0.56816924","0.55445737","0.5298501","0.52529526","0.5242817","0.5230332","0.52025527","0.51271504","0.5111258","0.50924855","0.50700384","0.5046472","0.5040559","0.5023257","0.5019368","0.49901193","0.49784297","0.49663934","0.49618027","0.4956633","0.49178258","0.4906687","0.48958197","0.4895619","0.48900127","0.48850393","0.48820964","0.48751518","0.48657155","0.48575747","0.4853053","0.485264","0.4852444","0.48478577","0.48428348","0.4839677","0.4836184","0.48334157","0.48216894","0.4813472","0.48130536","0.47997072","0.47831902","0.47790533","0.4775881","0.47685745","0.47678098","0.4766721","0.47661614","0.47641334","0.47629154","0.47597817","0.47569123","0.47515342","0.47482055","0.4748033","0.47406605","0.47400737","0.47388607","0.47346103","0.47295296","0.47275504","0.4726981","0.47221616","0.47002843","0.4696877","0.46929458","0.4691993","0.46917155","0.4686913","0.46855846","0.46853185","0.4681471","0.4681277","0.46734783","0.4671979","0.46719337","0.4664735","0.46582037","0.46562934","0.4653796","0.46533355","0.46429846","0.4640978","0.46379048","0.46339846","0.46328822","0.4631003","0.46298313","0.46288413","0.46273896","0.46264958","0.46248814","0.46182662","0.46162182","0.46148068","0.46133083","0.46130133","0.46122605","0.46116373","0.46027264"],"string":"[\n \"0.56816924\",\n \"0.55445737\",\n \"0.5298501\",\n \"0.52529526\",\n \"0.5242817\",\n \"0.5230332\",\n \"0.52025527\",\n \"0.51271504\",\n \"0.5111258\",\n \"0.50924855\",\n \"0.50700384\",\n \"0.5046472\",\n \"0.5040559\",\n \"0.5023257\",\n \"0.5019368\",\n \"0.49901193\",\n \"0.49784297\",\n \"0.49663934\",\n \"0.49618027\",\n \"0.4956633\",\n \"0.49178258\",\n \"0.4906687\",\n \"0.48958197\",\n \"0.4895619\",\n \"0.48900127\",\n \"0.48850393\",\n \"0.48820964\",\n \"0.48751518\",\n \"0.48657155\",\n \"0.48575747\",\n \"0.4853053\",\n \"0.485264\",\n \"0.4852444\",\n \"0.48478577\",\n \"0.48428348\",\n \"0.4839677\",\n \"0.4836184\",\n \"0.48334157\",\n \"0.48216894\",\n \"0.4813472\",\n \"0.48130536\",\n \"0.47997072\",\n \"0.47831902\",\n \"0.47790533\",\n \"0.4775881\",\n \"0.47685745\",\n \"0.47678098\",\n \"0.4766721\",\n \"0.47661614\",\n \"0.47641334\",\n \"0.47629154\",\n \"0.47597817\",\n \"0.47569123\",\n \"0.47515342\",\n \"0.47482055\",\n \"0.4748033\",\n \"0.47406605\",\n \"0.47400737\",\n \"0.47388607\",\n \"0.47346103\",\n \"0.47295296\",\n \"0.47275504\",\n \"0.4726981\",\n \"0.47221616\",\n \"0.47002843\",\n \"0.4696877\",\n \"0.46929458\",\n \"0.4691993\",\n \"0.46917155\",\n \"0.4686913\",\n \"0.46855846\",\n \"0.46853185\",\n \"0.4681471\",\n \"0.4681277\",\n \"0.46734783\",\n \"0.4671979\",\n \"0.46719337\",\n \"0.4664735\",\n \"0.46582037\",\n \"0.46562934\",\n \"0.4653796\",\n \"0.46533355\",\n \"0.46429846\",\n \"0.4640978\",\n \"0.46379048\",\n \"0.46339846\",\n \"0.46328822\",\n \"0.4631003\",\n \"0.46298313\",\n \"0.46288413\",\n \"0.46273896\",\n \"0.46264958\",\n \"0.46248814\",\n \"0.46182662\",\n \"0.46162182\",\n \"0.46148068\",\n \"0.46133083\",\n \"0.46130133\",\n \"0.46122605\",\n \"0.46116373\",\n \"0.46027264\"\n]","isConversational":false},"document_score":{"kind":"string","value":"0.0"},"document_rank":{"kind":"string","value":"-1"}}},{"rowIdx":16593,"cells":{"query":{"kind":"string","value":"Trap file with no M02 block gerber."},"document":{"kind":"string","value":"def test_no_eof(self):"},"metadata":{"kind":"string","value":"{\n \"objective\": {\n \"self\": [],\n \"paired\": [],\n \"triplet\": [\n [\n \"query\",\n \"document\",\n \"negatives\"\n ]\n ]\n }\n}"},"negatives":{"kind":"list like","value":["def cleanupV032backup(self):\n doCleanup = False\n if (os.path.isfile(self.MAPSTUDIO + 'm10_00_00_00.msb.bak')):\n self.msbio.open(self.MAPSTUDIO + 'm10_00_00_00.msb.bak')\n if (len(self.msbio.models.rows) >= 373):\n doCleanup = True\n\n if (doCleanup):\n print(\"Detected invalid .msb file backups from v0.3.2, attempting to fix.\")\n try:\n for i, iFile in enumerate(self.inputFiles):\n if (os.path.isfile(self.MAPCOPY + iFile + '.msb')):\n self.msbio.open(self.MAPCOPY + iFile + '.msb')\n self.msbio.models.rows = self.msbio.models.rows[:self.startIndices[i]]\n self.msbio.save(self.MAPSTUDIO + iFile + '.msb.bak', False)\n print(\"Fixed \" + self.MAPSTUDIO + iFile + '.msb.bak')\n else:\n print(\"Failed to fix backup: \" + self.MAPSTUDIO + iFile + '.msb.bak, ' + self.MAPCOPY + iFile + '.msb from previous use of the randomizer does not exist.')\n except:\n print(\"[ERROR] Failed to fix the backups.\")","def UnhandledPacket(Packet):\n\n\tglobal UnhandledFile\n\n\tif (UnhandledFile != None):\n\t\tUnhandledFile.write(Packet)","def test_fake_file(self):\n fits_file = os.path.join(self.datadir, 'monol_test_fake.evt')\n hen.fake.main(['-o', fits_file, '--instrument', 'FPMB'])\n info = hen.io.print_fits_info(fits_file, hdu=1)\n assert info['Instrument'] == 'FPMB'","def test_byte_loss(self):\n log.info('===== START TEST REAL FILE =====')\n\n # Telemetered\n file_path = os.path.join(RESOURCE_PATH, '11330408_SNA_SNA.txt')\n\n stream_handle = open(file_path, MODE_ASCII_READ)\n\n self.create_parser(stream_handle)\n\n particles = self.parser.get_records(3)\n\n log.debug(\"*** test_byte_loss Num particles %s\", len(particles))\n\n # check all the values against expected results.\n self.assert_particles(particles, 'byte_loss.yml', RESOURCE_PATH)\n stream_handle.close()\n\n log.info('===== END TEST BYTE LOSS =====')","def insert_bad_data():\n get_file_reply(files[2][0], files[2][1])","def test_malformed(self):\n fdesc, fname = tempfile.mkstemp()\n tfile = os.fdopen(fdesc, 'w')\n tfile.write(self.file_str2)\n tfile.close()\n assert_raises(Exception, grades.writers.GradesFile, fname)\n os.unlink(fname)","def unknown(self):\n self.add_file_string('Unknown file')\n self.should_copy = False","def skip_gutenberg_header(self, fp):\n for line in fp:\n if line.startswith('*END*THE SMALL PRINT!'):\n break","def test_single_chunk(caplog):\n # Need to override the test level set above\n caplog.set_level(logging.WARNING, 'metpy.io.nexrad')\n f = Level2File(get_test_data('Level2_KLBB_single_chunk'))\n assert len(f.sweeps) == 1\n assert 'Unable to read volume header' in caplog.text\n\n # Make sure the warning is not present if we pass the right kwarg.\n caplog.clear()\n Level2File(get_test_data('Level2_KLBB_single_chunk'), has_volume_header=False)\n assert 'Unable to read volume header' not in caplog.text","def abort_ber_meas(self):\r\r\n loggerCmw = logging.getLogger('abort_ber_meas')\r\r\n self.write('ABORt:WCDMa:SIGN:BER')\r\r\n loggerCmw.info(\"Aborting BER measurements\")\r\r\n time.sleep(1)","def test_missingDetectors(self):\n files = [getFile(fp)\n for fp in ['bwr_0_det0.m', 'bwr_noxy_det0.m']]\n self._raisesMisMatchError(files)\n self.assertMsgInLogs(\"ERROR\", \"detectors: Parser files\", partial=True)","def test_doubled_file():\n with contextlib.closing(get_test_data('Level2_KFTG_20150430_1419.ar2v')) as infile:\n data = infile.read()\n fobj = BytesIO(data + data)\n f = Level2File(fobj)\n assert len(f.sweeps) == 12","def process_full_file(self, code):\n return code","def test_large_import(self):\n # the original file (from the IDD) is a previous version of the file from\n # the data server for the gp03flmb platform\n self.create_sample_data_set_dir('node59p1_orig.dat', TELEM_DIR, 'node59p1.dat')\n self.assert_initialize()\n # one bad sample in here:\n # PH1236501_01D5u51F361E0_EC_162E has non ascii bytes at the end and is missing \\r\n result = self.data_subscribers.get_samples(DataParticleType.CONTROL, 1, 60)\n result = self.data_subscribers.get_samples(DataParticleType.SAMPLE, 49, 100)\n\n # this file is the more recent file off the data server for gp03flmb/d00001\n # this file appends more data to that in node59p1_orig\n self.create_sample_data_set_dir('node59p1.dat', TELEM_DIR)\n # several bad samples in here:\n # PH1236501_01D5u521208B4_A1_D274 doesn't have enough bytes (469 not 470)\n # PH1236501_01D5u52461BDC_CF_55BD doesn't have enough bytes (469 not 470)\n # PH1236501_01D5u5266BCF1_DA_6466 doesn't have enough bytes (469 not 470)\n # PH1236501_01DAu5288AF85_C9_7365, PH1236501_01DAu529E1BDF_42_4835\n # have extra bytes after the sample, not an error anymore\n # PH1236501_01D5u52B090DA_BA_8CC1 doesn't have enough bytes (469 not 470)\n # PH1236501_01DAu52B38839_BB_4134, PH1236501_01DAu52C8F493_34_3FC2\n # PH1236501_01DAu52ECE16B_79_F727, PH1236501_01DAu53024DC6_F2_7EC9 \n # have extra bytes after sample, not an error anymore\n result = self.data_subscribers.get_samples(DataParticleType.SAMPLE, 751, 430)","def test_readbadformat(self):\n\n self.assertRaises(ParseError, self.hw, self.badfile)","def test_real_file(self):\n log.info('===== START TEST BYTE LOSS =====')\n\n # Recovered\n file_path = os.path.join(RESOURCE_PATH, '11079364_SNA_SNA.txt')\n\n stream_handle = open(file_path, MODE_ASCII_READ)\n\n self.create_parser(stream_handle, telem_flag=False)\n\n particles = self.parser.get_records(182)\n\n log.debug(\"*** test_real_file Num particles %s\", len(particles))\n\n # check all the values against expected results.\n self.assert_particles(particles, '11079364_SNA_SNA_recov.yml', RESOURCE_PATH)\n self.assertEquals(self.exception_callback_value, [])\n stream_handle.close()\n\n # Telemetered\n file_path = os.path.join(RESOURCE_PATH, '11079419_SNA_SNA.txt')\n\n stream_handle = open(file_path, MODE_ASCII_READ)\n\n self.create_parser(stream_handle)\n\n particles = self.parser.get_records(172)\n\n log.debug(\"*** test_real_file Num particles %s\", len(particles))\n\n # check all the values against expected results.\n self.assert_particles(particles, '11079419_SNA_SNA_telem.yml', RESOURCE_PATH)\n stream_handle.close()\n\n log.info('===== END TEST REAL FILE =====')","def test_read_fail2(self):\n mod_fn = os.path.join(tests.TEST_DATA_PATH, 'segmentations', 'test_bad_data2.mod')\n with self.assertRaises(ValueError):\n modreader.get_data(mod_fn) # missing 'IEOF' end","def test08(self):\n logical_file_name = \"/store/mc/Fall08/BBJets250to500-madgraph/GEN-SIM-RAW/IDEAL_/%s/%i.root\" %(uid, 0)\n #print \"WARNING : DBS cannot list INVALID file, so for now this test is commented out\"\n self.api.updateFileStatus(logical_file_name=logical_file_name, is_file_valid=0)\n #listfile\n filesInDBS=self.api.listFiles(logical_file_name=logical_file_name, detail=True)\n self.assertEqual(len(filesInDBS), 1)\n self.assertEqual(filesInDBS[0]['is_file_valid'], 0)","def test_empty_file(self):\n\n temp = tempfile.NamedTemporaryFile()\n temp.flush()\n self.assertRaises(MalformedFileError, NBTFile, temp.name)","def test_harvester_new_file_exception_recovered(self):\n # create the file so that it is unreadable\n self.create_sample_data_set_dir(\n \"DOS15908_1st7_step1.DAT\",\n RECOV_DIR,\n \"DOS15909.DAT\",\n mode=000\n )\n\n # Start sampling and watch for an exception\n self.driver.start_sampling()\n\n self.assert_exception(IOError)\n\n # At this point the harvester thread is dead. The agent\n # exception handle should handle this case.","def test_fileDoesNotExist(self):\n fp = FilePath(self.mktemp())\n protocol = self.makeConnectedDccFileReceive(fp.path)\n\n self.allDataReceivedForProtocol(protocol, b\"I <3 Twisted\")\n\n self.assertEqual(fp.getContent(), b\"I <3 Twisted\")","def testEdgeMarkerGeneric0(self):\n outname = self.prefix+'.asap'\n self.res = sdcal(infile=self.rawfile,calmode='otf',markonly=True,outfile=outname,outform='ASAP')\n refdir = self._readref( self.reffiles[0] )\n self._checkfile( outname ) \n self._checkmarker( outname, refdir )","def test_read_0_2_smirnoff(self):\n ForceField(\n get_data_file_path(\n \"test_forcefields/smirnoff99Frosst_reference_0_2_spec.offxml\"\n )\n )","def test_DL_import_wrong_file_unserialized(self):\n filepath = '6.txt'\n wrong_file = open(filepath, 'x')\n wrong_file.write(\"This is not a serialized detector flow data\")\n wrong_file.close()\n # Check if exception was raised for wrong serialization\n with self.assertRaises(Exception):\n flow_processing_input.DetectorsLocation(9999, filepath)\n os.remove(filepath)","def skip_gutenberg_header(fp):\n for line in fp:\n if line.startswith('*END*THE SMALL PRINT!'):\n break","def test_file_read_bin_missing_file(self):\n with (self.assertRaises(IOError)):\n FileReader(self.bogus_path).read_bin()","def setUp(self):\n self.single_rfh2_message = open(\n os.path.join(self.messages_dir, \"single_rfh2.dat\"), \"rb\").read()\n self.single_rfh2_message_not_well_formed = \\\n self.single_rfh2_message[0:117] + self.single_rfh2_message[121:]","def test_read_0_1_smirnoff(self):\n ForceField(\n get_data_file_path(\n \"test_forcefields/smirnoff99Frosst_reference_0_1_spec.offxml\"\n )\n )","def test_old_format_for_tags(self):\n test_files = glob.glob(INPUT_HYPM_PATH + '/unit_*.mdd')\n test_files.extend(glob.glob(INPUT_FLMB_PATH + '/unit_*.mdd'))\n\n mdd.procall(test_files)\n\n data = self.read_full_file('node58p1.dat')\n if not self.check_for_tags(data):\n self.fail(\"Found header tag in data file\")\n\n data = self.read_full_file('node59p1.dat')\n if not self.check_for_tags(data):\n self.fail(\"Found header tag in data file\")","def test_fake_file_with_deadtime(self):\n fits_file = os.path.join(self.datadir, 'monol_test_fake_lc.evt')\n hen.fake.main(['--deadtime', '2.5e-3',\n '--ctrate', '2000',\n '-o', fits_file])","def _process_end_of_file(self):\n (nd_timestamp, non_data) = self._chunker.get_next_non_data()\n if non_data and len(non_data) > 0:\n message = \"Extra un-expected non-data bytes at the end of the file:%s\", non_data\n log.warn(message)\n self._exception_callback(RecoverableSampleException(message))","def prepare_bed_file(bed_file, output, ouf=False, save_rejected=None, only_chrom=None):\n new_lines = [] # keep updated lines\n rejected = [] # keep IDs of skipped transcripts + the reason why\n names = Counter() # we need to make sure that all names are unique\n allowed_re = re.compile(ALLOWED_CHARSET_RE).search\n broken_names = []\n\n f = open(bed_file, \"r\")\n for num, line in enumerate(f, 1):\n # parse bed file according to specification\n line_data = line.rstrip().split(\"\\t\")\n\n if len(line_data) != 12:\n f.close() # this is for sure an error\n # it is possible only if something except a bed12 was provided\n die(\n \"Error! Bed 12 file is required! Got a file with {len(line_data)} fields instead\"\n )\n\n chrom = line_data[0]\n if only_chrom and chrom != only_chrom:\n # TOGA allows to perform the analysis on a specific chromosome only\n # is so, we can skip all transcripts that located on other chromosomes\n continue\n chromStart = int(line_data[1])\n chromEnd = int(line_data[2])\n name = line_data[3] # gene_name usually\n corr_name = not bool(allowed_re(name))\n if corr_name is False:\n broken_names.append(name)\n # TODO: check weird characters in the transcript name\n # bed_score = int(line_data[4]) # never used\n # strand = line_data[5] # otherwise:\n # strand = True if line_data[5] == '+' else False\n thickStart = int(line_data[6])\n thickEnd = int(line_data[7])\n # itemRgb = line_data[8] # never used\n blockCount = int(line_data[9])\n blockSizes = [int(x) for x in line_data[10].split(\",\") if x != \"\"]\n blockStarts = [int(x) for x in line_data[11].split(\",\") if x != \"\"]\n blockEnds = [blockStarts[i] + blockSizes[i] for i in range(blockCount)]\n blockAbsStarts = [blockStarts[i] + chromStart for i in range(blockCount)]\n blockAbsEnds = [blockEnds[i] + chromStart for i in range(blockCount)]\n blockNewStarts, blockNewEnds = [], []\n names[name] += 1\n\n if thickStart > thickEnd:\n f.close() # according to bed12 specification this should never happen\n sys.stderr.write(f\"Problem occurred at line {num}, gene {name}\\n\")\n die(\"Error! Bed file is corrupted, thickEnd MUST be >= thickStart\")\n elif thickStart == thickEnd:\n # this means that this is a non-coding transcript\n # TOGA cannot process them: we can skip it\n rejected.append((name, \"No CDS\"))\n continue\n\n if thickStart < chromStart or thickEnd > chromEnd:\n # a very strange (but still possible) case\n f.close() # for sure an error with input data\n sys.stderr.write(f\"Problem occurred at line {num}, gene {name}\\n\")\n die(\"Error! Bed file is corrupted, thickRange is outside chromRange!\")\n\n # now select CDS only\n # we keep UTRs in the filtered file\n # however, we need CDS to check whether it's correct (% 3 == 0)\n for block_num in range(blockCount):\n blockStart = blockAbsStarts[block_num]\n blockEnd = blockAbsEnds[block_num]\n\n # skip the block if it is entirely UTR\n if blockEnd <= thickStart:\n continue\n elif blockStart >= thickEnd:\n continue\n\n # if we are here: this is not an entirely UTR exon\n # it might intersect the CDS border or to be in the CDS entirely\n # remove UTRs: block start must be >= CDS_start (thickStart)\n # block end must be <= CDS_end (thickEnd)\n blockNewStart = blockStart if blockStart >= thickStart else thickStart\n blockNewEnd = blockEnd if blockEnd <= thickEnd else thickEnd\n blockNewStarts.append(blockNewStart - thickStart)\n blockNewEnds.append(blockNewEnd - thickStart)\n\n if len(blockNewStarts) == 0:\n # even it thickStart != thickEnd this transcript still can be non-coding\n # but if there are no blocks in the CDS -> we can catch this\n rejected.append((name, \"No CDS\"))\n continue\n\n block_new_count = len(blockNewStarts)\n blockNewSizes = [\n blockNewEnds[i] - blockNewStarts[i] for i in range(block_new_count)\n ]\n\n if sum(blockNewSizes) % 3 != 0 and not ouf:\n # this is an out-of-frame (or incomplete transcript)\n # ideally CDS length should be divisible by 3\n # not ouf means that we like to keep such transcripts for some reason\n rejected.append((name, \"Out-of-frame gene\"))\n continue\n\n # we keep this transcript: add in to the list\n new_line = \"\\t\".join([str(x) for x in line_data])\n new_lines.append(new_line)\n f.close()\n\n # if not allowed characters in transcript names: list them\n if len(broken_names) > 0:\n eprint(\"Error! Some transcript names contain not allowed characters\")\n for t in broken_names:\n eprint(t)\n die(f\"Allowed characters are: {ALLOWED_CHARSET}\")\n # if there are non-unique transcript IDs: die\n # I kill it there, not earlier to show them altogether\n if any(v > 1 for v in names.values()):\n eprint(\"Error! There are non-uniq transcript IDs:\")\n duplicates = [k for k, v in names.items() if v > 1]\n for d in duplicates:\n eprint(d)\n die(\"Abort\")\n\n if len(new_lines) == 0:\n # no transcripts pass the filter: probably an input data mistake\n sys.exit(\n f\"Error! No reference annotation tracks left after filtering procedure! Abort\"\n )\n\n # write transcripts that passed the filter to the output file\n f = open(output, \"w\") if output != \"stdout\" else sys.stdout\n f.write(\"\\n\".join(new_lines) + \"\\n\")\n f.close() if output != \"stdout\" else None\n\n if save_rejected:\n # save transcripts that didn't pass the filter + reason why\n f = open(save_rejected, \"w\")\n for elem in rejected:\n f.write(f\"{elem[0]}\\t{elem[1]}\\n\")\n f.close()","def test_read_0_1_smirff(self):\n ForceField(\n get_data_file_path(\n \"test_forcefields/smirff99Frosst_reference_0_1_spec.offxml\"\n )\n )","def __checkFile(self, filename):\n \n try:\n with open(filename, 'r') as f:\n first_line = f.readline()\n \n if not len(first_line.split(\"\\t\")) == 19:\n raise BadProteomeScoutFile(\"N/A\")\n \n \n except:\n BadProteomeScoutFile(\"Invalid ProteomeScout flat file %s.\\nFile is invalid or corrupted\" % str(filename))","def test_not_implemented():\n for not_implemented_ext in ['.mef', '.nwb']:\n data_path = _TempDir()\n raw_fname = op.join(data_path, 'test' + not_implemented_ext)\n with open(raw_fname, 'w', encoding='utf-8'):\n pass\n with pytest.raises(ValueError, match=('there is no IO support for '\n 'this file format yet')):\n _read_raw(raw_fname)","def test_harvester_new_file_exception_recovered(self):\n # need to put data in the file, not just make an empty file for this to work\n self.create_sample_data_set_dir(\n \"DOS15908_1st7_step1.DAT\",\n RECOV_DIR,\n \"DOS15908.DAT\",\n mode=000,\n copy_metadata=False\n )\n\n self.assert_initialize(final_state=ResourceAgentState.COMMAND)\n\n self.event_subscribers.clear_events()\n self.assert_resource_command(DriverEvent.START_AUTOSAMPLE)\n self.assert_state_change(ResourceAgentState.LOST_CONNECTION, 90)\n self.assert_event_received(ResourceAgentConnectionLostErrorEvent, 10)\n\n self.clear_sample_data()\n self.create_sample_data_set_dir(\n \"DOS15908_1st7_step1.DAT\",\n RECOV_DIR,\n \"DOS15908.DAT\",\n copy_metadata=False\n )\n\n # Should automatically retry connect and transition to streaming\n self.assert_state_change(ResourceAgentState.STREAMING, 90)","def test_GFD_import_wrong_file_unserialized(self):\n filepath = '6.txt'\n wrong_file = open(filepath, 'x')\n wrong_file.write(\"This is not a serialized detector flow data\")\n wrong_file.close()\n # Check if exception was raised for wrong serialization\n with self.assertRaises(Exception):\n flow_processing_input.GroundFlowData(filepath)\n os.remove(filepath)","def test_read_fail1(self):\n mod_fn = os.path.join(tests.TEST_DATA_PATH, 'segmentations', 'test_bad_data1.mod')\n with self.assertRaises(ValueError):\n modreader.get_data(mod_fn) # missing 'IMOD' start","def test_02_not_exist(self):\n with self.assertLogs(\"borg\", \"WARNING\") as logger:\n self.api.extract(self.archive, self.file_3)\n message = logger.records[0].getMessage()\n self.assertRegex(\n message,\n r\".*?file_3.*never\",\n \"Warning not logged for bad path\",\n )","def test_readfile(self):\n fname = os.path.join(self.datadir, 'monol_testA_E3-50_rebin4_gti') + \\\n HEN_FILE_EXTENSION\n command = \"{0}\".format(fname)\n\n hen.io.main(command.split())","def test_harvester_new_file_exception(self):\n # need to put data in the file, not just make an empty file for this to work\n self.create_sample_data_set_dir('node59p1_step4.dat', TELEM_DIR, \"node59p1.dat\",\n mode=000)\n\n self.assert_initialize(final_state=ResourceAgentState.COMMAND)\n\n self.event_subscribers.clear_events()\n self.assert_resource_command(DriverEvent.START_AUTOSAMPLE)\n self.assert_state_change(ResourceAgentState.LOST_CONNECTION, 90)\n self.assert_event_received(ResourceAgentConnectionLostErrorEvent, 10)\n\n self.clear_sample_data()\n self.create_sample_data_set_dir('node59p1_step4.dat', TELEM_DIR, \"node59p1.dat\")\n\n # Should automatically retry connect and transition to streaming\n self.assert_state_change(ResourceAgentState.STREAMING, 90)","def test_incomplete_file(self):\n log.info(\"START INTEG TEST INCOMPLETE\")\n\n self.clear_sample_data()\n self.clear_async_data()\n\n # From sample file A0000010.DEC:\n # Flag record, first and last velocity record, time record,\n # but the end of Velocity record (all zeroes) is missing.\n filename = \"A1000002.DEC\"\n self.create_sample_data('incomplete_A0000002.DEC', filename)\n\n # Start sampling.\n self.driver.start_sampling()\n\n # an event catches the sample exception\n self.assert_event('ResourceAgentErrorEvent')\n\n # Verify that the entire file has been read.\n self.assert_file_ingested(filename)\n\n log.info(\"END INTEG TEST INCOMPLETE\")","def test_is_not_delicious_file(self):\r\n bad_file = StringIO.StringIO()\r\n bad_file.write('failing tests please')\r\n bad_file.seek(0)\r\n\r\n self.assertTrue(\r\n not DelXMLImporter.can_handle(bad_file),\r\n \"DelXMLImporter cannot handle this file\")\r\n\r\n bad_file.close()","def test_harvester_new_file_exception(self):\n # need to put data in the file, not just make an empty file for this to work\n self.create_sample_data_set_dir(\n 'node59p1_step4.dat',\n TELEM_DIR,\n \"node59p1.dat\",\n mode=000,\n copy_metadata=False\n )\n\n self.assert_initialize(final_state=ResourceAgentState.COMMAND)\n\n self.event_subscribers.clear_events()\n self.assert_resource_command(DriverEvent.START_AUTOSAMPLE)\n self.assert_state_change(ResourceAgentState.LOST_CONNECTION, 90)\n self.assert_event_received(ResourceAgentConnectionLostErrorEvent, 10)\n\n self.clear_sample_data()\n self.create_sample_data_set_dir(\n 'node59p1_step4.dat',\n TELEM_DIR,\n \"node59p1.dat\",\n copy_metadata=False\n )\n\n # Should automatically retry connect and transition to streaming\n self.assert_state_change(ResourceAgentState.STREAMING, 90)","def test_block_bad_signature(self):\n pass","def test_incomplete_file(self):\n log.info(\"START QUAL TEST INCOMPLETE FILE\")\n\n # From sample file A0000010.DEC:\n # Flag record, first and last velocity record, time record,\n # but the end of Velocity record (all zeroes) is missing.\n self.clear_sample_data()\n self.event_subscribers.clear_events()\n self.assert_initialize()\n self.create_sample_data('incomplete_A0000002.DEC', \"A1000002.DEC\")\n\n # Verify an event was raised and we are in our retry state.\n self.verify_queue_empty()\n self.assert_event_received(ResourceAgentErrorEvent, 10)\n self.assert_state_change(ResourceAgentState.STREAMING, 10)\n\n log.info(\"END QUAL TEST INCOMPLETE FILE\")","def test_harvester_new_file_exception(self):\n # create the file so that it is unreadable\n self.create_sample_data_set_dir(\n \"node59p1_step1.dat\",\n TELEM_DIR,\n \"node59p1.dat\",\n mode=000,\n copy_metadata=False\n )\n\n # Start sampling and watch for an exception\n self.driver.start_sampling()\n\n self.assert_exception(ValueError)\n\n # At this point the harvester thread is dead. The agent\n # exception handle should handle this case.","def checkIfAllowedToModify(self):\n\n oldBytes = b''\n testFileName = self.MAPSTUDIO + self.inputFiles[0] + '.msb'\n\n with open(testFileName, 'rb') as oldf:\n oldBytes = oldf.read()\n\n # Try writing something to the file\n\n try:\n with open(testFileName, 'wb') as outf:\n outf.write(b'TESTINGIFICANWRITEINTOTHISFILE')\n except:\n return False\n\n # Because apparently for _some_ reason it doesn't throw an error sometimes(?) so we confirm if the file was actually modified\n\n newBytes = b''\n with open(testFileName, 'rb') as oldf:\n newBytes = oldf.read()\n\n if (oldBytes == newBytes):\n return False\n\n # Restore the file to normal\n\n with open(testFileName, 'wb') as outf:\n outf.write(oldBytes)\n\n oldBytes = b''\n newBytes = b''\n\n return True","def test_harvester_new_file_exception(self):\n\n # create the file so that it is unreadable\n self.create_sample_data_set_dir(\"node59p1_step1.dat\", TELEM_DIR, \"node59p1.dat\",\n mode=000)\n\n # Start sampling and watch for an exception\n self.driver.start_sampling()\n\n self.assert_exception(ValueError)\n\n # At this point the harvester thread is dead. The agent\n # exception handle should handle this case.","def test_strain_redefined(generate_strain_redefined):\n fname = generate_strain_redefined\n try:\n process_files([fname])\n raise Exception('The redefined strain data and lack of stress data was not caught')\n except IOError:\n pass","def skip_gutenberg_header(fp):\n for line in fp:\n if line.startswith(''):\n break","def test_bad_protein_file():\n\n bad = random_filename()\n rv, out = getstatusoutput(f'{prg} --cdhit {cdhit} -p {bad}')\n assert rv > 0\n assert out.lower().startswith('usage:')\n assert re.search(f\"No such file or directory: '{bad}'\", out)","def reportFileCorruption(gpfn, sitemover):\n\n # except for lcgcp site mover (since it does not return a proper SURL, the consistency report is done in the site mover)\n _copytool, dummy = getCopytool(mode=\"get\")\n if _copytool != \"lcgcp\" and _copytool != \"lcg-cp\" and _copytool != \"storm\":\n if gpfn != \"\":\n try:\n sitemover.reportFileCorruption(gpfn)\n except Exception, e:\n tolog(\"!!WARNING!!1212!! Caught exception: %s\" % (e))\n else:\n tolog(\"Reported file corruption\")\n else:\n tolog(\"!!WARNING!!1990!! Can not report SURL for corrupt file to consistency server since SURL is an empty string\")\n else:\n tolog(\"(Already reported corrupted file)\")","def recover_data(infile: str, outfile: str, lsb: int, nbytes: int):\n if not lsb:\n return 7\n if not nbytes:\n return 8\n\n if not infile.endswith('.wav'):\n return 4\n\n try:\n lsb = int(lsb)\n except TypeError:\n lsb = lsb\n\n steganographer = Stego(infile, lsb)\n if steganographer.recover(outfile, nbytes):\n return 0\n\n cleanup(outfile)\n return 1","def test_is_not_delicious_file(self):\r\n bad_file = StringIO.StringIO()\r\n bad_file.write('failing tests please')\r\n bad_file.seek(0)\r\n\r\n self.assertTrue(\r\n not DelImporter.can_handle(bad_file),\r\n \"DelImporter cannot handle this file\")\r\n\r\n bad_file.close()","def test_bad_hsm():\n image_file = os.path.join('input','DECam_00241238_01.fits.fz')\n cat_file = os.path.join('input',\n 'DECam_00241238_01_psfcat_tb_maxmag_17.0_magcut_3.0_findstars.fits')\n psf_file = os.path.join('output','bad_hsm.fits')\n\n twodhist_file = os.path.join('output','bad_hsm_twod.pdf')\n whisker_file = os.path.join('output','bad_hsm_whisk.pdf')\n rho_file = os.path.join('output','bad_hsm_rho.pdf')\n shape_file = os.path.join('output','bad_hsm_shape.pdf')\n star_file = os.path.join('output','bad_hsm_star.pdf')\n hsm_file = os.path.join('output','bad_hsm_hsm.fits')\n hsm4_file = os.path.join('output','bad_hsm_hsm_fourth.fits')\n sizemag_file = os.path.join('output','bad_hsm_sizemag.png')\n\n stamp_size = 25\n\n # The configuration dict with the right input fields for the file we're using.\n config = {\n 'input' : {\n 'nstars': 8,\n 'image_file_name' : image_file,\n 'image_hdu' : 1,\n 'weight_hdu' : 3,\n 'badpix_hdu' : 2,\n 'cat_file_name' : cat_file,\n 'cat_hdu' : 2,\n # These next two are intentionally backwards. The PixelGrid will find some kind\n # of solution, but it will be complex garbage, and hsm will fail for them.\n 'x_col' : 'YWIN_IMAGE',\n 'y_col' : 'XWIN_IMAGE',\n 'sky_col' : 'BACKGROUND',\n 'stamp_size' : stamp_size,\n 'ra' : 'TELRA',\n 'dec' : 'TELDEC',\n 'gain' : 'GAINA',\n },\n 'output' : {\n 'file_name' : psf_file,\n 'stats' : [\n {\n 'type': 'TwoDHist',\n 'file_name': twodhist_file,\n },\n {\n 'type': 'Whisker',\n 'file_name': whisker_file,\n },\n { # Note: stats doesn't have to be a list.\n 'type': 'Rho',\n 'file_name': rho_file\n },\n {\n 'type': 'ShapeHist',\n 'file_name': shape_file,\n },\n {\n 'type': 'Star',\n 'file_name': star_file,\n },\n {\n 'type': 'SizeMag',\n 'file_name': sizemag_file,\n },\n {\n 'type': 'HSMCatalog',\n 'file_name': hsm_file,\n },\n {\n 'type': 'HSMCatalog',\n 'file_name': hsm4_file,\n 'fourth_order': True,\n },\n ],\n },\n 'psf' : {\n 'model' : {\n 'type' : 'PixelGrid',\n 'scale' : 0.3,\n 'size' : 10,\n 'interp': 'Lanczos(3)'\n },\n 'interp' : { 'type' : 'Mean' },\n 'outliers' : {\n 'type' : 'Chisq',\n 'nsigma' : 0.05 # This will throw out all but 1, which adds an additional\n # test of Star stats when nstars < nplot\n }\n },\n }\n if __name__ == '__main__':\n logger = piff.config.setup_logger(1)\n else:\n config['verbose'] = 0\n logger = None\n\n for f in [twodhist_file, rho_file, shape_file, star_file, hsm_file]:\n if os.path.exists(f):\n os.remove(f)\n\n piff.piffify(config, logger=logger)\n\n # Confirm that all but one star was rejected, since that was part of the intent of this test.\n psf = piff.read(psf_file)\n print('stars = ',psf.stars)\n print('nremoved = ',psf.nremoved)\n assert len(psf.stars) == 1\n assert psf.nremoved == 7 # There were 8 to start.\n\n for f in [twodhist_file, rho_file, shape_file, star_file, sizemag_file, hsm_file]:\n assert os.path.exists(f)\n\n # Check hsm file with bad measurements\n # The one star that was left still fails hsm measurement here.\n data = fitsio.read(hsm_file)\n for col in ['ra', 'dec', 'x', 'y', 'u', 'v',\n 'T_data', 'g1_data', 'g2_data',\n 'T_model', 'g1_model', 'g2_model',\n 'flux', 'reserve', 'flag_data', 'flag_model']:\n assert len(data[col]) == 1\n print('flag_data = ',data['flag_data'])\n print('flag_model = ',data['flag_model'])\n np.testing.assert_array_equal(data['flag_data'], 7)\n np.testing.assert_array_equal(data['flag_model'], 7)","def test_large_flmb(self):\n test_files_218 = glob.glob(INPUT_FLMB_PATH + '/unit_363-2013-218*.mdd')\n\n mdd.procall(test_files_218)\n\n data_orig = self.read_full_file('node59p1.dat')\n\n # two status files from different controllers, 12371 and 12365\n data_out_71 = self.read_full_file('node59p1_0.status_1237101.dat')\n self.check_sio_type(data_out_71, ['CS', 'PS'])\n data_out_65 = self.read_full_file('node59p1_0.status_1236501.dat')\n self.check_sio_type(data_out_65, ['CS', 'PS'])\n data_out = data_out_71\n data_out += data_out_65\n\n data_adcps = self.read_full_file('node59p1_0.adcps_1237111.dat')\n self.check_sio_type(data_adcps, ['AD'])\n data_out += data_adcps\n\n data_ctdmo = self.read_full_file('node59p1_0.ctdmo_1237100.dat')\n self.check_sio_type(data_ctdmo, ['CT', 'CO'])\n data_out += data_ctdmo\n\n data_dosta = self.read_full_file('node59p1_0.dosta_1236501.dat')\n self.check_sio_type(data_dosta, ['DO'])\n data_out += data_dosta\n\n data_flort = self.read_full_file('node59p1_0.flort_1236501.dat')\n self.check_sio_type(data_flort, ['FL'])\n data_out += data_flort\n\n data_phsen = self.read_full_file('node59p1_0.phsen_1236501.dat')\n self.check_sio_type(data_phsen, ['PH'])\n data_out += data_phsen\n\n if not TestSioUnpack.compare_sio_matches(data_orig, data_out):\n self.fail(\"Failed sio block compare\")\n\n test_files = glob.glob(INPUT_FLMB_PATH + '/unit_363-2013-205*.mdd')\n test_files_217 = glob.glob(INPUT_FLMB_PATH + '/unit_363-2013-217*.mdd')\n test_files_219 = glob.glob(INPUT_FLMB_PATH + '/unit_363-2013-219*.mdd')\n\n test_files.extend(test_files_217)\n test_files.extend(test_files_219)\n\n mdd.procall(test_files)\n\n data_out = self.compare_node59(1, data_out)\n\n test_files = glob.glob(INPUT_FLMB_PATH + '/unit_363-2013-233*.mdd')\n test_files_231 = glob.glob(INPUT_FLMB_PATH + '/unit_363-2013-231*.mdd')\n\n test_files.extend(test_files_231)\n\n mdd.procall(test_files)\n\n self.compare_node59(2, data_out)","def test_file_read_gzip_missing_file(self):\n with (self.assertRaises(IOError)):\n FileReader(self.bogus_path).read_gzip()","def attempt_file_reset(f):\r\n if hasattr(f, 'seek'):\r\n f.seek(0)","def write_no_seek(meta_file, data_block):\n position = meta_file.tell()\n # seek 0 bytes from the end of file (2)\n meta_file.seek(0, 2)\n meta_file.write(data_block)\n meta_file.seek(position)","def test_fake_file_xmm(self):\n fits_file = os.path.join(self.datadir, 'monol_test_fake_lc_xmm.evt')\n hen.fake.main(['--deadtime', '1e-4', '-m', 'XMM', '-i', 'epn',\n '--ctrate', '2000',\n '-o', fits_file])\n hdu_list = fits.open(fits_file)\n hdunames = [hdu.name for hdu in hdu_list]\n assert 'STDGTI01' in hdunames\n assert 'STDGTI02' in hdunames\n assert 'STDGTI07' in hdunames","def test_basic_mech_write(self):\n\n unit = btmux.parse_from_file(os.path.join(BTMUX_SAMPLE_DIR, 'AS7-D'))\n fobj = StringIO()\n write_to_file(unit, fobj)\n #print fobj.getvalue()\n # TODO: Compare to a golden standard.","def test_load_events_split(self):\n command = \\\n '{0} -g --min-length 0'.format(\n os.path.join(self.datadir, 'monol_testB.evt'))\n hen.read_events.main(command.split())\n new_filename = os.path.join(self.datadir,\n 'monol_testB_nustar_fpmb_gti000_ev' +\n HEN_FILE_EXTENSION)\n assert os.path.exists(new_filename)","def test_hiddenbinary(self):\n # copy file rules\n tmpfile = tempfile.NamedTemporaryFile(\n suffix='virus', prefix='fuglu-unittest', dir='/tmp')\n shutil.copy(TESTDATADIR + '/binaryattachment.eml', tmpfile.name)\n suspect = Suspect(\n 'sender@unittests.fuglu.org', 'recipient@unittests.fuglu.org', tmpfile.name)\n\n result = self.candidate.examine(suspect)\n if type(result) is tuple:\n result, message = result\n tmpfile.close()\n self.assertEqual(result, DELETE)","def process_file(file_name):\n pass # delete this line and replace with your code here","def test_mapping_file_removal(self):\r\n mf_exp, _ = parse_mapping_file_to_dict(self.MF_OUT_1)\r\n # bt doesn't change in this test\r\n bt_exp = parse_biom_table(self.BT_IN_1)\r\n mf_obs, bt_obs, nonshared_samples = \\\r\n sync_biom_and_mf(parse_mapping_file_to_dict(self.MF_IN_1)[0],\r\n parse_biom_table(self.BT_IN_1))\r\n self.assertEqual(mf_exp, mf_obs)\r\n self.assertEqual(bt_exp, bt_obs)\r\n self.assertEqual(nonshared_samples, set(['NotInOtuTable2',\r\n 'NotInOtuTable1']))","def test_lj_no_url(self):\n text = self.transfer('msg3.txt')\n assert self.mark not in text","def test_stress_not_in(generate_no_stress_one_file):\n fname = generate_no_stress_one_file\n with pytest.raises(Exception):\n process_files([fname])","def tearDown(self):\n try:\n os.remove(self.junk_file)\n except OSError as doh:\n if doh.errno == 2:\n # No such File, ignore\n pass\n else:\n raise","def test_strain_not_in(generate_no_strain_one_file):\n fname = generate_no_strain_one_file\n with pytest.raises(Exception) as f:\n process_files([fname])","def test_empty_file(self):\n with open(os.path.join(test_dir, \"empty_file.txt\")) as f:\n for idx, line in enumerate(reverse_readline(f)):\n raise ValueError(\"an empty file is being read!\")","def test_bad_file():\n\n bad = ''.join(random.choices(string.ascii_uppercase + string.digits, k=5))\n rv, out = getstatusoutput(f'{prg} -f {bad}')\n assert rv != 0\n assert re.match('usage:', out, re.I)\n assert re.search(f\"No such file or directory: '{bad}'\", out)","def test_export_to_mff_no_device():\n pytest.importorskip(\"mffpy\", \"0.5.7\")\n evoked = read_evokeds_mff(egi_evoked_fname, condition=\"Category 1\")\n evoked.info[\"device_info\"] = None\n with pytest.raises(ValueError, match=\"No device type.\"):\n export_evokeds(\"output.mff\", evoked)","def test_mapping_file_removal(self):\r\n mf_exp, _ = parse_mapping_file_to_dict(self.MF_OUT_3)\r\n # bt doesn't change in this test\r\n bt_exp = parse_biom_table(self.BT_OUT_3)\r\n mf_obs, bt_obs, nonshared_samples = \\\r\n sync_biom_and_mf(parse_mapping_file_to_dict(self.MF_IN_3)[0],\r\n parse_biom_table(self.BT_IN_1))\r\n self.assertEqual(mf_exp, mf_obs)\r\n self.assertEqual(bt_exp, bt_obs)\r\n self.assertEqual(nonshared_samples, set(['Sample4', 'NotInOtuTable2',\r\n 'NotInOtuTable1']))","def perform_general():\r\n print(\"Performing the \\\"indirect\\\" check on all blocks\")\r\n \r\n filename_part = \"fusedata.\"\r\n i_start = begining_block_number + 1 #1\r\n i_end = ending_block_number #25\r\n file_name = filename_part\r\n\r\n \r\n for i in range(i_start, (i_end + 1)):\r\n #opening each block available to us\r\n file_name = filename_part + str(i)\r\n #print \"file_name\"+file_name\r\n file_access = open (file_name,\"r+\")\r\n \r\n try:\r\n block_contents = json.load(file_access)\r\n file_access.close()\r\n except ValueError:\r\n print \"\\\"\"+file_name+\"\\\" not in json format (catch 1)\"\r\n file_access.close() \r\n continue\r\n \r\n # first performing the size check\r\n if(type(block_contents) == dict):\r\n # checking if the current parsed block is a file inode\r\n if((\"indirect\" in block_contents) == True):\r\n size_check(block_contents, file_name)\r\n perform_indirect(block_contents, file_name)\r\n \r\n #closing the file to effect changes\r\n file_access_2 = open (file_name,\"w\")\r\n json.dump(block_contents,file_access_2)\r\n file_access_2.close() \r\n \r\n\r\n \r\n print(\"Reached end of test\") \r\n \r\n print(\"-------------------------------\")","def test_stress_redefined(generate_stress_redefined):\n fname = generate_stress_redefined\n try:\n process_files([fname])\n raise Exception('The redefined stress data and lack of strain data was not caught')\n except IOError:\n pass","def test_bad_file():\n\n bad_file = random_string()\n letter = random.choice(string.ascii_lowercase)\n rv, out = getstatusoutput('{} {} -f {}'.format(prg, letter, bad_file))\n assert rv != 0\n expected = \"No such file or directory: '{}'\".format(bad_file)\n assert re.search(expected, out)","def sniff( self, filename ):\n handle = open(filename)\n line = handle.readline()\n\n #nb carac\n first = line.split()\n if ( not first[0].isdigit() ):\n return False\n\n ncar=int(first[0]);\n line = handle.readline()\n first = line.split()\n if ( not first[0].isdigit() ):\n return False\n if ( not first[1].isdigit() ):\n return False\n\n nfix=int(first[0]);\n ncov=int(first[1]);\n\n #nom des effets\n line = handle.readline()\n first = line.split()\n if ( len(first) < (nfix + ncov)):\n return False\n\n for i in range(ncar):\n line = handle.readline()\n first = line.split()\n if ( len(first) < (2+2*nfix+ncov) ):\n return False\n\n handle.close()\n\n return True","def test_read_xls_file_not_found(self):\r\n my_tape = Tape()\r\n my_tape.read_xls('bogus_tape_file')","def test_remove_file_group0(self):\n with copy_of_directory(assets.path_to('SBB0000F29300010000/data')) as tempdir:\n mets = OcrdMets(filename=join(tempdir, 'mets.xml'))\n self.assertEqual(len(mets.file_groups), 17)\n self.assertEqual(len(mets.find_all_files()), 35)\n # print()\n # before = sorted([x.ID for x in mets.find_all_files()])\n with self.assertRaisesRegex(Exception, \"not empty\"):\n mets.remove_file_group('OCR-D-GT-ALTO')\n mets.remove_file_group('OCR-D-GT-PAGE', recursive=True)\n # print([x for x in before if x not in sorted([x.ID for x in mets.find_all_files()])])\n self.assertEqual(len(mets.file_groups), 16)\n self.assertEqual(len(mets.find_all_files()), 33)","def test_ignore_empty_files(self):\n\n self.checker.config.file_header_ignore_empty_files = True\n node_mock = MagicMock()\n node_mock.stream.return_value.__enter__.return_value.read.return_value.decode.return_value = ''\n with self.assertNoMessages():\n self.checker.process_module(node_mock)","def process_rom_file(name):\n\n # Link the instruction rom file to the tb directory\n SRC_FILE = REPO_ROOT + '/tests/riscv-tests-simple/generated/' + name + \".verilog\"\n ROM_FILE = os.getcwd() + '/verilog.rom' # need to link the instruction ram file the the current directory\n if os.path.isfile(ROM_FILE):\n os.remove(ROM_FILE)\n os.symlink(SRC_FILE, ROM_FILE)\n\n FP = open('verilog.rom', \"r\")\n IRAM_FP = open('instr_ram.rom', \"w\")\n DRAM_FP = open('data_ram.rom', \"w\")\n\n iram = True\n for line in FP.readlines():\n if line.rstrip() == \"@01000000\":\n iram = False\n continue\n if iram:\n IRAM_FP.write(line)\n else:\n DRAM_FP.write(line)\n\n\n FP.close()\n IRAM_FP.close()\n DRAM_FP.close()","def test_invalid_flag_record(self):\n log.info(\"START INTEG TEST INVALID\")\n\n self.clear_sample_data()\n self.clear_async_data()\n\n # Made-up data with all flags except the first set to True.\n # First flag is not a zero or one.\n filename = \"A1000003.DEC\"\n self.create_sample_data('invalid_A0000003.DEC', filename)\n\n # Start sampling.\n self.driver.start_sampling()\n\n # an event catches the sample exception\n self.assert_event('ResourceAgentErrorEvent')\n\n # Verify that the entire file has been read.\n self.assert_file_ingested(filename)\n log.info(\"END INTEG TEST INVALID\")","def test_do_not_ignore_empty_files(self):\n\n node_mock = MagicMock()\n node_mock.stream.return_value.__enter__.return_value.read.return_value.decode.return_value = ''\n with self.assertAddsMessages(pylint.testutils.Message(\n msg_id='invalid-file-header',\n line=1,\n args=self.EXPECTED_HEADER)):\n self.checker.process_module(node_mock)","def file(self,file):\n self.lib.lammps_file(self.lmp,file.encode('utf-8'))","def test_no_tags(self):\n test_files = glob.glob(INPUT_GI_PATH + '/gi_*.mdd')\n\n mdd.procall(test_files)\n\n data = self.read_full_file('node16p1.dat')\n if not self.check_for_tags(data):\n self.fail(\"Found header tag in data file\")\n\n data = self.read_full_file('node17p1.dat')\n if not self.check_for_tags(data):\n self.fail(\"Found header tag in data file\")\n\n data = self.read_full_file('node14p1.dat')\n if not self.check_for_tags(data):\n self.fail(\"Found header tag in data file\")","def _process_file(self, path):\n\t\tself.getFailures(path)\n\t\ttry:\n\t\t\twhile True:\n\t\t\t\tticket = self.failManager.toBan()\n\t\t\t\tself.jail.putFailTicket(ticket)\n\t\texcept FailManagerEmpty:\n\t\t\tself.failManager.cleanup(MyTime.time())\n\t\tself.dateDetector.sortTemplate()\n\t\tself.__modified = False","def process_message(msg):\n global fout\n print(\"received \")\n if len(msg)==200: #is header or end\n msg_in=msg.decode(\"utf-8\",\"ignore\")\n msg_in=msg_in.split(\",,\")\n if msg_in[0]==\"header\": #header\n filename=extract_file_data(msg_in[1])\n file_out=\"copy-\"+filename\n fout=open(file_out,\"wb\") #use a different filename\n\n if msg_in[0]==\"end\": #is it really last packet?\n in_hash_final=in_hash_md5.hexdigest()\n if in_hash_final==msg_in[2]:\n print(\"File copied OK -valid hash \",in_hash_final)\n else:\n print(\"Bad file receive \",in_hash_final)\n return False\n else:\n if msg_in[0]!=\"header\":\n in_hash_md5.update(msg)\n return True\n else:\n return False\n else:\n in_hash_md5.update(msg)\n #msg_in=msg.decode(\"utf-8\",\"ignore\")\n if len(msg) <100:\n print(msg)\n return True","def test_noFilesFromAccept(self):\n return self._acceptFailureTest(ENFILE)","def _prepare_blocks():\n\n counter = blocks[0]['freeStart']\n maxBlocks = blocks[0]['maxBlocks']\n while(counter < maxBlocks) :\n try:\n # print (mount['parent'] + '/linddata.' + str(counter))\n f = open(mount['parent'] + '/linddata.' + str(counter), 'r') \n except IOError, e:\n return STATUS['M_BD']\n else :\n fdatastring = f.next()\n fdata = deserializedata(fdatastring)\n blocks[counter] = fdata\n counter += 1\n \n return STATUS['OK']","def assert_after_stop(self):\n super(parent.TestFileOutputDriver, self).assert_after_stop()\n assert(os.path.isfile(self.filepath))\n with open(self.filepath, 'rb') as fd:\n contents = fd.read()\n nt.assert_equal(contents, self.ply_file_contents)","def test_lint_fail_malformed(self, style):\n with ExpectedException(LinterFailure):\n run_linter_throw(\"path/to/file\",\n \"{s} path/to/file_wrong\\n{m}{e}\\n\",\n style,\n whitelist=[\"headerblock/filename\"])","def test_verify_clear_trace_mid_reassembly(self):\n\n self.pg_enable_capture()\n self.src_if.add_stream(self.fragments_400[0:-1])\n self.pg_start()\n\n self.logger.debug(self.vapi.cli(\"show trace\"))\n self.vapi.cli(\"clear trace\")\n\n self.src_if.add_stream(self.fragments_400[-1])\n self.pg_start()\n packets = self.dst_if.get_capture(len(self.pkt_infos))\n self.verify_capture(packets)","def fix_xfer_syntax(filename):\n\n current_syntax = get_xfer_syntax(filename)\n if (current_syntax == '1.2.840.10008.1.2.1' or \n current_syntax is None or\n current_syntax == '1.2.840.10008.1.2'):\n return (filename, filename)\n else:\n print(current_syntax)\n\n new_filename = tempfile.mktemp(prefix='iffpy')\n\n subprocess.run([\"gdcmconv\",\n \"-w\",\n \"-i\", filename,\n \"-o\", new_filename])\n\n if os.path.exists(new_filename):\n print(f\"Successfully converted file: {new_filename}\")\n return (new_filename, f\"decompressed;{filename}\")\n else:\n print(f\"Looks like this one failed: {new_filename}\")\n return (None, None)","def get_file_format(file):\n flag = None\n with open(file) as f:\n for line in f.readlines():\n MAT, MF, MT = read_control(line)[:3]\n if MF == 1 and MT == 451:\n i = 0\n C, i = read_cont([line], i)\n flag = C.N1\n break\n if flag is None:\n ftype = None\n elif flag == -11 or flag == -12:\n ftype = \"errorr\"\n elif flag == -1:\n ftype = \"gendf\"\n else:\n if C.L1 == 2:\n ftype = \"pendf\"\n else:\n ftype = \"endf6\"\n return ftype","def read(file):\n\n blocks = ['bus', 'load', 'fshunt', 'gen', 'branch', 'transf', 'area',\n 'twotermdc', 'vscdc', 'impedcorr', 'mtdc', 'msline', 'zone',\n 'interarea', 'owner', 'facts', 'swshunt', 'gne', 'Q']\n nol = [1, 1, 1, 1, 1, 4, 1,\n 0, 0, 0, 0, 0, 1,\n 0, 1, 0, 0, 0, 0]\n rawd = re.compile('rawd\\d\\d')\n\n retval = True\n version = 0\n b = 0 # current block index\n raw = {}\n for item in blocks:\n raw[item] = []\n\n data = []\n mdata = [] # multi-line data\n mline = 0 # line counter for multi-line models\n\n # parse file into raw with to_number conversions\n fid = open(file, 'r')\n for num, line in enumerate(fid.readlines()):\n line = line.strip()\n if num == 0: # get basemva and frequency\n data = line.split('/')[0]\n data = data.split(',')\n\n mva = float(data[1])\n freq = float(data[5])\n version = int(data[2])\n\n if not version:\n version = int(rawd.search(line).group(0).strip('rawd'))\n if version < 32 or version > 33:\n logging.warning('RAW file version is not 32 or 33. Error may occur.')\n continue\n elif num == 1: # store the case info line\n logging.info(line)\n continue\n elif num == 2:\n continue\n elif num >= 3:\n if line[0:2] == '0 ' or line[0:3] == ' 0 ': # end of block\n b += 1\n continue\n elif line[0] is 'Q': # end of file\n break\n data = line.split(',')\n\n data = [to_number(item) for item in data]\n mdata.append(data)\n mline += 1\n if mline == nol[b]:\n if nol[b] == 1:\n mdata = mdata[0]\n raw[blocks[b]].append(mdata)\n mdata = []\n mline = 0\n fid.close()\n\n # add device elements params and add to PSAT formatted dictionary\n\n for data in raw['bus']:\n \"\"\"version 32:\n 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10\n ID, NAME, BasekV, Type, Area Zone Owner Va, Vm, latitude longitude\n \"\"\"\n idx = data[0]\n ty = data[3]\n angle = data[8]\n try:\n lat = data[9]\n except:\n # logging.warning('<No Coordinates in .raw file>')\n param = {'idx': idx,\n 'name': data[1],\n 'Vn': data[2],\n 'type': data[3],\n 'area': data[4],\n 'voltage': data[7],\n 'region': data[5],\n 'owner': data[6],\n 'angle': angle,\n }\n psatlist = [data[0], data[2], data[7], angle, data[4], data[5]]\n else:\n param = {'idx': idx,\n 'name': data[1],\n 'Vn': data[2],\n 'type': data[3],\n 'area': data[4],\n 'voltage': data[7],\n 'region': data[5],\n 'owner': data[6],\n 'angle': angle,\n 'latitude': data[9],\n 'longitude': data[10]\n }\n psatlist = [data[0], data[2], data[7], angle, data[4], data[5], data[9], data[10]]\n Settings.Bus.append(psatlist)\n Settings.BusNames.append(data[1])\n # Add BusSTORE Dictionary For Later Reference\n Settings.BusStore[idx] = param\n\n xcoord = [34.560040, 34.938385, 34.360040, 40.5152473, 40.3142473, 36.527401, 36.857401, 36.687401, 36.856401,\n 40.487041, 36.903901, 36.702901, 35.832561, 33.386047, 33.185047, 37.105571, 37.104154, 33.706718,\n 37.103549, 36.703539, 37.103559, 36.703549, 36.033561, 35.631561, 36.032561, 35.732561, 36.525401,\n 36.857401, 49.869314, 50.969314, 51.979314, 52.481674, 54.973192, 56.276212, 41.734596, 34.551015,\n 34.652015, 34.537507, 34.587507, 34.157904, 33.714453, 33.762453, 39.548160, 39.496160, 34.313143,\n 34.545782, 34.380686, 34.111686, 34.137762, 34.118650, 34.158650, 33.918650, 33.718650, 34.018650,\n 34.018650, 34.018650, 34.018650, 34.018650, 34.312456, 34.315456, 34.243600, 34.566258, 34.565258,\n 46.064672, 46.565672, 45.514571, 45.606833, 45.806833, 44.890000, 45.596416, 45.295416, 45.891161,\n 47.954899, 46.511440, 45.913936, 45.713936, 46.669335, 47.954899, 47.624154, 43.784730, 44.482350,\n 42.006860, 42.934919, 42.731919, 43.013135, 44.068350, 43.558350, 42.438350, 42.938350, 44.068350,\n 43.558350, 43.048350, 42.638350, 44.068350, 43.558350, 43.048350, 42.638350, 43.620189, 39.120428,\n 40.398031, 35.216200, 35.215200, 36.202099, 39.777745, 39.539598, 37.052929, 35.403217, 35.352217,\n 36.807243, 39.567450, 40.807689, 40.806689, 41.008689, 39.555494, 37.954721, 38.406721, 38.906721,\n 38.656721]\n ycoord = [-109.277313, -110.303798, -109.777313, -107.546455, -107.546455, -108.325669, -108.654569, -108.486669,\n -108.325669, -107.185575, -111.390408, -111.390408, -111.448566, -112.860397, -112.659397, -108.243555,\n -108.441191, -112.322033, -111.590816, -111.190816, -111.190816, -111.590806, -111.648566, -111.248566,\n -111.249566, -111.647566, -108.655669, -108.323669, -122.150895, -122.150895, -122.150895, -121.61684,\n -121.924221, -122.21370, -108.790427, -117.568105, -117.538105, -118.607375, -118.658375, -118.280282,\n -118.146319, -118.096319, -112.52797, -112.72797, -118.690631, -118.389938, -118.478496, -118.478496,\n -118.299917, -118.095428, -118.095428, -118.095428, -118.095428, -118.195428, -118.395428, -117.995428,\n -117.795428, -117.995428, -118.481217, -118.891217, -118.391667, -117.166428, -117.368428, -106.60906,\n -106.80906, -122.681289, -121.114785, -122.113785, -123.29000, -121.312202, -121.114202, -106.612578,\n -118.997945, -112.88531, -120.692286, -120.693974, -119.571501, -120.997945, -122.219492, -118.77463,\n -121.019484, -121.316546, -114.419206, -114.419206, -120.956476, -120.79484, -120.93484, -121.216546,\n -121.156546, -121.215484, -121.135484, -121.255484, -121.175484, -121.013484, -120.733484, -121.053484,\n -120.973484, -118.865882, -122.073631, -122.263453, -120.847567, -120.900567, -120.129849, -122.142965,\n -122.262993, -121.021929, -119.450452, -119.450452, -121.779037, -122.276225, -122.135718, -121.935718,\n -121.935718, -121.24000, -121.18379, -121.10879, -121.27379, -121.23979]\n\n #for idx, line in enumerate(Settings.Bus):\n # line.extend([xcoord[idx], ycoord[idx]])\n\n maxV = 1.1\n minV = 0.9\n maxQ = 1\n minQ = 0\n convimp = 0\n status = 1\n loss = 1\n\n for data in raw['load']:\n \"\"\"version 32:\n 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11\n Bus, Id, Status, Area, Zone, PL(MW), QL (MW), IP, IQ, YP, YQ, OWNER\n \"\"\"\n\n busidx = data[0]\n vn = Settings.BusStore[busidx]['Vn']\n voltage = Settings.BusStore[busidx]['voltage']\n param = {'bus': busidx,\n 'Vn': vn,\n 'Sn': mva,\n 'p': (data[5] + data[7] * voltage + data[9] * voltage ** 2) / mva,\n 'q': (data[6] + data[8] * voltage - data[10] * voltage ** 2) / mva,\n 'owner': data[11],\n 'type': Settings.BusStore[busidx]['type'],\n 'voltage': voltage\n }\n\n psatlist = [busidx, mva, vn, param['p'], param['q'], maxV, minV, convimp, status]\n Settings.PQ.append(psatlist)\n \"\"\"CONFIRM THAT OTHER BUSES HAVE 0 P and 0 Q which are not added\"\"\"\n\n for data in raw['fshunt']:\n \"\"\"\n 0, 1, 2, 3, 4\n Bus, name, Status, g (MW), b (Mvar)\n \"\"\"\n busidx = data[0]\n vn = Settings.BusStore[busidx]['Vn']\n param = {'bus': busidx,\n 'Vn': vn,\n 'status': data[2],\n 'Sn': mva,\n 'g': data[3] / mva,\n 'b': data[4] / mva,\n }\n\n psatlist = [busidx, mva, vn, freq, param['g'], param['b'], param['status']]\n Settings.Shunt.append(psatlist)\n\n gen_idx = 0\n type = 6\n\n for data in raw['gen']:\n \"\"\"\n 0, 1, 2, 3, 4, 5, 6, 7, 8, 9,10,11, 12, 13, 14, 15, 16,17,18,19\n I,ID,PG,QG,QT,QB,VS,IREG,MBASE,ZR,ZX,RT,XT,GTAP,STAT,RMPCT,PT,PB,O1,F1\n \"\"\"\n busidx = data[0]\n vn = Settings.BusStore[busidx]['Vn']\n gen_mva = data[8]\n gen_idx += 1\n status = data[14]\n leak = 0\n param = {'Sn': gen_mva,\n 'Vn': vn,\n 'u': status,\n 'idx': gen_idx,\n 'bus': busidx,\n 'pg': status * data[2] / mva,\n 'qg': status * data[3] / mva,\n 'qmax': data[4] / mva,\n 'qmin': data[5] / mva,\n 'v0': data[6],\n 'ra': data[9], # ra armature resistance\n 'xs': data[10], # xs synchronous reactance\n 'pmax': data[16] / mva,\n 'pmin': data[17] / mva,\n }\n\n if Settings.BusStore[busidx]['type'] == 3: #Check Bus Type for Slack\n refangle = 0\n refBus = 1\n PGuess = 1\n swlist = [busidx, gen_mva, vn, param['v0'], refangle, param['qmax'], param['qmin'],\n maxV, minV, PGuess, loss, refBus, status]\n SW = swlist\n Settings.SW.append(swlist)\n Settings.SWStore[busidx] = param\n Settings.SynStore[busidx] = param\n continue\n\n if busidx not in Settings.BusStore.keys():\n \"\"\" Need data from .dyr file. Create initial list, then append data from .dyr\"\"\"\n else:\n # psatlist = [busidx, gen_mva, vn, freq, type, leak, param['ra'],param['xs']]\n # Syn.append(psatlist)\n Settings.SynStore[busidx] = param\n pvlist = [busidx, gen_mva, vn, param['pg'], Settings.BusStore[busidx]['voltage'],\n param['qmax'], param['qmin'], maxV, minV, loss, status]\n Settings.PV.append(pvlist)\n\n\n for data in raw['branch']:\n \"\"\"\n I,J,ID,R,X,B,RATEA,RATEB,RATEC,GI,BI,GJ,BJ,ST,LEN,O1,F1,...,O4,F4\n \"\"\"\n param = {'bus1': data[0],\n 'bus2': data[1],\n 'id' : data[2],\n 'r': data[3],\n 'x': data[4],\n 'b': data[5],\n 'rate_a': data[6],\n 'rate_b': data[7],\n 'rate_c': data[8],\n 'Vn': Settings.BusStore[data[0]]['Vn'],\n 'Vn2': Settings.BusStore[data[1]]['Vn'],\n 'length': data[14],\n 'Ilim': EMPTY,\n 'Plim': EMPTY,\n 'Slim': EMPTY,\n 'status': data[13]\n }\n\n psatlist = [param['bus1'], param['bus2'], param['rate_c'], param['Vn'], freq, EMPTY,\n param['length'], param['r'], param['x'], param['b'], param['Ilim'], param['Plim'], EMPTY, EMPTY,\n param['Slim'], param['status']]\n Settings.Lineij.append([data[0], data[1], data[2]])\n Settings.Lineji.append([data[1], data[0], data[2]])\n Settings.LineOrd[param['bus1']].append(psatlist)\n Settings.branches += 1\n Settings.linecount += 1\n Settings.LineBusMatij[param['bus2']].append(Settings.branches)\n Settings.LineBusMatji[param['bus1']].append(Settings.branches)\n\n for data in raw['transf']:\n \"\"\"\n I,J,K,CKT,CW,CZ,CM,MAG1,MAG2,NMETR,'NAME',STAT,O1,F1,...,O4,F4\n R1-2,X1-2,SBASE1-2\n WINDV1,NOMV1,ANG1,RATA1,RATB1,RATC1,COD1,CONT1,RMA1,RMI1,VMA1,VMI1,NTP1,TAB1,CR1,CX1\n WINDV2,NOMV2\n \"\"\"\n if len(data[1]) < 5:\n ty = 2\n else:\n ty = 3\n if ty == 3:\n continue\n # raise NotImplementedError('Three-winding transformer not implemented')\n\n tap = data[2][0]\n phi = data[2][2]\n\n if tap == 1 and phi == 0:\n trasf = False\n else:\n trasf = True\n param = {'trasf': trasf,\n 'bus1': data[0][0],\n 'bus2': data[0][1],\n 'u': data[0][11],\n 'b': data[0][8],\n 'r': data[1][0],\n 'x': data[1][1],\n 'tap': tap,\n 'phi': phi,\n 'rate_a': data[2][3],\n 'Vn': Settings.BusStore[busidx]['Vn'],\n 'Vn2': Settings.BusStore[busidx]['Vn'],\n # 'length': data[?][?], FIND CORRECT INDEX\n 'Ilim': EMPTY,\n 'Plim': EMPTY,\n 'Slim': EMPTY,\n }\n psatlist = [param['bus1'], param['bus2'], param['rate_a'], param['Vn'], freq, EMPTY,\n EMPTY, param['r'], param['x'], param['b'], param['Ilim'], param['Plim'], EMPTY, EMPTY,\n param['Slim'], param['u']]\n\n Settings.LineOrd[param['bus1']].append(psatlist)\n Settings.linecount += 1\n Settings.transformers += 1\n # ADD Line Data(All Branch Types) to Sys Param Dict after .dyr Transformer Data Added\n # Re-Order Line Data for correct sequence\n for key in Settings.LineOrd:\n for item in Settings.LineOrd[key]:\n Settings.Line.append(item)\n\n for data in raw['area']:\n Settings.Areas.append(data[4])\n\n for data in raw['zone']:\n Settings.Regions.append(data[1])\n\n return retval","def testEdgeMarkerRaster0(self):\n outname = self.prefix+'.asap'\n self.res = sdcal(infile=self.rawfile,calmode='otfraster',markonly=True,outfile=outname,outform='ASAP')\n refdir = self._readref( self.reffiles[0] )\n self._checkfile( outname ) \n self._checkmarker( outname, refdir )","def testEdgeMarkerGeneric1(self):\n outname = self.prefix+'.asap'\n self.res = sdcal(infile=self.rawfile,calmode='otf',fraction='3%',markonly=True,outfile=outname,outform='ASAP')\n refdir = self._readref( self.reffiles[1] )\n self._checkfile( outname ) \n self._checkmarker( outname, refdir )","def reserved_field(self) -> int:\n return unsigned_int(self._file_bytes, 0x06)","def add_fault_rupture_from_file(self, fault_filename):\n self.fault.add_patches_from_file(fault_filename) \n self.irst = 214","def remove_decay(slha_file, pid):\n\n print 'removing DECAY block %s from slha file %s' % (pid, slha_file)\n\n # rewrite slha file\n import shutil\n shutil.move(slha_file, slha_file+'.org')\n \n update = open(slha_file, 'w')\n\n skip = False\n for l in open(slha_file+'.org'):\n if l.startswith('DECAY %s '%pid):\n skip = True\n continue\n\n if l.startswith('DECAY '):\n skip = False\n \n if not skip:\n update.write(l)\n \n update.close()\n\n # remove also from MSSM.model file\n print 'removing decay of %s from MSSM.model file' % pid\n\n # rewrite MSSM.model file\n from PyJobTransformsCore.trfutil import get_files\n get_files( 'MSSM.model', keepDir=False, errorIfNotFound=True )\n\n import shutil\n shutil.move('MSSM.model', 'MSSM.model.org')\n \n update = open('MSSM.model', 'w')\n\n for l in open('MSSM.model.org'):\n if l.startswith('insert /Herwig/Shower/ShowerHandler:DecayInShower 0 %s '%pid):\n continue\n update.write(l)\n \n update.close()"],"string":"[\n \"def cleanupV032backup(self):\\n doCleanup = False\\n if (os.path.isfile(self.MAPSTUDIO + 'm10_00_00_00.msb.bak')):\\n self.msbio.open(self.MAPSTUDIO + 'm10_00_00_00.msb.bak')\\n if (len(self.msbio.models.rows) >= 373):\\n doCleanup = True\\n\\n if (doCleanup):\\n print(\\\"Detected invalid .msb file backups from v0.3.2, attempting to fix.\\\")\\n try:\\n for i, iFile in enumerate(self.inputFiles):\\n if (os.path.isfile(self.MAPCOPY + iFile + '.msb')):\\n self.msbio.open(self.MAPCOPY + iFile + '.msb')\\n self.msbio.models.rows = self.msbio.models.rows[:self.startIndices[i]]\\n self.msbio.save(self.MAPSTUDIO + iFile + '.msb.bak', False)\\n print(\\\"Fixed \\\" + self.MAPSTUDIO + iFile + '.msb.bak')\\n else:\\n print(\\\"Failed to fix backup: \\\" + self.MAPSTUDIO + iFile + '.msb.bak, ' + self.MAPCOPY + iFile + '.msb from previous use of the randomizer does not exist.')\\n except:\\n print(\\\"[ERROR] Failed to fix the backups.\\\")\",\n \"def UnhandledPacket(Packet):\\n\\n\\tglobal UnhandledFile\\n\\n\\tif (UnhandledFile != None):\\n\\t\\tUnhandledFile.write(Packet)\",\n \"def test_fake_file(self):\\n fits_file = os.path.join(self.datadir, 'monol_test_fake.evt')\\n hen.fake.main(['-o', fits_file, '--instrument', 'FPMB'])\\n info = hen.io.print_fits_info(fits_file, hdu=1)\\n assert info['Instrument'] == 'FPMB'\",\n \"def test_byte_loss(self):\\n log.info('===== START TEST REAL FILE =====')\\n\\n # Telemetered\\n file_path = os.path.join(RESOURCE_PATH, '11330408_SNA_SNA.txt')\\n\\n stream_handle = open(file_path, MODE_ASCII_READ)\\n\\n self.create_parser(stream_handle)\\n\\n particles = self.parser.get_records(3)\\n\\n log.debug(\\\"*** test_byte_loss Num particles %s\\\", len(particles))\\n\\n # check all the values against expected results.\\n self.assert_particles(particles, 'byte_loss.yml', RESOURCE_PATH)\\n stream_handle.close()\\n\\n log.info('===== END TEST BYTE LOSS =====')\",\n \"def insert_bad_data():\\n get_file_reply(files[2][0], files[2][1])\",\n \"def test_malformed(self):\\n fdesc, fname = tempfile.mkstemp()\\n tfile = os.fdopen(fdesc, 'w')\\n tfile.write(self.file_str2)\\n tfile.close()\\n assert_raises(Exception, grades.writers.GradesFile, fname)\\n os.unlink(fname)\",\n \"def unknown(self):\\n self.add_file_string('Unknown file')\\n self.should_copy = False\",\n \"def skip_gutenberg_header(self, fp):\\n for line in fp:\\n if line.startswith('*END*THE SMALL PRINT!'):\\n break\",\n \"def test_single_chunk(caplog):\\n # Need to override the test level set above\\n caplog.set_level(logging.WARNING, 'metpy.io.nexrad')\\n f = Level2File(get_test_data('Level2_KLBB_single_chunk'))\\n assert len(f.sweeps) == 1\\n assert 'Unable to read volume header' in caplog.text\\n\\n # Make sure the warning is not present if we pass the right kwarg.\\n caplog.clear()\\n Level2File(get_test_data('Level2_KLBB_single_chunk'), has_volume_header=False)\\n assert 'Unable to read volume header' not in caplog.text\",\n \"def abort_ber_meas(self):\\r\\r\\n loggerCmw = logging.getLogger('abort_ber_meas')\\r\\r\\n self.write('ABORt:WCDMa:SIGN:BER')\\r\\r\\n loggerCmw.info(\\\"Aborting BER measurements\\\")\\r\\r\\n time.sleep(1)\",\n \"def test_missingDetectors(self):\\n files = [getFile(fp)\\n for fp in ['bwr_0_det0.m', 'bwr_noxy_det0.m']]\\n self._raisesMisMatchError(files)\\n self.assertMsgInLogs(\\\"ERROR\\\", \\\"detectors: Parser files\\\", partial=True)\",\n \"def test_doubled_file():\\n with contextlib.closing(get_test_data('Level2_KFTG_20150430_1419.ar2v')) as infile:\\n data = infile.read()\\n fobj = BytesIO(data + data)\\n f = Level2File(fobj)\\n assert len(f.sweeps) == 12\",\n \"def process_full_file(self, code):\\n return code\",\n \"def test_large_import(self):\\n # the original file (from the IDD) is a previous version of the file from\\n # the data server for the gp03flmb platform\\n self.create_sample_data_set_dir('node59p1_orig.dat', TELEM_DIR, 'node59p1.dat')\\n self.assert_initialize()\\n # one bad sample in here:\\n # PH1236501_01D5u51F361E0_EC_162E has non ascii bytes at the end and is missing \\\\r\\n result = self.data_subscribers.get_samples(DataParticleType.CONTROL, 1, 60)\\n result = self.data_subscribers.get_samples(DataParticleType.SAMPLE, 49, 100)\\n\\n # this file is the more recent file off the data server for gp03flmb/d00001\\n # this file appends more data to that in node59p1_orig\\n self.create_sample_data_set_dir('node59p1.dat', TELEM_DIR)\\n # several bad samples in here:\\n # PH1236501_01D5u521208B4_A1_D274 doesn't have enough bytes (469 not 470)\\n # PH1236501_01D5u52461BDC_CF_55BD doesn't have enough bytes (469 not 470)\\n # PH1236501_01D5u5266BCF1_DA_6466 doesn't have enough bytes (469 not 470)\\n # PH1236501_01DAu5288AF85_C9_7365, PH1236501_01DAu529E1BDF_42_4835\\n # have extra bytes after the sample, not an error anymore\\n # PH1236501_01D5u52B090DA_BA_8CC1 doesn't have enough bytes (469 not 470)\\n # PH1236501_01DAu52B38839_BB_4134, PH1236501_01DAu52C8F493_34_3FC2\\n # PH1236501_01DAu52ECE16B_79_F727, PH1236501_01DAu53024DC6_F2_7EC9 \\n # have extra bytes after sample, not an error anymore\\n result = self.data_subscribers.get_samples(DataParticleType.SAMPLE, 751, 430)\",\n \"def test_readbadformat(self):\\n\\n self.assertRaises(ParseError, self.hw, self.badfile)\",\n \"def test_real_file(self):\\n log.info('===== START TEST BYTE LOSS =====')\\n\\n # Recovered\\n file_path = os.path.join(RESOURCE_PATH, '11079364_SNA_SNA.txt')\\n\\n stream_handle = open(file_path, MODE_ASCII_READ)\\n\\n self.create_parser(stream_handle, telem_flag=False)\\n\\n particles = self.parser.get_records(182)\\n\\n log.debug(\\\"*** test_real_file Num particles %s\\\", len(particles))\\n\\n # check all the values against expected results.\\n self.assert_particles(particles, '11079364_SNA_SNA_recov.yml', RESOURCE_PATH)\\n self.assertEquals(self.exception_callback_value, [])\\n stream_handle.close()\\n\\n # Telemetered\\n file_path = os.path.join(RESOURCE_PATH, '11079419_SNA_SNA.txt')\\n\\n stream_handle = open(file_path, MODE_ASCII_READ)\\n\\n self.create_parser(stream_handle)\\n\\n particles = self.parser.get_records(172)\\n\\n log.debug(\\\"*** test_real_file Num particles %s\\\", len(particles))\\n\\n # check all the values against expected results.\\n self.assert_particles(particles, '11079419_SNA_SNA_telem.yml', RESOURCE_PATH)\\n stream_handle.close()\\n\\n log.info('===== END TEST REAL FILE =====')\",\n \"def test_read_fail2(self):\\n mod_fn = os.path.join(tests.TEST_DATA_PATH, 'segmentations', 'test_bad_data2.mod')\\n with self.assertRaises(ValueError):\\n modreader.get_data(mod_fn) # missing 'IEOF' end\",\n \"def test08(self):\\n logical_file_name = \\\"/store/mc/Fall08/BBJets250to500-madgraph/GEN-SIM-RAW/IDEAL_/%s/%i.root\\\" %(uid, 0)\\n #print \\\"WARNING : DBS cannot list INVALID file, so for now this test is commented out\\\"\\n self.api.updateFileStatus(logical_file_name=logical_file_name, is_file_valid=0)\\n #listfile\\n filesInDBS=self.api.listFiles(logical_file_name=logical_file_name, detail=True)\\n self.assertEqual(len(filesInDBS), 1)\\n self.assertEqual(filesInDBS[0]['is_file_valid'], 0)\",\n \"def test_empty_file(self):\\n\\n temp = tempfile.NamedTemporaryFile()\\n temp.flush()\\n self.assertRaises(MalformedFileError, NBTFile, temp.name)\",\n \"def test_harvester_new_file_exception_recovered(self):\\n # create the file so that it is unreadable\\n self.create_sample_data_set_dir(\\n \\\"DOS15908_1st7_step1.DAT\\\",\\n RECOV_DIR,\\n \\\"DOS15909.DAT\\\",\\n mode=000\\n )\\n\\n # Start sampling and watch for an exception\\n self.driver.start_sampling()\\n\\n self.assert_exception(IOError)\\n\\n # At this point the harvester thread is dead. The agent\\n # exception handle should handle this case.\",\n \"def test_fileDoesNotExist(self):\\n fp = FilePath(self.mktemp())\\n protocol = self.makeConnectedDccFileReceive(fp.path)\\n\\n self.allDataReceivedForProtocol(protocol, b\\\"I <3 Twisted\\\")\\n\\n self.assertEqual(fp.getContent(), b\\\"I <3 Twisted\\\")\",\n \"def testEdgeMarkerGeneric0(self):\\n outname = self.prefix+'.asap'\\n self.res = sdcal(infile=self.rawfile,calmode='otf',markonly=True,outfile=outname,outform='ASAP')\\n refdir = self._readref( self.reffiles[0] )\\n self._checkfile( outname ) \\n self._checkmarker( outname, refdir )\",\n \"def test_read_0_2_smirnoff(self):\\n ForceField(\\n get_data_file_path(\\n \\\"test_forcefields/smirnoff99Frosst_reference_0_2_spec.offxml\\\"\\n )\\n )\",\n \"def test_DL_import_wrong_file_unserialized(self):\\n filepath = '6.txt'\\n wrong_file = open(filepath, 'x')\\n wrong_file.write(\\\"This is not a serialized detector flow data\\\")\\n wrong_file.close()\\n # Check if exception was raised for wrong serialization\\n with self.assertRaises(Exception):\\n flow_processing_input.DetectorsLocation(9999, filepath)\\n os.remove(filepath)\",\n \"def skip_gutenberg_header(fp):\\n for line in fp:\\n if line.startswith('*END*THE SMALL PRINT!'):\\n break\",\n \"def test_file_read_bin_missing_file(self):\\n with (self.assertRaises(IOError)):\\n FileReader(self.bogus_path).read_bin()\",\n \"def setUp(self):\\n self.single_rfh2_message = open(\\n os.path.join(self.messages_dir, \\\"single_rfh2.dat\\\"), \\\"rb\\\").read()\\n self.single_rfh2_message_not_well_formed = \\\\\\n self.single_rfh2_message[0:117] + self.single_rfh2_message[121:]\",\n \"def test_read_0_1_smirnoff(self):\\n ForceField(\\n get_data_file_path(\\n \\\"test_forcefields/smirnoff99Frosst_reference_0_1_spec.offxml\\\"\\n )\\n )\",\n \"def test_old_format_for_tags(self):\\n test_files = glob.glob(INPUT_HYPM_PATH + '/unit_*.mdd')\\n test_files.extend(glob.glob(INPUT_FLMB_PATH + '/unit_*.mdd'))\\n\\n mdd.procall(test_files)\\n\\n data = self.read_full_file('node58p1.dat')\\n if not self.check_for_tags(data):\\n self.fail(\\\"Found header tag in data file\\\")\\n\\n data = self.read_full_file('node59p1.dat')\\n if not self.check_for_tags(data):\\n self.fail(\\\"Found header tag in data file\\\")\",\n \"def test_fake_file_with_deadtime(self):\\n fits_file = os.path.join(self.datadir, 'monol_test_fake_lc.evt')\\n hen.fake.main(['--deadtime', '2.5e-3',\\n '--ctrate', '2000',\\n '-o', fits_file])\",\n \"def _process_end_of_file(self):\\n (nd_timestamp, non_data) = self._chunker.get_next_non_data()\\n if non_data and len(non_data) > 0:\\n message = \\\"Extra un-expected non-data bytes at the end of the file:%s\\\", non_data\\n log.warn(message)\\n self._exception_callback(RecoverableSampleException(message))\",\n \"def prepare_bed_file(bed_file, output, ouf=False, save_rejected=None, only_chrom=None):\\n new_lines = [] # keep updated lines\\n rejected = [] # keep IDs of skipped transcripts + the reason why\\n names = Counter() # we need to make sure that all names are unique\\n allowed_re = re.compile(ALLOWED_CHARSET_RE).search\\n broken_names = []\\n\\n f = open(bed_file, \\\"r\\\")\\n for num, line in enumerate(f, 1):\\n # parse bed file according to specification\\n line_data = line.rstrip().split(\\\"\\\\t\\\")\\n\\n if len(line_data) != 12:\\n f.close() # this is for sure an error\\n # it is possible only if something except a bed12 was provided\\n die(\\n \\\"Error! Bed 12 file is required! Got a file with {len(line_data)} fields instead\\\"\\n )\\n\\n chrom = line_data[0]\\n if only_chrom and chrom != only_chrom:\\n # TOGA allows to perform the analysis on a specific chromosome only\\n # is so, we can skip all transcripts that located on other chromosomes\\n continue\\n chromStart = int(line_data[1])\\n chromEnd = int(line_data[2])\\n name = line_data[3] # gene_name usually\\n corr_name = not bool(allowed_re(name))\\n if corr_name is False:\\n broken_names.append(name)\\n # TODO: check weird characters in the transcript name\\n # bed_score = int(line_data[4]) # never used\\n # strand = line_data[5] # otherwise:\\n # strand = True if line_data[5] == '+' else False\\n thickStart = int(line_data[6])\\n thickEnd = int(line_data[7])\\n # itemRgb = line_data[8] # never used\\n blockCount = int(line_data[9])\\n blockSizes = [int(x) for x in line_data[10].split(\\\",\\\") if x != \\\"\\\"]\\n blockStarts = [int(x) for x in line_data[11].split(\\\",\\\") if x != \\\"\\\"]\\n blockEnds = [blockStarts[i] + blockSizes[i] for i in range(blockCount)]\\n blockAbsStarts = [blockStarts[i] + chromStart for i in range(blockCount)]\\n blockAbsEnds = [blockEnds[i] + chromStart for i in range(blockCount)]\\n blockNewStarts, blockNewEnds = [], []\\n names[name] += 1\\n\\n if thickStart > thickEnd:\\n f.close() # according to bed12 specification this should never happen\\n sys.stderr.write(f\\\"Problem occurred at line {num}, gene {name}\\\\n\\\")\\n die(\\\"Error! Bed file is corrupted, thickEnd MUST be >= thickStart\\\")\\n elif thickStart == thickEnd:\\n # this means that this is a non-coding transcript\\n # TOGA cannot process them: we can skip it\\n rejected.append((name, \\\"No CDS\\\"))\\n continue\\n\\n if thickStart < chromStart or thickEnd > chromEnd:\\n # a very strange (but still possible) case\\n f.close() # for sure an error with input data\\n sys.stderr.write(f\\\"Problem occurred at line {num}, gene {name}\\\\n\\\")\\n die(\\\"Error! Bed file is corrupted, thickRange is outside chromRange!\\\")\\n\\n # now select CDS only\\n # we keep UTRs in the filtered file\\n # however, we need CDS to check whether it's correct (% 3 == 0)\\n for block_num in range(blockCount):\\n blockStart = blockAbsStarts[block_num]\\n blockEnd = blockAbsEnds[block_num]\\n\\n # skip the block if it is entirely UTR\\n if blockEnd <= thickStart:\\n continue\\n elif blockStart >= thickEnd:\\n continue\\n\\n # if we are here: this is not an entirely UTR exon\\n # it might intersect the CDS border or to be in the CDS entirely\\n # remove UTRs: block start must be >= CDS_start (thickStart)\\n # block end must be <= CDS_end (thickEnd)\\n blockNewStart = blockStart if blockStart >= thickStart else thickStart\\n blockNewEnd = blockEnd if blockEnd <= thickEnd else thickEnd\\n blockNewStarts.append(blockNewStart - thickStart)\\n blockNewEnds.append(blockNewEnd - thickStart)\\n\\n if len(blockNewStarts) == 0:\\n # even it thickStart != thickEnd this transcript still can be non-coding\\n # but if there are no blocks in the CDS -> we can catch this\\n rejected.append((name, \\\"No CDS\\\"))\\n continue\\n\\n block_new_count = len(blockNewStarts)\\n blockNewSizes = [\\n blockNewEnds[i] - blockNewStarts[i] for i in range(block_new_count)\\n ]\\n\\n if sum(blockNewSizes) % 3 != 0 and not ouf:\\n # this is an out-of-frame (or incomplete transcript)\\n # ideally CDS length should be divisible by 3\\n # not ouf means that we like to keep such transcripts for some reason\\n rejected.append((name, \\\"Out-of-frame gene\\\"))\\n continue\\n\\n # we keep this transcript: add in to the list\\n new_line = \\\"\\\\t\\\".join([str(x) for x in line_data])\\n new_lines.append(new_line)\\n f.close()\\n\\n # if not allowed characters in transcript names: list them\\n if len(broken_names) > 0:\\n eprint(\\\"Error! Some transcript names contain not allowed characters\\\")\\n for t in broken_names:\\n eprint(t)\\n die(f\\\"Allowed characters are: {ALLOWED_CHARSET}\\\")\\n # if there are non-unique transcript IDs: die\\n # I kill it there, not earlier to show them altogether\\n if any(v > 1 for v in names.values()):\\n eprint(\\\"Error! There are non-uniq transcript IDs:\\\")\\n duplicates = [k for k, v in names.items() if v > 1]\\n for d in duplicates:\\n eprint(d)\\n die(\\\"Abort\\\")\\n\\n if len(new_lines) == 0:\\n # no transcripts pass the filter: probably an input data mistake\\n sys.exit(\\n f\\\"Error! No reference annotation tracks left after filtering procedure! Abort\\\"\\n )\\n\\n # write transcripts that passed the filter to the output file\\n f = open(output, \\\"w\\\") if output != \\\"stdout\\\" else sys.stdout\\n f.write(\\\"\\\\n\\\".join(new_lines) + \\\"\\\\n\\\")\\n f.close() if output != \\\"stdout\\\" else None\\n\\n if save_rejected:\\n # save transcripts that didn't pass the filter + reason why\\n f = open(save_rejected, \\\"w\\\")\\n for elem in rejected:\\n f.write(f\\\"{elem[0]}\\\\t{elem[1]}\\\\n\\\")\\n f.close()\",\n \"def test_read_0_1_smirff(self):\\n ForceField(\\n get_data_file_path(\\n \\\"test_forcefields/smirff99Frosst_reference_0_1_spec.offxml\\\"\\n )\\n )\",\n \"def __checkFile(self, filename):\\n \\n try:\\n with open(filename, 'r') as f:\\n first_line = f.readline()\\n \\n if not len(first_line.split(\\\"\\\\t\\\")) == 19:\\n raise BadProteomeScoutFile(\\\"N/A\\\")\\n \\n \\n except:\\n BadProteomeScoutFile(\\\"Invalid ProteomeScout flat file %s.\\\\nFile is invalid or corrupted\\\" % str(filename))\",\n \"def test_not_implemented():\\n for not_implemented_ext in ['.mef', '.nwb']:\\n data_path = _TempDir()\\n raw_fname = op.join(data_path, 'test' + not_implemented_ext)\\n with open(raw_fname, 'w', encoding='utf-8'):\\n pass\\n with pytest.raises(ValueError, match=('there is no IO support for '\\n 'this file format yet')):\\n _read_raw(raw_fname)\",\n \"def test_harvester_new_file_exception_recovered(self):\\n # need to put data in the file, not just make an empty file for this to work\\n self.create_sample_data_set_dir(\\n \\\"DOS15908_1st7_step1.DAT\\\",\\n RECOV_DIR,\\n \\\"DOS15908.DAT\\\",\\n mode=000,\\n copy_metadata=False\\n )\\n\\n self.assert_initialize(final_state=ResourceAgentState.COMMAND)\\n\\n self.event_subscribers.clear_events()\\n self.assert_resource_command(DriverEvent.START_AUTOSAMPLE)\\n self.assert_state_change(ResourceAgentState.LOST_CONNECTION, 90)\\n self.assert_event_received(ResourceAgentConnectionLostErrorEvent, 10)\\n\\n self.clear_sample_data()\\n self.create_sample_data_set_dir(\\n \\\"DOS15908_1st7_step1.DAT\\\",\\n RECOV_DIR,\\n \\\"DOS15908.DAT\\\",\\n copy_metadata=False\\n )\\n\\n # Should automatically retry connect and transition to streaming\\n self.assert_state_change(ResourceAgentState.STREAMING, 90)\",\n \"def test_GFD_import_wrong_file_unserialized(self):\\n filepath = '6.txt'\\n wrong_file = open(filepath, 'x')\\n wrong_file.write(\\\"This is not a serialized detector flow data\\\")\\n wrong_file.close()\\n # Check if exception was raised for wrong serialization\\n with self.assertRaises(Exception):\\n flow_processing_input.GroundFlowData(filepath)\\n os.remove(filepath)\",\n \"def test_read_fail1(self):\\n mod_fn = os.path.join(tests.TEST_DATA_PATH, 'segmentations', 'test_bad_data1.mod')\\n with self.assertRaises(ValueError):\\n modreader.get_data(mod_fn) # missing 'IMOD' start\",\n \"def test_02_not_exist(self):\\n with self.assertLogs(\\\"borg\\\", \\\"WARNING\\\") as logger:\\n self.api.extract(self.archive, self.file_3)\\n message = logger.records[0].getMessage()\\n self.assertRegex(\\n message,\\n r\\\".*?file_3.*never\\\",\\n \\\"Warning not logged for bad path\\\",\\n )\",\n \"def test_readfile(self):\\n fname = os.path.join(self.datadir, 'monol_testA_E3-50_rebin4_gti') + \\\\\\n HEN_FILE_EXTENSION\\n command = \\\"{0}\\\".format(fname)\\n\\n hen.io.main(command.split())\",\n \"def test_harvester_new_file_exception(self):\\n # need to put data in the file, not just make an empty file for this to work\\n self.create_sample_data_set_dir('node59p1_step4.dat', TELEM_DIR, \\\"node59p1.dat\\\",\\n mode=000)\\n\\n self.assert_initialize(final_state=ResourceAgentState.COMMAND)\\n\\n self.event_subscribers.clear_events()\\n self.assert_resource_command(DriverEvent.START_AUTOSAMPLE)\\n self.assert_state_change(ResourceAgentState.LOST_CONNECTION, 90)\\n self.assert_event_received(ResourceAgentConnectionLostErrorEvent, 10)\\n\\n self.clear_sample_data()\\n self.create_sample_data_set_dir('node59p1_step4.dat', TELEM_DIR, \\\"node59p1.dat\\\")\\n\\n # Should automatically retry connect and transition to streaming\\n self.assert_state_change(ResourceAgentState.STREAMING, 90)\",\n \"def test_incomplete_file(self):\\n log.info(\\\"START INTEG TEST INCOMPLETE\\\")\\n\\n self.clear_sample_data()\\n self.clear_async_data()\\n\\n # From sample file A0000010.DEC:\\n # Flag record, first and last velocity record, time record,\\n # but the end of Velocity record (all zeroes) is missing.\\n filename = \\\"A1000002.DEC\\\"\\n self.create_sample_data('incomplete_A0000002.DEC', filename)\\n\\n # Start sampling.\\n self.driver.start_sampling()\\n\\n # an event catches the sample exception\\n self.assert_event('ResourceAgentErrorEvent')\\n\\n # Verify that the entire file has been read.\\n self.assert_file_ingested(filename)\\n\\n log.info(\\\"END INTEG TEST INCOMPLETE\\\")\",\n \"def test_is_not_delicious_file(self):\\r\\n bad_file = StringIO.StringIO()\\r\\n bad_file.write('failing tests please')\\r\\n bad_file.seek(0)\\r\\n\\r\\n self.assertTrue(\\r\\n not DelXMLImporter.can_handle(bad_file),\\r\\n \\\"DelXMLImporter cannot handle this file\\\")\\r\\n\\r\\n bad_file.close()\",\n \"def test_harvester_new_file_exception(self):\\n # need to put data in the file, not just make an empty file for this to work\\n self.create_sample_data_set_dir(\\n 'node59p1_step4.dat',\\n TELEM_DIR,\\n \\\"node59p1.dat\\\",\\n mode=000,\\n copy_metadata=False\\n )\\n\\n self.assert_initialize(final_state=ResourceAgentState.COMMAND)\\n\\n self.event_subscribers.clear_events()\\n self.assert_resource_command(DriverEvent.START_AUTOSAMPLE)\\n self.assert_state_change(ResourceAgentState.LOST_CONNECTION, 90)\\n self.assert_event_received(ResourceAgentConnectionLostErrorEvent, 10)\\n\\n self.clear_sample_data()\\n self.create_sample_data_set_dir(\\n 'node59p1_step4.dat',\\n TELEM_DIR,\\n \\\"node59p1.dat\\\",\\n copy_metadata=False\\n )\\n\\n # Should automatically retry connect and transition to streaming\\n self.assert_state_change(ResourceAgentState.STREAMING, 90)\",\n \"def test_block_bad_signature(self):\\n pass\",\n \"def test_incomplete_file(self):\\n log.info(\\\"START QUAL TEST INCOMPLETE FILE\\\")\\n\\n # From sample file A0000010.DEC:\\n # Flag record, first and last velocity record, time record,\\n # but the end of Velocity record (all zeroes) is missing.\\n self.clear_sample_data()\\n self.event_subscribers.clear_events()\\n self.assert_initialize()\\n self.create_sample_data('incomplete_A0000002.DEC', \\\"A1000002.DEC\\\")\\n\\n # Verify an event was raised and we are in our retry state.\\n self.verify_queue_empty()\\n self.assert_event_received(ResourceAgentErrorEvent, 10)\\n self.assert_state_change(ResourceAgentState.STREAMING, 10)\\n\\n log.info(\\\"END QUAL TEST INCOMPLETE FILE\\\")\",\n \"def test_harvester_new_file_exception(self):\\n # create the file so that it is unreadable\\n self.create_sample_data_set_dir(\\n \\\"node59p1_step1.dat\\\",\\n TELEM_DIR,\\n \\\"node59p1.dat\\\",\\n mode=000,\\n copy_metadata=False\\n )\\n\\n # Start sampling and watch for an exception\\n self.driver.start_sampling()\\n\\n self.assert_exception(ValueError)\\n\\n # At this point the harvester thread is dead. The agent\\n # exception handle should handle this case.\",\n \"def checkIfAllowedToModify(self):\\n\\n oldBytes = b''\\n testFileName = self.MAPSTUDIO + self.inputFiles[0] + '.msb'\\n\\n with open(testFileName, 'rb') as oldf:\\n oldBytes = oldf.read()\\n\\n # Try writing something to the file\\n\\n try:\\n with open(testFileName, 'wb') as outf:\\n outf.write(b'TESTINGIFICANWRITEINTOTHISFILE')\\n except:\\n return False\\n\\n # Because apparently for _some_ reason it doesn't throw an error sometimes(?) so we confirm if the file was actually modified\\n\\n newBytes = b''\\n with open(testFileName, 'rb') as oldf:\\n newBytes = oldf.read()\\n\\n if (oldBytes == newBytes):\\n return False\\n\\n # Restore the file to normal\\n\\n with open(testFileName, 'wb') as outf:\\n outf.write(oldBytes)\\n\\n oldBytes = b''\\n newBytes = b''\\n\\n return True\",\n \"def test_harvester_new_file_exception(self):\\n\\n # create the file so that it is unreadable\\n self.create_sample_data_set_dir(\\\"node59p1_step1.dat\\\", TELEM_DIR, \\\"node59p1.dat\\\",\\n mode=000)\\n\\n # Start sampling and watch for an exception\\n self.driver.start_sampling()\\n\\n self.assert_exception(ValueError)\\n\\n # At this point the harvester thread is dead. The agent\\n # exception handle should handle this case.\",\n \"def test_strain_redefined(generate_strain_redefined):\\n fname = generate_strain_redefined\\n try:\\n process_files([fname])\\n raise Exception('The redefined strain data and lack of stress data was not caught')\\n except IOError:\\n pass\",\n \"def skip_gutenberg_header(fp):\\n for line in fp:\\n if line.startswith(''):\\n break\",\n \"def test_bad_protein_file():\\n\\n bad = random_filename()\\n rv, out = getstatusoutput(f'{prg} --cdhit {cdhit} -p {bad}')\\n assert rv > 0\\n assert out.lower().startswith('usage:')\\n assert re.search(f\\\"No such file or directory: '{bad}'\\\", out)\",\n \"def reportFileCorruption(gpfn, sitemover):\\n\\n # except for lcgcp site mover (since it does not return a proper SURL, the consistency report is done in the site mover)\\n _copytool, dummy = getCopytool(mode=\\\"get\\\")\\n if _copytool != \\\"lcgcp\\\" and _copytool != \\\"lcg-cp\\\" and _copytool != \\\"storm\\\":\\n if gpfn != \\\"\\\":\\n try:\\n sitemover.reportFileCorruption(gpfn)\\n except Exception, e:\\n tolog(\\\"!!WARNING!!1212!! Caught exception: %s\\\" % (e))\\n else:\\n tolog(\\\"Reported file corruption\\\")\\n else:\\n tolog(\\\"!!WARNING!!1990!! Can not report SURL for corrupt file to consistency server since SURL is an empty string\\\")\\n else:\\n tolog(\\\"(Already reported corrupted file)\\\")\",\n \"def recover_data(infile: str, outfile: str, lsb: int, nbytes: int):\\n if not lsb:\\n return 7\\n if not nbytes:\\n return 8\\n\\n if not infile.endswith('.wav'):\\n return 4\\n\\n try:\\n lsb = int(lsb)\\n except TypeError:\\n lsb = lsb\\n\\n steganographer = Stego(infile, lsb)\\n if steganographer.recover(outfile, nbytes):\\n return 0\\n\\n cleanup(outfile)\\n return 1\",\n \"def test_is_not_delicious_file(self):\\r\\n bad_file = StringIO.StringIO()\\r\\n bad_file.write('failing tests please')\\r\\n bad_file.seek(0)\\r\\n\\r\\n self.assertTrue(\\r\\n not DelImporter.can_handle(bad_file),\\r\\n \\\"DelImporter cannot handle this file\\\")\\r\\n\\r\\n bad_file.close()\",\n \"def test_bad_hsm():\\n image_file = os.path.join('input','DECam_00241238_01.fits.fz')\\n cat_file = os.path.join('input',\\n 'DECam_00241238_01_psfcat_tb_maxmag_17.0_magcut_3.0_findstars.fits')\\n psf_file = os.path.join('output','bad_hsm.fits')\\n\\n twodhist_file = os.path.join('output','bad_hsm_twod.pdf')\\n whisker_file = os.path.join('output','bad_hsm_whisk.pdf')\\n rho_file = os.path.join('output','bad_hsm_rho.pdf')\\n shape_file = os.path.join('output','bad_hsm_shape.pdf')\\n star_file = os.path.join('output','bad_hsm_star.pdf')\\n hsm_file = os.path.join('output','bad_hsm_hsm.fits')\\n hsm4_file = os.path.join('output','bad_hsm_hsm_fourth.fits')\\n sizemag_file = os.path.join('output','bad_hsm_sizemag.png')\\n\\n stamp_size = 25\\n\\n # The configuration dict with the right input fields for the file we're using.\\n config = {\\n 'input' : {\\n 'nstars': 8,\\n 'image_file_name' : image_file,\\n 'image_hdu' : 1,\\n 'weight_hdu' : 3,\\n 'badpix_hdu' : 2,\\n 'cat_file_name' : cat_file,\\n 'cat_hdu' : 2,\\n # These next two are intentionally backwards. The PixelGrid will find some kind\\n # of solution, but it will be complex garbage, and hsm will fail for them.\\n 'x_col' : 'YWIN_IMAGE',\\n 'y_col' : 'XWIN_IMAGE',\\n 'sky_col' : 'BACKGROUND',\\n 'stamp_size' : stamp_size,\\n 'ra' : 'TELRA',\\n 'dec' : 'TELDEC',\\n 'gain' : 'GAINA',\\n },\\n 'output' : {\\n 'file_name' : psf_file,\\n 'stats' : [\\n {\\n 'type': 'TwoDHist',\\n 'file_name': twodhist_file,\\n },\\n {\\n 'type': 'Whisker',\\n 'file_name': whisker_file,\\n },\\n { # Note: stats doesn't have to be a list.\\n 'type': 'Rho',\\n 'file_name': rho_file\\n },\\n {\\n 'type': 'ShapeHist',\\n 'file_name': shape_file,\\n },\\n {\\n 'type': 'Star',\\n 'file_name': star_file,\\n },\\n {\\n 'type': 'SizeMag',\\n 'file_name': sizemag_file,\\n },\\n {\\n 'type': 'HSMCatalog',\\n 'file_name': hsm_file,\\n },\\n {\\n 'type': 'HSMCatalog',\\n 'file_name': hsm4_file,\\n 'fourth_order': True,\\n },\\n ],\\n },\\n 'psf' : {\\n 'model' : {\\n 'type' : 'PixelGrid',\\n 'scale' : 0.3,\\n 'size' : 10,\\n 'interp': 'Lanczos(3)'\\n },\\n 'interp' : { 'type' : 'Mean' },\\n 'outliers' : {\\n 'type' : 'Chisq',\\n 'nsigma' : 0.05 # This will throw out all but 1, which adds an additional\\n # test of Star stats when nstars < nplot\\n }\\n },\\n }\\n if __name__ == '__main__':\\n logger = piff.config.setup_logger(1)\\n else:\\n config['verbose'] = 0\\n logger = None\\n\\n for f in [twodhist_file, rho_file, shape_file, star_file, hsm_file]:\\n if os.path.exists(f):\\n os.remove(f)\\n\\n piff.piffify(config, logger=logger)\\n\\n # Confirm that all but one star was rejected, since that was part of the intent of this test.\\n psf = piff.read(psf_file)\\n print('stars = ',psf.stars)\\n print('nremoved = ',psf.nremoved)\\n assert len(psf.stars) == 1\\n assert psf.nremoved == 7 # There were 8 to start.\\n\\n for f in [twodhist_file, rho_file, shape_file, star_file, sizemag_file, hsm_file]:\\n assert os.path.exists(f)\\n\\n # Check hsm file with bad measurements\\n # The one star that was left still fails hsm measurement here.\\n data = fitsio.read(hsm_file)\\n for col in ['ra', 'dec', 'x', 'y', 'u', 'v',\\n 'T_data', 'g1_data', 'g2_data',\\n 'T_model', 'g1_model', 'g2_model',\\n 'flux', 'reserve', 'flag_data', 'flag_model']:\\n assert len(data[col]) == 1\\n print('flag_data = ',data['flag_data'])\\n print('flag_model = ',data['flag_model'])\\n np.testing.assert_array_equal(data['flag_data'], 7)\\n np.testing.assert_array_equal(data['flag_model'], 7)\",\n \"def test_large_flmb(self):\\n test_files_218 = glob.glob(INPUT_FLMB_PATH + '/unit_363-2013-218*.mdd')\\n\\n mdd.procall(test_files_218)\\n\\n data_orig = self.read_full_file('node59p1.dat')\\n\\n # two status files from different controllers, 12371 and 12365\\n data_out_71 = self.read_full_file('node59p1_0.status_1237101.dat')\\n self.check_sio_type(data_out_71, ['CS', 'PS'])\\n data_out_65 = self.read_full_file('node59p1_0.status_1236501.dat')\\n self.check_sio_type(data_out_65, ['CS', 'PS'])\\n data_out = data_out_71\\n data_out += data_out_65\\n\\n data_adcps = self.read_full_file('node59p1_0.adcps_1237111.dat')\\n self.check_sio_type(data_adcps, ['AD'])\\n data_out += data_adcps\\n\\n data_ctdmo = self.read_full_file('node59p1_0.ctdmo_1237100.dat')\\n self.check_sio_type(data_ctdmo, ['CT', 'CO'])\\n data_out += data_ctdmo\\n\\n data_dosta = self.read_full_file('node59p1_0.dosta_1236501.dat')\\n self.check_sio_type(data_dosta, ['DO'])\\n data_out += data_dosta\\n\\n data_flort = self.read_full_file('node59p1_0.flort_1236501.dat')\\n self.check_sio_type(data_flort, ['FL'])\\n data_out += data_flort\\n\\n data_phsen = self.read_full_file('node59p1_0.phsen_1236501.dat')\\n self.check_sio_type(data_phsen, ['PH'])\\n data_out += data_phsen\\n\\n if not TestSioUnpack.compare_sio_matches(data_orig, data_out):\\n self.fail(\\\"Failed sio block compare\\\")\\n\\n test_files = glob.glob(INPUT_FLMB_PATH + '/unit_363-2013-205*.mdd')\\n test_files_217 = glob.glob(INPUT_FLMB_PATH + '/unit_363-2013-217*.mdd')\\n test_files_219 = glob.glob(INPUT_FLMB_PATH + '/unit_363-2013-219*.mdd')\\n\\n test_files.extend(test_files_217)\\n test_files.extend(test_files_219)\\n\\n mdd.procall(test_files)\\n\\n data_out = self.compare_node59(1, data_out)\\n\\n test_files = glob.glob(INPUT_FLMB_PATH + '/unit_363-2013-233*.mdd')\\n test_files_231 = glob.glob(INPUT_FLMB_PATH + '/unit_363-2013-231*.mdd')\\n\\n test_files.extend(test_files_231)\\n\\n mdd.procall(test_files)\\n\\n self.compare_node59(2, data_out)\",\n \"def test_file_read_gzip_missing_file(self):\\n with (self.assertRaises(IOError)):\\n FileReader(self.bogus_path).read_gzip()\",\n \"def attempt_file_reset(f):\\r\\n if hasattr(f, 'seek'):\\r\\n f.seek(0)\",\n \"def write_no_seek(meta_file, data_block):\\n position = meta_file.tell()\\n # seek 0 bytes from the end of file (2)\\n meta_file.seek(0, 2)\\n meta_file.write(data_block)\\n meta_file.seek(position)\",\n \"def test_fake_file_xmm(self):\\n fits_file = os.path.join(self.datadir, 'monol_test_fake_lc_xmm.evt')\\n hen.fake.main(['--deadtime', '1e-4', '-m', 'XMM', '-i', 'epn',\\n '--ctrate', '2000',\\n '-o', fits_file])\\n hdu_list = fits.open(fits_file)\\n hdunames = [hdu.name for hdu in hdu_list]\\n assert 'STDGTI01' in hdunames\\n assert 'STDGTI02' in hdunames\\n assert 'STDGTI07' in hdunames\",\n \"def test_basic_mech_write(self):\\n\\n unit = btmux.parse_from_file(os.path.join(BTMUX_SAMPLE_DIR, 'AS7-D'))\\n fobj = StringIO()\\n write_to_file(unit, fobj)\\n #print fobj.getvalue()\\n # TODO: Compare to a golden standard.\",\n \"def test_load_events_split(self):\\n command = \\\\\\n '{0} -g --min-length 0'.format(\\n os.path.join(self.datadir, 'monol_testB.evt'))\\n hen.read_events.main(command.split())\\n new_filename = os.path.join(self.datadir,\\n 'monol_testB_nustar_fpmb_gti000_ev' +\\n HEN_FILE_EXTENSION)\\n assert os.path.exists(new_filename)\",\n \"def test_hiddenbinary(self):\\n # copy file rules\\n tmpfile = tempfile.NamedTemporaryFile(\\n suffix='virus', prefix='fuglu-unittest', dir='/tmp')\\n shutil.copy(TESTDATADIR + '/binaryattachment.eml', tmpfile.name)\\n suspect = Suspect(\\n 'sender@unittests.fuglu.org', 'recipient@unittests.fuglu.org', tmpfile.name)\\n\\n result = self.candidate.examine(suspect)\\n if type(result) is tuple:\\n result, message = result\\n tmpfile.close()\\n self.assertEqual(result, DELETE)\",\n \"def process_file(file_name):\\n pass # delete this line and replace with your code here\",\n \"def test_mapping_file_removal(self):\\r\\n mf_exp, _ = parse_mapping_file_to_dict(self.MF_OUT_1)\\r\\n # bt doesn't change in this test\\r\\n bt_exp = parse_biom_table(self.BT_IN_1)\\r\\n mf_obs, bt_obs, nonshared_samples = \\\\\\r\\n sync_biom_and_mf(parse_mapping_file_to_dict(self.MF_IN_1)[0],\\r\\n parse_biom_table(self.BT_IN_1))\\r\\n self.assertEqual(mf_exp, mf_obs)\\r\\n self.assertEqual(bt_exp, bt_obs)\\r\\n self.assertEqual(nonshared_samples, set(['NotInOtuTable2',\\r\\n 'NotInOtuTable1']))\",\n \"def test_lj_no_url(self):\\n text = self.transfer('msg3.txt')\\n assert self.mark not in text\",\n \"def test_stress_not_in(generate_no_stress_one_file):\\n fname = generate_no_stress_one_file\\n with pytest.raises(Exception):\\n process_files([fname])\",\n \"def tearDown(self):\\n try:\\n os.remove(self.junk_file)\\n except OSError as doh:\\n if doh.errno == 2:\\n # No such File, ignore\\n pass\\n else:\\n raise\",\n \"def test_strain_not_in(generate_no_strain_one_file):\\n fname = generate_no_strain_one_file\\n with pytest.raises(Exception) as f:\\n process_files([fname])\",\n \"def test_empty_file(self):\\n with open(os.path.join(test_dir, \\\"empty_file.txt\\\")) as f:\\n for idx, line in enumerate(reverse_readline(f)):\\n raise ValueError(\\\"an empty file is being read!\\\")\",\n \"def test_bad_file():\\n\\n bad = ''.join(random.choices(string.ascii_uppercase + string.digits, k=5))\\n rv, out = getstatusoutput(f'{prg} -f {bad}')\\n assert rv != 0\\n assert re.match('usage:', out, re.I)\\n assert re.search(f\\\"No such file or directory: '{bad}'\\\", out)\",\n \"def test_export_to_mff_no_device():\\n pytest.importorskip(\\\"mffpy\\\", \\\"0.5.7\\\")\\n evoked = read_evokeds_mff(egi_evoked_fname, condition=\\\"Category 1\\\")\\n evoked.info[\\\"device_info\\\"] = None\\n with pytest.raises(ValueError, match=\\\"No device type.\\\"):\\n export_evokeds(\\\"output.mff\\\", evoked)\",\n \"def test_mapping_file_removal(self):\\r\\n mf_exp, _ = parse_mapping_file_to_dict(self.MF_OUT_3)\\r\\n # bt doesn't change in this test\\r\\n bt_exp = parse_biom_table(self.BT_OUT_3)\\r\\n mf_obs, bt_obs, nonshared_samples = \\\\\\r\\n sync_biom_and_mf(parse_mapping_file_to_dict(self.MF_IN_3)[0],\\r\\n parse_biom_table(self.BT_IN_1))\\r\\n self.assertEqual(mf_exp, mf_obs)\\r\\n self.assertEqual(bt_exp, bt_obs)\\r\\n self.assertEqual(nonshared_samples, set(['Sample4', 'NotInOtuTable2',\\r\\n 'NotInOtuTable1']))\",\n \"def perform_general():\\r\\n print(\\\"Performing the \\\\\\\"indirect\\\\\\\" check on all blocks\\\")\\r\\n \\r\\n filename_part = \\\"fusedata.\\\"\\r\\n i_start = begining_block_number + 1 #1\\r\\n i_end = ending_block_number #25\\r\\n file_name = filename_part\\r\\n\\r\\n \\r\\n for i in range(i_start, (i_end + 1)):\\r\\n #opening each block available to us\\r\\n file_name = filename_part + str(i)\\r\\n #print \\\"file_name\\\"+file_name\\r\\n file_access = open (file_name,\\\"r+\\\")\\r\\n \\r\\n try:\\r\\n block_contents = json.load(file_access)\\r\\n file_access.close()\\r\\n except ValueError:\\r\\n print \\\"\\\\\\\"\\\"+file_name+\\\"\\\\\\\" not in json format (catch 1)\\\"\\r\\n file_access.close() \\r\\n continue\\r\\n \\r\\n # first performing the size check\\r\\n if(type(block_contents) == dict):\\r\\n # checking if the current parsed block is a file inode\\r\\n if((\\\"indirect\\\" in block_contents) == True):\\r\\n size_check(block_contents, file_name)\\r\\n perform_indirect(block_contents, file_name)\\r\\n \\r\\n #closing the file to effect changes\\r\\n file_access_2 = open (file_name,\\\"w\\\")\\r\\n json.dump(block_contents,file_access_2)\\r\\n file_access_2.close() \\r\\n \\r\\n\\r\\n \\r\\n print(\\\"Reached end of test\\\") \\r\\n \\r\\n print(\\\"-------------------------------\\\")\",\n \"def test_stress_redefined(generate_stress_redefined):\\n fname = generate_stress_redefined\\n try:\\n process_files([fname])\\n raise Exception('The redefined stress data and lack of strain data was not caught')\\n except IOError:\\n pass\",\n \"def test_bad_file():\\n\\n bad_file = random_string()\\n letter = random.choice(string.ascii_lowercase)\\n rv, out = getstatusoutput('{} {} -f {}'.format(prg, letter, bad_file))\\n assert rv != 0\\n expected = \\\"No such file or directory: '{}'\\\".format(bad_file)\\n assert re.search(expected, out)\",\n \"def sniff( self, filename ):\\n handle = open(filename)\\n line = handle.readline()\\n\\n #nb carac\\n first = line.split()\\n if ( not first[0].isdigit() ):\\n return False\\n\\n ncar=int(first[0]);\\n line = handle.readline()\\n first = line.split()\\n if ( not first[0].isdigit() ):\\n return False\\n if ( not first[1].isdigit() ):\\n return False\\n\\n nfix=int(first[0]);\\n ncov=int(first[1]);\\n\\n #nom des effets\\n line = handle.readline()\\n first = line.split()\\n if ( len(first) < (nfix + ncov)):\\n return False\\n\\n for i in range(ncar):\\n line = handle.readline()\\n first = line.split()\\n if ( len(first) < (2+2*nfix+ncov) ):\\n return False\\n\\n handle.close()\\n\\n return True\",\n \"def test_read_xls_file_not_found(self):\\r\\n my_tape = Tape()\\r\\n my_tape.read_xls('bogus_tape_file')\",\n \"def test_remove_file_group0(self):\\n with copy_of_directory(assets.path_to('SBB0000F29300010000/data')) as tempdir:\\n mets = OcrdMets(filename=join(tempdir, 'mets.xml'))\\n self.assertEqual(len(mets.file_groups), 17)\\n self.assertEqual(len(mets.find_all_files()), 35)\\n # print()\\n # before = sorted([x.ID for x in mets.find_all_files()])\\n with self.assertRaisesRegex(Exception, \\\"not empty\\\"):\\n mets.remove_file_group('OCR-D-GT-ALTO')\\n mets.remove_file_group('OCR-D-GT-PAGE', recursive=True)\\n # print([x for x in before if x not in sorted([x.ID for x in mets.find_all_files()])])\\n self.assertEqual(len(mets.file_groups), 16)\\n self.assertEqual(len(mets.find_all_files()), 33)\",\n \"def test_ignore_empty_files(self):\\n\\n self.checker.config.file_header_ignore_empty_files = True\\n node_mock = MagicMock()\\n node_mock.stream.return_value.__enter__.return_value.read.return_value.decode.return_value = ''\\n with self.assertNoMessages():\\n self.checker.process_module(node_mock)\",\n \"def process_rom_file(name):\\n\\n # Link the instruction rom file to the tb directory\\n SRC_FILE = REPO_ROOT + '/tests/riscv-tests-simple/generated/' + name + \\\".verilog\\\"\\n ROM_FILE = os.getcwd() + '/verilog.rom' # need to link the instruction ram file the the current directory\\n if os.path.isfile(ROM_FILE):\\n os.remove(ROM_FILE)\\n os.symlink(SRC_FILE, ROM_FILE)\\n\\n FP = open('verilog.rom', \\\"r\\\")\\n IRAM_FP = open('instr_ram.rom', \\\"w\\\")\\n DRAM_FP = open('data_ram.rom', \\\"w\\\")\\n\\n iram = True\\n for line in FP.readlines():\\n if line.rstrip() == \\\"@01000000\\\":\\n iram = False\\n continue\\n if iram:\\n IRAM_FP.write(line)\\n else:\\n DRAM_FP.write(line)\\n\\n\\n FP.close()\\n IRAM_FP.close()\\n DRAM_FP.close()\",\n \"def test_invalid_flag_record(self):\\n log.info(\\\"START INTEG TEST INVALID\\\")\\n\\n self.clear_sample_data()\\n self.clear_async_data()\\n\\n # Made-up data with all flags except the first set to True.\\n # First flag is not a zero or one.\\n filename = \\\"A1000003.DEC\\\"\\n self.create_sample_data('invalid_A0000003.DEC', filename)\\n\\n # Start sampling.\\n self.driver.start_sampling()\\n\\n # an event catches the sample exception\\n self.assert_event('ResourceAgentErrorEvent')\\n\\n # Verify that the entire file has been read.\\n self.assert_file_ingested(filename)\\n log.info(\\\"END INTEG TEST INVALID\\\")\",\n \"def test_do_not_ignore_empty_files(self):\\n\\n node_mock = MagicMock()\\n node_mock.stream.return_value.__enter__.return_value.read.return_value.decode.return_value = ''\\n with self.assertAddsMessages(pylint.testutils.Message(\\n msg_id='invalid-file-header',\\n line=1,\\n args=self.EXPECTED_HEADER)):\\n self.checker.process_module(node_mock)\",\n \"def file(self,file):\\n self.lib.lammps_file(self.lmp,file.encode('utf-8'))\",\n \"def test_no_tags(self):\\n test_files = glob.glob(INPUT_GI_PATH + '/gi_*.mdd')\\n\\n mdd.procall(test_files)\\n\\n data = self.read_full_file('node16p1.dat')\\n if not self.check_for_tags(data):\\n self.fail(\\\"Found header tag in data file\\\")\\n\\n data = self.read_full_file('node17p1.dat')\\n if not self.check_for_tags(data):\\n self.fail(\\\"Found header tag in data file\\\")\\n\\n data = self.read_full_file('node14p1.dat')\\n if not self.check_for_tags(data):\\n self.fail(\\\"Found header tag in data file\\\")\",\n \"def _process_file(self, path):\\n\\t\\tself.getFailures(path)\\n\\t\\ttry:\\n\\t\\t\\twhile True:\\n\\t\\t\\t\\tticket = self.failManager.toBan()\\n\\t\\t\\t\\tself.jail.putFailTicket(ticket)\\n\\t\\texcept FailManagerEmpty:\\n\\t\\t\\tself.failManager.cleanup(MyTime.time())\\n\\t\\tself.dateDetector.sortTemplate()\\n\\t\\tself.__modified = False\",\n \"def process_message(msg):\\n global fout\\n print(\\\"received \\\")\\n if len(msg)==200: #is header or end\\n msg_in=msg.decode(\\\"utf-8\\\",\\\"ignore\\\")\\n msg_in=msg_in.split(\\\",,\\\")\\n if msg_in[0]==\\\"header\\\": #header\\n filename=extract_file_data(msg_in[1])\\n file_out=\\\"copy-\\\"+filename\\n fout=open(file_out,\\\"wb\\\") #use a different filename\\n\\n if msg_in[0]==\\\"end\\\": #is it really last packet?\\n in_hash_final=in_hash_md5.hexdigest()\\n if in_hash_final==msg_in[2]:\\n print(\\\"File copied OK -valid hash \\\",in_hash_final)\\n else:\\n print(\\\"Bad file receive \\\",in_hash_final)\\n return False\\n else:\\n if msg_in[0]!=\\\"header\\\":\\n in_hash_md5.update(msg)\\n return True\\n else:\\n return False\\n else:\\n in_hash_md5.update(msg)\\n #msg_in=msg.decode(\\\"utf-8\\\",\\\"ignore\\\")\\n if len(msg) <100:\\n print(msg)\\n return True\",\n \"def test_noFilesFromAccept(self):\\n return self._acceptFailureTest(ENFILE)\",\n \"def _prepare_blocks():\\n\\n counter = blocks[0]['freeStart']\\n maxBlocks = blocks[0]['maxBlocks']\\n while(counter < maxBlocks) :\\n try:\\n # print (mount['parent'] + '/linddata.' + str(counter))\\n f = open(mount['parent'] + '/linddata.' + str(counter), 'r') \\n except IOError, e:\\n return STATUS['M_BD']\\n else :\\n fdatastring = f.next()\\n fdata = deserializedata(fdatastring)\\n blocks[counter] = fdata\\n counter += 1\\n \\n return STATUS['OK']\",\n \"def assert_after_stop(self):\\n super(parent.TestFileOutputDriver, self).assert_after_stop()\\n assert(os.path.isfile(self.filepath))\\n with open(self.filepath, 'rb') as fd:\\n contents = fd.read()\\n nt.assert_equal(contents, self.ply_file_contents)\",\n \"def test_lint_fail_malformed(self, style):\\n with ExpectedException(LinterFailure):\\n run_linter_throw(\\\"path/to/file\\\",\\n \\\"{s} path/to/file_wrong\\\\n{m}{e}\\\\n\\\",\\n style,\\n whitelist=[\\\"headerblock/filename\\\"])\",\n \"def test_verify_clear_trace_mid_reassembly(self):\\n\\n self.pg_enable_capture()\\n self.src_if.add_stream(self.fragments_400[0:-1])\\n self.pg_start()\\n\\n self.logger.debug(self.vapi.cli(\\\"show trace\\\"))\\n self.vapi.cli(\\\"clear trace\\\")\\n\\n self.src_if.add_stream(self.fragments_400[-1])\\n self.pg_start()\\n packets = self.dst_if.get_capture(len(self.pkt_infos))\\n self.verify_capture(packets)\",\n \"def fix_xfer_syntax(filename):\\n\\n current_syntax = get_xfer_syntax(filename)\\n if (current_syntax == '1.2.840.10008.1.2.1' or \\n current_syntax is None or\\n current_syntax == '1.2.840.10008.1.2'):\\n return (filename, filename)\\n else:\\n print(current_syntax)\\n\\n new_filename = tempfile.mktemp(prefix='iffpy')\\n\\n subprocess.run([\\\"gdcmconv\\\",\\n \\\"-w\\\",\\n \\\"-i\\\", filename,\\n \\\"-o\\\", new_filename])\\n\\n if os.path.exists(new_filename):\\n print(f\\\"Successfully converted file: {new_filename}\\\")\\n return (new_filename, f\\\"decompressed;{filename}\\\")\\n else:\\n print(f\\\"Looks like this one failed: {new_filename}\\\")\\n return (None, None)\",\n \"def get_file_format(file):\\n flag = None\\n with open(file) as f:\\n for line in f.readlines():\\n MAT, MF, MT = read_control(line)[:3]\\n if MF == 1 and MT == 451:\\n i = 0\\n C, i = read_cont([line], i)\\n flag = C.N1\\n break\\n if flag is None:\\n ftype = None\\n elif flag == -11 or flag == -12:\\n ftype = \\\"errorr\\\"\\n elif flag == -1:\\n ftype = \\\"gendf\\\"\\n else:\\n if C.L1 == 2:\\n ftype = \\\"pendf\\\"\\n else:\\n ftype = \\\"endf6\\\"\\n return ftype\",\n \"def read(file):\\n\\n blocks = ['bus', 'load', 'fshunt', 'gen', 'branch', 'transf', 'area',\\n 'twotermdc', 'vscdc', 'impedcorr', 'mtdc', 'msline', 'zone',\\n 'interarea', 'owner', 'facts', 'swshunt', 'gne', 'Q']\\n nol = [1, 1, 1, 1, 1, 4, 1,\\n 0, 0, 0, 0, 0, 1,\\n 0, 1, 0, 0, 0, 0]\\n rawd = re.compile('rawd\\\\d\\\\d')\\n\\n retval = True\\n version = 0\\n b = 0 # current block index\\n raw = {}\\n for item in blocks:\\n raw[item] = []\\n\\n data = []\\n mdata = [] # multi-line data\\n mline = 0 # line counter for multi-line models\\n\\n # parse file into raw with to_number conversions\\n fid = open(file, 'r')\\n for num, line in enumerate(fid.readlines()):\\n line = line.strip()\\n if num == 0: # get basemva and frequency\\n data = line.split('/')[0]\\n data = data.split(',')\\n\\n mva = float(data[1])\\n freq = float(data[5])\\n version = int(data[2])\\n\\n if not version:\\n version = int(rawd.search(line).group(0).strip('rawd'))\\n if version < 32 or version > 33:\\n logging.warning('RAW file version is not 32 or 33. Error may occur.')\\n continue\\n elif num == 1: # store the case info line\\n logging.info(line)\\n continue\\n elif num == 2:\\n continue\\n elif num >= 3:\\n if line[0:2] == '0 ' or line[0:3] == ' 0 ': # end of block\\n b += 1\\n continue\\n elif line[0] is 'Q': # end of file\\n break\\n data = line.split(',')\\n\\n data = [to_number(item) for item in data]\\n mdata.append(data)\\n mline += 1\\n if mline == nol[b]:\\n if nol[b] == 1:\\n mdata = mdata[0]\\n raw[blocks[b]].append(mdata)\\n mdata = []\\n mline = 0\\n fid.close()\\n\\n # add device elements params and add to PSAT formatted dictionary\\n\\n for data in raw['bus']:\\n \\\"\\\"\\\"version 32:\\n 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10\\n ID, NAME, BasekV, Type, Area Zone Owner Va, Vm, latitude longitude\\n \\\"\\\"\\\"\\n idx = data[0]\\n ty = data[3]\\n angle = data[8]\\n try:\\n lat = data[9]\\n except:\\n # logging.warning('<No Coordinates in .raw file>')\\n param = {'idx': idx,\\n 'name': data[1],\\n 'Vn': data[2],\\n 'type': data[3],\\n 'area': data[4],\\n 'voltage': data[7],\\n 'region': data[5],\\n 'owner': data[6],\\n 'angle': angle,\\n }\\n psatlist = [data[0], data[2], data[7], angle, data[4], data[5]]\\n else:\\n param = {'idx': idx,\\n 'name': data[1],\\n 'Vn': data[2],\\n 'type': data[3],\\n 'area': data[4],\\n 'voltage': data[7],\\n 'region': data[5],\\n 'owner': data[6],\\n 'angle': angle,\\n 'latitude': data[9],\\n 'longitude': data[10]\\n }\\n psatlist = [data[0], data[2], data[7], angle, data[4], data[5], data[9], data[10]]\\n Settings.Bus.append(psatlist)\\n Settings.BusNames.append(data[1])\\n # Add BusSTORE Dictionary For Later Reference\\n Settings.BusStore[idx] = param\\n\\n xcoord = [34.560040, 34.938385, 34.360040, 40.5152473, 40.3142473, 36.527401, 36.857401, 36.687401, 36.856401,\\n 40.487041, 36.903901, 36.702901, 35.832561, 33.386047, 33.185047, 37.105571, 37.104154, 33.706718,\\n 37.103549, 36.703539, 37.103559, 36.703549, 36.033561, 35.631561, 36.032561, 35.732561, 36.525401,\\n 36.857401, 49.869314, 50.969314, 51.979314, 52.481674, 54.973192, 56.276212, 41.734596, 34.551015,\\n 34.652015, 34.537507, 34.587507, 34.157904, 33.714453, 33.762453, 39.548160, 39.496160, 34.313143,\\n 34.545782, 34.380686, 34.111686, 34.137762, 34.118650, 34.158650, 33.918650, 33.718650, 34.018650,\\n 34.018650, 34.018650, 34.018650, 34.018650, 34.312456, 34.315456, 34.243600, 34.566258, 34.565258,\\n 46.064672, 46.565672, 45.514571, 45.606833, 45.806833, 44.890000, 45.596416, 45.295416, 45.891161,\\n 47.954899, 46.511440, 45.913936, 45.713936, 46.669335, 47.954899, 47.624154, 43.784730, 44.482350,\\n 42.006860, 42.934919, 42.731919, 43.013135, 44.068350, 43.558350, 42.438350, 42.938350, 44.068350,\\n 43.558350, 43.048350, 42.638350, 44.068350, 43.558350, 43.048350, 42.638350, 43.620189, 39.120428,\\n 40.398031, 35.216200, 35.215200, 36.202099, 39.777745, 39.539598, 37.052929, 35.403217, 35.352217,\\n 36.807243, 39.567450, 40.807689, 40.806689, 41.008689, 39.555494, 37.954721, 38.406721, 38.906721,\\n 38.656721]\\n ycoord = [-109.277313, -110.303798, -109.777313, -107.546455, -107.546455, -108.325669, -108.654569, -108.486669,\\n -108.325669, -107.185575, -111.390408, -111.390408, -111.448566, -112.860397, -112.659397, -108.243555,\\n -108.441191, -112.322033, -111.590816, -111.190816, -111.190816, -111.590806, -111.648566, -111.248566,\\n -111.249566, -111.647566, -108.655669, -108.323669, -122.150895, -122.150895, -122.150895, -121.61684,\\n -121.924221, -122.21370, -108.790427, -117.568105, -117.538105, -118.607375, -118.658375, -118.280282,\\n -118.146319, -118.096319, -112.52797, -112.72797, -118.690631, -118.389938, -118.478496, -118.478496,\\n -118.299917, -118.095428, -118.095428, -118.095428, -118.095428, -118.195428, -118.395428, -117.995428,\\n -117.795428, -117.995428, -118.481217, -118.891217, -118.391667, -117.166428, -117.368428, -106.60906,\\n -106.80906, -122.681289, -121.114785, -122.113785, -123.29000, -121.312202, -121.114202, -106.612578,\\n -118.997945, -112.88531, -120.692286, -120.693974, -119.571501, -120.997945, -122.219492, -118.77463,\\n -121.019484, -121.316546, -114.419206, -114.419206, -120.956476, -120.79484, -120.93484, -121.216546,\\n -121.156546, -121.215484, -121.135484, -121.255484, -121.175484, -121.013484, -120.733484, -121.053484,\\n -120.973484, -118.865882, -122.073631, -122.263453, -120.847567, -120.900567, -120.129849, -122.142965,\\n -122.262993, -121.021929, -119.450452, -119.450452, -121.779037, -122.276225, -122.135718, -121.935718,\\n -121.935718, -121.24000, -121.18379, -121.10879, -121.27379, -121.23979]\\n\\n #for idx, line in enumerate(Settings.Bus):\\n # line.extend([xcoord[idx], ycoord[idx]])\\n\\n maxV = 1.1\\n minV = 0.9\\n maxQ = 1\\n minQ = 0\\n convimp = 0\\n status = 1\\n loss = 1\\n\\n for data in raw['load']:\\n \\\"\\\"\\\"version 32:\\n 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11\\n Bus, Id, Status, Area, Zone, PL(MW), QL (MW), IP, IQ, YP, YQ, OWNER\\n \\\"\\\"\\\"\\n\\n busidx = data[0]\\n vn = Settings.BusStore[busidx]['Vn']\\n voltage = Settings.BusStore[busidx]['voltage']\\n param = {'bus': busidx,\\n 'Vn': vn,\\n 'Sn': mva,\\n 'p': (data[5] + data[7] * voltage + data[9] * voltage ** 2) / mva,\\n 'q': (data[6] + data[8] * voltage - data[10] * voltage ** 2) / mva,\\n 'owner': data[11],\\n 'type': Settings.BusStore[busidx]['type'],\\n 'voltage': voltage\\n }\\n\\n psatlist = [busidx, mva, vn, param['p'], param['q'], maxV, minV, convimp, status]\\n Settings.PQ.append(psatlist)\\n \\\"\\\"\\\"CONFIRM THAT OTHER BUSES HAVE 0 P and 0 Q which are not added\\\"\\\"\\\"\\n\\n for data in raw['fshunt']:\\n \\\"\\\"\\\"\\n 0, 1, 2, 3, 4\\n Bus, name, Status, g (MW), b (Mvar)\\n \\\"\\\"\\\"\\n busidx = data[0]\\n vn = Settings.BusStore[busidx]['Vn']\\n param = {'bus': busidx,\\n 'Vn': vn,\\n 'status': data[2],\\n 'Sn': mva,\\n 'g': data[3] / mva,\\n 'b': data[4] / mva,\\n }\\n\\n psatlist = [busidx, mva, vn, freq, param['g'], param['b'], param['status']]\\n Settings.Shunt.append(psatlist)\\n\\n gen_idx = 0\\n type = 6\\n\\n for data in raw['gen']:\\n \\\"\\\"\\\"\\n 0, 1, 2, 3, 4, 5, 6, 7, 8, 9,10,11, 12, 13, 14, 15, 16,17,18,19\\n I,ID,PG,QG,QT,QB,VS,IREG,MBASE,ZR,ZX,RT,XT,GTAP,STAT,RMPCT,PT,PB,O1,F1\\n \\\"\\\"\\\"\\n busidx = data[0]\\n vn = Settings.BusStore[busidx]['Vn']\\n gen_mva = data[8]\\n gen_idx += 1\\n status = data[14]\\n leak = 0\\n param = {'Sn': gen_mva,\\n 'Vn': vn,\\n 'u': status,\\n 'idx': gen_idx,\\n 'bus': busidx,\\n 'pg': status * data[2] / mva,\\n 'qg': status * data[3] / mva,\\n 'qmax': data[4] / mva,\\n 'qmin': data[5] / mva,\\n 'v0': data[6],\\n 'ra': data[9], # ra armature resistance\\n 'xs': data[10], # xs synchronous reactance\\n 'pmax': data[16] / mva,\\n 'pmin': data[17] / mva,\\n }\\n\\n if Settings.BusStore[busidx]['type'] == 3: #Check Bus Type for Slack\\n refangle = 0\\n refBus = 1\\n PGuess = 1\\n swlist = [busidx, gen_mva, vn, param['v0'], refangle, param['qmax'], param['qmin'],\\n maxV, minV, PGuess, loss, refBus, status]\\n SW = swlist\\n Settings.SW.append(swlist)\\n Settings.SWStore[busidx] = param\\n Settings.SynStore[busidx] = param\\n continue\\n\\n if busidx not in Settings.BusStore.keys():\\n \\\"\\\"\\\" Need data from .dyr file. Create initial list, then append data from .dyr\\\"\\\"\\\"\\n else:\\n # psatlist = [busidx, gen_mva, vn, freq, type, leak, param['ra'],param['xs']]\\n # Syn.append(psatlist)\\n Settings.SynStore[busidx] = param\\n pvlist = [busidx, gen_mva, vn, param['pg'], Settings.BusStore[busidx]['voltage'],\\n param['qmax'], param['qmin'], maxV, minV, loss, status]\\n Settings.PV.append(pvlist)\\n\\n\\n for data in raw['branch']:\\n \\\"\\\"\\\"\\n I,J,ID,R,X,B,RATEA,RATEB,RATEC,GI,BI,GJ,BJ,ST,LEN,O1,F1,...,O4,F4\\n \\\"\\\"\\\"\\n param = {'bus1': data[0],\\n 'bus2': data[1],\\n 'id' : data[2],\\n 'r': data[3],\\n 'x': data[4],\\n 'b': data[5],\\n 'rate_a': data[6],\\n 'rate_b': data[7],\\n 'rate_c': data[8],\\n 'Vn': Settings.BusStore[data[0]]['Vn'],\\n 'Vn2': Settings.BusStore[data[1]]['Vn'],\\n 'length': data[14],\\n 'Ilim': EMPTY,\\n 'Plim': EMPTY,\\n 'Slim': EMPTY,\\n 'status': data[13]\\n }\\n\\n psatlist = [param['bus1'], param['bus2'], param['rate_c'], param['Vn'], freq, EMPTY,\\n param['length'], param['r'], param['x'], param['b'], param['Ilim'], param['Plim'], EMPTY, EMPTY,\\n param['Slim'], param['status']]\\n Settings.Lineij.append([data[0], data[1], data[2]])\\n Settings.Lineji.append([data[1], data[0], data[2]])\\n Settings.LineOrd[param['bus1']].append(psatlist)\\n Settings.branches += 1\\n Settings.linecount += 1\\n Settings.LineBusMatij[param['bus2']].append(Settings.branches)\\n Settings.LineBusMatji[param['bus1']].append(Settings.branches)\\n\\n for data in raw['transf']:\\n \\\"\\\"\\\"\\n I,J,K,CKT,CW,CZ,CM,MAG1,MAG2,NMETR,'NAME',STAT,O1,F1,...,O4,F4\\n R1-2,X1-2,SBASE1-2\\n WINDV1,NOMV1,ANG1,RATA1,RATB1,RATC1,COD1,CONT1,RMA1,RMI1,VMA1,VMI1,NTP1,TAB1,CR1,CX1\\n WINDV2,NOMV2\\n \\\"\\\"\\\"\\n if len(data[1]) < 5:\\n ty = 2\\n else:\\n ty = 3\\n if ty == 3:\\n continue\\n # raise NotImplementedError('Three-winding transformer not implemented')\\n\\n tap = data[2][0]\\n phi = data[2][2]\\n\\n if tap == 1 and phi == 0:\\n trasf = False\\n else:\\n trasf = True\\n param = {'trasf': trasf,\\n 'bus1': data[0][0],\\n 'bus2': data[0][1],\\n 'u': data[0][11],\\n 'b': data[0][8],\\n 'r': data[1][0],\\n 'x': data[1][1],\\n 'tap': tap,\\n 'phi': phi,\\n 'rate_a': data[2][3],\\n 'Vn': Settings.BusStore[busidx]['Vn'],\\n 'Vn2': Settings.BusStore[busidx]['Vn'],\\n # 'length': data[?][?], FIND CORRECT INDEX\\n 'Ilim': EMPTY,\\n 'Plim': EMPTY,\\n 'Slim': EMPTY,\\n }\\n psatlist = [param['bus1'], param['bus2'], param['rate_a'], param['Vn'], freq, EMPTY,\\n EMPTY, param['r'], param['x'], param['b'], param['Ilim'], param['Plim'], EMPTY, EMPTY,\\n param['Slim'], param['u']]\\n\\n Settings.LineOrd[param['bus1']].append(psatlist)\\n Settings.linecount += 1\\n Settings.transformers += 1\\n # ADD Line Data(All Branch Types) to Sys Param Dict after .dyr Transformer Data Added\\n # Re-Order Line Data for correct sequence\\n for key in Settings.LineOrd:\\n for item in Settings.LineOrd[key]:\\n Settings.Line.append(item)\\n\\n for data in raw['area']:\\n Settings.Areas.append(data[4])\\n\\n for data in raw['zone']:\\n Settings.Regions.append(data[1])\\n\\n return retval\",\n \"def testEdgeMarkerRaster0(self):\\n outname = self.prefix+'.asap'\\n self.res = sdcal(infile=self.rawfile,calmode='otfraster',markonly=True,outfile=outname,outform='ASAP')\\n refdir = self._readref( self.reffiles[0] )\\n self._checkfile( outname ) \\n self._checkmarker( outname, refdir )\",\n \"def testEdgeMarkerGeneric1(self):\\n outname = self.prefix+'.asap'\\n self.res = sdcal(infile=self.rawfile,calmode='otf',fraction='3%',markonly=True,outfile=outname,outform='ASAP')\\n refdir = self._readref( self.reffiles[1] )\\n self._checkfile( outname ) \\n self._checkmarker( outname, refdir )\",\n \"def reserved_field(self) -> int:\\n return unsigned_int(self._file_bytes, 0x06)\",\n \"def add_fault_rupture_from_file(self, fault_filename):\\n self.fault.add_patches_from_file(fault_filename) \\n self.irst = 214\",\n \"def remove_decay(slha_file, pid):\\n\\n print 'removing DECAY block %s from slha file %s' % (pid, slha_file)\\n\\n # rewrite slha file\\n import shutil\\n shutil.move(slha_file, slha_file+'.org')\\n \\n update = open(slha_file, 'w')\\n\\n skip = False\\n for l in open(slha_file+'.org'):\\n if l.startswith('DECAY %s '%pid):\\n skip = True\\n continue\\n\\n if l.startswith('DECAY '):\\n skip = False\\n \\n if not skip:\\n update.write(l)\\n \\n update.close()\\n\\n # remove also from MSSM.model file\\n print 'removing decay of %s from MSSM.model file' % pid\\n\\n # rewrite MSSM.model file\\n from PyJobTransformsCore.trfutil import get_files\\n get_files( 'MSSM.model', keepDir=False, errorIfNotFound=True )\\n\\n import shutil\\n shutil.move('MSSM.model', 'MSSM.model.org')\\n \\n update = open('MSSM.model', 'w')\\n\\n for l in open('MSSM.model.org'):\\n if l.startswith('insert /Herwig/Shower/ShowerHandler:DecayInShower 0 %s '%pid):\\n continue\\n update.write(l)\\n \\n update.close()\"\n]","isConversational":false},"negative_scores":{"kind":"list like","value":["0.5411359","0.53538233","0.53510696","0.5252125","0.51773673","0.5137562","0.5103627","0.509049","0.50799817","0.50792575","0.5078129","0.5071632","0.50331587","0.5031816","0.50235265","0.5013143","0.50088","0.50076556","0.50074273","0.50043285","0.499754","0.49968338","0.49952057","0.49935654","0.49828312","0.49811938","0.49774918","0.4974507","0.49631417","0.4934815","0.49295175","0.49237406","0.49235472","0.4923465","0.48970228","0.4887948","0.48748115","0.4868853","0.4843847","0.48417908","0.48340252","0.48262402","0.47927514","0.4785978","0.47858602","0.4784409","0.47795084","0.47708705","0.4765409","0.47623903","0.4758797","0.47567454","0.4752668","0.4744526","0.47390434","0.47293332","0.47234082","0.47228065","0.4722628","0.47199568","0.4719874","0.47051215","0.46924284","0.4691592","0.46854225","0.46853384","0.46757784","0.46748656","0.46696606","0.46693522","0.46689782","0.4665559","0.46644107","0.4659074","0.46545315","0.46434414","0.46429384","0.46383616","0.46322525","0.4631426","0.46254858","0.46195364","0.46178943","0.4617591","0.4603625","0.45994565","0.4598308","0.45982447","0.45967394","0.4595963","0.4595639","0.4591717","0.4579677","0.45792744","0.45785388","0.4567873","0.45623472","0.45563298","0.4551226","0.45507994","0.45429474"],"string":"[\n \"0.5411359\",\n \"0.53538233\",\n \"0.53510696\",\n \"0.5252125\",\n \"0.51773673\",\n \"0.5137562\",\n \"0.5103627\",\n \"0.509049\",\n \"0.50799817\",\n \"0.50792575\",\n \"0.5078129\",\n \"0.5071632\",\n \"0.50331587\",\n \"0.5031816\",\n \"0.50235265\",\n \"0.5013143\",\n \"0.50088\",\n \"0.50076556\",\n \"0.50074273\",\n \"0.50043285\",\n \"0.499754\",\n \"0.49968338\",\n \"0.49952057\",\n \"0.49935654\",\n \"0.49828312\",\n \"0.49811938\",\n \"0.49774918\",\n \"0.4974507\",\n \"0.49631417\",\n \"0.4934815\",\n \"0.49295175\",\n \"0.49237406\",\n \"0.49235472\",\n \"0.4923465\",\n \"0.48970228\",\n \"0.4887948\",\n \"0.48748115\",\n \"0.4868853\",\n \"0.4843847\",\n \"0.48417908\",\n \"0.48340252\",\n \"0.48262402\",\n \"0.47927514\",\n \"0.4785978\",\n \"0.47858602\",\n \"0.4784409\",\n \"0.47795084\",\n \"0.47708705\",\n \"0.4765409\",\n \"0.47623903\",\n \"0.4758797\",\n \"0.47567454\",\n \"0.4752668\",\n \"0.4744526\",\n \"0.47390434\",\n \"0.47293332\",\n \"0.47234082\",\n \"0.47228065\",\n \"0.4722628\",\n \"0.47199568\",\n \"0.4719874\",\n \"0.47051215\",\n \"0.46924284\",\n \"0.4691592\",\n \"0.46854225\",\n \"0.46853384\",\n \"0.46757784\",\n \"0.46748656\",\n \"0.46696606\",\n \"0.46693522\",\n \"0.46689782\",\n \"0.4665559\",\n \"0.46644107\",\n \"0.4659074\",\n \"0.46545315\",\n \"0.46434414\",\n \"0.46429384\",\n \"0.46383616\",\n \"0.46322525\",\n \"0.4631426\",\n \"0.46254858\",\n \"0.46195364\",\n \"0.46178943\",\n \"0.4617591\",\n \"0.4603625\",\n \"0.45994565\",\n \"0.4598308\",\n \"0.45982447\",\n \"0.45967394\",\n \"0.4595963\",\n \"0.4595639\",\n \"0.4591717\",\n \"0.4579677\",\n \"0.45792744\",\n \"0.45785388\",\n \"0.4567873\",\n \"0.45623472\",\n \"0.45563298\",\n \"0.4551226\",\n \"0.45507994\",\n \"0.45429474\"\n]","isConversational":false},"document_score":{"kind":"string","value":"0.0"},"document_rank":{"kind":"string","value":"-1"}}},{"rowIdx":16594,"cells":{"query":{"kind":"string","value":"Trap offspec data in gerber file."},"document":{"kind":"string","value":"def test_alien_data(self):"},"metadata":{"kind":"string","value":"{\n \"objective\": {\n \"self\": [],\n \"paired\": [],\n \"triplet\": [\n [\n \"query\",\n \"document\",\n \"negatives\"\n ]\n ]\n }\n}"},"negatives":{"kind":"list like","value":["def add_fault_rupture_from_file(self, fault_filename):\n self.fault.add_patches_from_file(fault_filename) \n self.irst = 214","def test_fake_file(self):\n fits_file = os.path.join(self.datadir, 'monol_test_fake.evt')\n hen.fake.main(['-o', fits_file, '--instrument', 'FPMB'])\n info = hen.io.print_fits_info(fits_file, hdu=1)\n assert info['Instrument'] == 'FPMB'","def setUp(self):\n self.junk_file = '/tmp/asdfoowersdfuixlwles'","def hook_file_opened(self):","def test_process_data():\n afos_dump.process_data(\"\")","def test_fake_file_with_deadtime(self):\n fits_file = os.path.join(self.datadir, 'monol_test_fake_lc.evt')\n hen.fake.main(['--deadtime', '2.5e-3',\n '--ctrate', '2000',\n '-o', fits_file])","def test_DL_import_wrong_file_unserialized(self):\n filepath = '6.txt'\n wrong_file = open(filepath, 'x')\n wrong_file.write(\"This is not a serialized detector flow data\")\n wrong_file.close()\n # Check if exception was raised for wrong serialization\n with self.assertRaises(Exception):\n flow_processing_input.DetectorsLocation(9999, filepath)\n os.remove(filepath)","def setUp(self):\n self.single_rfh2_message = open(\n os.path.join(self.messages_dir, \"single_rfh2.dat\"), \"rb\").read()\n self.single_rfh2_message_not_well_formed = \\\n self.single_rfh2_message[0:117] + self.single_rfh2_message[121:]","def setUp(self):\n # parse the file\n self.plateMeas = PlateMeas(pathToPlate8131MeasFile)","def setup_file_handling(self, down_store, file_encoder, file_decoder, distributor, log_dir):\n self.__uplinker = fprime_gds.common.files.uplinker.FileUplinker(file_encoder)\n self.__downlinker = fprime_gds.common.files.downlinker.FileDownlinker(down_store, log_dir=log_dir)\n file_decoder.register(self.__downlinker)\n distributor.register(\"FW_PACKET_HAND\", self.__uplinker)","def handleExistingData(iIndent):\r\n\tglobal sEType, sEVar, sEData\r\n\r\n\t# If none, quit.\r\n\tif not sEType:\r\n\t\treturn\r\n\r\n\t# Skip if we have no data.\r\n\tif not sEData:\r\n\t\treturn\r\n\r\n\t# Insert tab level and comments into a header.\r\n\tsHead = (\" \" * iIndent) + \"/// \"\r\n\r\n\t# Sanitise data.\r\n\tsEData.rstrip()\r\n\r\n\t# Swap breaks for heads.\r\n\tsEData = sEData.replace(BREAK, \"\\n\" + sHead)\r\n\r\n\t# Write out the respective blocks.\r\n\tif sEType == BRIEF:\r\n\t\t#sEData = sEData.replace(\"<summary>\", \"\")\r\n\t\t#sEData = sEData.replace(\"</summary>\", \"\")\r\n\t\tpOutFile.write(sHead + \"<summary>\\n\")\r\n\t\tpOutFile.write(sHead + sEData + \"\\n\")\r\n\t\tpOutFile.write(sHead + \"</summary>\\n\")\r\n\r\n\telif sEType == PARAM:\r\n\t\tpOutFile.write(sHead + \"<param name=\\\"\" + str(sEVar) + \"\\\">\" + str(sEData) + \"</param>\\n\")\r\n\r\n\telif sEType == RETURN:\r\n\t\tpOutFile.write(sHead + \"<returns>\" + str(sEData) + \"</returns>\\n\")\r\n\r\n\telif sEType == AUTHOR:\r\n\t\tpOutFile.write(sHead + \"<author>\" + str(sEData) + \"</author>\\n\")\r\n\t\t\r\n\telif sEType == DATE:\r\n\t\tpOutFile.write(sHead + \"<date>\" + str(sEData) + \"</date>\\n\")\r\n\t\t\r\n\telif sEType == RETURN:\r\n\t\tpOutFile.write(sHead + \"<returns>\" + str(sEData) + \"</returns>\\n\")\r\n\r\n\telif sEType == REMARK:\r\n\t\tpOutFile.write(sHead + str(sEData) + \"\\n\")\r\n\r\n\t# Zap any leftover data.\r\n\tsEType = None\r\n\tsEVar = None\r\n\tsEData = \"\"","def rdspecdat(self):\n # TODO : ugh. this is crude. Should have some checks for file format\n # and probably better to use the astropy.io functions now.\n try:\n w, f, e = np.loadtxt(self.filename, unpack=True)\n except:\n w, f = np.loadtxt(self.filename, unpack=True)\n e = []","def preCommitFixup(self):\n log_method_call(self, self.name)\n # UEFI firmware/bootloader cannot read 1.1 or 1.2 metadata arrays\n if getattr(self.format, \"mountpoint\", None) == \"/boot/efi\":\n self.metadataVersion = \"1.0\"","def do_before_dump(self):\n self.checksummer.prepare_checksums()","def test_handle_info_reading():\n bids_root = _TempDir()\n\n # read in USA dataset, so it should find 50 Hz\n raw = _read_raw_fif(raw_fname)\n\n # write copy of raw with line freq of 60\n # bids basename and fname\n bids_path = BIDSPath(subject='01', session='01',\n task='audiovisual', run='01',\n root=bids_root)\n suffix = \"meg\"\n bids_fname = bids_path.copy().update(suffix=suffix,\n extension='.fif')\n write_raw_bids(raw, bids_path, overwrite=True)\n\n # find sidecar JSON fname\n bids_fname.update(datatype=suffix)\n sidecar_fname = _find_matching_sidecar(bids_fname, suffix=suffix,\n extension='.json')\n\n # assert that we get the same line frequency set\n raw = read_raw_bids(bids_path=bids_path)\n assert raw.info['line_freq'] == 60\n\n # 2. if line frequency is not set in raw file, then ValueError\n raw.info['line_freq'] = None\n with pytest.raises(ValueError, match=\"PowerLineFrequency .* required\"):\n write_raw_bids(raw, bids_path, overwrite=True)\n\n # make a copy of the sidecar in \"derivatives/\"\n # to check that we make sure we always get the right sidecar\n # in addition, it should not break the sidecar reading\n # in `read_raw_bids`\n deriv_dir = op.join(bids_root, \"derivatives\")\n sidecar_copy = op.join(deriv_dir, op.basename(sidecar_fname))\n os.mkdir(deriv_dir)\n with open(sidecar_fname, \"r\", encoding='utf-8') as fin:\n sidecar_json = json.load(fin)\n sidecar_json[\"PowerLineFrequency\"] = 45\n _write_json(sidecar_copy, sidecar_json)\n raw = read_raw_bids(bids_path=bids_path)\n assert raw.info['line_freq'] == 60\n\n # 3. assert that we get an error when sidecar json doesn't match\n _update_sidecar(sidecar_fname, \"PowerLineFrequency\", 55)\n with pytest.raises(ValueError, match=\"Line frequency in sidecar json\"):\n raw = read_raw_bids(bids_path=bids_path)\n assert raw.info['line_freq'] == 55","def insert_bad_data():\n get_file_reply(files[2][0], files[2][1])","def test_DL_import_wrong_file_serialized(self):\n filepath = '5.txt'\n with open(filepath, 'wb') as file:\n pickle.dump([\"This is a wrong dataset\"], file)\n # Check if exception was raised for wrong data type\n with self.assertRaises(Exception):\n flow_processing_input.DetectorsLocation(9999, filepath)\n os.remove(filepath)","def test_old_format_for_tags(self):\n test_files = glob.glob(INPUT_HYPM_PATH + '/unit_*.mdd')\n test_files.extend(glob.glob(INPUT_FLMB_PATH + '/unit_*.mdd'))\n\n mdd.procall(test_files)\n\n data = self.read_full_file('node58p1.dat')\n if not self.check_for_tags(data):\n self.fail(\"Found header tag in data file\")\n\n data = self.read_full_file('node59p1.dat')\n if not self.check_for_tags(data):\n self.fail(\"Found header tag in data file\")","def testEdgeMarkerGeneric0(self):\n outname = self.prefix+'.asap'\n self.res = sdcal(infile=self.rawfile,calmode='otf',markonly=True,outfile=outname,outform='ASAP')\n refdir = self._readref( self.reffiles[0] )\n self._checkfile( outname ) \n self._checkmarker( outname, refdir )","def test_is_not_delicious_file(self):\r\n bad_file = StringIO.StringIO()\r\n bad_file.write('failing tests please')\r\n bad_file.seek(0)\r\n\r\n self.assertTrue(\r\n not DelXMLImporter.can_handle(bad_file),\r\n \"DelXMLImporter cannot handle this file\")\r\n\r\n bad_file.close()","def test_is_not_delicious_file(self):\r\n bad_file = StringIO.StringIO()\r\n bad_file.write('failing tests please')\r\n bad_file.seek(0)\r\n\r\n self.assertTrue(\r\n not DelImporter.can_handle(bad_file),\r\n \"DelImporter cannot handle this file\")\r\n\r\n bad_file.close()","def add_fault_rupture_from_file(self,fault_filename):\n \n self.ricom.add_fault_rupture_from_file(fault_filename)","def test_pert_file(self):\n path, case = os.path.split(self.ieee14)\n\n # --- with pert file ---\n ss = andes.run('ieee14.raw', pert='pert.py',\n input_path=path, no_output=True, default_config=True,\n )\n ss.TDS.init()\n self.assertIsNotNone(ss.TDS.callpert)\n\n # --- without pert file ---\n ss = andes.run('ieee14.raw',\n input_path=path, no_output=True, default_config=True,\n )\n ss.TDS.init()\n self.assertIsNone(ss.TDS.callpert)","def read_input(self, specs):\n print('DEBUGG specs:', specs)","def test_real_file(self):\n log.info('===== START TEST BYTE LOSS =====')\n\n # Recovered\n file_path = os.path.join(RESOURCE_PATH, '11079364_SNA_SNA.txt')\n\n stream_handle = open(file_path, MODE_ASCII_READ)\n\n self.create_parser(stream_handle, telem_flag=False)\n\n particles = self.parser.get_records(182)\n\n log.debug(\"*** test_real_file Num particles %s\", len(particles))\n\n # check all the values against expected results.\n self.assert_particles(particles, '11079364_SNA_SNA_recov.yml', RESOURCE_PATH)\n self.assertEquals(self.exception_callback_value, [])\n stream_handle.close()\n\n # Telemetered\n file_path = os.path.join(RESOURCE_PATH, '11079419_SNA_SNA.txt')\n\n stream_handle = open(file_path, MODE_ASCII_READ)\n\n self.create_parser(stream_handle)\n\n particles = self.parser.get_records(172)\n\n log.debug(\"*** test_real_file Num particles %s\", len(particles))\n\n # check all the values against expected results.\n self.assert_particles(particles, '11079419_SNA_SNA_telem.yml', RESOURCE_PATH)\n stream_handle.close()\n\n log.info('===== END TEST REAL FILE =====')","def test_read_0_1_smirnoff(self):\n ForceField(\n get_data_file_path(\n \"test_forcefields/smirnoff99Frosst_reference_0_1_spec.offxml\"\n )\n )","def prepare_bed_file(bed_file, output, ouf=False, save_rejected=None, only_chrom=None):\n new_lines = [] # keep updated lines\n rejected = [] # keep IDs of skipped transcripts + the reason why\n names = Counter() # we need to make sure that all names are unique\n allowed_re = re.compile(ALLOWED_CHARSET_RE).search\n broken_names = []\n\n f = open(bed_file, \"r\")\n for num, line in enumerate(f, 1):\n # parse bed file according to specification\n line_data = line.rstrip().split(\"\\t\")\n\n if len(line_data) != 12:\n f.close() # this is for sure an error\n # it is possible only if something except a bed12 was provided\n die(\n \"Error! Bed 12 file is required! Got a file with {len(line_data)} fields instead\"\n )\n\n chrom = line_data[0]\n if only_chrom and chrom != only_chrom:\n # TOGA allows to perform the analysis on a specific chromosome only\n # is so, we can skip all transcripts that located on other chromosomes\n continue\n chromStart = int(line_data[1])\n chromEnd = int(line_data[2])\n name = line_data[3] # gene_name usually\n corr_name = not bool(allowed_re(name))\n if corr_name is False:\n broken_names.append(name)\n # TODO: check weird characters in the transcript name\n # bed_score = int(line_data[4]) # never used\n # strand = line_data[5] # otherwise:\n # strand = True if line_data[5] == '+' else False\n thickStart = int(line_data[6])\n thickEnd = int(line_data[7])\n # itemRgb = line_data[8] # never used\n blockCount = int(line_data[9])\n blockSizes = [int(x) for x in line_data[10].split(\",\") if x != \"\"]\n blockStarts = [int(x) for x in line_data[11].split(\",\") if x != \"\"]\n blockEnds = [blockStarts[i] + blockSizes[i] for i in range(blockCount)]\n blockAbsStarts = [blockStarts[i] + chromStart for i in range(blockCount)]\n blockAbsEnds = [blockEnds[i] + chromStart for i in range(blockCount)]\n blockNewStarts, blockNewEnds = [], []\n names[name] += 1\n\n if thickStart > thickEnd:\n f.close() # according to bed12 specification this should never happen\n sys.stderr.write(f\"Problem occurred at line {num}, gene {name}\\n\")\n die(\"Error! Bed file is corrupted, thickEnd MUST be >= thickStart\")\n elif thickStart == thickEnd:\n # this means that this is a non-coding transcript\n # TOGA cannot process them: we can skip it\n rejected.append((name, \"No CDS\"))\n continue\n\n if thickStart < chromStart or thickEnd > chromEnd:\n # a very strange (but still possible) case\n f.close() # for sure an error with input data\n sys.stderr.write(f\"Problem occurred at line {num}, gene {name}\\n\")\n die(\"Error! Bed file is corrupted, thickRange is outside chromRange!\")\n\n # now select CDS only\n # we keep UTRs in the filtered file\n # however, we need CDS to check whether it's correct (% 3 == 0)\n for block_num in range(blockCount):\n blockStart = blockAbsStarts[block_num]\n blockEnd = blockAbsEnds[block_num]\n\n # skip the block if it is entirely UTR\n if blockEnd <= thickStart:\n continue\n elif blockStart >= thickEnd:\n continue\n\n # if we are here: this is not an entirely UTR exon\n # it might intersect the CDS border or to be in the CDS entirely\n # remove UTRs: block start must be >= CDS_start (thickStart)\n # block end must be <= CDS_end (thickEnd)\n blockNewStart = blockStart if blockStart >= thickStart else thickStart\n blockNewEnd = blockEnd if blockEnd <= thickEnd else thickEnd\n blockNewStarts.append(blockNewStart - thickStart)\n blockNewEnds.append(blockNewEnd - thickStart)\n\n if len(blockNewStarts) == 0:\n # even it thickStart != thickEnd this transcript still can be non-coding\n # but if there are no blocks in the CDS -> we can catch this\n rejected.append((name, \"No CDS\"))\n continue\n\n block_new_count = len(blockNewStarts)\n blockNewSizes = [\n blockNewEnds[i] - blockNewStarts[i] for i in range(block_new_count)\n ]\n\n if sum(blockNewSizes) % 3 != 0 and not ouf:\n # this is an out-of-frame (or incomplete transcript)\n # ideally CDS length should be divisible by 3\n # not ouf means that we like to keep such transcripts for some reason\n rejected.append((name, \"Out-of-frame gene\"))\n continue\n\n # we keep this transcript: add in to the list\n new_line = \"\\t\".join([str(x) for x in line_data])\n new_lines.append(new_line)\n f.close()\n\n # if not allowed characters in transcript names: list them\n if len(broken_names) > 0:\n eprint(\"Error! Some transcript names contain not allowed characters\")\n for t in broken_names:\n eprint(t)\n die(f\"Allowed characters are: {ALLOWED_CHARSET}\")\n # if there are non-unique transcript IDs: die\n # I kill it there, not earlier to show them altogether\n if any(v > 1 for v in names.values()):\n eprint(\"Error! There are non-uniq transcript IDs:\")\n duplicates = [k for k, v in names.items() if v > 1]\n for d in duplicates:\n eprint(d)\n die(\"Abort\")\n\n if len(new_lines) == 0:\n # no transcripts pass the filter: probably an input data mistake\n sys.exit(\n f\"Error! No reference annotation tracks left after filtering procedure! Abort\"\n )\n\n # write transcripts that passed the filter to the output file\n f = open(output, \"w\") if output != \"stdout\" else sys.stdout\n f.write(\"\\n\".join(new_lines) + \"\\n\")\n f.close() if output != \"stdout\" else None\n\n if save_rejected:\n # save transcripts that didn't pass the filter + reason why\n f = open(save_rejected, \"w\")\n for elem in rejected:\n f.write(f\"{elem[0]}\\t{elem[1]}\\n\")\n f.close()","def setUp(self):\n self.epath = 'flyeye/tests/fixtures'\n self.dpath = join(self.epath, 'disc.silhouette')","def test_readfile_fits(self):\n fitsname = os.path.join(self.datadir, 'monol_testA.evt')\n command = \"{0}\".format(fitsname)\n\n hen.io.main(command.split())","def setUp(self):\n\n PyFunceble.load_config()\n\n StdoutBase.setUp(self)\n\n self.file = \"the_file_is_a_ghost\"\n self.to_print = {\n \"basic\": {\"hello\": 5, \"world\": 6, \"here\": 7, \"is\": 8, \"PyFunceble\": 10},\n \"size_constructor\": [5, 6, 7, 8, 9, 10],\n \"basic_string\": \"Hello, World!\",\n \"hosts\": {\"0.0.0.0\": 7, \"hello.world\": 11},\n }\n\n self.file_instance = PyFunceble.helpers.File(self.file)\n self.file_instance.delete()","def test_fake_file_from_input_lc(self):\n lcurve_in = os.path.join(self.datadir, 'lcurveA.fits')\n fits_file = os.path.join(self.datadir, 'monol_test_fake_lc.evt')\n hen.fake.main(['--lc', lcurve_in, '-o', fits_file])","def setUp(self):\n with open('test/0a6a357e.json') as read_file:\n self.tx_json_0a6a357e = json.load(read_file)\n with open('test/bip69-synth.json') as read_file:\n self.bip69_synth = json.load(read_file)","def gain_data_main():\n gainfile = os.path.join(DATA_PATH, \"zen.2457698.40355.xx.gain.calfits\")\n with uvtest.check_warnings(\n UserWarning,\n match=[\n \"telescope_location is not set. Using known values for HERA.\",\n \"antenna_positions are not set or are being overwritten. Using known \"\n \"values for HERA.\",\n ],\n ):\n gain_object = UVCal.from_file(gainfile, use_future_array_shapes=True)\n gain_object.freq_range = None\n\n yield gain_object\n\n del gain_object","def unknown(self):\n self.add_file_string('Unknown file')\n self.should_copy = False","def SetStructuredData(self, file): # real signature unknown; restored from __doc__\n pass","def test_load_rivers_config_major_forcing_data_file(self, config, config_dict, infile_dict, monkeypatch):\n test_output_file = 'Fraser_flow'\n monkeypatch.setitem(infile_dict['forcing_data_files'], 'major_river', test_output_file)\n config.rivers = Mock()\n config._read_yaml_file = Mock(return_value=config_dict)\n config._load_rivers_config(config_dict, infile_dict)\n assert config.rivers.output_files[\"major\"] == test_output_file","def test_import_report_malformed():\n with pytest.raises(DmarcImportError):\n import_feedback_report('<malform></ed>')","def test_read_0_2_smirnoff(self):\n ForceField(\n get_data_file_path(\n \"test_forcefields/smirnoff99Frosst_reference_0_2_spec.offxml\"\n )\n )","def test_readbadformat(self):\n\n self.assertRaises(ParseError, self.hw, self.badfile)","def test_pds_txt(self):\n lcurve_txt = os.path.join(self.datadir,\n 'lcurve_txt_lc' +\n HEN_FILE_EXTENSION)\n command = '{0} -f 128'.format(lcurve_txt)\n hen.fspec.main(command.split())","def test_is_delicious_file(self):\r\n good_file = self._get_del_file()\r\n self.assertTrue(\r\n DelXMLImporter.can_handle(good_file),\r\n \"DelXMLImporter should handle this file\")\r\n good_file.close()","def test_data_source_soaps_post(self):\n pass","def testEdgeMarkerGeneric1(self):\n outname = self.prefix+'.asap'\n self.res = sdcal(infile=self.rawfile,calmode='otf',fraction='3%',markonly=True,outfile=outname,outform='ASAP')\n refdir = self._readref( self.reffiles[1] )\n self._checkfile( outname ) \n self._checkmarker( outname, refdir )","def test_load_rivers_config_minor_forcing_data_file(self, config, config_dict, infile_dict, monkeypatch):\n test_output_file = 'Englishman_flow'\n monkeypatch.setitem(infile_dict['forcing_data_files'], 'minor_river', test_output_file)\n config.rivers = Mock()\n config._read_yaml_file = Mock(return_value=config_dict)\n config._load_rivers_config(config_dict, infile_dict)\n assert config.rivers.output_files[\"minor\"] == test_output_file","def test_strain_redefined(generate_strain_redefined):\n fname = generate_strain_redefined\n try:\n process_files([fname])\n raise Exception('The redefined strain data and lack of stress data was not caught')\n except IOError:\n pass","def preparePatch(self):\n if DEBUG > 1: sys.stderr.write(\"* preparePatch()\\n\")\n\n if self.patchLoaded:\n #Load PC with 0x0220.\n #This will invoke the patched bootstrap loader subroutines.\n self.bslTxRx(self.BSL_LOADPC, #Command: Load PC\n 0x0220) #Address to load into PC\n self.BSLMemAccessWarning = 0 #Error is removed within workaround code\n return","def _read_file(self):\n\n with open(self.file_name, 'rb') as f:\n new_test = struct.unpack('<l', f.read(8)[4:])[0]\n f.close()\n\n with open(self.file_name, 'rb') as f:\n old_test = struct.unpack('<h', f.read(6)[4:])[0]\n f.close()\n\n with open(self.file_name, 'rb') as f:\n other_test = struct.unpack('<l', f.read(20)[16:])[0]\n f.close()\n\n open_file = open(self.file_name, 'rb')\n\n if (other_test==202):\n raw = open_file.read(1236)[11:]\n self.model = '202'\n elif ((not new_test==102) and old_test==102):\n raw = open_file.read(1133)\n self.model = '102old'\n elif (new_test==102 and old_test==102):\n raw = open_file.read(1224)\n self.model = '102new'\n\n self.header = DpHeader(raw, self.model)\n\n self.data = DpData(open_file, \n self.model, \n self.header.interferogram_size, \n self.header.number_of_coadds, \n 2048*self.header.zero_fill,\n self.header.laser_wavelength_microns, \n self.header.dispersion_constant_xm,\n self.header.dispersion_constant_xb)\n\n open_file.close()","def test_read_raw_suggested(fname):\n with pytest.raises(ValueError, match='Try reading'):\n read_raw(fname)","def delay_data_main():\n delayfile = os.path.join(DATA_PATH, \"zen.2457698.40355.xx.delay.calfits\")\n with uvtest.check_warnings(\n UserWarning,\n match=[\n \"telescope_location is not set. Using known values for HERA.\",\n \"antenna_positions are not set or are being overwritten. Using known \"\n \"values for HERA.\",\n \"When converting a delay-style cal to future array shapes the flag_array\"\n \" (and input_flag_array if it exists) must drop the frequency axis\",\n ],\n ):\n delay_object = UVCal.from_file(delayfile, use_future_array_shapes=True)\n\n # yield the data for testing, then del after tests finish\n yield delay_object\n\n del delay_object","def _read_eeg(eeg_file):\r\n pass","def _process_end_of_file(self):\n (nd_timestamp, non_data) = self._chunker.get_next_non_data()\n if non_data and len(non_data) > 0:\n message = \"Extra un-expected non-data bytes at the end of the file:%s\", non_data\n log.warn(message)\n self._exception_callback(RecoverableSampleException(message))","def test_getters_no_ext(self, *args):\n test_data = WireProtocolData(DATA_FILE_NO_EXT)\n self._test_getters(test_data, *args)","def test_harvester_new_file_exception_recovered(self):\n # need to put data in the file, not just make an empty file for this to work\n self.create_sample_data_set_dir(\n \"DOS15908_1st7_step1.DAT\",\n RECOV_DIR,\n \"DOS15908.DAT\",\n mode=000,\n copy_metadata=False\n )\n\n self.assert_initialize(final_state=ResourceAgentState.COMMAND)\n\n self.event_subscribers.clear_events()\n self.assert_resource_command(DriverEvent.START_AUTOSAMPLE)\n self.assert_state_change(ResourceAgentState.LOST_CONNECTION, 90)\n self.assert_event_received(ResourceAgentConnectionLostErrorEvent, 10)\n\n self.clear_sample_data()\n self.create_sample_data_set_dir(\n \"DOS15908_1st7_step1.DAT\",\n RECOV_DIR,\n \"DOS15908.DAT\",\n copy_metadata=False\n )\n\n # Should automatically retry connect and transition to streaming\n self.assert_state_change(ResourceAgentState.STREAMING, 90)","def test_GFD_import_wrong_file_unserialized(self):\n filepath = '6.txt'\n wrong_file = open(filepath, 'x')\n wrong_file.write(\"This is not a serialized detector flow data\")\n wrong_file.close()\n # Check if exception was raised for wrong serialization\n with self.assertRaises(Exception):\n flow_processing_input.GroundFlowData(filepath)\n os.remove(filepath)","def _handle_dump_unknown(self, data, original):\n for key, val in original.items():\n if key not in self.fields:\n data[key] = val\n return data","def readAMBERTop(self, phys, filename):\r\n\r\n def skipLine(data):\r\n nl = data.index('\\n')\r\n return data[nl+1:len(data)]\r\n\r\n def jumpTo(data, target):\r\n fp = data.index(target)\r\n return data[fp:len(data)]\r\n\r\n def readRemove(data, size):\r\n retval = data[0:size-1]\r\n return data[size:len(data)]\r\n\r\n def getInteger(data):\r\n pos = 0\r\n retval = \"\"\r\n while (not data[pos].isdigit()):\r\n pos = pos + 1\r\n while (data[pos].isdigit()):\r\n retval = retval + data[pos]\r\n pos = pos + 1\r\n data = data[pos:len(data)]\r\n return int(retval), data\r\n\r\n def parse(data, arr, str, count, dtype, tupsize=1):\r\n data = jumpTo(data, \"%FLAG \"+str)\r\n data = jumpTo(data, \"%FORMAT\")\r\n numPerLine, data = getInteger(data)\r\n fieldsize, data = getInteger(data)\r\n data = skipLine(data) \r\n \r\n arr2 = []\r\n numread = 0\r\n for j in range(0, (tupsize*count-1) / numPerLine + 1):\r\n for i in range(0, numPerLine):\r\n if (tupsize == 1):\r\n arr.append(dtype(data[0:fieldsize].strip()))\r\n else:\r\n arr2.append(dtype(data[0:fieldsize].strip()))\r\n if (len(arr2) == tupsize):\r\n arr.append(arr2)\r\n arr2 = []\r\n numread += 1\r\n data = data[fieldsize:len(data)]\r\n if (numread == tupsize*count):\r\n break\r\n data = skipLine(data) \r\n return data\r\n\r\n def scan(data, str):\r\n return (data.count(str) != 0)\r\n\r\n\r\n f = open(filename, 'r')\r\n data = f.read()\r\n\r\n # First Line: VERSION ...\r\n data = skipLine(data)\r\n\r\n # Go To: %FLAG POINTERS\r\n data = jumpTo(data, '%FLAG POINTERS')\r\n\r\n data = jumpTo(data, '%FORMAT')\r\n numPerLine, data = getInteger(data)\r\n fieldsize, data = getInteger(data)\r\n data = skipLine(data)\r\n \r\n temp = []\r\n numread = 0\r\n for j in range(0, 31 / numPerLine + 1):\r\n for i in range(0, numPerLine):\r\n temp.append(int(data[0:8]))\r\n data = data[8:len(data)]\r\n numread += 1\r\n if (numread == 31):\r\n break\r\n data = skipLine(data)\r\n \r\n [natoms, ntypes, nbonh, mbona, ntheth, mtheta, nphih, mphia, nhparm, nparm, nnb, nres, nbona, ntheta, nphia, numbnd, numang, nptra, natyp, nphb, ifpert, nbper, ngper, ndper, mbper, mgper, mdper, ifbox, nmxrs, ifcap, numextra] = temp \r\n\r\n\r\n #################################################\r\n # Read AtomTypes\r\n atomnames = []\r\n charges = []\r\n masses = []\r\n atindex = []\r\n exclusions = []\r\n nparams = []\r\n reslabels = []\r\n respointers = []\r\n forceconstants = [[], [], []] # bond, angle, dihedral\r\n equilvals = [[], [], [[], []]] # bond, angle, dihedral\r\n scee_scales = []\r\n scnb_scales = []\r\n solty = []\r\n lj_acoef = []\r\n lj_bcoef = []\r\n\r\n data = parse(data, atomnames, \"ATOM_NAME\", natoms, str) \r\n data = parse(data, charges, \"CHARGE\", natoms, float)\r\n data = parse(data, masses, \"MASS\", natoms, float)\r\n data = parse(data, atindex, \"ATOM_TYPE_INDEX\", natoms, int)\r\n data = parse(data, exclusions, \"NUMBER_EXCLUDED_ATOMS\", natoms, int)\r\n data = parse(data, nparams, \"NONBONDED_PARM_INDEX\", ntypes*ntypes, int)\r\n data = parse(data, reslabels, \"RESIDUE_LABEL\", nres, str)\r\n data = parse(data, respointers, \"RESIDUE_POINTER\", nres, int)\r\n data = parse(data, forceconstants[0], \"BOND_FORCE_CONSTANT\", numbnd, float)\r\n data = parse(data, equilvals[0], \"BOND_EQUIL_VALUE\", numbnd, float)\r\n data = parse(data, forceconstants[1], \"ANGLE_FORCE_CONSTANT\", numang, float)\r\n data = parse(data, equilvals[1], \"ANGLE_EQUIL_VALUE\", numang, float)\r\n data = parse(data, forceconstants[2], \"DIHEDRAL_FORCE_CONSTANT\", nptra, float)\r\n data = parse(data, equilvals[2][0], \"DIHEDRAL_PERIODICITY\", nptra, float)\r\n data = parse(data, equilvals[2][1], \"DIHEDRAL_PHASE\", nptra, float)\r\n if (scan(data, \"SCEE_SCALE_FACTOR\")):\r\n data = parse(data, scee_scales, \"SCEE_SCALE_FACTORS\", nptra, float)\r\n else:\r\n for i in range(0, nptra):\r\n scee_scales.append(1.2) # Default \r\n if (scan(data, \"SCNB_SCALE_FACTOR\")):\r\n data = parse(data, scnb_scales, \"SCNB_SCALE_FACTORS\", nptra, float)\r\n else:\r\n for i in range(0, nptra):\r\n scnb_scales.append(2.0) # Default \r\n\r\n data = parse(data, solty, \"SOLTY\", natyp, float)\r\n data = parse(data, lj_acoef, \"LENNARD_JONES_ACOEF\", ntypes*(ntypes+1)/2, float)\r\n data = parse(data, lj_bcoef, \"LENNARD_JONES_BCOEF\", ntypes*(ntypes+1)/2, float)\r\n\r\n\r\n ##########################################################\r\n # STRUCTURE\r\n\r\n bonds = [[], []] # With H, Without H\r\n angles = [[], []] # With H, Without H\r\n dihedrals = [[], []] # With H, Without H\r\n impropers = [[], []] # With H, Without H\r\n excluded_atoms = [] \r\n hbond_acoef = []\r\n hbond_bcoef = []\r\n hbcut = []\r\n amber_atom_types = []\r\n tree_chain = []\r\n join_array = []\r\n irotat = []\r\n radii = []\r\n screen = []\r\n\r\n data = parse(data, bonds[0], \"BONDS_INC_HYDROGEN\", nbonh, int, 3)\r\n data = parse(data, bonds[1], \"BONDS_WITHOUT_HYDROGEN\", nbona, int, 3)\r\n data = parse(data, angles[0], \"ANGLES_INC_HYDROGEN\", ntheth, int, 4)\r\n data = parse(data, angles[1], \"ANGLES_WITHOUT_HYDROGEN\", ntheta, int, 4)\r\n data = parse(data, dihedrals[0], \"DIHEDRALS_INC_HYDROGEN\", nphih, int, 5)\r\n data = parse(data, dihedrals[1], \"DIHEDRALS_WITHOUT_HYDROGEN\", nphia, int, 5)\r\n \r\n # MERGE ARRAYS - PM HANDLES THE H+\r\n final_bonds = bonds[0] + bonds[1]\r\n final_angles = angles[0] + angles[1]\r\n final_dihedrals = dihedrals[0] + dihedrals[1]\r\n final_impropers = []\r\n \r\n # CLEAN UP THE TRASH\r\n del(bonds)\r\n del(angles)\r\n del(dihedrals)\r\n \r\n\r\n # Move impropers into their own array\r\n i = 0\r\n while (i < len(final_dihedrals)):\r\n if (final_dihedrals[i][2] < 0): # 1-4 exclusions are handled by our back end\r\n final_dihedrals[i][2] *= -1\r\n if (final_dihedrals[i][3] < 0):\r\n final_dihedrals[i][3] *= -1 # Make + again\r\n final_impropers.append(final_dihedrals[i])\r\n final_dihedrals.remove(final_dihedrals[i])\r\n i -= 1\r\n i += 1\r\n\r\n # Convert charge units\r\n for i in range(0, len(charges)):\r\n charges[i] /= 18.223\r\n\r\n\r\n data = parse(data, excluded_atoms, \"EXCLUDED_ATOMS_LIST\", nnb, int)\r\n data = parse(data, hbond_acoef, \"HBOND_ACOEF\", nphb, float)\r\n data = parse(data, hbond_bcoef, \"HBOND_BCOEF\", nphb, float)\r\n data = parse(data, hbcut, \"HBCUT\", nphb, float)\r\n data = parse(data, amber_atom_types, \"AMBER_ATOM_TYPE\", natoms, str)\r\n data = parse(data, tree_chain, \"TREE_CHAIN_CLASSIFICATION\", natoms, str)\r\n data = parse(data, join_array, \"JOIN_ARRAY\", natoms, int)\r\n data = parse(data, irotat, \"IROTAT\", natoms, int)\r\n data = parse(data, radii, \"RADII\", natoms, float)\r\n data = parse(data, screen, \"SCREEN\", natoms, float)\r\n\r\n # Further process dihedrals and impropers\r\n # Deal with multiplicity\r\n # A bit ugly, but the fastest for now\r\n # forceconstants[2][dihedrals[0][i][4]-1], int(equilvals[2][0][dihedrals[0][i][4]-1]), equilvals[2][1][dihedrals[0][i][4]-1]\r\n\r\n mult_di = dict()\r\n mult_im = dict()\r\n for i in range(0, len(final_dihedrals)):\r\n di_id = str(final_dihedrals[i][0])+' '+str(final_dihedrals[i][1])+' '+str(final_dihedrals[i][2])+' '+str(final_dihedrals[i][3])\r\n if (not mult_di.has_key(di_id)):\r\n mult_di[di_id] = [1, False, [forceconstants[2][final_dihedrals[i][4]-1]], [int(equilvals[2][0][final_dihedrals[i][4]-1])], [equilvals[2][1][final_dihedrals[i][4]-1]]]\r\n else:\r\n mult_di[di_id][0] += 1\r\n mult_di[di_id][2].append(forceconstants[2][final_dihedrals[i][4]-1])\r\n mult_di[di_id][3].append(int(equilvals[2][0][final_dihedrals[i][4]-1]))\r\n mult_di[di_id][4].append(equilvals[2][1][final_dihedrals[i][4]-1])\r\n \r\n for i in range(0, len(final_impropers)):\r\n im_id = str(final_impropers[i][0])+' '+str(final_impropers[i][1])+' '+str(final_impropers[i][2])+' '+str(final_impropers[i][3])\r\n if (not mult_im.has_key(di_id)):\r\n mult_im[im_id] = [1, False, [forceconstants[2][final_impropers[i][4]-1]], [int(equilvals[2][0][final_impropers[i][4]-1])], [equilvals[2][1][final_impropers[i][4]-1]]]\r\n else:\r\n mult_im[im_id][0] += 1\r\n mult_im[im_id][2].append(forceconstants[2][final_impropers[i][4]-1])\r\n mult_im[im_id][3].append(int(equilvals[2][0][final_impropers[i][4]-1]))\r\n mult_im[im_id][4].append(equilvals[2][1][final_impropers[i][4]-1])\r\n\r\n\r\n\r\n \r\n #[natoms, ntypes, nbonh, mbona, ntheth, mtheta, nphih, mphia, nhparm, nparm, nnb, nres, nbona, ntheta, nphia, numbnd, numang, nptra, natyp, nphb, ifpert, nbper, ngper, ndper, mbper, mgper, mdper, ifbox, nmxrs, ifcap, numextra] = temp \r\n #phys.myPSF.createAll(natoms, nbonh+mbona, ntheth+mtheta,\r\n # len(dihedrals[0])+len(dihedrals[1]),\r\n # len(impropers[0])+len(impropers[1]),\r\n # 0, 0, 0, 0)\r\n \r\n # Add atoms\r\n curres = 1\r\n for i in range(0, natoms):\r\n phys.myPSF.addAtom(i, 'SIM', curres, reslabels[curres-1],\r\n atomnames[i], atomnames[i], charges[i],\r\n masses[i]) \r\n if (curres != nres and i >= respointers[curres]):\r\n curres += 1\r\n\r\n # Add bonds\r\n for i in range(0, nbonh+nbona):\r\n phys.myPSF.addBond(i+1, final_bonds[i][0]/3+1, final_bonds[i][1]/3+1)\r\n phys.myPAR.addBond(i+1, atomnames[final_bonds[i][0]/3], atomnames[final_bonds[i][1]/3], forceconstants[0][final_bonds[i][2]/3], equilvals[0][final_bonds[i][2]/3])\r\n \r\n # Add angles\r\n for i in range(0, ntheth+ntheta):\r\n phys.myPSF.addAngle(i+1, final_angles[i][0]/3+1, final_angles[i][1]/3+1, final_angles[i][2]/3+1)\r\n phys.myPAR.addAngle(i+1, atomnames[final_angles[i][0]/3], atomnames[final_angles[i][1]/3], atomnames[final_angles[i][2]/3], forceconstants[1][final_angles[i][3]/3], equilvals[1][final_angles[i][3]/3])\r\n \r\n # Add dihedrals\r\n for i in range(0, len(final_dihedrals)):\r\n di_id = str(final_dihedrals[i][0])+' '+str(final_dihedrals[i][1])+' '+str(final_dihedrals[i][2])+' '+str(final_dihedrals[i][3])\r\n mult = mult_di[di_id][0]\r\n checked = mult_di[di_id][1]\r\n print di_id, \" \", mult\r\n if (not checked):\r\n if (mult == 1):\r\n phys.myPSF.addDihedral(i+1, final_dihedrals[i][0]/3+1, final_dihedrals[i][1]/3+1, int(numpy.abs(final_dihedrals[i][2]))/3+1, final_dihedrals[i][3]/3+1)\r\n phys.myPAR.addDihedral(i+1, atomnames[final_dihedrals[i][0]/3], atomnames[final_dihedrals[i][1]/3], atomnames[int(numpy.abs(final_dihedrals[i][2]))/3], atomnames[final_dihedrals[i][3]/3], forceconstants[2][final_dihedrals[i][4]-1], int(equilvals[2][0][final_dihedrals[i][4]-1]), equilvals[2][1][final_dihedrals[i][4]-1])\r\n else:\r\n mult_di[di_id][1] = True\r\n # Add dihedral with the appropriate multiplicity\r\n # Force constants, periodicity and phase shifts are in [2], [3], and [4] respectively\r\n fcvec = PARReader.VectorOfDouble()\r\n periodvec = PARReader.VectorOfInt()\r\n phasevec = PARReader.VectorOfDouble() \r\n for j in range(0, len(mult_di[di_id][2])):\r\n fcvec.push_back(mult_di[di_id][2][j])\r\n periodvec.push_back(mult_di[di_id][3][j])\r\n phasevec.push_back(mult_di[di_id][4][j])\r\n phys.myPSF.addDihedral(i+1, final_dihedrals[i][0]/3+1, final_dihedrals[i][1]/3+1, int(numpy.abs(final_dihedrals[i][2]))/3+1, final_dihedrals[i][3]/3+1)\r\n phys.myPAR.addDihedral(i+1, atomnames[final_dihedrals[i][0]/3], atomnames[final_dihedrals[i][1]/3], atomnames[int(numpy.abs(final_dihedrals[i][2]))/3], atomnames[final_dihedrals[i][3]/3], mult, fcvec, periodvec, phasevec)\r\n \r\n\r\n\r\n\r\n for i in range(0, len(final_impropers)):\r\n im_id = str(final_impropers[i][0])+' '+str(final_impropers[i][1])+' '+str(final_impropers[i][2])+' '+str(final_impropers[i][3])\r\n mult = mult_im[im_id][0]\r\n checked = mult_im[im_id][1]\r\n print im_id, \" \", mult\r\n if (not checked):\r\n if (mult == 1):\r\n phys.myPSF.addImproper(i+1, final_impropers[i][0]/3+1, final_impropers[i][1]/3+1, int(numpy.abs(final_impropers[i][2]))/3+1, final_impropers[i][3]/3+1)\r\n phys.myPAR.addImproper(i+1, atomnames[final_impropers[i][0]/3], atomnames[final_impropers[i][1]/3], atomnames[int(numpy.abs(final_impropers[i][2]))/3], atomnames[final_impropers[i][3]/3], forceconstants[2][final_impropers[i][4]-1], int(equilvals[2][0][final_impropers[i][4]-1]), equilvals[2][1][final_impropers[i][4]-1])\r\n else:\r\n mult_im[im_id][1] = True\r\n # Add dihedral with the appropriate multiplicity\r\n # Force constants, periodicity and phase shifts are in [2], [3], and [4] respectively\r\n fcvec = PARReader.VectorOfDouble()\r\n periodvec = PARReader.VectorOfInt()\r\n phasevec = PARReader.VectorOfDouble() \r\n for j in range(0, len(mult_im[im_id][2])):\r\n fcvec.push_back(mult_im[im_id][2][j])\r\n periodvec.push_back(mult_im[im_id][3][j])\r\n phasevec.push_back(mult_im[im_id][4][j])\r\n phys.myPSF.addImproper(i+1, final_impropers[i][0]/3+1, final_impropers[i][1]/3+1, int(numpy.abs(final_impropers[i][2]))/3+1, final_impropers[i][3]/3+1)\r\n phys.myPAR.addImproper(i+1, atomnames[final_impropers[i][0]/3], atomnames[final_impropers[i][1]/3], atomnames[int(numpy.abs(final_impropers[i][2]))/3], atomnames[final_impropers[i][3]/3], mult, fcvec, periodvec, phasevec)\r\n\r\n \r\n # Need to add garbage nonbonded stuff for now\r\n for i in range(0, natoms):\r\n phys.myPAR.addNonbonded(i, atomnames[i], 1, 1, 1, 1, 1, 1)\r\n\r\n # Add VDW parameters\r\n # AMBER has the Aij and Bij already in the parameter file\r\n # This actually makes life easier.\r\n # CHARMM does not, they simply have the original sigma and epsilon.\r\n # To compensate for this, for now we will leave the nonbondeds empty in phys.myPAR\r\n # We will then access the LennardJones parameter table in Topology directly\r\n k = 0\r\n phys.myTop.resizeLennardJonesParameters(ntypes)\r\n for i in range(0, ntypes):\r\n for j in range(i, ntypes):\r\n params = GenericTopology.LennardJonesParameters(lj_acoef[k], lj_bcoef[k])\r\n k += 1\r\n phys.myTop.setLennardJonesParameters(i, j, params)\r\n \r\n phys.myPAR.readFlag = 1\r\n phys.build()","def read_data(self, loc):\n pass","def setUp(self):\n self.setUpPyfakefs()\n with mock.patch.object(subprocess, 'Popen', side_effect=thor_mocks.mock_thor_start):\n self._analyzer = yara_analyzer.YaraAnalyzer()\n\n # Write target file.\n # pylint: disable=no-member\n self.fs.create_file('./target.exe', contents='This is definitely not an evil file. ^_^\\n')","def UnhandledPacket(Packet):\n\n\tglobal UnhandledFile\n\n\tif (UnhandledFile != None):\n\t\tUnhandledFile.write(Packet)","def read(self, filename): # real signature unknown; restored from __doc__\n pass","def test_harvester_new_file_exception_recovered(self):\n # create the file so that it is unreadable\n self.create_sample_data_set_dir(\n \"DOS15908_1st7_step1.DAT\",\n RECOV_DIR,\n \"DOS15909.DAT\",\n mode=000\n )\n\n # Start sampling and watch for an exception\n self.driver.start_sampling()\n\n self.assert_exception(IOError)\n\n # At this point the harvester thread is dead. The agent\n # exception handle should handle this case.","def test_fix_odk_sunmission(self):\n data = {\n \"@a\": \"a\",\n \"b\": \"b\",\n \"orx:meta\": \"should_not_be_there\"\n }\n\n fixed_data = sources.__fix_odk_data(data)\n\n self.assertEqual(fixed_data, {\n \"a\": \"a\",\n \"b\": \"b\"\n })","def test_bad_data(self):\r\n # LB180210_3_corrupted.PD0 has three records in it, the 2nd record was corrupted\r\n with open(os.path.join(RESOURCE_PATH, 'LB180210_3_corrupted.PD0'), 'rb') as stream_handle:\r\n\r\n parser = AdcpPd0Parser(self.config_recov, stream_handle, self.exception_callback)\r\n\r\n # try to get 3 particles, should only get 2 back\r\n # the second one should correspond to ensemble 3\r\n parser.get_records(3)\r\n\r\n log.debug('Exceptions : %s', self.exception_callback_value[0])\r\n\r\n self.assertEqual(len(self.exception_callback_value), 1)\r\n self.assert_(isinstance(self.exception_callback_value[0], RecoverableSampleException))","def test_is_delicious_file(self):\r\n good_file = self._get_del_file()\r\n\r\n self.assertTrue(\r\n DelImporter.can_handle(good_file),\r\n \"DelImporter should handle this file\")\r\n\r\n good_file.close()","def UnDumpInfo(self):\n filename = '%s/preprocess_info.yaml' % self.logdir\n f = open(filename,'r')\n self.info = yaml.load(f.read())\n f.close()","def test_read_0_1_smirff(self):\n ForceField(\n get_data_file_path(\n \"test_forcefields/smirff99Frosst_reference_0_1_spec.offxml\"\n )\n )","def package_data(self, data):\n pass","def test_bug1003(capfd):\n input_dir = get_input_path('bug1003')\n temp_dir = get_temp_dir_path('bug1003var')\n copytree(input_dir, temp_dir)\n ds_path = os.path.join(temp_dir, 'bug1003.designspace')\n runner(CMD + ['-o', 'd', f'_{ds_path}'])\n captured = capfd.readouterr()\n assert \"The input set requires compatibilization\" in captured.err","def handle_data(self, data):\n if verbose(): print(\"TIParser.handle_data(self, '%s')\" % (data))\n pass","def _read_bu_wig(self, handle, sequence_name):\n self.chromosomes[sequence_name] = () \n for line in handle:\n position, total, reverse, forward = line.rstrip(\"\\r\\n\").split()\n self.coverage[(sequence_name, position)] = (int(reverse), int(forward))","def test_doubled_file():\n with contextlib.closing(get_test_data('Level2_KFTG_20150430_1419.ar2v')) as infile:\n data = infile.read()\n fobj = BytesIO(data + data)\n f = Level2File(fobj)\n assert len(f.sweeps) == 12","def _autodetect_endianness(self):\n pos = self.file.tell()\n # Jump to the data sample format code.\n self.file.seek(3224, 1)\n format = unpack(b'>h', self.file.read(2))[0]\n # Check if valid.\n if format in DATA_SAMPLE_FORMAT_UNPACK_FUNCTIONS.keys():\n self.endian = '>'\n # Else test little endian.\n else:\n self.file.seek(-2, 1)\n format = unpack(b'<h', self.file.read(2))[0]\n if format in DATA_SAMPLE_FORMAT_UNPACK_FUNCTIONS.keys():\n self.endian = '<'\n else:\n msg = 'Unable to determine the endianness of the file. ' + \\\n 'Please specify it.'\n raise SEGYError(msg)\n # Jump to previous position.\n self.file.seek(pos, 0)","def __init__(self, raw_data_file,):\n self.raw_data_file = raw_data_file\n self.clean_data = self.cleanData()\n self.microtrip_data = []","def test_get_infile(self):\r\n pass # not practically testable, but obvious file I/O\r","def test_ddt_with_unknown_extends(self):\n # Setup test\n infilename = os.path.join(_SAMPLE_FILES_DIR, \"reg_good_ddt.xml\")\n filename = os.path.join(_TMP_DIR, \"reg_ddt_unknown_extends.xml\")\n out_source_name = \"physics_types_ddt_unknown_extends\"\n out_source = os.path.join(_TMP_DIR, out_source_name + '.F90')\n out_meta = os.path.join(_TMP_DIR, out_source_name + '.meta')\n remove_files([out_source, out_meta])\n tree, root = read_xml_file(infilename)\n # Change output filename\n for obj in root:\n oname = obj.get('name')\n if (obj.tag == 'file') and (oname == 'physics_types_ddt'):\n obj.set('name', out_source_name)\n for var in obj:\n ltype = var.get('type')\n if (var.tag == 'ddt') and (ltype == \"physics_state\"):\n var.set('extends', 'physics_tend')\n break\n # End if\n # End for\n break\n # End if\n # End for\n tree.write(filename)\n # Run test\n with self.assertRaises(ValueError) as verr:\n _ = gen_registry(filename, 'eul', {}, _TMP_DIR, 2,\n _SRC_MOD_DIR, _CAM_ROOT,\n loglevel=logging.ERROR,\n error_on_no_validate=True)\n # End with\n # Check exception message\n emsg = (\"DDT, 'physics_state', extends type 'physics_tend', \"\n \"however, this type is not known\")\n self.assertEqual(emsg, str(verr.exception))\n # Make sure no output files were created\n self.assertFalse(os.path.exists(out_meta))\n self.assertFalse(os.path.exists(out_source))","def __init__(self, message, file_handle, format):\n oh = open(file_handle, \"rU\")\n config.log.critical(\"Unrecognised file format\")\n print(\"-----------------------\")\n print(\"Diagnostic:\")\n print(\"0:\", oh.readline().rstrip(\"\\r\\n\"))\n print(\"1:\", oh.readline().rstrip(\"\\r\\n\"))\n print(\"2:\", oh.readline().rstrip(\"\\r\\n\"))\n print(\"3:\", oh.readline().rstrip(\"\\r\\n\"))\n if \"sniffer\" in format:\n print(\"Format Specifier: Sniffer (guess the file format)\")\n else:\n print(\n \"Format Specifier: %s\"\n % \" \".join(\"%s:%s\" % (key, format[key]) for key in format)\n )\n\n print(\"-----------------------\")\n config.log.critical(\"%s\" % (message,))\n print()","def record_fileprep(data):\n order_detail = OrderDetail.objects.get(ac_od_id=data['ac_od_id'])\n order_detail.fileprep = data['fileprep']\n return order_detail.save()","def _load_raw_file(self, tracker, seq, is_gt):\n\n # Only loaded when run to reduce minimum requirements\n from pycocotools import mask as mask_utils\n\n # File location\n if self.data_is_zipped:\n if is_gt:\n zip_file = os.path.join(self.gt_fol, 'data.zip')\n else:\n zip_file = os.path.join(self.tracker_fol, tracker, self.tracker_sub_fol + '.zip')\n file = seq + '.txt'\n else:\n zip_file = None\n if is_gt:\n file = self.config[\"GT_LOC_FORMAT\"].format(gt_folder=self.gt_fol, seq=seq)\n else:\n file = os.path.join(self.tracker_fol, tracker, self.tracker_sub_fol, seq + '.txt')\n\n # Ignore regions\n if is_gt:\n crowd_ignore_filter = {2: ['10']}\n else:\n crowd_ignore_filter = None\n\n # Load raw data from text file\n read_data, ignore_data = self._load_simple_text_file(file, crowd_ignore_filter=crowd_ignore_filter,\n is_zipped=self.data_is_zipped, zip_file=zip_file,\n force_delimiters=' ')\n\n # Convert data to required format\n num_timesteps = self.seq_lengths[seq]\n data_keys = ['ids', 'classes', 'dets']\n if is_gt:\n data_keys += ['gt_ignore_region']\n raw_data = {key: [None] * num_timesteps for key in data_keys}\n\n # Check for any extra time keys\n current_time_keys = [str(t) for t in range(num_timesteps)]\n extra_time_keys = [x for x in read_data.keys() if x not in current_time_keys]\n if len(extra_time_keys) > 0:\n if is_gt:\n text = 'Ground-truth'\n else:\n text = 'Tracking'\n raise TrackEvalException(\n text + ' data contains the following invalid timesteps in seq %s: ' % seq + ', '.join(\n [str(x) + ', ' for x in extra_time_keys]))\n\n for t in range(num_timesteps):\n time_key = str(t)\n # list to collect all masks of a timestep to check for overlapping areas\n all_masks = []\n if time_key in read_data.keys():\n try:\n raw_data['dets'][t] = [{'size': [int(region[3]), int(region[4])],\n 'counts': region[5].encode(encoding='UTF-8')}\n for region in read_data[time_key]]\n raw_data['ids'][t] = np.atleast_1d([region[1] for region in read_data[time_key]]).astype(int)\n raw_data['classes'][t] = np.atleast_1d([region[2] for region in read_data[time_key]]).astype(int)\n all_masks += raw_data['dets'][t]\n except IndexError:\n self._raise_index_error(is_gt, tracker, seq)\n except ValueError:\n self._raise_value_error(is_gt, tracker, seq)\n else:\n raw_data['dets'][t] = []\n raw_data['ids'][t] = np.empty(0).astype(int)\n raw_data['classes'][t] = np.empty(0).astype(int)\n if is_gt:\n if time_key in ignore_data.keys():\n try:\n time_ignore = [{'size': [int(region[3]), int(region[4])],\n 'counts': region[5].encode(encoding='UTF-8')}\n for region in ignore_data[time_key]]\n raw_data['gt_ignore_region'][t] = mask_utils.merge([mask for mask in time_ignore],\n intersect=False)\n all_masks += [raw_data['gt_ignore_region'][t]]\n except IndexError:\n self._raise_index_error(is_gt, tracker, seq)\n except ValueError:\n self._raise_value_error(is_gt, tracker, seq)\n else:\n raw_data['gt_ignore_region'][t] = mask_utils.merge([], intersect=False)\n\n # check for overlapping masks\n if all_masks:\n masks_merged = all_masks[0]\n for mask in all_masks[1:]:\n if mask_utils.area(mask_utils.merge([masks_merged, mask], intersect=True)) != 0.0:\n raise TrackEvalException(\n 'Tracker has overlapping masks. Tracker: ' + tracker + ' Seq: ' + seq + ' Timestep: ' + str(\n t))\n masks_merged = mask_utils.merge([masks_merged, mask], intersect=False)\n\n if is_gt:\n key_map = {'ids': 'gt_ids',\n 'classes': 'gt_classes',\n 'dets': 'gt_dets'}\n else:\n key_map = {'ids': 'tracker_ids',\n 'classes': 'tracker_classes',\n 'dets': 'tracker_dets'}\n for k, v in key_map.items():\n raw_data[v] = raw_data.pop(k)\n raw_data[\"num_timesteps\"] = num_timesteps\n raw_data['seq'] = seq\n return raw_data","def postprocess_file(config: Config, dfs: DFs) -> None:\n if SymbolDF.name in dfs:\n dfs[SymbolDF.name] = postprocess_symbols(config, dfs[SymbolDF.name])","def tell(self):\n ...","def test_read_fail2(self):\n mod_fn = os.path.join(tests.TEST_DATA_PATH, 'segmentations', 'test_bad_data2.mod')\n with self.assertRaises(ValueError):\n modreader.get_data(mod_fn) # missing 'IEOF' end","def setUp(self):\n self._file = 'test.g3'\n write_example_file(self._file)","def readdata(self,filename_): # 3\n res = self.__obj.readdataautoformat(filename_)\n if res != 0:\n result,msg = self.__getlasterror(res)\n raise Error(rescode(res),msg)","def tests_ti_file_get(self):\n super().indicator_get()","def _read_data(self):","def test_incomplete_file(self):\n log.info(\"START INTEG TEST INCOMPLETE\")\n\n self.clear_sample_data()\n self.clear_async_data()\n\n # From sample file A0000010.DEC:\n # Flag record, first and last velocity record, time record,\n # but the end of Velocity record (all zeroes) is missing.\n filename = \"A1000002.DEC\"\n self.create_sample_data('incomplete_A0000002.DEC', filename)\n\n # Start sampling.\n self.driver.start_sampling()\n\n # an event catches the sample exception\n self.assert_event('ResourceAgentErrorEvent')\n\n # Verify that the entire file has been read.\n self.assert_file_ingested(filename)\n\n log.info(\"END INTEG TEST INCOMPLETE\")","def post_process_trap(): \n #################### 0) assign internal values #################### \n from project_parameters import trapType,debug,trapFile,name,driveAmplitude,driveFrequency,Omega,dcplot,weightElectrodes,coefs,ax,az,phi,save,scale\n #from all_functions import find_saddle,plot_potential,dc_potential,set_voltages,exact_saddle,spher_harm_bas,spher_harm_exp,pfit,plotN\n import pickle\n\n with open(trapFile,'rb') as f:\n trap = pickle.load(f)\n\n qe = trap.configuration.charge\n mass = trap.configuration.mass\n Zval = trap.configuration.position\n r0 = trap.configuration.r0\n RFampl = driveAmplitude \n V0 = mass*(2*np.pi*Omega)**2*(r0*10**-3)**2/qe\n X,Y,Z=trap.instance.X,trap.instance.Y,trap.instance.Z \n data = trap.configuration\n dcVoltages = set_voltages()\n ne = len(weightElectrodes)\n E = trap.instance.E\n out = trap.configuration\n if debug.post_process_trap:\n print dcVoltages,np.max(dcVoltages)#np.sum(abs(dcVoltages))\n plotN(dcVoltages,trap,'set DC voltages') \n Vdc = dc_potential(trap,dcVoltages,E)\n #[IDC,JDC,KDC] = find_saddle(Vdc,X,Y,Z,3,Zval) \n #[XDC,YDC,ZDC] = exact_saddle(Vdc,X,Y,Z,3,Zval)\n #XDC,YDC,ZDC = X[IDC],150/scale,Z[KDC]\n #print XDC,YDC,ZDC,IDC,JDC,KDC\n #dcbasis,dcscale= spher_harm_bas(XDC,YDC,ZDC,X,Y,Z,4)\n #QQ = spher_harm_exp(Vdc,dcbasis,dcscale) \n #print QQ[0:9].T\n #1) RF Analysis\n print('RF Analysis') \n Vrf = RFampl*data.EL_RF\n [Irf,Jrf,Krf] = find_saddle(Vrf,X,Y,Z,2,Zval)\n if debug.post_process_trap:\n plot_potential(Vrf,X,Y,Z,dcplot,'weighted RF potential','V_{rf} (eV)',[Irf,Jrf,Krf])\n #2) DC Analysis\n print('DC Analysis')\n trap = dc_potential(trap,dcVoltages,E,update=None)\n Vdc = trap.instance.DC\n [Idc,Jdc,Kdc] = find_saddle(Vdc,X,Y,Z,3,Zval) # only used to calculate error at end\n if debug.post_process_trap:\n plot_potential(Vdc,X,Y,Z,'1D plots','full DC potential')\n #3) determine the exact saddles of the RF and DC\n trap = dc_potential(trap,dcVoltages,E)\n Vdc = trap.instance.DC\n print('Determining exact RF saddle...')\n [Xrf,Yrf,Zrf] = exact_saddle(Vrf,X,Y,Z,2,Zval) \n print('Determining exact DC saddle...')\n [Xdc,Ydc,Zdc] = exact_saddle(Vdc,X,Y,Z,3,Zval)\n #4) determine stray field (beginning of justAnalyzeTrap)\n print('Determining compensation due to E field...')\n nx,ny,nz=X.shape[0],Y.shape[0],Z.shape[0]\n x,y,z = np.zeros((nx,ny,nz)),np.zeros((nx,ny,nz)),np.zeros((nx,ny,nz))\n for i in range(nx):\n for j in range(ny):\n for k in range(nz):\n x[i,j,k] = X[i]\n y[i,j,k] = Y[j]\n z[i,j,k] = Z[k]\n VlessE = Vdc-E[0]*x-E[1]*y-E[2]*z\n [Xdc,Ydc,Zdc] = exact_saddle(VlessE,X,Y,Z,3) \n dist = np.sqrt((Xrf-Xdc)**2+(Yrf-Ydc)**2+(Zrf-Zdc)**2) \n #5) call pfit to built teh total field and determine the trap characteristics\n [fx,fy,fz,theta,Depth,Xe,Ye,Ze] = pfit(Vrf,Vdc,X,Y,Z,Irf,Jrf,Krf)#pfit(trap,E,Freq,RFampl)\n print('Stray field is ({0},{1},{2}) V/m.'.format(scale*E[0],scale*E[1],scale*E[2]))\n print('With this field, the compensation is optimized to {} micron.'.format(scale*dist))\n print('RF saddle: ({0},{1},{2})\\nDC saddle ({3},{4},{5}).'.format(Xrf,Yrf,Zrf,Xdc,Ydc,Zdc)) \n if debug.trap_depth:\n print('The trap escape position is at ({0},{1},{2}) microns, for a trap depth of {3} mV'.format(Xe*scale,Ye*scale,Ze*scale,Depth*scale))\n print('The trap frequencies are fx = {0} MHz, fy = {1} MHz, and fz = {2} MHz'.format(fx*10**-6,fy*10**-6,fz*10**-6))\n #6) Sanity testing; quality check no longer used\n if debug.post_process_trap:\n rfbasis,rfscale= spher_harm_bas(Xrf,Yrf,Zrf,X,Y,Z,2)\n Qrf = spher_harm_exp(Vrf,rfbasis,rfscale) \n if np.sqrt((Xrf-Xdc)**2+(Yrf-Ydc)**2+(Zrf-Zdc)**2)>0.008: \n print('Expanding DC with RF for saniy checking.')\n Qdc = spher_harm_exp(Vdc,rfbasis,rfscale) \n else:\n print('Expanding DC without RF for sanity checking.')\n dcbasis,dcscale= spher_harm_bas(Xdc,Ydc,Zdc,X,Y,Z,2)\n Qdc = spher_harm_exp(Vdc,dcbasis,dcscale) \n Arf = 2*np.sqrt( (3*Qrf[7])**2+(3*Qrf[8])**2 )\n Thetarf = 45*(Qrf[8]/abs(Qrf[8]))-90*np.arctan((3*Qrf[7])/(3*Qrf[8]))/np.pi\n Adc = 2*np.sqrt( (3*Qdc[7])**2+(3*Qdc[8])**2 )\n Thetadc = 45*(Qrf[8]/abs(Qrf[8]))-90*np.arctan((3*Qdc[7])/(3*Qdc[8]))/np.pi\n out.E = E\n out.miscompensation = dist\n out.ionpos = [Xrf,Yrf,Zdc]\n out.ionposIndex = [Irf,Jrf,Krf]\n out.frequency = [fx,fy,fz]\n out.theta = theta\n out.trap_depth = Depth/qe \n out.escapepos = [Xe,Ye,Ze]\n out.Quadrf = 2*np.array([Qrf[7]*3,Qrf[4]/2,Qrf[8]*6,-Qrf[6]*3,-Qrf[5]*3])\n out.Quaddc = 2*np.array([Qdc[7]*3,Qdc[4]/2,Qdc[8]*6,-Qdc[6]*3,-Qdc[5]*3])\n out.Arf = Arf\n out.Thetarf = Thetarf\n out.Adc = Adc\n out.Thetadc = Thetadc\n T = np.array([[2,-2,0,0,0],[-2,-2,0,0,0],[0,4,0,0,0],[0,0,1,0,0],[0,0,0,1,0],[0, 0,0,0,1]])\n Qdrf = out.Quadrf.T\n Qddc = out.Quaddc.T\n out.q = (1/V0)*T*Qdrf\n out.alpha = (2/V0)*T*Qddc\n out.Error = [X[Idc]-Xdc,Y[Jdc]-Ydc,Z[Kdc]-Zdc]\n #7) update the trapping field data structure with instance attributes\n trap.configuration=out\n trap.instance.driveAmplitude = driveAmplitude\n trap.instance.driveFrequency = driveFrequency\n trap.instance.coefs = coefs\n trap.instance.ax = ax\n trap.instance.az = az\n trap.instance.phi = phi\n trap.instance.ppt = True\n trap.instance.out = out\n if save==True:\n print('Saving '+trapFile+' as a data structure...')\n with open(trapFile,'wb') as f:\n pickle.dump(trap,f)\n return 'post_proccess_trap complete' #out # no output needed really","def process_file(self, data, filename):\n\n if data:\n data = self.update_province_info(data)\n self.get_province_info(data, filename)","def __init__(self, inFilename):\n\n self._prmtopVersion=None\n self._flags=[]\n self._raw_format={}\n self._raw_data={}\n self._has_nbfix_terms = False\n\n with open(inFilename, 'r') as fIn:\n for line in fIn:\n if line[0] == '%':\n if line.startswith('%VERSION'):\n tag, self._prmtopVersion = line.rstrip().split(None, 1)\n elif line.startswith('%FLAG'):\n tag, flag = line.rstrip().split(None, 1)\n self._flags.append(flag)\n self._raw_data[flag] = []\n elif line.startswith('%FORMAT'):\n format = line.rstrip()\n index0=format.index('(')\n index1=format.index(')')\n format = format[index0+1:index1]\n try:\n m = FORMAT_RE_PATTERN.search(format)\n self._raw_format[self._flags[-1]] = (format, m.group(1), m.group(2), int(m.group(3)), m.group(4))\n except:\n # We couldn't parse the format, so just treat the whole line as a single string.\n self._raw_format[self._flags[-1]] = (format, 1, 'a', 80, '')\n elif line.startswith('%COMMENT'):\n continue\n elif self._flags \\\n and 'TITLE'==self._flags[-1] \\\n and not self._raw_data['TITLE']:\n self._raw_data['TITLE'] = line.rstrip()\n else:\n flag=self._flags[-1]\n (format, numItems, itemType,\n iLength, itemPrecision) = self._getFormat(flag)\n line = line.rstrip()\n for index in range(0, len(line), iLength):\n item = line[index:index+iLength]\n if item:\n self._raw_data[flag].append(item.strip())\n # See if this is a CHAMBER-style topology file, which is not supported\n # for creating Systems\n self.chamber = 'CTITLE' in self._flags","def import_fix_dat(xrec=None):\n xrec = conf.get_current()\n\n\n regEx = re.compile(\"[A-Z]{5}\")\n \n inputfile = conf.work_dir(\"/xplane_unzipped/%s/earth_fix.dat\" % (xrec['zip_dir']))\n c = 0\n with open(inputfile) as readnav:\n \n for line in readnav:\n c += 1\n \n # Skip first three lines, hope Robin Peel will never change this behaviour ;-)\n if c < 4:\n pass\n else:\n \n if not line.startswith(\"99\"):\n \n lst = line.strip().split()\n fix_ident = str(lst[2])\n \n if fix_ident == \"NPOLE\":\n pass\n \n else:\n #//fix_center_lat84 = str(lst[0])\n #fix_center_lon84 = str(lst[1])\n maj = 1 if regEx.match(fix_ident) else 0\n # insert to db\n insert_fix( \n **dict(\n ident=fix_ident, major=maj,\n lat=str(lst[0]), lon=str(lst[1])\n )\n )\n \n ## We commit every x to make faster\n if c % 5000 == 0:\n print \" > fix: %s - %s of %s\" % (fix_ident, c, MAX_LINES_GUESS)\n\n \n idx_file = conf.raw_fix_path()","def unusedFromKDOTDataPreparation():","def test_load_events_noclobber(self):\n with catch_warnings() as w:\n command = \\\n '{0} --noclobber'.format(\n os.path.join(self.datadir, 'monol_testB.evt'))\n hen.read_events.main(command.split())\n assert str(w[0].message).strip().endswith(\n \"exists and using noclobber. Skipping\"), \\\n \"Unexpected warning output\"","def test_load_gtis(self):\n fits_file = os.path.join(self.datadir, 'monol_testA.evt')\n hen.io.load_gtis(fits_file)","def __init__(self, filename):\n config.log.critical(\"File '%s' is not a glbase binary file\" % filename)","def run():\n\twrite_fuel_data()","def tests_ti_file_get_tag(self, request: FixtureRequest):\n super().indicator_get_tag(request)","def _hook_data(self, data):\n if self.data_hook is not None:\n self.data_hook(data)","def import_gene_information(inputargs):\n\n global chainnams, chain\n chain = inputargs['chain']\n\n if inputargs['tags'] == \"extended\" and inputargs['species'] == \"mouse\":\n print(\"Please note that there is currently no extended tag set for mouse TCR genes.\\n\" \\\n \"Decombinator will now switch the tag set in use from \\'extended\\' to \\'original\\'.\\n\" \\\n \"In future, consider editing the script to change the default, \" \\\n \"or use the appropriate flags (-sp mouse -tg original).\")\n inputargs['tags'] = \"original\"\n\n if inputargs['tags'] == \"extended\" and (chain == 'g' or chain == 'd'):\n print(\"Please note that there is currently no extended tag set for gamma/delta TCR genes.\\n\" \\\n \"Decombinator will now switch the tag set in use from \\'extended\\' to \\'original\\'.\\n\" \\\n \"In future, consider editing the script to change the default, or use the appropriate flags.\")\n inputargs['tags'] = \"original\"\n\n # Check species information\n if inputargs['species'] not in [\"human\", \"mouse\"]:\n print(\"Species not recognised. Please select either \\'human\\' (default) or \\'mouse\\'.\\n\" \\\n \"If mouse is required by default, consider changing the default value in the script.\")\n sys.exit()\n\n # Look for tag and V/J fasta and cysteine position files: if these cannot be found in the working directory,\n # source them from GitHub repositories\n # Note that fasta/tag files fit the pattern \"species_tagset_gene.[fasta/tags]\"\n # I.e. \"[human/mouse]_[extended/original]_TR[A/B/G/D][V/J].[fasta/tags]\"\n\n for gene in ['v', 'j']:\n # Get FASTA data\n fasta_file = read_tcr_file(inputargs['species'], inputargs['tags'], gene, \"fasta\", inputargs['tagfastadir'])\n globals()[gene + \"_genes\"] = list(SeqIO.parse(fasta_file, \"fasta\"))\n\n globals()[gene + \"_regions\"] = [str( item.seq.upper()) for item in globals()[gene + \"_genes\"]]\n globals()[gene + \"_names\"] = [str(item.id.upper().split(\"|\")[1]) for item in globals()[gene + \"_genes\"]]\n\n # Get conserved translation residue sites and functionality data\n translation_file = open(read_tcr_file(inputargs['species'], inputargs['tags'], gene, \"translate\",\n inputargs['tagfastadir']),\"rt\")\n translate_data = [x.rstrip() for x in list(translation_file)]\n\n globals()[gene + \"_translate_position\"] = [int(x.split(\",\")[1]) for x in translate_data]\n globals()[gene + \"_translate_residue\"] = [x.split(\",\")[2] for x in translate_data]\n globals()[gene + \"_functionality\"] = [x.split(\",\")[3] for x in translate_data]\n\n if gene == 'v':\n \n if inputargs['species'] == \"human\":\n # Get germline CDR data\n cdr_file = open(read_tcr_file(inputargs['species'], inputargs['tags'], gene, \"cdrs\", inputargs['tagfastadir']), \"rt\")\n cdr_data = [x.rstrip() for x in list(cdr_file)]\n cdr_file.close()\n v_cdr1 = [x.split(\" \")[1] for x in cdr_data]\n v_cdr2 = [x.split(\" \")[2] for x in cdr_data]\n else:\n # cdr_file only exists for human - CDR1 and CDR2 only written to output tsv\n # for human. Otherwise create empty lists fo v_cdr1 and v_cdr2, to write empty\n # fields to output tsv\n v_cdr1 = [\"\"]*len(globals()[gene + \"_genes\"])\n v_cdr2 = [\"\"]*len(globals()[gene + \"_genes\"])\n\n return v_regions, j_regions, v_names, j_names, v_translate_position, v_translate_residue, \\\n j_translate_position, j_translate_residue, v_functionality, j_functionality, v_cdr1, v_cdr2","def calibrate(self, master):\n if master.referencetype == \"Block\":\n self.caldat = self.mw \n else:\n print(\"Kein gültiger Referenzsensortyp\")","def get_unknown_event(self, fixture_name: str) -> str:\n fixture_data = orjson.loads(\n self.webhook_fixture_data(\"semaphore\", fixture_name, file_type=\"json\")\n )\n fixture_data[\"revision\"][\"reference_type\"] = \"unknown\"\n return fixture_data","def read_evoked_lfp(probe,group,p,data):\n\n print('#### Low-pass filtering the data ####')\n \n\n nr_of_electrodes = p['nr_of_electrodes_per_group']\n save_file = p['path'] + '/probe_{:g}_group_{:g}/probe_{:g}_group_{:g}_evoked.pickle'.format(probe,group,probe,group)\n\n #Low pass filtering\n filt = lowpassFilter(rate = p['sample_rate'], high = p['cutoff_freq'], order = 3, axis = 1)\n filtered = filt(data)\n\n\n #Notch filtering\n #if p['notch_filt_freq'] != 0:\n # notchFilt = notchFilter(rate = p['sample_rate'], low = p['notch_filt_freq']-5, high = p['notch_filt_freq']+5, order = 3)\n #Reading the trigger timestamps (process varies depending on the file format\n\n if p['fileformat'] == 'dat':\n trigger_filepath = p['path'] + '/' + p['stim_file']\n with open(trigger_filepath, 'rb') as fid:\n trigger = np.fromfile(fid, np.int16)\n stim_timestamps = extract_stim_timestamps_der(trigger,p)\n\n elif p['fileformat'] == 'cont':\n\t\t#Reading the digital input from file\n trigger_filepath = p['path'] + '/all_channels.events'\n trigger_events = loadEvents(trigger_filepath)\n\n #Acquiring the timestamps of the ttl pulses\n timestamps = trigger_events['timestamps']\n eventId = trigger_events['eventId']\n eventType = trigger_events['eventType']\n channel = trigger_events['channel']\n\n timestamps_global = timestamps[eventType == 5]\n timestamps_ttl = []\n\n ttl_events = (eventType == 3)\n ttl_rise = (eventId == 1)\n\n for i in range(len(timestamps)):\n if (ttl_events[i]) and (ttl_rise[i]):\n timestamps_ttl = np.append(timestamps_ttl, timestamps[i])\n\n stim_timestamps = timestamps_ttl - timestamps_global[0]\n\n elif p['fileformat'] == 'rhd':\n trigger_all = []\n for file in range(len(p['rhd_file'])):\n data = read_data(p['path']+'/'+ p['rhd_file'][file])\n trigger = data['board_dig_in_data'][1]\n trigger_all = np.append(trigger_all, trigger)\n\n stim_timestamps = []\n for i in range(1,len(trigger_all)):\n if trigger_all[i-1] == 0 and trigger_all[i] == 1:\n stim_timestamps = np.append(stim_timestamps, i)\n\n evoked = read_evoked_lfp_from_stim_timestamps(filtered, stim_timestamps, p)\n\n #Save all evoked activity in a pickle file\n fid = open(save_file, 'wb')\n pickle.dump({'evoked':evoked, 'stim_timestamps':stim_timestamps}, fid, protocol=-1)\n fid.close()\n\n #Downsampling\n if(p['down_sample'] == True):\n down_sampled = signal.decimate(filtered, p['down_sample_rate'], zero_phase=True) #Downsampling signal\n small_sample_rate = p['sample_rate']/p['down_sample_rate']\n stim_downsampled = (stim_timestamps/p['down_sample_rate']).astype(int) #Shifting stim_timestamps\n\n evoked_downsampled = read_evoked_lfp_from_stim_timestamps_downsampled(down_sampled, stim_downsampled, p, small_sample_rate)\n\n #Save all evoked activity in a pickle file\n save_file = p['path'] + '/probe_{0}_group_{1}/probe_{2}_group_{3}_evoked_down_sampled.pickle'.format(probe,group,probe,group)\n fid = open(save_file, 'wb')\n pickle.dump({'evoked':evoked_downsampled, 'stim_timestamps':stim_downsampled}, fid, protocol=-1)\n fid.close()"],"string":"[\n \"def add_fault_rupture_from_file(self, fault_filename):\\n self.fault.add_patches_from_file(fault_filename) \\n self.irst = 214\",\n \"def test_fake_file(self):\\n fits_file = os.path.join(self.datadir, 'monol_test_fake.evt')\\n hen.fake.main(['-o', fits_file, '--instrument', 'FPMB'])\\n info = hen.io.print_fits_info(fits_file, hdu=1)\\n assert info['Instrument'] == 'FPMB'\",\n \"def setUp(self):\\n self.junk_file = '/tmp/asdfoowersdfuixlwles'\",\n \"def hook_file_opened(self):\",\n \"def test_process_data():\\n afos_dump.process_data(\\\"\\\")\",\n \"def test_fake_file_with_deadtime(self):\\n fits_file = os.path.join(self.datadir, 'monol_test_fake_lc.evt')\\n hen.fake.main(['--deadtime', '2.5e-3',\\n '--ctrate', '2000',\\n '-o', fits_file])\",\n \"def test_DL_import_wrong_file_unserialized(self):\\n filepath = '6.txt'\\n wrong_file = open(filepath, 'x')\\n wrong_file.write(\\\"This is not a serialized detector flow data\\\")\\n wrong_file.close()\\n # Check if exception was raised for wrong serialization\\n with self.assertRaises(Exception):\\n flow_processing_input.DetectorsLocation(9999, filepath)\\n os.remove(filepath)\",\n \"def setUp(self):\\n self.single_rfh2_message = open(\\n os.path.join(self.messages_dir, \\\"single_rfh2.dat\\\"), \\\"rb\\\").read()\\n self.single_rfh2_message_not_well_formed = \\\\\\n self.single_rfh2_message[0:117] + self.single_rfh2_message[121:]\",\n \"def setUp(self):\\n # parse the file\\n self.plateMeas = PlateMeas(pathToPlate8131MeasFile)\",\n \"def setup_file_handling(self, down_store, file_encoder, file_decoder, distributor, log_dir):\\n self.__uplinker = fprime_gds.common.files.uplinker.FileUplinker(file_encoder)\\n self.__downlinker = fprime_gds.common.files.downlinker.FileDownlinker(down_store, log_dir=log_dir)\\n file_decoder.register(self.__downlinker)\\n distributor.register(\\\"FW_PACKET_HAND\\\", self.__uplinker)\",\n \"def handleExistingData(iIndent):\\r\\n\\tglobal sEType, sEVar, sEData\\r\\n\\r\\n\\t# If none, quit.\\r\\n\\tif not sEType:\\r\\n\\t\\treturn\\r\\n\\r\\n\\t# Skip if we have no data.\\r\\n\\tif not sEData:\\r\\n\\t\\treturn\\r\\n\\r\\n\\t# Insert tab level and comments into a header.\\r\\n\\tsHead = (\\\" \\\" * iIndent) + \\\"/// \\\"\\r\\n\\r\\n\\t# Sanitise data.\\r\\n\\tsEData.rstrip()\\r\\n\\r\\n\\t# Swap breaks for heads.\\r\\n\\tsEData = sEData.replace(BREAK, \\\"\\\\n\\\" + sHead)\\r\\n\\r\\n\\t# Write out the respective blocks.\\r\\n\\tif sEType == BRIEF:\\r\\n\\t\\t#sEData = sEData.replace(\\\"<summary>\\\", \\\"\\\")\\r\\n\\t\\t#sEData = sEData.replace(\\\"</summary>\\\", \\\"\\\")\\r\\n\\t\\tpOutFile.write(sHead + \\\"<summary>\\\\n\\\")\\r\\n\\t\\tpOutFile.write(sHead + sEData + \\\"\\\\n\\\")\\r\\n\\t\\tpOutFile.write(sHead + \\\"</summary>\\\\n\\\")\\r\\n\\r\\n\\telif sEType == PARAM:\\r\\n\\t\\tpOutFile.write(sHead + \\\"<param name=\\\\\\\"\\\" + str(sEVar) + \\\"\\\\\\\">\\\" + str(sEData) + \\\"</param>\\\\n\\\")\\r\\n\\r\\n\\telif sEType == RETURN:\\r\\n\\t\\tpOutFile.write(sHead + \\\"<returns>\\\" + str(sEData) + \\\"</returns>\\\\n\\\")\\r\\n\\r\\n\\telif sEType == AUTHOR:\\r\\n\\t\\tpOutFile.write(sHead + \\\"<author>\\\" + str(sEData) + \\\"</author>\\\\n\\\")\\r\\n\\t\\t\\r\\n\\telif sEType == DATE:\\r\\n\\t\\tpOutFile.write(sHead + \\\"<date>\\\" + str(sEData) + \\\"</date>\\\\n\\\")\\r\\n\\t\\t\\r\\n\\telif sEType == RETURN:\\r\\n\\t\\tpOutFile.write(sHead + \\\"<returns>\\\" + str(sEData) + \\\"</returns>\\\\n\\\")\\r\\n\\r\\n\\telif sEType == REMARK:\\r\\n\\t\\tpOutFile.write(sHead + str(sEData) + \\\"\\\\n\\\")\\r\\n\\r\\n\\t# Zap any leftover data.\\r\\n\\tsEType = None\\r\\n\\tsEVar = None\\r\\n\\tsEData = \\\"\\\"\",\n \"def rdspecdat(self):\\n # TODO : ugh. this is crude. Should have some checks for file format\\n # and probably better to use the astropy.io functions now.\\n try:\\n w, f, e = np.loadtxt(self.filename, unpack=True)\\n except:\\n w, f = np.loadtxt(self.filename, unpack=True)\\n e = []\",\n \"def preCommitFixup(self):\\n log_method_call(self, self.name)\\n # UEFI firmware/bootloader cannot read 1.1 or 1.2 metadata arrays\\n if getattr(self.format, \\\"mountpoint\\\", None) == \\\"/boot/efi\\\":\\n self.metadataVersion = \\\"1.0\\\"\",\n \"def do_before_dump(self):\\n self.checksummer.prepare_checksums()\",\n \"def test_handle_info_reading():\\n bids_root = _TempDir()\\n\\n # read in USA dataset, so it should find 50 Hz\\n raw = _read_raw_fif(raw_fname)\\n\\n # write copy of raw with line freq of 60\\n # bids basename and fname\\n bids_path = BIDSPath(subject='01', session='01',\\n task='audiovisual', run='01',\\n root=bids_root)\\n suffix = \\\"meg\\\"\\n bids_fname = bids_path.copy().update(suffix=suffix,\\n extension='.fif')\\n write_raw_bids(raw, bids_path, overwrite=True)\\n\\n # find sidecar JSON fname\\n bids_fname.update(datatype=suffix)\\n sidecar_fname = _find_matching_sidecar(bids_fname, suffix=suffix,\\n extension='.json')\\n\\n # assert that we get the same line frequency set\\n raw = read_raw_bids(bids_path=bids_path)\\n assert raw.info['line_freq'] == 60\\n\\n # 2. if line frequency is not set in raw file, then ValueError\\n raw.info['line_freq'] = None\\n with pytest.raises(ValueError, match=\\\"PowerLineFrequency .* required\\\"):\\n write_raw_bids(raw, bids_path, overwrite=True)\\n\\n # make a copy of the sidecar in \\\"derivatives/\\\"\\n # to check that we make sure we always get the right sidecar\\n # in addition, it should not break the sidecar reading\\n # in `read_raw_bids`\\n deriv_dir = op.join(bids_root, \\\"derivatives\\\")\\n sidecar_copy = op.join(deriv_dir, op.basename(sidecar_fname))\\n os.mkdir(deriv_dir)\\n with open(sidecar_fname, \\\"r\\\", encoding='utf-8') as fin:\\n sidecar_json = json.load(fin)\\n sidecar_json[\\\"PowerLineFrequency\\\"] = 45\\n _write_json(sidecar_copy, sidecar_json)\\n raw = read_raw_bids(bids_path=bids_path)\\n assert raw.info['line_freq'] == 60\\n\\n # 3. assert that we get an error when sidecar json doesn't match\\n _update_sidecar(sidecar_fname, \\\"PowerLineFrequency\\\", 55)\\n with pytest.raises(ValueError, match=\\\"Line frequency in sidecar json\\\"):\\n raw = read_raw_bids(bids_path=bids_path)\\n assert raw.info['line_freq'] == 55\",\n \"def insert_bad_data():\\n get_file_reply(files[2][0], files[2][1])\",\n \"def test_DL_import_wrong_file_serialized(self):\\n filepath = '5.txt'\\n with open(filepath, 'wb') as file:\\n pickle.dump([\\\"This is a wrong dataset\\\"], file)\\n # Check if exception was raised for wrong data type\\n with self.assertRaises(Exception):\\n flow_processing_input.DetectorsLocation(9999, filepath)\\n os.remove(filepath)\",\n \"def test_old_format_for_tags(self):\\n test_files = glob.glob(INPUT_HYPM_PATH + '/unit_*.mdd')\\n test_files.extend(glob.glob(INPUT_FLMB_PATH + '/unit_*.mdd'))\\n\\n mdd.procall(test_files)\\n\\n data = self.read_full_file('node58p1.dat')\\n if not self.check_for_tags(data):\\n self.fail(\\\"Found header tag in data file\\\")\\n\\n data = self.read_full_file('node59p1.dat')\\n if not self.check_for_tags(data):\\n self.fail(\\\"Found header tag in data file\\\")\",\n \"def testEdgeMarkerGeneric0(self):\\n outname = self.prefix+'.asap'\\n self.res = sdcal(infile=self.rawfile,calmode='otf',markonly=True,outfile=outname,outform='ASAP')\\n refdir = self._readref( self.reffiles[0] )\\n self._checkfile( outname ) \\n self._checkmarker( outname, refdir )\",\n \"def test_is_not_delicious_file(self):\\r\\n bad_file = StringIO.StringIO()\\r\\n bad_file.write('failing tests please')\\r\\n bad_file.seek(0)\\r\\n\\r\\n self.assertTrue(\\r\\n not DelXMLImporter.can_handle(bad_file),\\r\\n \\\"DelXMLImporter cannot handle this file\\\")\\r\\n\\r\\n bad_file.close()\",\n \"def test_is_not_delicious_file(self):\\r\\n bad_file = StringIO.StringIO()\\r\\n bad_file.write('failing tests please')\\r\\n bad_file.seek(0)\\r\\n\\r\\n self.assertTrue(\\r\\n not DelImporter.can_handle(bad_file),\\r\\n \\\"DelImporter cannot handle this file\\\")\\r\\n\\r\\n bad_file.close()\",\n \"def add_fault_rupture_from_file(self,fault_filename):\\n \\n self.ricom.add_fault_rupture_from_file(fault_filename)\",\n \"def test_pert_file(self):\\n path, case = os.path.split(self.ieee14)\\n\\n # --- with pert file ---\\n ss = andes.run('ieee14.raw', pert='pert.py',\\n input_path=path, no_output=True, default_config=True,\\n )\\n ss.TDS.init()\\n self.assertIsNotNone(ss.TDS.callpert)\\n\\n # --- without pert file ---\\n ss = andes.run('ieee14.raw',\\n input_path=path, no_output=True, default_config=True,\\n )\\n ss.TDS.init()\\n self.assertIsNone(ss.TDS.callpert)\",\n \"def read_input(self, specs):\\n print('DEBUGG specs:', specs)\",\n \"def test_real_file(self):\\n log.info('===== START TEST BYTE LOSS =====')\\n\\n # Recovered\\n file_path = os.path.join(RESOURCE_PATH, '11079364_SNA_SNA.txt')\\n\\n stream_handle = open(file_path, MODE_ASCII_READ)\\n\\n self.create_parser(stream_handle, telem_flag=False)\\n\\n particles = self.parser.get_records(182)\\n\\n log.debug(\\\"*** test_real_file Num particles %s\\\", len(particles))\\n\\n # check all the values against expected results.\\n self.assert_particles(particles, '11079364_SNA_SNA_recov.yml', RESOURCE_PATH)\\n self.assertEquals(self.exception_callback_value, [])\\n stream_handle.close()\\n\\n # Telemetered\\n file_path = os.path.join(RESOURCE_PATH, '11079419_SNA_SNA.txt')\\n\\n stream_handle = open(file_path, MODE_ASCII_READ)\\n\\n self.create_parser(stream_handle)\\n\\n particles = self.parser.get_records(172)\\n\\n log.debug(\\\"*** test_real_file Num particles %s\\\", len(particles))\\n\\n # check all the values against expected results.\\n self.assert_particles(particles, '11079419_SNA_SNA_telem.yml', RESOURCE_PATH)\\n stream_handle.close()\\n\\n log.info('===== END TEST REAL FILE =====')\",\n \"def test_read_0_1_smirnoff(self):\\n ForceField(\\n get_data_file_path(\\n \\\"test_forcefields/smirnoff99Frosst_reference_0_1_spec.offxml\\\"\\n )\\n )\",\n \"def prepare_bed_file(bed_file, output, ouf=False, save_rejected=None, only_chrom=None):\\n new_lines = [] # keep updated lines\\n rejected = [] # keep IDs of skipped transcripts + the reason why\\n names = Counter() # we need to make sure that all names are unique\\n allowed_re = re.compile(ALLOWED_CHARSET_RE).search\\n broken_names = []\\n\\n f = open(bed_file, \\\"r\\\")\\n for num, line in enumerate(f, 1):\\n # parse bed file according to specification\\n line_data = line.rstrip().split(\\\"\\\\t\\\")\\n\\n if len(line_data) != 12:\\n f.close() # this is for sure an error\\n # it is possible only if something except a bed12 was provided\\n die(\\n \\\"Error! Bed 12 file is required! Got a file with {len(line_data)} fields instead\\\"\\n )\\n\\n chrom = line_data[0]\\n if only_chrom and chrom != only_chrom:\\n # TOGA allows to perform the analysis on a specific chromosome only\\n # is so, we can skip all transcripts that located on other chromosomes\\n continue\\n chromStart = int(line_data[1])\\n chromEnd = int(line_data[2])\\n name = line_data[3] # gene_name usually\\n corr_name = not bool(allowed_re(name))\\n if corr_name is False:\\n broken_names.append(name)\\n # TODO: check weird characters in the transcript name\\n # bed_score = int(line_data[4]) # never used\\n # strand = line_data[5] # otherwise:\\n # strand = True if line_data[5] == '+' else False\\n thickStart = int(line_data[6])\\n thickEnd = int(line_data[7])\\n # itemRgb = line_data[8] # never used\\n blockCount = int(line_data[9])\\n blockSizes = [int(x) for x in line_data[10].split(\\\",\\\") if x != \\\"\\\"]\\n blockStarts = [int(x) for x in line_data[11].split(\\\",\\\") if x != \\\"\\\"]\\n blockEnds = [blockStarts[i] + blockSizes[i] for i in range(blockCount)]\\n blockAbsStarts = [blockStarts[i] + chromStart for i in range(blockCount)]\\n blockAbsEnds = [blockEnds[i] + chromStart for i in range(blockCount)]\\n blockNewStarts, blockNewEnds = [], []\\n names[name] += 1\\n\\n if thickStart > thickEnd:\\n f.close() # according to bed12 specification this should never happen\\n sys.stderr.write(f\\\"Problem occurred at line {num}, gene {name}\\\\n\\\")\\n die(\\\"Error! Bed file is corrupted, thickEnd MUST be >= thickStart\\\")\\n elif thickStart == thickEnd:\\n # this means that this is a non-coding transcript\\n # TOGA cannot process them: we can skip it\\n rejected.append((name, \\\"No CDS\\\"))\\n continue\\n\\n if thickStart < chromStart or thickEnd > chromEnd:\\n # a very strange (but still possible) case\\n f.close() # for sure an error with input data\\n sys.stderr.write(f\\\"Problem occurred at line {num}, gene {name}\\\\n\\\")\\n die(\\\"Error! Bed file is corrupted, thickRange is outside chromRange!\\\")\\n\\n # now select CDS only\\n # we keep UTRs in the filtered file\\n # however, we need CDS to check whether it's correct (% 3 == 0)\\n for block_num in range(blockCount):\\n blockStart = blockAbsStarts[block_num]\\n blockEnd = blockAbsEnds[block_num]\\n\\n # skip the block if it is entirely UTR\\n if blockEnd <= thickStart:\\n continue\\n elif blockStart >= thickEnd:\\n continue\\n\\n # if we are here: this is not an entirely UTR exon\\n # it might intersect the CDS border or to be in the CDS entirely\\n # remove UTRs: block start must be >= CDS_start (thickStart)\\n # block end must be <= CDS_end (thickEnd)\\n blockNewStart = blockStart if blockStart >= thickStart else thickStart\\n blockNewEnd = blockEnd if blockEnd <= thickEnd else thickEnd\\n blockNewStarts.append(blockNewStart - thickStart)\\n blockNewEnds.append(blockNewEnd - thickStart)\\n\\n if len(blockNewStarts) == 0:\\n # even it thickStart != thickEnd this transcript still can be non-coding\\n # but if there are no blocks in the CDS -> we can catch this\\n rejected.append((name, \\\"No CDS\\\"))\\n continue\\n\\n block_new_count = len(blockNewStarts)\\n blockNewSizes = [\\n blockNewEnds[i] - blockNewStarts[i] for i in range(block_new_count)\\n ]\\n\\n if sum(blockNewSizes) % 3 != 0 and not ouf:\\n # this is an out-of-frame (or incomplete transcript)\\n # ideally CDS length should be divisible by 3\\n # not ouf means that we like to keep such transcripts for some reason\\n rejected.append((name, \\\"Out-of-frame gene\\\"))\\n continue\\n\\n # we keep this transcript: add in to the list\\n new_line = \\\"\\\\t\\\".join([str(x) for x in line_data])\\n new_lines.append(new_line)\\n f.close()\\n\\n # if not allowed characters in transcript names: list them\\n if len(broken_names) > 0:\\n eprint(\\\"Error! Some transcript names contain not allowed characters\\\")\\n for t in broken_names:\\n eprint(t)\\n die(f\\\"Allowed characters are: {ALLOWED_CHARSET}\\\")\\n # if there are non-unique transcript IDs: die\\n # I kill it there, not earlier to show them altogether\\n if any(v > 1 for v in names.values()):\\n eprint(\\\"Error! There are non-uniq transcript IDs:\\\")\\n duplicates = [k for k, v in names.items() if v > 1]\\n for d in duplicates:\\n eprint(d)\\n die(\\\"Abort\\\")\\n\\n if len(new_lines) == 0:\\n # no transcripts pass the filter: probably an input data mistake\\n sys.exit(\\n f\\\"Error! No reference annotation tracks left after filtering procedure! Abort\\\"\\n )\\n\\n # write transcripts that passed the filter to the output file\\n f = open(output, \\\"w\\\") if output != \\\"stdout\\\" else sys.stdout\\n f.write(\\\"\\\\n\\\".join(new_lines) + \\\"\\\\n\\\")\\n f.close() if output != \\\"stdout\\\" else None\\n\\n if save_rejected:\\n # save transcripts that didn't pass the filter + reason why\\n f = open(save_rejected, \\\"w\\\")\\n for elem in rejected:\\n f.write(f\\\"{elem[0]}\\\\t{elem[1]}\\\\n\\\")\\n f.close()\",\n \"def setUp(self):\\n self.epath = 'flyeye/tests/fixtures'\\n self.dpath = join(self.epath, 'disc.silhouette')\",\n \"def test_readfile_fits(self):\\n fitsname = os.path.join(self.datadir, 'monol_testA.evt')\\n command = \\\"{0}\\\".format(fitsname)\\n\\n hen.io.main(command.split())\",\n \"def setUp(self):\\n\\n PyFunceble.load_config()\\n\\n StdoutBase.setUp(self)\\n\\n self.file = \\\"the_file_is_a_ghost\\\"\\n self.to_print = {\\n \\\"basic\\\": {\\\"hello\\\": 5, \\\"world\\\": 6, \\\"here\\\": 7, \\\"is\\\": 8, \\\"PyFunceble\\\": 10},\\n \\\"size_constructor\\\": [5, 6, 7, 8, 9, 10],\\n \\\"basic_string\\\": \\\"Hello, World!\\\",\\n \\\"hosts\\\": {\\\"0.0.0.0\\\": 7, \\\"hello.world\\\": 11},\\n }\\n\\n self.file_instance = PyFunceble.helpers.File(self.file)\\n self.file_instance.delete()\",\n \"def test_fake_file_from_input_lc(self):\\n lcurve_in = os.path.join(self.datadir, 'lcurveA.fits')\\n fits_file = os.path.join(self.datadir, 'monol_test_fake_lc.evt')\\n hen.fake.main(['--lc', lcurve_in, '-o', fits_file])\",\n \"def setUp(self):\\n with open('test/0a6a357e.json') as read_file:\\n self.tx_json_0a6a357e = json.load(read_file)\\n with open('test/bip69-synth.json') as read_file:\\n self.bip69_synth = json.load(read_file)\",\n \"def gain_data_main():\\n gainfile = os.path.join(DATA_PATH, \\\"zen.2457698.40355.xx.gain.calfits\\\")\\n with uvtest.check_warnings(\\n UserWarning,\\n match=[\\n \\\"telescope_location is not set. Using known values for HERA.\\\",\\n \\\"antenna_positions are not set or are being overwritten. Using known \\\"\\n \\\"values for HERA.\\\",\\n ],\\n ):\\n gain_object = UVCal.from_file(gainfile, use_future_array_shapes=True)\\n gain_object.freq_range = None\\n\\n yield gain_object\\n\\n del gain_object\",\n \"def unknown(self):\\n self.add_file_string('Unknown file')\\n self.should_copy = False\",\n \"def SetStructuredData(self, file): # real signature unknown; restored from __doc__\\n pass\",\n \"def test_load_rivers_config_major_forcing_data_file(self, config, config_dict, infile_dict, monkeypatch):\\n test_output_file = 'Fraser_flow'\\n monkeypatch.setitem(infile_dict['forcing_data_files'], 'major_river', test_output_file)\\n config.rivers = Mock()\\n config._read_yaml_file = Mock(return_value=config_dict)\\n config._load_rivers_config(config_dict, infile_dict)\\n assert config.rivers.output_files[\\\"major\\\"] == test_output_file\",\n \"def test_import_report_malformed():\\n with pytest.raises(DmarcImportError):\\n import_feedback_report('<malform></ed>')\",\n \"def test_read_0_2_smirnoff(self):\\n ForceField(\\n get_data_file_path(\\n \\\"test_forcefields/smirnoff99Frosst_reference_0_2_spec.offxml\\\"\\n )\\n )\",\n \"def test_readbadformat(self):\\n\\n self.assertRaises(ParseError, self.hw, self.badfile)\",\n \"def test_pds_txt(self):\\n lcurve_txt = os.path.join(self.datadir,\\n 'lcurve_txt_lc' +\\n HEN_FILE_EXTENSION)\\n command = '{0} -f 128'.format(lcurve_txt)\\n hen.fspec.main(command.split())\",\n \"def test_is_delicious_file(self):\\r\\n good_file = self._get_del_file()\\r\\n self.assertTrue(\\r\\n DelXMLImporter.can_handle(good_file),\\r\\n \\\"DelXMLImporter should handle this file\\\")\\r\\n good_file.close()\",\n \"def test_data_source_soaps_post(self):\\n pass\",\n \"def testEdgeMarkerGeneric1(self):\\n outname = self.prefix+'.asap'\\n self.res = sdcal(infile=self.rawfile,calmode='otf',fraction='3%',markonly=True,outfile=outname,outform='ASAP')\\n refdir = self._readref( self.reffiles[1] )\\n self._checkfile( outname ) \\n self._checkmarker( outname, refdir )\",\n \"def test_load_rivers_config_minor_forcing_data_file(self, config, config_dict, infile_dict, monkeypatch):\\n test_output_file = 'Englishman_flow'\\n monkeypatch.setitem(infile_dict['forcing_data_files'], 'minor_river', test_output_file)\\n config.rivers = Mock()\\n config._read_yaml_file = Mock(return_value=config_dict)\\n config._load_rivers_config(config_dict, infile_dict)\\n assert config.rivers.output_files[\\\"minor\\\"] == test_output_file\",\n \"def test_strain_redefined(generate_strain_redefined):\\n fname = generate_strain_redefined\\n try:\\n process_files([fname])\\n raise Exception('The redefined strain data and lack of stress data was not caught')\\n except IOError:\\n pass\",\n \"def preparePatch(self):\\n if DEBUG > 1: sys.stderr.write(\\\"* preparePatch()\\\\n\\\")\\n\\n if self.patchLoaded:\\n #Load PC with 0x0220.\\n #This will invoke the patched bootstrap loader subroutines.\\n self.bslTxRx(self.BSL_LOADPC, #Command: Load PC\\n 0x0220) #Address to load into PC\\n self.BSLMemAccessWarning = 0 #Error is removed within workaround code\\n return\",\n \"def _read_file(self):\\n\\n with open(self.file_name, 'rb') as f:\\n new_test = struct.unpack('<l', f.read(8)[4:])[0]\\n f.close()\\n\\n with open(self.file_name, 'rb') as f:\\n old_test = struct.unpack('<h', f.read(6)[4:])[0]\\n f.close()\\n\\n with open(self.file_name, 'rb') as f:\\n other_test = struct.unpack('<l', f.read(20)[16:])[0]\\n f.close()\\n\\n open_file = open(self.file_name, 'rb')\\n\\n if (other_test==202):\\n raw = open_file.read(1236)[11:]\\n self.model = '202'\\n elif ((not new_test==102) and old_test==102):\\n raw = open_file.read(1133)\\n self.model = '102old'\\n elif (new_test==102 and old_test==102):\\n raw = open_file.read(1224)\\n self.model = '102new'\\n\\n self.header = DpHeader(raw, self.model)\\n\\n self.data = DpData(open_file, \\n self.model, \\n self.header.interferogram_size, \\n self.header.number_of_coadds, \\n 2048*self.header.zero_fill,\\n self.header.laser_wavelength_microns, \\n self.header.dispersion_constant_xm,\\n self.header.dispersion_constant_xb)\\n\\n open_file.close()\",\n \"def test_read_raw_suggested(fname):\\n with pytest.raises(ValueError, match='Try reading'):\\n read_raw(fname)\",\n \"def delay_data_main():\\n delayfile = os.path.join(DATA_PATH, \\\"zen.2457698.40355.xx.delay.calfits\\\")\\n with uvtest.check_warnings(\\n UserWarning,\\n match=[\\n \\\"telescope_location is not set. Using known values for HERA.\\\",\\n \\\"antenna_positions are not set or are being overwritten. Using known \\\"\\n \\\"values for HERA.\\\",\\n \\\"When converting a delay-style cal to future array shapes the flag_array\\\"\\n \\\" (and input_flag_array if it exists) must drop the frequency axis\\\",\\n ],\\n ):\\n delay_object = UVCal.from_file(delayfile, use_future_array_shapes=True)\\n\\n # yield the data for testing, then del after tests finish\\n yield delay_object\\n\\n del delay_object\",\n \"def _read_eeg(eeg_file):\\r\\n pass\",\n \"def _process_end_of_file(self):\\n (nd_timestamp, non_data) = self._chunker.get_next_non_data()\\n if non_data and len(non_data) > 0:\\n message = \\\"Extra un-expected non-data bytes at the end of the file:%s\\\", non_data\\n log.warn(message)\\n self._exception_callback(RecoverableSampleException(message))\",\n \"def test_getters_no_ext(self, *args):\\n test_data = WireProtocolData(DATA_FILE_NO_EXT)\\n self._test_getters(test_data, *args)\",\n \"def test_harvester_new_file_exception_recovered(self):\\n # need to put data in the file, not just make an empty file for this to work\\n self.create_sample_data_set_dir(\\n \\\"DOS15908_1st7_step1.DAT\\\",\\n RECOV_DIR,\\n \\\"DOS15908.DAT\\\",\\n mode=000,\\n copy_metadata=False\\n )\\n\\n self.assert_initialize(final_state=ResourceAgentState.COMMAND)\\n\\n self.event_subscribers.clear_events()\\n self.assert_resource_command(DriverEvent.START_AUTOSAMPLE)\\n self.assert_state_change(ResourceAgentState.LOST_CONNECTION, 90)\\n self.assert_event_received(ResourceAgentConnectionLostErrorEvent, 10)\\n\\n self.clear_sample_data()\\n self.create_sample_data_set_dir(\\n \\\"DOS15908_1st7_step1.DAT\\\",\\n RECOV_DIR,\\n \\\"DOS15908.DAT\\\",\\n copy_metadata=False\\n )\\n\\n # Should automatically retry connect and transition to streaming\\n self.assert_state_change(ResourceAgentState.STREAMING, 90)\",\n \"def test_GFD_import_wrong_file_unserialized(self):\\n filepath = '6.txt'\\n wrong_file = open(filepath, 'x')\\n wrong_file.write(\\\"This is not a serialized detector flow data\\\")\\n wrong_file.close()\\n # Check if exception was raised for wrong serialization\\n with self.assertRaises(Exception):\\n flow_processing_input.GroundFlowData(filepath)\\n os.remove(filepath)\",\n \"def _handle_dump_unknown(self, data, original):\\n for key, val in original.items():\\n if key not in self.fields:\\n data[key] = val\\n return data\",\n \"def readAMBERTop(self, phys, filename):\\r\\n\\r\\n def skipLine(data):\\r\\n nl = data.index('\\\\n')\\r\\n return data[nl+1:len(data)]\\r\\n\\r\\n def jumpTo(data, target):\\r\\n fp = data.index(target)\\r\\n return data[fp:len(data)]\\r\\n\\r\\n def readRemove(data, size):\\r\\n retval = data[0:size-1]\\r\\n return data[size:len(data)]\\r\\n\\r\\n def getInteger(data):\\r\\n pos = 0\\r\\n retval = \\\"\\\"\\r\\n while (not data[pos].isdigit()):\\r\\n pos = pos + 1\\r\\n while (data[pos].isdigit()):\\r\\n retval = retval + data[pos]\\r\\n pos = pos + 1\\r\\n data = data[pos:len(data)]\\r\\n return int(retval), data\\r\\n\\r\\n def parse(data, arr, str, count, dtype, tupsize=1):\\r\\n data = jumpTo(data, \\\"%FLAG \\\"+str)\\r\\n data = jumpTo(data, \\\"%FORMAT\\\")\\r\\n numPerLine, data = getInteger(data)\\r\\n fieldsize, data = getInteger(data)\\r\\n data = skipLine(data) \\r\\n \\r\\n arr2 = []\\r\\n numread = 0\\r\\n for j in range(0, (tupsize*count-1) / numPerLine + 1):\\r\\n for i in range(0, numPerLine):\\r\\n if (tupsize == 1):\\r\\n arr.append(dtype(data[0:fieldsize].strip()))\\r\\n else:\\r\\n arr2.append(dtype(data[0:fieldsize].strip()))\\r\\n if (len(arr2) == tupsize):\\r\\n arr.append(arr2)\\r\\n arr2 = []\\r\\n numread += 1\\r\\n data = data[fieldsize:len(data)]\\r\\n if (numread == tupsize*count):\\r\\n break\\r\\n data = skipLine(data) \\r\\n return data\\r\\n\\r\\n def scan(data, str):\\r\\n return (data.count(str) != 0)\\r\\n\\r\\n\\r\\n f = open(filename, 'r')\\r\\n data = f.read()\\r\\n\\r\\n # First Line: VERSION ...\\r\\n data = skipLine(data)\\r\\n\\r\\n # Go To: %FLAG POINTERS\\r\\n data = jumpTo(data, '%FLAG POINTERS')\\r\\n\\r\\n data = jumpTo(data, '%FORMAT')\\r\\n numPerLine, data = getInteger(data)\\r\\n fieldsize, data = getInteger(data)\\r\\n data = skipLine(data)\\r\\n \\r\\n temp = []\\r\\n numread = 0\\r\\n for j in range(0, 31 / numPerLine + 1):\\r\\n for i in range(0, numPerLine):\\r\\n temp.append(int(data[0:8]))\\r\\n data = data[8:len(data)]\\r\\n numread += 1\\r\\n if (numread == 31):\\r\\n break\\r\\n data = skipLine(data)\\r\\n \\r\\n [natoms, ntypes, nbonh, mbona, ntheth, mtheta, nphih, mphia, nhparm, nparm, nnb, nres, nbona, ntheta, nphia, numbnd, numang, nptra, natyp, nphb, ifpert, nbper, ngper, ndper, mbper, mgper, mdper, ifbox, nmxrs, ifcap, numextra] = temp \\r\\n\\r\\n\\r\\n #################################################\\r\\n # Read AtomTypes\\r\\n atomnames = []\\r\\n charges = []\\r\\n masses = []\\r\\n atindex = []\\r\\n exclusions = []\\r\\n nparams = []\\r\\n reslabels = []\\r\\n respointers = []\\r\\n forceconstants = [[], [], []] # bond, angle, dihedral\\r\\n equilvals = [[], [], [[], []]] # bond, angle, dihedral\\r\\n scee_scales = []\\r\\n scnb_scales = []\\r\\n solty = []\\r\\n lj_acoef = []\\r\\n lj_bcoef = []\\r\\n\\r\\n data = parse(data, atomnames, \\\"ATOM_NAME\\\", natoms, str) \\r\\n data = parse(data, charges, \\\"CHARGE\\\", natoms, float)\\r\\n data = parse(data, masses, \\\"MASS\\\", natoms, float)\\r\\n data = parse(data, atindex, \\\"ATOM_TYPE_INDEX\\\", natoms, int)\\r\\n data = parse(data, exclusions, \\\"NUMBER_EXCLUDED_ATOMS\\\", natoms, int)\\r\\n data = parse(data, nparams, \\\"NONBONDED_PARM_INDEX\\\", ntypes*ntypes, int)\\r\\n data = parse(data, reslabels, \\\"RESIDUE_LABEL\\\", nres, str)\\r\\n data = parse(data, respointers, \\\"RESIDUE_POINTER\\\", nres, int)\\r\\n data = parse(data, forceconstants[0], \\\"BOND_FORCE_CONSTANT\\\", numbnd, float)\\r\\n data = parse(data, equilvals[0], \\\"BOND_EQUIL_VALUE\\\", numbnd, float)\\r\\n data = parse(data, forceconstants[1], \\\"ANGLE_FORCE_CONSTANT\\\", numang, float)\\r\\n data = parse(data, equilvals[1], \\\"ANGLE_EQUIL_VALUE\\\", numang, float)\\r\\n data = parse(data, forceconstants[2], \\\"DIHEDRAL_FORCE_CONSTANT\\\", nptra, float)\\r\\n data = parse(data, equilvals[2][0], \\\"DIHEDRAL_PERIODICITY\\\", nptra, float)\\r\\n data = parse(data, equilvals[2][1], \\\"DIHEDRAL_PHASE\\\", nptra, float)\\r\\n if (scan(data, \\\"SCEE_SCALE_FACTOR\\\")):\\r\\n data = parse(data, scee_scales, \\\"SCEE_SCALE_FACTORS\\\", nptra, float)\\r\\n else:\\r\\n for i in range(0, nptra):\\r\\n scee_scales.append(1.2) # Default \\r\\n if (scan(data, \\\"SCNB_SCALE_FACTOR\\\")):\\r\\n data = parse(data, scnb_scales, \\\"SCNB_SCALE_FACTORS\\\", nptra, float)\\r\\n else:\\r\\n for i in range(0, nptra):\\r\\n scnb_scales.append(2.0) # Default \\r\\n\\r\\n data = parse(data, solty, \\\"SOLTY\\\", natyp, float)\\r\\n data = parse(data, lj_acoef, \\\"LENNARD_JONES_ACOEF\\\", ntypes*(ntypes+1)/2, float)\\r\\n data = parse(data, lj_bcoef, \\\"LENNARD_JONES_BCOEF\\\", ntypes*(ntypes+1)/2, float)\\r\\n\\r\\n\\r\\n ##########################################################\\r\\n # STRUCTURE\\r\\n\\r\\n bonds = [[], []] # With H, Without H\\r\\n angles = [[], []] # With H, Without H\\r\\n dihedrals = [[], []] # With H, Without H\\r\\n impropers = [[], []] # With H, Without H\\r\\n excluded_atoms = [] \\r\\n hbond_acoef = []\\r\\n hbond_bcoef = []\\r\\n hbcut = []\\r\\n amber_atom_types = []\\r\\n tree_chain = []\\r\\n join_array = []\\r\\n irotat = []\\r\\n radii = []\\r\\n screen = []\\r\\n\\r\\n data = parse(data, bonds[0], \\\"BONDS_INC_HYDROGEN\\\", nbonh, int, 3)\\r\\n data = parse(data, bonds[1], \\\"BONDS_WITHOUT_HYDROGEN\\\", nbona, int, 3)\\r\\n data = parse(data, angles[0], \\\"ANGLES_INC_HYDROGEN\\\", ntheth, int, 4)\\r\\n data = parse(data, angles[1], \\\"ANGLES_WITHOUT_HYDROGEN\\\", ntheta, int, 4)\\r\\n data = parse(data, dihedrals[0], \\\"DIHEDRALS_INC_HYDROGEN\\\", nphih, int, 5)\\r\\n data = parse(data, dihedrals[1], \\\"DIHEDRALS_WITHOUT_HYDROGEN\\\", nphia, int, 5)\\r\\n \\r\\n # MERGE ARRAYS - PM HANDLES THE H+\\r\\n final_bonds = bonds[0] + bonds[1]\\r\\n final_angles = angles[0] + angles[1]\\r\\n final_dihedrals = dihedrals[0] + dihedrals[1]\\r\\n final_impropers = []\\r\\n \\r\\n # CLEAN UP THE TRASH\\r\\n del(bonds)\\r\\n del(angles)\\r\\n del(dihedrals)\\r\\n \\r\\n\\r\\n # Move impropers into their own array\\r\\n i = 0\\r\\n while (i < len(final_dihedrals)):\\r\\n if (final_dihedrals[i][2] < 0): # 1-4 exclusions are handled by our back end\\r\\n final_dihedrals[i][2] *= -1\\r\\n if (final_dihedrals[i][3] < 0):\\r\\n final_dihedrals[i][3] *= -1 # Make + again\\r\\n final_impropers.append(final_dihedrals[i])\\r\\n final_dihedrals.remove(final_dihedrals[i])\\r\\n i -= 1\\r\\n i += 1\\r\\n\\r\\n # Convert charge units\\r\\n for i in range(0, len(charges)):\\r\\n charges[i] /= 18.223\\r\\n\\r\\n\\r\\n data = parse(data, excluded_atoms, \\\"EXCLUDED_ATOMS_LIST\\\", nnb, int)\\r\\n data = parse(data, hbond_acoef, \\\"HBOND_ACOEF\\\", nphb, float)\\r\\n data = parse(data, hbond_bcoef, \\\"HBOND_BCOEF\\\", nphb, float)\\r\\n data = parse(data, hbcut, \\\"HBCUT\\\", nphb, float)\\r\\n data = parse(data, amber_atom_types, \\\"AMBER_ATOM_TYPE\\\", natoms, str)\\r\\n data = parse(data, tree_chain, \\\"TREE_CHAIN_CLASSIFICATION\\\", natoms, str)\\r\\n data = parse(data, join_array, \\\"JOIN_ARRAY\\\", natoms, int)\\r\\n data = parse(data, irotat, \\\"IROTAT\\\", natoms, int)\\r\\n data = parse(data, radii, \\\"RADII\\\", natoms, float)\\r\\n data = parse(data, screen, \\\"SCREEN\\\", natoms, float)\\r\\n\\r\\n # Further process dihedrals and impropers\\r\\n # Deal with multiplicity\\r\\n # A bit ugly, but the fastest for now\\r\\n # forceconstants[2][dihedrals[0][i][4]-1], int(equilvals[2][0][dihedrals[0][i][4]-1]), equilvals[2][1][dihedrals[0][i][4]-1]\\r\\n\\r\\n mult_di = dict()\\r\\n mult_im = dict()\\r\\n for i in range(0, len(final_dihedrals)):\\r\\n di_id = str(final_dihedrals[i][0])+' '+str(final_dihedrals[i][1])+' '+str(final_dihedrals[i][2])+' '+str(final_dihedrals[i][3])\\r\\n if (not mult_di.has_key(di_id)):\\r\\n mult_di[di_id] = [1, False, [forceconstants[2][final_dihedrals[i][4]-1]], [int(equilvals[2][0][final_dihedrals[i][4]-1])], [equilvals[2][1][final_dihedrals[i][4]-1]]]\\r\\n else:\\r\\n mult_di[di_id][0] += 1\\r\\n mult_di[di_id][2].append(forceconstants[2][final_dihedrals[i][4]-1])\\r\\n mult_di[di_id][3].append(int(equilvals[2][0][final_dihedrals[i][4]-1]))\\r\\n mult_di[di_id][4].append(equilvals[2][1][final_dihedrals[i][4]-1])\\r\\n \\r\\n for i in range(0, len(final_impropers)):\\r\\n im_id = str(final_impropers[i][0])+' '+str(final_impropers[i][1])+' '+str(final_impropers[i][2])+' '+str(final_impropers[i][3])\\r\\n if (not mult_im.has_key(di_id)):\\r\\n mult_im[im_id] = [1, False, [forceconstants[2][final_impropers[i][4]-1]], [int(equilvals[2][0][final_impropers[i][4]-1])], [equilvals[2][1][final_impropers[i][4]-1]]]\\r\\n else:\\r\\n mult_im[im_id][0] += 1\\r\\n mult_im[im_id][2].append(forceconstants[2][final_impropers[i][4]-1])\\r\\n mult_im[im_id][3].append(int(equilvals[2][0][final_impropers[i][4]-1]))\\r\\n mult_im[im_id][4].append(equilvals[2][1][final_impropers[i][4]-1])\\r\\n\\r\\n\\r\\n\\r\\n \\r\\n #[natoms, ntypes, nbonh, mbona, ntheth, mtheta, nphih, mphia, nhparm, nparm, nnb, nres, nbona, ntheta, nphia, numbnd, numang, nptra, natyp, nphb, ifpert, nbper, ngper, ndper, mbper, mgper, mdper, ifbox, nmxrs, ifcap, numextra] = temp \\r\\n #phys.myPSF.createAll(natoms, nbonh+mbona, ntheth+mtheta,\\r\\n # len(dihedrals[0])+len(dihedrals[1]),\\r\\n # len(impropers[0])+len(impropers[1]),\\r\\n # 0, 0, 0, 0)\\r\\n \\r\\n # Add atoms\\r\\n curres = 1\\r\\n for i in range(0, natoms):\\r\\n phys.myPSF.addAtom(i, 'SIM', curres, reslabels[curres-1],\\r\\n atomnames[i], atomnames[i], charges[i],\\r\\n masses[i]) \\r\\n if (curres != nres and i >= respointers[curres]):\\r\\n curres += 1\\r\\n\\r\\n # Add bonds\\r\\n for i in range(0, nbonh+nbona):\\r\\n phys.myPSF.addBond(i+1, final_bonds[i][0]/3+1, final_bonds[i][1]/3+1)\\r\\n phys.myPAR.addBond(i+1, atomnames[final_bonds[i][0]/3], atomnames[final_bonds[i][1]/3], forceconstants[0][final_bonds[i][2]/3], equilvals[0][final_bonds[i][2]/3])\\r\\n \\r\\n # Add angles\\r\\n for i in range(0, ntheth+ntheta):\\r\\n phys.myPSF.addAngle(i+1, final_angles[i][0]/3+1, final_angles[i][1]/3+1, final_angles[i][2]/3+1)\\r\\n phys.myPAR.addAngle(i+1, atomnames[final_angles[i][0]/3], atomnames[final_angles[i][1]/3], atomnames[final_angles[i][2]/3], forceconstants[1][final_angles[i][3]/3], equilvals[1][final_angles[i][3]/3])\\r\\n \\r\\n # Add dihedrals\\r\\n for i in range(0, len(final_dihedrals)):\\r\\n di_id = str(final_dihedrals[i][0])+' '+str(final_dihedrals[i][1])+' '+str(final_dihedrals[i][2])+' '+str(final_dihedrals[i][3])\\r\\n mult = mult_di[di_id][0]\\r\\n checked = mult_di[di_id][1]\\r\\n print di_id, \\\" \\\", mult\\r\\n if (not checked):\\r\\n if (mult == 1):\\r\\n phys.myPSF.addDihedral(i+1, final_dihedrals[i][0]/3+1, final_dihedrals[i][1]/3+1, int(numpy.abs(final_dihedrals[i][2]))/3+1, final_dihedrals[i][3]/3+1)\\r\\n phys.myPAR.addDihedral(i+1, atomnames[final_dihedrals[i][0]/3], atomnames[final_dihedrals[i][1]/3], atomnames[int(numpy.abs(final_dihedrals[i][2]))/3], atomnames[final_dihedrals[i][3]/3], forceconstants[2][final_dihedrals[i][4]-1], int(equilvals[2][0][final_dihedrals[i][4]-1]), equilvals[2][1][final_dihedrals[i][4]-1])\\r\\n else:\\r\\n mult_di[di_id][1] = True\\r\\n # Add dihedral with the appropriate multiplicity\\r\\n # Force constants, periodicity and phase shifts are in [2], [3], and [4] respectively\\r\\n fcvec = PARReader.VectorOfDouble()\\r\\n periodvec = PARReader.VectorOfInt()\\r\\n phasevec = PARReader.VectorOfDouble() \\r\\n for j in range(0, len(mult_di[di_id][2])):\\r\\n fcvec.push_back(mult_di[di_id][2][j])\\r\\n periodvec.push_back(mult_di[di_id][3][j])\\r\\n phasevec.push_back(mult_di[di_id][4][j])\\r\\n phys.myPSF.addDihedral(i+1, final_dihedrals[i][0]/3+1, final_dihedrals[i][1]/3+1, int(numpy.abs(final_dihedrals[i][2]))/3+1, final_dihedrals[i][3]/3+1)\\r\\n phys.myPAR.addDihedral(i+1, atomnames[final_dihedrals[i][0]/3], atomnames[final_dihedrals[i][1]/3], atomnames[int(numpy.abs(final_dihedrals[i][2]))/3], atomnames[final_dihedrals[i][3]/3], mult, fcvec, periodvec, phasevec)\\r\\n \\r\\n\\r\\n\\r\\n\\r\\n for i in range(0, len(final_impropers)):\\r\\n im_id = str(final_impropers[i][0])+' '+str(final_impropers[i][1])+' '+str(final_impropers[i][2])+' '+str(final_impropers[i][3])\\r\\n mult = mult_im[im_id][0]\\r\\n checked = mult_im[im_id][1]\\r\\n print im_id, \\\" \\\", mult\\r\\n if (not checked):\\r\\n if (mult == 1):\\r\\n phys.myPSF.addImproper(i+1, final_impropers[i][0]/3+1, final_impropers[i][1]/3+1, int(numpy.abs(final_impropers[i][2]))/3+1, final_impropers[i][3]/3+1)\\r\\n phys.myPAR.addImproper(i+1, atomnames[final_impropers[i][0]/3], atomnames[final_impropers[i][1]/3], atomnames[int(numpy.abs(final_impropers[i][2]))/3], atomnames[final_impropers[i][3]/3], forceconstants[2][final_impropers[i][4]-1], int(equilvals[2][0][final_impropers[i][4]-1]), equilvals[2][1][final_impropers[i][4]-1])\\r\\n else:\\r\\n mult_im[im_id][1] = True\\r\\n # Add dihedral with the appropriate multiplicity\\r\\n # Force constants, periodicity and phase shifts are in [2], [3], and [4] respectively\\r\\n fcvec = PARReader.VectorOfDouble()\\r\\n periodvec = PARReader.VectorOfInt()\\r\\n phasevec = PARReader.VectorOfDouble() \\r\\n for j in range(0, len(mult_im[im_id][2])):\\r\\n fcvec.push_back(mult_im[im_id][2][j])\\r\\n periodvec.push_back(mult_im[im_id][3][j])\\r\\n phasevec.push_back(mult_im[im_id][4][j])\\r\\n phys.myPSF.addImproper(i+1, final_impropers[i][0]/3+1, final_impropers[i][1]/3+1, int(numpy.abs(final_impropers[i][2]))/3+1, final_impropers[i][3]/3+1)\\r\\n phys.myPAR.addImproper(i+1, atomnames[final_impropers[i][0]/3], atomnames[final_impropers[i][1]/3], atomnames[int(numpy.abs(final_impropers[i][2]))/3], atomnames[final_impropers[i][3]/3], mult, fcvec, periodvec, phasevec)\\r\\n\\r\\n \\r\\n # Need to add garbage nonbonded stuff for now\\r\\n for i in range(0, natoms):\\r\\n phys.myPAR.addNonbonded(i, atomnames[i], 1, 1, 1, 1, 1, 1)\\r\\n\\r\\n # Add VDW parameters\\r\\n # AMBER has the Aij and Bij already in the parameter file\\r\\n # This actually makes life easier.\\r\\n # CHARMM does not, they simply have the original sigma and epsilon.\\r\\n # To compensate for this, for now we will leave the nonbondeds empty in phys.myPAR\\r\\n # We will then access the LennardJones parameter table in Topology directly\\r\\n k = 0\\r\\n phys.myTop.resizeLennardJonesParameters(ntypes)\\r\\n for i in range(0, ntypes):\\r\\n for j in range(i, ntypes):\\r\\n params = GenericTopology.LennardJonesParameters(lj_acoef[k], lj_bcoef[k])\\r\\n k += 1\\r\\n phys.myTop.setLennardJonesParameters(i, j, params)\\r\\n \\r\\n phys.myPAR.readFlag = 1\\r\\n phys.build()\",\n \"def read_data(self, loc):\\n pass\",\n \"def setUp(self):\\n self.setUpPyfakefs()\\n with mock.patch.object(subprocess, 'Popen', side_effect=thor_mocks.mock_thor_start):\\n self._analyzer = yara_analyzer.YaraAnalyzer()\\n\\n # Write target file.\\n # pylint: disable=no-member\\n self.fs.create_file('./target.exe', contents='This is definitely not an evil file. ^_^\\\\n')\",\n \"def UnhandledPacket(Packet):\\n\\n\\tglobal UnhandledFile\\n\\n\\tif (UnhandledFile != None):\\n\\t\\tUnhandledFile.write(Packet)\",\n \"def read(self, filename): # real signature unknown; restored from __doc__\\n pass\",\n \"def test_harvester_new_file_exception_recovered(self):\\n # create the file so that it is unreadable\\n self.create_sample_data_set_dir(\\n \\\"DOS15908_1st7_step1.DAT\\\",\\n RECOV_DIR,\\n \\\"DOS15909.DAT\\\",\\n mode=000\\n )\\n\\n # Start sampling and watch for an exception\\n self.driver.start_sampling()\\n\\n self.assert_exception(IOError)\\n\\n # At this point the harvester thread is dead. The agent\\n # exception handle should handle this case.\",\n \"def test_fix_odk_sunmission(self):\\n data = {\\n \\\"@a\\\": \\\"a\\\",\\n \\\"b\\\": \\\"b\\\",\\n \\\"orx:meta\\\": \\\"should_not_be_there\\\"\\n }\\n\\n fixed_data = sources.__fix_odk_data(data)\\n\\n self.assertEqual(fixed_data, {\\n \\\"a\\\": \\\"a\\\",\\n \\\"b\\\": \\\"b\\\"\\n })\",\n \"def test_bad_data(self):\\r\\n # LB180210_3_corrupted.PD0 has three records in it, the 2nd record was corrupted\\r\\n with open(os.path.join(RESOURCE_PATH, 'LB180210_3_corrupted.PD0'), 'rb') as stream_handle:\\r\\n\\r\\n parser = AdcpPd0Parser(self.config_recov, stream_handle, self.exception_callback)\\r\\n\\r\\n # try to get 3 particles, should only get 2 back\\r\\n # the second one should correspond to ensemble 3\\r\\n parser.get_records(3)\\r\\n\\r\\n log.debug('Exceptions : %s', self.exception_callback_value[0])\\r\\n\\r\\n self.assertEqual(len(self.exception_callback_value), 1)\\r\\n self.assert_(isinstance(self.exception_callback_value[0], RecoverableSampleException))\",\n \"def test_is_delicious_file(self):\\r\\n good_file = self._get_del_file()\\r\\n\\r\\n self.assertTrue(\\r\\n DelImporter.can_handle(good_file),\\r\\n \\\"DelImporter should handle this file\\\")\\r\\n\\r\\n good_file.close()\",\n \"def UnDumpInfo(self):\\n filename = '%s/preprocess_info.yaml' % self.logdir\\n f = open(filename,'r')\\n self.info = yaml.load(f.read())\\n f.close()\",\n \"def test_read_0_1_smirff(self):\\n ForceField(\\n get_data_file_path(\\n \\\"test_forcefields/smirff99Frosst_reference_0_1_spec.offxml\\\"\\n )\\n )\",\n \"def package_data(self, data):\\n pass\",\n \"def test_bug1003(capfd):\\n input_dir = get_input_path('bug1003')\\n temp_dir = get_temp_dir_path('bug1003var')\\n copytree(input_dir, temp_dir)\\n ds_path = os.path.join(temp_dir, 'bug1003.designspace')\\n runner(CMD + ['-o', 'd', f'_{ds_path}'])\\n captured = capfd.readouterr()\\n assert \\\"The input set requires compatibilization\\\" in captured.err\",\n \"def handle_data(self, data):\\n if verbose(): print(\\\"TIParser.handle_data(self, '%s')\\\" % (data))\\n pass\",\n \"def _read_bu_wig(self, handle, sequence_name):\\n self.chromosomes[sequence_name] = () \\n for line in handle:\\n position, total, reverse, forward = line.rstrip(\\\"\\\\r\\\\n\\\").split()\\n self.coverage[(sequence_name, position)] = (int(reverse), int(forward))\",\n \"def test_doubled_file():\\n with contextlib.closing(get_test_data('Level2_KFTG_20150430_1419.ar2v')) as infile:\\n data = infile.read()\\n fobj = BytesIO(data + data)\\n f = Level2File(fobj)\\n assert len(f.sweeps) == 12\",\n \"def _autodetect_endianness(self):\\n pos = self.file.tell()\\n # Jump to the data sample format code.\\n self.file.seek(3224, 1)\\n format = unpack(b'>h', self.file.read(2))[0]\\n # Check if valid.\\n if format in DATA_SAMPLE_FORMAT_UNPACK_FUNCTIONS.keys():\\n self.endian = '>'\\n # Else test little endian.\\n else:\\n self.file.seek(-2, 1)\\n format = unpack(b'<h', self.file.read(2))[0]\\n if format in DATA_SAMPLE_FORMAT_UNPACK_FUNCTIONS.keys():\\n self.endian = '<'\\n else:\\n msg = 'Unable to determine the endianness of the file. ' + \\\\\\n 'Please specify it.'\\n raise SEGYError(msg)\\n # Jump to previous position.\\n self.file.seek(pos, 0)\",\n \"def __init__(self, raw_data_file,):\\n self.raw_data_file = raw_data_file\\n self.clean_data = self.cleanData()\\n self.microtrip_data = []\",\n \"def test_get_infile(self):\\r\\n pass # not practically testable, but obvious file I/O\\r\",\n \"def test_ddt_with_unknown_extends(self):\\n # Setup test\\n infilename = os.path.join(_SAMPLE_FILES_DIR, \\\"reg_good_ddt.xml\\\")\\n filename = os.path.join(_TMP_DIR, \\\"reg_ddt_unknown_extends.xml\\\")\\n out_source_name = \\\"physics_types_ddt_unknown_extends\\\"\\n out_source = os.path.join(_TMP_DIR, out_source_name + '.F90')\\n out_meta = os.path.join(_TMP_DIR, out_source_name + '.meta')\\n remove_files([out_source, out_meta])\\n tree, root = read_xml_file(infilename)\\n # Change output filename\\n for obj in root:\\n oname = obj.get('name')\\n if (obj.tag == 'file') and (oname == 'physics_types_ddt'):\\n obj.set('name', out_source_name)\\n for var in obj:\\n ltype = var.get('type')\\n if (var.tag == 'ddt') and (ltype == \\\"physics_state\\\"):\\n var.set('extends', 'physics_tend')\\n break\\n # End if\\n # End for\\n break\\n # End if\\n # End for\\n tree.write(filename)\\n # Run test\\n with self.assertRaises(ValueError) as verr:\\n _ = gen_registry(filename, 'eul', {}, _TMP_DIR, 2,\\n _SRC_MOD_DIR, _CAM_ROOT,\\n loglevel=logging.ERROR,\\n error_on_no_validate=True)\\n # End with\\n # Check exception message\\n emsg = (\\\"DDT, 'physics_state', extends type 'physics_tend', \\\"\\n \\\"however, this type is not known\\\")\\n self.assertEqual(emsg, str(verr.exception))\\n # Make sure no output files were created\\n self.assertFalse(os.path.exists(out_meta))\\n self.assertFalse(os.path.exists(out_source))\",\n \"def __init__(self, message, file_handle, format):\\n oh = open(file_handle, \\\"rU\\\")\\n config.log.critical(\\\"Unrecognised file format\\\")\\n print(\\\"-----------------------\\\")\\n print(\\\"Diagnostic:\\\")\\n print(\\\"0:\\\", oh.readline().rstrip(\\\"\\\\r\\\\n\\\"))\\n print(\\\"1:\\\", oh.readline().rstrip(\\\"\\\\r\\\\n\\\"))\\n print(\\\"2:\\\", oh.readline().rstrip(\\\"\\\\r\\\\n\\\"))\\n print(\\\"3:\\\", oh.readline().rstrip(\\\"\\\\r\\\\n\\\"))\\n if \\\"sniffer\\\" in format:\\n print(\\\"Format Specifier: Sniffer (guess the file format)\\\")\\n else:\\n print(\\n \\\"Format Specifier: %s\\\"\\n % \\\" \\\".join(\\\"%s:%s\\\" % (key, format[key]) for key in format)\\n )\\n\\n print(\\\"-----------------------\\\")\\n config.log.critical(\\\"%s\\\" % (message,))\\n print()\",\n \"def record_fileprep(data):\\n order_detail = OrderDetail.objects.get(ac_od_id=data['ac_od_id'])\\n order_detail.fileprep = data['fileprep']\\n return order_detail.save()\",\n \"def _load_raw_file(self, tracker, seq, is_gt):\\n\\n # Only loaded when run to reduce minimum requirements\\n from pycocotools import mask as mask_utils\\n\\n # File location\\n if self.data_is_zipped:\\n if is_gt:\\n zip_file = os.path.join(self.gt_fol, 'data.zip')\\n else:\\n zip_file = os.path.join(self.tracker_fol, tracker, self.tracker_sub_fol + '.zip')\\n file = seq + '.txt'\\n else:\\n zip_file = None\\n if is_gt:\\n file = self.config[\\\"GT_LOC_FORMAT\\\"].format(gt_folder=self.gt_fol, seq=seq)\\n else:\\n file = os.path.join(self.tracker_fol, tracker, self.tracker_sub_fol, seq + '.txt')\\n\\n # Ignore regions\\n if is_gt:\\n crowd_ignore_filter = {2: ['10']}\\n else:\\n crowd_ignore_filter = None\\n\\n # Load raw data from text file\\n read_data, ignore_data = self._load_simple_text_file(file, crowd_ignore_filter=crowd_ignore_filter,\\n is_zipped=self.data_is_zipped, zip_file=zip_file,\\n force_delimiters=' ')\\n\\n # Convert data to required format\\n num_timesteps = self.seq_lengths[seq]\\n data_keys = ['ids', 'classes', 'dets']\\n if is_gt:\\n data_keys += ['gt_ignore_region']\\n raw_data = {key: [None] * num_timesteps for key in data_keys}\\n\\n # Check for any extra time keys\\n current_time_keys = [str(t) for t in range(num_timesteps)]\\n extra_time_keys = [x for x in read_data.keys() if x not in current_time_keys]\\n if len(extra_time_keys) > 0:\\n if is_gt:\\n text = 'Ground-truth'\\n else:\\n text = 'Tracking'\\n raise TrackEvalException(\\n text + ' data contains the following invalid timesteps in seq %s: ' % seq + ', '.join(\\n [str(x) + ', ' for x in extra_time_keys]))\\n\\n for t in range(num_timesteps):\\n time_key = str(t)\\n # list to collect all masks of a timestep to check for overlapping areas\\n all_masks = []\\n if time_key in read_data.keys():\\n try:\\n raw_data['dets'][t] = [{'size': [int(region[3]), int(region[4])],\\n 'counts': region[5].encode(encoding='UTF-8')}\\n for region in read_data[time_key]]\\n raw_data['ids'][t] = np.atleast_1d([region[1] for region in read_data[time_key]]).astype(int)\\n raw_data['classes'][t] = np.atleast_1d([region[2] for region in read_data[time_key]]).astype(int)\\n all_masks += raw_data['dets'][t]\\n except IndexError:\\n self._raise_index_error(is_gt, tracker, seq)\\n except ValueError:\\n self._raise_value_error(is_gt, tracker, seq)\\n else:\\n raw_data['dets'][t] = []\\n raw_data['ids'][t] = np.empty(0).astype(int)\\n raw_data['classes'][t] = np.empty(0).astype(int)\\n if is_gt:\\n if time_key in ignore_data.keys():\\n try:\\n time_ignore = [{'size': [int(region[3]), int(region[4])],\\n 'counts': region[5].encode(encoding='UTF-8')}\\n for region in ignore_data[time_key]]\\n raw_data['gt_ignore_region'][t] = mask_utils.merge([mask for mask in time_ignore],\\n intersect=False)\\n all_masks += [raw_data['gt_ignore_region'][t]]\\n except IndexError:\\n self._raise_index_error(is_gt, tracker, seq)\\n except ValueError:\\n self._raise_value_error(is_gt, tracker, seq)\\n else:\\n raw_data['gt_ignore_region'][t] = mask_utils.merge([], intersect=False)\\n\\n # check for overlapping masks\\n if all_masks:\\n masks_merged = all_masks[0]\\n for mask in all_masks[1:]:\\n if mask_utils.area(mask_utils.merge([masks_merged, mask], intersect=True)) != 0.0:\\n raise TrackEvalException(\\n 'Tracker has overlapping masks. Tracker: ' + tracker + ' Seq: ' + seq + ' Timestep: ' + str(\\n t))\\n masks_merged = mask_utils.merge([masks_merged, mask], intersect=False)\\n\\n if is_gt:\\n key_map = {'ids': 'gt_ids',\\n 'classes': 'gt_classes',\\n 'dets': 'gt_dets'}\\n else:\\n key_map = {'ids': 'tracker_ids',\\n 'classes': 'tracker_classes',\\n 'dets': 'tracker_dets'}\\n for k, v in key_map.items():\\n raw_data[v] = raw_data.pop(k)\\n raw_data[\\\"num_timesteps\\\"] = num_timesteps\\n raw_data['seq'] = seq\\n return raw_data\",\n \"def postprocess_file(config: Config, dfs: DFs) -> None:\\n if SymbolDF.name in dfs:\\n dfs[SymbolDF.name] = postprocess_symbols(config, dfs[SymbolDF.name])\",\n \"def tell(self):\\n ...\",\n \"def test_read_fail2(self):\\n mod_fn = os.path.join(tests.TEST_DATA_PATH, 'segmentations', 'test_bad_data2.mod')\\n with self.assertRaises(ValueError):\\n modreader.get_data(mod_fn) # missing 'IEOF' end\",\n \"def setUp(self):\\n self._file = 'test.g3'\\n write_example_file(self._file)\",\n \"def readdata(self,filename_): # 3\\n res = self.__obj.readdataautoformat(filename_)\\n if res != 0:\\n result,msg = self.__getlasterror(res)\\n raise Error(rescode(res),msg)\",\n \"def tests_ti_file_get(self):\\n super().indicator_get()\",\n \"def _read_data(self):\",\n \"def test_incomplete_file(self):\\n log.info(\\\"START INTEG TEST INCOMPLETE\\\")\\n\\n self.clear_sample_data()\\n self.clear_async_data()\\n\\n # From sample file A0000010.DEC:\\n # Flag record, first and last velocity record, time record,\\n # but the end of Velocity record (all zeroes) is missing.\\n filename = \\\"A1000002.DEC\\\"\\n self.create_sample_data('incomplete_A0000002.DEC', filename)\\n\\n # Start sampling.\\n self.driver.start_sampling()\\n\\n # an event catches the sample exception\\n self.assert_event('ResourceAgentErrorEvent')\\n\\n # Verify that the entire file has been read.\\n self.assert_file_ingested(filename)\\n\\n log.info(\\\"END INTEG TEST INCOMPLETE\\\")\",\n \"def post_process_trap(): \\n #################### 0) assign internal values #################### \\n from project_parameters import trapType,debug,trapFile,name,driveAmplitude,driveFrequency,Omega,dcplot,weightElectrodes,coefs,ax,az,phi,save,scale\\n #from all_functions import find_saddle,plot_potential,dc_potential,set_voltages,exact_saddle,spher_harm_bas,spher_harm_exp,pfit,plotN\\n import pickle\\n\\n with open(trapFile,'rb') as f:\\n trap = pickle.load(f)\\n\\n qe = trap.configuration.charge\\n mass = trap.configuration.mass\\n Zval = trap.configuration.position\\n r0 = trap.configuration.r0\\n RFampl = driveAmplitude \\n V0 = mass*(2*np.pi*Omega)**2*(r0*10**-3)**2/qe\\n X,Y,Z=trap.instance.X,trap.instance.Y,trap.instance.Z \\n data = trap.configuration\\n dcVoltages = set_voltages()\\n ne = len(weightElectrodes)\\n E = trap.instance.E\\n out = trap.configuration\\n if debug.post_process_trap:\\n print dcVoltages,np.max(dcVoltages)#np.sum(abs(dcVoltages))\\n plotN(dcVoltages,trap,'set DC voltages') \\n Vdc = dc_potential(trap,dcVoltages,E)\\n #[IDC,JDC,KDC] = find_saddle(Vdc,X,Y,Z,3,Zval) \\n #[XDC,YDC,ZDC] = exact_saddle(Vdc,X,Y,Z,3,Zval)\\n #XDC,YDC,ZDC = X[IDC],150/scale,Z[KDC]\\n #print XDC,YDC,ZDC,IDC,JDC,KDC\\n #dcbasis,dcscale= spher_harm_bas(XDC,YDC,ZDC,X,Y,Z,4)\\n #QQ = spher_harm_exp(Vdc,dcbasis,dcscale) \\n #print QQ[0:9].T\\n #1) RF Analysis\\n print('RF Analysis') \\n Vrf = RFampl*data.EL_RF\\n [Irf,Jrf,Krf] = find_saddle(Vrf,X,Y,Z,2,Zval)\\n if debug.post_process_trap:\\n plot_potential(Vrf,X,Y,Z,dcplot,'weighted RF potential','V_{rf} (eV)',[Irf,Jrf,Krf])\\n #2) DC Analysis\\n print('DC Analysis')\\n trap = dc_potential(trap,dcVoltages,E,update=None)\\n Vdc = trap.instance.DC\\n [Idc,Jdc,Kdc] = find_saddle(Vdc,X,Y,Z,3,Zval) # only used to calculate error at end\\n if debug.post_process_trap:\\n plot_potential(Vdc,X,Y,Z,'1D plots','full DC potential')\\n #3) determine the exact saddles of the RF and DC\\n trap = dc_potential(trap,dcVoltages,E)\\n Vdc = trap.instance.DC\\n print('Determining exact RF saddle...')\\n [Xrf,Yrf,Zrf] = exact_saddle(Vrf,X,Y,Z,2,Zval) \\n print('Determining exact DC saddle...')\\n [Xdc,Ydc,Zdc] = exact_saddle(Vdc,X,Y,Z,3,Zval)\\n #4) determine stray field (beginning of justAnalyzeTrap)\\n print('Determining compensation due to E field...')\\n nx,ny,nz=X.shape[0],Y.shape[0],Z.shape[0]\\n x,y,z = np.zeros((nx,ny,nz)),np.zeros((nx,ny,nz)),np.zeros((nx,ny,nz))\\n for i in range(nx):\\n for j in range(ny):\\n for k in range(nz):\\n x[i,j,k] = X[i]\\n y[i,j,k] = Y[j]\\n z[i,j,k] = Z[k]\\n VlessE = Vdc-E[0]*x-E[1]*y-E[2]*z\\n [Xdc,Ydc,Zdc] = exact_saddle(VlessE,X,Y,Z,3) \\n dist = np.sqrt((Xrf-Xdc)**2+(Yrf-Ydc)**2+(Zrf-Zdc)**2) \\n #5) call pfit to built teh total field and determine the trap characteristics\\n [fx,fy,fz,theta,Depth,Xe,Ye,Ze] = pfit(Vrf,Vdc,X,Y,Z,Irf,Jrf,Krf)#pfit(trap,E,Freq,RFampl)\\n print('Stray field is ({0},{1},{2}) V/m.'.format(scale*E[0],scale*E[1],scale*E[2]))\\n print('With this field, the compensation is optimized to {} micron.'.format(scale*dist))\\n print('RF saddle: ({0},{1},{2})\\\\nDC saddle ({3},{4},{5}).'.format(Xrf,Yrf,Zrf,Xdc,Ydc,Zdc)) \\n if debug.trap_depth:\\n print('The trap escape position is at ({0},{1},{2}) microns, for a trap depth of {3} mV'.format(Xe*scale,Ye*scale,Ze*scale,Depth*scale))\\n print('The trap frequencies are fx = {0} MHz, fy = {1} MHz, and fz = {2} MHz'.format(fx*10**-6,fy*10**-6,fz*10**-6))\\n #6) Sanity testing; quality check no longer used\\n if debug.post_process_trap:\\n rfbasis,rfscale= spher_harm_bas(Xrf,Yrf,Zrf,X,Y,Z,2)\\n Qrf = spher_harm_exp(Vrf,rfbasis,rfscale) \\n if np.sqrt((Xrf-Xdc)**2+(Yrf-Ydc)**2+(Zrf-Zdc)**2)>0.008: \\n print('Expanding DC with RF for saniy checking.')\\n Qdc = spher_harm_exp(Vdc,rfbasis,rfscale) \\n else:\\n print('Expanding DC without RF for sanity checking.')\\n dcbasis,dcscale= spher_harm_bas(Xdc,Ydc,Zdc,X,Y,Z,2)\\n Qdc = spher_harm_exp(Vdc,dcbasis,dcscale) \\n Arf = 2*np.sqrt( (3*Qrf[7])**2+(3*Qrf[8])**2 )\\n Thetarf = 45*(Qrf[8]/abs(Qrf[8]))-90*np.arctan((3*Qrf[7])/(3*Qrf[8]))/np.pi\\n Adc = 2*np.sqrt( (3*Qdc[7])**2+(3*Qdc[8])**2 )\\n Thetadc = 45*(Qrf[8]/abs(Qrf[8]))-90*np.arctan((3*Qdc[7])/(3*Qdc[8]))/np.pi\\n out.E = E\\n out.miscompensation = dist\\n out.ionpos = [Xrf,Yrf,Zdc]\\n out.ionposIndex = [Irf,Jrf,Krf]\\n out.frequency = [fx,fy,fz]\\n out.theta = theta\\n out.trap_depth = Depth/qe \\n out.escapepos = [Xe,Ye,Ze]\\n out.Quadrf = 2*np.array([Qrf[7]*3,Qrf[4]/2,Qrf[8]*6,-Qrf[6]*3,-Qrf[5]*3])\\n out.Quaddc = 2*np.array([Qdc[7]*3,Qdc[4]/2,Qdc[8]*6,-Qdc[6]*3,-Qdc[5]*3])\\n out.Arf = Arf\\n out.Thetarf = Thetarf\\n out.Adc = Adc\\n out.Thetadc = Thetadc\\n T = np.array([[2,-2,0,0,0],[-2,-2,0,0,0],[0,4,0,0,0],[0,0,1,0,0],[0,0,0,1,0],[0, 0,0,0,1]])\\n Qdrf = out.Quadrf.T\\n Qddc = out.Quaddc.T\\n out.q = (1/V0)*T*Qdrf\\n out.alpha = (2/V0)*T*Qddc\\n out.Error = [X[Idc]-Xdc,Y[Jdc]-Ydc,Z[Kdc]-Zdc]\\n #7) update the trapping field data structure with instance attributes\\n trap.configuration=out\\n trap.instance.driveAmplitude = driveAmplitude\\n trap.instance.driveFrequency = driveFrequency\\n trap.instance.coefs = coefs\\n trap.instance.ax = ax\\n trap.instance.az = az\\n trap.instance.phi = phi\\n trap.instance.ppt = True\\n trap.instance.out = out\\n if save==True:\\n print('Saving '+trapFile+' as a data structure...')\\n with open(trapFile,'wb') as f:\\n pickle.dump(trap,f)\\n return 'post_proccess_trap complete' #out # no output needed really\",\n \"def process_file(self, data, filename):\\n\\n if data:\\n data = self.update_province_info(data)\\n self.get_province_info(data, filename)\",\n \"def __init__(self, inFilename):\\n\\n self._prmtopVersion=None\\n self._flags=[]\\n self._raw_format={}\\n self._raw_data={}\\n self._has_nbfix_terms = False\\n\\n with open(inFilename, 'r') as fIn:\\n for line in fIn:\\n if line[0] == '%':\\n if line.startswith('%VERSION'):\\n tag, self._prmtopVersion = line.rstrip().split(None, 1)\\n elif line.startswith('%FLAG'):\\n tag, flag = line.rstrip().split(None, 1)\\n self._flags.append(flag)\\n self._raw_data[flag] = []\\n elif line.startswith('%FORMAT'):\\n format = line.rstrip()\\n index0=format.index('(')\\n index1=format.index(')')\\n format = format[index0+1:index1]\\n try:\\n m = FORMAT_RE_PATTERN.search(format)\\n self._raw_format[self._flags[-1]] = (format, m.group(1), m.group(2), int(m.group(3)), m.group(4))\\n except:\\n # We couldn't parse the format, so just treat the whole line as a single string.\\n self._raw_format[self._flags[-1]] = (format, 1, 'a', 80, '')\\n elif line.startswith('%COMMENT'):\\n continue\\n elif self._flags \\\\\\n and 'TITLE'==self._flags[-1] \\\\\\n and not self._raw_data['TITLE']:\\n self._raw_data['TITLE'] = line.rstrip()\\n else:\\n flag=self._flags[-1]\\n (format, numItems, itemType,\\n iLength, itemPrecision) = self._getFormat(flag)\\n line = line.rstrip()\\n for index in range(0, len(line), iLength):\\n item = line[index:index+iLength]\\n if item:\\n self._raw_data[flag].append(item.strip())\\n # See if this is a CHAMBER-style topology file, which is not supported\\n # for creating Systems\\n self.chamber = 'CTITLE' in self._flags\",\n \"def import_fix_dat(xrec=None):\\n xrec = conf.get_current()\\n\\n\\n regEx = re.compile(\\\"[A-Z]{5}\\\")\\n \\n inputfile = conf.work_dir(\\\"/xplane_unzipped/%s/earth_fix.dat\\\" % (xrec['zip_dir']))\\n c = 0\\n with open(inputfile) as readnav:\\n \\n for line in readnav:\\n c += 1\\n \\n # Skip first three lines, hope Robin Peel will never change this behaviour ;-)\\n if c < 4:\\n pass\\n else:\\n \\n if not line.startswith(\\\"99\\\"):\\n \\n lst = line.strip().split()\\n fix_ident = str(lst[2])\\n \\n if fix_ident == \\\"NPOLE\\\":\\n pass\\n \\n else:\\n #//fix_center_lat84 = str(lst[0])\\n #fix_center_lon84 = str(lst[1])\\n maj = 1 if regEx.match(fix_ident) else 0\\n # insert to db\\n insert_fix( \\n **dict(\\n ident=fix_ident, major=maj,\\n lat=str(lst[0]), lon=str(lst[1])\\n )\\n )\\n \\n ## We commit every x to make faster\\n if c % 5000 == 0:\\n print \\\" > fix: %s - %s of %s\\\" % (fix_ident, c, MAX_LINES_GUESS)\\n\\n \\n idx_file = conf.raw_fix_path()\",\n \"def unusedFromKDOTDataPreparation():\",\n \"def test_load_events_noclobber(self):\\n with catch_warnings() as w:\\n command = \\\\\\n '{0} --noclobber'.format(\\n os.path.join(self.datadir, 'monol_testB.evt'))\\n hen.read_events.main(command.split())\\n assert str(w[0].message).strip().endswith(\\n \\\"exists and using noclobber. Skipping\\\"), \\\\\\n \\\"Unexpected warning output\\\"\",\n \"def test_load_gtis(self):\\n fits_file = os.path.join(self.datadir, 'monol_testA.evt')\\n hen.io.load_gtis(fits_file)\",\n \"def __init__(self, filename):\\n config.log.critical(\\\"File '%s' is not a glbase binary file\\\" % filename)\",\n \"def run():\\n\\twrite_fuel_data()\",\n \"def tests_ti_file_get_tag(self, request: FixtureRequest):\\n super().indicator_get_tag(request)\",\n \"def _hook_data(self, data):\\n if self.data_hook is not None:\\n self.data_hook(data)\",\n \"def import_gene_information(inputargs):\\n\\n global chainnams, chain\\n chain = inputargs['chain']\\n\\n if inputargs['tags'] == \\\"extended\\\" and inputargs['species'] == \\\"mouse\\\":\\n print(\\\"Please note that there is currently no extended tag set for mouse TCR genes.\\\\n\\\" \\\\\\n \\\"Decombinator will now switch the tag set in use from \\\\'extended\\\\' to \\\\'original\\\\'.\\\\n\\\" \\\\\\n \\\"In future, consider editing the script to change the default, \\\" \\\\\\n \\\"or use the appropriate flags (-sp mouse -tg original).\\\")\\n inputargs['tags'] = \\\"original\\\"\\n\\n if inputargs['tags'] == \\\"extended\\\" and (chain == 'g' or chain == 'd'):\\n print(\\\"Please note that there is currently no extended tag set for gamma/delta TCR genes.\\\\n\\\" \\\\\\n \\\"Decombinator will now switch the tag set in use from \\\\'extended\\\\' to \\\\'original\\\\'.\\\\n\\\" \\\\\\n \\\"In future, consider editing the script to change the default, or use the appropriate flags.\\\")\\n inputargs['tags'] = \\\"original\\\"\\n\\n # Check species information\\n if inputargs['species'] not in [\\\"human\\\", \\\"mouse\\\"]:\\n print(\\\"Species not recognised. Please select either \\\\'human\\\\' (default) or \\\\'mouse\\\\'.\\\\n\\\" \\\\\\n \\\"If mouse is required by default, consider changing the default value in the script.\\\")\\n sys.exit()\\n\\n # Look for tag and V/J fasta and cysteine position files: if these cannot be found in the working directory,\\n # source them from GitHub repositories\\n # Note that fasta/tag files fit the pattern \\\"species_tagset_gene.[fasta/tags]\\\"\\n # I.e. \\\"[human/mouse]_[extended/original]_TR[A/B/G/D][V/J].[fasta/tags]\\\"\\n\\n for gene in ['v', 'j']:\\n # Get FASTA data\\n fasta_file = read_tcr_file(inputargs['species'], inputargs['tags'], gene, \\\"fasta\\\", inputargs['tagfastadir'])\\n globals()[gene + \\\"_genes\\\"] = list(SeqIO.parse(fasta_file, \\\"fasta\\\"))\\n\\n globals()[gene + \\\"_regions\\\"] = [str( item.seq.upper()) for item in globals()[gene + \\\"_genes\\\"]]\\n globals()[gene + \\\"_names\\\"] = [str(item.id.upper().split(\\\"|\\\")[1]) for item in globals()[gene + \\\"_genes\\\"]]\\n\\n # Get conserved translation residue sites and functionality data\\n translation_file = open(read_tcr_file(inputargs['species'], inputargs['tags'], gene, \\\"translate\\\",\\n inputargs['tagfastadir']),\\\"rt\\\")\\n translate_data = [x.rstrip() for x in list(translation_file)]\\n\\n globals()[gene + \\\"_translate_position\\\"] = [int(x.split(\\\",\\\")[1]) for x in translate_data]\\n globals()[gene + \\\"_translate_residue\\\"] = [x.split(\\\",\\\")[2] for x in translate_data]\\n globals()[gene + \\\"_functionality\\\"] = [x.split(\\\",\\\")[3] for x in translate_data]\\n\\n if gene == 'v':\\n \\n if inputargs['species'] == \\\"human\\\":\\n # Get germline CDR data\\n cdr_file = open(read_tcr_file(inputargs['species'], inputargs['tags'], gene, \\\"cdrs\\\", inputargs['tagfastadir']), \\\"rt\\\")\\n cdr_data = [x.rstrip() for x in list(cdr_file)]\\n cdr_file.close()\\n v_cdr1 = [x.split(\\\" \\\")[1] for x in cdr_data]\\n v_cdr2 = [x.split(\\\" \\\")[2] for x in cdr_data]\\n else:\\n # cdr_file only exists for human - CDR1 and CDR2 only written to output tsv\\n # for human. Otherwise create empty lists fo v_cdr1 and v_cdr2, to write empty\\n # fields to output tsv\\n v_cdr1 = [\\\"\\\"]*len(globals()[gene + \\\"_genes\\\"])\\n v_cdr2 = [\\\"\\\"]*len(globals()[gene + \\\"_genes\\\"])\\n\\n return v_regions, j_regions, v_names, j_names, v_translate_position, v_translate_residue, \\\\\\n j_translate_position, j_translate_residue, v_functionality, j_functionality, v_cdr1, v_cdr2\",\n \"def calibrate(self, master):\\n if master.referencetype == \\\"Block\\\":\\n self.caldat = self.mw \\n else:\\n print(\\\"Kein gültiger Referenzsensortyp\\\")\",\n \"def get_unknown_event(self, fixture_name: str) -> str:\\n fixture_data = orjson.loads(\\n self.webhook_fixture_data(\\\"semaphore\\\", fixture_name, file_type=\\\"json\\\")\\n )\\n fixture_data[\\\"revision\\\"][\\\"reference_type\\\"] = \\\"unknown\\\"\\n return fixture_data\",\n \"def read_evoked_lfp(probe,group,p,data):\\n\\n print('#### Low-pass filtering the data ####')\\n \\n\\n nr_of_electrodes = p['nr_of_electrodes_per_group']\\n save_file = p['path'] + '/probe_{:g}_group_{:g}/probe_{:g}_group_{:g}_evoked.pickle'.format(probe,group,probe,group)\\n\\n #Low pass filtering\\n filt = lowpassFilter(rate = p['sample_rate'], high = p['cutoff_freq'], order = 3, axis = 1)\\n filtered = filt(data)\\n\\n\\n #Notch filtering\\n #if p['notch_filt_freq'] != 0:\\n # notchFilt = notchFilter(rate = p['sample_rate'], low = p['notch_filt_freq']-5, high = p['notch_filt_freq']+5, order = 3)\\n #Reading the trigger timestamps (process varies depending on the file format\\n\\n if p['fileformat'] == 'dat':\\n trigger_filepath = p['path'] + '/' + p['stim_file']\\n with open(trigger_filepath, 'rb') as fid:\\n trigger = np.fromfile(fid, np.int16)\\n stim_timestamps = extract_stim_timestamps_der(trigger,p)\\n\\n elif p['fileformat'] == 'cont':\\n\\t\\t#Reading the digital input from file\\n trigger_filepath = p['path'] + '/all_channels.events'\\n trigger_events = loadEvents(trigger_filepath)\\n\\n #Acquiring the timestamps of the ttl pulses\\n timestamps = trigger_events['timestamps']\\n eventId = trigger_events['eventId']\\n eventType = trigger_events['eventType']\\n channel = trigger_events['channel']\\n\\n timestamps_global = timestamps[eventType == 5]\\n timestamps_ttl = []\\n\\n ttl_events = (eventType == 3)\\n ttl_rise = (eventId == 1)\\n\\n for i in range(len(timestamps)):\\n if (ttl_events[i]) and (ttl_rise[i]):\\n timestamps_ttl = np.append(timestamps_ttl, timestamps[i])\\n\\n stim_timestamps = timestamps_ttl - timestamps_global[0]\\n\\n elif p['fileformat'] == 'rhd':\\n trigger_all = []\\n for file in range(len(p['rhd_file'])):\\n data = read_data(p['path']+'/'+ p['rhd_file'][file])\\n trigger = data['board_dig_in_data'][1]\\n trigger_all = np.append(trigger_all, trigger)\\n\\n stim_timestamps = []\\n for i in range(1,len(trigger_all)):\\n if trigger_all[i-1] == 0 and trigger_all[i] == 1:\\n stim_timestamps = np.append(stim_timestamps, i)\\n\\n evoked = read_evoked_lfp_from_stim_timestamps(filtered, stim_timestamps, p)\\n\\n #Save all evoked activity in a pickle file\\n fid = open(save_file, 'wb')\\n pickle.dump({'evoked':evoked, 'stim_timestamps':stim_timestamps}, fid, protocol=-1)\\n fid.close()\\n\\n #Downsampling\\n if(p['down_sample'] == True):\\n down_sampled = signal.decimate(filtered, p['down_sample_rate'], zero_phase=True) #Downsampling signal\\n small_sample_rate = p['sample_rate']/p['down_sample_rate']\\n stim_downsampled = (stim_timestamps/p['down_sample_rate']).astype(int) #Shifting stim_timestamps\\n\\n evoked_downsampled = read_evoked_lfp_from_stim_timestamps_downsampled(down_sampled, stim_downsampled, p, small_sample_rate)\\n\\n #Save all evoked activity in a pickle file\\n save_file = p['path'] + '/probe_{0}_group_{1}/probe_{2}_group_{3}_evoked_down_sampled.pickle'.format(probe,group,probe,group)\\n fid = open(save_file, 'wb')\\n pickle.dump({'evoked':evoked_downsampled, 'stim_timestamps':stim_downsampled}, fid, protocol=-1)\\n fid.close()\"\n]","isConversational":false},"negative_scores":{"kind":"list like","value":["0.55719537","0.5494891","0.51716053","0.51296675","0.5104879","0.5093885","0.50897896","0.50862515","0.5061046","0.50539726","0.5030481","0.5016976","0.50007325","0.4999721","0.49765038","0.4970551","0.4964387","0.4937533","0.4932086","0.49242124","0.4913246","0.49125105","0.4908097","0.49050215","0.4899774","0.48698184","0.4853567","0.48311684","0.4830347","0.4812253","0.48072535","0.4798691","0.47905138","0.47821388","0.47784656","0.47757137","0.4771618","0.47698247","0.47670168","0.4754711","0.4750666","0.47430438","0.47293633","0.47167426","0.46986276","0.46950787","0.46915","0.46882027","0.46853372","0.46830285","0.46822444","0.4674154","0.46733686","0.4669663","0.4657619","0.4652506","0.46524775","0.4651378","0.46493372","0.46375382","0.46336478","0.46331784","0.4626136","0.46251404","0.46219414","0.4616999","0.46151367","0.4606046","0.45884174","0.45856878","0.4585532","0.45836568","0.45629117","0.45628685","0.4556165","0.45503297","0.4544869","0.4544305","0.45429817","0.45371613","0.45370686","0.45357707","0.453387","0.45302904","0.4530276","0.45265672","0.45249832","0.45234966","0.45217794","0.45191437","0.45165828","0.45164126","0.45163533","0.45116925","0.4511101","0.45038503","0.449653","0.44894186","0.4486692","0.44848445","0.44716924"],"string":"[\n \"0.55719537\",\n \"0.5494891\",\n \"0.51716053\",\n \"0.51296675\",\n \"0.5104879\",\n \"0.5093885\",\n \"0.50897896\",\n \"0.50862515\",\n \"0.5061046\",\n \"0.50539726\",\n \"0.5030481\",\n \"0.5016976\",\n \"0.50007325\",\n \"0.4999721\",\n \"0.49765038\",\n \"0.4970551\",\n \"0.4964387\",\n \"0.4937533\",\n \"0.4932086\",\n \"0.49242124\",\n \"0.4913246\",\n \"0.49125105\",\n \"0.4908097\",\n \"0.49050215\",\n \"0.4899774\",\n \"0.48698184\",\n \"0.4853567\",\n \"0.48311684\",\n \"0.4830347\",\n \"0.4812253\",\n \"0.48072535\",\n \"0.4798691\",\n \"0.47905138\",\n \"0.47821388\",\n \"0.47784656\",\n \"0.47757137\",\n \"0.4771618\",\n \"0.47698247\",\n \"0.47670168\",\n \"0.4754711\",\n \"0.4750666\",\n \"0.47430438\",\n \"0.47293633\",\n \"0.47167426\",\n \"0.46986276\",\n \"0.46950787\",\n \"0.46915\",\n \"0.46882027\",\n \"0.46853372\",\n \"0.46830285\",\n \"0.46822444\",\n \"0.4674154\",\n \"0.46733686\",\n \"0.4669663\",\n \"0.4657619\",\n \"0.4652506\",\n \"0.46524775\",\n \"0.4651378\",\n \"0.46493372\",\n \"0.46375382\",\n \"0.46336478\",\n \"0.46331784\",\n \"0.4626136\",\n \"0.46251404\",\n \"0.46219414\",\n \"0.4616999\",\n \"0.46151367\",\n \"0.4606046\",\n \"0.45884174\",\n \"0.45856878\",\n \"0.4585532\",\n \"0.45836568\",\n \"0.45629117\",\n \"0.45628685\",\n \"0.4556165\",\n \"0.45503297\",\n \"0.4544869\",\n \"0.4544305\",\n \"0.45429817\",\n \"0.45371613\",\n \"0.45370686\",\n \"0.45357707\",\n \"0.453387\",\n \"0.45302904\",\n \"0.4530276\",\n \"0.45265672\",\n \"0.45249832\",\n \"0.45234966\",\n \"0.45217794\",\n \"0.45191437\",\n \"0.45165828\",\n \"0.45164126\",\n \"0.45163533\",\n \"0.45116925\",\n \"0.4511101\",\n \"0.45038503\",\n \"0.449653\",\n \"0.44894186\",\n \"0.4486692\",\n \"0.44848445\",\n \"0.44716924\"\n]","isConversational":false},"document_score":{"kind":"string","value":"0.0"},"document_rank":{"kind":"string","value":"-1"}}},{"rowIdx":16595,"cells":{"query":{"kind":"string","value":"Trap long arc in single quadrant mode."},"document":{"kind":"string","value":"def test_single_quadrant(self):"},"metadata":{"kind":"string","value":"{\n \"objective\": {\n \"self\": [],\n \"paired\": [],\n \"triplet\": [\n [\n \"query\",\n \"document\",\n \"negatives\"\n ]\n ]\n }\n}"},"negatives":{"kind":"list like","value":["def place_rebar_long_torsion(as_tl_req, d):\r\n \"\"\"as_tl_req - area of longitudinal reinforcement required for torsion\"\"\"\r\n \"\"\"d - preferred diameter (this is initially the flexural rebar diameter. If not enough, chose one diameter above\"\"\"\r\n \"\"\"returns a list with [n, d] where n is number of bars and d diameter of bar\"\"\"\r\n\r\n diameters = [12, 16, 20, 25, 32, 40]\r\n ix = diameters.index(d)\r\n\r\n while ix < len(diameters)-1: # while loop to run through every diameters possible\r\n\r\n as_t = 4 * np.pi * d ** 2 / 4\r\n\r\n if as_t > as_tl_req: # in case provided area is enough, break\r\n a = [4, d]\r\n break\r\n\r\n else:\r\n d = diameters[ix+1]\r\n ix += 1\r\n\r\n if as_t < as_tl_req: # final check in case provided area is not enough\r\n a = [0, 0]\r\n\r\n return a","def trapezoid_area(lower, leg , upper):\n area = (((upper+lower)/2)*leg)\n return area","def GetLoCorner(self):\n ...","def Oneside( x, y0, y1, r):\n\n true = 1\n size_x = np.shape( x )\n if not size_x: size_x = [0]\n\n if size_x[ 0 ] == 0:\n if x == 0: return x\n elif abs( x ) >= r: return Arc( x, y0, y1, r )\n yh = sqrt( r*r - x*x )\n if ( y0 <= -yh ):\n if ( y1 <= -yh ) : return Arc( x, y0, y1, r )\n elif ( y1 <= yh ) : return Arc( x, y0, -yh, r ) \\\n + Chord( x, -yh, y1 )\n else : return Arc( x, y0, -yh, r ) \\\n + Chord( x, -yh, yh ) + Arc( x, yh, y1, r )\n \n elif ( y0 < yh ):\n if ( y1 <= -yh ) : return Chord( x, y0, -yh ) \\\n + Arc( x, -yh, y1, r )\n elif ( y1 <= yh ) : return Chord( x, y0, y1 )\n else : return Chord( x, y0, yh ) + Arc( x, yh, y1, r )\n\n else :\n if ( y1 <= -yh ) : return Arc( x, y0, yh, r ) \\\n + Chord( x, yh, -yh ) + Arc( x, -yh, y1, r )\n elif ( y1 <= yh ) : return Arc( x, y0, yh, r ) + Chord( x, yh, y1 )\n else : return Arc( x, y0, y1, r )\n\n else :\n ans2 = x\n t0 = where( x == 0)[0]\n count = len(t0)\n if count == len( x ): return ans2\n\n ans = x * 0\n yh = x * 0\n to = where( abs( x ) >= r)[0]\n tocount = len(to)\n ti = where( abs( x ) < r)[0]\n ticount = len(ti)\n if tocount != 0: ans[ to ] = Arc( x[to], y0[to], y1[to], r )\n if ticount == 0: return ans\n \n yh[ ti ] = sqrt( r*r - x[ti]*x[ti] )\n \n t1 = where( np.less_equal(y0[ti],-yh[ti]) )[0]\n count = len(t1)\n if count != 0:\n i = ti[ t1 ]\n\n t2 = where( np.less_equal(y1[i],-yh[i]))[0]\n count = len(t2)\n if count != 0:\n j = ti[ t1[ t2 ] ]\n ans[j] = Arc( x[j], y0[j], y1[j], r )\n\n t2 = where( ( greater(y1[i],-yh[i]) ) &\n ( less_equal(y1[i],yh[i]) ))[0]\n count = len(t2)\n if count != 0:\n j = ti[ t1[ t2 ] ]\n ans[j] = Arc( x[j], y0[j], -yh[j], r ) \\\n + Chord( x[j], -yh[j], y1[j] )\n\n t2 = where( greater(y1[i], yh[i]) )[0]\n count = len(t2)\n\n if count != 0:\n j = ti[ t1[ t2 ] ]\n ans[j] = Arc( x[j], y0[j], -yh[j], r ) \\\n + Chord( x[j], -yh[j], yh[j] ) \\\n + Arc( x[j], yh[j], y1[j], r )\n \n t1 = where( ( greater(y0[ti],-yh[ti]) ) & \n ( less(y0[ti],yh[ti]) ))[0] \n count = len(t1)\n if count != 0:\n i = ti[ t1 ]\n\n t2 = where( np.less_equal(y1[i],-yh[i]))[0]\n count = len(t2)\n if count != 0:\n j = ti[ t1[ t2 ] ]\n ans[j] = Chord( x[j], y0[j], -yh[j] ) \\\n + Arc( x[j], -yh[j], y1[j], r )\n \n\n t2 = where( ( greater(y1[i], -yh[i]) ) & \n ( less_equal(y1[i], yh[i]) ))[0]\n count = len(t2)\n\n if count != 0:\n j = ti[ t1[ t2 ] ]\n ans[j] = Chord( x[j], y0[j], y1[j] )\n\n t2 = where( greater(y1[i], yh[i]))[0]\n count = len(t2)\n if count != 0:\n j = ti[ t1[ t2 ] ]\n ans[j] = Chord( x[j], y0[j], yh[j] ) \\\n + Arc( x[j], yh[j], y1[j], r )\n\n t1 = where( greater_equal(y0[ti], yh[ti]))[0] \n count = len(t1)\n if count != 0:\n i = ti[ t1 ]\n\n t2 = where ( np.less_equal(y1[i], -yh[i]))[0] \n count = len(t2)\n if count != 0:\n j = ti[ t1[ t2 ] ]\n ans[j] = Arc( x[j], y0[j], yh[j], r ) \\\n + Chord( x[j], yh[j], -yh[j] ) \\\n + Arc( x[j], -yh[j], y1[j], r )\n\n t2 = where( ( greater(y1[i], -yh[i]) ) & \n ( less_equal(y1[i], yh[i]) ))[0]\n count = len(t2)\n if count != 0:\n j = ti[ t1[ t2 ] ]\n ans[j] = Arc( x[j], y0[j], yh[j], r ) \\\n + Chord( x[j], yh[j], y1[j] )\n\n t2 = where( greater(y1[i], yh[i]))[0]\n count = len(t2)\n if count != 0:\n j = ti[ t1[ t2 ] ]\n ans[j] = Arc( x[j], y0[j], y1[j], r )\n\n return ans","def triangular_area():\n print(1*1/2, 2*2/2, 3*3/2, 4*4/2, 5*5/2, 6*6/2, 7*7/2, 8*8/2, 9*9/2,\n 10*10/2)","def quarterarc_trench(self,r, width, gap, x0, y0, orient='NE', npoints=20):\n inside = self.quarterarc(r, gap, x0, y0, orientation=orient, npoints=npoints)\n outside = self.quarterarc(r + gap + width, gap, x0, y0, orientation=orient, \n npoints=npoints)\n return [inside, outside]","def proz_manually ():\r\n Check_180turn(left_boundary,right_boundary)\r\n ABS() # Baseline correction \r\n XCMD(\"closeall\",WAIT_TILL_DONE)","def halfarc_trench(self,r, width, gap, x0, y0, orient='E', npoints=40):\n inside = self.halfarc(r, gap, x0, y0, orientation=orient, npoints=npoints)\n outside = self.halfarc(r + gap + width, gap, x0, y0, orientation=orient, npoints=npoints)\n return [inside, outside]","def horizontal_arcs_iglu():\n arc(screen, BLACK, (50, 560, 300, 20), 3.14, 0)\n arc(screen, BLACK, (60, 510, 280, 20), 3.14, 0)\n arc(screen, BLACK, (80, 460, 240, 20), 3.14, 0)\n arc(screen, BLACK, (120, 420, 160, 20), 3.14, 0)","def do_altangle(self):\n nave = 10000\n x, y, z, angle = cbp.phidget.main(nave)\n current_angle = angle\n #print(current_angle)\n self.altangle = current_angle\n return current_angle","def settle(self):\n if (self.angle >= self.max_angle) or (\n self.angle <= -self.max_angle\n ): # time to reverse\n print(\"reverse\", self.angle, self.max_angle)\n self.speed *= -0.9 # damped\n self.max_angle *= 0.9\n if self.speed > 0:\n self.angle = self.max_angle\n else:\n self.angle = -self.max_angle\n\n self.angle += radians(self.speed)\n print(self.angle, self.max_angle, self.speed)\n self.x = self.cx + self.length * sin(self.angle)\n self.y = self.cy + self.length * cos(self.angle)","def echointro(self,longver_): # 3\n res = self.__obj.echointro(longver_)\n if res != 0:\n raise Error(rescode(res),\"\")","def lendiag(self):\n if self.y <= self.x:\n return self.y\n else:\n return self.x","def LED_angle():\n right = np.transpose(vision.pqr_l)\n print(right)\n if not right.size:\n return\n else:\n angle = np.arctan2(right[0, 1], right[0, 0]) * 180 / pi\n if angle > -15:\n leds.off()\n else:\n leds.on()","def check_angle_of_arcs(self):\n\n if self.thin_arc_start_angle >= 3600:\n self.thin_arc_start_angle %= 360\n self.thin_arc_start_angle += 360\n\n elif self.thin_arc_start_angle <= -3600:\n self.thin_arc_start_angle %= 360\n self.thin_arc_start_angle -= 360\n\n if self.thin_arc_end_angle >= 3600:\n self.thin_arc_end_angle %= 360\n self.thin_arc_end_angle += 360\n\n elif self.thin_arc_end_angle <= -3600:\n self.thin_arc_end_angle %= 360\n self.thin_arc_end_angle -= 360\n\n if self.thick_arc_start_angle >= 3600:\n self.thick_arc_start_angle %= 360\n self.thick_arc_start_angle += 360\n\n elif self.thick_arc_start_angle <= -3600:\n self.thick_arc_start_angle %= 360\n self.thick_arc_start_angle -= 360\n\n if self.thick_arc_end_angle >= 3600:\n self.thick_arc_end_angle %= 360\n self.thick_arc_end_angle += 360\n\n elif self.thick_arc_end_angle <= -3600:\n self.thick_arc_end_angle %= 360\n self.thick_arc_end_angle -= 360","def square_area(side):\n return side**2","def diag_line((lat0, lon0, alt0), (lat, lon, alt), k=5):\n\tlats = np.linspace(lat0, lat, k)\n\tlons = np.linspace(lon0, lon, k)\n\talts = np.linspace(alt0, alt, k)\n\tp = zip(lats, lons, alts)\n\treturn p","def op_rad(self, args):\n self.require_stack(1)\n val1 = self.stack.pop()\n self.stack.append(decimal.radians(val1))","def Agl2ArcLen(self,agl):\r\n\r\n return (self.distance_between_wheels/2)*agl","def epicycloid(r, n, t):\n first = True\n t.up()\n i = 1\n while True:\n theata = i * get_radian() / 10\n i += 1\n x = r * (cos(theata)+(1/n)*cos(n*theata))\n y = r * (sin(theata)+(1/n)*sin(n*theata))\n t.goto(x, y)\n if first == True:\n t.pd()\n first = False\n s = ([round(x, 5), round(y, 5)])\n else:\n if s == [round(x, 5), round(y, 5)]:\n break\n t.up()","def radius_step(radius, num_longtidues, num_latitudes, time):\n step = int(exp(time))\n radius['long_down'] = radius['long_down'] - step\n if radius['long_down'] <= 0:\n radius['long_down'] = 0\n radius['long_up'] = radius['long_up'] + step\n if radius['long_up'] >= num_longtidues - 1:\n radius['long_up'] = num_longtidues - 1\n radius['lat_down'] = radius['lat_down'] - step\n if radius['lat_down'] <= 0:\n radius['lat_down'] = 0\n radius['lat_up'] = radius['lat_up'] + step\n if radius['lat_up'] >= num_latitudes - 1:\n radius['lat_up'] = num_latitudes - 1","def rotate_arcs(self):\n\n if self.arc_direction:\n self.thick_arc_start_angle -= 5\n self.thick_arc_end_angle -= 5\n\n self.thin_arc_start_angle += 5\n self.thin_arc_end_angle += 5\n else:\n self.thick_arc_start_angle += 5\n self.thick_arc_end_angle += 5\n\n self.thin_arc_start_angle -= 5\n self.thin_arc_end_angle -= 5","def test_trapezoid_area(self):\n self.assertEqual(16, trapezoid_area(\n self.values['base_minor'], self.values['base_major'], self.values['height']))","def delta_long(self, other_coord):\n\n delta_rad = other_coord.long.rad - self.long.rad\n\n return AngleRad(delta_rad)","def quadrant(coordinates: tuple, center: tuple):\n angle = calculate_angle(center, coordinates)\n if angle =< 90:\n return \"LL\"\n if angle =< 180:\n return \"UL\"\n if angle =< 270:\n return \"UR\"\n return \"LR\"","def arm(self):\n pass","def cube_area(edge : number) -> number:\n area = 6*edge*edge\n\n return area","def _corner_moravec(*args, **kwargs): # real signature unknown\n pass","def draw_long_shape():\n turtle.fillcolor('blue')\n draw_block()\n turtle.forward(50)\n draw_block()\n turtle.forward(50)\n draw_block()\n turtle.forward(50)\n draw_block()\n turtle.back(150)","def corrRing(self, angle):\n c =\"/cli:python /app:matrix /cmd:setcorring\" + str(float(angle))\n self.sendCMDstring(c)","def mark_sq8(self):\n self.drive_inches(15, 400)\n self.turn_degrees(90, 400)\n self.drive_inches(13, 400)\n ev3.Sound.speak('Place Mark').wait()\n self.arm_calibration()\n self.drive_inches(-13, 400)\n self.turn_degrees(-90, 400)\n self.drive_inches(-15, 400)","def trapezoid_area(base_minor, base_major, height):\n return ((base_major + base_minor) / 2 ) * height","def testRadial(self):\n self.doTest(afwGeom.makeRadialTransform([0, 1.01, 1e-7]))","def testRadial(self):\n self.doTest(afwGeom.makeRadialTransform([0, 1.01, 1e-7]))","def trapArea(base1, base2, height):\n return base1 + base2 * 1/2 * height","def area_circle(r):\n return (r ** 2) * math.pi","def _determine_quadrant(row, column) -> QuadrantEnum:\n if row < 4 and column < 5:\n return QuadrantEnum.TOP_LEFT\n elif row < 4 and column >= 5:\n return QuadrantEnum.TOP_RIGHT\n elif row >= 4 and column < 5:\n return QuadrantEnum.BOTTOM_LEFT\n else:\n return QuadrantEnum.BOTTOM_RIGHT","def Intarea( xc, yc, r, x0, x1, y0, y1):\n\n#\n# Shift the objects so that the circle is at the origin.\n#\n x0 = x0 - xc\n y0 = y0 - yc\n x1 = x1 - xc\n y1 = y1 - yc\n\n return Oneside( x1, y0, y1, r ) + Oneside( y1, -x1, -x0, r ) +\\\n Oneside( -x0, -y1, -y0, r ) + Oneside( -y0, x0, x1, r )","def area_equilat(side):\n\treturn side/2 * math.sqrt(side**2 - (side/2)**2)","def get_quadrant(azi, posang1, posang2, full=False):\n ang1, ang2 = posang1, posang2\n maxazipos = len(azi)\n\n def get_sl(a, b, clock=1):\n if clock == 1:\n if a < b:\n return list(range(a, b + 1))\n else:\n return [*range(a, maxazipos), *range(0, b + 1)]\n else:\n if a > b:\n return list(range(a, b - 1, -1))\n else:\n return [*range(a, -1, -1), *range(maxazipos - 1, b - 1, -1)]\n\n if ang1 > ang2:\n dist1 = ang1 - ang2\n dist2 = maxazipos - dist1\n mid1 = ang1 + dist1 // 2\n if mid1 >= maxazipos:\n mid1 -= maxazipos\n\n mid2 = ang1 - dist2 // 2\n if mid2 < 0:\n mid2 += maxazipos\n\n quad = [None] * 4\n if not full:\n quad[0] = get_sl(ang1, mid1, 1)\n quad[1] = get_sl(ang1, mid2, -1)\n quad[2] = get_sl(ang2, mid2, 1)\n quad[3] = get_sl(ang2, mid1, -1)\n else:\n quad[0] = get_sl(ang1, ang2, 1)\n quad[1] = get_sl(ang1, ang2, -1)\n quad[2] = get_sl(ang2, ang1, 1)\n quad[3] = get_sl(ang2, ang1, -1)\n\n else:\n dist1 = ang2 - ang1\n dist2 = maxazipos - dist1\n mid1 = ang1 + dist1 // 2\n if mid1 >= maxazipos:\n mid1 -= maxazipos\n\n mid2 = ang1 - dist2 // 2\n if mid2 < 0:\n mid2 += maxazipos\n\n quad = [None] * 4\n if not full:\n quad[0] = get_sl(ang1, mid1, 1)\n quad[1] = get_sl(ang1, mid2, -1)\n quad[2] = get_sl(ang2, mid2, 1)\n quad[3] = get_sl(ang2, mid1, -1)\n else:\n quad[0] = get_sl(ang1, ang2, 1)\n quad[1] = get_sl(ang1, ang2, -1)\n quad[2] = get_sl(ang2, ang1, 1)\n quad[3] = get_sl(ang2, ang1, -1)\n\n return quad","def _determine_quadrant(self, row, column) -> QuadrantEnum:\n if row < 4 and column < 5:\n return QuadrantEnum.TOP_LEFT\n elif row < 4 and column >= 5:\n return QuadrantEnum.TOP_RIGHT\n elif row >= 4 and column < 5:\n return QuadrantEnum.BOTTOM_LEFT\n else:\n return QuadrantEnum.BOTTOM_RIGHT","def fireEast(self):\n self.rotate('e')\n gun = Laser(self)\n gun.shoot('e')\n self.agent.actionCompleted()","def turnRightDiag(ev3):\n ev3.set_angle(\"A\", \"30\", \"45\")\n ev3.set_angle(\"B\", \"-30\", \"-45\")\n ev3.set_angle(\"C\", \"30\", \"45\")","def Arc( x, y0, y1, r):\n return 0.5 * r*r * ( np.arctan( (y1).astype(float)/(x).astype(float) ) - np.arctan( (y0).astype(float)/(x).astype(float) ) )","def mark_sq4(self):\n self.drive_inches(8.5, 400)\n self.turn_degrees(90, 400)\n self.drive_inches(6.5, 400)\n ev3.Sound.speak('Place Mark').wait()\n self.arm_calibration()\n self.drive_inches(-6.5, 400)\n self.turn_degrees(-90, 400)\n self.drive_inches(-8.5, 400)","def __around_long_row(self):\n list_of_cord = []\n for i in range(-self.rad, self.rad + 1):\n for j in range(-self.rad, self.rad + 1):\n if (i == 0 and j == 0) or (i != 0 and j == 1):\n continue\n list_of_cord.append((i, j))\n return list_of_cord","def checkRing(self, verbose = 0):\n angleSum = self.tfs.ANGLE.sum()\n if self.verbose: print (\"check\")\n print (\"---------------------------------- \\n Checking, if ring is closed: \\n\", \"angleSum = \", angleSum)\n twoPi = 2*pi\n \n if angleSum != twoPi:\n fudge = 2*pi - angleSum\n print (\" ** Ring not closed - offset of: \", fudge)","def __bcc_left_diagonals(self) -> cq.cq.Workplane:\n # In a cuboid ABCDA1B1C1D1 this is the angle C1AD\n #angle_C1AD = 90 - degrees(acos(2**-.5))\n angle_C1AD = 90 - degrees(acos(0.5))\n angle_CAD = 90 - degrees(acos(sqrt(2/3)))\n pseudo_unit_cell_size = sqrt(2/3)*self.unit_cell_size\n corner_points = np.array(\n [(0, 0),\n (self.bcc_unit_cell_size, 0),\n (self.bcc_unit_cell_size, self.unit_cell_size),\n (0, self.unit_cell_size)]\n )\n result = (\n cq.Workplane(\"XY\")\n .pushPoints(corner_points)\n .eachpointAdaptive(\n create_bcc_diagonal_strut,\n callback_extra_args = [\n {\"unit_cell_size\": pseudo_unit_cell_size,\n \"radius\": self.strut_radius,\n \"angle_x\": - angle_CAD,\n \"angle_y\": angle_C1AD},\n {\"unit_cell_size\": 0.5 * pseudo_unit_cell_size,\n \"radius\": self.strut_radius,\n \"angle_x\": - angle_CAD,\n \"angle_y\": - angle_C1AD},\n {\"unit_cell_size\": 0.5 * pseudo_unit_cell_size,\n \"radius\": self.strut_radius,\n \"angle_x\": angle_CAD,\n \"angle_y\": - angle_C1AD},\n {\"unit_cell_size\": pseudo_unit_cell_size,\n \"radius\": self.strut_radius,\n \"angle_x\": angle_CAD,\n \"angle_y\": angle_C1AD}\n ],\n useLocalCoords = True\n )\n )\n return result","def quadrant(pAx, pAy, pBx, pBy):\n###############################################################################\n\n if (pBx>pAx and pBy>pAy):\n return 1\n elif (pBx<pAx and pBy>pAy):\n return 2\n elif (pBx<pAx and pBy<pAy):\n return 3\n elif (pBx>pAx and pBy<pAy):\n return 4\n else:\n return 0","def area_circle(l):\n a = math.pi * ((l / 2) ** 2)\n return a","def closer_ang(x,a,dir=0):\r\n if dir == 0:\r\n return a + smaller_ang(x-a)\r\n elif dir == 1:\r\n return a + (x-a)%(2*pi)\r\n elif dir == -1:\r\n return a + (x-a)%(2*pi) - 2*pi","def test_euler_angles_1q_hard_thetas(self, gate):\n self.check_one_qubit_euler_angles(Operator(gate))","def _O_and_O2_correction(self, alt):\n _O_and_O2_correction_fast(alt, self.Texo)","def rayleigh_noscale(th):\n c = np.cos(th)\n c2 = c**2\n return 0.5*np.array([[c2+1 , c2-1 , 0 , 0],\n [c2-1 , c2+1 , 0 , 0],\n [0 , 0 , 2*c , 0],\n [0 , 0 , 0 , 2*c]])","def rotate_quadrant(self, quadrant, direction):\n direction = Direction(direction)\n self.play_area[quadrant].rotate(direction)","def doubleClick(self, event):\n doRotation = False\n\n self.can.focus_force()\n interCircle = self.findInter(event.x, event.y)\n if interCircle:\n xa, ya, xb, yb = self.can.coords(interCircle)\n inter = ((xa + xb)/2, (ya + yb)/2)\n for seg in self.segs:\n if (not doRotation) and (seg.getStartPoint() == inter):\n doRotation = True\n lastInter = inter\n if doRotation:\n seg.place(lastInter)\n seg.rotate(pi/2)\n lastInter = seg.getEndPoint()\n\n self.wipe(self.segs)","def _H_correction(self, alt):\n _H_correction_fast(alt, self.Texo)","def long(self, amount):","def GetHiCorner(self):\n ...","def drawE8(\n pl=57, ## Parallel length\n gw=12.5, ## Gauge width\n tw=20, ## Grip width\n tl=50.0, ## Grip length\n rd=12.5, ## Radius\n):\n import numpy as np\n A = tw/2. - gw/2.\n th = -90.-np.arccos((rd-A)/rd)*180./np.pi\n x = rd * np.sin(th*np.pi/180.)\n ## Round...\n th0=-90\n th_delta=np.arccos((rd-A)/rd)*180/np.pi\n th1=th0+th_delta\n ths=np.linspace(th0*np.pi/180.,th1*np.pi/180.)\n xs = rd*np.cos(ths)\n ys = rd*np.sin(ths)\n ## translate xs,ys\n xs = xs + (x-xs[-1])\n ys = ys + (-A+tw-ys[-1])\n xyRound=[xs.tolist(),ys.tolist()]\n \n \n ## parallel\n x0,y0=xs[0],ys[0]\n xyParallel = [[x0-0.5*pl,x0],[y0,y0]]\n \n ## Right grip\n XS=[x+tl,x+tl,x][::-1]\n YS=[-A+0.5*tw,-A+tw,-A+tw][::-1]\n xyRG=[XS,YS]\n \n x=xyParallel[0]+xyRound[0]+xyRG[0]\n y=xyParallel[1]+xyRound[1]+xyRG[1]\n \n xyCoords=np.array([x,y])\n \n # print xyCoords.shape\n \n ## translate the coordinate so that the center of gravity is (0,0)\n xyCoords[0]=xyCoords[0]-xyCoords[0][0]\n xyCoords[1]=xyCoords[1]-xyCoords[1][-1]\n # plot(xyCoords[0],xyCoords[1],'-')\n \n ## Apply 2-fold symmetry.\n sym0 =[[ 1,0],[0, 1]] ## Identical\n sym1 =[[-1,0],[0, 1]] ## Reflect y axis\n sym2 =[[ 1,0],[0,-1]] ## Reflect x axis\n sym3 =[[-1,0],[0,-1]] ## Reflect origin\n \n sym = np.array([sym0,sym2,sym3,sym1])\n # plot(xyCoords[0,0],xyCoords[1,0],'x')\n\n xyTot=[[],[]]\n for i in range(len(sym)):\n symOp = sym[i][:,:]# (2,2)\n temp = np.tensordot(symOp,xyCoords,axes=[1,0])\n if i==1 or i==3:\n temp[0]=temp[0][::-1]\n temp[1]=temp[1][::-1]\n elif i==0 or i==2:\n temp=temp[::]\n\n for j in range(len(temp[0])):\n xyTot[0].append(temp[0][j])\n xyTot[1].append(temp[1][j])\n\n xyTot=np.array(xyTot)\n\n\n x0=min(xyTot[0])\n y0=min(xyTot[1])+tw/2.\n\n xyTot[0] = xyTot[0] - x0\n xyTot[1] = xyTot[1] - y0\n\n return xyTot","def arm1_maker(size=60, color='0x9C661F'):\n arm = GArc(size, size+30, 100, 200)\n arm.filled = True\n arm.fill_color = color\n return arm","def polar_tth_corr_map_rygg_pinhole(tth, eta, instrument, absorption_length,\n pinhole_thickness, pinhole_radius,\n num_phi_elements=60):\n panels = list(instrument.detectors.values())\n return calc_tth_rygg_pinhole(panels, absorption_length, tth, eta,\n pinhole_thickness, pinhole_radius,\n num_phi_elements) - tth","def area(r):\n return np.pi * (r ** 2)","def test_euler_angles_1q_clifford(self, clifford):\n self.check_one_qubit_euler_angles(clifford)","def arccosh(a):","def right_twist(self):\n self.turn_by_deg(180)\n #time.sleep(.1)\n self.stop()\n self.turn_by_deg(180)\n #time.sleep(.1)\n self.stop()","def increase_right_boundary(self):\n self.R = self.R + 1.0\n self.Ne = self.Ne + 1","def diag():\n tt.left(90)\n tt.forward(50)\n tt.left(135)\n tt.down()\n tt.forward(50*sqrt(2))\n tt.up()\n tt.left(135)\n tt.forward(60)","def question_c():\n 4*math.pi*(r**2)","def test_wrap_at_180():\n spiral_arm = survey.get_spiral_slice(track = \"CrF\", \n wrap_at_180 = True)\n spiral_arm2 = survey.get_spiral_slice(track = \"Carina_far\", \n wrap_at_180 = True)\n\n assert np.allclose(spiral_arm[\"INTEN\"], spiral_arm2[\"INTEN\"], equal_nan = True)","def _is_trivial_angle(rad: float, atol: float) -> bool:\n return abs(rad) < atol or abs(abs(rad) - np.pi / 4) < atol","def choice_4(side_ac, side_cb, angle_acb, precision):\r\n c_squared = math.pow(side_cb, 2) + math.pow(side_ac, 2) - 2 * side_cb * side_ac * \\\r\n math.cos(math.radians(angle_acb))\r\n side_ab = math.sqrt(c_squared)\r\n side_ab = '{:.{prec}f}'.format(side_ab, prec=precision)\r\n print(\"Side AB is \" + str(side_ab) + \"\\n\")","def arc(r, mv_direction):\n \n vert_amount = 80\n arc_vert_amount = int(vert_amount / 2);\n edge = 2 * r * math.sin(math.radians(360 / (2 * vert_amount)))\n polygon_angle = (vert_amount - 2) / vert_amount * 180\n angle = 180 - polygon_angle\n \n for i in range(arc_vert_amount):\n if i == 0: \n rotate_turtle(polygon_angle / 2, not mv_direction)\n else:\n rotate_turtle(angle, mv_direction)\n turtle.forward(edge)","def create_rink():\n\n # RINK\n coords = OFFSET, OFFSET, OFFSET+22*SCALE, OFFSET+22*SCALE\n canvas.create_arc(coords, start=90, extent=90, fill=WHITE, outline=\"\")\n coords = OFFSET, HEIGHT-OFFSET-22*SCALE, OFFSET+22*SCALE, HEIGHT-OFFSET\n canvas.create_arc(coords, start=180, extent=90, fill=WHITE, outline=WHITE)\n coords = WIDTH-OFFSET-22*SCALE, HEIGHT-OFFSET-22*SCALE, WIDTH-OFFSET, HEIGHT-OFFSET\n canvas.create_arc(coords, start=270, extent=90, fill=WHITE, outline=WHITE)\n coords = WIDTH-OFFSET-22*SCALE, OFFSET, WIDTH-OFFSET, OFFSET+22*SCALE\n canvas.create_arc(coords, start=0, extent=90, fill=WHITE, outline=WHITE)\n coords = OFFSET+11*SCALE, OFFSET, WIDTH-OFFSET-11*SCALE, OFFSET, WIDTH-OFFSET-11*SCALE, HEIGHT-OFFSET, OFFSET+11*SCALE, HEIGHT-OFFSET\n canvas.create_polygon(coords, fill=WHITE, outline=WHITE)\n coords = OFFSET, OFFSET+11*SCALE, WIDTH-OFFSET, OFFSET+11*SCALE, WIDTH-OFFSET, HEIGHT-OFFSET-11*SCALE, OFFSET, HEIGHT-OFFSET-11*SCALE\n canvas.create_polygon(coords, fill=WHITE, outline=WHITE)\n\n # CENTER CIRCLE\n coords = WIDTH/2-15*SCALE, HEIGHT/2-15*SCALE, WIDTH/2+15*SCALE, HEIGHT/2+15*SCALE\n canvas.create_oval(coords, outline=BLUE, width=2, fill=WHITE)\n\n # HALF CENTER CIRCLE\n coords = WIDTH/2-10*SCALE, HEIGHT-OFFSET-10*SCALE, WIDTH/2+10*SCALE, HEIGHT-OFFSET+10*SCALE\n canvas.create_arc(coords, outline=RED, width=2, start=0, extent=180)\n\n # GOAL AREA\n # - Left\n # - - Crease\n coords = OFFSET+5*SCALE, HEIGHT/2-6*SCALE, OFFSET+17*SCALE, HEIGHT/2+6*SCALE\n canvas.create_arc(coords, fill=LIGHT_BLUE, start=318, extent=84, outline=\"\")\n canvas.create_arc(coords, outline=RED, start=318, extent=84, style=ARC)\n coords = OFFSET+11*SCALE, HEIGHT/2-4*SCALE, OFFSET+15.5*SCALE, HEIGHT/2-4*SCALE, OFFSET+15.5*SCALE, HEIGHT/2+4*SCALE, OFFSET+11*SCALE, HEIGHT/2+4*SCALE\n canvas.create_polygon(coords, fill=LIGHT_BLUE, outline=\"\")\n coords = OFFSET+11*SCALE, HEIGHT/2-4*SCALE, OFFSET+15.2*SCALE+1, HEIGHT/2-4*SCALE\n canvas.create_line(coords, fill=RED)\n coords = OFFSET+15.2*SCALE+1, HEIGHT/2+4*SCALE, OFFSET+11*SCALE, HEIGHT/2+4*SCALE\n canvas.create_line(coords, fill=RED)\n # - - Restricted Area\n coords = OFFSET, HEIGHT/2-14*SCALE, OFFSET+11*SCALE, HEIGHT/2-9*SCALE\n canvas.create_line(coords, fill=RED)\n coords = OFFSET, HEIGHT/2+14*SCALE, OFFSET+11*SCALE, HEIGHT/2+9*SCALE\n canvas.create_line(coords, fill=RED)\n # - - Goal\n coords = OFFSET+8*SCALE, HEIGHT/2-3*SCALE, OFFSET+11*SCALE, HEIGHT/2-3*SCALE, OFFSET+11*SCALE, HEIGHT/2+3*SCALE, OFFSET+8*SCALE, HEIGHT/2+3*SCALE\n canvas.create_polygon(coords, fill=GRAY, outline=RED)\n # - Right\n # - - Crease\n coords = WIDTH-(OFFSET+5*SCALE), HEIGHT/2-6*SCALE, WIDTH-(OFFSET+17*SCALE), HEIGHT/2+6*SCALE\n canvas.create_arc(coords, fill=LIGHT_BLUE, start=138, extent=84, outline=\"\")\n canvas.create_arc(coords, outline=RED, start=138, extent=84, style=ARC)\n coords = WIDTH-(OFFSET+11*SCALE), HEIGHT/2-4*SCALE, WIDTH-(OFFSET+15.5*SCALE), HEIGHT/2-4*SCALE, WIDTH-(OFFSET+15.5*SCALE), HEIGHT/2+4*SCALE, WIDTH-(OFFSET+11*SCALE), HEIGHT/2+4*SCALE\n canvas.create_polygon(coords, fill=LIGHT_BLUE, outline=\"\")\n coords = WIDTH-(OFFSET+11*SCALE), HEIGHT/2-4*SCALE, WIDTH-(OFFSET+15.2*SCALE+1), HEIGHT/2-4*SCALE\n canvas.create_line(coords, fill=RED)\n coords = WIDTH-(OFFSET+15.2*SCALE+1), HEIGHT/2+4*SCALE, WIDTH-(OFFSET+11*SCALE), HEIGHT/2+4*SCALE\n canvas.create_line(coords, fill=RED)\n # - - Restricted Area\n coords = WIDTH-OFFSET, HEIGHT/2-14*SCALE, WIDTH-OFFSET-11*SCALE, HEIGHT/2-9*SCALE\n canvas.create_line(coords, fill=RED)\n coords = WIDTH-OFFSET, HEIGHT/2+14*SCALE, WIDTH-OFFSET-11*SCALE, HEIGHT/2+9*SCALE\n canvas.create_line(coords, fill=RED)\n # - - Goal\n coords = WIDTH-(OFFSET+8*SCALE), HEIGHT/2-3*SCALE, WIDTH-(OFFSET+11*SCALE), HEIGHT/2-3*SCALE, WIDTH-(OFFSET+11*SCALE), HEIGHT/2+3*SCALE, WIDTH-(OFFSET+8*SCALE), HEIGHT/2+3*SCALE\n canvas.create_polygon(coords, fill=GRAY, outline=RED)\n\n # LINES\n # - Left Baseline\n coords = OFFSET+11*SCALE, OFFSET, OFFSET+11*SCALE, HEIGHT-OFFSET\n canvas.create_line(coords, fill=RED, width=1.5)\n # - Right Baseline\n coords = WIDTH-OFFSET-11*SCALE, OFFSET, WIDTH-OFFSET-11*SCALE, HEIGHT-OFFSET\n canvas.create_line(coords, fill=RED, width=1.5)\n # - Left Blueline\n coords = OFFSET+70*SCALE, OFFSET, OFFSET+70*SCALE, HEIGHT-OFFSET\n canvas.create_line(coords, fill=BLUE, width=7)\n # - Right Blueline\n coords = WIDTH-(OFFSET+70*SCALE), OFFSET, WIDTH-(OFFSET+70*SCALE), HEIGHT-OFFSET\n canvas.create_line(coords, fill=BLUE, width=7)\n # - Redline\n coords = WIDTH/2, OFFSET, WIDTH/2, HEIGHT-OFFSET\n canvas.create_line(coords, fill=RED, width=7)\n coords = WIDTH/2, OFFSET, WIDTH/2, HEIGHT-OFFSET\n canvas.create_line(coords, fill=WHITE, width=5, dash=(9,9))\n\n # RINK OUTLINE\n coords = OFFSET, OFFSET, OFFSET+22*SCALE, OFFSET+22*SCALE\n canvas.create_arc(coords, start=90, extent=90, outline=BLACK, style=ARC, width=2)\n coords = OFFSET, HEIGHT-OFFSET-22*SCALE, OFFSET+22*SCALE, HEIGHT-OFFSET\n canvas.create_arc(coords, start=180, extent=90, outline=BLACK, style=ARC, width=2)\n coords = WIDTH-OFFSET-22*SCALE, HEIGHT-OFFSET-22*SCALE, WIDTH-OFFSET, HEIGHT-OFFSET\n canvas.create_arc(coords, start=270, extent=90, outline=BLACK, style=ARC, width=2)\n coords = WIDTH-OFFSET-22*SCALE, OFFSET, WIDTH-OFFSET, OFFSET+22*SCALE\n canvas.create_arc(coords, start=0, extent=90, outline=BLACK, style=ARC, width=2)\n coords = OFFSET+11*SCALE, OFFSET, WIDTH-OFFSET-11*SCALE, OFFSET\n canvas.create_line(coords, fill=BLACK, width=2)\n coords = WIDTH-OFFSET, OFFSET+11*SCALE, WIDTH-OFFSET, HEIGHT-OFFSET-11*SCALE\n canvas.create_line(coords, fill=BLACK, width=2)\n coords = WIDTH-OFFSET-11*SCALE, HEIGHT-OFFSET, OFFSET+11*SCALE, HEIGHT-OFFSET\n canvas.create_line(coords, fill=BLACK, width=2)\n coords = OFFSET, OFFSET+11*SCALE, OFFSET, HEIGHT-OFFSET-11*SCALE\n canvas.create_line(coords, fill=BLACK, width=2)\n\n\n # CENTER DOT\n coords = WIDTH/2-1*SCALE-1, HEIGHT/2-1*SCALE-1, WIDTH/2+1*SCALE+1, HEIGHT/2+1*SCALE+1\n canvas.create_oval(coords, outline=WHITE, fill=BLUE)\n\n # FACEOFF\n # - Top Left\n # - - Ticks\n coords = OFFSET+29.5*SCALE, HEIGHT/2-39*SCALE, OFFSET+29.5*SCALE, HEIGHT/2-5*SCALE\n canvas.create_line(coords, fill=RED, width=2)\n coords = OFFSET+32.5*SCALE, HEIGHT/2-39*SCALE, OFFSET+32.5*SCALE, HEIGHT/2-5*SCALE\n canvas.create_line(coords, fill=RED, width=2)\n # - - Circles\n coords = OFFSET+16*SCALE, HEIGHT/2-37*SCALE, OFFSET+46*SCALE, HEIGHT/2-7*SCALE\n canvas.create_oval(coords, outline=RED, width=2, fill=WHITE)\n coords = OFFSET+30*SCALE, HEIGHT/2-23*SCALE, OFFSET+32*SCALE, HEIGHT/2-21*SCALE\n canvas.create_oval(coords, fill=RED, outline=\"\")\n # - - Cross\n coords = OFFSET+25*SCALE, HEIGHT/2-22.8*SCALE, OFFSET+29*SCALE, HEIGHT/2-22.8*SCALE, OFFSET+29*SCALE, HEIGHT/2-25.8*SCALE\n canvas.create_line(coords, fill=RED, width=2)\n coords = OFFSET+25*SCALE, HEIGHT/2-21.2*SCALE, OFFSET+29*SCALE, HEIGHT/2-21.2*SCALE, OFFSET+29*SCALE, HEIGHT/2-18.2*SCALE\n canvas.create_line(coords, fill=RED, width=2)\n coords = OFFSET+37*SCALE, HEIGHT/2-22.8*SCALE, OFFSET+33*SCALE, HEIGHT/2-22.8*SCALE, OFFSET+33*SCALE, HEIGHT/2-25.8*SCALE\n canvas.create_line(coords, fill=RED, width=2)\n coords = OFFSET+37*SCALE, HEIGHT/2-21.2*SCALE, OFFSET+33*SCALE, HEIGHT/2-21.2*SCALE, OFFSET+33*SCALE, HEIGHT/2-18.2*SCALE\n canvas.create_line(coords, fill=RED, width=2)\n # - Bottom Left\n # - - Ticks\n coords = OFFSET+29.5*SCALE, HEIGHT/2+39*SCALE, OFFSET+29.5*SCALE, HEIGHT/2+5*SCALE\n canvas.create_line(coords, fill=RED, width=2)\n coords = OFFSET+32.5*SCALE, HEIGHT/2+39*SCALE, OFFSET+32.5*SCALE, HEIGHT/2+5*SCALE\n canvas.create_line(coords, fill=RED, width=2)\n # - - Circles\n coords = OFFSET+16*SCALE, HEIGHT/2+37*SCALE, OFFSET+46*SCALE, HEIGHT/2+7*SCALE\n canvas.create_oval(coords, outline=RED, width=2, fill=WHITE)\n coords = OFFSET+30*SCALE, HEIGHT/2+23*SCALE, OFFSET+32*SCALE, HEIGHT/2+21*SCALE\n canvas.create_oval(coords, fill=RED, outline=\"\")\n # - - Cross\n coords = OFFSET+25*SCALE, HEIGHT/2+22.8*SCALE, OFFSET+29*SCALE, HEIGHT/2+22.8*SCALE, OFFSET+29*SCALE, HEIGHT/2+25.8*SCALE\n canvas.create_line(coords, fill=RED, width=2)\n coords = OFFSET+25*SCALE, HEIGHT/2+21.2*SCALE, OFFSET+29*SCALE, HEIGHT/2+21.2*SCALE, OFFSET+29*SCALE, HEIGHT/2+18.2*SCALE\n canvas.create_line(coords, fill=RED, width=2)\n coords = OFFSET+37*SCALE, HEIGHT/2+22.8*SCALE, OFFSET+33*SCALE, HEIGHT/2+22.8*SCALE, OFFSET+33*SCALE, HEIGHT/2+25.8*SCALE\n canvas.create_line(coords, fill=RED, width=2)\n coords = OFFSET+37*SCALE, HEIGHT/2+21.2*SCALE, OFFSET+33*SCALE, HEIGHT/2+21.2*SCALE, OFFSET+33*SCALE, HEIGHT/2+18.2*SCALE\n canvas.create_line(coords, fill=RED, width=2)\n # - Top Right\n # - - Ticks\n coords = WIDTH-(OFFSET+29.5*SCALE), HEIGHT/2-39*SCALE, WIDTH-(OFFSET+29.5*SCALE), HEIGHT/2-5*SCALE\n canvas.create_line(coords, fill=RED, width=2)\n coords = WIDTH-(OFFSET+32.5*SCALE), HEIGHT/2-39*SCALE, WIDTH-(OFFSET+32.5*SCALE), HEIGHT/2-5*SCALE\n canvas.create_line(coords, fill=RED, width=2)\n # - - Circles\n coords = WIDTH-(OFFSET+16*SCALE), HEIGHT/2-37*SCALE, WIDTH-(OFFSET+46*SCALE), HEIGHT/2-7*SCALE\n canvas.create_oval(coords, outline=RED, width=2, fill=WHITE)\n coords = WIDTH-(OFFSET+30*SCALE), HEIGHT/2-23*SCALE, WIDTH-(OFFSET+32*SCALE), HEIGHT/2-21*SCALE\n canvas.create_oval(coords, fill=RED, outline=\"\")\n # - - Cross\n coords = WIDTH-(OFFSET+25*SCALE), HEIGHT/2-22.8*SCALE, WIDTH-(OFFSET+29*SCALE), HEIGHT/2-22.8*SCALE, WIDTH-(OFFSET+29*SCALE), HEIGHT/2-25.8*SCALE\n canvas.create_line(coords, fill=RED, width=2)\n coords = WIDTH-(OFFSET+25*SCALE), HEIGHT/2-21.2*SCALE, WIDTH-(OFFSET+29*SCALE), HEIGHT/2-21.2*SCALE, WIDTH-(OFFSET+29*SCALE), HEIGHT/2-18.2*SCALE\n canvas.create_line(coords, fill=RED, width=2)\n coords = WIDTH-(OFFSET+37*SCALE), HEIGHT/2-22.8*SCALE, WIDTH-(OFFSET+33*SCALE), HEIGHT/2-22.8*SCALE, WIDTH-(OFFSET+33*SCALE), HEIGHT/2-25.8*SCALE\n canvas.create_line(coords, fill=RED, width=2)\n coords = WIDTH-(OFFSET+37*SCALE), HEIGHT/2-21.2*SCALE, WIDTH-(OFFSET+33*SCALE), HEIGHT/2-21.2*SCALE, WIDTH-(OFFSET+33*SCALE), HEIGHT/2-18.2*SCALE\n canvas.create_line(coords, fill=RED, width=2)\n # - Bottom Right\n # - - Ticks\n coords = WIDTH-(OFFSET+29.5*SCALE), HEIGHT/2+39*SCALE, WIDTH-(OFFSET+29.5*SCALE), HEIGHT/2+5*SCALE\n canvas.create_line(coords, fill=RED, width=2)\n coords = WIDTH-(OFFSET+32.5*SCALE), HEIGHT/2+39*SCALE, WIDTH-(OFFSET+32.5*SCALE), HEIGHT/2+5*SCALE\n canvas.create_line(coords, fill=RED, width=2)\n # - - Circles\n coords = WIDTH-(OFFSET+16*SCALE), HEIGHT/2+37*SCALE, WIDTH-(OFFSET+46*SCALE), HEIGHT/2+7*SCALE\n canvas.create_oval(coords, outline=RED, width=2, fill=WHITE)\n coords = WIDTH-(OFFSET+30*SCALE), HEIGHT/2+23*SCALE, WIDTH-(OFFSET+32*SCALE), HEIGHT/2+21*SCALE\n canvas.create_oval(coords, fill=RED, outline=\"\")\n # - - Cross\n coords = WIDTH-(OFFSET+25*SCALE), HEIGHT/2+22.8*SCALE, WIDTH-(OFFSET+29*SCALE), HEIGHT/2+22.8*SCALE, WIDTH-(OFFSET+29*SCALE), HEIGHT/2+25.8*SCALE\n canvas.create_line(coords, fill=RED, width=2)\n coords = WIDTH-(OFFSET+25*SCALE), HEIGHT/2+21.2*SCALE, WIDTH-(OFFSET+29*SCALE), HEIGHT/2+21.2*SCALE, WIDTH-(OFFSET+29*SCALE), HEIGHT/2+18.2*SCALE\n canvas.create_line(coords, fill=RED, width=2)\n coords = WIDTH-(OFFSET+37*SCALE), HEIGHT/2+22.8*SCALE, WIDTH-(OFFSET+33*SCALE), HEIGHT/2+22.8*SCALE, WIDTH-(OFFSET+33*SCALE), HEIGHT/2+25.8*SCALE\n canvas.create_line(coords, fill=RED, width=2)\n coords = WIDTH-(OFFSET+37*SCALE), HEIGHT/2+21.2*SCALE, WIDTH-(OFFSET+33*SCALE), HEIGHT/2+21.2*SCALE, WIDTH-(OFFSET+33*SCALE), HEIGHT/2+18.2*SCALE\n canvas.create_line(coords, fill=RED, width=2)\n\n # NEUTRAL ZONE FACEOFF\n # - Top Left\n coords = WIDTH/2-21*SCALE, HEIGHT/2-23*SCALE, WIDTH/2-19*SCALE, HEIGHT/2-21*SCALE\n canvas.create_oval(coords, outline=\"\", fill=RED)\n # - Bottom Left\n coords = WIDTH/2-21*SCALE, HEIGHT/2+23*SCALE, WIDTH/2-19*SCALE, HEIGHT/2+21*SCALE\n canvas.create_oval(coords, outline=\"\", fill=RED)\n # - Top Right\n coords = WIDTH/2+21*SCALE, HEIGHT/2-23*SCALE, WIDTH/2+19*SCALE, HEIGHT/2-21*SCALE\n canvas.create_oval(coords, outline=\"\", fill=RED)\n # - Bottom Right\n coords = WIDTH/2+21*SCALE, HEIGHT/2+23*SCALE, WIDTH/2+19*SCALE, HEIGHT/2+21*SCALE\n canvas.create_oval(coords, outline=\"\", fill=RED)\n\n\n canvas.grid(row=1, columnspan=5)","def l8_refl_toa_band_func(dn, cos_theta, refl_mult, refl_add):\n refl_toa = np.copy(dn).astype(np.float64)\n refl_toa *= refl_mult\n refl_toa += refl_add\n refl_toa /= cos_theta\n np.clip(refl_toa, 0.0001, 1, out=refl_toa)\n return refl_toa","def _confined_angle_0(a):\n while a < 0:\n a += 2*_math.pi\n while a >= 2*_math.pi:\n a -= 2*_math.pi\n return a","def area(length, hypotenuse):\n side = int(length)* hypotenuse\n return round(side*2, 2) # returns the rounded area of the roof.","def _triangle_areas(self, point):\n vertex_0, vertex_1, vertex_2 = self._vertices(point)\n len_edge_12 = gs.linalg.norm((vertex_1 - vertex_2), axis=-1)\n len_edge_02 = gs.linalg.norm((vertex_0 - vertex_2), axis=-1)\n len_edge_01 = gs.linalg.norm((vertex_0 - vertex_1), axis=-1)\n half_perimeter = 0.5 * (len_edge_12 + len_edge_02 + len_edge_01)\n return gs.sqrt(\n (\n half_perimeter\n * (half_perimeter - len_edge_12)\n * (half_perimeter - len_edge_02)\n * (half_perimeter - len_edge_01)\n ).clip(min=1e-6)\n )","def __bcc_diagonals(self) -> cq.cq.Workplane:\n # In a cuboid ABCDA1B1C1D1 this is the angle C1AD\n #angle_C1AD = 90 - degrees(acos(2**-.5))\n angle_C1AD = 90 - degrees(acos(0.5))\n angle_CAD = 90 - degrees(acos(sqrt(2/3)))\n pseudo_unit_cell_size = sqrt(2/3)*self.unit_cell_size\n corner_points = np.array(\n [(0, 0),\n (self.bcc_unit_cell_size, 0),\n (self.bcc_unit_cell_size, self.unit_cell_size),\n (0, self.unit_cell_size)]\n )\n result = (\n cq.Workplane(\"XY\")\n .pushPoints(corner_points)\n .eachpointAdaptive(\n create_bcc_diagonal_strut,\n callback_extra_args = [\n {\"unit_cell_size\": pseudo_unit_cell_size,\n \"radius\": self.strut_radius,\n \"angle_x\": - angle_CAD,\n \"angle_y\": angle_C1AD},\n {\"unit_cell_size\": pseudo_unit_cell_size,\n \"radius\": self.strut_radius,\n \"angle_x\": - angle_CAD,\n \"angle_y\": - angle_C1AD},\n {\"unit_cell_size\": pseudo_unit_cell_size,\n \"radius\": self.strut_radius,\n \"angle_x\": angle_CAD,\n \"angle_y\": - angle_C1AD},\n {\"unit_cell_size\": pseudo_unit_cell_size,\n \"radius\": self.strut_radius,\n \"angle_x\": angle_CAD,\n \"angle_y\": angle_C1AD}\n ],\n useLocalCoords = True\n )\n )\n return result","def create_left_right_tangent(self):\n self.arc_incident_tan = Arc(\n start_angle = PI/2 + self.incident_angle,\n angle = PI/2 - self.incident_angle,\n radius = self.arc_incident_tan_radius,\n color = self.arc_incident_color,\n arc_center = self.mirror_origin\n )\n\n theta_in_tan_pos_offset = -2.0 * RIGHT + 0.8 * UP\n self.tex_theta_in_tan = TexMobject(r\"90^{\\circ}\",\n r\"-\",\n r\"\\theta_{i}\",\n color=self.tex_theta_in_color).\\\n move_to(self.mirror_origin + theta_in_tan_pos_offset)\n\n self.arc_reflected_tan = Arc(\n start_angle = 0,\n angle = PI/2 - self.reflected_angle,\n radius = self.arc_reflected_tan_radius,\n color = self.arc_reflected_color,\n arc_center = self.mirror_origin\n )\n\n theta_out_tan_pos_offset = 2.0 * RIGHT + 0.8 * UP\n self.tex_theta_ref_tan = TexMobject(r\"90^{\\circ}\",\n r\"-\",\n r\"\\theta_{r}\",\n color=self.tex_theta_ref_color).\\\n move_to(self.mirror_origin + theta_out_tan_pos_offset)","def test_fix_antimeridian(self):\n globe = self.read_feature('Global_Ocean')\n fc = FeatureCollection()\n name = 'Antarctic Box'\n feature = {\n 'type': 'Feature',\n 'properties': {\n 'name': name,\n 'tags': '',\n 'object': 'region',\n 'component': 'ocean',\n 'author': 'Xylar Asay-Davis'\n },\n 'geometry': {\n 'type': 'Polygon',\n 'coordinates': [\n [\n [\n 190.000000,\n -70.000000\n ],\n [\n 190.000000,\n -90.000000\n ],\n [\n 180.000000,\n -90.000000\n ],\n [\n 170.000000,\n -90.000000\n ],\n [\n 170.000000,\n -70.000000\n ],\n [\n 180.000000,\n -70.000000\n ],\n [\n 190.000000,\n -70.000000\n ]\n ]\n ]\n }\n }\n fc.add_feature(feature=feature)\n self.check_feature(fc.features[0],\n expected_name=name,\n expected_type='Polygon')\n fixed = fc.fix_antimeridian()\n self.check_feature(fixed.features[0],\n expected_name=name,\n expected_type='MultiPolygon')\n\n geom = globe.features[0]['geometry']\n globe_shape = shapely.geometry.shape(geom)\n\n geom = fixed.features[0]['geometry']\n shape = shapely.geometry.shape(geom)\n assert isinstance(shape, shapely.geometry.MultiPolygon)\n # make sure the fixed polygons are within -180 to 180 deg. lon.\n assert shapely.covers(globe_shape, shape)","def stokes_right_circular():\n return np.array([1, 0, 0, 1])","def quarter_chord(self) -> np.ndarray:\n return 0.75 * self.xyz_le + 0.25 * self.xyz_te()","def arc_n(self, xn ,yn, rn, start, stop):\n x = round(xn * self.width)\n y = round(yn * self.height)\n r = round(rn * min(self.width, self.height))\n self.arc(x, y, r, start, stop)","def draw_arc_outline(center_x, center_y, width, height, color, start_angle,\n end_angle, border_width=1, tilt_angle=0):\n num_segments = 128\n GL.glEnable(GL.GL_BLEND)\n GL.glBlendFunc(GL.GL_SRC_ALPHA, GL.GL_ONE_MINUS_SRC_ALPHA)\n GL.glEnable(GL.GL_LINE_SMOOTH)\n GL.glHint(GL.GL_LINE_SMOOTH_HINT, GL.GL_NICEST)\n GL.glHint(GL.GL_POLYGON_SMOOTH_HINT, GL.GL_NICEST)\n\n GL.glLoadIdentity()\n GL.glTranslatef(center_x, center_y, 0)\n GL.glRotatef(tilt_angle, 0, 0, 1)\n GL.glLineWidth(border_width)\n\n # Set color\n if len(color) == 4:\n GL.glColor4ub(color[0], color[1], color[2], color[3])\n elif len(color) == 3:\n GL.glColor4ub(color[0], color[1], color[2], 255)\n\n GL.glBegin(GL.GL_LINE_STRIP)\n\n start_segment = int(start_angle / 360 * num_segments)\n end_segment = int(end_angle / 360 * num_segments)\n\n for segment in range(start_segment, end_segment + 1):\n theta = 2.0 * 3.1415926 * segment / num_segments\n\n x = width * math.cos(theta)\n y = height * math.sin(theta)\n\n GL.glVertex3f(x, y, 0.5)\n\n GL.glEnd()\n GL.glLoadIdentity()","def step(self):\n r, c = self.ant_r, self.ant_c\n if self.grid[r][c] == LangtonAnt.WHITE:\n self.direction = rotate_counterclock(self.direction)\n self.grid[r][c] = LangtonAnt.BLACK\n else:\n self.direction = rotate_clockwise(self.direction)\n self.grid[r][c] = LangtonAnt.WHITE\n\n self.ant_r -= self.direction[1]\n self.ant_c += self.direction[0]","def nine_punishment(self):\n self.direction_clock_wise = not self.direction_clock_wise","def test_rhombus_area(self):\n self.assertEqual(17.5, rhombus_area(\n self.values['diagonal_1'], self.values['diagonal_2']))","def closer_angle(x, a, dir=0):\n if dir == 0:\n return a + smaller_angle(x-a)\n elif dir == 1:\n return a + (x-a)%(2*np.pi)\n elif dir == -1:\n return a + (x-a)%(2*np.pi) - 2*np.pi","def _confined_angle_pi(a):\n while a<-_math.pi:\n a+=2*_math.pi\n while a>=_math.pi:\n a-=2*_math.pi\n return a","def area_rectangulo(b,h):\n area = b*h\n print \"El area es: \",area","def getEdgeAngle():\n '''\n returns angle a\n a\n ◿\n b c\n '''\n ANGLE_OFFSET = 8 # How far off the angle measurements are in degrees.\n THRESHOLD = 220 # How much light must be reflected to 'notice' the desk.\n angle = 0\n while angle < panTilt.TLT_RANGE:\n angle += 1\n panTilt.tilt(int(angle))\n deskDetected = ir.readWithDelay()\n # print \"Angle:\", angle + ANGLE_OFFSET, \", ir reading:\", deskDetected\n if deskDetected > THRESHOLD or angle == panTilt.TLT_RANGE:\n # print \"-----------------------\"\n break # Break out of looking downwards loop\n panTilt.up() # Look up again\n return 90 - angle - ANGLE_OFFSET","def AddDimRadial(self,center,chordPnt,leaderLength):\n\t\treturn self.Space.AddDimRadial(center,chordPnt,leaderLength)","def slopecal(ton):\r\n global _ton_old\r\n global _slope\r\n\r\n print(\"ton: \", ton, \" _ton_old: \", _ton_old, \" substraction: \", round((ton - _ton_old),2))\r\n\r\n if round((ton - _ton_old), 2) >= 5:\r\n _slope = 1\r\n if round((ton - _ton_old), 2) <= -10:\r\n _slope = -1\r\n _ton_old = ton","def GetArc(arc):\r\n pass","def redfearn(lat, lon, false_easting=None, false_northing=None,\r\n zone=None, central_meridian=None, scale_factor=None):\r\n\r\n\r\n from math import pi, sqrt, sin, cos, tan\r\n \r\n\r\n\r\n #GDA Specifications\r\n a = 6378137.0 #Semi major axis\r\n inverse_flattening = 298.257222101 #1/f\r\n if scale_factor is None:\r\n K0 = 0.9996 #Central scale factor \r\n else:\r\n K0 = scale_factor\r\n #print 'scale', K0\r\n zone_width = 6 #Degrees\r\n\r\n longitude_of_central_meridian_zone0 = -183 \r\n longitude_of_western_edge_zone0 = -186\r\n\r\n if false_easting is None:\r\n false_easting = 500000\r\n\r\n if false_northing is None:\r\n if lat < 0:\r\n false_northing = 10000000 #Southern hemisphere\r\n else:\r\n false_northing = 0 #Northern hemisphere)\r\n \r\n \r\n #Derived constants\r\n f = 1.0/inverse_flattening\r\n b = a*(1-f) #Semi minor axis\r\n\r\n e2 = 2*f - f*f# = f*(2-f) = (a^2-b^2/a^2 #Eccentricity\r\n e = sqrt(e2)\r\n e2_ = e2/(1-e2) # = (a^2-b^2)/b^2 #Second eccentricity\r\n e_ = sqrt(e2_)\r\n e4 = e2*e2\r\n e6 = e2*e4\r\n\r\n #Foot point latitude\r\n n = (a-b)/(a+b) #Same as e2 - why ?\r\n n2 = n*n\r\n n3 = n*n2\r\n n4 = n2*n2\r\n\r\n G = a*(1-n)*(1-n2)*(1+9*n2/4+225*n4/64)*pi/180\r\n\r\n\r\n phi = lat*pi/180 #Convert latitude to radians\r\n\r\n sinphi = sin(phi) \r\n sin2phi = sin(2*phi)\r\n sin4phi = sin(4*phi)\r\n sin6phi = sin(6*phi)\r\n\r\n cosphi = cos(phi)\r\n cosphi2 = cosphi*cosphi\r\n cosphi3 = cosphi*cosphi2\r\n cosphi4 = cosphi2*cosphi2\r\n cosphi5 = cosphi*cosphi4 \r\n cosphi6 = cosphi2*cosphi4\r\n cosphi7 = cosphi*cosphi6\r\n cosphi8 = cosphi4*cosphi4 \r\n\r\n t = tan(phi)\r\n t2 = t*t\r\n t4 = t2*t2\r\n t6 = t2*t4\r\n \r\n #Radius of Curvature\r\n rho = a*(1-e2)/(1-e2*sinphi*sinphi)**1.5\r\n nu = a/(1-e2*sinphi*sinphi)**0.5\r\n psi = nu/rho\r\n psi2 = psi*psi\r\n psi3 = psi*psi2\r\n psi4 = psi2*psi2\r\n\r\n\r\n\r\n #Meridian distance\r\n\r\n A0 = 1 - e2/4 - 3*e4/64 - 5*e6/256\r\n A2 = 3.0/8*(e2+e4/4+15*e6/128)\r\n A4 = 15.0/256*(e4+3*e6/4)\r\n A6 = 35*e6/3072\r\n \r\n term1 = a*A0*phi\r\n term2 = -a*A2*sin2phi\r\n term3 = a*A4*sin4phi\r\n term4 = -a*A6*sin6phi\r\n\r\n m = term1 + term2 + term3 + term4 #OK\r\n\r\n if zone is not None and central_meridian is not None:\r\n msg = 'You specified both zone and central_meridian. Provide only one of them'\r\n raise Exception, msg\r\n \r\n # Zone\r\n if zone is None:\r\n zone = int((lon - longitude_of_western_edge_zone0)/zone_width)\r\n\r\n # Central meridian\r\n if central_meridian is None:\r\n central_meridian = zone*zone_width+longitude_of_central_meridian_zone0\r\n else:\r\n zone = -1\r\n\r\n omega = (lon-central_meridian)*pi/180 #Relative longitude (radians)\r\n omega2 = omega*omega\r\n omega3 = omega*omega2\r\n omega4 = omega2*omega2\r\n omega5 = omega*omega4\r\n omega6 = omega3*omega3\r\n omega7 = omega*omega6\r\n omega8 = omega4*omega4\r\n \r\n #Northing\r\n term1 = nu*sinphi*cosphi*omega2/2 \r\n term2 = nu*sinphi*cosphi3*(4*psi2+psi-t2)*omega4/24\r\n term3 = nu*sinphi*cosphi5*\\\r\n (8*psi4*(11-24*t2)-28*psi3*(1-6*t2)+\\\r\n psi2*(1-32*t2)-psi*2*t2+t4-t2)*omega6/720\r\n term4 = nu*sinphi*cosphi7*(1385-3111*t2+543*t4-t6)*omega8/40320\r\n northing = false_northing + K0*(m + term1 + term2 + term3 + term4)\r\n\r\n #Easting\r\n term1 = nu*omega*cosphi\r\n term2 = nu*cosphi3*(psi-t2)*omega3/6\r\n term3 = nu*cosphi5*(4*psi3*(1-6*t2)+psi2*(1+8*t2)-2*psi*t2+t4)*omega5/120\r\n term4 = nu*cosphi7*(61-479*t2+179*t4-t6)*omega7/5040\r\n easting = false_easting + K0*(term1 + term2 + term3 + term4)\r\n \r\n return zone, easting, northing","def arm_and_takeoff(vehicle, target_alt, loiter_time):\n util.log_info(\"Checking if armable.\")\n \n wait_count = 0\n while not vehicle.is_armable:\n time.sleep(.2)\n wait_count = wait_count + 1\n \n if wait_count % 25 == 0:\n util.log_warning(\"Vehicle not armable.\")\n \n if wait_count >= 100:\n util.log_warning(\"Unable to arm. Abort.\")\n shared.status['abort'] = True\n return False\n\n util.log_info(\"Switching to GUIDED and Arming.\")\n set_mode(vehicle, \"GUIDED\")\n\n util.log_debug(\"Arming...\")\n vehicle.armed = True\n time.sleep(3)\n \n wait_count = 0\n while True:\n time.sleep(.5)\n wait_count = wait_count + 1\n \n if vehicle.armed :\n util.log_info(\"Armed.\")\n break\n \n elif wait_count % 10 == 0:\n util.log_warning('Retry arming.')\n \n if wait_count >= 20:\n util.log_warning(\"Arming failed. Abort.\")\n shared.status['abort'] = True\n return False\n\n vehicle.simple_takeoff(target_alt) \n\n # Wait until the vehicle reaches a safe altitude (95%), or otherwise the command \n # after Vehicle.simple_takeoff will execute immediately, causing unexpected results.\n while True:\n util.log_debug(\"Altitude: %s\" % vehicle.location.global_relative_frame.alt) \n if vehicle.location.global_relative_frame.alt >= target_alt - shared.ALT_TOLERANCE:\n util.log_info(\"Target altitude reached: %s m.\" % vehicle.location.global_relative_frame.alt)\n break\n\n time.sleep(.5)\n \n time.sleep(loiter_time)\n return True","def decelOutsideBorder(self):\n if self.isOutsideBorder():\n if self.rotation == 0:\n self.currentAccel = 0\n else:\n self.currentAccel = self.currentAccel/1.01","def rad(area) :\n return sqrt(area/pi)","def test_polar_angle_normal_case(self):\n point1 = np.array([1, 1])\n point2 = np.array([2, 2])\n pol_angle = convex_hull.polar_angle(point2, point1)\n\n self.assertEqual(round(math.tan(pol_angle)), 1)"],"string":"[\n \"def place_rebar_long_torsion(as_tl_req, d):\\r\\n \\\"\\\"\\\"as_tl_req - area of longitudinal reinforcement required for torsion\\\"\\\"\\\"\\r\\n \\\"\\\"\\\"d - preferred diameter (this is initially the flexural rebar diameter. If not enough, chose one diameter above\\\"\\\"\\\"\\r\\n \\\"\\\"\\\"returns a list with [n, d] where n is number of bars and d diameter of bar\\\"\\\"\\\"\\r\\n\\r\\n diameters = [12, 16, 20, 25, 32, 40]\\r\\n ix = diameters.index(d)\\r\\n\\r\\n while ix < len(diameters)-1: # while loop to run through every diameters possible\\r\\n\\r\\n as_t = 4 * np.pi * d ** 2 / 4\\r\\n\\r\\n if as_t > as_tl_req: # in case provided area is enough, break\\r\\n a = [4, d]\\r\\n break\\r\\n\\r\\n else:\\r\\n d = diameters[ix+1]\\r\\n ix += 1\\r\\n\\r\\n if as_t < as_tl_req: # final check in case provided area is not enough\\r\\n a = [0, 0]\\r\\n\\r\\n return a\",\n \"def trapezoid_area(lower, leg , upper):\\n area = (((upper+lower)/2)*leg)\\n return area\",\n \"def GetLoCorner(self):\\n ...\",\n \"def Oneside( x, y0, y1, r):\\n\\n true = 1\\n size_x = np.shape( x )\\n if not size_x: size_x = [0]\\n\\n if size_x[ 0 ] == 0:\\n if x == 0: return x\\n elif abs( x ) >= r: return Arc( x, y0, y1, r )\\n yh = sqrt( r*r - x*x )\\n if ( y0 <= -yh ):\\n if ( y1 <= -yh ) : return Arc( x, y0, y1, r )\\n elif ( y1 <= yh ) : return Arc( x, y0, -yh, r ) \\\\\\n + Chord( x, -yh, y1 )\\n else : return Arc( x, y0, -yh, r ) \\\\\\n + Chord( x, -yh, yh ) + Arc( x, yh, y1, r )\\n \\n elif ( y0 < yh ):\\n if ( y1 <= -yh ) : return Chord( x, y0, -yh ) \\\\\\n + Arc( x, -yh, y1, r )\\n elif ( y1 <= yh ) : return Chord( x, y0, y1 )\\n else : return Chord( x, y0, yh ) + Arc( x, yh, y1, r )\\n\\n else :\\n if ( y1 <= -yh ) : return Arc( x, y0, yh, r ) \\\\\\n + Chord( x, yh, -yh ) + Arc( x, -yh, y1, r )\\n elif ( y1 <= yh ) : return Arc( x, y0, yh, r ) + Chord( x, yh, y1 )\\n else : return Arc( x, y0, y1, r )\\n\\n else :\\n ans2 = x\\n t0 = where( x == 0)[0]\\n count = len(t0)\\n if count == len( x ): return ans2\\n\\n ans = x * 0\\n yh = x * 0\\n to = where( abs( x ) >= r)[0]\\n tocount = len(to)\\n ti = where( abs( x ) < r)[0]\\n ticount = len(ti)\\n if tocount != 0: ans[ to ] = Arc( x[to], y0[to], y1[to], r )\\n if ticount == 0: return ans\\n \\n yh[ ti ] = sqrt( r*r - x[ti]*x[ti] )\\n \\n t1 = where( np.less_equal(y0[ti],-yh[ti]) )[0]\\n count = len(t1)\\n if count != 0:\\n i = ti[ t1 ]\\n\\n t2 = where( np.less_equal(y1[i],-yh[i]))[0]\\n count = len(t2)\\n if count != 0:\\n j = ti[ t1[ t2 ] ]\\n ans[j] = Arc( x[j], y0[j], y1[j], r )\\n\\n t2 = where( ( greater(y1[i],-yh[i]) ) &\\n ( less_equal(y1[i],yh[i]) ))[0]\\n count = len(t2)\\n if count != 0:\\n j = ti[ t1[ t2 ] ]\\n ans[j] = Arc( x[j], y0[j], -yh[j], r ) \\\\\\n + Chord( x[j], -yh[j], y1[j] )\\n\\n t2 = where( greater(y1[i], yh[i]) )[0]\\n count = len(t2)\\n\\n if count != 0:\\n j = ti[ t1[ t2 ] ]\\n ans[j] = Arc( x[j], y0[j], -yh[j], r ) \\\\\\n + Chord( x[j], -yh[j], yh[j] ) \\\\\\n + Arc( x[j], yh[j], y1[j], r )\\n \\n t1 = where( ( greater(y0[ti],-yh[ti]) ) & \\n ( less(y0[ti],yh[ti]) ))[0] \\n count = len(t1)\\n if count != 0:\\n i = ti[ t1 ]\\n\\n t2 = where( np.less_equal(y1[i],-yh[i]))[0]\\n count = len(t2)\\n if count != 0:\\n j = ti[ t1[ t2 ] ]\\n ans[j] = Chord( x[j], y0[j], -yh[j] ) \\\\\\n + Arc( x[j], -yh[j], y1[j], r )\\n \\n\\n t2 = where( ( greater(y1[i], -yh[i]) ) & \\n ( less_equal(y1[i], yh[i]) ))[0]\\n count = len(t2)\\n\\n if count != 0:\\n j = ti[ t1[ t2 ] ]\\n ans[j] = Chord( x[j], y0[j], y1[j] )\\n\\n t2 = where( greater(y1[i], yh[i]))[0]\\n count = len(t2)\\n if count != 0:\\n j = ti[ t1[ t2 ] ]\\n ans[j] = Chord( x[j], y0[j], yh[j] ) \\\\\\n + Arc( x[j], yh[j], y1[j], r )\\n\\n t1 = where( greater_equal(y0[ti], yh[ti]))[0] \\n count = len(t1)\\n if count != 0:\\n i = ti[ t1 ]\\n\\n t2 = where ( np.less_equal(y1[i], -yh[i]))[0] \\n count = len(t2)\\n if count != 0:\\n j = ti[ t1[ t2 ] ]\\n ans[j] = Arc( x[j], y0[j], yh[j], r ) \\\\\\n + Chord( x[j], yh[j], -yh[j] ) \\\\\\n + Arc( x[j], -yh[j], y1[j], r )\\n\\n t2 = where( ( greater(y1[i], -yh[i]) ) & \\n ( less_equal(y1[i], yh[i]) ))[0]\\n count = len(t2)\\n if count != 0:\\n j = ti[ t1[ t2 ] ]\\n ans[j] = Arc( x[j], y0[j], yh[j], r ) \\\\\\n + Chord( x[j], yh[j], y1[j] )\\n\\n t2 = where( greater(y1[i], yh[i]))[0]\\n count = len(t2)\\n if count != 0:\\n j = ti[ t1[ t2 ] ]\\n ans[j] = Arc( x[j], y0[j], y1[j], r )\\n\\n return ans\",\n \"def triangular_area():\\n print(1*1/2, 2*2/2, 3*3/2, 4*4/2, 5*5/2, 6*6/2, 7*7/2, 8*8/2, 9*9/2,\\n 10*10/2)\",\n \"def quarterarc_trench(self,r, width, gap, x0, y0, orient='NE', npoints=20):\\n inside = self.quarterarc(r, gap, x0, y0, orientation=orient, npoints=npoints)\\n outside = self.quarterarc(r + gap + width, gap, x0, y0, orientation=orient, \\n npoints=npoints)\\n return [inside, outside]\",\n \"def proz_manually ():\\r\\n Check_180turn(left_boundary,right_boundary)\\r\\n ABS() # Baseline correction \\r\\n XCMD(\\\"closeall\\\",WAIT_TILL_DONE)\",\n \"def halfarc_trench(self,r, width, gap, x0, y0, orient='E', npoints=40):\\n inside = self.halfarc(r, gap, x0, y0, orientation=orient, npoints=npoints)\\n outside = self.halfarc(r + gap + width, gap, x0, y0, orientation=orient, npoints=npoints)\\n return [inside, outside]\",\n \"def horizontal_arcs_iglu():\\n arc(screen, BLACK, (50, 560, 300, 20), 3.14, 0)\\n arc(screen, BLACK, (60, 510, 280, 20), 3.14, 0)\\n arc(screen, BLACK, (80, 460, 240, 20), 3.14, 0)\\n arc(screen, BLACK, (120, 420, 160, 20), 3.14, 0)\",\n \"def do_altangle(self):\\n nave = 10000\\n x, y, z, angle = cbp.phidget.main(nave)\\n current_angle = angle\\n #print(current_angle)\\n self.altangle = current_angle\\n return current_angle\",\n \"def settle(self):\\n if (self.angle >= self.max_angle) or (\\n self.angle <= -self.max_angle\\n ): # time to reverse\\n print(\\\"reverse\\\", self.angle, self.max_angle)\\n self.speed *= -0.9 # damped\\n self.max_angle *= 0.9\\n if self.speed > 0:\\n self.angle = self.max_angle\\n else:\\n self.angle = -self.max_angle\\n\\n self.angle += radians(self.speed)\\n print(self.angle, self.max_angle, self.speed)\\n self.x = self.cx + self.length * sin(self.angle)\\n self.y = self.cy + self.length * cos(self.angle)\",\n \"def echointro(self,longver_): # 3\\n res = self.__obj.echointro(longver_)\\n if res != 0:\\n raise Error(rescode(res),\\\"\\\")\",\n \"def lendiag(self):\\n if self.y <= self.x:\\n return self.y\\n else:\\n return self.x\",\n \"def LED_angle():\\n right = np.transpose(vision.pqr_l)\\n print(right)\\n if not right.size:\\n return\\n else:\\n angle = np.arctan2(right[0, 1], right[0, 0]) * 180 / pi\\n if angle > -15:\\n leds.off()\\n else:\\n leds.on()\",\n \"def check_angle_of_arcs(self):\\n\\n if self.thin_arc_start_angle >= 3600:\\n self.thin_arc_start_angle %= 360\\n self.thin_arc_start_angle += 360\\n\\n elif self.thin_arc_start_angle <= -3600:\\n self.thin_arc_start_angle %= 360\\n self.thin_arc_start_angle -= 360\\n\\n if self.thin_arc_end_angle >= 3600:\\n self.thin_arc_end_angle %= 360\\n self.thin_arc_end_angle += 360\\n\\n elif self.thin_arc_end_angle <= -3600:\\n self.thin_arc_end_angle %= 360\\n self.thin_arc_end_angle -= 360\\n\\n if self.thick_arc_start_angle >= 3600:\\n self.thick_arc_start_angle %= 360\\n self.thick_arc_start_angle += 360\\n\\n elif self.thick_arc_start_angle <= -3600:\\n self.thick_arc_start_angle %= 360\\n self.thick_arc_start_angle -= 360\\n\\n if self.thick_arc_end_angle >= 3600:\\n self.thick_arc_end_angle %= 360\\n self.thick_arc_end_angle += 360\\n\\n elif self.thick_arc_end_angle <= -3600:\\n self.thick_arc_end_angle %= 360\\n self.thick_arc_end_angle -= 360\",\n \"def square_area(side):\\n return side**2\",\n \"def diag_line((lat0, lon0, alt0), (lat, lon, alt), k=5):\\n\\tlats = np.linspace(lat0, lat, k)\\n\\tlons = np.linspace(lon0, lon, k)\\n\\talts = np.linspace(alt0, alt, k)\\n\\tp = zip(lats, lons, alts)\\n\\treturn p\",\n \"def op_rad(self, args):\\n self.require_stack(1)\\n val1 = self.stack.pop()\\n self.stack.append(decimal.radians(val1))\",\n \"def Agl2ArcLen(self,agl):\\r\\n\\r\\n return (self.distance_between_wheels/2)*agl\",\n \"def epicycloid(r, n, t):\\n first = True\\n t.up()\\n i = 1\\n while True:\\n theata = i * get_radian() / 10\\n i += 1\\n x = r * (cos(theata)+(1/n)*cos(n*theata))\\n y = r * (sin(theata)+(1/n)*sin(n*theata))\\n t.goto(x, y)\\n if first == True:\\n t.pd()\\n first = False\\n s = ([round(x, 5), round(y, 5)])\\n else:\\n if s == [round(x, 5), round(y, 5)]:\\n break\\n t.up()\",\n \"def radius_step(radius, num_longtidues, num_latitudes, time):\\n step = int(exp(time))\\n radius['long_down'] = radius['long_down'] - step\\n if radius['long_down'] <= 0:\\n radius['long_down'] = 0\\n radius['long_up'] = radius['long_up'] + step\\n if radius['long_up'] >= num_longtidues - 1:\\n radius['long_up'] = num_longtidues - 1\\n radius['lat_down'] = radius['lat_down'] - step\\n if radius['lat_down'] <= 0:\\n radius['lat_down'] = 0\\n radius['lat_up'] = radius['lat_up'] + step\\n if radius['lat_up'] >= num_latitudes - 1:\\n radius['lat_up'] = num_latitudes - 1\",\n \"def rotate_arcs(self):\\n\\n if self.arc_direction:\\n self.thick_arc_start_angle -= 5\\n self.thick_arc_end_angle -= 5\\n\\n self.thin_arc_start_angle += 5\\n self.thin_arc_end_angle += 5\\n else:\\n self.thick_arc_start_angle += 5\\n self.thick_arc_end_angle += 5\\n\\n self.thin_arc_start_angle -= 5\\n self.thin_arc_end_angle -= 5\",\n \"def test_trapezoid_area(self):\\n self.assertEqual(16, trapezoid_area(\\n self.values['base_minor'], self.values['base_major'], self.values['height']))\",\n \"def delta_long(self, other_coord):\\n\\n delta_rad = other_coord.long.rad - self.long.rad\\n\\n return AngleRad(delta_rad)\",\n \"def quadrant(coordinates: tuple, center: tuple):\\n angle = calculate_angle(center, coordinates)\\n if angle =< 90:\\n return \\\"LL\\\"\\n if angle =< 180:\\n return \\\"UL\\\"\\n if angle =< 270:\\n return \\\"UR\\\"\\n return \\\"LR\\\"\",\n \"def arm(self):\\n pass\",\n \"def cube_area(edge : number) -> number:\\n area = 6*edge*edge\\n\\n return area\",\n \"def _corner_moravec(*args, **kwargs): # real signature unknown\\n pass\",\n \"def draw_long_shape():\\n turtle.fillcolor('blue')\\n draw_block()\\n turtle.forward(50)\\n draw_block()\\n turtle.forward(50)\\n draw_block()\\n turtle.forward(50)\\n draw_block()\\n turtle.back(150)\",\n \"def corrRing(self, angle):\\n c =\\\"/cli:python /app:matrix /cmd:setcorring\\\" + str(float(angle))\\n self.sendCMDstring(c)\",\n \"def mark_sq8(self):\\n self.drive_inches(15, 400)\\n self.turn_degrees(90, 400)\\n self.drive_inches(13, 400)\\n ev3.Sound.speak('Place Mark').wait()\\n self.arm_calibration()\\n self.drive_inches(-13, 400)\\n self.turn_degrees(-90, 400)\\n self.drive_inches(-15, 400)\",\n \"def trapezoid_area(base_minor, base_major, height):\\n return ((base_major + base_minor) / 2 ) * height\",\n \"def testRadial(self):\\n self.doTest(afwGeom.makeRadialTransform([0, 1.01, 1e-7]))\",\n \"def testRadial(self):\\n self.doTest(afwGeom.makeRadialTransform([0, 1.01, 1e-7]))\",\n \"def trapArea(base1, base2, height):\\n return base1 + base2 * 1/2 * height\",\n \"def area_circle(r):\\n return (r ** 2) * math.pi\",\n \"def _determine_quadrant(row, column) -> QuadrantEnum:\\n if row < 4 and column < 5:\\n return QuadrantEnum.TOP_LEFT\\n elif row < 4 and column >= 5:\\n return QuadrantEnum.TOP_RIGHT\\n elif row >= 4 and column < 5:\\n return QuadrantEnum.BOTTOM_LEFT\\n else:\\n return QuadrantEnum.BOTTOM_RIGHT\",\n \"def Intarea( xc, yc, r, x0, x1, y0, y1):\\n\\n#\\n# Shift the objects so that the circle is at the origin.\\n#\\n x0 = x0 - xc\\n y0 = y0 - yc\\n x1 = x1 - xc\\n y1 = y1 - yc\\n\\n return Oneside( x1, y0, y1, r ) + Oneside( y1, -x1, -x0, r ) +\\\\\\n Oneside( -x0, -y1, -y0, r ) + Oneside( -y0, x0, x1, r )\",\n \"def area_equilat(side):\\n\\treturn side/2 * math.sqrt(side**2 - (side/2)**2)\",\n \"def get_quadrant(azi, posang1, posang2, full=False):\\n ang1, ang2 = posang1, posang2\\n maxazipos = len(azi)\\n\\n def get_sl(a, b, clock=1):\\n if clock == 1:\\n if a < b:\\n return list(range(a, b + 1))\\n else:\\n return [*range(a, maxazipos), *range(0, b + 1)]\\n else:\\n if a > b:\\n return list(range(a, b - 1, -1))\\n else:\\n return [*range(a, -1, -1), *range(maxazipos - 1, b - 1, -1)]\\n\\n if ang1 > ang2:\\n dist1 = ang1 - ang2\\n dist2 = maxazipos - dist1\\n mid1 = ang1 + dist1 // 2\\n if mid1 >= maxazipos:\\n mid1 -= maxazipos\\n\\n mid2 = ang1 - dist2 // 2\\n if mid2 < 0:\\n mid2 += maxazipos\\n\\n quad = [None] * 4\\n if not full:\\n quad[0] = get_sl(ang1, mid1, 1)\\n quad[1] = get_sl(ang1, mid2, -1)\\n quad[2] = get_sl(ang2, mid2, 1)\\n quad[3] = get_sl(ang2, mid1, -1)\\n else:\\n quad[0] = get_sl(ang1, ang2, 1)\\n quad[1] = get_sl(ang1, ang2, -1)\\n quad[2] = get_sl(ang2, ang1, 1)\\n quad[3] = get_sl(ang2, ang1, -1)\\n\\n else:\\n dist1 = ang2 - ang1\\n dist2 = maxazipos - dist1\\n mid1 = ang1 + dist1 // 2\\n if mid1 >= maxazipos:\\n mid1 -= maxazipos\\n\\n mid2 = ang1 - dist2 // 2\\n if mid2 < 0:\\n mid2 += maxazipos\\n\\n quad = [None] * 4\\n if not full:\\n quad[0] = get_sl(ang1, mid1, 1)\\n quad[1] = get_sl(ang1, mid2, -1)\\n quad[2] = get_sl(ang2, mid2, 1)\\n quad[3] = get_sl(ang2, mid1, -1)\\n else:\\n quad[0] = get_sl(ang1, ang2, 1)\\n quad[1] = get_sl(ang1, ang2, -1)\\n quad[2] = get_sl(ang2, ang1, 1)\\n quad[3] = get_sl(ang2, ang1, -1)\\n\\n return quad\",\n \"def _determine_quadrant(self, row, column) -> QuadrantEnum:\\n if row < 4 and column < 5:\\n return QuadrantEnum.TOP_LEFT\\n elif row < 4 and column >= 5:\\n return QuadrantEnum.TOP_RIGHT\\n elif row >= 4 and column < 5:\\n return QuadrantEnum.BOTTOM_LEFT\\n else:\\n return QuadrantEnum.BOTTOM_RIGHT\",\n \"def fireEast(self):\\n self.rotate('e')\\n gun = Laser(self)\\n gun.shoot('e')\\n self.agent.actionCompleted()\",\n \"def turnRightDiag(ev3):\\n ev3.set_angle(\\\"A\\\", \\\"30\\\", \\\"45\\\")\\n ev3.set_angle(\\\"B\\\", \\\"-30\\\", \\\"-45\\\")\\n ev3.set_angle(\\\"C\\\", \\\"30\\\", \\\"45\\\")\",\n \"def Arc( x, y0, y1, r):\\n return 0.5 * r*r * ( np.arctan( (y1).astype(float)/(x).astype(float) ) - np.arctan( (y0).astype(float)/(x).astype(float) ) )\",\n \"def mark_sq4(self):\\n self.drive_inches(8.5, 400)\\n self.turn_degrees(90, 400)\\n self.drive_inches(6.5, 400)\\n ev3.Sound.speak('Place Mark').wait()\\n self.arm_calibration()\\n self.drive_inches(-6.5, 400)\\n self.turn_degrees(-90, 400)\\n self.drive_inches(-8.5, 400)\",\n \"def __around_long_row(self):\\n list_of_cord = []\\n for i in range(-self.rad, self.rad + 1):\\n for j in range(-self.rad, self.rad + 1):\\n if (i == 0 and j == 0) or (i != 0 and j == 1):\\n continue\\n list_of_cord.append((i, j))\\n return list_of_cord\",\n \"def checkRing(self, verbose = 0):\\n angleSum = self.tfs.ANGLE.sum()\\n if self.verbose: print (\\\"check\\\")\\n print (\\\"---------------------------------- \\\\n Checking, if ring is closed: \\\\n\\\", \\\"angleSum = \\\", angleSum)\\n twoPi = 2*pi\\n \\n if angleSum != twoPi:\\n fudge = 2*pi - angleSum\\n print (\\\" ** Ring not closed - offset of: \\\", fudge)\",\n \"def __bcc_left_diagonals(self) -> cq.cq.Workplane:\\n # In a cuboid ABCDA1B1C1D1 this is the angle C1AD\\n #angle_C1AD = 90 - degrees(acos(2**-.5))\\n angle_C1AD = 90 - degrees(acos(0.5))\\n angle_CAD = 90 - degrees(acos(sqrt(2/3)))\\n pseudo_unit_cell_size = sqrt(2/3)*self.unit_cell_size\\n corner_points = np.array(\\n [(0, 0),\\n (self.bcc_unit_cell_size, 0),\\n (self.bcc_unit_cell_size, self.unit_cell_size),\\n (0, self.unit_cell_size)]\\n )\\n result = (\\n cq.Workplane(\\\"XY\\\")\\n .pushPoints(corner_points)\\n .eachpointAdaptive(\\n create_bcc_diagonal_strut,\\n callback_extra_args = [\\n {\\\"unit_cell_size\\\": pseudo_unit_cell_size,\\n \\\"radius\\\": self.strut_radius,\\n \\\"angle_x\\\": - angle_CAD,\\n \\\"angle_y\\\": angle_C1AD},\\n {\\\"unit_cell_size\\\": 0.5 * pseudo_unit_cell_size,\\n \\\"radius\\\": self.strut_radius,\\n \\\"angle_x\\\": - angle_CAD,\\n \\\"angle_y\\\": - angle_C1AD},\\n {\\\"unit_cell_size\\\": 0.5 * pseudo_unit_cell_size,\\n \\\"radius\\\": self.strut_radius,\\n \\\"angle_x\\\": angle_CAD,\\n \\\"angle_y\\\": - angle_C1AD},\\n {\\\"unit_cell_size\\\": pseudo_unit_cell_size,\\n \\\"radius\\\": self.strut_radius,\\n \\\"angle_x\\\": angle_CAD,\\n \\\"angle_y\\\": angle_C1AD}\\n ],\\n useLocalCoords = True\\n )\\n )\\n return result\",\n \"def quadrant(pAx, pAy, pBx, pBy):\\n###############################################################################\\n\\n if (pBx>pAx and pBy>pAy):\\n return 1\\n elif (pBx<pAx and pBy>pAy):\\n return 2\\n elif (pBx<pAx and pBy<pAy):\\n return 3\\n elif (pBx>pAx and pBy<pAy):\\n return 4\\n else:\\n return 0\",\n \"def area_circle(l):\\n a = math.pi * ((l / 2) ** 2)\\n return a\",\n \"def closer_ang(x,a,dir=0):\\r\\n if dir == 0:\\r\\n return a + smaller_ang(x-a)\\r\\n elif dir == 1:\\r\\n return a + (x-a)%(2*pi)\\r\\n elif dir == -1:\\r\\n return a + (x-a)%(2*pi) - 2*pi\",\n \"def test_euler_angles_1q_hard_thetas(self, gate):\\n self.check_one_qubit_euler_angles(Operator(gate))\",\n \"def _O_and_O2_correction(self, alt):\\n _O_and_O2_correction_fast(alt, self.Texo)\",\n \"def rayleigh_noscale(th):\\n c = np.cos(th)\\n c2 = c**2\\n return 0.5*np.array([[c2+1 , c2-1 , 0 , 0],\\n [c2-1 , c2+1 , 0 , 0],\\n [0 , 0 , 2*c , 0],\\n [0 , 0 , 0 , 2*c]])\",\n \"def rotate_quadrant(self, quadrant, direction):\\n direction = Direction(direction)\\n self.play_area[quadrant].rotate(direction)\",\n \"def doubleClick(self, event):\\n doRotation = False\\n\\n self.can.focus_force()\\n interCircle = self.findInter(event.x, event.y)\\n if interCircle:\\n xa, ya, xb, yb = self.can.coords(interCircle)\\n inter = ((xa + xb)/2, (ya + yb)/2)\\n for seg in self.segs:\\n if (not doRotation) and (seg.getStartPoint() == inter):\\n doRotation = True\\n lastInter = inter\\n if doRotation:\\n seg.place(lastInter)\\n seg.rotate(pi/2)\\n lastInter = seg.getEndPoint()\\n\\n self.wipe(self.segs)\",\n \"def _H_correction(self, alt):\\n _H_correction_fast(alt, self.Texo)\",\n \"def long(self, amount):\",\n \"def GetHiCorner(self):\\n ...\",\n \"def drawE8(\\n pl=57, ## Parallel length\\n gw=12.5, ## Gauge width\\n tw=20, ## Grip width\\n tl=50.0, ## Grip length\\n rd=12.5, ## Radius\\n):\\n import numpy as np\\n A = tw/2. - gw/2.\\n th = -90.-np.arccos((rd-A)/rd)*180./np.pi\\n x = rd * np.sin(th*np.pi/180.)\\n ## Round...\\n th0=-90\\n th_delta=np.arccos((rd-A)/rd)*180/np.pi\\n th1=th0+th_delta\\n ths=np.linspace(th0*np.pi/180.,th1*np.pi/180.)\\n xs = rd*np.cos(ths)\\n ys = rd*np.sin(ths)\\n ## translate xs,ys\\n xs = xs + (x-xs[-1])\\n ys = ys + (-A+tw-ys[-1])\\n xyRound=[xs.tolist(),ys.tolist()]\\n \\n \\n ## parallel\\n x0,y0=xs[0],ys[0]\\n xyParallel = [[x0-0.5*pl,x0],[y0,y0]]\\n \\n ## Right grip\\n XS=[x+tl,x+tl,x][::-1]\\n YS=[-A+0.5*tw,-A+tw,-A+tw][::-1]\\n xyRG=[XS,YS]\\n \\n x=xyParallel[0]+xyRound[0]+xyRG[0]\\n y=xyParallel[1]+xyRound[1]+xyRG[1]\\n \\n xyCoords=np.array([x,y])\\n \\n # print xyCoords.shape\\n \\n ## translate the coordinate so that the center of gravity is (0,0)\\n xyCoords[0]=xyCoords[0]-xyCoords[0][0]\\n xyCoords[1]=xyCoords[1]-xyCoords[1][-1]\\n # plot(xyCoords[0],xyCoords[1],'-')\\n \\n ## Apply 2-fold symmetry.\\n sym0 =[[ 1,0],[0, 1]] ## Identical\\n sym1 =[[-1,0],[0, 1]] ## Reflect y axis\\n sym2 =[[ 1,0],[0,-1]] ## Reflect x axis\\n sym3 =[[-1,0],[0,-1]] ## Reflect origin\\n \\n sym = np.array([sym0,sym2,sym3,sym1])\\n # plot(xyCoords[0,0],xyCoords[1,0],'x')\\n\\n xyTot=[[],[]]\\n for i in range(len(sym)):\\n symOp = sym[i][:,:]# (2,2)\\n temp = np.tensordot(symOp,xyCoords,axes=[1,0])\\n if i==1 or i==3:\\n temp[0]=temp[0][::-1]\\n temp[1]=temp[1][::-1]\\n elif i==0 or i==2:\\n temp=temp[::]\\n\\n for j in range(len(temp[0])):\\n xyTot[0].append(temp[0][j])\\n xyTot[1].append(temp[1][j])\\n\\n xyTot=np.array(xyTot)\\n\\n\\n x0=min(xyTot[0])\\n y0=min(xyTot[1])+tw/2.\\n\\n xyTot[0] = xyTot[0] - x0\\n xyTot[1] = xyTot[1] - y0\\n\\n return xyTot\",\n \"def arm1_maker(size=60, color='0x9C661F'):\\n arm = GArc(size, size+30, 100, 200)\\n arm.filled = True\\n arm.fill_color = color\\n return arm\",\n \"def polar_tth_corr_map_rygg_pinhole(tth, eta, instrument, absorption_length,\\n pinhole_thickness, pinhole_radius,\\n num_phi_elements=60):\\n panels = list(instrument.detectors.values())\\n return calc_tth_rygg_pinhole(panels, absorption_length, tth, eta,\\n pinhole_thickness, pinhole_radius,\\n num_phi_elements) - tth\",\n \"def area(r):\\n return np.pi * (r ** 2)\",\n \"def test_euler_angles_1q_clifford(self, clifford):\\n self.check_one_qubit_euler_angles(clifford)\",\n \"def arccosh(a):\",\n \"def right_twist(self):\\n self.turn_by_deg(180)\\n #time.sleep(.1)\\n self.stop()\\n self.turn_by_deg(180)\\n #time.sleep(.1)\\n self.stop()\",\n \"def increase_right_boundary(self):\\n self.R = self.R + 1.0\\n self.Ne = self.Ne + 1\",\n \"def diag():\\n tt.left(90)\\n tt.forward(50)\\n tt.left(135)\\n tt.down()\\n tt.forward(50*sqrt(2))\\n tt.up()\\n tt.left(135)\\n tt.forward(60)\",\n \"def question_c():\\n 4*math.pi*(r**2)\",\n \"def test_wrap_at_180():\\n spiral_arm = survey.get_spiral_slice(track = \\\"CrF\\\", \\n wrap_at_180 = True)\\n spiral_arm2 = survey.get_spiral_slice(track = \\\"Carina_far\\\", \\n wrap_at_180 = True)\\n\\n assert np.allclose(spiral_arm[\\\"INTEN\\\"], spiral_arm2[\\\"INTEN\\\"], equal_nan = True)\",\n \"def _is_trivial_angle(rad: float, atol: float) -> bool:\\n return abs(rad) < atol or abs(abs(rad) - np.pi / 4) < atol\",\n \"def choice_4(side_ac, side_cb, angle_acb, precision):\\r\\n c_squared = math.pow(side_cb, 2) + math.pow(side_ac, 2) - 2 * side_cb * side_ac * \\\\\\r\\n math.cos(math.radians(angle_acb))\\r\\n side_ab = math.sqrt(c_squared)\\r\\n side_ab = '{:.{prec}f}'.format(side_ab, prec=precision)\\r\\n print(\\\"Side AB is \\\" + str(side_ab) + \\\"\\\\n\\\")\",\n \"def arc(r, mv_direction):\\n \\n vert_amount = 80\\n arc_vert_amount = int(vert_amount / 2);\\n edge = 2 * r * math.sin(math.radians(360 / (2 * vert_amount)))\\n polygon_angle = (vert_amount - 2) / vert_amount * 180\\n angle = 180 - polygon_angle\\n \\n for i in range(arc_vert_amount):\\n if i == 0: \\n rotate_turtle(polygon_angle / 2, not mv_direction)\\n else:\\n rotate_turtle(angle, mv_direction)\\n turtle.forward(edge)\",\n \"def create_rink():\\n\\n # RINK\\n coords = OFFSET, OFFSET, OFFSET+22*SCALE, OFFSET+22*SCALE\\n canvas.create_arc(coords, start=90, extent=90, fill=WHITE, outline=\\\"\\\")\\n coords = OFFSET, HEIGHT-OFFSET-22*SCALE, OFFSET+22*SCALE, HEIGHT-OFFSET\\n canvas.create_arc(coords, start=180, extent=90, fill=WHITE, outline=WHITE)\\n coords = WIDTH-OFFSET-22*SCALE, HEIGHT-OFFSET-22*SCALE, WIDTH-OFFSET, HEIGHT-OFFSET\\n canvas.create_arc(coords, start=270, extent=90, fill=WHITE, outline=WHITE)\\n coords = WIDTH-OFFSET-22*SCALE, OFFSET, WIDTH-OFFSET, OFFSET+22*SCALE\\n canvas.create_arc(coords, start=0, extent=90, fill=WHITE, outline=WHITE)\\n coords = OFFSET+11*SCALE, OFFSET, WIDTH-OFFSET-11*SCALE, OFFSET, WIDTH-OFFSET-11*SCALE, HEIGHT-OFFSET, OFFSET+11*SCALE, HEIGHT-OFFSET\\n canvas.create_polygon(coords, fill=WHITE, outline=WHITE)\\n coords = OFFSET, OFFSET+11*SCALE, WIDTH-OFFSET, OFFSET+11*SCALE, WIDTH-OFFSET, HEIGHT-OFFSET-11*SCALE, OFFSET, HEIGHT-OFFSET-11*SCALE\\n canvas.create_polygon(coords, fill=WHITE, outline=WHITE)\\n\\n # CENTER CIRCLE\\n coords = WIDTH/2-15*SCALE, HEIGHT/2-15*SCALE, WIDTH/2+15*SCALE, HEIGHT/2+15*SCALE\\n canvas.create_oval(coords, outline=BLUE, width=2, fill=WHITE)\\n\\n # HALF CENTER CIRCLE\\n coords = WIDTH/2-10*SCALE, HEIGHT-OFFSET-10*SCALE, WIDTH/2+10*SCALE, HEIGHT-OFFSET+10*SCALE\\n canvas.create_arc(coords, outline=RED, width=2, start=0, extent=180)\\n\\n # GOAL AREA\\n # - Left\\n # - - Crease\\n coords = OFFSET+5*SCALE, HEIGHT/2-6*SCALE, OFFSET+17*SCALE, HEIGHT/2+6*SCALE\\n canvas.create_arc(coords, fill=LIGHT_BLUE, start=318, extent=84, outline=\\\"\\\")\\n canvas.create_arc(coords, outline=RED, start=318, extent=84, style=ARC)\\n coords = OFFSET+11*SCALE, HEIGHT/2-4*SCALE, OFFSET+15.5*SCALE, HEIGHT/2-4*SCALE, OFFSET+15.5*SCALE, HEIGHT/2+4*SCALE, OFFSET+11*SCALE, HEIGHT/2+4*SCALE\\n canvas.create_polygon(coords, fill=LIGHT_BLUE, outline=\\\"\\\")\\n coords = OFFSET+11*SCALE, HEIGHT/2-4*SCALE, OFFSET+15.2*SCALE+1, HEIGHT/2-4*SCALE\\n canvas.create_line(coords, fill=RED)\\n coords = OFFSET+15.2*SCALE+1, HEIGHT/2+4*SCALE, OFFSET+11*SCALE, HEIGHT/2+4*SCALE\\n canvas.create_line(coords, fill=RED)\\n # - - Restricted Area\\n coords = OFFSET, HEIGHT/2-14*SCALE, OFFSET+11*SCALE, HEIGHT/2-9*SCALE\\n canvas.create_line(coords, fill=RED)\\n coords = OFFSET, HEIGHT/2+14*SCALE, OFFSET+11*SCALE, HEIGHT/2+9*SCALE\\n canvas.create_line(coords, fill=RED)\\n # - - Goal\\n coords = OFFSET+8*SCALE, HEIGHT/2-3*SCALE, OFFSET+11*SCALE, HEIGHT/2-3*SCALE, OFFSET+11*SCALE, HEIGHT/2+3*SCALE, OFFSET+8*SCALE, HEIGHT/2+3*SCALE\\n canvas.create_polygon(coords, fill=GRAY, outline=RED)\\n # - Right\\n # - - Crease\\n coords = WIDTH-(OFFSET+5*SCALE), HEIGHT/2-6*SCALE, WIDTH-(OFFSET+17*SCALE), HEIGHT/2+6*SCALE\\n canvas.create_arc(coords, fill=LIGHT_BLUE, start=138, extent=84, outline=\\\"\\\")\\n canvas.create_arc(coords, outline=RED, start=138, extent=84, style=ARC)\\n coords = WIDTH-(OFFSET+11*SCALE), HEIGHT/2-4*SCALE, WIDTH-(OFFSET+15.5*SCALE), HEIGHT/2-4*SCALE, WIDTH-(OFFSET+15.5*SCALE), HEIGHT/2+4*SCALE, WIDTH-(OFFSET+11*SCALE), HEIGHT/2+4*SCALE\\n canvas.create_polygon(coords, fill=LIGHT_BLUE, outline=\\\"\\\")\\n coords = WIDTH-(OFFSET+11*SCALE), HEIGHT/2-4*SCALE, WIDTH-(OFFSET+15.2*SCALE+1), HEIGHT/2-4*SCALE\\n canvas.create_line(coords, fill=RED)\\n coords = WIDTH-(OFFSET+15.2*SCALE+1), HEIGHT/2+4*SCALE, WIDTH-(OFFSET+11*SCALE), HEIGHT/2+4*SCALE\\n canvas.create_line(coords, fill=RED)\\n # - - Restricted Area\\n coords = WIDTH-OFFSET, HEIGHT/2-14*SCALE, WIDTH-OFFSET-11*SCALE, HEIGHT/2-9*SCALE\\n canvas.create_line(coords, fill=RED)\\n coords = WIDTH-OFFSET, HEIGHT/2+14*SCALE, WIDTH-OFFSET-11*SCALE, HEIGHT/2+9*SCALE\\n canvas.create_line(coords, fill=RED)\\n # - - Goal\\n coords = WIDTH-(OFFSET+8*SCALE), HEIGHT/2-3*SCALE, WIDTH-(OFFSET+11*SCALE), HEIGHT/2-3*SCALE, WIDTH-(OFFSET+11*SCALE), HEIGHT/2+3*SCALE, WIDTH-(OFFSET+8*SCALE), HEIGHT/2+3*SCALE\\n canvas.create_polygon(coords, fill=GRAY, outline=RED)\\n\\n # LINES\\n # - Left Baseline\\n coords = OFFSET+11*SCALE, OFFSET, OFFSET+11*SCALE, HEIGHT-OFFSET\\n canvas.create_line(coords, fill=RED, width=1.5)\\n # - Right Baseline\\n coords = WIDTH-OFFSET-11*SCALE, OFFSET, WIDTH-OFFSET-11*SCALE, HEIGHT-OFFSET\\n canvas.create_line(coords, fill=RED, width=1.5)\\n # - Left Blueline\\n coords = OFFSET+70*SCALE, OFFSET, OFFSET+70*SCALE, HEIGHT-OFFSET\\n canvas.create_line(coords, fill=BLUE, width=7)\\n # - Right Blueline\\n coords = WIDTH-(OFFSET+70*SCALE), OFFSET, WIDTH-(OFFSET+70*SCALE), HEIGHT-OFFSET\\n canvas.create_line(coords, fill=BLUE, width=7)\\n # - Redline\\n coords = WIDTH/2, OFFSET, WIDTH/2, HEIGHT-OFFSET\\n canvas.create_line(coords, fill=RED, width=7)\\n coords = WIDTH/2, OFFSET, WIDTH/2, HEIGHT-OFFSET\\n canvas.create_line(coords, fill=WHITE, width=5, dash=(9,9))\\n\\n # RINK OUTLINE\\n coords = OFFSET, OFFSET, OFFSET+22*SCALE, OFFSET+22*SCALE\\n canvas.create_arc(coords, start=90, extent=90, outline=BLACK, style=ARC, width=2)\\n coords = OFFSET, HEIGHT-OFFSET-22*SCALE, OFFSET+22*SCALE, HEIGHT-OFFSET\\n canvas.create_arc(coords, start=180, extent=90, outline=BLACK, style=ARC, width=2)\\n coords = WIDTH-OFFSET-22*SCALE, HEIGHT-OFFSET-22*SCALE, WIDTH-OFFSET, HEIGHT-OFFSET\\n canvas.create_arc(coords, start=270, extent=90, outline=BLACK, style=ARC, width=2)\\n coords = WIDTH-OFFSET-22*SCALE, OFFSET, WIDTH-OFFSET, OFFSET+22*SCALE\\n canvas.create_arc(coords, start=0, extent=90, outline=BLACK, style=ARC, width=2)\\n coords = OFFSET+11*SCALE, OFFSET, WIDTH-OFFSET-11*SCALE, OFFSET\\n canvas.create_line(coords, fill=BLACK, width=2)\\n coords = WIDTH-OFFSET, OFFSET+11*SCALE, WIDTH-OFFSET, HEIGHT-OFFSET-11*SCALE\\n canvas.create_line(coords, fill=BLACK, width=2)\\n coords = WIDTH-OFFSET-11*SCALE, HEIGHT-OFFSET, OFFSET+11*SCALE, HEIGHT-OFFSET\\n canvas.create_line(coords, fill=BLACK, width=2)\\n coords = OFFSET, OFFSET+11*SCALE, OFFSET, HEIGHT-OFFSET-11*SCALE\\n canvas.create_line(coords, fill=BLACK, width=2)\\n\\n\\n # CENTER DOT\\n coords = WIDTH/2-1*SCALE-1, HEIGHT/2-1*SCALE-1, WIDTH/2+1*SCALE+1, HEIGHT/2+1*SCALE+1\\n canvas.create_oval(coords, outline=WHITE, fill=BLUE)\\n\\n # FACEOFF\\n # - Top Left\\n # - - Ticks\\n coords = OFFSET+29.5*SCALE, HEIGHT/2-39*SCALE, OFFSET+29.5*SCALE, HEIGHT/2-5*SCALE\\n canvas.create_line(coords, fill=RED, width=2)\\n coords = OFFSET+32.5*SCALE, HEIGHT/2-39*SCALE, OFFSET+32.5*SCALE, HEIGHT/2-5*SCALE\\n canvas.create_line(coords, fill=RED, width=2)\\n # - - Circles\\n coords = OFFSET+16*SCALE, HEIGHT/2-37*SCALE, OFFSET+46*SCALE, HEIGHT/2-7*SCALE\\n canvas.create_oval(coords, outline=RED, width=2, fill=WHITE)\\n coords = OFFSET+30*SCALE, HEIGHT/2-23*SCALE, OFFSET+32*SCALE, HEIGHT/2-21*SCALE\\n canvas.create_oval(coords, fill=RED, outline=\\\"\\\")\\n # - - Cross\\n coords = OFFSET+25*SCALE, HEIGHT/2-22.8*SCALE, OFFSET+29*SCALE, HEIGHT/2-22.8*SCALE, OFFSET+29*SCALE, HEIGHT/2-25.8*SCALE\\n canvas.create_line(coords, fill=RED, width=2)\\n coords = OFFSET+25*SCALE, HEIGHT/2-21.2*SCALE, OFFSET+29*SCALE, HEIGHT/2-21.2*SCALE, OFFSET+29*SCALE, HEIGHT/2-18.2*SCALE\\n canvas.create_line(coords, fill=RED, width=2)\\n coords = OFFSET+37*SCALE, HEIGHT/2-22.8*SCALE, OFFSET+33*SCALE, HEIGHT/2-22.8*SCALE, OFFSET+33*SCALE, HEIGHT/2-25.8*SCALE\\n canvas.create_line(coords, fill=RED, width=2)\\n coords = OFFSET+37*SCALE, HEIGHT/2-21.2*SCALE, OFFSET+33*SCALE, HEIGHT/2-21.2*SCALE, OFFSET+33*SCALE, HEIGHT/2-18.2*SCALE\\n canvas.create_line(coords, fill=RED, width=2)\\n # - Bottom Left\\n # - - Ticks\\n coords = OFFSET+29.5*SCALE, HEIGHT/2+39*SCALE, OFFSET+29.5*SCALE, HEIGHT/2+5*SCALE\\n canvas.create_line(coords, fill=RED, width=2)\\n coords = OFFSET+32.5*SCALE, HEIGHT/2+39*SCALE, OFFSET+32.5*SCALE, HEIGHT/2+5*SCALE\\n canvas.create_line(coords, fill=RED, width=2)\\n # - - Circles\\n coords = OFFSET+16*SCALE, HEIGHT/2+37*SCALE, OFFSET+46*SCALE, HEIGHT/2+7*SCALE\\n canvas.create_oval(coords, outline=RED, width=2, fill=WHITE)\\n coords = OFFSET+30*SCALE, HEIGHT/2+23*SCALE, OFFSET+32*SCALE, HEIGHT/2+21*SCALE\\n canvas.create_oval(coords, fill=RED, outline=\\\"\\\")\\n # - - Cross\\n coords = OFFSET+25*SCALE, HEIGHT/2+22.8*SCALE, OFFSET+29*SCALE, HEIGHT/2+22.8*SCALE, OFFSET+29*SCALE, HEIGHT/2+25.8*SCALE\\n canvas.create_line(coords, fill=RED, width=2)\\n coords = OFFSET+25*SCALE, HEIGHT/2+21.2*SCALE, OFFSET+29*SCALE, HEIGHT/2+21.2*SCALE, OFFSET+29*SCALE, HEIGHT/2+18.2*SCALE\\n canvas.create_line(coords, fill=RED, width=2)\\n coords = OFFSET+37*SCALE, HEIGHT/2+22.8*SCALE, OFFSET+33*SCALE, HEIGHT/2+22.8*SCALE, OFFSET+33*SCALE, HEIGHT/2+25.8*SCALE\\n canvas.create_line(coords, fill=RED, width=2)\\n coords = OFFSET+37*SCALE, HEIGHT/2+21.2*SCALE, OFFSET+33*SCALE, HEIGHT/2+21.2*SCALE, OFFSET+33*SCALE, HEIGHT/2+18.2*SCALE\\n canvas.create_line(coords, fill=RED, width=2)\\n # - Top Right\\n # - - Ticks\\n coords = WIDTH-(OFFSET+29.5*SCALE), HEIGHT/2-39*SCALE, WIDTH-(OFFSET+29.5*SCALE), HEIGHT/2-5*SCALE\\n canvas.create_line(coords, fill=RED, width=2)\\n coords = WIDTH-(OFFSET+32.5*SCALE), HEIGHT/2-39*SCALE, WIDTH-(OFFSET+32.5*SCALE), HEIGHT/2-5*SCALE\\n canvas.create_line(coords, fill=RED, width=2)\\n # - - Circles\\n coords = WIDTH-(OFFSET+16*SCALE), HEIGHT/2-37*SCALE, WIDTH-(OFFSET+46*SCALE), HEIGHT/2-7*SCALE\\n canvas.create_oval(coords, outline=RED, width=2, fill=WHITE)\\n coords = WIDTH-(OFFSET+30*SCALE), HEIGHT/2-23*SCALE, WIDTH-(OFFSET+32*SCALE), HEIGHT/2-21*SCALE\\n canvas.create_oval(coords, fill=RED, outline=\\\"\\\")\\n # - - Cross\\n coords = WIDTH-(OFFSET+25*SCALE), HEIGHT/2-22.8*SCALE, WIDTH-(OFFSET+29*SCALE), HEIGHT/2-22.8*SCALE, WIDTH-(OFFSET+29*SCALE), HEIGHT/2-25.8*SCALE\\n canvas.create_line(coords, fill=RED, width=2)\\n coords = WIDTH-(OFFSET+25*SCALE), HEIGHT/2-21.2*SCALE, WIDTH-(OFFSET+29*SCALE), HEIGHT/2-21.2*SCALE, WIDTH-(OFFSET+29*SCALE), HEIGHT/2-18.2*SCALE\\n canvas.create_line(coords, fill=RED, width=2)\\n coords = WIDTH-(OFFSET+37*SCALE), HEIGHT/2-22.8*SCALE, WIDTH-(OFFSET+33*SCALE), HEIGHT/2-22.8*SCALE, WIDTH-(OFFSET+33*SCALE), HEIGHT/2-25.8*SCALE\\n canvas.create_line(coords, fill=RED, width=2)\\n coords = WIDTH-(OFFSET+37*SCALE), HEIGHT/2-21.2*SCALE, WIDTH-(OFFSET+33*SCALE), HEIGHT/2-21.2*SCALE, WIDTH-(OFFSET+33*SCALE), HEIGHT/2-18.2*SCALE\\n canvas.create_line(coords, fill=RED, width=2)\\n # - Bottom Right\\n # - - Ticks\\n coords = WIDTH-(OFFSET+29.5*SCALE), HEIGHT/2+39*SCALE, WIDTH-(OFFSET+29.5*SCALE), HEIGHT/2+5*SCALE\\n canvas.create_line(coords, fill=RED, width=2)\\n coords = WIDTH-(OFFSET+32.5*SCALE), HEIGHT/2+39*SCALE, WIDTH-(OFFSET+32.5*SCALE), HEIGHT/2+5*SCALE\\n canvas.create_line(coords, fill=RED, width=2)\\n # - - Circles\\n coords = WIDTH-(OFFSET+16*SCALE), HEIGHT/2+37*SCALE, WIDTH-(OFFSET+46*SCALE), HEIGHT/2+7*SCALE\\n canvas.create_oval(coords, outline=RED, width=2, fill=WHITE)\\n coords = WIDTH-(OFFSET+30*SCALE), HEIGHT/2+23*SCALE, WIDTH-(OFFSET+32*SCALE), HEIGHT/2+21*SCALE\\n canvas.create_oval(coords, fill=RED, outline=\\\"\\\")\\n # - - Cross\\n coords = WIDTH-(OFFSET+25*SCALE), HEIGHT/2+22.8*SCALE, WIDTH-(OFFSET+29*SCALE), HEIGHT/2+22.8*SCALE, WIDTH-(OFFSET+29*SCALE), HEIGHT/2+25.8*SCALE\\n canvas.create_line(coords, fill=RED, width=2)\\n coords = WIDTH-(OFFSET+25*SCALE), HEIGHT/2+21.2*SCALE, WIDTH-(OFFSET+29*SCALE), HEIGHT/2+21.2*SCALE, WIDTH-(OFFSET+29*SCALE), HEIGHT/2+18.2*SCALE\\n canvas.create_line(coords, fill=RED, width=2)\\n coords = WIDTH-(OFFSET+37*SCALE), HEIGHT/2+22.8*SCALE, WIDTH-(OFFSET+33*SCALE), HEIGHT/2+22.8*SCALE, WIDTH-(OFFSET+33*SCALE), HEIGHT/2+25.8*SCALE\\n canvas.create_line(coords, fill=RED, width=2)\\n coords = WIDTH-(OFFSET+37*SCALE), HEIGHT/2+21.2*SCALE, WIDTH-(OFFSET+33*SCALE), HEIGHT/2+21.2*SCALE, WIDTH-(OFFSET+33*SCALE), HEIGHT/2+18.2*SCALE\\n canvas.create_line(coords, fill=RED, width=2)\\n\\n # NEUTRAL ZONE FACEOFF\\n # - Top Left\\n coords = WIDTH/2-21*SCALE, HEIGHT/2-23*SCALE, WIDTH/2-19*SCALE, HEIGHT/2-21*SCALE\\n canvas.create_oval(coords, outline=\\\"\\\", fill=RED)\\n # - Bottom Left\\n coords = WIDTH/2-21*SCALE, HEIGHT/2+23*SCALE, WIDTH/2-19*SCALE, HEIGHT/2+21*SCALE\\n canvas.create_oval(coords, outline=\\\"\\\", fill=RED)\\n # - Top Right\\n coords = WIDTH/2+21*SCALE, HEIGHT/2-23*SCALE, WIDTH/2+19*SCALE, HEIGHT/2-21*SCALE\\n canvas.create_oval(coords, outline=\\\"\\\", fill=RED)\\n # - Bottom Right\\n coords = WIDTH/2+21*SCALE, HEIGHT/2+23*SCALE, WIDTH/2+19*SCALE, HEIGHT/2+21*SCALE\\n canvas.create_oval(coords, outline=\\\"\\\", fill=RED)\\n\\n\\n canvas.grid(row=1, columnspan=5)\",\n \"def l8_refl_toa_band_func(dn, cos_theta, refl_mult, refl_add):\\n refl_toa = np.copy(dn).astype(np.float64)\\n refl_toa *= refl_mult\\n refl_toa += refl_add\\n refl_toa /= cos_theta\\n np.clip(refl_toa, 0.0001, 1, out=refl_toa)\\n return refl_toa\",\n \"def _confined_angle_0(a):\\n while a < 0:\\n a += 2*_math.pi\\n while a >= 2*_math.pi:\\n a -= 2*_math.pi\\n return a\",\n \"def area(length, hypotenuse):\\n side = int(length)* hypotenuse\\n return round(side*2, 2) # returns the rounded area of the roof.\",\n \"def _triangle_areas(self, point):\\n vertex_0, vertex_1, vertex_2 = self._vertices(point)\\n len_edge_12 = gs.linalg.norm((vertex_1 - vertex_2), axis=-1)\\n len_edge_02 = gs.linalg.norm((vertex_0 - vertex_2), axis=-1)\\n len_edge_01 = gs.linalg.norm((vertex_0 - vertex_1), axis=-1)\\n half_perimeter = 0.5 * (len_edge_12 + len_edge_02 + len_edge_01)\\n return gs.sqrt(\\n (\\n half_perimeter\\n * (half_perimeter - len_edge_12)\\n * (half_perimeter - len_edge_02)\\n * (half_perimeter - len_edge_01)\\n ).clip(min=1e-6)\\n )\",\n \"def __bcc_diagonals(self) -> cq.cq.Workplane:\\n # In a cuboid ABCDA1B1C1D1 this is the angle C1AD\\n #angle_C1AD = 90 - degrees(acos(2**-.5))\\n angle_C1AD = 90 - degrees(acos(0.5))\\n angle_CAD = 90 - degrees(acos(sqrt(2/3)))\\n pseudo_unit_cell_size = sqrt(2/3)*self.unit_cell_size\\n corner_points = np.array(\\n [(0, 0),\\n (self.bcc_unit_cell_size, 0),\\n (self.bcc_unit_cell_size, self.unit_cell_size),\\n (0, self.unit_cell_size)]\\n )\\n result = (\\n cq.Workplane(\\\"XY\\\")\\n .pushPoints(corner_points)\\n .eachpointAdaptive(\\n create_bcc_diagonal_strut,\\n callback_extra_args = [\\n {\\\"unit_cell_size\\\": pseudo_unit_cell_size,\\n \\\"radius\\\": self.strut_radius,\\n \\\"angle_x\\\": - angle_CAD,\\n \\\"angle_y\\\": angle_C1AD},\\n {\\\"unit_cell_size\\\": pseudo_unit_cell_size,\\n \\\"radius\\\": self.strut_radius,\\n \\\"angle_x\\\": - angle_CAD,\\n \\\"angle_y\\\": - angle_C1AD},\\n {\\\"unit_cell_size\\\": pseudo_unit_cell_size,\\n \\\"radius\\\": self.strut_radius,\\n \\\"angle_x\\\": angle_CAD,\\n \\\"angle_y\\\": - angle_C1AD},\\n {\\\"unit_cell_size\\\": pseudo_unit_cell_size,\\n \\\"radius\\\": self.strut_radius,\\n \\\"angle_x\\\": angle_CAD,\\n \\\"angle_y\\\": angle_C1AD}\\n ],\\n useLocalCoords = True\\n )\\n )\\n return result\",\n \"def create_left_right_tangent(self):\\n self.arc_incident_tan = Arc(\\n start_angle = PI/2 + self.incident_angle,\\n angle = PI/2 - self.incident_angle,\\n radius = self.arc_incident_tan_radius,\\n color = self.arc_incident_color,\\n arc_center = self.mirror_origin\\n )\\n\\n theta_in_tan_pos_offset = -2.0 * RIGHT + 0.8 * UP\\n self.tex_theta_in_tan = TexMobject(r\\\"90^{\\\\circ}\\\",\\n r\\\"-\\\",\\n r\\\"\\\\theta_{i}\\\",\\n color=self.tex_theta_in_color).\\\\\\n move_to(self.mirror_origin + theta_in_tan_pos_offset)\\n\\n self.arc_reflected_tan = Arc(\\n start_angle = 0,\\n angle = PI/2 - self.reflected_angle,\\n radius = self.arc_reflected_tan_radius,\\n color = self.arc_reflected_color,\\n arc_center = self.mirror_origin\\n )\\n\\n theta_out_tan_pos_offset = 2.0 * RIGHT + 0.8 * UP\\n self.tex_theta_ref_tan = TexMobject(r\\\"90^{\\\\circ}\\\",\\n r\\\"-\\\",\\n r\\\"\\\\theta_{r}\\\",\\n color=self.tex_theta_ref_color).\\\\\\n move_to(self.mirror_origin + theta_out_tan_pos_offset)\",\n \"def test_fix_antimeridian(self):\\n globe = self.read_feature('Global_Ocean')\\n fc = FeatureCollection()\\n name = 'Antarctic Box'\\n feature = {\\n 'type': 'Feature',\\n 'properties': {\\n 'name': name,\\n 'tags': '',\\n 'object': 'region',\\n 'component': 'ocean',\\n 'author': 'Xylar Asay-Davis'\\n },\\n 'geometry': {\\n 'type': 'Polygon',\\n 'coordinates': [\\n [\\n [\\n 190.000000,\\n -70.000000\\n ],\\n [\\n 190.000000,\\n -90.000000\\n ],\\n [\\n 180.000000,\\n -90.000000\\n ],\\n [\\n 170.000000,\\n -90.000000\\n ],\\n [\\n 170.000000,\\n -70.000000\\n ],\\n [\\n 180.000000,\\n -70.000000\\n ],\\n [\\n 190.000000,\\n -70.000000\\n ]\\n ]\\n ]\\n }\\n }\\n fc.add_feature(feature=feature)\\n self.check_feature(fc.features[0],\\n expected_name=name,\\n expected_type='Polygon')\\n fixed = fc.fix_antimeridian()\\n self.check_feature(fixed.features[0],\\n expected_name=name,\\n expected_type='MultiPolygon')\\n\\n geom = globe.features[0]['geometry']\\n globe_shape = shapely.geometry.shape(geom)\\n\\n geom = fixed.features[0]['geometry']\\n shape = shapely.geometry.shape(geom)\\n assert isinstance(shape, shapely.geometry.MultiPolygon)\\n # make sure the fixed polygons are within -180 to 180 deg. lon.\\n assert shapely.covers(globe_shape, shape)\",\n \"def stokes_right_circular():\\n return np.array([1, 0, 0, 1])\",\n \"def quarter_chord(self) -> np.ndarray:\\n return 0.75 * self.xyz_le + 0.25 * self.xyz_te()\",\n \"def arc_n(self, xn ,yn, rn, start, stop):\\n x = round(xn * self.width)\\n y = round(yn * self.height)\\n r = round(rn * min(self.width, self.height))\\n self.arc(x, y, r, start, stop)\",\n \"def draw_arc_outline(center_x, center_y, width, height, color, start_angle,\\n end_angle, border_width=1, tilt_angle=0):\\n num_segments = 128\\n GL.glEnable(GL.GL_BLEND)\\n GL.glBlendFunc(GL.GL_SRC_ALPHA, GL.GL_ONE_MINUS_SRC_ALPHA)\\n GL.glEnable(GL.GL_LINE_SMOOTH)\\n GL.glHint(GL.GL_LINE_SMOOTH_HINT, GL.GL_NICEST)\\n GL.glHint(GL.GL_POLYGON_SMOOTH_HINT, GL.GL_NICEST)\\n\\n GL.glLoadIdentity()\\n GL.glTranslatef(center_x, center_y, 0)\\n GL.glRotatef(tilt_angle, 0, 0, 1)\\n GL.glLineWidth(border_width)\\n\\n # Set color\\n if len(color) == 4:\\n GL.glColor4ub(color[0], color[1], color[2], color[3])\\n elif len(color) == 3:\\n GL.glColor4ub(color[0], color[1], color[2], 255)\\n\\n GL.glBegin(GL.GL_LINE_STRIP)\\n\\n start_segment = int(start_angle / 360 * num_segments)\\n end_segment = int(end_angle / 360 * num_segments)\\n\\n for segment in range(start_segment, end_segment + 1):\\n theta = 2.0 * 3.1415926 * segment / num_segments\\n\\n x = width * math.cos(theta)\\n y = height * math.sin(theta)\\n\\n GL.glVertex3f(x, y, 0.5)\\n\\n GL.glEnd()\\n GL.glLoadIdentity()\",\n \"def step(self):\\n r, c = self.ant_r, self.ant_c\\n if self.grid[r][c] == LangtonAnt.WHITE:\\n self.direction = rotate_counterclock(self.direction)\\n self.grid[r][c] = LangtonAnt.BLACK\\n else:\\n self.direction = rotate_clockwise(self.direction)\\n self.grid[r][c] = LangtonAnt.WHITE\\n\\n self.ant_r -= self.direction[1]\\n self.ant_c += self.direction[0]\",\n \"def nine_punishment(self):\\n self.direction_clock_wise = not self.direction_clock_wise\",\n \"def test_rhombus_area(self):\\n self.assertEqual(17.5, rhombus_area(\\n self.values['diagonal_1'], self.values['diagonal_2']))\",\n \"def closer_angle(x, a, dir=0):\\n if dir == 0:\\n return a + smaller_angle(x-a)\\n elif dir == 1:\\n return a + (x-a)%(2*np.pi)\\n elif dir == -1:\\n return a + (x-a)%(2*np.pi) - 2*np.pi\",\n \"def _confined_angle_pi(a):\\n while a<-_math.pi:\\n a+=2*_math.pi\\n while a>=_math.pi:\\n a-=2*_math.pi\\n return a\",\n \"def area_rectangulo(b,h):\\n area = b*h\\n print \\\"El area es: \\\",area\",\n \"def getEdgeAngle():\\n '''\\n returns angle a\\n a\\n ◿\\n b c\\n '''\\n ANGLE_OFFSET = 8 # How far off the angle measurements are in degrees.\\n THRESHOLD = 220 # How much light must be reflected to 'notice' the desk.\\n angle = 0\\n while angle < panTilt.TLT_RANGE:\\n angle += 1\\n panTilt.tilt(int(angle))\\n deskDetected = ir.readWithDelay()\\n # print \\\"Angle:\\\", angle + ANGLE_OFFSET, \\\", ir reading:\\\", deskDetected\\n if deskDetected > THRESHOLD or angle == panTilt.TLT_RANGE:\\n # print \\\"-----------------------\\\"\\n break # Break out of looking downwards loop\\n panTilt.up() # Look up again\\n return 90 - angle - ANGLE_OFFSET\",\n \"def AddDimRadial(self,center,chordPnt,leaderLength):\\n\\t\\treturn self.Space.AddDimRadial(center,chordPnt,leaderLength)\",\n \"def slopecal(ton):\\r\\n global _ton_old\\r\\n global _slope\\r\\n\\r\\n print(\\\"ton: \\\", ton, \\\" _ton_old: \\\", _ton_old, \\\" substraction: \\\", round((ton - _ton_old),2))\\r\\n\\r\\n if round((ton - _ton_old), 2) >= 5:\\r\\n _slope = 1\\r\\n if round((ton - _ton_old), 2) <= -10:\\r\\n _slope = -1\\r\\n _ton_old = ton\",\n \"def GetArc(arc):\\r\\n pass\",\n \"def redfearn(lat, lon, false_easting=None, false_northing=None,\\r\\n zone=None, central_meridian=None, scale_factor=None):\\r\\n\\r\\n\\r\\n from math import pi, sqrt, sin, cos, tan\\r\\n \\r\\n\\r\\n\\r\\n #GDA Specifications\\r\\n a = 6378137.0 #Semi major axis\\r\\n inverse_flattening = 298.257222101 #1/f\\r\\n if scale_factor is None:\\r\\n K0 = 0.9996 #Central scale factor \\r\\n else:\\r\\n K0 = scale_factor\\r\\n #print 'scale', K0\\r\\n zone_width = 6 #Degrees\\r\\n\\r\\n longitude_of_central_meridian_zone0 = -183 \\r\\n longitude_of_western_edge_zone0 = -186\\r\\n\\r\\n if false_easting is None:\\r\\n false_easting = 500000\\r\\n\\r\\n if false_northing is None:\\r\\n if lat < 0:\\r\\n false_northing = 10000000 #Southern hemisphere\\r\\n else:\\r\\n false_northing = 0 #Northern hemisphere)\\r\\n \\r\\n \\r\\n #Derived constants\\r\\n f = 1.0/inverse_flattening\\r\\n b = a*(1-f) #Semi minor axis\\r\\n\\r\\n e2 = 2*f - f*f# = f*(2-f) = (a^2-b^2/a^2 #Eccentricity\\r\\n e = sqrt(e2)\\r\\n e2_ = e2/(1-e2) # = (a^2-b^2)/b^2 #Second eccentricity\\r\\n e_ = sqrt(e2_)\\r\\n e4 = e2*e2\\r\\n e6 = e2*e4\\r\\n\\r\\n #Foot point latitude\\r\\n n = (a-b)/(a+b) #Same as e2 - why ?\\r\\n n2 = n*n\\r\\n n3 = n*n2\\r\\n n4 = n2*n2\\r\\n\\r\\n G = a*(1-n)*(1-n2)*(1+9*n2/4+225*n4/64)*pi/180\\r\\n\\r\\n\\r\\n phi = lat*pi/180 #Convert latitude to radians\\r\\n\\r\\n sinphi = sin(phi) \\r\\n sin2phi = sin(2*phi)\\r\\n sin4phi = sin(4*phi)\\r\\n sin6phi = sin(6*phi)\\r\\n\\r\\n cosphi = cos(phi)\\r\\n cosphi2 = cosphi*cosphi\\r\\n cosphi3 = cosphi*cosphi2\\r\\n cosphi4 = cosphi2*cosphi2\\r\\n cosphi5 = cosphi*cosphi4 \\r\\n cosphi6 = cosphi2*cosphi4\\r\\n cosphi7 = cosphi*cosphi6\\r\\n cosphi8 = cosphi4*cosphi4 \\r\\n\\r\\n t = tan(phi)\\r\\n t2 = t*t\\r\\n t4 = t2*t2\\r\\n t6 = t2*t4\\r\\n \\r\\n #Radius of Curvature\\r\\n rho = a*(1-e2)/(1-e2*sinphi*sinphi)**1.5\\r\\n nu = a/(1-e2*sinphi*sinphi)**0.5\\r\\n psi = nu/rho\\r\\n psi2 = psi*psi\\r\\n psi3 = psi*psi2\\r\\n psi4 = psi2*psi2\\r\\n\\r\\n\\r\\n\\r\\n #Meridian distance\\r\\n\\r\\n A0 = 1 - e2/4 - 3*e4/64 - 5*e6/256\\r\\n A2 = 3.0/8*(e2+e4/4+15*e6/128)\\r\\n A4 = 15.0/256*(e4+3*e6/4)\\r\\n A6 = 35*e6/3072\\r\\n \\r\\n term1 = a*A0*phi\\r\\n term2 = -a*A2*sin2phi\\r\\n term3 = a*A4*sin4phi\\r\\n term4 = -a*A6*sin6phi\\r\\n\\r\\n m = term1 + term2 + term3 + term4 #OK\\r\\n\\r\\n if zone is not None and central_meridian is not None:\\r\\n msg = 'You specified both zone and central_meridian. Provide only one of them'\\r\\n raise Exception, msg\\r\\n \\r\\n # Zone\\r\\n if zone is None:\\r\\n zone = int((lon - longitude_of_western_edge_zone0)/zone_width)\\r\\n\\r\\n # Central meridian\\r\\n if central_meridian is None:\\r\\n central_meridian = zone*zone_width+longitude_of_central_meridian_zone0\\r\\n else:\\r\\n zone = -1\\r\\n\\r\\n omega = (lon-central_meridian)*pi/180 #Relative longitude (radians)\\r\\n omega2 = omega*omega\\r\\n omega3 = omega*omega2\\r\\n omega4 = omega2*omega2\\r\\n omega5 = omega*omega4\\r\\n omega6 = omega3*omega3\\r\\n omega7 = omega*omega6\\r\\n omega8 = omega4*omega4\\r\\n \\r\\n #Northing\\r\\n term1 = nu*sinphi*cosphi*omega2/2 \\r\\n term2 = nu*sinphi*cosphi3*(4*psi2+psi-t2)*omega4/24\\r\\n term3 = nu*sinphi*cosphi5*\\\\\\r\\n (8*psi4*(11-24*t2)-28*psi3*(1-6*t2)+\\\\\\r\\n psi2*(1-32*t2)-psi*2*t2+t4-t2)*omega6/720\\r\\n term4 = nu*sinphi*cosphi7*(1385-3111*t2+543*t4-t6)*omega8/40320\\r\\n northing = false_northing + K0*(m + term1 + term2 + term3 + term4)\\r\\n\\r\\n #Easting\\r\\n term1 = nu*omega*cosphi\\r\\n term2 = nu*cosphi3*(psi-t2)*omega3/6\\r\\n term3 = nu*cosphi5*(4*psi3*(1-6*t2)+psi2*(1+8*t2)-2*psi*t2+t4)*omega5/120\\r\\n term4 = nu*cosphi7*(61-479*t2+179*t4-t6)*omega7/5040\\r\\n easting = false_easting + K0*(term1 + term2 + term3 + term4)\\r\\n \\r\\n return zone, easting, northing\",\n \"def arm_and_takeoff(vehicle, target_alt, loiter_time):\\n util.log_info(\\\"Checking if armable.\\\")\\n \\n wait_count = 0\\n while not vehicle.is_armable:\\n time.sleep(.2)\\n wait_count = wait_count + 1\\n \\n if wait_count % 25 == 0:\\n util.log_warning(\\\"Vehicle not armable.\\\")\\n \\n if wait_count >= 100:\\n util.log_warning(\\\"Unable to arm. Abort.\\\")\\n shared.status['abort'] = True\\n return False\\n\\n util.log_info(\\\"Switching to GUIDED and Arming.\\\")\\n set_mode(vehicle, \\\"GUIDED\\\")\\n\\n util.log_debug(\\\"Arming...\\\")\\n vehicle.armed = True\\n time.sleep(3)\\n \\n wait_count = 0\\n while True:\\n time.sleep(.5)\\n wait_count = wait_count + 1\\n \\n if vehicle.armed :\\n util.log_info(\\\"Armed.\\\")\\n break\\n \\n elif wait_count % 10 == 0:\\n util.log_warning('Retry arming.')\\n \\n if wait_count >= 20:\\n util.log_warning(\\\"Arming failed. Abort.\\\")\\n shared.status['abort'] = True\\n return False\\n\\n vehicle.simple_takeoff(target_alt) \\n\\n # Wait until the vehicle reaches a safe altitude (95%), or otherwise the command \\n # after Vehicle.simple_takeoff will execute immediately, causing unexpected results.\\n while True:\\n util.log_debug(\\\"Altitude: %s\\\" % vehicle.location.global_relative_frame.alt) \\n if vehicle.location.global_relative_frame.alt >= target_alt - shared.ALT_TOLERANCE:\\n util.log_info(\\\"Target altitude reached: %s m.\\\" % vehicle.location.global_relative_frame.alt)\\n break\\n\\n time.sleep(.5)\\n \\n time.sleep(loiter_time)\\n return True\",\n \"def decelOutsideBorder(self):\\n if self.isOutsideBorder():\\n if self.rotation == 0:\\n self.currentAccel = 0\\n else:\\n self.currentAccel = self.currentAccel/1.01\",\n \"def rad(area) :\\n return sqrt(area/pi)\",\n \"def test_polar_angle_normal_case(self):\\n point1 = np.array([1, 1])\\n point2 = np.array([2, 2])\\n pol_angle = convex_hull.polar_angle(point2, point1)\\n\\n self.assertEqual(round(math.tan(pol_angle)), 1)\"\n]","isConversational":false},"negative_scores":{"kind":"list like","value":["0.51212114","0.503686","0.500466","0.49968642","0.49456814","0.4928112","0.4917071","0.48972583","0.48096138","0.48058507","0.47610927","0.4761016","0.47439614","0.47282705","0.47250915","0.47182012","0.47141975","0.47103226","0.47048694","0.47028008","0.4698094","0.46844405","0.46564132","0.4637103","0.46258566","0.46199593","0.46190676","0.46163186","0.46075577","0.45921886","0.4582551","0.45782408","0.4564016","0.4564016","0.45620373","0.4557938","0.45547226","0.4545062","0.45422927","0.45375913","0.4528103","0.45272765","0.45215315","0.45141056","0.451182","0.4508992","0.44931066","0.4493009","0.44795388","0.44722542","0.44597822","0.44485328","0.4440624","0.4428098","0.4426644","0.44215047","0.441914","0.4407792","0.4406124","0.43941","0.43865335","0.4382187","0.43755633","0.43731645","0.4370133","0.4369455","0.43553248","0.43534544","0.4352612","0.43508613","0.43508187","0.43504715","0.4346106","0.43436342","0.4335063","0.43325272","0.4330793","0.4328586","0.43253055","0.43210703","0.43171534","0.4314756","0.43143982","0.43126875","0.43111914","0.43096915","0.43086338","0.43034527","0.43012968","0.4298269","0.4290787","0.4286278","0.42857856","0.4283203","0.4274733","0.42740625","0.42686456","0.4268004","0.42665657","0.42596895"],"string":"[\n \"0.51212114\",\n \"0.503686\",\n \"0.500466\",\n \"0.49968642\",\n \"0.49456814\",\n \"0.4928112\",\n \"0.4917071\",\n \"0.48972583\",\n \"0.48096138\",\n \"0.48058507\",\n \"0.47610927\",\n \"0.4761016\",\n \"0.47439614\",\n \"0.47282705\",\n \"0.47250915\",\n \"0.47182012\",\n \"0.47141975\",\n \"0.47103226\",\n \"0.47048694\",\n \"0.47028008\",\n \"0.4698094\",\n \"0.46844405\",\n \"0.46564132\",\n \"0.4637103\",\n \"0.46258566\",\n \"0.46199593\",\n \"0.46190676\",\n \"0.46163186\",\n \"0.46075577\",\n \"0.45921886\",\n \"0.4582551\",\n \"0.45782408\",\n \"0.4564016\",\n \"0.4564016\",\n \"0.45620373\",\n \"0.4557938\",\n \"0.45547226\",\n \"0.4545062\",\n \"0.45422927\",\n \"0.45375913\",\n \"0.4528103\",\n \"0.45272765\",\n \"0.45215315\",\n \"0.45141056\",\n \"0.451182\",\n \"0.4508992\",\n \"0.44931066\",\n \"0.4493009\",\n \"0.44795388\",\n \"0.44722542\",\n \"0.44597822\",\n \"0.44485328\",\n \"0.4440624\",\n \"0.4428098\",\n \"0.4426644\",\n \"0.44215047\",\n \"0.441914\",\n \"0.4407792\",\n \"0.4406124\",\n \"0.43941\",\n \"0.43865335\",\n \"0.4382187\",\n \"0.43755633\",\n \"0.43731645\",\n \"0.4370133\",\n \"0.4369455\",\n \"0.43553248\",\n \"0.43534544\",\n \"0.4352612\",\n \"0.43508613\",\n \"0.43508187\",\n \"0.43504715\",\n \"0.4346106\",\n \"0.43436342\",\n \"0.4335063\",\n \"0.43325272\",\n \"0.4330793\",\n \"0.4328586\",\n \"0.43253055\",\n \"0.43210703\",\n \"0.43171534\",\n \"0.4314756\",\n \"0.43143982\",\n \"0.43126875\",\n \"0.43111914\",\n \"0.43096915\",\n \"0.43086338\",\n \"0.43034527\",\n \"0.43012968\",\n \"0.4298269\",\n \"0.4290787\",\n \"0.4286278\",\n \"0.42857856\",\n \"0.4283203\",\n \"0.4274733\",\n \"0.42740625\",\n \"0.42686456\",\n \"0.4268004\",\n \"0.42665657\",\n \"0.42596895\"\n]","isConversational":false},"document_score":{"kind":"string","value":"0.46925488"},"document_rank":{"kind":"string","value":"21"}}},{"rowIdx":16596,"cells":{"query":{"kind":"string","value":"Trap unsuccessful outline fill closure."},"document":{"kind":"string","value":"def test_open_fill(self):"},"metadata":{"kind":"string","value":"{\n \"objective\": {\n \"self\": [],\n \"paired\": [],\n \"triplet\": [\n [\n \"query\",\n \"document\",\n \"negatives\"\n ]\n ]\n }\n}"},"negatives":{"kind":"list like","value":["def end_fill():\n turtleTmp.end_fill()","def test_outline_fills(self):\n image = self.design.layout.layers[0].images[0]\n assert len(image.fills) == 2","def fillbox(self,event=None):\n \n pass","def update_fill(self, event):\r\n\r\n if event.type == 'FILL':\r\n self.update_positions_from_fill(event)\r\n self.update_holdings_from_fill(event)","def update_fill(self, event):\n if event.type == 'FILL':\n self.update_positions_from_fill(event)\n self.update_holdings_from_fill(event)","def update_fill(self, event):\n if event.type == 'FILL':\n self.update_positions_from_fill(event)\n self.update_holdings_from_fill(event)","def stop_filling(self, signum, frame):\n self._filling = False","def stroke(self):\n yield\n self._impl.stroke()","def _handle_border(self, i_row, i_col, adj_opp_cells, check_func, loc):\n check_func(i_row, i_col, adj_opp_cells, loc)\n #check_func will be any of the five functions listed below","def stroke(self, path, clr):\n pass","def excepthook(self, type, value, tb):\n \n self.InteractiveTB(type, value, tb, tb_offset=0)\n if self.InteractiveTB.call_pdb and self.has_readline:\n self.readline.set_completer(self.Completer.complete)","def test_area_error_when_normalize_but_no_fill_color_stack():\n result = CliRunner().invoke(area, [\"-N\", *NORMAL_ARGS])\n assert result.exit_code == 1\n assert (\n \"ConflictingArgs: -c/--colorvar needs to be specified when creating a normalized (i.e. stacked) chart\"\n in result.output.strip()\n )","def __exit__(self, exc_type, exc_value, exc_tb) -> None:\n lib.wlr_seat_keyboard_end_grab(self._seat)","def fill(self, color):","def __exit__(self, exception, value, trace):\n self.manual_exit()","def fill(self):\n return self._turtle.fill()","def fill(self, path, clr):\n pass","def _draw_outline(self) -> None:\n stroke = self.border_thickness\n\n # draw outline rectangle\n for _w in range(self.widget_width):\n for line in range(stroke):\n self._bitmap[_w, line] = 1\n self._bitmap[_w, self.widget_height - 1 - line] = 1\n for _h in range(self.widget_height):\n for line in range(stroke):\n self._bitmap[line, _h] = 1\n self._bitmap[self.widget_width - 1 - line, _h] = 1","def EndDraw(self):\r\n\r\n pass","def fill(self, colour: int, /) -> None:","def __exit__(self, _type, value, traceback):\n self.obj.write(\"]\")\n self.obj.close()","def onA(self, event):\r\n if event.state == 4:\r\n self.selectAll()\r\n return \"break\"","def stop_loss_on_fill(self, stop_loss_on_fill):\n\n self._stop_loss_on_fill = stop_loss_on_fill","def stop_loss_on_fill(self, stop_loss_on_fill):\n\n self._stop_loss_on_fill = stop_loss_on_fill","def __exit__(exc_type, value, traceback):\n del exc_type\n del value\n del traceback\n\n IndentedLogger._indent_level -= 1\n\n if (IndentedLogger._indent_level == 0 and\n IndentedLogger._printed_on_secondary_indents):\n print_message(\"\\n\")\n IndentedLogger._printed_on_secondary_indents = False","def _clear(self, event):\n if self.ignore(event) or self._changed_canvas():\n return\n self._background = self.canvas.copy_from_bbox(self.ax.bbox)\n self.ax.draw_artist(self._checks)\n if hasattr(self, '_lines'):\n for l1, l2 in self._lines:\n self.ax.draw_artist(l1)\n self.ax.draw_artist(l2)","def update_fill(self, event):\n if event.type == 'FILL':\n self.update_positions_from_fill(event)\n self.update_prices_from_fill(event)\n self.update_holdings_from_fill(event)","def __exit__(self, _type, _value, _traceback):\n self.dispose()","def fill_row(nono, row):\n # Filling inside the blocks\n changed_1 = fill_inside_of_the_blocks(nono, row)\n # Marking as empty beggining of the line\n changed_2 = fill_beggining_of_the_row(nono, row)\n # Marking as empty end of the line\n changed_3 = fill_end_of_the_row(nono, row)\n # Marking as empty area between blocks\n changed_4 = fill_between_the_blocks(nono, row)\n\n sth_changed = changed_1 or changed_2 or changed_3 or changed_4\n\n # if nonogram is in the interactive mode, update plot\n if nono.mode_data.is_interactive_plot_active() and sth_changed:\n nono.update_plot()\n\n return sth_changed","def fill(layer, event):\n # on press\n layer.fill(layer.coordinates, layer._value, layer.selected_label)","def remove_stroke(settings):\r\n if settings.fillstyle == 'border':\r\n settings.fillstyle = 'none'\r\n elif settings.fillstyle == 'fill+border':\r\n settings.fg = settings.bg\r\n settings.fillstyle = 'fill'","def flush(self):\n if self.fill:\n self._turtle.fill(False)\n self._turtle.fill(True)","def line(self, arg, fill):\n pass","def fix_elevation(self):\n selected_segment = \\\n self.controller.shared_data.obj_track.selected_segment_idx\n segment_idx = selected_segment[0]\n segment = \\\n self.controller.shared_data.obj_track.get_segment(segment_idx)\n\n if len(selected_segment) == 1:\n if segment.shape[0] > constants.fix_thr:\n try:\n self.controller.shared_data.obj_track.fix_elevation(\n segment_idx)\n except ValueError:\n self.controller.shared_data.obj_track.smooth_elevation(\n segment_idx)\n else:\n self.controller.shared_data.obj_track.smooth_elevation(\n segment_idx)\n\n plots.update_plots(\n self.controller.shared_data.obj_track,\n self.controller.shared_data.ax_track,\n self.controller.shared_data.ax_ele,\n self.controller.shared_data.ax_track_info,\n canvas=self.controller.shared_data.canvas)\n\n elif len(selected_segment) > 1:\n messagebox.showerror('Warning',\n 'More than one segment is selected')\n elif len(selected_segment) == 0:\n messagebox.showerror('Warning',\n 'No segment is selected')","def fix_nonerrors(self):\n if not self.only_error:\n return\n self.line = None\n self.filename = None","def ic_fill():\n text = \"! Add missing Atoms and assign them coordinates\\n\"\n text += \"ic fill preserve\\nic param\\nic build\\nhbuild\\n\\n\"\n return text","def correctPending(self):\n if self.lastPainted:\n self.doPaint(self.lastPainted[0], self.lastPainted[1], self.colors['idle'], \"gray75\")\n self.lastPainted = None","def begin_fill(*args,**kwargs):\n if(len(args)==2 and len(kwargs)==0):\n turtleTmp.begin_fill(args[0], args[1])\n elif (len(args)==1 and len(kwargs)==0):\n turtleTmp.begin_fill(args[0], turtleTmp.color)\n elif (len(args)==0 and len(kwargs)==1):\n if(\"borderColor\" in kwargs):\n turtleTmp.begin_fill(kwargs[\"borderColor\"], turtleTmp.color)\n else:\n turtleTmp.begin_fill(turtleTmp.color, kwargs[\"fillColor\"])\n elif (len(args)==1 and len(kwargs)==1):\n if(\"borderColor\" in kwargs):\n turtleTmp.begin_fill(kwargs[\"borderColor\"], args[0])\n else:\n turtleTmp.begin_fill(args[0], kwargs[\"fillColor\"])\n elif(len(kwargs)==2 and len(args)==0):\n turtleTmp.begin_fill(kwargs[\"borderColor\"], kwargs[\"fillColor\"])\n else:\n turtleTmp.begin_fill(turtleTmp.color, turtleTmp.color)","def _settle_shape(self, shape):\n if shape:\n for block in shape.blocks:\n self.array[block.row_position][block.column_position] = block\n self.remove_completed_lines()","def trailing_stop_loss_on_fill(self, trailing_stop_loss_on_fill):\n\n self._trailing_stop_loss_on_fill = trailing_stop_loss_on_fill","def trailing_stop_loss_on_fill(self, trailing_stop_loss_on_fill):\n\n self._trailing_stop_loss_on_fill = trailing_stop_loss_on_fill","def fill():\n # Switch in edit mode\n bpy.ops.object.mode_set(mode = 'EDIT')\n \n # Fill hole\n bpy.ops.mesh.fill()","def testSettled(self):\n self.injectEvent(safe.Grabbing.GRABBED)\n self.assertCurrentState(safe.Surface)","def validate(self):\n self.parent.copyCurrentWinState(self.pltw)\n if self.incr:\n self.pltw.blklst[self.blkno][self.ypos] = self.data[2]\n else:\n self.pltw.blklst[self.blkno][self.ypos] = self.data[2][::-1]\n self.pltw.dirty = True\n self.pltw.activecurv = self.cpos\n self.pltw.updatePlot()\n self.parent.updateUI()\n self.hide()","def paint(self):\r\n self.canvas.delete(tkinter.ALL)\r\n self.visit(self.tree.root)","def validate(self):\n self.parent.copyCurrentWinState(self.pltw)\n self.pltw.blklst[self.blkno][self.ypos] = self.data[2]\n self.pltw.dirty = True\n self.pltw.activecurv = self.cpos\n self.pltw.updatePlot()\n self.parent.smoothtyp = self.type\n self.parent.smoothFilter = self.nfilter\n self.parent.smoothpass = self.npass\n self.parent.updateUI()\n self.hide()","def setOutline(self, color):\n self._reconfig(\"outline\", color)","def fill(self, color):\n self.format.fill(self, color)","def _switch(self):\n self.fill= not self.fill","def fill(self, fill_rule='nonzero', preserve=False):\n self._impl.new_path()\n yield\n if fill_rule is 'evenodd':\n self._impl.fill(fill_rule, preserve)\n else:\n self._impl.fill('nonzero', preserve)","def exit(self):\n if self.currentEditor is not None:\n self.currentEditor.highlight()\n self.currentEditor = None\n \n for editor in self.editors:\n editor.refreshCoverageAnnotations()\n \n self.__setSbFile()","def on_size(self, *args):\n self.canvas.before.clear()\n if hasattr(self, 'warn'):\n color = (.8, 0, 0) if self.warn else (0, .5, 0)\n else:\n color = (0, .5, 0)\n with self.canvas.before:\n Color(*color, 0.25)\n Rectangle(pos=self.pos, size=self.size)","def validate(self):\n self.pltw.blklst[self.blkno][self.ypos] = self.data[2]\n self.pltw.updatePlot()\n self.pltw.dirty = True\n self.parent.fitmodel = self.model\n self.pltw.activecurv = self.cpos\n self.parent.updateUI()\n self.hide()","def fill(self, x, y, color):\n raise NotImplementedError # Override this function in the Solution classes","def grabComplete(self): #$NON-NLS-1$\r","def validate(self):\n self.pltw.blklst[self.blkno][self.ypos] = self.data[2]\n self.pltw.updatePlot()\n self.pltw.dirty = True\n self.pltw.activecurv = self.cpos\n self.parent.updateUI()\n self.hide()","def validate(self):\n self.pltw.blklst[self.blkno][self.ypos] = self.data[2]\n self.pltw.updatePlot()\n self.pltw.dirty = True\n self.pltw.activecurv = self.cpos\n self.parent.updateUI()\n self.hide()","def _clear(self):\n self._fillitem = self._fillpath = None\n for item in self.items:\n self.screen._delete(item)\n self.currentLineItem = self.screen._createline()\n self.currentLine = []\n if self._drawing:\n self.currentLine.append(self._position)\n self.items = [self.currentLineItem]\n self.clearstamps()","def end(self):\n #self.manipulator_restore()\n #self.header_text_restore()\n #self.cursor_modal_restore()\n pass","def _finalize_strokes(self, strokes, lines=None):\n for i, offsets in tqdm(enumerate(strokes)):\n if lines and not lines[i]:\n print(\"Empty line? Stroke:\")\n print(offsets[:10])\n continue\n\n offsets[:, :2] *= 1.5\n curr_strokes = drawing.offsets_to_coords(offsets)\n curr_strokes = drawing.denoise(curr_strokes)\n curr_strokes[:, :2] = drawing.align(curr_strokes[:, :2])\n\n # Normalize\n curr_strokes[:, 1] -= np.min(curr_strokes[:, 1])\n max_y = np.max(curr_strokes[:, 1])\n if max_y:\n curr_strokes[:, :2] /= max_y\n else:\n warnings.warn(f\"max y is zero {curr_strokes}\")\n\n # Convert end points to start points\n #curr_strokes = eos_to_sos(curr_strokes)\n\n yield curr_strokes","def test_mark_status_after_single_area_perturbation(self):\n F = FaultDiagnosis(\"tests/TOY_graph.csv\")\n F.simulate_area_perturbation([\"area1\"])\n\n mark_status_after_area_perturbation = {\n '2': 'ACTIVE',\n '3': 'ACTIVE',\n '4': 'ACTIVE',\n '5': 'ACTIVE',\n '6': 'ACTIVE',\n '7': 'ACTIVE',\n '8': 'ACTIVE',\n '9': 'ACTIVE',\n '10': 'ACTIVE',\n '11': 'ACTIVE',\n '12': 'ACTIVE',\n '13': 'ACTIVE',\n '14': 'ACTIVE',\n '15': 'ACTIVE',\n '16': 'ACTIVE',\n '17': 'ACTIVE',\n '18': 'ACTIVE',\n '19': 'ACTIVE'\n }\n\n self.assertDictEqual(\n mark_status_after_area_perturbation,\n F.G.mark_status,\n msg=\"FINAL MARK STATUS failure: perturbation in area 1\")","def finishStroke(self, pos):\n windowX = pos[0] - self.window.rect[0]\n windowY = pos[1] - self.window.rect[1]\n endPos = (windowX, windowY)\n if self.strokePos:\n self.strokes.append( (self.strokePos, endPos, self.color) )\n self.setDirty()\n self.strokePos = endPos","def try_decoration(self, func):\n while True:\n try:\n func()\n break\n except:\n print(\"\")","def handler(signum, frame, spinner):\n spinner.red.fail(\"✘\")\n spinner.stop()","def _focus_exit(self):\n self._switch(exiting=True)","def remove_fill(settings):\r\n if settings.fillstyle == 'fill':\r\n settings.fillstyle = 'none'\r\n\r\n elif settings.fillstyle == 'fill+border':\r\n settings.fillstyle = 'border'\r\n return","def on_fill(self, oid, body):\n\t\tlogger.info('Consuming filled Order')\n\t\tfill = body['fill']\n\n\t\t# update the position first\n\t\tself.pos[fill.symbol].on_fill(fill)\n\n\t\t# getting data from the fill event\n\t\tQ = fill.quantity\n\t\tK, D, C = fill.fill_cost, fill.fill_type, fill.commission\n\n\t\tcost = D.value * K * Q\n\n\t\tself.commission += C\n\t\tself.cash -= cost + C","def __exit__(self, exc_type, exc_val, exc_tb):\n self._finalize()\n # Do not return anything to pass on all other exceptions.","def clear_entry(event):\n\tbackground = event.widget.config()['background'][-1];\n\tif(background==ERROR_COLOR):\n\t\tevent.widget.delete(0, \"end\")\n\t\tevent.widget.config(bg=WHITE)\n\tfeedback.config(text=\"\", fg=ERROR_COLOR);","def FillupArea(self):\r\n\r\n drillsize = self.FromUserUnit(float(self.m_txtViaDrillSize.GetValue()))\r\n viasize = self.FromUserUnit(float(self.m_txtViaSize.GetValue()))\r\n step_x = self.FromUserUnit(float(self.m_txtHSpacing.GetValue()))\r\n step_y = self.FromUserUnit(float(self.m_txtVSpacing.GetValue()))\r\n clearance = self.FromUserUnit(float(self.m_txtClearance.GetValue()))\r\n self.randomize = self.m_chkRandomize.GetValue()\r\n self.clearance = clearance\r\n bbox = self.area.GetBoundingBox()\r\n top = bbox.GetTop()\r\n bottom = bbox.GetBottom()\r\n right = bbox.GetRight()\r\n left = bbox.GetLeft()\r\n netname = self.m_cbNet.GetStringSelection()\r\n netcode = self.board.GetNetcodeFromNetname(netname)\r\n # commit = pcbnew.COMMIT()\r\n viacount = 0\r\n x = left\r\n\r\n # Cycle trough area bounding box checking and implanting vias\r\n layer = self.area.GetLayer()\r\n\r\n while x <= right:\r\n y = top\r\n while y <= bottom:\r\n if self.randomize:\r\n xp = x + random.uniform(-1, 1) * step_x / 5\r\n yp = y + random.uniform(-1, 1) * step_y / 5\r\n else:\r\n xp = x\r\n yp = y\r\n\r\n if hasattr(pcbnew, 'VECTOR2I'):\r\n p = pcbnew.VECTOR2I(xp, yp)\r\n else:\r\n if(hasattr(pcbnew, 'wxPoint')):\r\n p = pcbnew.wxPoint(xp, yp)\r\n\r\n if self.area.HitTestFilledArea(layer, p, 0):\r\n via = pcbnew.PCB_VIA(self.board)\r\n via.SetPosition(p)\r\n via.SetLayer(layer)\r\n via.SetNetCode(netcode)\r\n # Set up via with clearance added to its size-> bounding box check will be OK in worst case, may be too conservative, but additional checks are possible if needed\r\n # TODO: possibly take the clearance from the PCB settings instead of the dialog\r\n # Clearance is all around -> *2\r\n via.SetDrill(drillsize + 2 * clearance)\r\n via.SetWidth(viasize + 2 * clearance)\r\n # via.SetTimeStamp(__timecode__)\r\n if not self.CheckOverlap(via):\r\n # Check clearance only if clearance value differs from 0 (disabled)\r\n if (clearance == 0) or self.CheckClearance(via, self.area, clearance):\r\n via.SetWidth(viasize)\r\n via.SetDrill(drillsize)\r\n self.board.Add(via)\r\n # commit.Add(via)\r\n self.pcb_group.AddItem(via)\r\n viacount += 1\r\n y += step_y\r\n x += step_x\r\n\r\n if viacount > 0:\r\n wx.MessageBox(_(u\"Implanted: %d vias!\") % viacount)\r\n # commit.Push()\r\n pcbnew.Refresh()\r\n else:\r\n wx.MessageBox(_(u\"No vias implanted!\"))","def move_draught_end(event):\n global red_draughts, white_draughts\n global board_array\n global old_point\n global die_1_num, die_2_num, doubles\n draught = board.find_withtag(CURRENT)[0]\n #Figure out which point they want to put it on\n bottom = (event.y-click_offset[1] >= board_height//2)\n point_left_edges = [board_divisions*i for i in xrange(0,15) if i != 7]\n is_red = draught in red_draughts\n if bottom == False:\n new_point = 12+point_left_edges.index(min(point_left_edges, key=lambda x:abs(x-event.x+click_offset[0])))\n else:\n new_point = 13-point_left_edges.index(min(point_left_edges, key=lambda x:abs(x-event.x+click_offset[0]))) \n #Check legality\n if(board_array[new_point][1] > 1 and is_red) or (board_array[new_point][0] > 1 and not is_red): #if too many opposite color on square\n draw_draughts()\n return\n if(board_array[0][0] > 0 and is_red and old_point != 0)or(board_array[25][1] > 0 and not is_red and old_point != 25):#Obligated to move off bar first\n draw_draughts()\n return\n if(new_point == 0 and not is_red): #if white trying to bear off\n for i in xrange(7,26):\n if(board_array[i][1] > 0): #If white has a piece outside home, can't bear off\n draw_draughts()\n return\n if(new_point == 25 and is_red): #if red trying to bear off\n for i in xrange(0,18):\n if(board_array[i][0] > 0): #If red has a piece outside home, can't bear off\n draw_draughts()\n return \n \n if(new_point-old_point == die_1_num and is_red) or (old_point-new_point == die_1_num and not is_red):\n if(doubles == False) or (die_2_num != 0):\n die_1_num = 0\n else: \n die_2_num = die_1_num\n doubles = False\n elif(new_point-old_point == die_2_num and is_red) or (old_point-new_point == die_2_num and not is_red):\n if(doubles == False) or (die_1_num != 0):\n die_2_num = 0\n else: \n die_1_num = die_2_num\n doubles = False\n else: #Can't move there on this roll\n draw_draughts()\n return\n update_dice()\n #Update board_array\n if is_red:\n board_array[old_point][0] -= 1\n board_array[new_point][0] += 1\n if(board_array[new_point][1] == 1): #Handle hits\n board_array[new_point][1] -= 1\n board_array[25][1] += 1\n else:\n board_array[old_point][1] -= 1\n board_array[new_point][1] += 1\n if(board_array[new_point][0] == 1): #Handle hits\n board_array[new_point][0] -= 1\n board_array[0][0] += 1\n\n draw_draughts()\n if(die_1_num == 0 and die_2_num == 0):\n comp_turn()","async def __aexit__(self, exc_type, exc_val, exc_tb):\n pass","def test_05_valid_stroke(self):\n stroke_record = SwimRecord(stroke='doggie paddle')\n try:\n stroke_record.full_clean()\n except ValidationError as e:\n self.assertTrue(\"doggie paddle is not a valid stroke\" in e.message_dict['stroke'])","def BraceBadLight(self, pos):\n # Check if we are still alive or not, as this may be called\n # after we have been deleted.\n if self:\n super(EditraBaseStc, self).BraceBadLight(pos)","def setFill(self, fill):\n self.area_show = fill","def visit(self):\n self.tree = self.recursive_visit(self.tree)\n # assert self.current_line == self.tree.absolute_bounding_box.bottom_right.line","def fill_single_street():\n if facing_north():\n if not on_beeper():\n if not front_is_clear():\n turn_right()\n move()\n if not on_beeper():\n turn_around()\n # back to the initial position\n move()\n turn_around()\n fill_one_line()","def let_shape_fall(self):\n if self.falling_shape:\n self.falling_shape.lower_shape_by_one_row()\n if self.shape_cannot_be_placed(self.falling_shape):\n self.falling_shape.raise_shape_by_one_row()\n if self.shape_cannot_be_placed(self.falling_shape):\n self.end_game()\n else:\n self.settle_falilng_shape()\n return True","def assertion_errored(self, func, exception):","def __gotoBrace(self):\n self.activeWindow().moveToMatchingBrace()","def _go_to_first_blank(self, box):\n for y in range(4, 41):\n self.box2.move(y, 4)\n if chr(self.box2.inch() & 0xFF) == ' ': # binary and because char is in bottom 8 bits.\n self.box2.move(y + 1, 4)\n if chr(self.box2.inch() & 0xFF) == ' ': # look for 2 blank lines in a raw\n y, x = self.box2.getyx() # store position, we can add new alert below\n try:\n if chr(self.box2.inch(y + 1, x) & 0xFF) == ' ':\n return y\n except curses.error: # this is the case where we had 2 blank lines but these were the last 2 lines\n pass # of the screen. We can't /n + write two lines so we need to proceed to screen scrolling\n # screen is filled with alerts\n self.box2.scrollok(True)\n self.box2.move(4, 4)\n self.box2.setscrreg(4, 41)\n self.box2.scroll(4)\n self.box2.box() # need to redraw borders\n return self._go_to_first_blank(self.box2)","def test_invalidate_error():\n \n test_object = fa.read_in_envision(data_csv=plate_2_repeat, platemap_csv=plate_map_file, data_type='plate', size=384)\n test_object.invalidate() # execute the invalidate function without specifying well ids, rows or columns to be invalidated","def show_crash(self): \n # Allows lander to crash on to moon's surface\n if self.lander_polygon:\n self.lander_polygon.undraw()\n self.lander_polygon = graphics.Polygon(graphics.Point(self.win.width / 2 - 10, 0),\n graphics.Point(self.win.width/2 - 3, 10),\n graphics.Point(self.win.width/2 + 3, 10),\n graphics.Point(self.win.width/2 + 10, 0))\n self.lander_polygon.setFill(\"blue\")\n self.lander_polygon.draw(self.win)\n \n self.text = graphics.Text(graphics.Point(150, 90), 'You crashed! Oh no!')\n self.text.draw(self.win)\n \n # Draws fire around crashed lander\n self.fire = graphics.Polygon(graphics.Point(110, 0), graphics.Point(110, 20), graphics.Point(120, 15), graphics.Point(130, 20), graphics.Point(130, 0), graphics.Point(110, 0))\n self.fire.setFill('red')\n self.fire.draw(self.win)\n \n # Draws more fire around crashed lander\n self.fire_2 = graphics.Polygon(graphics.Point(170, 0), graphics.Point(170, 20), graphics.Point(180, 15), graphics.Point(190, 20), graphics.Point(190, 0), graphics.Point(170, 0))\n self.fire_2.setFill('red')\n self.fire_2.draw(self.win)\n print(\"Crash! Oh noes!\")","def _finalize(cls, ret, counter, fill_value):\n pass","def reset_cause():","def assertion_failed(self, func, exception):","def fill(self) -> int:\n return self._fill_color","def on_step(self) -> None:\r\n\r\n if self.board == None:\r\n return\r\n\r\n TkState.disable(self.edit_menu.winfo_children())\r\n TkState.enable([self.reset_button])\r\n self.anim_board.next_gen()\r\n self.on_new_generation()\r\n self.painter.draw_board()","def border(self):\n ...","def Redraw(self):\n print(\"EMPTY VIEW REDRAW\")","def __exit__(\r\n self, exc_type: Type,\r\n exc_value: Any,\r\n traceback: Any) -> None:\r\n from apysc.expression import expression_file_util\r\n from apysc.expression import last_scope\r\n from apysc.expression.last_scope import LastScope\r\n from apysc.type import revert_interface\r\n revert_interface.revert_each_scope_vars(\r\n snapshot_name=self._snapshot_name,\r\n locals_=self._locals, globals_=self._globals)\r\n self._indent.__exit__()\r\n expression_file_util.append_js_expression(expression='}')\r\n last_scope.set_last_scope(value=LastScope.FOR)","def _draw_handler(self, bpy_dummy_self, bpy_dummy_context):\r\n self._drawRays()","def clear_complete_lines():\n global board\n\n\n nb = []\n fn = []\n for idl, line in enumerate(board):\n if 0 in line:\n # Not full\n nb.append(line)\n else:\n fn.append(idl)\n\n if fn:\n # Update the board information\n board = new_board_lines(len(fn)) + nb\n\n # clear\n d_line = [obj for obj in scene.objects if type(obj) is box and obj.y in fn]\n for _ in xrange(10):\n rate(20)\n for obj in d_line:\n obj.opacity -= 0.1\n for obj in d_line:\n obj.visible = 0\n\n\n # decline\n for n in fn:\n for obj in (obj for obj in scene.objects if type(obj) is box and obj.y < n):\n obj.y += 1\n\n return fn","def outline(color=\"white\", linewidth=3, **kwargs):\n return [pe.withStroke(linewidth=linewidth, foreground=color, **kwargs)]","def __exit__(self, exc_type, exc_value, traceback):\n pass","def check_if_filled(self, new_cell, cell_color, filled_edges, filled_surrounded):\n new_cell_color = self.get_color(new_cell)\n if new_cell_color != cell_color:\n return False\n\n if new_cell not in filled_edges + filled_surrounded:\n filled_edges.append(new_cell)\n\n return True","def __exit__(self, exc_type, exc_value, traceback):\n return None","def fix_bug(self):\n self.bugged = False\n self.error_prob = 0.0","def setFilled(self, fill):\n isFilled = fill\n repaint()","def _handle_reset(self):\n # reset own state\n self.grbl_version = None\n self.in_check_mode = False\n self.line_active = False\n # wait for init\n self._wait_for_grbl_init()","def test_reset_limit_on_dedent(self):\n indenter = indent.Indenter()\n indenter.indentation = -2\n self.assertRaises(ValueError, indenter.dedent)\n indenter.indentation = -1\n self.assertRaises(ValueError, indenter.dedent)\n indenter.indentation = 0\n self.assertRaises(ValueError, indenter.dedent)\n indenter.indentation = +1\n indenter.dedent()\n indenter.indentation = +2\n indenter.dedent()"],"string":"[\n \"def end_fill():\\n turtleTmp.end_fill()\",\n \"def test_outline_fills(self):\\n image = self.design.layout.layers[0].images[0]\\n assert len(image.fills) == 2\",\n \"def fillbox(self,event=None):\\n \\n pass\",\n \"def update_fill(self, event):\\r\\n\\r\\n if event.type == 'FILL':\\r\\n self.update_positions_from_fill(event)\\r\\n self.update_holdings_from_fill(event)\",\n \"def update_fill(self, event):\\n if event.type == 'FILL':\\n self.update_positions_from_fill(event)\\n self.update_holdings_from_fill(event)\",\n \"def update_fill(self, event):\\n if event.type == 'FILL':\\n self.update_positions_from_fill(event)\\n self.update_holdings_from_fill(event)\",\n \"def stop_filling(self, signum, frame):\\n self._filling = False\",\n \"def stroke(self):\\n yield\\n self._impl.stroke()\",\n \"def _handle_border(self, i_row, i_col, adj_opp_cells, check_func, loc):\\n check_func(i_row, i_col, adj_opp_cells, loc)\\n #check_func will be any of the five functions listed below\",\n \"def stroke(self, path, clr):\\n pass\",\n \"def excepthook(self, type, value, tb):\\n \\n self.InteractiveTB(type, value, tb, tb_offset=0)\\n if self.InteractiveTB.call_pdb and self.has_readline:\\n self.readline.set_completer(self.Completer.complete)\",\n \"def test_area_error_when_normalize_but_no_fill_color_stack():\\n result = CliRunner().invoke(area, [\\\"-N\\\", *NORMAL_ARGS])\\n assert result.exit_code == 1\\n assert (\\n \\\"ConflictingArgs: -c/--colorvar needs to be specified when creating a normalized (i.e. stacked) chart\\\"\\n in result.output.strip()\\n )\",\n \"def __exit__(self, exc_type, exc_value, exc_tb) -> None:\\n lib.wlr_seat_keyboard_end_grab(self._seat)\",\n \"def fill(self, color):\",\n \"def __exit__(self, exception, value, trace):\\n self.manual_exit()\",\n \"def fill(self):\\n return self._turtle.fill()\",\n \"def fill(self, path, clr):\\n pass\",\n \"def _draw_outline(self) -> None:\\n stroke = self.border_thickness\\n\\n # draw outline rectangle\\n for _w in range(self.widget_width):\\n for line in range(stroke):\\n self._bitmap[_w, line] = 1\\n self._bitmap[_w, self.widget_height - 1 - line] = 1\\n for _h in range(self.widget_height):\\n for line in range(stroke):\\n self._bitmap[line, _h] = 1\\n self._bitmap[self.widget_width - 1 - line, _h] = 1\",\n \"def EndDraw(self):\\r\\n\\r\\n pass\",\n \"def fill(self, colour: int, /) -> None:\",\n \"def __exit__(self, _type, value, traceback):\\n self.obj.write(\\\"]\\\")\\n self.obj.close()\",\n \"def onA(self, event):\\r\\n if event.state == 4:\\r\\n self.selectAll()\\r\\n return \\\"break\\\"\",\n \"def stop_loss_on_fill(self, stop_loss_on_fill):\\n\\n self._stop_loss_on_fill = stop_loss_on_fill\",\n \"def stop_loss_on_fill(self, stop_loss_on_fill):\\n\\n self._stop_loss_on_fill = stop_loss_on_fill\",\n \"def __exit__(exc_type, value, traceback):\\n del exc_type\\n del value\\n del traceback\\n\\n IndentedLogger._indent_level -= 1\\n\\n if (IndentedLogger._indent_level == 0 and\\n IndentedLogger._printed_on_secondary_indents):\\n print_message(\\\"\\\\n\\\")\\n IndentedLogger._printed_on_secondary_indents = False\",\n \"def _clear(self, event):\\n if self.ignore(event) or self._changed_canvas():\\n return\\n self._background = self.canvas.copy_from_bbox(self.ax.bbox)\\n self.ax.draw_artist(self._checks)\\n if hasattr(self, '_lines'):\\n for l1, l2 in self._lines:\\n self.ax.draw_artist(l1)\\n self.ax.draw_artist(l2)\",\n \"def update_fill(self, event):\\n if event.type == 'FILL':\\n self.update_positions_from_fill(event)\\n self.update_prices_from_fill(event)\\n self.update_holdings_from_fill(event)\",\n \"def __exit__(self, _type, _value, _traceback):\\n self.dispose()\",\n \"def fill_row(nono, row):\\n # Filling inside the blocks\\n changed_1 = fill_inside_of_the_blocks(nono, row)\\n # Marking as empty beggining of the line\\n changed_2 = fill_beggining_of_the_row(nono, row)\\n # Marking as empty end of the line\\n changed_3 = fill_end_of_the_row(nono, row)\\n # Marking as empty area between blocks\\n changed_4 = fill_between_the_blocks(nono, row)\\n\\n sth_changed = changed_1 or changed_2 or changed_3 or changed_4\\n\\n # if nonogram is in the interactive mode, update plot\\n if nono.mode_data.is_interactive_plot_active() and sth_changed:\\n nono.update_plot()\\n\\n return sth_changed\",\n \"def fill(layer, event):\\n # on press\\n layer.fill(layer.coordinates, layer._value, layer.selected_label)\",\n \"def remove_stroke(settings):\\r\\n if settings.fillstyle == 'border':\\r\\n settings.fillstyle = 'none'\\r\\n elif settings.fillstyle == 'fill+border':\\r\\n settings.fg = settings.bg\\r\\n settings.fillstyle = 'fill'\",\n \"def flush(self):\\n if self.fill:\\n self._turtle.fill(False)\\n self._turtle.fill(True)\",\n \"def line(self, arg, fill):\\n pass\",\n \"def fix_elevation(self):\\n selected_segment = \\\\\\n self.controller.shared_data.obj_track.selected_segment_idx\\n segment_idx = selected_segment[0]\\n segment = \\\\\\n self.controller.shared_data.obj_track.get_segment(segment_idx)\\n\\n if len(selected_segment) == 1:\\n if segment.shape[0] > constants.fix_thr:\\n try:\\n self.controller.shared_data.obj_track.fix_elevation(\\n segment_idx)\\n except ValueError:\\n self.controller.shared_data.obj_track.smooth_elevation(\\n segment_idx)\\n else:\\n self.controller.shared_data.obj_track.smooth_elevation(\\n segment_idx)\\n\\n plots.update_plots(\\n self.controller.shared_data.obj_track,\\n self.controller.shared_data.ax_track,\\n self.controller.shared_data.ax_ele,\\n self.controller.shared_data.ax_track_info,\\n canvas=self.controller.shared_data.canvas)\\n\\n elif len(selected_segment) > 1:\\n messagebox.showerror('Warning',\\n 'More than one segment is selected')\\n elif len(selected_segment) == 0:\\n messagebox.showerror('Warning',\\n 'No segment is selected')\",\n \"def fix_nonerrors(self):\\n if not self.only_error:\\n return\\n self.line = None\\n self.filename = None\",\n \"def ic_fill():\\n text = \\\"! Add missing Atoms and assign them coordinates\\\\n\\\"\\n text += \\\"ic fill preserve\\\\nic param\\\\nic build\\\\nhbuild\\\\n\\\\n\\\"\\n return text\",\n \"def correctPending(self):\\n if self.lastPainted:\\n self.doPaint(self.lastPainted[0], self.lastPainted[1], self.colors['idle'], \\\"gray75\\\")\\n self.lastPainted = None\",\n \"def begin_fill(*args,**kwargs):\\n if(len(args)==2 and len(kwargs)==0):\\n turtleTmp.begin_fill(args[0], args[1])\\n elif (len(args)==1 and len(kwargs)==0):\\n turtleTmp.begin_fill(args[0], turtleTmp.color)\\n elif (len(args)==0 and len(kwargs)==1):\\n if(\\\"borderColor\\\" in kwargs):\\n turtleTmp.begin_fill(kwargs[\\\"borderColor\\\"], turtleTmp.color)\\n else:\\n turtleTmp.begin_fill(turtleTmp.color, kwargs[\\\"fillColor\\\"])\\n elif (len(args)==1 and len(kwargs)==1):\\n if(\\\"borderColor\\\" in kwargs):\\n turtleTmp.begin_fill(kwargs[\\\"borderColor\\\"], args[0])\\n else:\\n turtleTmp.begin_fill(args[0], kwargs[\\\"fillColor\\\"])\\n elif(len(kwargs)==2 and len(args)==0):\\n turtleTmp.begin_fill(kwargs[\\\"borderColor\\\"], kwargs[\\\"fillColor\\\"])\\n else:\\n turtleTmp.begin_fill(turtleTmp.color, turtleTmp.color)\",\n \"def _settle_shape(self, shape):\\n if shape:\\n for block in shape.blocks:\\n self.array[block.row_position][block.column_position] = block\\n self.remove_completed_lines()\",\n \"def trailing_stop_loss_on_fill(self, trailing_stop_loss_on_fill):\\n\\n self._trailing_stop_loss_on_fill = trailing_stop_loss_on_fill\",\n \"def trailing_stop_loss_on_fill(self, trailing_stop_loss_on_fill):\\n\\n self._trailing_stop_loss_on_fill = trailing_stop_loss_on_fill\",\n \"def fill():\\n # Switch in edit mode\\n bpy.ops.object.mode_set(mode = 'EDIT')\\n \\n # Fill hole\\n bpy.ops.mesh.fill()\",\n \"def testSettled(self):\\n self.injectEvent(safe.Grabbing.GRABBED)\\n self.assertCurrentState(safe.Surface)\",\n \"def validate(self):\\n self.parent.copyCurrentWinState(self.pltw)\\n if self.incr:\\n self.pltw.blklst[self.blkno][self.ypos] = self.data[2]\\n else:\\n self.pltw.blklst[self.blkno][self.ypos] = self.data[2][::-1]\\n self.pltw.dirty = True\\n self.pltw.activecurv = self.cpos\\n self.pltw.updatePlot()\\n self.parent.updateUI()\\n self.hide()\",\n \"def paint(self):\\r\\n self.canvas.delete(tkinter.ALL)\\r\\n self.visit(self.tree.root)\",\n \"def validate(self):\\n self.parent.copyCurrentWinState(self.pltw)\\n self.pltw.blklst[self.blkno][self.ypos] = self.data[2]\\n self.pltw.dirty = True\\n self.pltw.activecurv = self.cpos\\n self.pltw.updatePlot()\\n self.parent.smoothtyp = self.type\\n self.parent.smoothFilter = self.nfilter\\n self.parent.smoothpass = self.npass\\n self.parent.updateUI()\\n self.hide()\",\n \"def setOutline(self, color):\\n self._reconfig(\\\"outline\\\", color)\",\n \"def fill(self, color):\\n self.format.fill(self, color)\",\n \"def _switch(self):\\n self.fill= not self.fill\",\n \"def fill(self, fill_rule='nonzero', preserve=False):\\n self._impl.new_path()\\n yield\\n if fill_rule is 'evenodd':\\n self._impl.fill(fill_rule, preserve)\\n else:\\n self._impl.fill('nonzero', preserve)\",\n \"def exit(self):\\n if self.currentEditor is not None:\\n self.currentEditor.highlight()\\n self.currentEditor = None\\n \\n for editor in self.editors:\\n editor.refreshCoverageAnnotations()\\n \\n self.__setSbFile()\",\n \"def on_size(self, *args):\\n self.canvas.before.clear()\\n if hasattr(self, 'warn'):\\n color = (.8, 0, 0) if self.warn else (0, .5, 0)\\n else:\\n color = (0, .5, 0)\\n with self.canvas.before:\\n Color(*color, 0.25)\\n Rectangle(pos=self.pos, size=self.size)\",\n \"def validate(self):\\n self.pltw.blklst[self.blkno][self.ypos] = self.data[2]\\n self.pltw.updatePlot()\\n self.pltw.dirty = True\\n self.parent.fitmodel = self.model\\n self.pltw.activecurv = self.cpos\\n self.parent.updateUI()\\n self.hide()\",\n \"def fill(self, x, y, color):\\n raise NotImplementedError # Override this function in the Solution classes\",\n \"def grabComplete(self): #$NON-NLS-1$\\r\",\n \"def validate(self):\\n self.pltw.blklst[self.blkno][self.ypos] = self.data[2]\\n self.pltw.updatePlot()\\n self.pltw.dirty = True\\n self.pltw.activecurv = self.cpos\\n self.parent.updateUI()\\n self.hide()\",\n \"def validate(self):\\n self.pltw.blklst[self.blkno][self.ypos] = self.data[2]\\n self.pltw.updatePlot()\\n self.pltw.dirty = True\\n self.pltw.activecurv = self.cpos\\n self.parent.updateUI()\\n self.hide()\",\n \"def _clear(self):\\n self._fillitem = self._fillpath = None\\n for item in self.items:\\n self.screen._delete(item)\\n self.currentLineItem = self.screen._createline()\\n self.currentLine = []\\n if self._drawing:\\n self.currentLine.append(self._position)\\n self.items = [self.currentLineItem]\\n self.clearstamps()\",\n \"def end(self):\\n #self.manipulator_restore()\\n #self.header_text_restore()\\n #self.cursor_modal_restore()\\n pass\",\n \"def _finalize_strokes(self, strokes, lines=None):\\n for i, offsets in tqdm(enumerate(strokes)):\\n if lines and not lines[i]:\\n print(\\\"Empty line? Stroke:\\\")\\n print(offsets[:10])\\n continue\\n\\n offsets[:, :2] *= 1.5\\n curr_strokes = drawing.offsets_to_coords(offsets)\\n curr_strokes = drawing.denoise(curr_strokes)\\n curr_strokes[:, :2] = drawing.align(curr_strokes[:, :2])\\n\\n # Normalize\\n curr_strokes[:, 1] -= np.min(curr_strokes[:, 1])\\n max_y = np.max(curr_strokes[:, 1])\\n if max_y:\\n curr_strokes[:, :2] /= max_y\\n else:\\n warnings.warn(f\\\"max y is zero {curr_strokes}\\\")\\n\\n # Convert end points to start points\\n #curr_strokes = eos_to_sos(curr_strokes)\\n\\n yield curr_strokes\",\n \"def test_mark_status_after_single_area_perturbation(self):\\n F = FaultDiagnosis(\\\"tests/TOY_graph.csv\\\")\\n F.simulate_area_perturbation([\\\"area1\\\"])\\n\\n mark_status_after_area_perturbation = {\\n '2': 'ACTIVE',\\n '3': 'ACTIVE',\\n '4': 'ACTIVE',\\n '5': 'ACTIVE',\\n '6': 'ACTIVE',\\n '7': 'ACTIVE',\\n '8': 'ACTIVE',\\n '9': 'ACTIVE',\\n '10': 'ACTIVE',\\n '11': 'ACTIVE',\\n '12': 'ACTIVE',\\n '13': 'ACTIVE',\\n '14': 'ACTIVE',\\n '15': 'ACTIVE',\\n '16': 'ACTIVE',\\n '17': 'ACTIVE',\\n '18': 'ACTIVE',\\n '19': 'ACTIVE'\\n }\\n\\n self.assertDictEqual(\\n mark_status_after_area_perturbation,\\n F.G.mark_status,\\n msg=\\\"FINAL MARK STATUS failure: perturbation in area 1\\\")\",\n \"def finishStroke(self, pos):\\n windowX = pos[0] - self.window.rect[0]\\n windowY = pos[1] - self.window.rect[1]\\n endPos = (windowX, windowY)\\n if self.strokePos:\\n self.strokes.append( (self.strokePos, endPos, self.color) )\\n self.setDirty()\\n self.strokePos = endPos\",\n \"def try_decoration(self, func):\\n while True:\\n try:\\n func()\\n break\\n except:\\n print(\\\"\\\")\",\n \"def handler(signum, frame, spinner):\\n spinner.red.fail(\\\"✘\\\")\\n spinner.stop()\",\n \"def _focus_exit(self):\\n self._switch(exiting=True)\",\n \"def remove_fill(settings):\\r\\n if settings.fillstyle == 'fill':\\r\\n settings.fillstyle = 'none'\\r\\n\\r\\n elif settings.fillstyle == 'fill+border':\\r\\n settings.fillstyle = 'border'\\r\\n return\",\n \"def on_fill(self, oid, body):\\n\\t\\tlogger.info('Consuming filled Order')\\n\\t\\tfill = body['fill']\\n\\n\\t\\t# update the position first\\n\\t\\tself.pos[fill.symbol].on_fill(fill)\\n\\n\\t\\t# getting data from the fill event\\n\\t\\tQ = fill.quantity\\n\\t\\tK, D, C = fill.fill_cost, fill.fill_type, fill.commission\\n\\n\\t\\tcost = D.value * K * Q\\n\\n\\t\\tself.commission += C\\n\\t\\tself.cash -= cost + C\",\n \"def __exit__(self, exc_type, exc_val, exc_tb):\\n self._finalize()\\n # Do not return anything to pass on all other exceptions.\",\n \"def clear_entry(event):\\n\\tbackground = event.widget.config()['background'][-1];\\n\\tif(background==ERROR_COLOR):\\n\\t\\tevent.widget.delete(0, \\\"end\\\")\\n\\t\\tevent.widget.config(bg=WHITE)\\n\\tfeedback.config(text=\\\"\\\", fg=ERROR_COLOR);\",\n \"def FillupArea(self):\\r\\n\\r\\n drillsize = self.FromUserUnit(float(self.m_txtViaDrillSize.GetValue()))\\r\\n viasize = self.FromUserUnit(float(self.m_txtViaSize.GetValue()))\\r\\n step_x = self.FromUserUnit(float(self.m_txtHSpacing.GetValue()))\\r\\n step_y = self.FromUserUnit(float(self.m_txtVSpacing.GetValue()))\\r\\n clearance = self.FromUserUnit(float(self.m_txtClearance.GetValue()))\\r\\n self.randomize = self.m_chkRandomize.GetValue()\\r\\n self.clearance = clearance\\r\\n bbox = self.area.GetBoundingBox()\\r\\n top = bbox.GetTop()\\r\\n bottom = bbox.GetBottom()\\r\\n right = bbox.GetRight()\\r\\n left = bbox.GetLeft()\\r\\n netname = self.m_cbNet.GetStringSelection()\\r\\n netcode = self.board.GetNetcodeFromNetname(netname)\\r\\n # commit = pcbnew.COMMIT()\\r\\n viacount = 0\\r\\n x = left\\r\\n\\r\\n # Cycle trough area bounding box checking and implanting vias\\r\\n layer = self.area.GetLayer()\\r\\n\\r\\n while x <= right:\\r\\n y = top\\r\\n while y <= bottom:\\r\\n if self.randomize:\\r\\n xp = x + random.uniform(-1, 1) * step_x / 5\\r\\n yp = y + random.uniform(-1, 1) * step_y / 5\\r\\n else:\\r\\n xp = x\\r\\n yp = y\\r\\n\\r\\n if hasattr(pcbnew, 'VECTOR2I'):\\r\\n p = pcbnew.VECTOR2I(xp, yp)\\r\\n else:\\r\\n if(hasattr(pcbnew, 'wxPoint')):\\r\\n p = pcbnew.wxPoint(xp, yp)\\r\\n\\r\\n if self.area.HitTestFilledArea(layer, p, 0):\\r\\n via = pcbnew.PCB_VIA(self.board)\\r\\n via.SetPosition(p)\\r\\n via.SetLayer(layer)\\r\\n via.SetNetCode(netcode)\\r\\n # Set up via with clearance added to its size-> bounding box check will be OK in worst case, may be too conservative, but additional checks are possible if needed\\r\\n # TODO: possibly take the clearance from the PCB settings instead of the dialog\\r\\n # Clearance is all around -> *2\\r\\n via.SetDrill(drillsize + 2 * clearance)\\r\\n via.SetWidth(viasize + 2 * clearance)\\r\\n # via.SetTimeStamp(__timecode__)\\r\\n if not self.CheckOverlap(via):\\r\\n # Check clearance only if clearance value differs from 0 (disabled)\\r\\n if (clearance == 0) or self.CheckClearance(via, self.area, clearance):\\r\\n via.SetWidth(viasize)\\r\\n via.SetDrill(drillsize)\\r\\n self.board.Add(via)\\r\\n # commit.Add(via)\\r\\n self.pcb_group.AddItem(via)\\r\\n viacount += 1\\r\\n y += step_y\\r\\n x += step_x\\r\\n\\r\\n if viacount > 0:\\r\\n wx.MessageBox(_(u\\\"Implanted: %d vias!\\\") % viacount)\\r\\n # commit.Push()\\r\\n pcbnew.Refresh()\\r\\n else:\\r\\n wx.MessageBox(_(u\\\"No vias implanted!\\\"))\",\n \"def move_draught_end(event):\\n global red_draughts, white_draughts\\n global board_array\\n global old_point\\n global die_1_num, die_2_num, doubles\\n draught = board.find_withtag(CURRENT)[0]\\n #Figure out which point they want to put it on\\n bottom = (event.y-click_offset[1] >= board_height//2)\\n point_left_edges = [board_divisions*i for i in xrange(0,15) if i != 7]\\n is_red = draught in red_draughts\\n if bottom == False:\\n new_point = 12+point_left_edges.index(min(point_left_edges, key=lambda x:abs(x-event.x+click_offset[0])))\\n else:\\n new_point = 13-point_left_edges.index(min(point_left_edges, key=lambda x:abs(x-event.x+click_offset[0]))) \\n #Check legality\\n if(board_array[new_point][1] > 1 and is_red) or (board_array[new_point][0] > 1 and not is_red): #if too many opposite color on square\\n draw_draughts()\\n return\\n if(board_array[0][0] > 0 and is_red and old_point != 0)or(board_array[25][1] > 0 and not is_red and old_point != 25):#Obligated to move off bar first\\n draw_draughts()\\n return\\n if(new_point == 0 and not is_red): #if white trying to bear off\\n for i in xrange(7,26):\\n if(board_array[i][1] > 0): #If white has a piece outside home, can't bear off\\n draw_draughts()\\n return\\n if(new_point == 25 and is_red): #if red trying to bear off\\n for i in xrange(0,18):\\n if(board_array[i][0] > 0): #If red has a piece outside home, can't bear off\\n draw_draughts()\\n return \\n \\n if(new_point-old_point == die_1_num and is_red) or (old_point-new_point == die_1_num and not is_red):\\n if(doubles == False) or (die_2_num != 0):\\n die_1_num = 0\\n else: \\n die_2_num = die_1_num\\n doubles = False\\n elif(new_point-old_point == die_2_num and is_red) or (old_point-new_point == die_2_num and not is_red):\\n if(doubles == False) or (die_1_num != 0):\\n die_2_num = 0\\n else: \\n die_1_num = die_2_num\\n doubles = False\\n else: #Can't move there on this roll\\n draw_draughts()\\n return\\n update_dice()\\n #Update board_array\\n if is_red:\\n board_array[old_point][0] -= 1\\n board_array[new_point][0] += 1\\n if(board_array[new_point][1] == 1): #Handle hits\\n board_array[new_point][1] -= 1\\n board_array[25][1] += 1\\n else:\\n board_array[old_point][1] -= 1\\n board_array[new_point][1] += 1\\n if(board_array[new_point][0] == 1): #Handle hits\\n board_array[new_point][0] -= 1\\n board_array[0][0] += 1\\n\\n draw_draughts()\\n if(die_1_num == 0 and die_2_num == 0):\\n comp_turn()\",\n \"async def __aexit__(self, exc_type, exc_val, exc_tb):\\n pass\",\n \"def test_05_valid_stroke(self):\\n stroke_record = SwimRecord(stroke='doggie paddle')\\n try:\\n stroke_record.full_clean()\\n except ValidationError as e:\\n self.assertTrue(\\\"doggie paddle is not a valid stroke\\\" in e.message_dict['stroke'])\",\n \"def BraceBadLight(self, pos):\\n # Check if we are still alive or not, as this may be called\\n # after we have been deleted.\\n if self:\\n super(EditraBaseStc, self).BraceBadLight(pos)\",\n \"def setFill(self, fill):\\n self.area_show = fill\",\n \"def visit(self):\\n self.tree = self.recursive_visit(self.tree)\\n # assert self.current_line == self.tree.absolute_bounding_box.bottom_right.line\",\n \"def fill_single_street():\\n if facing_north():\\n if not on_beeper():\\n if not front_is_clear():\\n turn_right()\\n move()\\n if not on_beeper():\\n turn_around()\\n # back to the initial position\\n move()\\n turn_around()\\n fill_one_line()\",\n \"def let_shape_fall(self):\\n if self.falling_shape:\\n self.falling_shape.lower_shape_by_one_row()\\n if self.shape_cannot_be_placed(self.falling_shape):\\n self.falling_shape.raise_shape_by_one_row()\\n if self.shape_cannot_be_placed(self.falling_shape):\\n self.end_game()\\n else:\\n self.settle_falilng_shape()\\n return True\",\n \"def assertion_errored(self, func, exception):\",\n \"def __gotoBrace(self):\\n self.activeWindow().moveToMatchingBrace()\",\n \"def _go_to_first_blank(self, box):\\n for y in range(4, 41):\\n self.box2.move(y, 4)\\n if chr(self.box2.inch() & 0xFF) == ' ': # binary and because char is in bottom 8 bits.\\n self.box2.move(y + 1, 4)\\n if chr(self.box2.inch() & 0xFF) == ' ': # look for 2 blank lines in a raw\\n y, x = self.box2.getyx() # store position, we can add new alert below\\n try:\\n if chr(self.box2.inch(y + 1, x) & 0xFF) == ' ':\\n return y\\n except curses.error: # this is the case where we had 2 blank lines but these were the last 2 lines\\n pass # of the screen. We can't /n + write two lines so we need to proceed to screen scrolling\\n # screen is filled with alerts\\n self.box2.scrollok(True)\\n self.box2.move(4, 4)\\n self.box2.setscrreg(4, 41)\\n self.box2.scroll(4)\\n self.box2.box() # need to redraw borders\\n return self._go_to_first_blank(self.box2)\",\n \"def test_invalidate_error():\\n \\n test_object = fa.read_in_envision(data_csv=plate_2_repeat, platemap_csv=plate_map_file, data_type='plate', size=384)\\n test_object.invalidate() # execute the invalidate function without specifying well ids, rows or columns to be invalidated\",\n \"def show_crash(self): \\n # Allows lander to crash on to moon's surface\\n if self.lander_polygon:\\n self.lander_polygon.undraw()\\n self.lander_polygon = graphics.Polygon(graphics.Point(self.win.width / 2 - 10, 0),\\n graphics.Point(self.win.width/2 - 3, 10),\\n graphics.Point(self.win.width/2 + 3, 10),\\n graphics.Point(self.win.width/2 + 10, 0))\\n self.lander_polygon.setFill(\\\"blue\\\")\\n self.lander_polygon.draw(self.win)\\n \\n self.text = graphics.Text(graphics.Point(150, 90), 'You crashed! Oh no!')\\n self.text.draw(self.win)\\n \\n # Draws fire around crashed lander\\n self.fire = graphics.Polygon(graphics.Point(110, 0), graphics.Point(110, 20), graphics.Point(120, 15), graphics.Point(130, 20), graphics.Point(130, 0), graphics.Point(110, 0))\\n self.fire.setFill('red')\\n self.fire.draw(self.win)\\n \\n # Draws more fire around crashed lander\\n self.fire_2 = graphics.Polygon(graphics.Point(170, 0), graphics.Point(170, 20), graphics.Point(180, 15), graphics.Point(190, 20), graphics.Point(190, 0), graphics.Point(170, 0))\\n self.fire_2.setFill('red')\\n self.fire_2.draw(self.win)\\n print(\\\"Crash! Oh noes!\\\")\",\n \"def _finalize(cls, ret, counter, fill_value):\\n pass\",\n \"def reset_cause():\",\n \"def assertion_failed(self, func, exception):\",\n \"def fill(self) -> int:\\n return self._fill_color\",\n \"def on_step(self) -> None:\\r\\n\\r\\n if self.board == None:\\r\\n return\\r\\n\\r\\n TkState.disable(self.edit_menu.winfo_children())\\r\\n TkState.enable([self.reset_button])\\r\\n self.anim_board.next_gen()\\r\\n self.on_new_generation()\\r\\n self.painter.draw_board()\",\n \"def border(self):\\n ...\",\n \"def Redraw(self):\\n print(\\\"EMPTY VIEW REDRAW\\\")\",\n \"def __exit__(\\r\\n self, exc_type: Type,\\r\\n exc_value: Any,\\r\\n traceback: Any) -> None:\\r\\n from apysc.expression import expression_file_util\\r\\n from apysc.expression import last_scope\\r\\n from apysc.expression.last_scope import LastScope\\r\\n from apysc.type import revert_interface\\r\\n revert_interface.revert_each_scope_vars(\\r\\n snapshot_name=self._snapshot_name,\\r\\n locals_=self._locals, globals_=self._globals)\\r\\n self._indent.__exit__()\\r\\n expression_file_util.append_js_expression(expression='}')\\r\\n last_scope.set_last_scope(value=LastScope.FOR)\",\n \"def _draw_handler(self, bpy_dummy_self, bpy_dummy_context):\\r\\n self._drawRays()\",\n \"def clear_complete_lines():\\n global board\\n\\n\\n nb = []\\n fn = []\\n for idl, line in enumerate(board):\\n if 0 in line:\\n # Not full\\n nb.append(line)\\n else:\\n fn.append(idl)\\n\\n if fn:\\n # Update the board information\\n board = new_board_lines(len(fn)) + nb\\n\\n # clear\\n d_line = [obj for obj in scene.objects if type(obj) is box and obj.y in fn]\\n for _ in xrange(10):\\n rate(20)\\n for obj in d_line:\\n obj.opacity -= 0.1\\n for obj in d_line:\\n obj.visible = 0\\n\\n\\n # decline\\n for n in fn:\\n for obj in (obj for obj in scene.objects if type(obj) is box and obj.y < n):\\n obj.y += 1\\n\\n return fn\",\n \"def outline(color=\\\"white\\\", linewidth=3, **kwargs):\\n return [pe.withStroke(linewidth=linewidth, foreground=color, **kwargs)]\",\n \"def __exit__(self, exc_type, exc_value, traceback):\\n pass\",\n \"def check_if_filled(self, new_cell, cell_color, filled_edges, filled_surrounded):\\n new_cell_color = self.get_color(new_cell)\\n if new_cell_color != cell_color:\\n return False\\n\\n if new_cell not in filled_edges + filled_surrounded:\\n filled_edges.append(new_cell)\\n\\n return True\",\n \"def __exit__(self, exc_type, exc_value, traceback):\\n return None\",\n \"def fix_bug(self):\\n self.bugged = False\\n self.error_prob = 0.0\",\n \"def setFilled(self, fill):\\n isFilled = fill\\n repaint()\",\n \"def _handle_reset(self):\\n # reset own state\\n self.grbl_version = None\\n self.in_check_mode = False\\n self.line_active = False\\n # wait for init\\n self._wait_for_grbl_init()\",\n \"def test_reset_limit_on_dedent(self):\\n indenter = indent.Indenter()\\n indenter.indentation = -2\\n self.assertRaises(ValueError, indenter.dedent)\\n indenter.indentation = -1\\n self.assertRaises(ValueError, indenter.dedent)\\n indenter.indentation = 0\\n self.assertRaises(ValueError, indenter.dedent)\\n indenter.indentation = +1\\n indenter.dedent()\\n indenter.indentation = +2\\n indenter.dedent()\"\n]","isConversational":false},"negative_scores":{"kind":"list like","value":["0.5995263","0.5990204","0.5509914","0.5184432","0.51762307","0.51762307","0.514419","0.51174825","0.50964","0.50798017","0.50475687","0.50426537","0.5025028","0.49561536","0.4947993","0.49472082","0.4876335","0.484599","0.48382837","0.48201862","0.4810579","0.48016107","0.47980425","0.47980425","0.47471458","0.47437802","0.4725151","0.4717904","0.47136936","0.47032598","0.4689915","0.4688131","0.46770594","0.46637228","0.465358","0.46431342","0.4638058","0.46222612","0.461166","0.4605203","0.4605203","0.45765212","0.45735478","0.45696697","0.45670786","0.45597717","0.45581457","0.45546922","0.45507312","0.45466542","0.45422244","0.45420757","0.45402375","0.45358363","0.45317674","0.45286304","0.45286304","0.45266372","0.4518734","0.4513378","0.45056453","0.45032403","0.44968188","0.4496139","0.44938922","0.44884625","0.44826794","0.4475901","0.44731233","0.44719186","0.44718203","0.44695935","0.44657442","0.44586766","0.44575647","0.44546","0.44505316","0.4447684","0.44436517","0.4438722","0.4433152","0.44318193","0.44281194","0.44265792","0.44265786","0.44223633","0.4415045","0.44136658","0.4403939","0.44032592","0.43953544","0.43904632","0.43888074","0.43879852","0.43856162","0.4374106","0.43693456","0.43653017","0.4359466","0.4358965","0.43568054"],"string":"[\n \"0.5995263\",\n \"0.5990204\",\n \"0.5509914\",\n \"0.5184432\",\n \"0.51762307\",\n \"0.51762307\",\n \"0.514419\",\n \"0.51174825\",\n \"0.50964\",\n \"0.50798017\",\n \"0.50475687\",\n \"0.50426537\",\n \"0.5025028\",\n \"0.49561536\",\n \"0.4947993\",\n \"0.49472082\",\n \"0.4876335\",\n \"0.484599\",\n \"0.48382837\",\n \"0.48201862\",\n \"0.4810579\",\n \"0.48016107\",\n \"0.47980425\",\n \"0.47980425\",\n \"0.47471458\",\n \"0.47437802\",\n \"0.4725151\",\n \"0.4717904\",\n \"0.47136936\",\n \"0.47032598\",\n \"0.4689915\",\n \"0.4688131\",\n \"0.46770594\",\n \"0.46637228\",\n \"0.465358\",\n \"0.46431342\",\n \"0.4638058\",\n \"0.46222612\",\n \"0.461166\",\n \"0.4605203\",\n \"0.4605203\",\n \"0.45765212\",\n \"0.45735478\",\n \"0.45696697\",\n \"0.45670786\",\n \"0.45597717\",\n \"0.45581457\",\n \"0.45546922\",\n \"0.45507312\",\n \"0.45466542\",\n \"0.45422244\",\n \"0.45420757\",\n \"0.45402375\",\n \"0.45358363\",\n \"0.45317674\",\n \"0.45286304\",\n \"0.45286304\",\n \"0.45266372\",\n \"0.4518734\",\n \"0.4513378\",\n \"0.45056453\",\n \"0.45032403\",\n \"0.44968188\",\n \"0.4496139\",\n \"0.44938922\",\n \"0.44884625\",\n \"0.44826794\",\n \"0.4475901\",\n \"0.44731233\",\n \"0.44719186\",\n \"0.44718203\",\n \"0.44695935\",\n \"0.44657442\",\n \"0.44586766\",\n \"0.44575647\",\n \"0.44546\",\n \"0.44505316\",\n \"0.4447684\",\n \"0.44436517\",\n \"0.4438722\",\n \"0.4433152\",\n \"0.44318193\",\n \"0.44281194\",\n \"0.44265792\",\n \"0.44265786\",\n \"0.44223633\",\n \"0.4415045\",\n \"0.44136658\",\n \"0.4403939\",\n \"0.44032592\",\n \"0.43953544\",\n \"0.43904632\",\n \"0.43888074\",\n \"0.43879852\",\n \"0.43856162\",\n \"0.4374106\",\n \"0.43693456\",\n \"0.43653017\",\n \"0.4359466\",\n \"0.4358965\",\n \"0.43568054\"\n]","isConversational":false},"document_score":{"kind":"string","value":"0.0"},"document_rank":{"kind":"string","value":"-1"}}},{"rowIdx":16597,"cells":{"query":{"kind":"string","value":"Trap nonlinear smear gerber."},"document":{"kind":"string","value":"def test_arc_smear(self):"},"metadata":{"kind":"string","value":"{\n \"objective\": {\n \"self\": [],\n \"paired\": [],\n \"triplet\": [\n [\n \"query\",\n \"document\",\n \"negatives\"\n ]\n ]\n }\n}"},"negatives":{"kind":"list like","value":["def post_process_trap(): \n #################### 0) assign internal values #################### \n from project_parameters import trapType,debug,trapFile,name,driveAmplitude,driveFrequency,Omega,dcplot,weightElectrodes,coefs,ax,az,phi,save,scale\n #from all_functions import find_saddle,plot_potential,dc_potential,set_voltages,exact_saddle,spher_harm_bas,spher_harm_exp,pfit,plotN\n import pickle\n\n with open(trapFile,'rb') as f:\n trap = pickle.load(f)\n\n qe = trap.configuration.charge\n mass = trap.configuration.mass\n Zval = trap.configuration.position\n r0 = trap.configuration.r0\n RFampl = driveAmplitude \n V0 = mass*(2*np.pi*Omega)**2*(r0*10**-3)**2/qe\n X,Y,Z=trap.instance.X,trap.instance.Y,trap.instance.Z \n data = trap.configuration\n dcVoltages = set_voltages()\n ne = len(weightElectrodes)\n E = trap.instance.E\n out = trap.configuration\n if debug.post_process_trap:\n print dcVoltages,np.max(dcVoltages)#np.sum(abs(dcVoltages))\n plotN(dcVoltages,trap,'set DC voltages') \n Vdc = dc_potential(trap,dcVoltages,E)\n #[IDC,JDC,KDC] = find_saddle(Vdc,X,Y,Z,3,Zval) \n #[XDC,YDC,ZDC] = exact_saddle(Vdc,X,Y,Z,3,Zval)\n #XDC,YDC,ZDC = X[IDC],150/scale,Z[KDC]\n #print XDC,YDC,ZDC,IDC,JDC,KDC\n #dcbasis,dcscale= spher_harm_bas(XDC,YDC,ZDC,X,Y,Z,4)\n #QQ = spher_harm_exp(Vdc,dcbasis,dcscale) \n #print QQ[0:9].T\n #1) RF Analysis\n print('RF Analysis') \n Vrf = RFampl*data.EL_RF\n [Irf,Jrf,Krf] = find_saddle(Vrf,X,Y,Z,2,Zval)\n if debug.post_process_trap:\n plot_potential(Vrf,X,Y,Z,dcplot,'weighted RF potential','V_{rf} (eV)',[Irf,Jrf,Krf])\n #2) DC Analysis\n print('DC Analysis')\n trap = dc_potential(trap,dcVoltages,E,update=None)\n Vdc = trap.instance.DC\n [Idc,Jdc,Kdc] = find_saddle(Vdc,X,Y,Z,3,Zval) # only used to calculate error at end\n if debug.post_process_trap:\n plot_potential(Vdc,X,Y,Z,'1D plots','full DC potential')\n #3) determine the exact saddles of the RF and DC\n trap = dc_potential(trap,dcVoltages,E)\n Vdc = trap.instance.DC\n print('Determining exact RF saddle...')\n [Xrf,Yrf,Zrf] = exact_saddle(Vrf,X,Y,Z,2,Zval) \n print('Determining exact DC saddle...')\n [Xdc,Ydc,Zdc] = exact_saddle(Vdc,X,Y,Z,3,Zval)\n #4) determine stray field (beginning of justAnalyzeTrap)\n print('Determining compensation due to E field...')\n nx,ny,nz=X.shape[0],Y.shape[0],Z.shape[0]\n x,y,z = np.zeros((nx,ny,nz)),np.zeros((nx,ny,nz)),np.zeros((nx,ny,nz))\n for i in range(nx):\n for j in range(ny):\n for k in range(nz):\n x[i,j,k] = X[i]\n y[i,j,k] = Y[j]\n z[i,j,k] = Z[k]\n VlessE = Vdc-E[0]*x-E[1]*y-E[2]*z\n [Xdc,Ydc,Zdc] = exact_saddle(VlessE,X,Y,Z,3) \n dist = np.sqrt((Xrf-Xdc)**2+(Yrf-Ydc)**2+(Zrf-Zdc)**2) \n #5) call pfit to built teh total field and determine the trap characteristics\n [fx,fy,fz,theta,Depth,Xe,Ye,Ze] = pfit(Vrf,Vdc,X,Y,Z,Irf,Jrf,Krf)#pfit(trap,E,Freq,RFampl)\n print('Stray field is ({0},{1},{2}) V/m.'.format(scale*E[0],scale*E[1],scale*E[2]))\n print('With this field, the compensation is optimized to {} micron.'.format(scale*dist))\n print('RF saddle: ({0},{1},{2})\\nDC saddle ({3},{4},{5}).'.format(Xrf,Yrf,Zrf,Xdc,Ydc,Zdc)) \n if debug.trap_depth:\n print('The trap escape position is at ({0},{1},{2}) microns, for a trap depth of {3} mV'.format(Xe*scale,Ye*scale,Ze*scale,Depth*scale))\n print('The trap frequencies are fx = {0} MHz, fy = {1} MHz, and fz = {2} MHz'.format(fx*10**-6,fy*10**-6,fz*10**-6))\n #6) Sanity testing; quality check no longer used\n if debug.post_process_trap:\n rfbasis,rfscale= spher_harm_bas(Xrf,Yrf,Zrf,X,Y,Z,2)\n Qrf = spher_harm_exp(Vrf,rfbasis,rfscale) \n if np.sqrt((Xrf-Xdc)**2+(Yrf-Ydc)**2+(Zrf-Zdc)**2)>0.008: \n print('Expanding DC with RF for saniy checking.')\n Qdc = spher_harm_exp(Vdc,rfbasis,rfscale) \n else:\n print('Expanding DC without RF for sanity checking.')\n dcbasis,dcscale= spher_harm_bas(Xdc,Ydc,Zdc,X,Y,Z,2)\n Qdc = spher_harm_exp(Vdc,dcbasis,dcscale) \n Arf = 2*np.sqrt( (3*Qrf[7])**2+(3*Qrf[8])**2 )\n Thetarf = 45*(Qrf[8]/abs(Qrf[8]))-90*np.arctan((3*Qrf[7])/(3*Qrf[8]))/np.pi\n Adc = 2*np.sqrt( (3*Qdc[7])**2+(3*Qdc[8])**2 )\n Thetadc = 45*(Qrf[8]/abs(Qrf[8]))-90*np.arctan((3*Qdc[7])/(3*Qdc[8]))/np.pi\n out.E = E\n out.miscompensation = dist\n out.ionpos = [Xrf,Yrf,Zdc]\n out.ionposIndex = [Irf,Jrf,Krf]\n out.frequency = [fx,fy,fz]\n out.theta = theta\n out.trap_depth = Depth/qe \n out.escapepos = [Xe,Ye,Ze]\n out.Quadrf = 2*np.array([Qrf[7]*3,Qrf[4]/2,Qrf[8]*6,-Qrf[6]*3,-Qrf[5]*3])\n out.Quaddc = 2*np.array([Qdc[7]*3,Qdc[4]/2,Qdc[8]*6,-Qdc[6]*3,-Qdc[5]*3])\n out.Arf = Arf\n out.Thetarf = Thetarf\n out.Adc = Adc\n out.Thetadc = Thetadc\n T = np.array([[2,-2,0,0,0],[-2,-2,0,0,0],[0,4,0,0,0],[0,0,1,0,0],[0,0,0,1,0],[0, 0,0,0,1]])\n Qdrf = out.Quadrf.T\n Qddc = out.Quaddc.T\n out.q = (1/V0)*T*Qdrf\n out.alpha = (2/V0)*T*Qddc\n out.Error = [X[Idc]-Xdc,Y[Jdc]-Ydc,Z[Kdc]-Zdc]\n #7) update the trapping field data structure with instance attributes\n trap.configuration=out\n trap.instance.driveAmplitude = driveAmplitude\n trap.instance.driveFrequency = driveFrequency\n trap.instance.coefs = coefs\n trap.instance.ax = ax\n trap.instance.az = az\n trap.instance.phi = phi\n trap.instance.ppt = True\n trap.instance.out = out\n if save==True:\n print('Saving '+trapFile+' as a data structure...')\n with open(trapFile,'wb') as f:\n pickle.dump(trap,f)\n return 'post_proccess_trap complete' #out # no output needed really","def backpropagating(self): \n\n ######################### Configure the sensor inputs given the movement of the agent ######################### \n sensors_result_N = self.agent.sensors(self, direction=3) + self.agent.get_energy_coarsed()+\\\n self.agent.rotate_previousAction(3)+[int(self.agent.get_previous_collision())]\n sensors_result_O = self.agent.sensors(self, direction=2) + self.agent.get_energy_coarsed()+\\\n self.agent.rotate_previousAction(2) + [int(self.agent.get_previous_collision())]\n sensors_result_S = self.agent.sensors(self, direction=1) + self.agent.get_energy_coarsed()+\\\n self.agent.rotate_previousAction(1) + [int(self.agent.get_previous_collision())]\n sensors_result_E = self.agent.sensors(self, direction=0) + self.agent.get_energy_coarsed()+\\\n self.agent.rotate_previousAction(0) + [int(self.agent.get_previous_collision())]\n\n input_nn_N = np.asarray(sensors_result_N).astype(int) # input when the Nord action is performed \n input_nn_O = np.asarray(sensors_result_O).astype(int) # input when the West action is performed\n input_nn_S = np.asarray(sensors_result_S).astype(int) # input when the South action is performed\n input_nn_E = np.asarray(sensors_result_E).astype(int) # input when the West action is performed\n\n l_input = [input_nn_E.reshape(1,145),input_nn_S.reshape(1,145),input_nn_O.reshape(1,145),input_nn_N.reshape(1,145)]\n ######################### Configure the sensor inputs given the movement of the agent #########################\n\n print(\"The reward in baskpropagating is %f\" %(self.agent.reward) ) \n parameters = [self.gamma, self.agent.reward]\n Ui = self.U_list[self.agent.get_previousAction().index(1)]\n\n if not self.end:\n U_list_y = [self.nn.predict(input_nn_E.reshape(1,145)),\\\n self.nn.predict(input_nn_S.reshape(1,145)),\\\n self.nn.predict(input_nn_O.reshape(1,145)),\\\n self.nn.predict(input_nn_N.reshape(1,145))] \n #print(U_list_y)\n maxU = np.max(U_list_y)\n #print(np.max(U_list_y))\n index_input_maxU = np.argmax(U_list_y) # the input given for the backprogating is the one with the maximum utility\n input_target = l_input[index_input_maxU] # The input target with the max utility, add to the tuple given during the experience replay\n uprime = self.agent.reward + self.gamma * maxU # input of the utility with the best value\n \n else:\n uprime = self.agent.reward\n input_target = np.array(None)\n \n action = self.agent.get_previousAction().index(1)\n input_nn = self.input_list[action]\n ##### Add to the lesson the action chose in order to go the next state, \n ##### the next state after to have performed the action, and the reward given\n if(self.action_proba[action] > 0.01): # the Pl minimum to choose the action corresponding to the action policy, cf to the paper part experience replay\n #next_states = [copy.deepcopy(input_nn_E).reshape(1,145), copy.deepcopy(input_nn_S).reshape(1,145), copy.deepcopy(input_nn_O).reshape(1,145), copy.deepcopy(input_nn_N).reshape(1,145)]\n self.memory.append((input_nn,action,np.asarray(copy.deepcopy(l_input)),self.agent.reward)) # We add the experiment to the memory of the agent \n \n ############################\n self.nn.train_one_step_other(input_nn,uprime)\n #self.nn.train(input_nn,tf.convert_to_tensor([[uprime]])) # use the method fit to train the neural network","def sandwich(self):\n if self.game.rules[\"capture\"] == \"custodial_capture\":\n self.remove_self()\n if self.game.rules[\"trapping\"]:\n for trapped_neighbor in [neighbor for neighbor in self.get_neighbors() if neighbor.trapped and self.position in neighbor.get_sandwichers() and len(neighbor.get_sandwichers()) == 2]:\n trapped_neighbor.untrap()\n self.trap()","def stack_nonlinearity(self):\n self.flow = self.NONLINEARITY[0](self.flow)","def fill_gas_tank(self):\r\n\t\tprint(\"This car doesn't need a gas tank.\")","def fill_gas_tank(self):\n print(\"This car doesn't need a gas tank!\")","def fill_gas_tank(self):\n print(\"This car doesn't need a gas tank!\")","def trap_knobs():\n print('Executing trap_knobs...')\n #0) Define parameters and heck to see what scripts have been run\n from project_parameters import save,debug,trapFile,elMap,electrodes,multipoles,name,simulationDirectory,reg,trapType\n #from all_functions import nullspace,plotN\n import pickle\n with open(trapFile,'rb') as f:\n trap = pickle.load(f)\n if trap.configuration.expand_field!=True:\n return 'You must run expand_field first!'\n if trap.configuration.trap_knobs and not debug.trap_knobs:\n return 'Already executed trap_knobs.'\n #1) redefine parameters with shorthand and run sanity checks\n totE = len(electrodes) # numTotalElectrodes\n totM = len(multipoles) # numTotalMultipoles\n assert totE == trap.numElectrodes # Make sure that the total number of electrodes includes the RF.\n tc = trap.configuration\n mc = tc.multipoleCoefficients # this is the original, maximum-length multipole coefficients matrix (multipoles,electrodes)\n for row in range(totM):\n #row+=1\n if abs(np.sum(mc[row,:])) < 10**-50: # arbitrarily small\n return 'trap_knobs: row {} is all 0, can not solve least square, stopping trap knobs'.format(row)\n #2) Apply electrode mapping by clearing some electrodes and adding them to the new map\n # mapping one to an unused electrode should turn it off as well\n for index in range(totE):\n if index != elMap[index]:\n mc[:,elMap[index]] += mc[:,index] # combine the electrode to its mapping\n electrodes[index] = 0 # clear the mapped electrode, implemented in part 3\n useE = int(np.sum(electrodes)) # numUsedElectrodes\n useM = int(np.sum(multipoles)) # numUsedMultipoles\n eo = np.sqrt(useM)-1 # expansionOrder\n #3) build a reduced array of multipole coefficients to invert\n MC = np.zeros((useM,useE)) # reduced matrix to build up and invert\n ML = 0\n for ml in range(totM):\n if multipoles[ml]:\n EL = 0 # clear the electrode indexing before looping through electrodes again for new multipole\n for el in range(totE):\n if electrodes[el]:\n MC[ML,EL] = mc[ml,el]\n EL += 1\n ML += 1\n print('trap_knobs: with electrode and multipole constraints, the coefficient matrix size is ({0},{1}).'.format(MC.shape[0],MC.shape[1]))\n #4) numerially invert the multipole coefficients to get the multipole controls, one multipole at a time\n # solve the equation MC*A = B, where the matrix made from all A vectors is C\n C = np.zeros((useE,useM)) # multipole controls (electrodes,multipoles) will be the inverse of multipole coefficents \n for mult in range(useM):\n B = np.zeros(useM)\n B[mult] = 1\n A = np.linalg.lstsq(MC,B)[0]\n C[:,mult] = A\n #5) calculate the nullspace and regularize if the coefficients matrix is sufficiently overdetermined\n if useM < useE:\n K = nullspace(MC)\n else:\n print('There is no nullspace because the coefficient matrix is rank deficient.\\nThere can be no regularization.')\n K = None\n reg = False\n if reg:\n for mult in range(useM):\n Cv = C[:,mult].T\n Lambda = np.linalg.lstsq(K,Cv)[0]\n test=np.dot(K,Lambda)\n C[:,mult] = C[:,mult]-test \n #6) expand the matrix back out again, with zero at all unused electrodes and multipoles; same as #3 with everything flipped\n c = np.zeros((totE,totM)) \n EL = 0\n for el in range(totE):\n if electrodes[el]:\n ML = 0 # clear the electrode indexing before looping through electrodes again for new multipole\n for ml in range(totM):\n if multipoles[ml]:\n c[el,ml] = C[EL,ML]\n ML += 1\n EL += 1\n #7) plot the multipole controls in teh trap geometry\n if debug.trap_knobs:\n for ml in range(totM):\n if multipoles[ml]:\n plot = c[:,ml]\n plotN(plot,trap,'Multipole {}'.format(ml)) \n #8) update instance configuration with multipole controls to be used bu dc_voltages in post_process_trap\n tc.multipoleKernel = K\n tc.multipoleControl = c\n tc.trap_knobs = True\n trap.configuration=tc\n #8.5) change the order of the columns of c for labrad\n # originally (after constant) Ez,Ey,Ex,U3,U4,U2,U5,U1,...,Y4-4,...,Y40,...,Y44\n # we want it to be Ex,Ey,Ez,U2,U1,U3,U5,U4,...,Y40 and then end before any of the other 4th order terms\n# cc = c.copy()\n# cc[:,1] = c[:,3] # Ex\n# cc[:,2] = c[:,1] # Ey\n# cc[:,3] = c[:,2] # Ez\n# cc[:,4] = c[:,6] # U2\n# cc[:,5] = c[:,8]\n# cc[:,6] = 0 # U3\n# cc[:,16]= c[:,20]# Y40\n# cc[:,20]= 0\n cc = c\n #9) save trap and save c as a text file (called the \"C\" file for Labrad)\n if save: \n print('Saving '+name+' as a data structure...')\n with open(trapFile,'wb') as f:\n pickle.dump(trap,f)\n #ct = cc[1:totE,1:17] #eliminate the RF electrode and constant multipole; eliminate everything past Y40\n ct = cc[1:totE,1:25] # only eliminate the constant\n text = np.zeros((ct.shape[0])*(ct.shape[1]))\n for j in range(ct.shape[1]):\n for i in range(ct.shape[0]):\n text[j*ct.shape[0]+i] = ct[i,j]\n np.savetxt(simulationDirectory+name+'.txt',text,delimiter=',')\n return 'Completed trap_knobs.'","def fill_gas_tank(self):\n print(\"\\nThis car doesn't need a gas tank!\")","def processTick(self, tick):\n\n self.lastRerouteCounter += 1\n # reroute every x ticks based on config value\n if self.lastRerouteCounter >= CustomRouter.reRouteEveryTicks and CustomRouter.reRouteEveryTicks > 0:\n self.lastRerouteCounter = 0\n if self.smartCar:\n try:\n oldRoute = self.currentRouterResult.route\n currentEdgeID = traci.vehicle.getRoadID(self.id)\n nextNodeID = Network.getEdgeIDsToNode(currentEdgeID).getID()\n self.currentRouterResult = CustomRouter.route(nextNodeID, self.targetID, tick, self)\n traci.vehicle.setRoute(self.id, [currentEdgeID] + self.currentRouterResult.route)\n # print(\"OLD: \" + str(oldRoute) + \" - NEW: \" + str(self.currentRouterResult.route))\n except IndexError as e:\n # print(e)\n pass\n except traci.exceptions.TraCIException as e:\n # print(e)\n pass\n\n roadID = traci.vehicle.getSubscriptionResults(self.id)[80]\n if roadID != self.currentEdgeID and self.smartCar:\n if self.currentEdgeBeginTick is not None:\n CustomRouter.applyEdgeDurationToAverage(self.currentEdgeID, tick - self.currentEdgeBeginTick, tick)\n # CSVLogger.logEvent(\"edge\", [tick, self.currentEdgeID,\n # tick - self.currentEdgeBeginTick, self.id])\n # log to kafak\n # msg = dict()\n # msg[\"tick\"] = tick\n # msg[\"edgeID\"] = self.currentEdgeID,\n # msg[\"duration\"] = tick - self.currentEdgeBeginTick\n # print(\"changed route to: \" + roadID)\n self.currentEdgeBeginTick = tick\n self.currentEdgeID = roadID\n pass","def dummyF(self, arg, signal, sender):\n \n if self.isDead == True:\n return\n \n \n #print \"DUMMY\"\n if self.aborting:\n self.aborting = False\n self.isActive = False\n self.__orderQueue.popleft()\n del self.slaveTalk\n self.slaveTalk = None\n# self.__orderQueue.popleft()\n try:\n self.releaseLock()\n except:\n pass\n #print \"No lock, actually.\" \n dispatcher.send('SLAVE_PARSE_QUEUE', self, '')","def trig_conditions(tr):\n \n\n \n ##############\n #TRACE RELATED\n ##############\n avg_tr = np.average(tr)\n \n shifted_tr = tr - avg_tr \n \n abs_tr = abs(shifted_tr)\n \n sort_tr = np.sort(abs_tr)\n \n tr_99 = sort_tr[int(0.999*len(sort_tr))]\n\n #95% noise to signal area ratio calculation\n area_big = tr_99 * int(0.95*len(sort_tr))\n \n area_small = np.sum(sort_tr[:int(0.95*len(sort_tr))])\n \n \n area_condition = area_small / area_big; print area_condition\n \n # if signal is quite noisy, use recursive STALTA, else use classic STALTA\n \n df = tr.stats.sampling_rate\n \n \n if area_condition <= 0.1:\n \n print(\"CLEAN SIGNAL!\\n\")\n\n ctf = abs(1-carlSTATrig(tr.data, int(5 * df), int(10 * df), 0.0001, 0.0001))\n \n sort_ctf = np.sort(ctf)\n \n ctf_low = sort_ctf[int(0.80*len(sort_ctf))]\n \n ctf_99 = sort_ctf[int(0.999*len(sort_ctf))]\n \n max_trig = ctf_99\n \n trig_on = ctf_low + 0.4 * (max_trig - ctf_low)\n\n trig_off = 0.8 * trig_on\n \n if not max_trig > 1.25 * ctf_low:\n trig_on = 0; trig_off = 0;\n \n \n \n elif 0.1 < area_condition < 0.16:\n \n print(\"NOISY SIGNAL!\\n\")\n\n ctf = abs(1-recSTALTA(tr.data, int(5 * df), int(10 * df)))\n \n sort_ctf = np.sort(ctf)\n \n ctf_low = sort_ctf[int(0.90*len(sort_ctf))]\n \n ctf_99 = sort_ctf[int(0.999*len(sort_ctf))]\n \n max_trig = ctf_99\n \n trig_on = ctf_low + 0.4 * (max_trig - ctf_low)\n\n trig_off = 0.8 * trig_on\n \n if not max_trig > 1.25 * ctf_low:\n trig_on = 0; trig_off = 0;\n \n else:\n print(\"TRACE TOO NOISY TO DETECT SIGNAL!\")\n trig_on = 0; trig_off = 0;\n ctf = abs(1-recSTALTA(tr.data, int(5 * df), int(10 * df)))\n\n \n\n\n\n \n\n \n \n ############\n #ctf RELATED\n ############\n\n \n #set conditional for noise. This is MINIMUM threshold.\n #ctf_avg = np.average(ctf)\n #ctf_mode = scipy.stats.mode(ctf)\n #ctf_std = np.std(ctf)\n \n\n \n \n #plt.figure()\n #plt.plot(sort_ctf)\n #plt.show()\n\n \n\n \n \n \n return trig_on, trig_off, ctf","def fill_gas_tank(self):\n print(\"This car doesn't have a gas tank!\")","def arm(self):\n error(\"Attempted to access abstract trigger arming function.\")","def louder():\n try:\n ttsEng.louder()\n except Exception, e:\n logging.error(e)","def lidar_callback(self, data):\n ranges = data.ranges\n proc_ranges = self.preprocess_lidar(ranges)\n drive_st_msg = AckermannDriveStamped()\n drive_msg = AckermannDrive()\n prev_drive = AckermannDrive()\n prev_drive_st_msg = AckermannDriveStamped()\n \n\n #Find closest point to LiDAR\n minPointIdx = 0\n for i in range(proc_ranges) :\n if proc_ranges[i] < proc_ranges[minPointIdx] :\n minPointIdx = i\n\n carLength = rospy.get_param(\"wheelbase\")\n carWidth = rospy.get_param(\"width\")\n avoidRadius = math.sqrt(math.pow(carLength, 2) + math.pow(carWidth, 2) + 1)\n angleToConsider = math.atan(avoidRadius / proc_ranges[minPointIdx])\n numPointsReplace = math.ceil(angleToConsider / data.angle_increment)\n\n for i in range(numPointsReplace) :\n proc_ranges[minPointIdx - i] = 0\n proc_ranges[minPointIdx + i] = 0\n \n maxGap = 0\n count = 0\n idxStartGap = 0\n idxEndGap = 0\n for i in range(proc_ranges) :\n if proc_ranges[i] != 0 :\n if count == 0:\n idxStartGap = i\n count += 1\n else :\n if count > maxGap :\n maxGap = count\n idxEndGap = i - 1\n count = 0\n\n bestPoint = self.find_best_point(idxStartGap, idxEndGap, proc_ranges)\n finalSteeringAngle = data.angle_min + data.angle_increment * bestPoint\n drive_msg.steering_angle = finalSteeringAngle\n if abs(drive_msg.steering_angle < 10):\n drive_msg.speed = 5\n elif abs(drive_msg.steering_angle < 20):\n drive_msg.speed = 2\n else:\n drive_msg.speed = 1\n\n prev_drive = drive_msg\n drive_st_msg.drive = drive_msg\n prev_drive_st_msg.drive = prev_drive\n\n if proc_ranges[bestPoint] > 3: \n self.drive_pub.publish(prev_drive_st_msg)\n else :\n self.drive_pub.publish(drive_st_msg)\n\n\n\n #Eliminate all points inside 'bubble' (set them to zero) \n\n #Find max length gap \n\n #Find the best point in the gap \n\n #Publish Drive message","def spillAlle(self):\r\n for sang in self._sanger:\r\n print(f\"Nå spilles følgende: {sang}\")","def relax(self):\n rospy.loginfo('Now Arm will be relax')\n self.go_with2([0, 0, 0, 0, 0])","def __init__(self, trap=2.5*10**16, Keq=1.0*10**17,\n EHdecay=1.0*10**-10, Etrap=2.0*10**-10, FHloss=8.0*10**-12,\n G3decay = 0, step=200*ps, pretime=2, reprate=80000000,\n verbose=False, trackQ=False, scalar=1, Gdecay=0, GHdecay=0,\n tolerance=0.005, G2decay=0. ,Gescape=1., Gform=1., G3loss=0.):\n # Some other variables used\n self.tolerance = tolerance\n self.scalar = scalar\n self.verbose = verbose\n self.reprate = reprate\n self.duration = 1.00 / reprate\n self.step = step\n self.steps = int(self.duration / self.step)\n self.powers = []\n self.pretime = pretime\n # Variables which hold state densities\n self.exciton = []\n self.hole = []\n self.electron = []\n self.trap = (trap) # Total number of traps\n self.filled = [] # Filled traps\n self.signal = []\n self.xsignal = []\n self.ehsignal = []\n self.xloss = []\n self.tloss = []\n self.pulses = []\n self.qk = []\n self.trackQ = trackQ\n # Rate and equilibrium constants, corrected for time step size\n self.Keq = Gescape/Gform # Equilibrium constant for X<-->e+h\n self.EHdecay = (EHdecay * step) # e+h->ground\n self.Etrap = (Etrap * step) # e+trap->filled\n self.FHloss = (FHloss * step) # filled+h->ground\n self.Gdecay = Gdecay * step\n self.G2decay = G2decay * step\n self.G3decay = G3decay * step\n self.GHdecay = GHdecay * step\n self.Gescape = Gescape * step\n self.G3loss = G3loss * step\n self.Gform = Gform * step","def disarm(self):\n pass","def _handle_mt_relax_error(self, calculation):\n self.ctx.restart_calc = calculation\n self.ctx.is_finished = True\n self.report('FLEUR calculation failed due to MT overlap. Can be fixed via RelaxBaseWorkChain')\n self.results()\n return ProcessHandlerReport(True, self.exit_codes.ERROR_MT_RADII_RELAX)","def Transformer(robot1,robot2): \n #with a 50% change surgery will be triggered\n return Random_Actuation.surgery(\"Transformer\",robot1,robot2,50)","def inverse_kinematics_baxter(TM_W0_Gtool, arm_side):\n\n # Get all constants for the distances and transformations for Baxter\n Constants = constants_baxter.GetConstants()\n L0 = Constants.L0\n L1 = Constants.L1\n L2 = Constants.L2\n L3 = Constants.L3\n L4 = Constants.L4\n L6 = Constants.L6\n L = Constants.L\n h = Constants.h\n H = Constants.H\n LH = Constants.LH\n TM_W0_BL = Constants.TM_W0_BL\n TM_W0_BR = Constants.TM_W0_BR\n TM_BL_0 = Constants.TM_BL_0\n TM_BR_0 = Constants.TM_BR_0\n TM_7_GL = Constants.TM_7_GL\n TM_7_GR = Constants.TM_7_GR\n\n # Apply inverse kinematics for the left arm\n if arm_side == \"left\":\n # Understanding the corresponding TM from the article, this can be solved:\n TM_0_6 = np.dot(np.dot(np.linalg.inv(np.dot(TM_W0_BL,TM_BL_0)), TM_W0_Gtool), np.linalg.inv((TM_7_GR)))\n\n # Find theta1\n PX_0_4 = TM_0_6[0, 3]\n PY_0_4 = TM_0_6[1, 3]\n\n theta1 = math.atan2(PY_0_4, PX_0_4)\n\n # Find theta2\n PZ_0_4 = TM_0_6[2, 3]\n E = 2*LH*(L1 - PX_0_4/math.cos(theta1))\n F = 2*LH*PZ_0_4\n G = (PX_0_4**2)/((math.cos(theta1))**2) + L1**2 + LH**2 - L4**2 + PZ_0_4**2 - 2*L1*PX_0_4/math.cos(theta1)\n\n\n if (E**2 + F**2 - G**2)>0:\n t1 = (-F + math.sqrt(E**2 + F**2 - G**2))/(G - E)\n else: \n t1 = (-F - 0)/(G - E)\n theta2 = 2*math.atan(t1)\n\n # We make only use the real part (img is not significant most of the times)\n #if (E**2 + F**2 - G**2)>0:\n #t2 = (-F - math.sqrt(E**2 + F**2 - G**2))/(G - E)\n #else:\n #t2 = (-F - 0)/(G - E)\n #theta2 = 2*math.atan(t2)\n\n\n\n # Find theta4\n theta4 = math.atan2(-PZ_0_4 - LH*math.sin(theta2), PX_0_4/math.cos(theta1) - L1 - LH*math.cos(theta2)) - theta2\n\n # Find theta5\n DH_0_3 = np.array([[0, 0, 0, theta1],\n [-math.pi/2, L1, 0, theta2],\n [0, LH, 0, theta4 + math.pi/2]])\n\n TM_0_3 = denavit_hartenberg.denavit_hartenberg(DH_0_3, 0)\n R_0_3 = TM_0_3[0:3, 0:3]\n\n R_0_6 = TM_0_6[0:3, 0:3]\n\n R_3_6 = np.dot(np.linalg.inv(R_0_3), R_0_6)\n\n theta5 = math.atan2(R_3_6[2,2], R_3_6[0,2])\n\n # Find theta7\n theta7 = math.atan2(-R_3_6[1,1], R_3_6[1,0])\n\n\n # Find theta6\n theta6 = math.atan2(R_3_6[1,0]/math.cos(theta7), -R_3_6[1,2])\n\n\n return [theta1, theta2, theta4, theta5, theta6, theta7]","def propagate(satellite):","def test_ridge_warning_in_fit_mle(self):\n # Create a variable for the fit_mle function's kwargs.\n # The print_res = False arguments are to make sure strings aren't\n # printed to the console unnecessarily.\n kwargs = {\"ridge\": 0.5,\n \"print_res\": False}\n\n # Test to make sure that the ridge warning message is printed when\n # using the ridge keyword argument\n with warnings.catch_warnings(record=True) as w:\n # Use this filter to always trigger the UserWarnings\n warnings.simplefilter('always', UserWarning)\n\n self.base_clog.fit_mle(self.fake_all_params, **kwargs)\n self.assertGreaterEqual(len(w), 1)\n self.assertIsInstance(w[0].category, type(UserWarning))\n self.assertIn(clog._ridge_warning_msg, str(w[0].message))\n\n return None","def test_no_backg_subt():\n \n test_object = fa.read_in_envision(data_csv=HsHis6_PEX5C_vs_HsPEX5C, platemap_csv=Hs_His6_PEX5C_vs_HsPEX5C_platemap, data_type='plate', size=384)\n test_object.calculate_r_i(correct=True, plot_i=False, thr=80)","def handler(signum, frame):\n m.signal()","def signal_vwap(self):\n pass","def non_social_action_SB(self):\n self.pumpRate = 0.4\n if not self.agent.done:\n self.action_gating()","def add_dcdisorder(self):\n # Add gaussian noise to pinning energies\n if self.lp['V0_pin_gauss'] > 0:\n self.Omg += self.lp['V0_pin_gauss']*np.random.randn(len(self.xy_inner))\n raise RuntimeError('Adding gaussian disorder: are you sure you want to proceed?')\n if self.lp['V0_spring_gauss'] > 0:\n print 'This is not done correctly here'\n self.OmK += self.lp['V0_spring_gauss'] * np.random.randn(np.shape(self.lattice.KL)[0],\n np.shape(self.lattice.KL)[1])\n sys.exit()\n\n if self.lp['V0_pin_flat'] > 0 or self.lp['V0_spring_flat'] > 0:\n # Note that we multiply by two so that V0_pin_flat is the HALF width of the distribution\n flat_disorder = (np.random.rand(len(self.xy_inner))) * 2 - 1.0\n\n if self.lp['V0_pin_flat'] > 0:\n self.Omg += self.lp['V0_pin_flat'] * flat_disorder\n if self.lp['Omg'] < 0:\n self.Omg[self.Omg > 0] = 0.\n elif self.lp['Omg'] > 0:\n self.Omg[self.Omg < 0] = 0.\n\n print('magnetic_gyro_lattice_class.py: V0_pin_flat=', self.lp['V0_pin_flat'])\n print(self.Omg)\n\n if self.lp['V0_spring_flat'] > 0:\n to_add = self.lp['V0_spring_flat'] * flat_disorder[:, np.newaxis] * np.ones_like(self.OmK)\n self.OmK[np.abs(self.OmK) > 0] += to_add[np.abs(self.OmK) > 0]\n if self.lp['Omk'] < 0:\n self.OmK[self.OmK > 0] = 0.\n elif self.lp['Omk'] > 0:\n self.OmK[self.OmK < 0] = 0.\n\n print('magnetic_gyro_lattice_class.py: OmK after flat disorder= ')\n print(self.OmK)\n # sys.exit()","def fill_gas_tank(self):\n print(\"\\nThis car need a gas tank!\")","def _stop_attack(self):\n self._add_malicious_blocks_to_honest_dag()\n self._competing_chain_tip_gid = None\n self._first_parallel_block_gid = None","def step(self):\n self.world.slosh_oceans()\n self.world.transfer_energy_vertically()\n self.world.transfer_energy_horizontally()\n self.world.absorb_energy_from_core()\n self.world.absorb_energy_from_sun(self.sun)","def arm(self):\n pass","def _step_snell(self) -> None:\n self.snell.step()","def test_pump_bypass_on_reverse_flow(use_numba):\n net = pandapipes.create_empty_network(\"net\", add_stdtypes=True)\n\n j1 = pandapipes.create_junction(net, pn_bar=5, tfluid_k=283.15)\n j2 = pandapipes.create_junction(net, pn_bar=5, tfluid_k=283.15)\n j3 = pandapipes.create_junction(net, pn_bar=5, tfluid_k=283.15)\n j4 = pandapipes.create_junction(net, pn_bar=5, tfluid_k=283.15)\n\n pandapipes.create_pipe(net, j1, j2, std_type='125_PE_80_SDR_11', k_mm=1., length_km=10)\n pandapipes.create_pipe(net, j3, j4, std_type='125_PE_80_SDR_11', k_mm=1., length_km=12)\n pandapipes.create_ext_grid(net, j1, 5, 283.15, type=\"p\")\n pandapipes.create_pump(net, j2, j3, std_type='P1')\n pandapipes.create_source(net, j4, 0.02333)\n\n pandapipes.create_fluid_from_lib(net, \"hgas\", overwrite=True)\n\n pandapipes.pipeflow(net, stop_condition=\"tol\", iter=3, friction_model=\"nikuradse\",\n mode=\"hydraulics\", transient=False, nonlinear_method=\"automatic\",\n tol_p=1e-4, tol_v=1e-4, use_numba=use_numba)\n\n assert net.res_pump.deltap_bar.isin([0]).all()\n assert np.isclose(net.res_junction.loc[1, \"p_bar\"], net.res_junction.loc[2, \"p_bar\"])","def lower_arm(self):\r\n # ---------------------------------------------------------------------\r\n # Done: 8. Implement this method; it is a ONE-LINER!\r\n # ---------------------------------------------------------------------\r\n if self.is_calibrated == False:\r\n self.calibrate_arm()\r\n self.move_arm_to_position(0)#America\r","def handle_thrusters(self, data):\n self.thrs_current = np.roll(self.thrs_current, -1, axis=1) # roll the vector (shift)\n self.thrs_current[0:4, -1] = data.current[0:4] # selected thrusters only\n\n self.thrs_energy += THR_VNOM * np.trapz(self.thrs_current, dx=THR_FRAME, axis=1)\n self.energy_last = np.sum(self.thrs_energy)","def stop_emission(self, detailed_signal): # reliably restored by inspect\n pass","def stop_emission(self, detailed_signal): # reliably restored by inspect\n pass","def stop_emission(self, detailed_signal): # reliably restored by inspect\n pass","def stop_emission(self, detailed_signal): # reliably restored by inspect\n pass","def stop_emission(self, detailed_signal): # reliably restored by inspect\n pass","def stop_emission(self, detailed_signal): # reliably restored by inspect\n pass","def stop_emission(self, detailed_signal): # reliably restored by inspect\n pass","def stop_emission(self, detailed_signal): # reliably restored by inspect\n pass","def stop_emission(self, detailed_signal): # reliably restored by inspect\n pass","def stop_emission(self, detailed_signal): # reliably restored by inspect\n pass","def stop_emission(self, detailed_signal): # reliably restored by inspect\n pass","def stop_emission(self, detailed_signal): # reliably restored by inspect\n pass","def stop_emission(self, detailed_signal): # reliably restored by inspect\n pass","def stop_emission(self, detailed_signal): # reliably restored by inspect\n pass","def stop_emission(self, detailed_signal): # reliably restored by inspect\n pass","def stop_emission(self, detailed_signal): # reliably restored by inspect\n pass","def stop_emission(self, detailed_signal): # reliably restored by inspect\n pass","def __post_init__(self):\n if self.steering == Direction.FWD:\n raise ValueError(\"Steering can't be FORWARD.\")","def postSI(self):\n # for cell in self.cells:\n # cell.resetTotOrdFlux()\n self.depth = 0","def BackSubstitution(self, Force):\n\t\tpass","def process_changeroot(self):\n self.__changeroot()","def simulation_step(self):\n if not self.np_trajectory.size:\n #No trajectory to go to.....\n return\n closest_ind = self.find_closest_trajectory_pose()\n ref_ind = (closest_ind + 30) # closest_ind + numpy.round(self.v / 4)\n traj_len = len(self.np_trajectory[0])\n if self.loop is True:\n ref_ind = ref_ind % traj_len\n else:\n if ref_ind > traj_len-1:\n ref_ind = traj_len-1\n if closest_ind == traj_len-1:\n self.at_dest = True\n else:\n ref_ind = closest_ind\n ref_state = self.np_trajectory[:, int(ref_ind)]\n\n # update vehicle state.\n '''if self.class_name == 'TruckVehicle':\n self.update_vehicle_state_qualisys()\n self.UDP_receive()\n if self.data == \"-1.00\":\n self.set_control_commands_pp(ref_state, ref_ind)\n else:\n steer = int(self.data[-6:-3])\n throttle = int(self.data[:-6]) + 5\n hw_port.set_command(throttle,steer,2)\n self.update_truck_hardware()\n else:\n self.set_control_commands(ref_state)\n self.update_vehicle_state()'''\n\n self.set_control_commands(ref_state, ref_ind)\n self.update_vehicle_state()\n\n # publish vehicle state.\n vehicle_state = msgs.VehicleState(self.vehicle_id, self.class_name,\n self.x, self.y, self.yaw, self.v)\n self.pub_state.publish(vehicle_state)\n self.update_current_node()\n\n #The way that the stop light waiting works, this is necessary\n if not self.waiting_at_stop:\n self.check_for_traffic_light()\n self.get_traffic()","async def unexpected_ball_received(self):\n # We do nothing in that case","def ungrasp(self):\n\t\t#rospy.init_node('Robotiq2FGripperSimpleController')\n\t\t\n\t\tpub = rospy.Publisher('Robotiq2FGripperRobotOutput', outputMsg.Robotiq2FGripper_robot_output)\n\n\t\tcommand = outputMsg.Robotiq2FGripper_robot_output();\n\t\ttimeout = 2.5\n\t\ttimeout_start = time.time()\n\t\twhile time.time() < timeout_start + timeout:\n\t\t#rospy.sleep(0.5)\n\t\t\t#command = genCommand(askForCommand(command), command) \n\t\t\tcommand = self.genCommand('r', command)\n\t\t\tpub.publish(command)\n\t\t\trospy.sleep(1)\n\t\t\tcommand = self.genCommand('a', command)\n\t\t\tpub.publish(command)\n\t\t\trospy.sleep(1)\n\t\t\t#command = self.genCommand('c', command)\n\t\t\t#pub.publish(command)\n\t\t\t#rospy.sleep(1)","def reset_cause():","def __init__(self, *args, **kwargs):\n super(G16SL1024AFR98, self).__init__(guard_count=16, *args, **kwargs)","def _perturbInPlaceHard(self):\n die","def signal_kernel(self, signum: int):","def shar():\n pass","def raise_arm(self):\r\n self.arm_motor.turn_on(self.speed)\r\n while not self.arm_touch_sensor.is_pressed():\r\n pass\r\n self.arm_motor.turn_off()\r\n\r\n # ---------------------------------------------------------------------\r\n # Done: 6. Implement this method; it is a ONE-LINER! (not)\r\n # ---------------------------------------------------------------------\r","def __init__(self, *args, **kwargs):\n super(G1SL1024AFR98, self).__init__(guard_count=1, *args, **kwargs)","def receive(self, signal, direction=None, polarization=None,\n force_real=True):\n super().receive(signal=signal, direction=direction,\n polarization=polarization,\n force_real=force_real)","def receive(self, signal, direction=None, polarization=None,\n force_real=True):\n super().receive(signal=signal, direction=direction,\n polarization=polarization,\n force_real=force_real)","def signal(self):\n pass","def calculate_axial_transport(my_cell, t):\n\n phi_si, phi_se, phi_di, phi_de, phi_sm, phi_dm = my_cell.membrane_potentials()\n\n j_Na_diff_i = my_cell.j_k_diff(my_cell.D_Na, my_cell.lamda_i, my_cell.Na_si, my_cell.Na_di)*my_cell.A_i*N_A\n Na_akkum_diff_i = scipy.integrate.cumtrapz(j_Na_diff_i, t, initial=0)\n\n j_Na_drift_i = my_cell.j_k_drift(my_cell.D_Na, my_cell.Z_Na, my_cell.lamda_i, my_cell.Na_si, my_cell.Na_di, phi_si, phi_di)*my_cell.A_i*N_A\n Na_akkum_drift_i = scipy.integrate.cumtrapz(j_Na_drift_i, t, initial=0)\n\n j_K_diff_i = my_cell.j_k_diff(my_cell.D_K, my_cell.lamda_i, my_cell.K_si, my_cell.K_di)*my_cell.A_i*N_A\n K_akkum_diff_i = scipy.integrate.cumtrapz(j_K_diff_i, t, initial=0)\n\n j_K_drift_i = my_cell.j_k_drift(my_cell.D_K, my_cell.Z_K, my_cell.lamda_i, my_cell.K_si, my_cell.K_di, phi_si, phi_di)*my_cell.A_i*N_A\n K_akkum_drift_i = scipy.integrate.cumtrapz(j_K_drift_i, t, initial=0)\n\n j_Cl_diff_i = my_cell.j_k_diff(my_cell.D_Cl, my_cell.lamda_i, my_cell.Cl_si, my_cell.Cl_di)*my_cell.A_i*N_A\n Cl_akkum_diff_i = scipy.integrate.cumtrapz(j_Cl_diff_i, t, initial=0)\n\n j_Cl_drift_i = my_cell.j_k_drift(my_cell.D_Cl, my_cell.Z_Cl, my_cell.lamda_i, my_cell.Cl_si, my_cell.Cl_di, phi_si, phi_di)*my_cell.A_i*N_A\n Cl_akkum_drift_i = scipy.integrate.cumtrapz(j_Cl_drift_i, t, initial=0)\n\n j_Ca_diff_i = my_cell.j_k_diff(my_cell.D_Ca, my_cell.lamda_i, my_cell.free_Ca_si, my_cell.free_Ca_di)*my_cell.A_i*N_A\n Ca_akkum_diff_i = scipy.integrate.cumtrapz(j_Ca_diff_i, t, initial=0)\n\n j_Ca_drift_i = my_cell.j_k_drift(my_cell.D_Ca, my_cell.Z_Ca, my_cell.lamda_i, my_cell.free_Ca_si, my_cell.free_Ca_di, phi_si, phi_di)*my_cell.A_i*N_A\n Ca_akkum_drift_i = scipy.integrate.cumtrapz(j_Ca_drift_i, t, initial=0)\n\n j_e_diff_i = (j_Na_diff_i + j_K_diff_i + 2*j_Ca_diff_i - j_Cl_diff_i)\n j_e_drift_i = (j_Na_drift_i + j_K_drift_i + 2*j_Ca_drift_i - j_Cl_drift_i)\n e_akkum_diff_i = (Na_akkum_diff_i*my_cell.Z_Na + K_akkum_diff_i*my_cell.Z_K + Cl_akkum_diff_i*my_cell.Z_Cl + Ca_akkum_diff_i*my_cell.Z_Ca)\n e_akkum_drift_i = (Na_akkum_drift_i*my_cell.Z_Na + K_akkum_drift_i*my_cell.Z_K + Cl_akkum_drift_i*my_cell.Z_Cl + Ca_akkum_drift_i*my_cell.Z_Ca)\n\n j_Na_diff_e = my_cell.j_k_diff(my_cell.D_Na, my_cell.lamda_e, my_cell.Na_se, my_cell.Na_de)*my_cell.A_e*N_A\n Na_akkum_diff_e = scipy.integrate.cumtrapz(j_Na_diff_e, t, initial=0)\n\n j_Na_drift_e = my_cell.j_k_drift(my_cell.D_Na, my_cell.Z_Na, my_cell.lamda_e, my_cell.Na_se, my_cell.Na_de, phi_se, phi_de)*my_cell.A_e*N_A\n Na_akkum_drift_e = scipy.integrate.cumtrapz(j_Na_drift_e, t, initial=0)\n\n j_K_diff_e = my_cell.j_k_diff(my_cell.D_K, my_cell.lamda_e, my_cell.K_se, my_cell.K_de)*my_cell.A_e*N_A\n K_akkum_diff_e = scipy.integrate.cumtrapz(j_K_diff_e, t, initial=0)\n\n j_K_drift_e = my_cell.j_k_drift(my_cell.D_K, my_cell.Z_K, my_cell.lamda_e, my_cell.K_se, my_cell.K_de, phi_se, phi_de)*my_cell.A_e*N_A\n K_akkum_drift_e = scipy.integrate.cumtrapz(j_K_drift_e, t, initial=0)\n\n j_Cl_diff_e = my_cell.j_k_diff(my_cell.D_Cl, my_cell.lamda_e, my_cell.Cl_se, my_cell.Cl_de)*my_cell.A_e*N_A\n Cl_akkum_diff_e = scipy.integrate.cumtrapz(j_Cl_diff_e, t, initial=0)\n\n j_Cl_drift_e = my_cell.j_k_drift(my_cell.D_Cl, my_cell.Z_Cl, my_cell.lamda_e, my_cell.Cl_se, my_cell.Cl_de, phi_se, phi_de)*my_cell.A_e*N_A\n Cl_akkum_drift_e = scipy.integrate.cumtrapz(j_Cl_drift_e, t, initial=0)\n\n j_Ca_diff_e = my_cell.j_k_diff(my_cell.D_Ca, my_cell.lamda_e, my_cell.Ca_se, my_cell.Ca_de)*my_cell.A_e*N_A\n Ca_akkum_diff_e = scipy.integrate.cumtrapz(j_Ca_diff_e, t, initial=0)\n\n j_Ca_drift_e = my_cell.j_k_drift(my_cell.D_Ca, my_cell.Z_Ca, my_cell.lamda_e, my_cell.Ca_se, my_cell.Ca_de, phi_se, phi_de)*my_cell.A_e*N_A\n Ca_akkum_drift_e = scipy.integrate.cumtrapz(j_Ca_drift_e, t, initial=0)\n\n j_e_diff_e = (j_Na_diff_e + j_K_diff_e + 2*j_Ca_diff_e - j_Cl_diff_e)\n j_e_drift_e = (j_Na_drift_e + j_K_drift_e + 2*j_Ca_drift_e - j_Cl_drift_e)\n e_akkum_diff_e = (Na_akkum_diff_e*my_cell.Z_Na + K_akkum_diff_e*my_cell.Z_K + Cl_akkum_diff_e*my_cell.Z_Cl + Ca_akkum_diff_e*my_cell.Z_Ca)\n e_akkum_drift_e = (Na_akkum_drift_e*my_cell.Z_Na + K_akkum_drift_e*my_cell.Z_K + Cl_akkum_drift_e*my_cell.Z_Cl + Ca_akkum_drift_e*my_cell.Z_Ca)\n\n return j_e_drift_i, j_e_diff_i, e_akkum_drift_i, e_akkum_diff_i, Na_akkum_drift_i, Na_akkum_diff_i, K_akkum_drift_i, K_akkum_diff_i, Cl_akkum_drift_i, Cl_akkum_diff_i, Ca_akkum_drift_i, Ca_akkum_diff_i, \\\n j_e_drift_e, j_e_diff_e, e_akkum_drift_e, e_akkum_diff_e, Na_akkum_drift_e, Na_akkum_diff_e, K_akkum_drift_e, K_akkum_diff_e, Cl_akkum_drift_e, Cl_akkum_diff_e, Ca_akkum_drift_e, Ca_akkum_diff_e","def softclippingHGMevaluation(input_generator,branches,iden_method,Plot,reference=None):\n for t in range(8,11):\n t = t / 10.0\n p = 1.0 - t\n input_signal = input_generator.GetOutput()\n nl_functions = [nlsp.function_factory.softclip(power=p),]*branches\n filter_spec_tofind = nlsp.log_bpfilter(branches=branches, input=input_signal)\n ref_nlsystem = nlsp.HammersteinGroupModel_up(input_signal=input_signal,\n nonlinear_functions=nl_functions,\n filter_irs=filter_spec_tofind,\n max_harmonics=range(1,branches+1))\n\n found_filter_spec, nl_functions = iden_method(input_generator,ref_nlsystem.GetOutput(),branches)\n iden_nlsystem = nlsp.HammersteinGroupModel_up(input_signal=input_signal,\n nonlinear_functions=nl_functions,\n filter_irs=found_filter_spec,\n max_harmonics=range(1,branches+1))\n # sine = sumpf.modules.SineWaveGenerator(frequency=5000.0,phase=0.0,samplingrate=input_signal.GetSamplingRate(),length=len(input_signal)).GetSignal()\n sine = sumpf.modules.SweepGenerator(samplingrate=input_signal.GetSamplingRate(),length=len(input_signal)).GetSignal()\n ref_nlsystem.SetInput(sine)\n iden_nlsystem.SetInput(sine)\n if reference is not None:\n reference = nlsp.change_length_signal(reference,length=len(input_signal))\n ref_nlsystem.SetInput(reference)\n iden_nlsystem.SetInput(reference)\n\n if Plot is True:\n plot.relabelandplot(sumpf.modules.FourierTransform(ref_nlsystem.GetOutput()).GetSpectrum(),\"Reference System\",show=False)\n plot.relabelandplot(sumpf.modules.FourierTransform(iden_nlsystem.GetOutput()).GetSpectrum(),\"Identified System\",show=False)\n print \"SNR between Reference and Identified output for symmetric hardclipping HGM(threshold:%r): %r\" %(t,nlsp.snr(ref_nlsystem.GetOutput(),\n iden_nlsystem.GetOutput()))","def _extrap_post_proc_hook(cls, gas_df):\n\n # Testing showed that N2O and CH4 at least were very succeptible to an ever increasing seasonal cycle amplitude\n # as the extrapolation backward in time got further and further. This is the simplest fix, a 12 month average\n # wipes out the seasonal cycle, and since the central tendency didn't get messed up, this result is at least\n # reasonable.\n #\n # We allow Pandas to fill in values at the beginning (limit_direction='backward') with the nearest value to keep\n # the data frame defined over the full date range. Yes this will flatten the trend out in those first six\n # months, but since those first six months contribute very little to the age-spectrum average concentration for\n # any time period relevant to TCCON, that's not going to affect the priors much. A proper linear extrapolation\n # would be better long-term.\n #\n # Alternately, data from sites like\n # https://www.eea.europa.eu/data-and-maps/daviz/atmospheric-concentration-of-carbon-dioxide-4\n # that extend back further could be used to at least get the shape of the trends. If early (pre 1990) data\n # becomes crucial, that is probably the best approach.\n smoothed_conc = gas_df.dmf_mean.rolling(window=12, center=True).mean().interpolate(method='index', limit_direction='backward')\n xx = gas_df.latency < 0\n gas_df.loc[xx, 'dmf_mean'] = smoothed_conc\n return gas_df","def on_R2(self):\r\n self.log()","def pdb2pka_desolv_backgr(self,residue):\n protein,routines,forcefield,apbs_setup,lig_titgrps = pdb2pka.pre_init(pdbfilename=self.pdbfile,\n ff='parse',\n ligand=None,\n verbose=1)\n mypkaRoutines = pdb2pka.pKaRoutines(protein, routines, forcefield,apbs_setup)\n #\n # Find our group\n #\n sp=residue.split(':')\n chainid=sp[0]\n #if chainid!='':\n # raise Exception,'pKD cannot handle PDB files with ChainIDs!'\n resnum=int(sp[1])\n target=sp[2]\n mypkaRoutines.findTitratableGroups()\n this_pKa=None\n for pKa in mypkaRoutines.pKas:\n print pKa.residue\n print pKa.uniqueid\n print pKa.residue.resSeq,resnum, pKa.residue.chainID,'CID',chainid,pKa.residue.name,target,pKa.pKaGroup.name,target\n #if pKa.residue.resSeq==resnum and pKa.residue.chainID==chainid and pKa.residue.name==target and pKa.pKaGroup.name==target:\n if pKa.residue.resSeq==resnum and pKa.residue.chainID==chainid and pKa.residue.name==target and pKa.pKaGroup.name==target:\n this_pKa=pKa\n break\n if not this_pKa:\n raise Exception,'Could not find inserted titratable group'\n mypkaRoutines.calculateBackground(onlypKa=pKa)\n mypkaRoutines.calculateDesolvation(onlypKa=pKa)\n #\n # Get the intrinsic pKa\n #\n pKaGroup=pKa.pKaGroup\n Gtype=pKa.pKaGroup.type\n #\n # We measure intrinsic pKa values against a single reference state\n #\n desolv=[]\n backgr=[]\n import math\n ln10=math.log(10)\n for titration in pKaGroup.DefTitrations:\n #\n # Find an uncharged reference state\n #\n ref_state=mypkaRoutines.neutral_ref_state[pKa][titration]\n all_states=titration.allstates\n all_states.sort()\n for state in all_states:\n if mypkaRoutines.is_charged(pKa,titration,state)==1:\n dpKa_desolv=(pKa.desolvation[state]-pKa.desolvation[ref_state])/ln10\n dpKa_backgr=(pKa.background[state]-pKa.background[ref_state])/ln10\n #\n # Make acid and base modifications\n #\n if Gtype=='base':\n dpKa_desolv=-dpKa_desolv\n dpKa_backgr=-dpKa_backgr\n #\n # Now calculate intrinsic pKa\n #\n backgr.append(dpKa_backgr)\n desolv.append(dpKa_desolv)\n intpKa=titration.modelpKa+dpKa_desolv+dpKa_backgr\n #print 'Energy difference for %s -> %s [reference state] is %5.2f pKa units' %(state,ref_state,intpKa)\n pKa.intrinsic_pKa[state]=intpKa\n else:\n #\n # Neutral states - why do we treat them differently?\n #\n dpKa_desolv=(pKa.desolvation[state]-pKa.desolvation[ref_state])/ln10\n dpKa_backgr=(pKa.background[state]-pKa.background[ref_state])/ln10\n #\n # Make acid and base modifications\n #\n if Gtype=='base':\n dpKa_desolv=-dpKa_desolv\n dpKa_backgr=-dpKa_backgr\n backgr.append(dpKa_backgr)\n desolv.append(dpKa_desolv)\n dpKa=dpKa_desolv+dpKa_backgr\n #print 'Energy difference for %s -> %s [reference state] is %5.2f kT' %(state,ref_state,dpKa)\n pKa.intrinsic_pKa[state]=dpKa\n #print '-----------------'\n #\n # One value is zero, so just get the avg of the rest\n #\n des_sum=0.0\n for val in desolv:\n des_sum=des_sum+val\n des_sum=des_sum/float(len(desolv)-1)\n #\n bac_sum=0.0\n for val in backgr:\n bac_sum=bac_sum+val\n bac_sum=bac_sum/float(len(backgr)-1)\n return {residue:des_sum},{residue:bac_sum}","def event11510450():\n header(11510450, 1)\n if_does_not_have_tae_event(0, CHR.Gwyndolin, 600)\n if_has_tae_event(0, CHR.Gwyndolin, 600)\n\n flag.disable_chunk(11515150, 11515151)\n flag.enable_random_in_chunk(11515150, 11515151)\n chr.disable(CHR.Gwyndolin)\n wait(1.0)\n\n # First two warps are always forward.\n skip_if_event_flag_on(2, 11515110)\n run_event_with_slot(11515110, 0, args=(1512710, 11515110))\n restart()\n skip_if_event_flag_on(2, 11515111)\n run_event_with_slot(11515110, 1, args=(1512711, 11515111))\n restart()\n\n for warp_number in range(2, 40):\n skip_if_event_flag_on(7, 11515110 + warp_number)\n\n skip_if_event_flag_on(2, 11515151)\n # Standard forward warp.\n run_event_with_slot(11515110, warp_number, args=(1512710 + warp_number, 11515110 + warp_number))\n skip(2)\n # Backward warp.\n flag.disable(11515110 + warp_number - 1) # Lose corridor progress.\n run_event_with_slot(11515110, warp_number - 2, args=(1512710 + warp_number - 2, 11515110 + warp_number - 2))\n\n chr.rotate_to_face_entity(CHR.Gwyndolin, CHR.Player)\n restart()","def TAY(self, *_):\n self.reg.Y = self.reg.A\n self.reg.N = self.reg.Y << 7\n self.reg.Z = self.reg.Y == 0","def ApplyXErrors( ErrorNum,array,type,L,CorrLen):\n\n if type == 1:\n #run across every element in the array\n for i in range(len(array[:,0,0])):\n for j in range(2):\n for k in range(len(array[0,0,:])):\n if random.random() >1- 1.*ErrorNum/(L*L): #rand chance of bitflip\n array[i,j,k] = -1*array[i,j,k] #apply bitflip if true\n return(array)\n\n elif type == 2:\n \"\"\"creates a number of errors on the grid. rather than having a chance of\n getting a certain number of errors, this one doesnt stop generating errors\n until you get a specified number of error.\n Two flips on the one qubit is counted as one error. This model may need to\n be changed to count it as no error. But this isnt necessilarly needed.\"\"\"\n numerrsLeft = ErrorNum\n while numerrsLeft != 0:\n Ri = int(round(random.random()*L)) -1\n Rj = int(round(random.random()*1)) -1 #int(r.rand()*2)\n Rk = int(round(random.random()*L)) -1\n if int(array[Ri,Rj,Rk]) == 1:\n array[Ri,Rj,Rk] = -1*array[Ri,Rj,Rk] #apply bitflip if true\n numerrsLeft += -1\n return(array)\n\n elif type == 4:\n \"\"\"creates a random walk with a set walk length\"\"\"\n ErrorChains = ErrorNum\n movements = []\n distances=[]\n while ErrorChains != 0: #this loop creates 1 chain\n Ri = randik(L)#create start location of walk\n Rj = randj()\n Rk = randik(L)\n walk=[] #this will be a list of tuples\n walk += [[Ri,Rk]] #create anyon\n i = 0 #set walk len counter-> could apply gauss dist here\n while i != CorrLen: #here we will just create the walk.\n nextstep=[]\n dice = int(4*random.random()) #randomly choose move direction\n if dice==0:\n #if its intersecting the walk;\n nextstep = [[walk[i][0],modpos(walk[i][1],L,-1)]]\n walk += nextstep\n\n if dice ==1 :\n nextstep = [[walk[i][0],modpos(walk[i][1],L,+1)]]\n walk += nextstep\n\n if dice == 2:\n nextstep = [[modpos(walk[i][0],L,-1),walk[i][1]]]\n walk += nextstep\n\n if dice == 3:\n nextstep = [[modpos(walk[i][0],L,-1),walk[i][1]]]\n walk += nextstep\n i+=1\n ErrorChains += -1\n movements += [walk] #combine all walks\n return(GetFlippedPoints(movements,array))\n\n elif type == 5:\n \"\"\"Self avoiding version of 4 (with self intersections)\"\"\"\n ErrorChains = ErrorNum\n movements = []\n distances=[]\n while ErrorChains != 0: #this loop creates 1 chain\n Ri = randik(L)\n Rj = ()\n Rk = randik(L)\n walk=[] #this will be a list of tuples\n walk += [[Ri,Rk]] #create anyon\n i = 0 #set walk len counter-> could apply gauss dist here\n while i != CorrLen: #here we will just create the walk.\n nextstep=[]\n dice = int(4*random.random()) #randomly choose move direction\n if dice == 0:\n #if its intersecting the walk;\n nextstep = [[walk[i][0],modpos(walk[i][1],L,-1)]]\n try:#if next step in walk:\n if nextstep[0] in walk:\n continue#try again.\n except:#if not in walk:\n pass#add to walk.\n walk += nextstep\n\n if dice == 1:\n nextstep = [[walk[i][0],modpos(walk[i][1],L,+1)]]\n try:\n if nextstep[0] in walk:\n continue\n except:\n pass\n walk += nextstep\n\n if dice == 2:\n nextstep = [[modpos(walk[i][0],L,-1),walk[i][1]]]\n try:\n if nextstep[0] in walk:\n continue\n except:\n pass\n walk += nextstep\n\n if dice == 3:\n nextstep = [[modpos(walk[i][0],L,-1),walk[i][1]]]\n try:\n if nextstep[0] in walk:\n continue\n except:\n pass\n walk += nextstep\n i+=1\n ErrorChains += -1\n movements += [walk] #combine all walks\n return(GetFlippedPoints(movements,array))\n elif type == 6:\n \"\"\"fixed version of 4\n a walk of set length, with self intersections. this one also doesnt 'cancel itself out' when it crosses over itself NOT IMPLEMENTED YET\"\"\"\n ErrorChains = ErrorNum\n movements = []\n distances=[]\n while ErrorChains != 0: #this loop creates 1 chain\n Ri = randik(L)#create start location of walk\n Rj = randj()\n Rk = randik(L)\n walk=[] #this will be a list of tuples\n walk += [[Ri,Rj,Rk]] #create anyon\n i = 0 #set walk len counter-> could apply gauss dist here\n while i != CorrLen: #here we will just create the walk.\n\n nextstep=[]\n dice = int(4*random.random()) #randomly choose move direction\n if dice==0:\n if Rj == 0:\n nextstep = [walk[i][0], walk[i][1]^1, modpos(walk[i][2],L,-1)]#removed extra bracket\n if Rj == 1:\n nextstep = [modpos(walk[i][0],L,-1), walk[i][1]^1, walk[i][2]]\n\n if dice ==1 :\n if Rj == 0:\n nextstep = [modpos(walk[i][0],L,1), walk[i][1]^1, walk[i][2]]\n if Rj == 1:\n nextstep = [walk[i][0], walk[i][1]^1, walk[i][2]]\n\n if dice == 2:\n if Rj == 0:\n nextstep = [modpos(walk[i][0],L,1), walk[i][1]^1, walk[i][2]]\n if Rj == 1:\n nextstep = [walk[i][0], walk[i][1]^1, modpos(walk[i][2],L,1)]\n\n if dice == 3:\n if Rj == 0:\n nextstep = [walk[i][0], walk[i][1]^1, walk[i][2]]\n if Rj == 1:\n nextstep = [modpos(walk[i][0], L, -1) , walk[i][1]^1, modpos(walk[i][2],L,1)]\n walk += [nextstep]\n i+=1\n ErrorChains += -1\n movements += [walk] #combine all walk\n return(GetFlippedPoints3(movements,array))","def tare_force(crush):\n tare = hanging_force(crush)\n if abs(tare) >= 0.25:\n set_trace()\n # assert abs(tare) < 0.25, f\"Excessive hanging force detected: {tare:.3f}\"\n crush['Force (N)'] = crush['Force (N)'] - tare\n return crush","def fix_jump(self):\n pass","def abort_ber_meas(self):\r\r\n loggerCmw = logging.getLogger('abort_ber_meas')\r\r\n self.write('ABORt:WCDMa:SIGN:BER')\r\r\n loggerCmw.info(\"Aborting BER measurements\")\r\r\n time.sleep(1)","def power_output_existing_thermal_rule(_m, g, y, s, t):\r\n\r\n if y != m.Y.last() and t != m.T.last():\r\n return (- m.sigma_1[g, y, s, t] + m.sigma_2[g, y, s, t]\r\n + m.sigma_20[g, y, s, t] - m.sigma_20[g, y, s, t + 1]\r\n - m.sigma_23[g, y, s, t] + m.sigma_23[g, y, s, t + 1]\r\n - m.lamb[self.k(m, g), y, s, t]\r\n + ((m.DELTA[y] * m.RHO[y, s]) * (\r\n m.C_MC[g, y] + ((m.EMISSIONS_RATE[g] - m.baseline[y]) * m.permit_price[y])))\r\n == 0)\r\n\r\n elif y != m.Y.last() and t == m.T.last():\r\n return (- m.sigma_1[g, y, s, t] + m.sigma_2[g, y, s, t]\r\n + m.sigma_20[g, y, s, t]\r\n - m.sigma_23[g, y, s, t]\r\n - m.lamb[self.k(m, g), y, s, t]\r\n + ((m.DELTA[y] * m.RHO[y, s]) * (\r\n m.C_MC[g, y] + ((m.EMISSIONS_RATE[g] - m.baseline[y]) * m.permit_price[y])))\r\n == 0)\r\n\r\n elif y == m.Y.last() and t != m.T.last():\r\n return (- m.sigma_1[g, y, s, t] + m.sigma_2[g, y, s, t]\r\n + m.sigma_20[g, y, s, t] - m.sigma_20[g, y, s, t + 1]\r\n - m.sigma_23[g, y, s, t] + m.sigma_23[g, y, s, t + 1]\r\n - m.lamb[self.k(m, g), y, s, t]\r\n + ((m.DELTA[y] * m.RHO[y, s]) * (1 + (1 / m.INTEREST_RATE)) * (\r\n m.C_MC[g, y] + ((m.EMISSIONS_RATE[g] - m.baseline[y]) * m.permit_price[y])))\r\n == 0)\r\n\r\n elif y == m.Y.last() and t == m.T.last():\r\n return (- m.sigma_1[g, y, s, t] + m.sigma_2[g, y, s, t]\r\n + m.sigma_20[g, y, s, t]\r\n - m.sigma_23[g, y, s, t]\r\n - m.lamb[self.k(m, g), y, s, t]\r\n + ((m.DELTA[y] * m.RHO[y, s]) * (1 + (1 / m.INTEREST_RATE)) * (\r\n m.C_MC[g, y] + ((m.EMISSIONS_RATE[g] - m.baseline[y]) * m.permit_price[y])))\r\n == 0)\r\n\r\n else:\r\n raise Exception(f'Unhandled case: {g, y, s, t}')","def adapt_steering(position):\n center = RESOLUTIONX / 2\n offset = center - position\n steerfactor = offset / 10\n CRL_CAR.steer(steerfactor)\n logging.info(position)","def recursiveTraceJumptablese(ea, function=False):","def stop():\n twister = Twist(linear=Vector3(x=0,y=0,z=0),angular=Vector3(x=0,y=0,z=0))\n pub.publish(twister)\n global has_bumped\n has_bumped = True","def test_14_missing_nonbonded_handler(self, force_field):\n top = Molecule.from_smiles(\"CCCC\").to_topology()\n\n ff_no_vdw = copy.deepcopy(force_field)\n ff_no_electrostatics = copy.deepcopy(force_field)\n\n ff_no_vdw.deregister_parameter_handler(\"vdW\")\n\n ff_no_electrostatics.deregister_parameter_handler(\"Electrostatics\")\n ff_no_electrostatics.deregister_parameter_handler(\"ToolkitAM1BCC\")\n\n sys_no_electrostatics = ff_no_electrostatics.create_openmm_system(top)\n\n np.testing.assert_almost_equal(\n actual=get_14_scaling_factors(sys_no_electrostatics)[1],\n desired=ff_no_electrostatics[\"vdW\"].scale14,\n decimal=8,\n )\n\n sys_no_vdw = ff_no_vdw.create_openmm_system(top)\n np.testing.assert_almost_equal(\n actual=get_14_scaling_factors(sys_no_vdw)[0],\n desired=ff_no_vdw[\"Electrostatics\"].scale14,\n decimal=8,\n )","def noCheck():\n dislin.nochek()","def do_solvate( ingro, outgro, inouttop, water = 'ffamber_tip3p.gro', verbose = False, use_big_vdwradii = False, FF = 'ffamber99sb'):\n\n #Copy top/gro files to a temporary working directory where we will do this setup before copying back. This is necessary because of issues with 3.3.x genbox, requiring input/output topology to be in working directory\n tempdir = tempfile.mkdtemp()\n shutil.copy(inouttop, os.path.join(tempdir, 'tmp.top') )\n shutil.copy(ingro, os.path.join( tempdir, 'tmp.gro') )\n startdir = os.getcwd()\n os.chdir( tempdir )\n\n if use_big_vdwradii: \n make_big_vdwradii('.') \n\n #Ensure forcefield\n ensure_forcefield( 'tmp.top', 'tmp.top', FF = FF )\n\n #Run genbox \n if verbose: print \"Running in temporary directory %s...\" % tempdir\n cmd = 'genbox -cp tmp.gro -p tmp.top -o out.gro -cs %(water)s' % vars()\n output = rungmx( cmd, verbose = verbose)\n if verbose: print output\n\n #Compile name of itp file and edit topology to include this\n wateritp = water.replace('.gro','.itp')\n #Edit topology file to replace spc.itp with this\n file = open( 'tmp.top', 'r')\n text = file.readlines()\n file.close()\n try:\n idx = text.index('#include \"spc.itp\"\\n')\n text[idx ] = '#include \"%(wateritp)s\"\\n' % vars()\n except ValueError:\n #Check if it already includes correct water model\n try:\n #If this works then we leave as is\n idx = text.index('#include \"%(wateritp)s\"\\n' % vars() )\n except ValueError:\n #If it is still not found, add the includejust before the SYSTEM section\n idx = 0\n while '[ system ]' not in text[idx]: #Find system line\n idx+=1\n text[idx] = '#include \"%(wateritp)s\"\\n' % vars() + text[idx]\n file = open( 'tmp.top', 'w')\n file.writelines( text )\n file.close()\n \n #Parse output and figure out the number of waters, typically SOL\n tmp = output.split('\\n')\n tmp.reverse()\n for line in tmp:\n if 'Number of SOL ' in line: break\n if not 'Number of SOL' in line: nwaters = None #Not found\n else:\n nwaters = int( line.split()[-1] )\n\n #Copy files back and cleanup\n os.chdir(startdir)\n shutil.copy( os.path.join(tempdir, 'tmp.top'), inouttop )\n shutil.copy( os.path.join(tempdir, 'out.gro'), outgro )\n shutil.rmtree( tempdir)\n\n return output, nwaters","def handler(signum, frame):\n logging.warning(\"Got a {} signal. Doing nothing\".format(signum))","def clean_linear_track_error(self):\r\n return self._arm.clean_linear_track_error()","def insert_motor(burt,axis=[-0.05,0,0],angle=45.0,max_force=35):\r\n iter = 45\r\n travel_thresh = abs(axis[0])-0.003\r\n burt.set_tcp(wp.motor_centroid)\r\n start_pose = burt.getl()\r\n burt.force_move(axis,acc=0.1,vel=0.01,force=max_force)\r\n end_pose = burt.getl()\r\n dif = end_pose[0]-start_pose[0]\r\n axis[0] -= dif\r\n #print(dif)\r\n if abs(dif)<travel_thresh:\r\n #have hit the fixing plate so hunt\r\n burt.movel_tool([-0.0005,0,0,0,0,0])\r\n time.sleep(0.1)\r\n start_force = burt.get_forces()[0]\r\n force = start_force\r\n print(\"hunting start force: \",start_force)\r\n for i in range(0,iter):\r\n burt.movel_tool([0,0,0,0,-(angle*pi)/(iter*180.0),0],acc=0.1)\r\n burt.translatel([end_pose[0]-0.0005,end_pose[1],end_pose[2]],acc=0.1)\r\n time.sleep(0.1)\r\n force = burt.get_forces()[0]\r\n print(\"measured force: \",force)\r\n if abs(force)<abs(0.2*start_force):\r\n burt.force_move(axis,acc=0.1,vel=0.01,force=max_force)\r\n \r\n burt.set_tcp(wp.pincher_tcp)\r\n return True\r\n burt.set_tcp(wp.pincher_tcp)\r\n return False\r\n burt.set_tcp(wp.pincher_tcp)\r\n return True","def simulationTwoDrugsDelayedTreatment():\n\n # TODO","def test_low_voltage_passing_signal(self):\n data = gen_random_data(-0.5, 0.5, self.channels)\n self.assertFalse(self.lowvoltage_rule.is_broken(data))","def signal_kernel(self, signum):\n pass","def trap_depth(V,X,Y,Z,Im,Jm,Km): \n from project_parameters import debug,scale,position\n #from all_functions import sum_of_e_field,spher_harm_bas,spher_harm_exp,spher_harm_cmp,find_saddle\n def a(a,N):\n \"\"\"Shortcut function to convert array x into a row vector.\"\"\" \n a=np.ravel(a, order='F') # Same order\n return a\n N1,N2,N3=V.shape\n N=N1*N2*N3\n [Ex,Ey,Ez]=np.gradient(V,abs(X[1]-X[0])/scale,abs(Y[1]-Y[0])/scale,abs(Z[1]-Z[0])/scale)\n E=np.sqrt(Ex**2+Ey**2+Ez**2)\n # identify the escape position and height by checking each point\n minElectricField=np.max(E) # initialize as maximum E field magnitude\n distance=0\n escapeHeight=1\n escapePosition=[0,0,0]\n [Im,Jm,Km] = find_saddle(V,X,Y,Z,3)\n Vm = V[Im,Jm,Km]\n for i in range(N1):\n for j in range(N2):\n for k in range(N3):\n if E[i,j,k]<minElectricField:\n distance=abs(np.sqrt((Im-i)**2+(Jm-j)**2+(Km-k)**2)) \n if distance > 6:\n minElectricField=E[i,j,k]\n escapeHeight=V[i,j,k]\n escapePosition=[i,j,k]\n if debug.trap_depth: \n print E[i,j,k],V[i,j,k],[i,j,k],distance\n check=1 \n if debug.trap_depth: \n print minElectricField,escapeHeight,escapePosition,distance \n if distance<check:\n print('trap_depth.py: Escape point too close to trap minimum. Improve grid resolution or extend grid.')\n if escapeHeight>0.2:\n print('trap_depth.py: Escape point parameter too high. Improve grid resolution or extend grid.')\n D=escapeHeight-Vm\n [Ie,Je,Ke]=escapePosition\n [Xe,Ye,Ze]=[X[Ie],Y[Je],Z[Ke]] \n return [D,Xe,Ye,Ze]","def chase_laser(self):\r\n print(\"Meeeeow\\n\")","def force ( r, e ):\n from math import isclose\n\n # Parameters of the Gay-Berne potential \n # \n # The key parameters are \n # mu, nu ................ the exponents \n # kappa and kappa' ....... the anisotropies \n # kappa is the ratio of intermolecular separations \n # sigma_e / sigma_s i.e. end-to-end / side-by-side \n # kappa' is the ratio of well depths \n # epsilon_s / epsilon_e i.e. side-by-side / end-to-end \n # The derived parameters are chi and chi' \n # chi = (kappa**2 - 1) / (kappa**2+1) \n # chi' = (z - 1) / (z + 1)\n # where z = (kappa') ** ( 1 / mu ) \n # \n # For convenience kappa' is spelt xappa, chi' is spelt xhi\n # We choose units such that sigma_s = 1.0 and epsilon_0 = 1.0\n # Two of the following three varieties should be commented out\n\n # Original Gay-Berne-deMiguel potential [J. Chem. Phys, 74, 3316; Mol. Phys. 74, 405 (1991)]\n mu, nu, kappa, xappa = 2, 1, 3.0, 5.0\n\n # # Luckhurst-Phippen potential [Liq. Cryst., 8, 451 (1990)]\n # mu, nu, kappa, xappa = 1, 2, 3.0, 5.0\n\n # # Berardi-Zannoni potential [J. Chem. Soc. Faraday Trans., 89, 4069 (1993)]\n # mu, nu, kappa, xappa = 1, 3, 3.0, 5.0\n\n # Derived parameters\n chi = (kappa**2 - 1.0) / (kappa**2+1.0)\n xhi = (xappa**(1.0/mu) - 1.0) / (xappa**(1.0/mu) + 1.0)\n\n # Cutoff distance; normally we would use a larger value\n r_cut = 4.0\n \n assert r.shape == (n,3), 'Incorrect shape of r'\n assert e.shape == (n,3), 'Incorrect shape of e'\n\n # Notation to match appendix\n i = 0\n j = 1\n\n ei = e[i,:]\n ej = e[j,:]\n assert isclose(np.sum(ei**2),1.0), 'Non-unit vector {} {} {}'.format(*ei)\n assert isclose(np.sum(ej**2),1.0), 'Non-unit vector {} {} {}'.format(*ej)\n\n rij = r[i,:] - r[j,:]\n rij_mag = np.sqrt( np.sum(rij**2) ) # Magnitude of separation vector\n sij = rij / rij_mag # Unit vector\n ci = np.dot( ei, sij )\n cj = np.dot( ej, sij )\n cij = np.dot( ei, ej )\n cp = ci + cj\n cm = ci - cj\n\n # Sigma formula\n cpchi = cp/(1.0+chi*cij)\n cmchi = cm/(1.0-chi*cij)\n sigma = 1.0/np.sqrt(1.0-0.5*chi*(cp*cpchi+cm*cmchi))\n\n # Epsilon formula\n eps1 = 1.0/np.sqrt(1.0-(chi*cij)**2) # Depends on chi, not xhi\n cpxhi = cp/(1.0+xhi*cij)\n cmxhi = cm/(1.0-xhi*cij)\n eps2 = 1.0-0.5*xhi*(cp*cpxhi+cm*cmxhi) # Depends on xhi\n epsilon = (eps1**nu) * (eps2**mu)\n\n # Potential at rij\n rho = rij_mag - sigma + 1.0\n rho6 = 1.0 / rho**6\n rho12 = rho6**2\n rhoterm = 4.0*(rho12 - rho6) # Needed for forces and torques\n drhoterm = -24.0 * (2.0 * rho12 - rho6) / rho # Needed for forces and torques\n pot = epsilon*rhoterm\n\n # Potential at r_cut\n rho = r_cut - sigma + 1.0\n rho6 = 1.0 / rho**6\n rho12 = rho6**2\n cutterm = 4.0*(rho12 - rho6) # Needed for cutoff forces and torques\n dcutterm = -24.0 * (2.0 * rho12 - rho6) / rho # Needed for cutoff forces and torques\n pot = pot - epsilon * cutterm\n\n # Derivatives of sigma\n prefac = 0.5*chi*sigma**3\n dsig_dci = prefac*(cpchi+cmchi)\n dsig_dcj = prefac*(cpchi-cmchi)\n prefac = prefac*(0.5*chi)\n dsig_dcij = -prefac*(cpchi**2-cmchi**2)\n\n # Derivatives of epsilon\n prefac = -mu*xhi*(eps1**nu)*eps2**(mu-1)\n deps_dci = prefac*(cpxhi+cmxhi)\n deps_dcj = prefac*(cpxhi-cmxhi)\n prefac = prefac*(0.5*xhi)\n deps_dcij = -prefac*(cpxhi**2-cmxhi**2) # From derivative of eps2\n deps_dcij = deps_dcij + nu*(chi**2)*(eps1**(nu+2))*(eps2**mu)*cij # From derivative of eps1\n\n # Derivatives of potential\n dpot_drij = epsilon * drhoterm\n dpot_dci = rhoterm * deps_dci - epsilon * drhoterm * dsig_dci\n dpot_dcj = rhoterm * deps_dcj - epsilon * drhoterm * dsig_dcj\n dpot_dcij = rhoterm * deps_dcij - epsilon * drhoterm * dsig_dcij\n\n # Standard formula for forces and torque gradients\n fij = -dpot_drij*sij - dpot_dci*(ei-ci*sij)/rij_mag - dpot_dcj*(ej-cj*sij)/rij_mag\n gi = dpot_dci*sij + dpot_dcij*ej\n gj = dpot_dcj*sij + dpot_dcij*ei\n\n # Derivatives of potential at cutoff\n dpot_drij = epsilon * dcutterm\n dpot_dci = cutterm * deps_dci - epsilon * dcutterm * dsig_dci\n dpot_dcj = cutterm * deps_dcj - epsilon * dcutterm * dsig_dcj\n dpot_dcij = cutterm * deps_dcij - epsilon * dcutterm * dsig_dcij\n\n # Standard formula for forces and torque gradients (without dpot_drij term)\n fij = fij + dpot_dci*(ei-ci*sij)/rij_mag + dpot_dcj*(ej-cj*sij)/rij_mag\n gi = gi - ( dpot_dci*sij + dpot_dcij*ej ) \n gj = gj - ( dpot_dcj*sij + dpot_dcij*ei ) \n\n # Final forces and torques\n f = np.empty_like(r)\n t = np.empty_like(r)\n f[i,:] = fij\n f[j,:] = -fij\n t[i,:] = -np.cross(ei,gi)\n t[j,:] = -np.cross(ej,gj)\n\n return pot, f, t","def give_treat(self, num_treats = 1):\n for x in range(0,num_treats):\n GPIO.output(self.treat_pin, 0)\n time.sleep(.5)\n GPIO.output(self.treat_pin, 1)\n time.sleep(.5)\n return","def scan_received(self, msg):\n # print msg\n if not(self.initialized):\n # wait for initialization to complete\n return\n\n if not(self.tf_listener.canTransform(self.base_frame,msg.header.frame_id,msg.header.stamp)):\n # need to know how to transform the laser to the base frame\n # this will be given by either Gazebo or neato_node\n return\n\n if not(self.tf_listener.canTransform(self.base_frame,self.odom_frame,msg.header.stamp)):\n # need to know how to transform between base and odometric frames\n # this will eventually be published by either Gazebo or neato_node\n return\n\n # print 'msg.header.frame_id', msg.header.frame_id\n # calculate pose of laser relative ot the robot base\n p = PoseStamped(header=Header(stamp=rospy.Time(0),\n frame_id=msg.header.frame_id))\n self.laser_pose = self.tf_listener.transformPose(self.base_frame,p)\n\n # find out where the robot thinks it is based on its odometry\n # listener.getLatestCommonTime(\"/base_link\",object_pose_in.header.frame_id)\n # p = PoseStamped(header=Header(stamp=msg.header.stamp,\n p = PoseStamped(header=Header(stamp=self.tf_listener.getLatestCommonTime(self.base_frame, self.map_frame),\n # p = PoseStamped(header=Header(stamp=rospy.Time.now(),\n frame_id=self.base_frame),\n pose=Pose())\n # p_aux = PoseStamped(header=Header(stamp=self.tf_listener.getLatestCommonTime(\"/base_link\",\"/map\"),\n p_aux = PoseStamped(header=Header(stamp=self.tf_listener.getLatestCommonTime(self.odom_frame, self.map_frame),\n # p_aux = PoseStamped(header=Header(stamp=rospy.Time.now(),\n frame_id=self.odom_frame),\n pose=Pose())\n odom_aux = self.tf_listener.transformPose(self.map_frame, p_aux)\n odom_aux_xy_theta = convert_pose_to_xy_and_theta(odom_aux.pose)\n # print 'odom_aux_xy_theta', odom_aux_xy_theta\n\n self.odom_pose = self.tf_listener.transformPose(self.odom_frame, p)\n # print 'self.odom_pose', self.odom_pose\n # (trans, root) = self.tf_listener.lookupTransform(self.odom_frame, self.base_frame, rospy.Time(0))\n # self.odom_pose = trans\n # print trans, root\n new_odom_xy_theta = convert_pose_to_xy_and_theta(self.odom_pose.pose)\n # new_odom_xy_theta = convert_pose_to_xy_and_theta(self.laser_pose.pose)\n xy_theta_aux = (new_odom_xy_theta[0]+odom_aux_xy_theta[0], \n new_odom_xy_theta[1]+odom_aux_xy_theta[1], new_odom_xy_theta[2])\n self.xy_theta_aux = xy_theta_aux\n\n if not(self.particle_cloud):\n self.initialize_particle_cloud(xy_theta_aux)\n self.current_odom_xy_theta = new_odom_xy_theta\n\n elif (math.fabs(new_odom_xy_theta[0] - self.current_odom_xy_theta[0]) > self.linear_mov or\n math.fabs(new_odom_xy_theta[1] - self.current_odom_xy_theta[1]) > self.linear_mov or\n math.fabs(new_odom_xy_theta[2] - self.current_odom_xy_theta[2]) > self.angular_mov):\n\n self.update_particles_with_odom(msg)\n self.update_particles_with_laser(msg)\n self.resample_particles()\n\n self.publish_particles(msg)"],"string":"[\n \"def post_process_trap(): \\n #################### 0) assign internal values #################### \\n from project_parameters import trapType,debug,trapFile,name,driveAmplitude,driveFrequency,Omega,dcplot,weightElectrodes,coefs,ax,az,phi,save,scale\\n #from all_functions import find_saddle,plot_potential,dc_potential,set_voltages,exact_saddle,spher_harm_bas,spher_harm_exp,pfit,plotN\\n import pickle\\n\\n with open(trapFile,'rb') as f:\\n trap = pickle.load(f)\\n\\n qe = trap.configuration.charge\\n mass = trap.configuration.mass\\n Zval = trap.configuration.position\\n r0 = trap.configuration.r0\\n RFampl = driveAmplitude \\n V0 = mass*(2*np.pi*Omega)**2*(r0*10**-3)**2/qe\\n X,Y,Z=trap.instance.X,trap.instance.Y,trap.instance.Z \\n data = trap.configuration\\n dcVoltages = set_voltages()\\n ne = len(weightElectrodes)\\n E = trap.instance.E\\n out = trap.configuration\\n if debug.post_process_trap:\\n print dcVoltages,np.max(dcVoltages)#np.sum(abs(dcVoltages))\\n plotN(dcVoltages,trap,'set DC voltages') \\n Vdc = dc_potential(trap,dcVoltages,E)\\n #[IDC,JDC,KDC] = find_saddle(Vdc,X,Y,Z,3,Zval) \\n #[XDC,YDC,ZDC] = exact_saddle(Vdc,X,Y,Z,3,Zval)\\n #XDC,YDC,ZDC = X[IDC],150/scale,Z[KDC]\\n #print XDC,YDC,ZDC,IDC,JDC,KDC\\n #dcbasis,dcscale= spher_harm_bas(XDC,YDC,ZDC,X,Y,Z,4)\\n #QQ = spher_harm_exp(Vdc,dcbasis,dcscale) \\n #print QQ[0:9].T\\n #1) RF Analysis\\n print('RF Analysis') \\n Vrf = RFampl*data.EL_RF\\n [Irf,Jrf,Krf] = find_saddle(Vrf,X,Y,Z,2,Zval)\\n if debug.post_process_trap:\\n plot_potential(Vrf,X,Y,Z,dcplot,'weighted RF potential','V_{rf} (eV)',[Irf,Jrf,Krf])\\n #2) DC Analysis\\n print('DC Analysis')\\n trap = dc_potential(trap,dcVoltages,E,update=None)\\n Vdc = trap.instance.DC\\n [Idc,Jdc,Kdc] = find_saddle(Vdc,X,Y,Z,3,Zval) # only used to calculate error at end\\n if debug.post_process_trap:\\n plot_potential(Vdc,X,Y,Z,'1D plots','full DC potential')\\n #3) determine the exact saddles of the RF and DC\\n trap = dc_potential(trap,dcVoltages,E)\\n Vdc = trap.instance.DC\\n print('Determining exact RF saddle...')\\n [Xrf,Yrf,Zrf] = exact_saddle(Vrf,X,Y,Z,2,Zval) \\n print('Determining exact DC saddle...')\\n [Xdc,Ydc,Zdc] = exact_saddle(Vdc,X,Y,Z,3,Zval)\\n #4) determine stray field (beginning of justAnalyzeTrap)\\n print('Determining compensation due to E field...')\\n nx,ny,nz=X.shape[0],Y.shape[0],Z.shape[0]\\n x,y,z = np.zeros((nx,ny,nz)),np.zeros((nx,ny,nz)),np.zeros((nx,ny,nz))\\n for i in range(nx):\\n for j in range(ny):\\n for k in range(nz):\\n x[i,j,k] = X[i]\\n y[i,j,k] = Y[j]\\n z[i,j,k] = Z[k]\\n VlessE = Vdc-E[0]*x-E[1]*y-E[2]*z\\n [Xdc,Ydc,Zdc] = exact_saddle(VlessE,X,Y,Z,3) \\n dist = np.sqrt((Xrf-Xdc)**2+(Yrf-Ydc)**2+(Zrf-Zdc)**2) \\n #5) call pfit to built teh total field and determine the trap characteristics\\n [fx,fy,fz,theta,Depth,Xe,Ye,Ze] = pfit(Vrf,Vdc,X,Y,Z,Irf,Jrf,Krf)#pfit(trap,E,Freq,RFampl)\\n print('Stray field is ({0},{1},{2}) V/m.'.format(scale*E[0],scale*E[1],scale*E[2]))\\n print('With this field, the compensation is optimized to {} micron.'.format(scale*dist))\\n print('RF saddle: ({0},{1},{2})\\\\nDC saddle ({3},{4},{5}).'.format(Xrf,Yrf,Zrf,Xdc,Ydc,Zdc)) \\n if debug.trap_depth:\\n print('The trap escape position is at ({0},{1},{2}) microns, for a trap depth of {3} mV'.format(Xe*scale,Ye*scale,Ze*scale,Depth*scale))\\n print('The trap frequencies are fx = {0} MHz, fy = {1} MHz, and fz = {2} MHz'.format(fx*10**-6,fy*10**-6,fz*10**-6))\\n #6) Sanity testing; quality check no longer used\\n if debug.post_process_trap:\\n rfbasis,rfscale= spher_harm_bas(Xrf,Yrf,Zrf,X,Y,Z,2)\\n Qrf = spher_harm_exp(Vrf,rfbasis,rfscale) \\n if np.sqrt((Xrf-Xdc)**2+(Yrf-Ydc)**2+(Zrf-Zdc)**2)>0.008: \\n print('Expanding DC with RF for saniy checking.')\\n Qdc = spher_harm_exp(Vdc,rfbasis,rfscale) \\n else:\\n print('Expanding DC without RF for sanity checking.')\\n dcbasis,dcscale= spher_harm_bas(Xdc,Ydc,Zdc,X,Y,Z,2)\\n Qdc = spher_harm_exp(Vdc,dcbasis,dcscale) \\n Arf = 2*np.sqrt( (3*Qrf[7])**2+(3*Qrf[8])**2 )\\n Thetarf = 45*(Qrf[8]/abs(Qrf[8]))-90*np.arctan((3*Qrf[7])/(3*Qrf[8]))/np.pi\\n Adc = 2*np.sqrt( (3*Qdc[7])**2+(3*Qdc[8])**2 )\\n Thetadc = 45*(Qrf[8]/abs(Qrf[8]))-90*np.arctan((3*Qdc[7])/(3*Qdc[8]))/np.pi\\n out.E = E\\n out.miscompensation = dist\\n out.ionpos = [Xrf,Yrf,Zdc]\\n out.ionposIndex = [Irf,Jrf,Krf]\\n out.frequency = [fx,fy,fz]\\n out.theta = theta\\n out.trap_depth = Depth/qe \\n out.escapepos = [Xe,Ye,Ze]\\n out.Quadrf = 2*np.array([Qrf[7]*3,Qrf[4]/2,Qrf[8]*6,-Qrf[6]*3,-Qrf[5]*3])\\n out.Quaddc = 2*np.array([Qdc[7]*3,Qdc[4]/2,Qdc[8]*6,-Qdc[6]*3,-Qdc[5]*3])\\n out.Arf = Arf\\n out.Thetarf = Thetarf\\n out.Adc = Adc\\n out.Thetadc = Thetadc\\n T = np.array([[2,-2,0,0,0],[-2,-2,0,0,0],[0,4,0,0,0],[0,0,1,0,0],[0,0,0,1,0],[0, 0,0,0,1]])\\n Qdrf = out.Quadrf.T\\n Qddc = out.Quaddc.T\\n out.q = (1/V0)*T*Qdrf\\n out.alpha = (2/V0)*T*Qddc\\n out.Error = [X[Idc]-Xdc,Y[Jdc]-Ydc,Z[Kdc]-Zdc]\\n #7) update the trapping field data structure with instance attributes\\n trap.configuration=out\\n trap.instance.driveAmplitude = driveAmplitude\\n trap.instance.driveFrequency = driveFrequency\\n trap.instance.coefs = coefs\\n trap.instance.ax = ax\\n trap.instance.az = az\\n trap.instance.phi = phi\\n trap.instance.ppt = True\\n trap.instance.out = out\\n if save==True:\\n print('Saving '+trapFile+' as a data structure...')\\n with open(trapFile,'wb') as f:\\n pickle.dump(trap,f)\\n return 'post_proccess_trap complete' #out # no output needed really\",\n \"def backpropagating(self): \\n\\n ######################### Configure the sensor inputs given the movement of the agent ######################### \\n sensors_result_N = self.agent.sensors(self, direction=3) + self.agent.get_energy_coarsed()+\\\\\\n self.agent.rotate_previousAction(3)+[int(self.agent.get_previous_collision())]\\n sensors_result_O = self.agent.sensors(self, direction=2) + self.agent.get_energy_coarsed()+\\\\\\n self.agent.rotate_previousAction(2) + [int(self.agent.get_previous_collision())]\\n sensors_result_S = self.agent.sensors(self, direction=1) + self.agent.get_energy_coarsed()+\\\\\\n self.agent.rotate_previousAction(1) + [int(self.agent.get_previous_collision())]\\n sensors_result_E = self.agent.sensors(self, direction=0) + self.agent.get_energy_coarsed()+\\\\\\n self.agent.rotate_previousAction(0) + [int(self.agent.get_previous_collision())]\\n\\n input_nn_N = np.asarray(sensors_result_N).astype(int) # input when the Nord action is performed \\n input_nn_O = np.asarray(sensors_result_O).astype(int) # input when the West action is performed\\n input_nn_S = np.asarray(sensors_result_S).astype(int) # input when the South action is performed\\n input_nn_E = np.asarray(sensors_result_E).astype(int) # input when the West action is performed\\n\\n l_input = [input_nn_E.reshape(1,145),input_nn_S.reshape(1,145),input_nn_O.reshape(1,145),input_nn_N.reshape(1,145)]\\n ######################### Configure the sensor inputs given the movement of the agent #########################\\n\\n print(\\\"The reward in baskpropagating is %f\\\" %(self.agent.reward) ) \\n parameters = [self.gamma, self.agent.reward]\\n Ui = self.U_list[self.agent.get_previousAction().index(1)]\\n\\n if not self.end:\\n U_list_y = [self.nn.predict(input_nn_E.reshape(1,145)),\\\\\\n self.nn.predict(input_nn_S.reshape(1,145)),\\\\\\n self.nn.predict(input_nn_O.reshape(1,145)),\\\\\\n self.nn.predict(input_nn_N.reshape(1,145))] \\n #print(U_list_y)\\n maxU = np.max(U_list_y)\\n #print(np.max(U_list_y))\\n index_input_maxU = np.argmax(U_list_y) # the input given for the backprogating is the one with the maximum utility\\n input_target = l_input[index_input_maxU] # The input target with the max utility, add to the tuple given during the experience replay\\n uprime = self.agent.reward + self.gamma * maxU # input of the utility with the best value\\n \\n else:\\n uprime = self.agent.reward\\n input_target = np.array(None)\\n \\n action = self.agent.get_previousAction().index(1)\\n input_nn = self.input_list[action]\\n ##### Add to the lesson the action chose in order to go the next state, \\n ##### the next state after to have performed the action, and the reward given\\n if(self.action_proba[action] > 0.01): # the Pl minimum to choose the action corresponding to the action policy, cf to the paper part experience replay\\n #next_states = [copy.deepcopy(input_nn_E).reshape(1,145), copy.deepcopy(input_nn_S).reshape(1,145), copy.deepcopy(input_nn_O).reshape(1,145), copy.deepcopy(input_nn_N).reshape(1,145)]\\n self.memory.append((input_nn,action,np.asarray(copy.deepcopy(l_input)),self.agent.reward)) # We add the experiment to the memory of the agent \\n \\n ############################\\n self.nn.train_one_step_other(input_nn,uprime)\\n #self.nn.train(input_nn,tf.convert_to_tensor([[uprime]])) # use the method fit to train the neural network\",\n \"def sandwich(self):\\n if self.game.rules[\\\"capture\\\"] == \\\"custodial_capture\\\":\\n self.remove_self()\\n if self.game.rules[\\\"trapping\\\"]:\\n for trapped_neighbor in [neighbor for neighbor in self.get_neighbors() if neighbor.trapped and self.position in neighbor.get_sandwichers() and len(neighbor.get_sandwichers()) == 2]:\\n trapped_neighbor.untrap()\\n self.trap()\",\n \"def stack_nonlinearity(self):\\n self.flow = self.NONLINEARITY[0](self.flow)\",\n \"def fill_gas_tank(self):\\r\\n\\t\\tprint(\\\"This car doesn't need a gas tank.\\\")\",\n \"def fill_gas_tank(self):\\n print(\\\"This car doesn't need a gas tank!\\\")\",\n \"def fill_gas_tank(self):\\n print(\\\"This car doesn't need a gas tank!\\\")\",\n \"def trap_knobs():\\n print('Executing trap_knobs...')\\n #0) Define parameters and heck to see what scripts have been run\\n from project_parameters import save,debug,trapFile,elMap,electrodes,multipoles,name,simulationDirectory,reg,trapType\\n #from all_functions import nullspace,plotN\\n import pickle\\n with open(trapFile,'rb') as f:\\n trap = pickle.load(f)\\n if trap.configuration.expand_field!=True:\\n return 'You must run expand_field first!'\\n if trap.configuration.trap_knobs and not debug.trap_knobs:\\n return 'Already executed trap_knobs.'\\n #1) redefine parameters with shorthand and run sanity checks\\n totE = len(electrodes) # numTotalElectrodes\\n totM = len(multipoles) # numTotalMultipoles\\n assert totE == trap.numElectrodes # Make sure that the total number of electrodes includes the RF.\\n tc = trap.configuration\\n mc = tc.multipoleCoefficients # this is the original, maximum-length multipole coefficients matrix (multipoles,electrodes)\\n for row in range(totM):\\n #row+=1\\n if abs(np.sum(mc[row,:])) < 10**-50: # arbitrarily small\\n return 'trap_knobs: row {} is all 0, can not solve least square, stopping trap knobs'.format(row)\\n #2) Apply electrode mapping by clearing some electrodes and adding them to the new map\\n # mapping one to an unused electrode should turn it off as well\\n for index in range(totE):\\n if index != elMap[index]:\\n mc[:,elMap[index]] += mc[:,index] # combine the electrode to its mapping\\n electrodes[index] = 0 # clear the mapped electrode, implemented in part 3\\n useE = int(np.sum(electrodes)) # numUsedElectrodes\\n useM = int(np.sum(multipoles)) # numUsedMultipoles\\n eo = np.sqrt(useM)-1 # expansionOrder\\n #3) build a reduced array of multipole coefficients to invert\\n MC = np.zeros((useM,useE)) # reduced matrix to build up and invert\\n ML = 0\\n for ml in range(totM):\\n if multipoles[ml]:\\n EL = 0 # clear the electrode indexing before looping through electrodes again for new multipole\\n for el in range(totE):\\n if electrodes[el]:\\n MC[ML,EL] = mc[ml,el]\\n EL += 1\\n ML += 1\\n print('trap_knobs: with electrode and multipole constraints, the coefficient matrix size is ({0},{1}).'.format(MC.shape[0],MC.shape[1]))\\n #4) numerially invert the multipole coefficients to get the multipole controls, one multipole at a time\\n # solve the equation MC*A = B, where the matrix made from all A vectors is C\\n C = np.zeros((useE,useM)) # multipole controls (electrodes,multipoles) will be the inverse of multipole coefficents \\n for mult in range(useM):\\n B = np.zeros(useM)\\n B[mult] = 1\\n A = np.linalg.lstsq(MC,B)[0]\\n C[:,mult] = A\\n #5) calculate the nullspace and regularize if the coefficients matrix is sufficiently overdetermined\\n if useM < useE:\\n K = nullspace(MC)\\n else:\\n print('There is no nullspace because the coefficient matrix is rank deficient.\\\\nThere can be no regularization.')\\n K = None\\n reg = False\\n if reg:\\n for mult in range(useM):\\n Cv = C[:,mult].T\\n Lambda = np.linalg.lstsq(K,Cv)[0]\\n test=np.dot(K,Lambda)\\n C[:,mult] = C[:,mult]-test \\n #6) expand the matrix back out again, with zero at all unused electrodes and multipoles; same as #3 with everything flipped\\n c = np.zeros((totE,totM)) \\n EL = 0\\n for el in range(totE):\\n if electrodes[el]:\\n ML = 0 # clear the electrode indexing before looping through electrodes again for new multipole\\n for ml in range(totM):\\n if multipoles[ml]:\\n c[el,ml] = C[EL,ML]\\n ML += 1\\n EL += 1\\n #7) plot the multipole controls in teh trap geometry\\n if debug.trap_knobs:\\n for ml in range(totM):\\n if multipoles[ml]:\\n plot = c[:,ml]\\n plotN(plot,trap,'Multipole {}'.format(ml)) \\n #8) update instance configuration with multipole controls to be used bu dc_voltages in post_process_trap\\n tc.multipoleKernel = K\\n tc.multipoleControl = c\\n tc.trap_knobs = True\\n trap.configuration=tc\\n #8.5) change the order of the columns of c for labrad\\n # originally (after constant) Ez,Ey,Ex,U3,U4,U2,U5,U1,...,Y4-4,...,Y40,...,Y44\\n # we want it to be Ex,Ey,Ez,U2,U1,U3,U5,U4,...,Y40 and then end before any of the other 4th order terms\\n# cc = c.copy()\\n# cc[:,1] = c[:,3] # Ex\\n# cc[:,2] = c[:,1] # Ey\\n# cc[:,3] = c[:,2] # Ez\\n# cc[:,4] = c[:,6] # U2\\n# cc[:,5] = c[:,8]\\n# cc[:,6] = 0 # U3\\n# cc[:,16]= c[:,20]# Y40\\n# cc[:,20]= 0\\n cc = c\\n #9) save trap and save c as a text file (called the \\\"C\\\" file for Labrad)\\n if save: \\n print('Saving '+name+' as a data structure...')\\n with open(trapFile,'wb') as f:\\n pickle.dump(trap,f)\\n #ct = cc[1:totE,1:17] #eliminate the RF electrode and constant multipole; eliminate everything past Y40\\n ct = cc[1:totE,1:25] # only eliminate the constant\\n text = np.zeros((ct.shape[0])*(ct.shape[1]))\\n for j in range(ct.shape[1]):\\n for i in range(ct.shape[0]):\\n text[j*ct.shape[0]+i] = ct[i,j]\\n np.savetxt(simulationDirectory+name+'.txt',text,delimiter=',')\\n return 'Completed trap_knobs.'\",\n \"def fill_gas_tank(self):\\n print(\\\"\\\\nThis car doesn't need a gas tank!\\\")\",\n \"def processTick(self, tick):\\n\\n self.lastRerouteCounter += 1\\n # reroute every x ticks based on config value\\n if self.lastRerouteCounter >= CustomRouter.reRouteEveryTicks and CustomRouter.reRouteEveryTicks > 0:\\n self.lastRerouteCounter = 0\\n if self.smartCar:\\n try:\\n oldRoute = self.currentRouterResult.route\\n currentEdgeID = traci.vehicle.getRoadID(self.id)\\n nextNodeID = Network.getEdgeIDsToNode(currentEdgeID).getID()\\n self.currentRouterResult = CustomRouter.route(nextNodeID, self.targetID, tick, self)\\n traci.vehicle.setRoute(self.id, [currentEdgeID] + self.currentRouterResult.route)\\n # print(\\\"OLD: \\\" + str(oldRoute) + \\\" - NEW: \\\" + str(self.currentRouterResult.route))\\n except IndexError as e:\\n # print(e)\\n pass\\n except traci.exceptions.TraCIException as e:\\n # print(e)\\n pass\\n\\n roadID = traci.vehicle.getSubscriptionResults(self.id)[80]\\n if roadID != self.currentEdgeID and self.smartCar:\\n if self.currentEdgeBeginTick is not None:\\n CustomRouter.applyEdgeDurationToAverage(self.currentEdgeID, tick - self.currentEdgeBeginTick, tick)\\n # CSVLogger.logEvent(\\\"edge\\\", [tick, self.currentEdgeID,\\n # tick - self.currentEdgeBeginTick, self.id])\\n # log to kafak\\n # msg = dict()\\n # msg[\\\"tick\\\"] = tick\\n # msg[\\\"edgeID\\\"] = self.currentEdgeID,\\n # msg[\\\"duration\\\"] = tick - self.currentEdgeBeginTick\\n # print(\\\"changed route to: \\\" + roadID)\\n self.currentEdgeBeginTick = tick\\n self.currentEdgeID = roadID\\n pass\",\n \"def dummyF(self, arg, signal, sender):\\n \\n if self.isDead == True:\\n return\\n \\n \\n #print \\\"DUMMY\\\"\\n if self.aborting:\\n self.aborting = False\\n self.isActive = False\\n self.__orderQueue.popleft()\\n del self.slaveTalk\\n self.slaveTalk = None\\n# self.__orderQueue.popleft()\\n try:\\n self.releaseLock()\\n except:\\n pass\\n #print \\\"No lock, actually.\\\" \\n dispatcher.send('SLAVE_PARSE_QUEUE', self, '')\",\n \"def trig_conditions(tr):\\n \\n\\n \\n ##############\\n #TRACE RELATED\\n ##############\\n avg_tr = np.average(tr)\\n \\n shifted_tr = tr - avg_tr \\n \\n abs_tr = abs(shifted_tr)\\n \\n sort_tr = np.sort(abs_tr)\\n \\n tr_99 = sort_tr[int(0.999*len(sort_tr))]\\n\\n #95% noise to signal area ratio calculation\\n area_big = tr_99 * int(0.95*len(sort_tr))\\n \\n area_small = np.sum(sort_tr[:int(0.95*len(sort_tr))])\\n \\n \\n area_condition = area_small / area_big; print area_condition\\n \\n # if signal is quite noisy, use recursive STALTA, else use classic STALTA\\n \\n df = tr.stats.sampling_rate\\n \\n \\n if area_condition <= 0.1:\\n \\n print(\\\"CLEAN SIGNAL!\\\\n\\\")\\n\\n ctf = abs(1-carlSTATrig(tr.data, int(5 * df), int(10 * df), 0.0001, 0.0001))\\n \\n sort_ctf = np.sort(ctf)\\n \\n ctf_low = sort_ctf[int(0.80*len(sort_ctf))]\\n \\n ctf_99 = sort_ctf[int(0.999*len(sort_ctf))]\\n \\n max_trig = ctf_99\\n \\n trig_on = ctf_low + 0.4 * (max_trig - ctf_low)\\n\\n trig_off = 0.8 * trig_on\\n \\n if not max_trig > 1.25 * ctf_low:\\n trig_on = 0; trig_off = 0;\\n \\n \\n \\n elif 0.1 < area_condition < 0.16:\\n \\n print(\\\"NOISY SIGNAL!\\\\n\\\")\\n\\n ctf = abs(1-recSTALTA(tr.data, int(5 * df), int(10 * df)))\\n \\n sort_ctf = np.sort(ctf)\\n \\n ctf_low = sort_ctf[int(0.90*len(sort_ctf))]\\n \\n ctf_99 = sort_ctf[int(0.999*len(sort_ctf))]\\n \\n max_trig = ctf_99\\n \\n trig_on = ctf_low + 0.4 * (max_trig - ctf_low)\\n\\n trig_off = 0.8 * trig_on\\n \\n if not max_trig > 1.25 * ctf_low:\\n trig_on = 0; trig_off = 0;\\n \\n else:\\n print(\\\"TRACE TOO NOISY TO DETECT SIGNAL!\\\")\\n trig_on = 0; trig_off = 0;\\n ctf = abs(1-recSTALTA(tr.data, int(5 * df), int(10 * df)))\\n\\n \\n\\n\\n\\n \\n\\n \\n \\n ############\\n #ctf RELATED\\n ############\\n\\n \\n #set conditional for noise. This is MINIMUM threshold.\\n #ctf_avg = np.average(ctf)\\n #ctf_mode = scipy.stats.mode(ctf)\\n #ctf_std = np.std(ctf)\\n \\n\\n \\n \\n #plt.figure()\\n #plt.plot(sort_ctf)\\n #plt.show()\\n\\n \\n\\n \\n \\n \\n return trig_on, trig_off, ctf\",\n \"def fill_gas_tank(self):\\n print(\\\"This car doesn't have a gas tank!\\\")\",\n \"def arm(self):\\n error(\\\"Attempted to access abstract trigger arming function.\\\")\",\n \"def louder():\\n try:\\n ttsEng.louder()\\n except Exception, e:\\n logging.error(e)\",\n \"def lidar_callback(self, data):\\n ranges = data.ranges\\n proc_ranges = self.preprocess_lidar(ranges)\\n drive_st_msg = AckermannDriveStamped()\\n drive_msg = AckermannDrive()\\n prev_drive = AckermannDrive()\\n prev_drive_st_msg = AckermannDriveStamped()\\n \\n\\n #Find closest point to LiDAR\\n minPointIdx = 0\\n for i in range(proc_ranges) :\\n if proc_ranges[i] < proc_ranges[minPointIdx] :\\n minPointIdx = i\\n\\n carLength = rospy.get_param(\\\"wheelbase\\\")\\n carWidth = rospy.get_param(\\\"width\\\")\\n avoidRadius = math.sqrt(math.pow(carLength, 2) + math.pow(carWidth, 2) + 1)\\n angleToConsider = math.atan(avoidRadius / proc_ranges[minPointIdx])\\n numPointsReplace = math.ceil(angleToConsider / data.angle_increment)\\n\\n for i in range(numPointsReplace) :\\n proc_ranges[minPointIdx - i] = 0\\n proc_ranges[minPointIdx + i] = 0\\n \\n maxGap = 0\\n count = 0\\n idxStartGap = 0\\n idxEndGap = 0\\n for i in range(proc_ranges) :\\n if proc_ranges[i] != 0 :\\n if count == 0:\\n idxStartGap = i\\n count += 1\\n else :\\n if count > maxGap :\\n maxGap = count\\n idxEndGap = i - 1\\n count = 0\\n\\n bestPoint = self.find_best_point(idxStartGap, idxEndGap, proc_ranges)\\n finalSteeringAngle = data.angle_min + data.angle_increment * bestPoint\\n drive_msg.steering_angle = finalSteeringAngle\\n if abs(drive_msg.steering_angle < 10):\\n drive_msg.speed = 5\\n elif abs(drive_msg.steering_angle < 20):\\n drive_msg.speed = 2\\n else:\\n drive_msg.speed = 1\\n\\n prev_drive = drive_msg\\n drive_st_msg.drive = drive_msg\\n prev_drive_st_msg.drive = prev_drive\\n\\n if proc_ranges[bestPoint] > 3: \\n self.drive_pub.publish(prev_drive_st_msg)\\n else :\\n self.drive_pub.publish(drive_st_msg)\\n\\n\\n\\n #Eliminate all points inside 'bubble' (set them to zero) \\n\\n #Find max length gap \\n\\n #Find the best point in the gap \\n\\n #Publish Drive message\",\n \"def spillAlle(self):\\r\\n for sang in self._sanger:\\r\\n print(f\\\"Nå spilles følgende: {sang}\\\")\",\n \"def relax(self):\\n rospy.loginfo('Now Arm will be relax')\\n self.go_with2([0, 0, 0, 0, 0])\",\n \"def __init__(self, trap=2.5*10**16, Keq=1.0*10**17,\\n EHdecay=1.0*10**-10, Etrap=2.0*10**-10, FHloss=8.0*10**-12,\\n G3decay = 0, step=200*ps, pretime=2, reprate=80000000,\\n verbose=False, trackQ=False, scalar=1, Gdecay=0, GHdecay=0,\\n tolerance=0.005, G2decay=0. ,Gescape=1., Gform=1., G3loss=0.):\\n # Some other variables used\\n self.tolerance = tolerance\\n self.scalar = scalar\\n self.verbose = verbose\\n self.reprate = reprate\\n self.duration = 1.00 / reprate\\n self.step = step\\n self.steps = int(self.duration / self.step)\\n self.powers = []\\n self.pretime = pretime\\n # Variables which hold state densities\\n self.exciton = []\\n self.hole = []\\n self.electron = []\\n self.trap = (trap) # Total number of traps\\n self.filled = [] # Filled traps\\n self.signal = []\\n self.xsignal = []\\n self.ehsignal = []\\n self.xloss = []\\n self.tloss = []\\n self.pulses = []\\n self.qk = []\\n self.trackQ = trackQ\\n # Rate and equilibrium constants, corrected for time step size\\n self.Keq = Gescape/Gform # Equilibrium constant for X<-->e+h\\n self.EHdecay = (EHdecay * step) # e+h->ground\\n self.Etrap = (Etrap * step) # e+trap->filled\\n self.FHloss = (FHloss * step) # filled+h->ground\\n self.Gdecay = Gdecay * step\\n self.G2decay = G2decay * step\\n self.G3decay = G3decay * step\\n self.GHdecay = GHdecay * step\\n self.Gescape = Gescape * step\\n self.G3loss = G3loss * step\\n self.Gform = Gform * step\",\n \"def disarm(self):\\n pass\",\n \"def _handle_mt_relax_error(self, calculation):\\n self.ctx.restart_calc = calculation\\n self.ctx.is_finished = True\\n self.report('FLEUR calculation failed due to MT overlap. Can be fixed via RelaxBaseWorkChain')\\n self.results()\\n return ProcessHandlerReport(True, self.exit_codes.ERROR_MT_RADII_RELAX)\",\n \"def Transformer(robot1,robot2): \\n #with a 50% change surgery will be triggered\\n return Random_Actuation.surgery(\\\"Transformer\\\",robot1,robot2,50)\",\n \"def inverse_kinematics_baxter(TM_W0_Gtool, arm_side):\\n\\n # Get all constants for the distances and transformations for Baxter\\n Constants = constants_baxter.GetConstants()\\n L0 = Constants.L0\\n L1 = Constants.L1\\n L2 = Constants.L2\\n L3 = Constants.L3\\n L4 = Constants.L4\\n L6 = Constants.L6\\n L = Constants.L\\n h = Constants.h\\n H = Constants.H\\n LH = Constants.LH\\n TM_W0_BL = Constants.TM_W0_BL\\n TM_W0_BR = Constants.TM_W0_BR\\n TM_BL_0 = Constants.TM_BL_0\\n TM_BR_0 = Constants.TM_BR_0\\n TM_7_GL = Constants.TM_7_GL\\n TM_7_GR = Constants.TM_7_GR\\n\\n # Apply inverse kinematics for the left arm\\n if arm_side == \\\"left\\\":\\n # Understanding the corresponding TM from the article, this can be solved:\\n TM_0_6 = np.dot(np.dot(np.linalg.inv(np.dot(TM_W0_BL,TM_BL_0)), TM_W0_Gtool), np.linalg.inv((TM_7_GR)))\\n\\n # Find theta1\\n PX_0_4 = TM_0_6[0, 3]\\n PY_0_4 = TM_0_6[1, 3]\\n\\n theta1 = math.atan2(PY_0_4, PX_0_4)\\n\\n # Find theta2\\n PZ_0_4 = TM_0_6[2, 3]\\n E = 2*LH*(L1 - PX_0_4/math.cos(theta1))\\n F = 2*LH*PZ_0_4\\n G = (PX_0_4**2)/((math.cos(theta1))**2) + L1**2 + LH**2 - L4**2 + PZ_0_4**2 - 2*L1*PX_0_4/math.cos(theta1)\\n\\n\\n if (E**2 + F**2 - G**2)>0:\\n t1 = (-F + math.sqrt(E**2 + F**2 - G**2))/(G - E)\\n else: \\n t1 = (-F - 0)/(G - E)\\n theta2 = 2*math.atan(t1)\\n\\n # We make only use the real part (img is not significant most of the times)\\n #if (E**2 + F**2 - G**2)>0:\\n #t2 = (-F - math.sqrt(E**2 + F**2 - G**2))/(G - E)\\n #else:\\n #t2 = (-F - 0)/(G - E)\\n #theta2 = 2*math.atan(t2)\\n\\n\\n\\n # Find theta4\\n theta4 = math.atan2(-PZ_0_4 - LH*math.sin(theta2), PX_0_4/math.cos(theta1) - L1 - LH*math.cos(theta2)) - theta2\\n\\n # Find theta5\\n DH_0_3 = np.array([[0, 0, 0, theta1],\\n [-math.pi/2, L1, 0, theta2],\\n [0, LH, 0, theta4 + math.pi/2]])\\n\\n TM_0_3 = denavit_hartenberg.denavit_hartenberg(DH_0_3, 0)\\n R_0_3 = TM_0_3[0:3, 0:3]\\n\\n R_0_6 = TM_0_6[0:3, 0:3]\\n\\n R_3_6 = np.dot(np.linalg.inv(R_0_3), R_0_6)\\n\\n theta5 = math.atan2(R_3_6[2,2], R_3_6[0,2])\\n\\n # Find theta7\\n theta7 = math.atan2(-R_3_6[1,1], R_3_6[1,0])\\n\\n\\n # Find theta6\\n theta6 = math.atan2(R_3_6[1,0]/math.cos(theta7), -R_3_6[1,2])\\n\\n\\n return [theta1, theta2, theta4, theta5, theta6, theta7]\",\n \"def propagate(satellite):\",\n \"def test_ridge_warning_in_fit_mle(self):\\n # Create a variable for the fit_mle function's kwargs.\\n # The print_res = False arguments are to make sure strings aren't\\n # printed to the console unnecessarily.\\n kwargs = {\\\"ridge\\\": 0.5,\\n \\\"print_res\\\": False}\\n\\n # Test to make sure that the ridge warning message is printed when\\n # using the ridge keyword argument\\n with warnings.catch_warnings(record=True) as w:\\n # Use this filter to always trigger the UserWarnings\\n warnings.simplefilter('always', UserWarning)\\n\\n self.base_clog.fit_mle(self.fake_all_params, **kwargs)\\n self.assertGreaterEqual(len(w), 1)\\n self.assertIsInstance(w[0].category, type(UserWarning))\\n self.assertIn(clog._ridge_warning_msg, str(w[0].message))\\n\\n return None\",\n \"def test_no_backg_subt():\\n \\n test_object = fa.read_in_envision(data_csv=HsHis6_PEX5C_vs_HsPEX5C, platemap_csv=Hs_His6_PEX5C_vs_HsPEX5C_platemap, data_type='plate', size=384)\\n test_object.calculate_r_i(correct=True, plot_i=False, thr=80)\",\n \"def handler(signum, frame):\\n m.signal()\",\n \"def signal_vwap(self):\\n pass\",\n \"def non_social_action_SB(self):\\n self.pumpRate = 0.4\\n if not self.agent.done:\\n self.action_gating()\",\n \"def add_dcdisorder(self):\\n # Add gaussian noise to pinning energies\\n if self.lp['V0_pin_gauss'] > 0:\\n self.Omg += self.lp['V0_pin_gauss']*np.random.randn(len(self.xy_inner))\\n raise RuntimeError('Adding gaussian disorder: are you sure you want to proceed?')\\n if self.lp['V0_spring_gauss'] > 0:\\n print 'This is not done correctly here'\\n self.OmK += self.lp['V0_spring_gauss'] * np.random.randn(np.shape(self.lattice.KL)[0],\\n np.shape(self.lattice.KL)[1])\\n sys.exit()\\n\\n if self.lp['V0_pin_flat'] > 0 or self.lp['V0_spring_flat'] > 0:\\n # Note that we multiply by two so that V0_pin_flat is the HALF width of the distribution\\n flat_disorder = (np.random.rand(len(self.xy_inner))) * 2 - 1.0\\n\\n if self.lp['V0_pin_flat'] > 0:\\n self.Omg += self.lp['V0_pin_flat'] * flat_disorder\\n if self.lp['Omg'] < 0:\\n self.Omg[self.Omg > 0] = 0.\\n elif self.lp['Omg'] > 0:\\n self.Omg[self.Omg < 0] = 0.\\n\\n print('magnetic_gyro_lattice_class.py: V0_pin_flat=', self.lp['V0_pin_flat'])\\n print(self.Omg)\\n\\n if self.lp['V0_spring_flat'] > 0:\\n to_add = self.lp['V0_spring_flat'] * flat_disorder[:, np.newaxis] * np.ones_like(self.OmK)\\n self.OmK[np.abs(self.OmK) > 0] += to_add[np.abs(self.OmK) > 0]\\n if self.lp['Omk'] < 0:\\n self.OmK[self.OmK > 0] = 0.\\n elif self.lp['Omk'] > 0:\\n self.OmK[self.OmK < 0] = 0.\\n\\n print('magnetic_gyro_lattice_class.py: OmK after flat disorder= ')\\n print(self.OmK)\\n # sys.exit()\",\n \"def fill_gas_tank(self):\\n print(\\\"\\\\nThis car need a gas tank!\\\")\",\n \"def _stop_attack(self):\\n self._add_malicious_blocks_to_honest_dag()\\n self._competing_chain_tip_gid = None\\n self._first_parallel_block_gid = None\",\n \"def step(self):\\n self.world.slosh_oceans()\\n self.world.transfer_energy_vertically()\\n self.world.transfer_energy_horizontally()\\n self.world.absorb_energy_from_core()\\n self.world.absorb_energy_from_sun(self.sun)\",\n \"def arm(self):\\n pass\",\n \"def _step_snell(self) -> None:\\n self.snell.step()\",\n \"def test_pump_bypass_on_reverse_flow(use_numba):\\n net = pandapipes.create_empty_network(\\\"net\\\", add_stdtypes=True)\\n\\n j1 = pandapipes.create_junction(net, pn_bar=5, tfluid_k=283.15)\\n j2 = pandapipes.create_junction(net, pn_bar=5, tfluid_k=283.15)\\n j3 = pandapipes.create_junction(net, pn_bar=5, tfluid_k=283.15)\\n j4 = pandapipes.create_junction(net, pn_bar=5, tfluid_k=283.15)\\n\\n pandapipes.create_pipe(net, j1, j2, std_type='125_PE_80_SDR_11', k_mm=1., length_km=10)\\n pandapipes.create_pipe(net, j3, j4, std_type='125_PE_80_SDR_11', k_mm=1., length_km=12)\\n pandapipes.create_ext_grid(net, j1, 5, 283.15, type=\\\"p\\\")\\n pandapipes.create_pump(net, j2, j3, std_type='P1')\\n pandapipes.create_source(net, j4, 0.02333)\\n\\n pandapipes.create_fluid_from_lib(net, \\\"hgas\\\", overwrite=True)\\n\\n pandapipes.pipeflow(net, stop_condition=\\\"tol\\\", iter=3, friction_model=\\\"nikuradse\\\",\\n mode=\\\"hydraulics\\\", transient=False, nonlinear_method=\\\"automatic\\\",\\n tol_p=1e-4, tol_v=1e-4, use_numba=use_numba)\\n\\n assert net.res_pump.deltap_bar.isin([0]).all()\\n assert np.isclose(net.res_junction.loc[1, \\\"p_bar\\\"], net.res_junction.loc[2, \\\"p_bar\\\"])\",\n \"def lower_arm(self):\\r\\n # ---------------------------------------------------------------------\\r\\n # Done: 8. Implement this method; it is a ONE-LINER!\\r\\n # ---------------------------------------------------------------------\\r\\n if self.is_calibrated == False:\\r\\n self.calibrate_arm()\\r\\n self.move_arm_to_position(0)#America\\r\",\n \"def handle_thrusters(self, data):\\n self.thrs_current = np.roll(self.thrs_current, -1, axis=1) # roll the vector (shift)\\n self.thrs_current[0:4, -1] = data.current[0:4] # selected thrusters only\\n\\n self.thrs_energy += THR_VNOM * np.trapz(self.thrs_current, dx=THR_FRAME, axis=1)\\n self.energy_last = np.sum(self.thrs_energy)\",\n \"def stop_emission(self, detailed_signal): # reliably restored by inspect\\n pass\",\n \"def stop_emission(self, detailed_signal): # reliably restored by inspect\\n pass\",\n \"def stop_emission(self, detailed_signal): # reliably restored by inspect\\n pass\",\n \"def stop_emission(self, detailed_signal): # reliably restored by inspect\\n pass\",\n \"def stop_emission(self, detailed_signal): # reliably restored by inspect\\n pass\",\n \"def stop_emission(self, detailed_signal): # reliably restored by inspect\\n pass\",\n \"def stop_emission(self, detailed_signal): # reliably restored by inspect\\n pass\",\n \"def stop_emission(self, detailed_signal): # reliably restored by inspect\\n pass\",\n \"def stop_emission(self, detailed_signal): # reliably restored by inspect\\n pass\",\n \"def stop_emission(self, detailed_signal): # reliably restored by inspect\\n pass\",\n \"def stop_emission(self, detailed_signal): # reliably restored by inspect\\n pass\",\n \"def stop_emission(self, detailed_signal): # reliably restored by inspect\\n pass\",\n \"def stop_emission(self, detailed_signal): # reliably restored by inspect\\n pass\",\n \"def stop_emission(self, detailed_signal): # reliably restored by inspect\\n pass\",\n \"def stop_emission(self, detailed_signal): # reliably restored by inspect\\n pass\",\n \"def stop_emission(self, detailed_signal): # reliably restored by inspect\\n pass\",\n \"def stop_emission(self, detailed_signal): # reliably restored by inspect\\n pass\",\n \"def __post_init__(self):\\n if self.steering == Direction.FWD:\\n raise ValueError(\\\"Steering can't be FORWARD.\\\")\",\n \"def postSI(self):\\n # for cell in self.cells:\\n # cell.resetTotOrdFlux()\\n self.depth = 0\",\n \"def BackSubstitution(self, Force):\\n\\t\\tpass\",\n \"def process_changeroot(self):\\n self.__changeroot()\",\n \"def simulation_step(self):\\n if not self.np_trajectory.size:\\n #No trajectory to go to.....\\n return\\n closest_ind = self.find_closest_trajectory_pose()\\n ref_ind = (closest_ind + 30) # closest_ind + numpy.round(self.v / 4)\\n traj_len = len(self.np_trajectory[0])\\n if self.loop is True:\\n ref_ind = ref_ind % traj_len\\n else:\\n if ref_ind > traj_len-1:\\n ref_ind = traj_len-1\\n if closest_ind == traj_len-1:\\n self.at_dest = True\\n else:\\n ref_ind = closest_ind\\n ref_state = self.np_trajectory[:, int(ref_ind)]\\n\\n # update vehicle state.\\n '''if self.class_name == 'TruckVehicle':\\n self.update_vehicle_state_qualisys()\\n self.UDP_receive()\\n if self.data == \\\"-1.00\\\":\\n self.set_control_commands_pp(ref_state, ref_ind)\\n else:\\n steer = int(self.data[-6:-3])\\n throttle = int(self.data[:-6]) + 5\\n hw_port.set_command(throttle,steer,2)\\n self.update_truck_hardware()\\n else:\\n self.set_control_commands(ref_state)\\n self.update_vehicle_state()'''\\n\\n self.set_control_commands(ref_state, ref_ind)\\n self.update_vehicle_state()\\n\\n # publish vehicle state.\\n vehicle_state = msgs.VehicleState(self.vehicle_id, self.class_name,\\n self.x, self.y, self.yaw, self.v)\\n self.pub_state.publish(vehicle_state)\\n self.update_current_node()\\n\\n #The way that the stop light waiting works, this is necessary\\n if not self.waiting_at_stop:\\n self.check_for_traffic_light()\\n self.get_traffic()\",\n \"async def unexpected_ball_received(self):\\n # We do nothing in that case\",\n \"def ungrasp(self):\\n\\t\\t#rospy.init_node('Robotiq2FGripperSimpleController')\\n\\t\\t\\n\\t\\tpub = rospy.Publisher('Robotiq2FGripperRobotOutput', outputMsg.Robotiq2FGripper_robot_output)\\n\\n\\t\\tcommand = outputMsg.Robotiq2FGripper_robot_output();\\n\\t\\ttimeout = 2.5\\n\\t\\ttimeout_start = time.time()\\n\\t\\twhile time.time() < timeout_start + timeout:\\n\\t\\t#rospy.sleep(0.5)\\n\\t\\t\\t#command = genCommand(askForCommand(command), command) \\n\\t\\t\\tcommand = self.genCommand('r', command)\\n\\t\\t\\tpub.publish(command)\\n\\t\\t\\trospy.sleep(1)\\n\\t\\t\\tcommand = self.genCommand('a', command)\\n\\t\\t\\tpub.publish(command)\\n\\t\\t\\trospy.sleep(1)\\n\\t\\t\\t#command = self.genCommand('c', command)\\n\\t\\t\\t#pub.publish(command)\\n\\t\\t\\t#rospy.sleep(1)\",\n \"def reset_cause():\",\n \"def __init__(self, *args, **kwargs):\\n super(G16SL1024AFR98, self).__init__(guard_count=16, *args, **kwargs)\",\n \"def _perturbInPlaceHard(self):\\n die\",\n \"def signal_kernel(self, signum: int):\",\n \"def shar():\\n pass\",\n \"def raise_arm(self):\\r\\n self.arm_motor.turn_on(self.speed)\\r\\n while not self.arm_touch_sensor.is_pressed():\\r\\n pass\\r\\n self.arm_motor.turn_off()\\r\\n\\r\\n # ---------------------------------------------------------------------\\r\\n # Done: 6. Implement this method; it is a ONE-LINER! (not)\\r\\n # ---------------------------------------------------------------------\\r\",\n \"def __init__(self, *args, **kwargs):\\n super(G1SL1024AFR98, self).__init__(guard_count=1, *args, **kwargs)\",\n \"def receive(self, signal, direction=None, polarization=None,\\n force_real=True):\\n super().receive(signal=signal, direction=direction,\\n polarization=polarization,\\n force_real=force_real)\",\n \"def receive(self, signal, direction=None, polarization=None,\\n force_real=True):\\n super().receive(signal=signal, direction=direction,\\n polarization=polarization,\\n force_real=force_real)\",\n \"def signal(self):\\n pass\",\n \"def calculate_axial_transport(my_cell, t):\\n\\n phi_si, phi_se, phi_di, phi_de, phi_sm, phi_dm = my_cell.membrane_potentials()\\n\\n j_Na_diff_i = my_cell.j_k_diff(my_cell.D_Na, my_cell.lamda_i, my_cell.Na_si, my_cell.Na_di)*my_cell.A_i*N_A\\n Na_akkum_diff_i = scipy.integrate.cumtrapz(j_Na_diff_i, t, initial=0)\\n\\n j_Na_drift_i = my_cell.j_k_drift(my_cell.D_Na, my_cell.Z_Na, my_cell.lamda_i, my_cell.Na_si, my_cell.Na_di, phi_si, phi_di)*my_cell.A_i*N_A\\n Na_akkum_drift_i = scipy.integrate.cumtrapz(j_Na_drift_i, t, initial=0)\\n\\n j_K_diff_i = my_cell.j_k_diff(my_cell.D_K, my_cell.lamda_i, my_cell.K_si, my_cell.K_di)*my_cell.A_i*N_A\\n K_akkum_diff_i = scipy.integrate.cumtrapz(j_K_diff_i, t, initial=0)\\n\\n j_K_drift_i = my_cell.j_k_drift(my_cell.D_K, my_cell.Z_K, my_cell.lamda_i, my_cell.K_si, my_cell.K_di, phi_si, phi_di)*my_cell.A_i*N_A\\n K_akkum_drift_i = scipy.integrate.cumtrapz(j_K_drift_i, t, initial=0)\\n\\n j_Cl_diff_i = my_cell.j_k_diff(my_cell.D_Cl, my_cell.lamda_i, my_cell.Cl_si, my_cell.Cl_di)*my_cell.A_i*N_A\\n Cl_akkum_diff_i = scipy.integrate.cumtrapz(j_Cl_diff_i, t, initial=0)\\n\\n j_Cl_drift_i = my_cell.j_k_drift(my_cell.D_Cl, my_cell.Z_Cl, my_cell.lamda_i, my_cell.Cl_si, my_cell.Cl_di, phi_si, phi_di)*my_cell.A_i*N_A\\n Cl_akkum_drift_i = scipy.integrate.cumtrapz(j_Cl_drift_i, t, initial=0)\\n\\n j_Ca_diff_i = my_cell.j_k_diff(my_cell.D_Ca, my_cell.lamda_i, my_cell.free_Ca_si, my_cell.free_Ca_di)*my_cell.A_i*N_A\\n Ca_akkum_diff_i = scipy.integrate.cumtrapz(j_Ca_diff_i, t, initial=0)\\n\\n j_Ca_drift_i = my_cell.j_k_drift(my_cell.D_Ca, my_cell.Z_Ca, my_cell.lamda_i, my_cell.free_Ca_si, my_cell.free_Ca_di, phi_si, phi_di)*my_cell.A_i*N_A\\n Ca_akkum_drift_i = scipy.integrate.cumtrapz(j_Ca_drift_i, t, initial=0)\\n\\n j_e_diff_i = (j_Na_diff_i + j_K_diff_i + 2*j_Ca_diff_i - j_Cl_diff_i)\\n j_e_drift_i = (j_Na_drift_i + j_K_drift_i + 2*j_Ca_drift_i - j_Cl_drift_i)\\n e_akkum_diff_i = (Na_akkum_diff_i*my_cell.Z_Na + K_akkum_diff_i*my_cell.Z_K + Cl_akkum_diff_i*my_cell.Z_Cl + Ca_akkum_diff_i*my_cell.Z_Ca)\\n e_akkum_drift_i = (Na_akkum_drift_i*my_cell.Z_Na + K_akkum_drift_i*my_cell.Z_K + Cl_akkum_drift_i*my_cell.Z_Cl + Ca_akkum_drift_i*my_cell.Z_Ca)\\n\\n j_Na_diff_e = my_cell.j_k_diff(my_cell.D_Na, my_cell.lamda_e, my_cell.Na_se, my_cell.Na_de)*my_cell.A_e*N_A\\n Na_akkum_diff_e = scipy.integrate.cumtrapz(j_Na_diff_e, t, initial=0)\\n\\n j_Na_drift_e = my_cell.j_k_drift(my_cell.D_Na, my_cell.Z_Na, my_cell.lamda_e, my_cell.Na_se, my_cell.Na_de, phi_se, phi_de)*my_cell.A_e*N_A\\n Na_akkum_drift_e = scipy.integrate.cumtrapz(j_Na_drift_e, t, initial=0)\\n\\n j_K_diff_e = my_cell.j_k_diff(my_cell.D_K, my_cell.lamda_e, my_cell.K_se, my_cell.K_de)*my_cell.A_e*N_A\\n K_akkum_diff_e = scipy.integrate.cumtrapz(j_K_diff_e, t, initial=0)\\n\\n j_K_drift_e = my_cell.j_k_drift(my_cell.D_K, my_cell.Z_K, my_cell.lamda_e, my_cell.K_se, my_cell.K_de, phi_se, phi_de)*my_cell.A_e*N_A\\n K_akkum_drift_e = scipy.integrate.cumtrapz(j_K_drift_e, t, initial=0)\\n\\n j_Cl_diff_e = my_cell.j_k_diff(my_cell.D_Cl, my_cell.lamda_e, my_cell.Cl_se, my_cell.Cl_de)*my_cell.A_e*N_A\\n Cl_akkum_diff_e = scipy.integrate.cumtrapz(j_Cl_diff_e, t, initial=0)\\n\\n j_Cl_drift_e = my_cell.j_k_drift(my_cell.D_Cl, my_cell.Z_Cl, my_cell.lamda_e, my_cell.Cl_se, my_cell.Cl_de, phi_se, phi_de)*my_cell.A_e*N_A\\n Cl_akkum_drift_e = scipy.integrate.cumtrapz(j_Cl_drift_e, t, initial=0)\\n\\n j_Ca_diff_e = my_cell.j_k_diff(my_cell.D_Ca, my_cell.lamda_e, my_cell.Ca_se, my_cell.Ca_de)*my_cell.A_e*N_A\\n Ca_akkum_diff_e = scipy.integrate.cumtrapz(j_Ca_diff_e, t, initial=0)\\n\\n j_Ca_drift_e = my_cell.j_k_drift(my_cell.D_Ca, my_cell.Z_Ca, my_cell.lamda_e, my_cell.Ca_se, my_cell.Ca_de, phi_se, phi_de)*my_cell.A_e*N_A\\n Ca_akkum_drift_e = scipy.integrate.cumtrapz(j_Ca_drift_e, t, initial=0)\\n\\n j_e_diff_e = (j_Na_diff_e + j_K_diff_e + 2*j_Ca_diff_e - j_Cl_diff_e)\\n j_e_drift_e = (j_Na_drift_e + j_K_drift_e + 2*j_Ca_drift_e - j_Cl_drift_e)\\n e_akkum_diff_e = (Na_akkum_diff_e*my_cell.Z_Na + K_akkum_diff_e*my_cell.Z_K + Cl_akkum_diff_e*my_cell.Z_Cl + Ca_akkum_diff_e*my_cell.Z_Ca)\\n e_akkum_drift_e = (Na_akkum_drift_e*my_cell.Z_Na + K_akkum_drift_e*my_cell.Z_K + Cl_akkum_drift_e*my_cell.Z_Cl + Ca_akkum_drift_e*my_cell.Z_Ca)\\n\\n return j_e_drift_i, j_e_diff_i, e_akkum_drift_i, e_akkum_diff_i, Na_akkum_drift_i, Na_akkum_diff_i, K_akkum_drift_i, K_akkum_diff_i, Cl_akkum_drift_i, Cl_akkum_diff_i, Ca_akkum_drift_i, Ca_akkum_diff_i, \\\\\\n j_e_drift_e, j_e_diff_e, e_akkum_drift_e, e_akkum_diff_e, Na_akkum_drift_e, Na_akkum_diff_e, K_akkum_drift_e, K_akkum_diff_e, Cl_akkum_drift_e, Cl_akkum_diff_e, Ca_akkum_drift_e, Ca_akkum_diff_e\",\n \"def softclippingHGMevaluation(input_generator,branches,iden_method,Plot,reference=None):\\n for t in range(8,11):\\n t = t / 10.0\\n p = 1.0 - t\\n input_signal = input_generator.GetOutput()\\n nl_functions = [nlsp.function_factory.softclip(power=p),]*branches\\n filter_spec_tofind = nlsp.log_bpfilter(branches=branches, input=input_signal)\\n ref_nlsystem = nlsp.HammersteinGroupModel_up(input_signal=input_signal,\\n nonlinear_functions=nl_functions,\\n filter_irs=filter_spec_tofind,\\n max_harmonics=range(1,branches+1))\\n\\n found_filter_spec, nl_functions = iden_method(input_generator,ref_nlsystem.GetOutput(),branches)\\n iden_nlsystem = nlsp.HammersteinGroupModel_up(input_signal=input_signal,\\n nonlinear_functions=nl_functions,\\n filter_irs=found_filter_spec,\\n max_harmonics=range(1,branches+1))\\n # sine = sumpf.modules.SineWaveGenerator(frequency=5000.0,phase=0.0,samplingrate=input_signal.GetSamplingRate(),length=len(input_signal)).GetSignal()\\n sine = sumpf.modules.SweepGenerator(samplingrate=input_signal.GetSamplingRate(),length=len(input_signal)).GetSignal()\\n ref_nlsystem.SetInput(sine)\\n iden_nlsystem.SetInput(sine)\\n if reference is not None:\\n reference = nlsp.change_length_signal(reference,length=len(input_signal))\\n ref_nlsystem.SetInput(reference)\\n iden_nlsystem.SetInput(reference)\\n\\n if Plot is True:\\n plot.relabelandplot(sumpf.modules.FourierTransform(ref_nlsystem.GetOutput()).GetSpectrum(),\\\"Reference System\\\",show=False)\\n plot.relabelandplot(sumpf.modules.FourierTransform(iden_nlsystem.GetOutput()).GetSpectrum(),\\\"Identified System\\\",show=False)\\n print \\\"SNR between Reference and Identified output for symmetric hardclipping HGM(threshold:%r): %r\\\" %(t,nlsp.snr(ref_nlsystem.GetOutput(),\\n iden_nlsystem.GetOutput()))\",\n \"def _extrap_post_proc_hook(cls, gas_df):\\n\\n # Testing showed that N2O and CH4 at least were very succeptible to an ever increasing seasonal cycle amplitude\\n # as the extrapolation backward in time got further and further. This is the simplest fix, a 12 month average\\n # wipes out the seasonal cycle, and since the central tendency didn't get messed up, this result is at least\\n # reasonable.\\n #\\n # We allow Pandas to fill in values at the beginning (limit_direction='backward') with the nearest value to keep\\n # the data frame defined over the full date range. Yes this will flatten the trend out in those first six\\n # months, but since those first six months contribute very little to the age-spectrum average concentration for\\n # any time period relevant to TCCON, that's not going to affect the priors much. A proper linear extrapolation\\n # would be better long-term.\\n #\\n # Alternately, data from sites like\\n # https://www.eea.europa.eu/data-and-maps/daviz/atmospheric-concentration-of-carbon-dioxide-4\\n # that extend back further could be used to at least get the shape of the trends. If early (pre 1990) data\\n # becomes crucial, that is probably the best approach.\\n smoothed_conc = gas_df.dmf_mean.rolling(window=12, center=True).mean().interpolate(method='index', limit_direction='backward')\\n xx = gas_df.latency < 0\\n gas_df.loc[xx, 'dmf_mean'] = smoothed_conc\\n return gas_df\",\n \"def on_R2(self):\\r\\n self.log()\",\n \"def pdb2pka_desolv_backgr(self,residue):\\n protein,routines,forcefield,apbs_setup,lig_titgrps = pdb2pka.pre_init(pdbfilename=self.pdbfile,\\n ff='parse',\\n ligand=None,\\n verbose=1)\\n mypkaRoutines = pdb2pka.pKaRoutines(protein, routines, forcefield,apbs_setup)\\n #\\n # Find our group\\n #\\n sp=residue.split(':')\\n chainid=sp[0]\\n #if chainid!='':\\n # raise Exception,'pKD cannot handle PDB files with ChainIDs!'\\n resnum=int(sp[1])\\n target=sp[2]\\n mypkaRoutines.findTitratableGroups()\\n this_pKa=None\\n for pKa in mypkaRoutines.pKas:\\n print pKa.residue\\n print pKa.uniqueid\\n print pKa.residue.resSeq,resnum, pKa.residue.chainID,'CID',chainid,pKa.residue.name,target,pKa.pKaGroup.name,target\\n #if pKa.residue.resSeq==resnum and pKa.residue.chainID==chainid and pKa.residue.name==target and pKa.pKaGroup.name==target:\\n if pKa.residue.resSeq==resnum and pKa.residue.chainID==chainid and pKa.residue.name==target and pKa.pKaGroup.name==target:\\n this_pKa=pKa\\n break\\n if not this_pKa:\\n raise Exception,'Could not find inserted titratable group'\\n mypkaRoutines.calculateBackground(onlypKa=pKa)\\n mypkaRoutines.calculateDesolvation(onlypKa=pKa)\\n #\\n # Get the intrinsic pKa\\n #\\n pKaGroup=pKa.pKaGroup\\n Gtype=pKa.pKaGroup.type\\n #\\n # We measure intrinsic pKa values against a single reference state\\n #\\n desolv=[]\\n backgr=[]\\n import math\\n ln10=math.log(10)\\n for titration in pKaGroup.DefTitrations:\\n #\\n # Find an uncharged reference state\\n #\\n ref_state=mypkaRoutines.neutral_ref_state[pKa][titration]\\n all_states=titration.allstates\\n all_states.sort()\\n for state in all_states:\\n if mypkaRoutines.is_charged(pKa,titration,state)==1:\\n dpKa_desolv=(pKa.desolvation[state]-pKa.desolvation[ref_state])/ln10\\n dpKa_backgr=(pKa.background[state]-pKa.background[ref_state])/ln10\\n #\\n # Make acid and base modifications\\n #\\n if Gtype=='base':\\n dpKa_desolv=-dpKa_desolv\\n dpKa_backgr=-dpKa_backgr\\n #\\n # Now calculate intrinsic pKa\\n #\\n backgr.append(dpKa_backgr)\\n desolv.append(dpKa_desolv)\\n intpKa=titration.modelpKa+dpKa_desolv+dpKa_backgr\\n #print 'Energy difference for %s -> %s [reference state] is %5.2f pKa units' %(state,ref_state,intpKa)\\n pKa.intrinsic_pKa[state]=intpKa\\n else:\\n #\\n # Neutral states - why do we treat them differently?\\n #\\n dpKa_desolv=(pKa.desolvation[state]-pKa.desolvation[ref_state])/ln10\\n dpKa_backgr=(pKa.background[state]-pKa.background[ref_state])/ln10\\n #\\n # Make acid and base modifications\\n #\\n if Gtype=='base':\\n dpKa_desolv=-dpKa_desolv\\n dpKa_backgr=-dpKa_backgr\\n backgr.append(dpKa_backgr)\\n desolv.append(dpKa_desolv)\\n dpKa=dpKa_desolv+dpKa_backgr\\n #print 'Energy difference for %s -> %s [reference state] is %5.2f kT' %(state,ref_state,dpKa)\\n pKa.intrinsic_pKa[state]=dpKa\\n #print '-----------------'\\n #\\n # One value is zero, so just get the avg of the rest\\n #\\n des_sum=0.0\\n for val in desolv:\\n des_sum=des_sum+val\\n des_sum=des_sum/float(len(desolv)-1)\\n #\\n bac_sum=0.0\\n for val in backgr:\\n bac_sum=bac_sum+val\\n bac_sum=bac_sum/float(len(backgr)-1)\\n return {residue:des_sum},{residue:bac_sum}\",\n \"def event11510450():\\n header(11510450, 1)\\n if_does_not_have_tae_event(0, CHR.Gwyndolin, 600)\\n if_has_tae_event(0, CHR.Gwyndolin, 600)\\n\\n flag.disable_chunk(11515150, 11515151)\\n flag.enable_random_in_chunk(11515150, 11515151)\\n chr.disable(CHR.Gwyndolin)\\n wait(1.0)\\n\\n # First two warps are always forward.\\n skip_if_event_flag_on(2, 11515110)\\n run_event_with_slot(11515110, 0, args=(1512710, 11515110))\\n restart()\\n skip_if_event_flag_on(2, 11515111)\\n run_event_with_slot(11515110, 1, args=(1512711, 11515111))\\n restart()\\n\\n for warp_number in range(2, 40):\\n skip_if_event_flag_on(7, 11515110 + warp_number)\\n\\n skip_if_event_flag_on(2, 11515151)\\n # Standard forward warp.\\n run_event_with_slot(11515110, warp_number, args=(1512710 + warp_number, 11515110 + warp_number))\\n skip(2)\\n # Backward warp.\\n flag.disable(11515110 + warp_number - 1) # Lose corridor progress.\\n run_event_with_slot(11515110, warp_number - 2, args=(1512710 + warp_number - 2, 11515110 + warp_number - 2))\\n\\n chr.rotate_to_face_entity(CHR.Gwyndolin, CHR.Player)\\n restart()\",\n \"def TAY(self, *_):\\n self.reg.Y = self.reg.A\\n self.reg.N = self.reg.Y << 7\\n self.reg.Z = self.reg.Y == 0\",\n \"def ApplyXErrors( ErrorNum,array,type,L,CorrLen):\\n\\n if type == 1:\\n #run across every element in the array\\n for i in range(len(array[:,0,0])):\\n for j in range(2):\\n for k in range(len(array[0,0,:])):\\n if random.random() >1- 1.*ErrorNum/(L*L): #rand chance of bitflip\\n array[i,j,k] = -1*array[i,j,k] #apply bitflip if true\\n return(array)\\n\\n elif type == 2:\\n \\\"\\\"\\\"creates a number of errors on the grid. rather than having a chance of\\n getting a certain number of errors, this one doesnt stop generating errors\\n until you get a specified number of error.\\n Two flips on the one qubit is counted as one error. This model may need to\\n be changed to count it as no error. But this isnt necessilarly needed.\\\"\\\"\\\"\\n numerrsLeft = ErrorNum\\n while numerrsLeft != 0:\\n Ri = int(round(random.random()*L)) -1\\n Rj = int(round(random.random()*1)) -1 #int(r.rand()*2)\\n Rk = int(round(random.random()*L)) -1\\n if int(array[Ri,Rj,Rk]) == 1:\\n array[Ri,Rj,Rk] = -1*array[Ri,Rj,Rk] #apply bitflip if true\\n numerrsLeft += -1\\n return(array)\\n\\n elif type == 4:\\n \\\"\\\"\\\"creates a random walk with a set walk length\\\"\\\"\\\"\\n ErrorChains = ErrorNum\\n movements = []\\n distances=[]\\n while ErrorChains != 0: #this loop creates 1 chain\\n Ri = randik(L)#create start location of walk\\n Rj = randj()\\n Rk = randik(L)\\n walk=[] #this will be a list of tuples\\n walk += [[Ri,Rk]] #create anyon\\n i = 0 #set walk len counter-> could apply gauss dist here\\n while i != CorrLen: #here we will just create the walk.\\n nextstep=[]\\n dice = int(4*random.random()) #randomly choose move direction\\n if dice==0:\\n #if its intersecting the walk;\\n nextstep = [[walk[i][0],modpos(walk[i][1],L,-1)]]\\n walk += nextstep\\n\\n if dice ==1 :\\n nextstep = [[walk[i][0],modpos(walk[i][1],L,+1)]]\\n walk += nextstep\\n\\n if dice == 2:\\n nextstep = [[modpos(walk[i][0],L,-1),walk[i][1]]]\\n walk += nextstep\\n\\n if dice == 3:\\n nextstep = [[modpos(walk[i][0],L,-1),walk[i][1]]]\\n walk += nextstep\\n i+=1\\n ErrorChains += -1\\n movements += [walk] #combine all walks\\n return(GetFlippedPoints(movements,array))\\n\\n elif type == 5:\\n \\\"\\\"\\\"Self avoiding version of 4 (with self intersections)\\\"\\\"\\\"\\n ErrorChains = ErrorNum\\n movements = []\\n distances=[]\\n while ErrorChains != 0: #this loop creates 1 chain\\n Ri = randik(L)\\n Rj = ()\\n Rk = randik(L)\\n walk=[] #this will be a list of tuples\\n walk += [[Ri,Rk]] #create anyon\\n i = 0 #set walk len counter-> could apply gauss dist here\\n while i != CorrLen: #here we will just create the walk.\\n nextstep=[]\\n dice = int(4*random.random()) #randomly choose move direction\\n if dice == 0:\\n #if its intersecting the walk;\\n nextstep = [[walk[i][0],modpos(walk[i][1],L,-1)]]\\n try:#if next step in walk:\\n if nextstep[0] in walk:\\n continue#try again.\\n except:#if not in walk:\\n pass#add to walk.\\n walk += nextstep\\n\\n if dice == 1:\\n nextstep = [[walk[i][0],modpos(walk[i][1],L,+1)]]\\n try:\\n if nextstep[0] in walk:\\n continue\\n except:\\n pass\\n walk += nextstep\\n\\n if dice == 2:\\n nextstep = [[modpos(walk[i][0],L,-1),walk[i][1]]]\\n try:\\n if nextstep[0] in walk:\\n continue\\n except:\\n pass\\n walk += nextstep\\n\\n if dice == 3:\\n nextstep = [[modpos(walk[i][0],L,-1),walk[i][1]]]\\n try:\\n if nextstep[0] in walk:\\n continue\\n except:\\n pass\\n walk += nextstep\\n i+=1\\n ErrorChains += -1\\n movements += [walk] #combine all walks\\n return(GetFlippedPoints(movements,array))\\n elif type == 6:\\n \\\"\\\"\\\"fixed version of 4\\n a walk of set length, with self intersections. this one also doesnt 'cancel itself out' when it crosses over itself NOT IMPLEMENTED YET\\\"\\\"\\\"\\n ErrorChains = ErrorNum\\n movements = []\\n distances=[]\\n while ErrorChains != 0: #this loop creates 1 chain\\n Ri = randik(L)#create start location of walk\\n Rj = randj()\\n Rk = randik(L)\\n walk=[] #this will be a list of tuples\\n walk += [[Ri,Rj,Rk]] #create anyon\\n i = 0 #set walk len counter-> could apply gauss dist here\\n while i != CorrLen: #here we will just create the walk.\\n\\n nextstep=[]\\n dice = int(4*random.random()) #randomly choose move direction\\n if dice==0:\\n if Rj == 0:\\n nextstep = [walk[i][0], walk[i][1]^1, modpos(walk[i][2],L,-1)]#removed extra bracket\\n if Rj == 1:\\n nextstep = [modpos(walk[i][0],L,-1), walk[i][1]^1, walk[i][2]]\\n\\n if dice ==1 :\\n if Rj == 0:\\n nextstep = [modpos(walk[i][0],L,1), walk[i][1]^1, walk[i][2]]\\n if Rj == 1:\\n nextstep = [walk[i][0], walk[i][1]^1, walk[i][2]]\\n\\n if dice == 2:\\n if Rj == 0:\\n nextstep = [modpos(walk[i][0],L,1), walk[i][1]^1, walk[i][2]]\\n if Rj == 1:\\n nextstep = [walk[i][0], walk[i][1]^1, modpos(walk[i][2],L,1)]\\n\\n if dice == 3:\\n if Rj == 0:\\n nextstep = [walk[i][0], walk[i][1]^1, walk[i][2]]\\n if Rj == 1:\\n nextstep = [modpos(walk[i][0], L, -1) , walk[i][1]^1, modpos(walk[i][2],L,1)]\\n walk += [nextstep]\\n i+=1\\n ErrorChains += -1\\n movements += [walk] #combine all walk\\n return(GetFlippedPoints3(movements,array))\",\n \"def tare_force(crush):\\n tare = hanging_force(crush)\\n if abs(tare) >= 0.25:\\n set_trace()\\n # assert abs(tare) < 0.25, f\\\"Excessive hanging force detected: {tare:.3f}\\\"\\n crush['Force (N)'] = crush['Force (N)'] - tare\\n return crush\",\n \"def fix_jump(self):\\n pass\",\n \"def abort_ber_meas(self):\\r\\r\\n loggerCmw = logging.getLogger('abort_ber_meas')\\r\\r\\n self.write('ABORt:WCDMa:SIGN:BER')\\r\\r\\n loggerCmw.info(\\\"Aborting BER measurements\\\")\\r\\r\\n time.sleep(1)\",\n \"def power_output_existing_thermal_rule(_m, g, y, s, t):\\r\\n\\r\\n if y != m.Y.last() and t != m.T.last():\\r\\n return (- m.sigma_1[g, y, s, t] + m.sigma_2[g, y, s, t]\\r\\n + m.sigma_20[g, y, s, t] - m.sigma_20[g, y, s, t + 1]\\r\\n - m.sigma_23[g, y, s, t] + m.sigma_23[g, y, s, t + 1]\\r\\n - m.lamb[self.k(m, g), y, s, t]\\r\\n + ((m.DELTA[y] * m.RHO[y, s]) * (\\r\\n m.C_MC[g, y] + ((m.EMISSIONS_RATE[g] - m.baseline[y]) * m.permit_price[y])))\\r\\n == 0)\\r\\n\\r\\n elif y != m.Y.last() and t == m.T.last():\\r\\n return (- m.sigma_1[g, y, s, t] + m.sigma_2[g, y, s, t]\\r\\n + m.sigma_20[g, y, s, t]\\r\\n - m.sigma_23[g, y, s, t]\\r\\n - m.lamb[self.k(m, g), y, s, t]\\r\\n + ((m.DELTA[y] * m.RHO[y, s]) * (\\r\\n m.C_MC[g, y] + ((m.EMISSIONS_RATE[g] - m.baseline[y]) * m.permit_price[y])))\\r\\n == 0)\\r\\n\\r\\n elif y == m.Y.last() and t != m.T.last():\\r\\n return (- m.sigma_1[g, y, s, t] + m.sigma_2[g, y, s, t]\\r\\n + m.sigma_20[g, y, s, t] - m.sigma_20[g, y, s, t + 1]\\r\\n - m.sigma_23[g, y, s, t] + m.sigma_23[g, y, s, t + 1]\\r\\n - m.lamb[self.k(m, g), y, s, t]\\r\\n + ((m.DELTA[y] * m.RHO[y, s]) * (1 + (1 / m.INTEREST_RATE)) * (\\r\\n m.C_MC[g, y] + ((m.EMISSIONS_RATE[g] - m.baseline[y]) * m.permit_price[y])))\\r\\n == 0)\\r\\n\\r\\n elif y == m.Y.last() and t == m.T.last():\\r\\n return (- m.sigma_1[g, y, s, t] + m.sigma_2[g, y, s, t]\\r\\n + m.sigma_20[g, y, s, t]\\r\\n - m.sigma_23[g, y, s, t]\\r\\n - m.lamb[self.k(m, g), y, s, t]\\r\\n + ((m.DELTA[y] * m.RHO[y, s]) * (1 + (1 / m.INTEREST_RATE)) * (\\r\\n m.C_MC[g, y] + ((m.EMISSIONS_RATE[g] - m.baseline[y]) * m.permit_price[y])))\\r\\n == 0)\\r\\n\\r\\n else:\\r\\n raise Exception(f'Unhandled case: {g, y, s, t}')\",\n \"def adapt_steering(position):\\n center = RESOLUTIONX / 2\\n offset = center - position\\n steerfactor = offset / 10\\n CRL_CAR.steer(steerfactor)\\n logging.info(position)\",\n \"def recursiveTraceJumptablese(ea, function=False):\",\n \"def stop():\\n twister = Twist(linear=Vector3(x=0,y=0,z=0),angular=Vector3(x=0,y=0,z=0))\\n pub.publish(twister)\\n global has_bumped\\n has_bumped = True\",\n \"def test_14_missing_nonbonded_handler(self, force_field):\\n top = Molecule.from_smiles(\\\"CCCC\\\").to_topology()\\n\\n ff_no_vdw = copy.deepcopy(force_field)\\n ff_no_electrostatics = copy.deepcopy(force_field)\\n\\n ff_no_vdw.deregister_parameter_handler(\\\"vdW\\\")\\n\\n ff_no_electrostatics.deregister_parameter_handler(\\\"Electrostatics\\\")\\n ff_no_electrostatics.deregister_parameter_handler(\\\"ToolkitAM1BCC\\\")\\n\\n sys_no_electrostatics = ff_no_electrostatics.create_openmm_system(top)\\n\\n np.testing.assert_almost_equal(\\n actual=get_14_scaling_factors(sys_no_electrostatics)[1],\\n desired=ff_no_electrostatics[\\\"vdW\\\"].scale14,\\n decimal=8,\\n )\\n\\n sys_no_vdw = ff_no_vdw.create_openmm_system(top)\\n np.testing.assert_almost_equal(\\n actual=get_14_scaling_factors(sys_no_vdw)[0],\\n desired=ff_no_vdw[\\\"Electrostatics\\\"].scale14,\\n decimal=8,\\n )\",\n \"def noCheck():\\n dislin.nochek()\",\n \"def do_solvate( ingro, outgro, inouttop, water = 'ffamber_tip3p.gro', verbose = False, use_big_vdwradii = False, FF = 'ffamber99sb'):\\n\\n #Copy top/gro files to a temporary working directory where we will do this setup before copying back. This is necessary because of issues with 3.3.x genbox, requiring input/output topology to be in working directory\\n tempdir = tempfile.mkdtemp()\\n shutil.copy(inouttop, os.path.join(tempdir, 'tmp.top') )\\n shutil.copy(ingro, os.path.join( tempdir, 'tmp.gro') )\\n startdir = os.getcwd()\\n os.chdir( tempdir )\\n\\n if use_big_vdwradii: \\n make_big_vdwradii('.') \\n\\n #Ensure forcefield\\n ensure_forcefield( 'tmp.top', 'tmp.top', FF = FF )\\n\\n #Run genbox \\n if verbose: print \\\"Running in temporary directory %s...\\\" % tempdir\\n cmd = 'genbox -cp tmp.gro -p tmp.top -o out.gro -cs %(water)s' % vars()\\n output = rungmx( cmd, verbose = verbose)\\n if verbose: print output\\n\\n #Compile name of itp file and edit topology to include this\\n wateritp = water.replace('.gro','.itp')\\n #Edit topology file to replace spc.itp with this\\n file = open( 'tmp.top', 'r')\\n text = file.readlines()\\n file.close()\\n try:\\n idx = text.index('#include \\\"spc.itp\\\"\\\\n')\\n text[idx ] = '#include \\\"%(wateritp)s\\\"\\\\n' % vars()\\n except ValueError:\\n #Check if it already includes correct water model\\n try:\\n #If this works then we leave as is\\n idx = text.index('#include \\\"%(wateritp)s\\\"\\\\n' % vars() )\\n except ValueError:\\n #If it is still not found, add the includejust before the SYSTEM section\\n idx = 0\\n while '[ system ]' not in text[idx]: #Find system line\\n idx+=1\\n text[idx] = '#include \\\"%(wateritp)s\\\"\\\\n' % vars() + text[idx]\\n file = open( 'tmp.top', 'w')\\n file.writelines( text )\\n file.close()\\n \\n #Parse output and figure out the number of waters, typically SOL\\n tmp = output.split('\\\\n')\\n tmp.reverse()\\n for line in tmp:\\n if 'Number of SOL ' in line: break\\n if not 'Number of SOL' in line: nwaters = None #Not found\\n else:\\n nwaters = int( line.split()[-1] )\\n\\n #Copy files back and cleanup\\n os.chdir(startdir)\\n shutil.copy( os.path.join(tempdir, 'tmp.top'), inouttop )\\n shutil.copy( os.path.join(tempdir, 'out.gro'), outgro )\\n shutil.rmtree( tempdir)\\n\\n return output, nwaters\",\n \"def handler(signum, frame):\\n logging.warning(\\\"Got a {} signal. Doing nothing\\\".format(signum))\",\n \"def clean_linear_track_error(self):\\r\\n return self._arm.clean_linear_track_error()\",\n \"def insert_motor(burt,axis=[-0.05,0,0],angle=45.0,max_force=35):\\r\\n iter = 45\\r\\n travel_thresh = abs(axis[0])-0.003\\r\\n burt.set_tcp(wp.motor_centroid)\\r\\n start_pose = burt.getl()\\r\\n burt.force_move(axis,acc=0.1,vel=0.01,force=max_force)\\r\\n end_pose = burt.getl()\\r\\n dif = end_pose[0]-start_pose[0]\\r\\n axis[0] -= dif\\r\\n #print(dif)\\r\\n if abs(dif)<travel_thresh:\\r\\n #have hit the fixing plate so hunt\\r\\n burt.movel_tool([-0.0005,0,0,0,0,0])\\r\\n time.sleep(0.1)\\r\\n start_force = burt.get_forces()[0]\\r\\n force = start_force\\r\\n print(\\\"hunting start force: \\\",start_force)\\r\\n for i in range(0,iter):\\r\\n burt.movel_tool([0,0,0,0,-(angle*pi)/(iter*180.0),0],acc=0.1)\\r\\n burt.translatel([end_pose[0]-0.0005,end_pose[1],end_pose[2]],acc=0.1)\\r\\n time.sleep(0.1)\\r\\n force = burt.get_forces()[0]\\r\\n print(\\\"measured force: \\\",force)\\r\\n if abs(force)<abs(0.2*start_force):\\r\\n burt.force_move(axis,acc=0.1,vel=0.01,force=max_force)\\r\\n \\r\\n burt.set_tcp(wp.pincher_tcp)\\r\\n return True\\r\\n burt.set_tcp(wp.pincher_tcp)\\r\\n return False\\r\\n burt.set_tcp(wp.pincher_tcp)\\r\\n return True\",\n \"def simulationTwoDrugsDelayedTreatment():\\n\\n # TODO\",\n \"def test_low_voltage_passing_signal(self):\\n data = gen_random_data(-0.5, 0.5, self.channels)\\n self.assertFalse(self.lowvoltage_rule.is_broken(data))\",\n \"def signal_kernel(self, signum):\\n pass\",\n \"def trap_depth(V,X,Y,Z,Im,Jm,Km): \\n from project_parameters import debug,scale,position\\n #from all_functions import sum_of_e_field,spher_harm_bas,spher_harm_exp,spher_harm_cmp,find_saddle\\n def a(a,N):\\n \\\"\\\"\\\"Shortcut function to convert array x into a row vector.\\\"\\\"\\\" \\n a=np.ravel(a, order='F') # Same order\\n return a\\n N1,N2,N3=V.shape\\n N=N1*N2*N3\\n [Ex,Ey,Ez]=np.gradient(V,abs(X[1]-X[0])/scale,abs(Y[1]-Y[0])/scale,abs(Z[1]-Z[0])/scale)\\n E=np.sqrt(Ex**2+Ey**2+Ez**2)\\n # identify the escape position and height by checking each point\\n minElectricField=np.max(E) # initialize as maximum E field magnitude\\n distance=0\\n escapeHeight=1\\n escapePosition=[0,0,0]\\n [Im,Jm,Km] = find_saddle(V,X,Y,Z,3)\\n Vm = V[Im,Jm,Km]\\n for i in range(N1):\\n for j in range(N2):\\n for k in range(N3):\\n if E[i,j,k]<minElectricField:\\n distance=abs(np.sqrt((Im-i)**2+(Jm-j)**2+(Km-k)**2)) \\n if distance > 6:\\n minElectricField=E[i,j,k]\\n escapeHeight=V[i,j,k]\\n escapePosition=[i,j,k]\\n if debug.trap_depth: \\n print E[i,j,k],V[i,j,k],[i,j,k],distance\\n check=1 \\n if debug.trap_depth: \\n print minElectricField,escapeHeight,escapePosition,distance \\n if distance<check:\\n print('trap_depth.py: Escape point too close to trap minimum. Improve grid resolution or extend grid.')\\n if escapeHeight>0.2:\\n print('trap_depth.py: Escape point parameter too high. Improve grid resolution or extend grid.')\\n D=escapeHeight-Vm\\n [Ie,Je,Ke]=escapePosition\\n [Xe,Ye,Ze]=[X[Ie],Y[Je],Z[Ke]] \\n return [D,Xe,Ye,Ze]\",\n \"def chase_laser(self):\\r\\n print(\\\"Meeeeow\\\\n\\\")\",\n \"def force ( r, e ):\\n from math import isclose\\n\\n # Parameters of the Gay-Berne potential \\n # \\n # The key parameters are \\n # mu, nu ................ the exponents \\n # kappa and kappa' ....... the anisotropies \\n # kappa is the ratio of intermolecular separations \\n # sigma_e / sigma_s i.e. end-to-end / side-by-side \\n # kappa' is the ratio of well depths \\n # epsilon_s / epsilon_e i.e. side-by-side / end-to-end \\n # The derived parameters are chi and chi' \\n # chi = (kappa**2 - 1) / (kappa**2+1) \\n # chi' = (z - 1) / (z + 1)\\n # where z = (kappa') ** ( 1 / mu ) \\n # \\n # For convenience kappa' is spelt xappa, chi' is spelt xhi\\n # We choose units such that sigma_s = 1.0 and epsilon_0 = 1.0\\n # Two of the following three varieties should be commented out\\n\\n # Original Gay-Berne-deMiguel potential [J. Chem. Phys, 74, 3316; Mol. Phys. 74, 405 (1991)]\\n mu, nu, kappa, xappa = 2, 1, 3.0, 5.0\\n\\n # # Luckhurst-Phippen potential [Liq. Cryst., 8, 451 (1990)]\\n # mu, nu, kappa, xappa = 1, 2, 3.0, 5.0\\n\\n # # Berardi-Zannoni potential [J. Chem. Soc. Faraday Trans., 89, 4069 (1993)]\\n # mu, nu, kappa, xappa = 1, 3, 3.0, 5.0\\n\\n # Derived parameters\\n chi = (kappa**2 - 1.0) / (kappa**2+1.0)\\n xhi = (xappa**(1.0/mu) - 1.0) / (xappa**(1.0/mu) + 1.0)\\n\\n # Cutoff distance; normally we would use a larger value\\n r_cut = 4.0\\n \\n assert r.shape == (n,3), 'Incorrect shape of r'\\n assert e.shape == (n,3), 'Incorrect shape of e'\\n\\n # Notation to match appendix\\n i = 0\\n j = 1\\n\\n ei = e[i,:]\\n ej = e[j,:]\\n assert isclose(np.sum(ei**2),1.0), 'Non-unit vector {} {} {}'.format(*ei)\\n assert isclose(np.sum(ej**2),1.0), 'Non-unit vector {} {} {}'.format(*ej)\\n\\n rij = r[i,:] - r[j,:]\\n rij_mag = np.sqrt( np.sum(rij**2) ) # Magnitude of separation vector\\n sij = rij / rij_mag # Unit vector\\n ci = np.dot( ei, sij )\\n cj = np.dot( ej, sij )\\n cij = np.dot( ei, ej )\\n cp = ci + cj\\n cm = ci - cj\\n\\n # Sigma formula\\n cpchi = cp/(1.0+chi*cij)\\n cmchi = cm/(1.0-chi*cij)\\n sigma = 1.0/np.sqrt(1.0-0.5*chi*(cp*cpchi+cm*cmchi))\\n\\n # Epsilon formula\\n eps1 = 1.0/np.sqrt(1.0-(chi*cij)**2) # Depends on chi, not xhi\\n cpxhi = cp/(1.0+xhi*cij)\\n cmxhi = cm/(1.0-xhi*cij)\\n eps2 = 1.0-0.5*xhi*(cp*cpxhi+cm*cmxhi) # Depends on xhi\\n epsilon = (eps1**nu) * (eps2**mu)\\n\\n # Potential at rij\\n rho = rij_mag - sigma + 1.0\\n rho6 = 1.0 / rho**6\\n rho12 = rho6**2\\n rhoterm = 4.0*(rho12 - rho6) # Needed for forces and torques\\n drhoterm = -24.0 * (2.0 * rho12 - rho6) / rho # Needed for forces and torques\\n pot = epsilon*rhoterm\\n\\n # Potential at r_cut\\n rho = r_cut - sigma + 1.0\\n rho6 = 1.0 / rho**6\\n rho12 = rho6**2\\n cutterm = 4.0*(rho12 - rho6) # Needed for cutoff forces and torques\\n dcutterm = -24.0 * (2.0 * rho12 - rho6) / rho # Needed for cutoff forces and torques\\n pot = pot - epsilon * cutterm\\n\\n # Derivatives of sigma\\n prefac = 0.5*chi*sigma**3\\n dsig_dci = prefac*(cpchi+cmchi)\\n dsig_dcj = prefac*(cpchi-cmchi)\\n prefac = prefac*(0.5*chi)\\n dsig_dcij = -prefac*(cpchi**2-cmchi**2)\\n\\n # Derivatives of epsilon\\n prefac = -mu*xhi*(eps1**nu)*eps2**(mu-1)\\n deps_dci = prefac*(cpxhi+cmxhi)\\n deps_dcj = prefac*(cpxhi-cmxhi)\\n prefac = prefac*(0.5*xhi)\\n deps_dcij = -prefac*(cpxhi**2-cmxhi**2) # From derivative of eps2\\n deps_dcij = deps_dcij + nu*(chi**2)*(eps1**(nu+2))*(eps2**mu)*cij # From derivative of eps1\\n\\n # Derivatives of potential\\n dpot_drij = epsilon * drhoterm\\n dpot_dci = rhoterm * deps_dci - epsilon * drhoterm * dsig_dci\\n dpot_dcj = rhoterm * deps_dcj - epsilon * drhoterm * dsig_dcj\\n dpot_dcij = rhoterm * deps_dcij - epsilon * drhoterm * dsig_dcij\\n\\n # Standard formula for forces and torque gradients\\n fij = -dpot_drij*sij - dpot_dci*(ei-ci*sij)/rij_mag - dpot_dcj*(ej-cj*sij)/rij_mag\\n gi = dpot_dci*sij + dpot_dcij*ej\\n gj = dpot_dcj*sij + dpot_dcij*ei\\n\\n # Derivatives of potential at cutoff\\n dpot_drij = epsilon * dcutterm\\n dpot_dci = cutterm * deps_dci - epsilon * dcutterm * dsig_dci\\n dpot_dcj = cutterm * deps_dcj - epsilon * dcutterm * dsig_dcj\\n dpot_dcij = cutterm * deps_dcij - epsilon * dcutterm * dsig_dcij\\n\\n # Standard formula for forces and torque gradients (without dpot_drij term)\\n fij = fij + dpot_dci*(ei-ci*sij)/rij_mag + dpot_dcj*(ej-cj*sij)/rij_mag\\n gi = gi - ( dpot_dci*sij + dpot_dcij*ej ) \\n gj = gj - ( dpot_dcj*sij + dpot_dcij*ei ) \\n\\n # Final forces and torques\\n f = np.empty_like(r)\\n t = np.empty_like(r)\\n f[i,:] = fij\\n f[j,:] = -fij\\n t[i,:] = -np.cross(ei,gi)\\n t[j,:] = -np.cross(ej,gj)\\n\\n return pot, f, t\",\n \"def give_treat(self, num_treats = 1):\\n for x in range(0,num_treats):\\n GPIO.output(self.treat_pin, 0)\\n time.sleep(.5)\\n GPIO.output(self.treat_pin, 1)\\n time.sleep(.5)\\n return\",\n \"def scan_received(self, msg):\\n # print msg\\n if not(self.initialized):\\n # wait for initialization to complete\\n return\\n\\n if not(self.tf_listener.canTransform(self.base_frame,msg.header.frame_id,msg.header.stamp)):\\n # need to know how to transform the laser to the base frame\\n # this will be given by either Gazebo or neato_node\\n return\\n\\n if not(self.tf_listener.canTransform(self.base_frame,self.odom_frame,msg.header.stamp)):\\n # need to know how to transform between base and odometric frames\\n # this will eventually be published by either Gazebo or neato_node\\n return\\n\\n # print 'msg.header.frame_id', msg.header.frame_id\\n # calculate pose of laser relative ot the robot base\\n p = PoseStamped(header=Header(stamp=rospy.Time(0),\\n frame_id=msg.header.frame_id))\\n self.laser_pose = self.tf_listener.transformPose(self.base_frame,p)\\n\\n # find out where the robot thinks it is based on its odometry\\n # listener.getLatestCommonTime(\\\"/base_link\\\",object_pose_in.header.frame_id)\\n # p = PoseStamped(header=Header(stamp=msg.header.stamp,\\n p = PoseStamped(header=Header(stamp=self.tf_listener.getLatestCommonTime(self.base_frame, self.map_frame),\\n # p = PoseStamped(header=Header(stamp=rospy.Time.now(),\\n frame_id=self.base_frame),\\n pose=Pose())\\n # p_aux = PoseStamped(header=Header(stamp=self.tf_listener.getLatestCommonTime(\\\"/base_link\\\",\\\"/map\\\"),\\n p_aux = PoseStamped(header=Header(stamp=self.tf_listener.getLatestCommonTime(self.odom_frame, self.map_frame),\\n # p_aux = PoseStamped(header=Header(stamp=rospy.Time.now(),\\n frame_id=self.odom_frame),\\n pose=Pose())\\n odom_aux = self.tf_listener.transformPose(self.map_frame, p_aux)\\n odom_aux_xy_theta = convert_pose_to_xy_and_theta(odom_aux.pose)\\n # print 'odom_aux_xy_theta', odom_aux_xy_theta\\n\\n self.odom_pose = self.tf_listener.transformPose(self.odom_frame, p)\\n # print 'self.odom_pose', self.odom_pose\\n # (trans, root) = self.tf_listener.lookupTransform(self.odom_frame, self.base_frame, rospy.Time(0))\\n # self.odom_pose = trans\\n # print trans, root\\n new_odom_xy_theta = convert_pose_to_xy_and_theta(self.odom_pose.pose)\\n # new_odom_xy_theta = convert_pose_to_xy_and_theta(self.laser_pose.pose)\\n xy_theta_aux = (new_odom_xy_theta[0]+odom_aux_xy_theta[0], \\n new_odom_xy_theta[1]+odom_aux_xy_theta[1], new_odom_xy_theta[2])\\n self.xy_theta_aux = xy_theta_aux\\n\\n if not(self.particle_cloud):\\n self.initialize_particle_cloud(xy_theta_aux)\\n self.current_odom_xy_theta = new_odom_xy_theta\\n\\n elif (math.fabs(new_odom_xy_theta[0] - self.current_odom_xy_theta[0]) > self.linear_mov or\\n math.fabs(new_odom_xy_theta[1] - self.current_odom_xy_theta[1]) > self.linear_mov or\\n math.fabs(new_odom_xy_theta[2] - self.current_odom_xy_theta[2]) > self.angular_mov):\\n\\n self.update_particles_with_odom(msg)\\n self.update_particles_with_laser(msg)\\n self.resample_particles()\\n\\n self.publish_particles(msg)\"\n]","isConversational":false},"negative_scores":{"kind":"list like","value":["0.54921705","0.52793443","0.52202374","0.521817","0.5195716","0.51095015","0.51095015","0.50273573","0.49843332","0.4955213","0.4955092","0.49494436","0.49199587","0.4883605","0.48833477","0.48775414","0.48286638","0.4825539","0.48209244","0.48204193","0.48141426","0.4807129","0.47532773","0.47503415","0.47471726","0.47464758","0.47390127","0.47350103","0.47120303","0.47007617","0.4696892","0.46957847","0.46947375","0.46457806","0.46438563","0.4631186","0.46302795","0.46268338","0.4625729","0.4625729","0.4625729","0.4625729","0.4625729","0.4625729","0.4625729","0.4625729","0.4625729","0.4625729","0.4625729","0.4625729","0.4625729","0.4625729","0.4625729","0.4625729","0.4625729","0.46235552","0.46173808","0.46138588","0.45978895","0.45974186","0.4592608","0.45892143","0.45854837","0.4580625","0.45764738","0.4571548","0.45707646","0.45502022","0.4535626","0.452896","0.452896","0.45217133","0.45207274","0.4516627","0.45157278","0.4511957","0.45111364","0.45087364","0.45087203","0.4508636","0.45076805","0.4499684","0.449607","0.44950107","0.4490045","0.44879776","0.44846973","0.4481199","0.44808856","0.44802868","0.4475829","0.4473084","0.44715306","0.4469648","0.44672543","0.4456875","0.4448412","0.44408903","0.44408652","0.44386578","0.44329023"],"string":"[\n \"0.54921705\",\n \"0.52793443\",\n \"0.52202374\",\n \"0.521817\",\n \"0.5195716\",\n \"0.51095015\",\n \"0.51095015\",\n \"0.50273573\",\n \"0.49843332\",\n \"0.4955213\",\n \"0.4955092\",\n \"0.49494436\",\n \"0.49199587\",\n \"0.4883605\",\n \"0.48833477\",\n \"0.48775414\",\n \"0.48286638\",\n \"0.4825539\",\n \"0.48209244\",\n \"0.48204193\",\n \"0.48141426\",\n \"0.4807129\",\n \"0.47532773\",\n \"0.47503415\",\n \"0.47471726\",\n \"0.47464758\",\n \"0.47390127\",\n \"0.47350103\",\n \"0.47120303\",\n \"0.47007617\",\n \"0.4696892\",\n \"0.46957847\",\n \"0.46947375\",\n \"0.46457806\",\n \"0.46438563\",\n \"0.4631186\",\n \"0.46302795\",\n \"0.46268338\",\n \"0.4625729\",\n \"0.4625729\",\n \"0.4625729\",\n \"0.4625729\",\n \"0.4625729\",\n \"0.4625729\",\n \"0.4625729\",\n \"0.4625729\",\n \"0.4625729\",\n \"0.4625729\",\n \"0.4625729\",\n \"0.4625729\",\n \"0.4625729\",\n \"0.4625729\",\n \"0.4625729\",\n \"0.4625729\",\n \"0.4625729\",\n \"0.46235552\",\n \"0.46173808\",\n \"0.46138588\",\n \"0.45978895\",\n \"0.45974186\",\n \"0.4592608\",\n \"0.45892143\",\n \"0.45854837\",\n \"0.4580625\",\n \"0.45764738\",\n \"0.4571548\",\n \"0.45707646\",\n \"0.45502022\",\n \"0.4535626\",\n \"0.452896\",\n \"0.452896\",\n \"0.45217133\",\n \"0.45207274\",\n \"0.4516627\",\n \"0.45157278\",\n \"0.4511957\",\n \"0.45111364\",\n \"0.45087364\",\n \"0.45087203\",\n \"0.4508636\",\n \"0.45076805\",\n \"0.4499684\",\n \"0.449607\",\n \"0.44950107\",\n \"0.4490045\",\n \"0.44879776\",\n \"0.44846973\",\n \"0.4481199\",\n \"0.44808856\",\n \"0.44802868\",\n \"0.4475829\",\n \"0.4473084\",\n \"0.44715306\",\n \"0.4469648\",\n \"0.44672543\",\n \"0.4456875\",\n \"0.4448412\",\n \"0.44408903\",\n \"0.44408652\",\n \"0.44386578\",\n \"0.44329023\"\n]","isConversational":false},"document_score":{"kind":"string","value":"0.0"},"document_rank":{"kind":"string","value":"-1"}}},{"rowIdx":16598,"cells":{"query":{"kind":"string","value":"Subscibe a set of event keys for a callback."},"document":{"kind":"string","value":"def subscribe(callback, keys):\n assert type(keys) in (set, list, tuple)\n _subscribers[callback] = keys"},"metadata":{"kind":"string","value":"{\n \"objective\": {\n \"self\": [],\n \"paired\": [],\n \"triplet\": [\n [\n \"query\",\n \"document\",\n \"negatives\"\n ]\n ]\n }\n}"},"negatives":{"kind":"list like","value":["def _handle_key_event(self, key, modifiers, mapping):\n if key in mapping:\n for callback in mapping[key]:\n callback()","def make_keyhandler(events):\n def handler(key):\n for k in events:\n if key == simplegui.KEY_MAP[k]:\n events[k]()\n return handler","def key_press(keys):\n return lambda e: e.key if e.type == pygame.KEYDOWN \\\n and e.key in keys else EventConsumerInfo.DONT_CARE","def __init__(self, events, terminate_callback):\n self.events = events\n self.terminate_callback = terminate_callback\n for event in self.events:\n if event.button is not None:\n event.button = mouse.Button(event.button)\n if event.key is not None:\n event.key = event.key.replace('\\'', '')\n event.key = event.key.replace('Key.', '')\n if event.key in keyboard.Key.__dict__:\n event.key = keyboard.Key.__dict__[event.key]","def key_event(self, key: Any, action: Any):\n pass","def on_key_press(self, key, callback):\n self._key_press_mappings.setdefault(key, []).append(callback)","def keysAll():","def __master_key_callback(self, window, key, scancode, action, mods):\n self.call_key_callback(window, key, scancode, action, mods, keyboard=self)","def handle_sc_event(store, changed_keys, info):\n\n for key in changed_keys:\n SC_HANDLERS[key](key=key, info=info)","def read_keys(self) -> list[KeyPress]:","def _on_key_press(self, event):","def keys():\n\n global pressed_keys\n pressed_keys = []\n\n the_keys = pygame.key.get_pressed()\n\n # check if keys in keymap are pressed\n for key in KEYMAP:\n if the_keys[key[\"name\"]]:\n\n # Check if pressed key is already pressed\n is_present = False\n for p_key in pressed_keys:\n if p_key == key[\"action\"]:\n is_present = True\n\n # Toggle action in list\n if is_present:\n pressed_keys.pop(pressed_keys.index(key[\"action\"]))\n else:\n pressed_keys.append(key[\"action\"])","def ev_KEYUP(self, event):","def set_button_callbacks(self):\n\t\tfor floor, channel in enumerate(INPUT.IN_BUTTONS):\n\t\t\tself.signalPoller.add_callback_to_channel(channel, partial(self.button_pressed_callback, ORDERDIR.IN, floor))\n\n\t\tfor floor, channel in enumerate(INPUT.UP_BUTTONS):\n\t\t\tself.signalPoller.add_callback_to_channel(channel, partial(self.button_pressed_callback, ORDERDIR.UP, floor))\n\n\t\tfor floor, channel in enumerate(INPUT.DOWN_BUTTONS):\n\t\t\tself.signalPoller.add_callback_to_channel(channel, partial(self.button_pressed_callback, ORDERDIR.DOWN, floor))","def enable_key_callback(self, v):\n pass","def on_key_down(self, key, callback):\n self._key_down_mappings.setdefault(key, []).append(callback)","def bind_modifiers(widget, event:Callable, button='Button-1',\n modes=frozendict({'Shift': KeyModes.SHIFT, 'Control': KeyModes.CONTROL, 'Alt': KeyModes.ALT, })):\n widget.bind(button, event)\n for modifier, keymode in modes.items():\n # We must provide 'keymode' as a default argument in the lambda expression (as method parameters are\n # only evaluated once), otherwise it will end up referencing the last value in the modes dictionary.\n widget.bind(f\"<{modifier}-{button}>\", lambda bind_event, mode=keymode: event(bind_event, mode))","def _control_keys(self, command):\n return [key for key, comm in self.KEY_TO_COMMAND.items() if comm == command]","def ev_KEYDOWN(self, event):","def check_special_callback(self, key_name):\n if key_name in self.reserved_keys:\n #Trying to set a special callback for a reserved key\n raise CallbackException(1, \"Special callback for {} can't be set because it's one of the reserved keys\".format(key_name))\n elif key_name in self.nonmaskable_keymap:\n #Key is already used in a non-maskable callback\n raise CallbackException(2, \"Special callback for {} can't be set because it's already set as nonmaskable\".format(key_name))\n elif key_name in self.maskable_keymap: \n #Key is already used in a maskable callback\n raise CallbackException(3, \"Special callback for {} can't be set because it's already set as maskable\".format(key_name))","def many(keys: List[str]):\n for key in keys:\n actions.key(key)","def bindKeys(self):\r\n self.c.bind(\"<Button-1>\",self.seek)\r\n self.c.bind(\"<MouseWheel>\",self.app.zoom)\r\n self.c.bind(\"<Button-3>\",self.peek)","def _on_key_release(self, event):","def on_key_event(self, key):\n pass","def bindHotkeys(self):\r\n self.root.bind(\"s\",self.pause)\r\n self.root.bind(\"p\",self.play)\r\n self.root.bind(\"x\",self.stop)\r\n self.root.bind(\"<Right>\",lambda event, t=10: self.skipFor(event,t=t))\r\n self.root.bind(\"<Left>\",lambda event, t=-10: self.skipFor(event,t=t))\r\n self.bindDPHotkeys()","def on_keydown(self, keys, game) -> None:\n pass","def onkey(self, fun, key):\n if fun is None:\n if key in self._keys:\n self._keys.remove(key)\n elif key not in self._keys:\n self._keys.append(key)\n self._onkeyrelease(fun, key)","def set_events(self):\r\n\r\n self.canvas.bind(\"<Button-1>\", self.event_click_left)\r\n self.bind(\"<Return>\", self.event_return)","def onEvent(self, eventKey, callback):\n\n #-------------------- \n # Construct callback dict if it doesn't exist.\n #--------------------\n if not hasattr(self, 'eventCallbacks__'):\n self.eventCallbacks__ = {}\n for eventType in self.EVENT_TYPES:\n self.eventCallbacks__[str(eventType)] = []\n\n\n if not eventKey in self.EVENT_TYPES:\n raise Exception(\"Xnat.io (onEvent): invalid event type '%s'\"%(eventKey))\n self.eventCallbacks__[eventKey].append(callback)","def CmdHandler(self, *events: str, colon: bool = False,\n ircv3: bool = False) -> Callable:\n ...","def setupShortcuts(self):\n\n macros = (\n (\"Ctrl+Return\", self.segmentNeedle),\n (\"Ctrl+z\", self.logic.deleteLastNeedle),\n )\n\n for keys,f in macros:\n k = qt.QKeySequence(keys)\n s = qt.QShortcut(k,slicer.util.mainWindow())\n s.connect('activated()', f)\n s.connect('activatedAmbiguously()', f)\n print \"SlicerRC - '%s' -> '%s'\" % (keys, f.__name__)","def __command_handler__(self, commands, handler):\n message_set = self.event.text.split(u' ')\n for command in commands:\n if command in message_set:\n handler(self.event, self.vk)\n break","def ev_keydown(self, event: KeyDown) -> None:","def key_callback(option,opt_str,value,parser):\n if \"--epi-key\" in opt_str:\n parser.values.epi_keys.append(value)\n elif \"--exclude\" in opt_str:\n parser.values.exclude_paths.append(value)","def event(self,events):\n for event in events:\n if event.type == KEYDOWN:\n if event.key == K_RETURN:#starts the game\n self.game.gotoMain()\n #print \"r\"\n if event.key == K_ESCAPE:#quits the game\n sys.exit(0)","def keyevent(self, keyname):\n self.adb.key_events(keyname)","def setShortcuts(self):\n self.game.app.accept('mouse1', self.onMouse1Down)\n self.game.app.accept('mouse3', self.onMouse2Down)\n self.game.app.accept('space', self.onSpaceBarClear)\n if self.enableMouseCamControl == 1:\n self.game.app.accept('wheel_up', self.onMouseWheelUp)\n self.game.app.accept('wheel_down', self.onMouseWheelDown)","def _multiple_callbacks(callbacks, *args, **kwargs):\n if isinstance(callbacks, list):\n for cb in callbacks:\n cb(*args, **kwargs)\n return\n if callbacks:\n callbacks(*args, **kwargs)","def register_callbacks(self, cbs):\n assert isinstance(cbs, dict) # cbs must be a dictionary\n cbs_key_list = list(cbs.keys())\n enum_key_list = [enum.value for enum in self._action_type_enum]\n \n # TODO replace by check for compulsory keys only, all action types do not apply to all actions\n #assert(len(set(enum_key_list) - set(cbs_key_list)) == 0)\n\n self._cbs = {}\n for key in cbs_key_list: # check syntax\n print \"Registered callback for action %s\" % key\n self._cbs[key] = cbs[key]\n rospy.logdebug(\"Callbacks registered.\")","def cb_key_combo_default(data, signal, signal_data):\n global esc_pressed, vi_buffer, cmd_text\n\n # If Esc was pressed, strip the Esc part from the pressed keys.\n # Example: user presses Esc followed by i. This is detected as \"\\x01[i\",\n # but we only want to handle \"i\".\n keys = signal_data\n if esc_pressed or esc_pressed == -2:\n if keys.startswith(\"\\x01[\" * esc_pressed):\n # Multiples of 3 seem to \"cancel\" themselves,\n # e.g. Esc-Esc-Esc-Alt-j-11 is detected as \"\\x01[\\x01[\\x01\"\n # followed by \"\\x01[j11\" (two different signals).\n if signal_data == \"\\x01[\" * 3:\n esc_pressed = -1 # `cb_check_esc()` will increment it to 0.\n else:\n esc_pressed = 0\n # This can happen if a valid combination is started but interrupted\n # with Esc, such as Ctrl-W→Esc→w which would send two signals:\n # \"\\x01W\\x01[\" then \"\\x01W\\x01[w\".\n # In that case, we still need to handle the next signal (\"\\x01W\\x01[w\")\n # so we use the special value \"-2\".\n else:\n esc_pressed = -2\n keys = keys.split(\"\\x01[\")[-1] # Remove the \"Esc\" part(s).\n # Ctrl-Space.\n elif keys == \"\\x01@\":\n set_mode(\"NORMAL\")\n return weechat.WEECHAT_RC_OK_EAT\n\n # Nothing to do here.\n if mode == \"INSERT\":\n return weechat.WEECHAT_RC_OK\n\n # We're in Replace mode — allow \"normal\" key presses (e.g. \"a\") and\n # overwrite the next character with them, but let the other key presses\n # pass normally (e.g. backspace, arrow keys, etc).\n if mode == \"REPLACE\":\n if len(keys) == 1:\n weechat.command(\"\", \"/input delete_next_char\")\n elif keys == \"\\x01?\":\n weechat.command(\"\", \"/input move_previous_char\")\n return weechat.WEECHAT_RC_OK_EAT\n return weechat.WEECHAT_RC_OK\n\n # We're catching keys! Only \"normal\" key presses interest us (e.g. \"a\"),\n # not complex ones (e.g. backspace).\n if len(keys) == 1 and catching_keys_data['amount']:\n catching_keys_data['keys'] += keys\n catching_keys_data['amount'] -= 1\n # Done catching keys, execute the callback.\n if catching_keys_data['amount'] == 0:\n globals()[catching_keys_data['callback']]()\n vi_buffer = \"\"\n weechat.bar_item_update(\"vi_buffer\")\n return weechat.WEECHAT_RC_OK_EAT\n\n # We're in command-line mode.\n if cmd_text:\n # Backspace key.\n if keys == \"\\x01?\":\n # Remove the last character from our command line.\n cmd_text = list(cmd_text)\n del cmd_text[-1]\n cmd_text = \"\".join(cmd_text)\n # Return key.\n elif keys == \"\\x01M\":\n weechat.hook_timer(1, 0, 1, \"cb_exec_cmd\", cmd_text)\n cmd_text = \"\"\n # Input.\n elif len(keys) == 1:\n cmd_text += keys\n # Update (and maybe hide) the bar item.\n weechat.bar_item_update(\"cmd_text\")\n if not cmd_text:\n weechat.command(\"\", \"/bar hide vi_cmd\")\n return weechat.WEECHAT_RC_OK_EAT\n # Enter command mode.\n elif keys == \":\":\n cmd_text += \":\"\n weechat.command(\"\", \"/bar show vi_cmd\")\n weechat.bar_item_update(\"cmd_text\")\n return weechat.WEECHAT_RC_OK_EAT\n\n # Add key to the buffer.\n vi_buffer += keys\n weechat.bar_item_update(\"vi_buffer\")\n if not vi_buffer:\n return weechat.WEECHAT_RC_OK\n\n # Check if the keys have a (partial or full) match. If so, also get the\n # keys without the count. (These are the actual keys we should handle.)\n # After that, `vi_buffer` is only used for display purposes — only\n # `vi_keys` is checked for all the handling.\n # If no matches are found, the keys buffer is cleared.\n matched, vi_keys, count = get_keys_and_count(vi_buffer)\n if not matched:\n vi_buffer = \"\"\n return weechat.WEECHAT_RC_OK_EAT\n\n buf = weechat.current_buffer()\n input_line = weechat.buffer_get_string(buf, \"input\")\n cur = weechat.buffer_get_integer(buf, \"input_pos\")\n\n # It's a key. If the corresponding value is a string, we assume it's a\n # WeeChat command. Otherwise, it's a method we'll call.\n if vi_keys in VI_KEYS:\n if isinstance(VI_KEYS[vi_keys], str):\n for _ in range(max(count, 1)):\n # This is to avoid crashing WeeChat on script reloads/unloads,\n # because no hooks must still be running when a script is\n # reloaded or unloaded.\n if VI_KEYS[vi_keys] == \"/input return\":\n return weechat.WEECHAT_RC_OK\n weechat.command(\"\", VI_KEYS[vi_keys])\n current_cur = weechat.buffer_get_integer(buf, \"input_pos\")\n set_cur(buf, input_line, current_cur)\n else:\n VI_KEYS[vi_keys](buf, input_line, cur, count)\n # It's a motion (e.g. \"w\") — call `motion_X()` where X is the motion, then\n # set the cursor's position to what that function returned.\n elif vi_keys in VI_MOTIONS:\n if vi_keys in SPECIAL_CHARS:\n func = \"motion_%s\" % SPECIAL_CHARS[vi_keys]\n else:\n func = \"motion_%s\" % vi_keys\n end, _, _ = globals()[func](input_line, cur, count)\n set_cur(buf, input_line, end)\n # It's an operator + motion (e.g. \"dw\") — call `motion_X()` (where X is\n # the motion), then we call `operator_Y()` (where Y is the operator)\n # with the position `motion_X()` returned. `operator_Y()` should then\n # handle changing the input line.\n elif (len(vi_keys) > 1 and\n vi_keys[0] in VI_OPERATORS and\n vi_keys[1:] in VI_MOTIONS):\n if vi_keys[1:] in SPECIAL_CHARS:\n func = \"motion_%s\" % SPECIAL_CHARS[vi_keys[1:]]\n else:\n func = \"motion_%s\" % vi_keys[1:]\n pos, overwrite, catching = globals()[func](input_line, cur, count)\n # If it's a catching motion, we don't want to call the operator just\n # yet -- this code will run again when the motion is complete, at which\n # point we will.\n if not catching:\n oper = \"operator_%s\" % vi_keys[0]\n globals()[oper](buf, input_line, cur, pos, overwrite)\n # The combo isn't completed yet (e.g. just \"d\").\n else:\n return weechat.WEECHAT_RC_OK_EAT\n\n # We've already handled the key combo, so clear the keys buffer.\n if not catching_keys_data['amount']:\n vi_buffer = \"\"\n weechat.bar_item_update(\"vi_buffer\")\n return weechat.WEECHAT_RC_OK_EAT","def on_events(self, add_callback=None, set_callback=None, del_callback=None):\n self.on_add(add_callback)\n self.on_set(set_callback)\n self.on_del(del_callback)","def subscribe_callbacks(self, *args):\n for arg in args:\n self.callbacks.append(arg)","def _callbackKeyButton(self, channel):\n if self._myKey.readKeyButton(channel) == 0:\n self.onKeyButtonDown(channel)\n return\n\n if self._myKey.readKeyButton(channel) == 1:\n self.onKeyButtonUp(channel)\n return","def keys():","def _type_keys(keys):\n FlaUIKeyboard.TypeSimultaneously(keys)","def cb_multi_hello(self, name):\n\n def cb_function(event):\n print(\"Hello %s!\"%name)\n\n return cb_function","def set_callback(self, key_name, callback):\n self.keymap[key_name] = callback","def key_handler(self):\n \n self.pressed = waitKey(1) & 255 #wait for keypress for 10 ms\n if self.pressed == 27: #exit program on 'esc'\n print \"exiting...\"\n self.camera.cam.release()\n exit()\n \n for key in self.key_controls.keys():\n if chr(self.pressed) == key:\n self.key_controls[key]()","def process_key(self, key):\n # Global and nonmaskable callbacks are supposed to work\n # even when the screen backlight is off\n #\n # First, querying global callbacks - they're more important than\n # even the current proxy nonmaskable callbacks\n logger.debug(\"Received key: {}\".format(key))\n if key in self.global_keymap:\n callback = self.global_keymap[key]\n self.handle_callback(callback, key, type=\"global\")\n return\n # Now, all the callbacks are either proxy callbacks or backlight-related\n # Saving a reference to current_proxy, in case it changes during the lookup\n current_proxy = self.get_current_proxy()\n if key in current_proxy.nonmaskable_keymap:\n callback = current_proxy.nonmaskable_keymap[key]\n self.handle_callback(callback, key, type=\"nonmaskable\", context_name=current_proxy.context_alias)\n return\n # Checking backlight state, turning it on if necessary\n if callable(self.backlight_cb):\n try:\n # backlight_cb turns on the backligth as a side effect\n backlight_was_off = self.backlight_cb()\n except:\n logger.exception(\"Exception while calling the backlight check callback!\")\n else:\n # If backlight was off, ignore the keypress\n if backlight_was_off is True:\n return\n # Now, all the other callbacks of the proxy:\n # Simple callbacks\n if key in current_proxy.keymap:\n callback = current_proxy.keymap[key]\n self.handle_callback(callback, key, context_name=current_proxy.context_alias)\n #Maskable callbacks\n elif key in current_proxy.maskable_keymap:\n callback = current_proxy.maskable_keymap[key]\n self.handle_callback(callback, key, type=\"maskable\", context_name=current_proxy.context_alias)\n #Keycode streaming\n elif callable(current_proxy.streaming):\n self.handle_callback(current_proxy.streaming, key, pass_key=True, type=\"streaming\", context_name=current_proxy.context_alias)\n else:\n logger.debug(\"Key {} has no handlers - ignored!\".format(key))\n pass #No handler for the key","def cbhandler(cls, session, cb_input):\n commandhandler = dict()\n commandhandler.update(dict({'sleep': cls.sleep}))\n commandhandler.update(dict({'dupsession': cls.reinitsession}))\n for i in range(len(cb_input)):\n command = cb_input[i]['cmd']\n arg = cb_input[i]['arg']\n if command in commandhandler.keys():\n cb_input[i]['ret'] = commandhandler[command](arg, session)\n else:\n print(\"Unknown command passed\", command)\n cls.log(3, \"Unknown command passed\", command)","def sync(self):\n available = self.count\n if available > 0:\n available = available + 2\n buf = self.read_keypad(available)\n for raw in buf:\n evt = KeyEvent(_seesaw_key((raw >> 2) & 0x3F), raw & 0x3)\n if (\n evt.number < _NEO_TRELLIS_NUM_KEYS\n and self.callbacks[evt.number] is not None\n ):\n self.callbacks[evt.number](evt)","def set_callbacks(self, **dic_functions):\n for action in self.interface.CALLBACKS:\n try:\n f = dic_functions[action]\n except KeyError:\n pass\n else:\n setattr(self.interface.callbacks, action, f)\n manquantes = [\n a for a in self.interface.CALLBACKS if not a in dic_functions]\n if not manquantes:\n logging.debug(\n f\"{self.__class__.__name__} : Tous les callbacks demandés sont fournis.\")\n else:\n logging.warning(\n f\"{self.__class__.__name__} didn't set asked callbacks {manquantes}\")","def _add_event_callback(self):\n for gpio_channel in self.registered_gpio:\n self.gpio_add_event_callback(gpio_channel)","def on_key_release(self, key, callback):\n self._key_release_mappings.setdefault(key, []).append(callback)","def wait_for_keys(self, *keys, timeout=0, sleeptime=0):\n if len(keys) == 1 and _is_iterable(keys[0]):\n keys = keys[0]\n\n return self.listen_until_return(Handler.key_press(keys), timeout=timeout,\n sleeptime=sleeptime)","def _GetMacKeyBindings():\n # A good reference for these: http://www.yellowbrain.com/stc/keymap.html\n return [\n # Move/select/delete by word\n (wx.stc.STC_KEY_LEFT, wx.stc.STC_SCMOD_ALT,\n wx.stc.STC_CMD_WORDLEFT),\n (wx.stc.STC_KEY_RIGHT, wx.stc.STC_SCMOD_ALT,\n wx.stc.STC_CMD_WORDRIGHT),\n (wx.stc.STC_KEY_LEFT, ALT_SHIFT, wx.stc.STC_CMD_WORDLEFTEXTEND),\n (wx.stc.STC_KEY_RIGHT, ALT_SHIFT, wx.stc.STC_CMD_WORDRIGHTEXTEND),\n (wx.stc.STC_KEY_BACK, wx.stc.STC_SCMOD_ALT,\n wx.stc.STC_CMD_DELWORDLEFT),\n (wx.stc.STC_KEY_DELETE, wx.stc.STC_SCMOD_ALT,\n wx.stc.STC_CMD_DELWORDRIGHT),\n (wx.stc.STC_KEY_BACK, ALT_SHIFT, wx.stc.STC_CMD_DELWORDRIGHT),\n (wx.stc.STC_KEY_DELETE, ALT_SHIFT, wx.stc.STC_CMD_DELWORDLEFT),\n\n # Move/select/delete by line\n (wx.stc.STC_KEY_LEFT, wx.stc.STC_SCMOD_CTRL,\n wx.stc.STC_CMD_VCHOME),\n (wx.stc.STC_KEY_LEFT, CTRL_SHIFT, wx.stc.STC_CMD_VCHOMEEXTEND),\n (wx.stc.STC_KEY_RIGHT, wx.stc.STC_SCMOD_CTRL,\n wx.stc.STC_CMD_LINEEND),\n (wx.stc.STC_KEY_RIGHT, CTRL_SHIFT, wx.stc.STC_CMD_LINEENDEXTEND),\n (wx.stc.STC_KEY_BACK, wx.stc.STC_SCMOD_CTRL,\n wx.stc.STC_CMD_DELLINELEFT),\n (wx.stc.STC_KEY_DELETE, wx.stc.STC_SCMOD_CTRL,\n wx.stc.STC_CMD_DELLINERIGHT),\n (wx.stc.STC_KEY_BACK, CTRL_SHIFT, wx.stc.STC_CMD_DELLINERIGHT),\n (wx.stc.STC_KEY_DELETE, CTRL_SHIFT, wx.stc.STC_CMD_DELLINELEFT),\n\n # By-character deletion behavior\n (wx.stc.STC_KEY_BACK, wx.stc.STC_SCMOD_NORM,\n wx.stc.STC_CMD_DELETEBACK),\n (wx.stc.STC_KEY_DELETE, wx.stc.STC_SCMOD_SHIFT,\n wx.stc.STC_CMD_DELETEBACK),\n\n # NOTE: The following two are a special case, since Scintilla\n # doesn't have a forward-delete action. So here we just cancel any\n # tip our auto-completion display, and then implement forward\n # delete in OnKeyDown.\n #(wx.stc.STC_KEY_DELETE, 0, wx.stc.STC_CMD_CANCEL),\n # Disabled as it breaks some keyboard functionality\n # NOTE: forward delete on mac is Fn+Delete and works fine\n # (wx.stc.STC_KEY_BACK, wx.stc.STC_SCMOD_SHIFT,\n # wx.stc.STC_CMD_CANCEL),\n ]","def check_events(self):\n for event in pygame.event.get():\n if event.type == pygame.KEYDOWN:\n if event.key == pygame.K_ESCAPE:\n self.menu_running = False\n if event.key == pygame.K_RETURN:\n self.START_KEY = True\n if event.key == pygame.K_BACKSPACE:\n self.BACK_KEY = True \n if event.key == pygame.K_DOWN:\n self.DOWN_KEY = True\n if event.key == pygame.K_UP:\n self.UP_KEY = True","def cb_key_pressed(data, signal, signal_data):\n global last_signal_time\n last_signal_time = time.time()\n if signal_data == \"\\x01[\":\n # In 50ms, check if any other keys were pressed. If not, it's Esc!\n weechat.hook_timer(50, 0, 1, \"cb_check_esc\",\n \"{:f}\".format(last_signal_time))\n return weechat.WEECHAT_RC_OK","def event_handler(self):\r\n for event in pygame.event.get():\r\n if event.type == QUIT:\r\n pygame.quit()\r\n sys.exit()\r\n elif event.type == MOUSEBUTTONDOWN and event.button == LEFT_CLICK:\r\n self.left_mouse_down_handler(event)\r\n elif event.type == MOUSEBUTTONUP and event.button == LEFT_CLICK:\r\n self.left_mouse_up_handler(event)\r\n elif event.type == MOUSEBUTTONDOWN and event.button == RIGHT_CLICK:\r\n self.right_mouse_down_handler(event)\r\n elif event.type == MOUSEBUTTONUP and event.button == RIGHT_CLICK:\r\n self.right_mouse_up_handler(event)\r\n elif event.type == MOUSEMOTION:\r\n self.mouse_motion_handler(event)\r\n elif event.type == MOUSEBUTTONUP and event.button in [2, 4, 5]:\r\n self.shortcut_click(event)","def keys(self, pattern=\"*\"):\n return self._command(b'KEYS', pattern, handler=list_of_keys)","def _handleEvents(self):\n\n pygame.event.pump()\n keyboardState = pygame.key.get_pressed()\n for key in Game.BoundControls:\n Game.ControlState[Game.Controls[key]] = keyboardState[key]\n if Game.ControlState[Game.Quit]:\n self._quit()","def slot_keypress(self, gox, (key)):\r\n pass","def initActions(self):\n\n\t\t#\n\t\t# this is super confusing to me, this is also defined in bToolBar\n\t\t# todo: where do I define it?????\n\t\t# if we define in both places,we get\n\t\t# WARNING: QAction::event: Ambiguous shortcut overload: 1\n\t\t'''\n\t\tmyName = '1'\n\t\tkeyboardAction1 = QtWidgets.QAction(myName, self)\n\t\tkeyboardAction1.setShortcut('1')# or 'Ctrl+r' or '&r' for alt+r\n\t\tkeyboardAction1.setToolTip('Set 1 [1]')\n\t\tkeyboardAction1.triggered.connect(lambda state, myName=myName: self.myAction_callback(myName))\n\t\tself.addAction(keyboardAction1)\n\t\t'''\n\n\t\t#\n\t\tmyName = 'Set Bad'\n\t\ttoggleBadAction = QtWidgets.QAction(myName, self)\n\t\ttoggleBadAction.setShortcut('b')# or 'Ctrl+r' or '&r' for alt+r\n\t\ttoggleBadAction.setToolTip('Set Bad [b]')\n\t\ttoggleBadAction.triggered.connect(lambda state, myName=myName: self.myAction_callback(myName))\n\t\tself.addAction(toggleBadAction)\n\n\t\t#\n\t\tmyName = 'Set Good'\n\t\ttoggleBadAction = QtWidgets.QAction(myName, self)\n\t\ttoggleBadAction.setShortcut('g')# or 'Ctrl+r' or '&r' for alt+r\n\t\ttoggleBadAction.setToolTip('Set Good [g]')\n\t\ttoggleBadAction.triggered.connect(lambda state, myName=myName: self.myAction_callback(myName))\n\t\tself.addAction(toggleBadAction)\n\n\t\t#\n\t\tmyName = 'Increase Tracing Sliding-Z'\n\t\ttoggleBadAction = QtWidgets.QAction(myName, self)\n\t\t#toggleBadAction.setShortcut('Shift+QtCore.Qt.Key_Plus')# or 'Ctrl+r' or '&r' for alt+r\n\t\t#myKeySequence = QtGui.QKeySequence(QtCore.Qt.Key_Shift + QtCore.Qt.Key_G)\n\t\tmyKeySequence = '.'\n\t\ttoggleBadAction.setShortcut(myKeySequence)# or 'Ctrl+r' or '&r' for alt+r\n\t\ttoggleBadAction.setToolTip('Increase Tracing Sliding-Z [.]')\n\t\ttoggleBadAction.triggered.connect(lambda state, myName=myName: self.myAction_callback(myName))\n\t\tself.addAction(toggleBadAction)\n\n\t\tmyName = 'Decrease Tracing Sliding-Z'\n\t\ttoggleBadAction = QtWidgets.QAction(myName, self)\n\t\t#toggleBadAction.setShortcut('Shift+QtCore.Qt.Key_Plus')# or 'Ctrl+r' or '&r' for alt+r\n\t\t#myKeySequence = QtGui.QKeySequence(QtCore.Qt.Key_Shift + QtCore.Qt.Key_G)\n\t\tmyKeySequence = ','\n\t\ttoggleBadAction.setShortcut(myKeySequence)# or 'Ctrl+r' or '&r' for alt+r\n\t\ttoggleBadAction.setToolTip('Decrease Tracing Sliding-Z [,]')\n\t\ttoggleBadAction.triggered.connect(lambda state, myName=myName: self.myAction_callback(myName))\n\t\tself.addAction(toggleBadAction)\n\n\t\t#\n\t\tmyName = 'Increase Sliding-Z'\n\t\ttoggleBadAction = QtWidgets.QAction(myName, self)\n\t\tmyKeySequence = QtGui.QKeySequence(QtCore.Qt.Key_Greater)\n\t\ttoggleBadAction.setShortcut(myKeySequence)# or 'Ctrl+r' or '&r' for alt+r\n\t\ttoggleBadAction.setToolTip('Increase Tracing Sliding-Z [>]')\n\t\ttoggleBadAction.triggered.connect(lambda state, myName=myName: self.myAction_callback(myName))\n\t\tself.addAction(toggleBadAction)\n\n\t\tmyName = 'Decrease Sliding-Z'\n\t\ttoggleBadAction = QtWidgets.QAction(myName, self)\n\t\t#toggleBadAction.setShortcut('Shift+QtCore.Qt.Key_Plus')# or 'Ctrl+r' or '&r' for alt+r\n\t\tmyKeySequence = QtGui.QKeySequence(QtCore.Qt.Key_Less)\n\t\ttoggleBadAction.setShortcut(myKeySequence)# or 'Ctrl+r' or '&r' for alt+r\n\t\ttoggleBadAction.setToolTip('Decrease Sliding-Z [<]')\n\t\ttoggleBadAction.triggered.connect(lambda state, myName=myName: self.myAction_callback(myName))\n\t\tself.addAction(toggleBadAction)\n\n\t\t'''\n\t\tfor action in self.actions():\n\t\t\tprint(' bStackWidget action:', action, action.text(), action.shortcut().toString())\n\t\t'''\n\t\t#print('bScatterPlotWidget.actions():', self.actions())","def _process_events(self, events):\n # Seperate modifiers and keys\n modifiers = []\n key_act_tuples = []\n for e in events:\n if e == []:\n pass\n elif e[0] in self.modifiers:\n modifiers.append(e[0])\n elif e[0] in self.keys:\n key_act_tuples.append(e)\n else:\n raise ValueError\n # Create processed events\n new_events = []\n new_events.append((None, None, None)) # The default event\n for key, key_act in key_act_tuples:\n new_events.append((key, key_act, None)) # None for any modifiers\n new_events.append((key, key_act, tuple(set(modifiers))))\n return new_events","def wait_for_keys_modified(self, *keys, modifiers_to_check=_mod_keys,\n timeout=0, sleeptime=0.001):\n\n set_mods = pygame.key.get_mods()\n return frozenset.union(\n frozenset([self.wait_for_keys(*keys, timeout=timeout, sleeptime=sleeptime)]),\n EventListener._contained_modifiers(set_mods, modifiers_to_check))","def signal_callbacks(self):\n for name in self.lookup_dict[self.__class__]:\n yield name, getattr(self, name)","def key_press_event(self, event):\n pass","def Handler(self, *events: str, colon: bool = False,\n ircv3: bool = False) -> Callable:\n ...","def on_events(self, insert_callback=None, set_callback=None,\n del_callback=None, reverse_callback=None, sort_callback=None):\n self.on_insert(insert_callback)\n self.on_set(set_callback)\n self.on_del(del_callback)\n self.on_reverse(reverse_callback)\n self.on_sort(sort_callback)","def event_loop(self):\n for event in pg.event.get():\n if event.type == pg.QUIT:\n self.done = True\n elif event.type in (pg.KEYDOWN, pg.KEYUP):\n self.keys = pg.key.get_pressed()","def wait_for_n_keypresses(self, key, n=1):\n my_const = \"key_consumed\"\n counter = 0\n\n def keypress_listener(e): return my_const \\\n if e.type == pygame.KEYDOWN and e.key == key \\\n else EventConsumerInfo.DONT_CARE\n\n while counter < n:\n if self.listen(keypress_listener) == my_const:\n counter += 1","def _get_mods(evt):\n mods = []\n mods += [keys.CONTROL] if evt.ControlDown() else []\n mods += [keys.ALT] if evt.AltDown() else []\n mods += [keys.SHIFT] if evt.ShiftDown() else []\n mods += [keys.META] if evt.MetaDown() else []\n return mods","def bind_keys_to_modes(self):\n for i,button in enumerate(self.mode_select.buttons, 1):\n key = getattr(pg, \"K_{}\".format(i))\n button.bind_key(key)","def run_callbacks(self, **kwargs):\n for callback in self.CALLBACKS:\n getattr(self, callback)(**kwargs)","def _run_callback() -> None:\n\n if keys.ANY_KEY in self._bindings:\n method, _ = self._bindings[keys.ANY_KEY]\n method(self, key)","def get_pygame_events(self):\n for event in pygame.event.get():\n if event.type in self.registered_pygame_handlers:\n for handler in self.registered_pygame_handlers[event.type]:\n\n if (event.type == pygame.KEYDOWN or\n event.type == pygame.KEYUP):\n handler(event.key, event.mod)\n else:\n handler()","def processKeyPressEvent(self, e):\n event = (int(e.modifiers()),e.key())\n# print \"<%x %x>\" % event, event\n# def f(d, stack):\n# for k,v in d.items():\n# stack.append(k)\n# if isinstance(v,dict):\n# f(v, stack)\n# else:\n# for x in stack:\n# print \"[%x %x]\" % x, x\n# print\n# stack.pop()\n# stack = []\n# f(self.AKH_keyBindings, stack)\n\n if event in self.AKH_keyBindingsWaiting:\n found = self.AKH_keyBindingsWaiting[event]\n elif event in self.AKH_keyBindings:\n found = self.AKH_keyBindings[event]\n else:\n key = event[1]\n if key!=QtCore.Qt.Key_Control and \\\n key!=QtCore.Qt.Key_Alt and \\\n key!=QtCore.Qt.Key_Shift:\n self.AKH_keyBindingsWaiting = {}\n return False\n if type(found) == dict:\n self.AKH_keyBindingsWaiting = found\n else:\n found()\n return True","def keypress(self, event):\n events = {\n '1': lambda: self.slot.set(1),\n '2': lambda: self.slot.set(2),\n '6': lambda: self.digits.set(6),\n '8': lambda: self.digits.set(8),\n }\n try:\n events[event.keysym]()\n except KeyError:\n pass\n if event.keysym in ('1', '2', 'Return', 'Enter'):\n self.get_totp()\n self.root.wm_withdraw()","def set_callbacks(self):\n\t\tself.set_floor_callbacks()\n\t\tself.set_button_callbacks()\n\t\tself.set_stop_callback()","def check_events(ai, var, screen, ship, shots, enemies, charges, shields, blasters, hub):\r\n\tfor event in pygame.event.get():\r\n\t\tif event.type == pygame.QUIT:\r\n\t\t\tsys.exit()\r\n\t\telif event.type == pygame.KEYDOWN:\r\n\t\t\tkey_down(event, ai, var, screen, ship, shots, enemies, charges, shields, hub)\r\n\t\telif event.type == pygame.KEYUP:\r\n\t\t\tkey_up(event, ai, var, screen, ship, charges, shields, blasters, hub)","def iterkeys(self, *args, **kwargs):\n self.__iter__(*args, **kwargs)","def _set_keys(self, listOfKeys):\n self._keys = listOfKeys","def __enableControls(self):\n for key in self._keyMap.keys():\n self.__acceptKeyDown(key)\n self.__acceptKeyUp(key)","def _onkeypress(self, fun, key=None):\n if fun is None:\n if key is None:\n self.cv.unbind(\"<KeyPress>\", None)\n else:\n self.cv.unbind(\"<KeyPress-%s>\" % key, None)\n else:\n def eventfun(event):\n fun()\n if key is None:\n self.cv.bind(\"<KeyPress>\", eventfun)\n else:\n self.cv.bind(\"<KeyPress-%s>\" % key, eventfun)","def releaseKeyButtons(self):\n self._myKey.removeKeyButtonEvent([\n CONFIG_KEY.BUTTON_ACT_A,\n CONFIG_KEY.BUTTON_ACT_B,\n CONFIG_KEY.BUTTON_JOY_UP,\n CONFIG_KEY.BUTTON_JOY_DOWN,\n CONFIG_KEY.BUTTON_JOY_LEFT,\n CONFIG_KEY.BUTTON_JOY_RIGHT,\n CONFIG_KEY.BUTTON_JOY_OK\n ])","def test_callback_keys(self):\n\n class Artist(Model):\n pass\n\n assert isinstance(Artist._callbacks, dict)\n assert 'before_save' in Artist._callbacks\n assert 'after_save' in Artist._callbacks\n assert 'before_delete' in Artist._callbacks\n assert 'after_delete' in Artist._callbacks\n assert 'after_init' in Artist._callbacks","def handle_events(self):\n keys = pygame.key.get_pressed()\n if self.game_manager.game_state == GameState.Running:\n if self.arcade:\n self.game_manager.control_players_arcade(self.joysticks) \n else:\n self.game_manager.control_players(keys)\n elif self.arcade:\n self.ui.arcade_control(self.joysticks[1])\n\n\n for event in pygame.event.get():\n if event.type == pygame.QUIT:\n self.game_manager.game_state = GameState.Quit \n if self.game_manager.game_state == GameState.Finished or\\\n self.game_manager.game_state == GameState.Menu :\n if event.type == pygame.KEYDOWN and not self.arcade:\n self.ui.control(event.key)\n #self.start_new_game(GameMode.EatToSurvive)","def initKeyButtons(self, mode = \"INT\"):\n if mode.upper() == \"INT\":\n try:\n self._myKey.configKeyButtons(\n enableButtons = [\n {\"id\":CONFIG_KEY.BUTTON_ACT_A, \"callback\":self._callbackKeyButton},\n {\"id\":CONFIG_KEY.BUTTON_ACT_B, \"callback\":self._callbackKeyButton},\n {\"id\":CONFIG_KEY.BUTTON_JOY_UP, \"callback\":self._callbackKeyButton},\n {\"id\":CONFIG_KEY.BUTTON_JOY_DOWN, \"callback\":self._callbackKeyButton},\n {\"id\":CONFIG_KEY.BUTTON_JOY_LEFT, \"callback\":self._callbackKeyButton},\n {\"id\":CONFIG_KEY.BUTTON_JOY_RIGHT, \"callback\":self._callbackKeyButton},\n {\"id\":CONFIG_KEY.BUTTON_JOY_OK, \"callback\":self._callbackKeyButton}\n ],\n bounceTime = DEF_BOUNCE_TIME_SHORT_MON )\n except:\n pass\n\n if mode.upper() == \"QUERY\":\n self._myKey.configKeyButtons([\n {\"id\":CONFIG_KEY.BUTTON_ACT_A, \"callback\":None},\n {\"id\":CONFIG_KEY.BUTTON_ACT_B, \"callback\":None},\n {\"id\":CONFIG_KEY.BUTTON_JOY_OK, \"callback\":None},\n {\"id\":CONFIG_KEY.BUTTON_JOY_UP, \"callback\":None},\n {\"id\":CONFIG_KEY.BUTTON_JOY_DOWN, \"callback\":None},\n {\"id\":CONFIG_KEY.BUTTON_JOY_LEFT, \"callback\":None},\n {\"id\":CONFIG_KEY.BUTTON_JOY_RIGHT, \"callback\":None}\n ])","def events_delete_btns(self):\n events = pg.event.get()\n for btn in self.delete_btns:\n btn.listen(events)","def send_keys(*input_seq):\n for chunk in input_seq:\n if isinstance(chunk, int):\n send_key_event(chunk)\n yield timeout(10)\n elif isinstance(chunk, str):\n for c in chunk:\n if c == \"\\n\":\n send_key_event(GDK_RETURN)\n else:\n send_key_event(ord(c))\n yield timeout(10)","def init_keystrokes(self):\n import x84.bbs.session\n term = x84.bbs.session.getterminal()\n self.keyset['home'].append(term.KEY_HOME)\n self.keyset['end'].append(term.KEY_END)\n self.keyset['pgup'].append(term.KEY_PGUP)\n self.keyset['pgdown'].append(term.KEY_PGDOWN)\n self.keyset['up'].append(term.KEY_UP)\n self.keyset['down'].append(term.KEY_DOWN)\n self.keyset['down'].append(term.KEY_ENTER)\n self.keyset['exit'].append(term.KEY_ESCAPE)","def keypress_handler(self, caller, event):\n ## Handle right arrow key press\n if event.keyval == 65363:\n self.tetris.right()\n\n ## Handle left arrow key press\n elif event.keyval == 65361:\n self.tetris.left()\n\n ## Handle up arrow key press\n elif event.keyval == 65362:\n self.tetris.rotate()\n\n ## Handle down arrow key press\n elif event.keyval == 65364:\n self.tetris.jump()\n\n ## Handle spacebar or pause key press\n elif event.keyval in (32, 65299): ## Spacebar \n self.tetris.pause()\n \n ## Call redraw on game\n self.tetris.call_redraw()","def get_keys(self):\n return [(['up', 'down', 'pg.up', 'pg.down'],\n 'navigate through the fields.'),\n (['esc'], 'backtrack to the previous pane or exit.'),\n (['F1', '?'], 'open this pane help.')]","def setupKeyMappings(self) :\n\t\t# first create keyMap object with default values\n\t\tself.keyMap = { \"left\":0, \"right\":0, \\\n\t\t\t\t\"forward\":0, \"backward\":0, \"dash\":0, \\\n\t\t\t\t\"slide-left\":0, \"slide-right\":0, \\\n \t\t\t\t\"cam-up\":0, \"cam-down\":0, \\\n\t\t\t\t\"cam-left\":0, \"cam-right\":0, \\\n\t\t\t\t\"zoom-in\":0, \"zoom-out\":0, \\\n\t\t\t\t\"reset-view\":0, \"view\":0}\n\t\t\n\t\t# now setup keyboard events that modify keyMap thru setKey\n\t\tself.accept(\"escape\", sys.exit)\n\n\t\t# turn help text on/off\n\t\tself.accept(\"h\", self.setKey, [\"help\",1])\n\t\tself.accept(\"h-up\", self.setKey, [\"help\",0])\n\n\t\t# movement controls\n\t\tself.accept(\"arrow_left\", self.setKey, [\"left\",1])\n\t\tself.accept(\"arrow_left-up\", self.setKey, [\"left\",0])\n\t\tself.accept(\"arrow_right\", self.setKey, [\"right\",1])\n\t\tself.accept(\"arrow_right-up\", self.setKey, [\"right\",0])\n\n\t\tself.accept(\"arrow_up\", self.setKey, [\"forward\",1])\n\t\tself.accept(\"arrow_up-up\", self.setKey, [\"forward\",0])\n \t\tself.accept(\"arrow_down\", self.setKey, [\"backward\",1])\n \t\tself.accept(\"arrow_down-up\", self.setKey, [\"backward\",0])\n\n \t\tself.accept(\",\", self.setKey, [\"slide-left\",1])\n \t\tself.accept(\",-up\", self.setKey, [\"slide-left\",0])\n \t\tself.accept(\".\", self.setKey, [\"slide-right\",1])\n \t\tself.accept(\".-up\", self.setKey, [\"slide-right\",0])\n\n\t\tself.accept(\"alt-arrow_up\", self.setKey, [\"dash\", 1])\n \t\tself.accept(\"alt-up\", self.setKey, [\"dash\", 0])\n\n\t\t# camera direction contols\n\t\tself.accept(\"shift-arrow_up\", self.setKey, [\"cam-up\",1])\n\t\tself.accept(\"shift-arrow_down\", self.setKey, [\"cam-down\",1])\n\t\tself.accept(\"shift-arrow_left\", self.setKey, [\"cam-left\",1])\n\t\tself.accept(\"shift-arrow_right\", self.setKey, [\"cam-right\",1])\t\n\n\t\t# zoom controls\n\t\tself.accept(\"z\", self.setKey, [\"zoom-in\",1])\n\t\tself.accept(\"z-up\", self.setKey, [\"zoom-in\",0])\n \t\tself.accept(\"shift-z\", self.setKey, [\"zoom-out\",1])\n\t\tself.accept(\"r\", self.setKey, [\"reset-view\",1]) \n\t\tself.accept(\"r-up\", self.setKey, [\"reset-view\",0]) \n\n\t\tself.accept(\"v\", self.setKey, [\"view\",1])\n\t\tself.accept(\"v-up\", self.setKey, [\"view\",0])","def ev_keyup(self, event: KeyUp) -> None:","def add_callbacks(am, ifttkey, ifttevent):\n if _debug:\n print(\"add_callbacks\", am)\n\n xurl = IFTT_URL.format(ifttevent, ifttkey)\n for c in am.mac_targets.values():\n call_val = {\n 'url': xurl,\n 'id': c.name,\n 'cur_val': -1\n }\n c.add_callback(iftt_callback, call_val)","def whait_for_keys_press(prompt, key1, key2, key3, key4):\n print(prompt)\n while True:\n Key_pressed = curses.wrapper(main)\n #if Key_pressed != (-1): print(Key_pressed) # displays number of key\n if Key_pressed == key1:\n break\n if Key_pressed == key2:\n break\n if Key_pressed == key3:\n break \n if Key_pressed == key4:\n break \n time.sleep(0.1)\n return Key_pressed","def addHandlers(self, handlers):\n self._eventHandlers.update(handlers)\n keys = self._eventHandlers.keys()\n pygame.event.set_allowed(keys)","def _key_press_event(self, event):\n if event.key() == 'escape':\n self.close()\n\n if event.text() == 'h':\n self._show_help()\n\n if event.text() in ('=', '+', '-'):\n self._zoom(sign=-2 * (event.text() == '-') + 1, draw=True)\n\n # Changing slices\n if event.key() in (QtCore.Qt.Key_Up, QtCore.Qt.Key_Down,\n QtCore.Qt.Key_Left, QtCore.Qt.Key_Right,\n QtCore.Qt.Key_Comma, QtCore.Qt.Key_Period,\n QtCore.Qt.Key_PageUp, QtCore.Qt.Key_PageDown):\n ras = np.array(self._ras)\n if event.key() in (QtCore.Qt.Key_Up, QtCore.Qt.Key_Down):\n ras[2] += 2 * (event.key() == QtCore.Qt.Key_Up) - 1\n elif event.key() in (QtCore.Qt.Key_Left, QtCore.Qt.Key_Right):\n ras[0] += 2 * (event.key() == QtCore.Qt.Key_Right) - 1\n else:\n ras[1] += 2 * (event.key() == QtCore.Qt.Key_PageUp or\n event.key() == QtCore.Qt.Key_Period) - 1\n self._set_ras(ras)","def keypress_signal_from_behaviors_coding_map(self, event):\n self.keyPressEvent(event)"],"string":"[\n \"def _handle_key_event(self, key, modifiers, mapping):\\n if key in mapping:\\n for callback in mapping[key]:\\n callback()\",\n \"def make_keyhandler(events):\\n def handler(key):\\n for k in events:\\n if key == simplegui.KEY_MAP[k]:\\n events[k]()\\n return handler\",\n \"def key_press(keys):\\n return lambda e: e.key if e.type == pygame.KEYDOWN \\\\\\n and e.key in keys else EventConsumerInfo.DONT_CARE\",\n \"def __init__(self, events, terminate_callback):\\n self.events = events\\n self.terminate_callback = terminate_callback\\n for event in self.events:\\n if event.button is not None:\\n event.button = mouse.Button(event.button)\\n if event.key is not None:\\n event.key = event.key.replace('\\\\'', '')\\n event.key = event.key.replace('Key.', '')\\n if event.key in keyboard.Key.__dict__:\\n event.key = keyboard.Key.__dict__[event.key]\",\n \"def key_event(self, key: Any, action: Any):\\n pass\",\n \"def on_key_press(self, key, callback):\\n self._key_press_mappings.setdefault(key, []).append(callback)\",\n \"def keysAll():\",\n \"def __master_key_callback(self, window, key, scancode, action, mods):\\n self.call_key_callback(window, key, scancode, action, mods, keyboard=self)\",\n \"def handle_sc_event(store, changed_keys, info):\\n\\n for key in changed_keys:\\n SC_HANDLERS[key](key=key, info=info)\",\n \"def read_keys(self) -> list[KeyPress]:\",\n \"def _on_key_press(self, event):\",\n \"def keys():\\n\\n global pressed_keys\\n pressed_keys = []\\n\\n the_keys = pygame.key.get_pressed()\\n\\n # check if keys in keymap are pressed\\n for key in KEYMAP:\\n if the_keys[key[\\\"name\\\"]]:\\n\\n # Check if pressed key is already pressed\\n is_present = False\\n for p_key in pressed_keys:\\n if p_key == key[\\\"action\\\"]:\\n is_present = True\\n\\n # Toggle action in list\\n if is_present:\\n pressed_keys.pop(pressed_keys.index(key[\\\"action\\\"]))\\n else:\\n pressed_keys.append(key[\\\"action\\\"])\",\n \"def ev_KEYUP(self, event):\",\n \"def set_button_callbacks(self):\\n\\t\\tfor floor, channel in enumerate(INPUT.IN_BUTTONS):\\n\\t\\t\\tself.signalPoller.add_callback_to_channel(channel, partial(self.button_pressed_callback, ORDERDIR.IN, floor))\\n\\n\\t\\tfor floor, channel in enumerate(INPUT.UP_BUTTONS):\\n\\t\\t\\tself.signalPoller.add_callback_to_channel(channel, partial(self.button_pressed_callback, ORDERDIR.UP, floor))\\n\\n\\t\\tfor floor, channel in enumerate(INPUT.DOWN_BUTTONS):\\n\\t\\t\\tself.signalPoller.add_callback_to_channel(channel, partial(self.button_pressed_callback, ORDERDIR.DOWN, floor))\",\n \"def enable_key_callback(self, v):\\n pass\",\n \"def on_key_down(self, key, callback):\\n self._key_down_mappings.setdefault(key, []).append(callback)\",\n \"def bind_modifiers(widget, event:Callable, button='Button-1',\\n modes=frozendict({'Shift': KeyModes.SHIFT, 'Control': KeyModes.CONTROL, 'Alt': KeyModes.ALT, })):\\n widget.bind(button, event)\\n for modifier, keymode in modes.items():\\n # We must provide 'keymode' as a default argument in the lambda expression (as method parameters are\\n # only evaluated once), otherwise it will end up referencing the last value in the modes dictionary.\\n widget.bind(f\\\"<{modifier}-{button}>\\\", lambda bind_event, mode=keymode: event(bind_event, mode))\",\n \"def _control_keys(self, command):\\n return [key for key, comm in self.KEY_TO_COMMAND.items() if comm == command]\",\n \"def ev_KEYDOWN(self, event):\",\n \"def check_special_callback(self, key_name):\\n if key_name in self.reserved_keys:\\n #Trying to set a special callback for a reserved key\\n raise CallbackException(1, \\\"Special callback for {} can't be set because it's one of the reserved keys\\\".format(key_name))\\n elif key_name in self.nonmaskable_keymap:\\n #Key is already used in a non-maskable callback\\n raise CallbackException(2, \\\"Special callback for {} can't be set because it's already set as nonmaskable\\\".format(key_name))\\n elif key_name in self.maskable_keymap: \\n #Key is already used in a maskable callback\\n raise CallbackException(3, \\\"Special callback for {} can't be set because it's already set as maskable\\\".format(key_name))\",\n \"def many(keys: List[str]):\\n for key in keys:\\n actions.key(key)\",\n \"def bindKeys(self):\\r\\n self.c.bind(\\\"<Button-1>\\\",self.seek)\\r\\n self.c.bind(\\\"<MouseWheel>\\\",self.app.zoom)\\r\\n self.c.bind(\\\"<Button-3>\\\",self.peek)\",\n \"def _on_key_release(self, event):\",\n \"def on_key_event(self, key):\\n pass\",\n \"def bindHotkeys(self):\\r\\n self.root.bind(\\\"s\\\",self.pause)\\r\\n self.root.bind(\\\"p\\\",self.play)\\r\\n self.root.bind(\\\"x\\\",self.stop)\\r\\n self.root.bind(\\\"<Right>\\\",lambda event, t=10: self.skipFor(event,t=t))\\r\\n self.root.bind(\\\"<Left>\\\",lambda event, t=-10: self.skipFor(event,t=t))\\r\\n self.bindDPHotkeys()\",\n \"def on_keydown(self, keys, game) -> None:\\n pass\",\n \"def onkey(self, fun, key):\\n if fun is None:\\n if key in self._keys:\\n self._keys.remove(key)\\n elif key not in self._keys:\\n self._keys.append(key)\\n self._onkeyrelease(fun, key)\",\n \"def set_events(self):\\r\\n\\r\\n self.canvas.bind(\\\"<Button-1>\\\", self.event_click_left)\\r\\n self.bind(\\\"<Return>\\\", self.event_return)\",\n \"def onEvent(self, eventKey, callback):\\n\\n #-------------------- \\n # Construct callback dict if it doesn't exist.\\n #--------------------\\n if not hasattr(self, 'eventCallbacks__'):\\n self.eventCallbacks__ = {}\\n for eventType in self.EVENT_TYPES:\\n self.eventCallbacks__[str(eventType)] = []\\n\\n\\n if not eventKey in self.EVENT_TYPES:\\n raise Exception(\\\"Xnat.io (onEvent): invalid event type '%s'\\\"%(eventKey))\\n self.eventCallbacks__[eventKey].append(callback)\",\n \"def CmdHandler(self, *events: str, colon: bool = False,\\n ircv3: bool = False) -> Callable:\\n ...\",\n \"def setupShortcuts(self):\\n\\n macros = (\\n (\\\"Ctrl+Return\\\", self.segmentNeedle),\\n (\\\"Ctrl+z\\\", self.logic.deleteLastNeedle),\\n )\\n\\n for keys,f in macros:\\n k = qt.QKeySequence(keys)\\n s = qt.QShortcut(k,slicer.util.mainWindow())\\n s.connect('activated()', f)\\n s.connect('activatedAmbiguously()', f)\\n print \\\"SlicerRC - '%s' -> '%s'\\\" % (keys, f.__name__)\",\n \"def __command_handler__(self, commands, handler):\\n message_set = self.event.text.split(u' ')\\n for command in commands:\\n if command in message_set:\\n handler(self.event, self.vk)\\n break\",\n \"def ev_keydown(self, event: KeyDown) -> None:\",\n \"def key_callback(option,opt_str,value,parser):\\n if \\\"--epi-key\\\" in opt_str:\\n parser.values.epi_keys.append(value)\\n elif \\\"--exclude\\\" in opt_str:\\n parser.values.exclude_paths.append(value)\",\n \"def event(self,events):\\n for event in events:\\n if event.type == KEYDOWN:\\n if event.key == K_RETURN:#starts the game\\n self.game.gotoMain()\\n #print \\\"r\\\"\\n if event.key == K_ESCAPE:#quits the game\\n sys.exit(0)\",\n \"def keyevent(self, keyname):\\n self.adb.key_events(keyname)\",\n \"def setShortcuts(self):\\n self.game.app.accept('mouse1', self.onMouse1Down)\\n self.game.app.accept('mouse3', self.onMouse2Down)\\n self.game.app.accept('space', self.onSpaceBarClear)\\n if self.enableMouseCamControl == 1:\\n self.game.app.accept('wheel_up', self.onMouseWheelUp)\\n self.game.app.accept('wheel_down', self.onMouseWheelDown)\",\n \"def _multiple_callbacks(callbacks, *args, **kwargs):\\n if isinstance(callbacks, list):\\n for cb in callbacks:\\n cb(*args, **kwargs)\\n return\\n if callbacks:\\n callbacks(*args, **kwargs)\",\n \"def register_callbacks(self, cbs):\\n assert isinstance(cbs, dict) # cbs must be a dictionary\\n cbs_key_list = list(cbs.keys())\\n enum_key_list = [enum.value for enum in self._action_type_enum]\\n \\n # TODO replace by check for compulsory keys only, all action types do not apply to all actions\\n #assert(len(set(enum_key_list) - set(cbs_key_list)) == 0)\\n\\n self._cbs = {}\\n for key in cbs_key_list: # check syntax\\n print \\\"Registered callback for action %s\\\" % key\\n self._cbs[key] = cbs[key]\\n rospy.logdebug(\\\"Callbacks registered.\\\")\",\n \"def cb_key_combo_default(data, signal, signal_data):\\n global esc_pressed, vi_buffer, cmd_text\\n\\n # If Esc was pressed, strip the Esc part from the pressed keys.\\n # Example: user presses Esc followed by i. This is detected as \\\"\\\\x01[i\\\",\\n # but we only want to handle \\\"i\\\".\\n keys = signal_data\\n if esc_pressed or esc_pressed == -2:\\n if keys.startswith(\\\"\\\\x01[\\\" * esc_pressed):\\n # Multiples of 3 seem to \\\"cancel\\\" themselves,\\n # e.g. Esc-Esc-Esc-Alt-j-11 is detected as \\\"\\\\x01[\\\\x01[\\\\x01\\\"\\n # followed by \\\"\\\\x01[j11\\\" (two different signals).\\n if signal_data == \\\"\\\\x01[\\\" * 3:\\n esc_pressed = -1 # `cb_check_esc()` will increment it to 0.\\n else:\\n esc_pressed = 0\\n # This can happen if a valid combination is started but interrupted\\n # with Esc, such as Ctrl-W→Esc→w which would send two signals:\\n # \\\"\\\\x01W\\\\x01[\\\" then \\\"\\\\x01W\\\\x01[w\\\".\\n # In that case, we still need to handle the next signal (\\\"\\\\x01W\\\\x01[w\\\")\\n # so we use the special value \\\"-2\\\".\\n else:\\n esc_pressed = -2\\n keys = keys.split(\\\"\\\\x01[\\\")[-1] # Remove the \\\"Esc\\\" part(s).\\n # Ctrl-Space.\\n elif keys == \\\"\\\\x01@\\\":\\n set_mode(\\\"NORMAL\\\")\\n return weechat.WEECHAT_RC_OK_EAT\\n\\n # Nothing to do here.\\n if mode == \\\"INSERT\\\":\\n return weechat.WEECHAT_RC_OK\\n\\n # We're in Replace mode — allow \\\"normal\\\" key presses (e.g. \\\"a\\\") and\\n # overwrite the next character with them, but let the other key presses\\n # pass normally (e.g. backspace, arrow keys, etc).\\n if mode == \\\"REPLACE\\\":\\n if len(keys) == 1:\\n weechat.command(\\\"\\\", \\\"/input delete_next_char\\\")\\n elif keys == \\\"\\\\x01?\\\":\\n weechat.command(\\\"\\\", \\\"/input move_previous_char\\\")\\n return weechat.WEECHAT_RC_OK_EAT\\n return weechat.WEECHAT_RC_OK\\n\\n # We're catching keys! Only \\\"normal\\\" key presses interest us (e.g. \\\"a\\\"),\\n # not complex ones (e.g. backspace).\\n if len(keys) == 1 and catching_keys_data['amount']:\\n catching_keys_data['keys'] += keys\\n catching_keys_data['amount'] -= 1\\n # Done catching keys, execute the callback.\\n if catching_keys_data['amount'] == 0:\\n globals()[catching_keys_data['callback']]()\\n vi_buffer = \\\"\\\"\\n weechat.bar_item_update(\\\"vi_buffer\\\")\\n return weechat.WEECHAT_RC_OK_EAT\\n\\n # We're in command-line mode.\\n if cmd_text:\\n # Backspace key.\\n if keys == \\\"\\\\x01?\\\":\\n # Remove the last character from our command line.\\n cmd_text = list(cmd_text)\\n del cmd_text[-1]\\n cmd_text = \\\"\\\".join(cmd_text)\\n # Return key.\\n elif keys == \\\"\\\\x01M\\\":\\n weechat.hook_timer(1, 0, 1, \\\"cb_exec_cmd\\\", cmd_text)\\n cmd_text = \\\"\\\"\\n # Input.\\n elif len(keys) == 1:\\n cmd_text += keys\\n # Update (and maybe hide) the bar item.\\n weechat.bar_item_update(\\\"cmd_text\\\")\\n if not cmd_text:\\n weechat.command(\\\"\\\", \\\"/bar hide vi_cmd\\\")\\n return weechat.WEECHAT_RC_OK_EAT\\n # Enter command mode.\\n elif keys == \\\":\\\":\\n cmd_text += \\\":\\\"\\n weechat.command(\\\"\\\", \\\"/bar show vi_cmd\\\")\\n weechat.bar_item_update(\\\"cmd_text\\\")\\n return weechat.WEECHAT_RC_OK_EAT\\n\\n # Add key to the buffer.\\n vi_buffer += keys\\n weechat.bar_item_update(\\\"vi_buffer\\\")\\n if not vi_buffer:\\n return weechat.WEECHAT_RC_OK\\n\\n # Check if the keys have a (partial or full) match. If so, also get the\\n # keys without the count. (These are the actual keys we should handle.)\\n # After that, `vi_buffer` is only used for display purposes — only\\n # `vi_keys` is checked for all the handling.\\n # If no matches are found, the keys buffer is cleared.\\n matched, vi_keys, count = get_keys_and_count(vi_buffer)\\n if not matched:\\n vi_buffer = \\\"\\\"\\n return weechat.WEECHAT_RC_OK_EAT\\n\\n buf = weechat.current_buffer()\\n input_line = weechat.buffer_get_string(buf, \\\"input\\\")\\n cur = weechat.buffer_get_integer(buf, \\\"input_pos\\\")\\n\\n # It's a key. If the corresponding value is a string, we assume it's a\\n # WeeChat command. Otherwise, it's a method we'll call.\\n if vi_keys in VI_KEYS:\\n if isinstance(VI_KEYS[vi_keys], str):\\n for _ in range(max(count, 1)):\\n # This is to avoid crashing WeeChat on script reloads/unloads,\\n # because no hooks must still be running when a script is\\n # reloaded or unloaded.\\n if VI_KEYS[vi_keys] == \\\"/input return\\\":\\n return weechat.WEECHAT_RC_OK\\n weechat.command(\\\"\\\", VI_KEYS[vi_keys])\\n current_cur = weechat.buffer_get_integer(buf, \\\"input_pos\\\")\\n set_cur(buf, input_line, current_cur)\\n else:\\n VI_KEYS[vi_keys](buf, input_line, cur, count)\\n # It's a motion (e.g. \\\"w\\\") — call `motion_X()` where X is the motion, then\\n # set the cursor's position to what that function returned.\\n elif vi_keys in VI_MOTIONS:\\n if vi_keys in SPECIAL_CHARS:\\n func = \\\"motion_%s\\\" % SPECIAL_CHARS[vi_keys]\\n else:\\n func = \\\"motion_%s\\\" % vi_keys\\n end, _, _ = globals()[func](input_line, cur, count)\\n set_cur(buf, input_line, end)\\n # It's an operator + motion (e.g. \\\"dw\\\") — call `motion_X()` (where X is\\n # the motion), then we call `operator_Y()` (where Y is the operator)\\n # with the position `motion_X()` returned. `operator_Y()` should then\\n # handle changing the input line.\\n elif (len(vi_keys) > 1 and\\n vi_keys[0] in VI_OPERATORS and\\n vi_keys[1:] in VI_MOTIONS):\\n if vi_keys[1:] in SPECIAL_CHARS:\\n func = \\\"motion_%s\\\" % SPECIAL_CHARS[vi_keys[1:]]\\n else:\\n func = \\\"motion_%s\\\" % vi_keys[1:]\\n pos, overwrite, catching = globals()[func](input_line, cur, count)\\n # If it's a catching motion, we don't want to call the operator just\\n # yet -- this code will run again when the motion is complete, at which\\n # point we will.\\n if not catching:\\n oper = \\\"operator_%s\\\" % vi_keys[0]\\n globals()[oper](buf, input_line, cur, pos, overwrite)\\n # The combo isn't completed yet (e.g. just \\\"d\\\").\\n else:\\n return weechat.WEECHAT_RC_OK_EAT\\n\\n # We've already handled the key combo, so clear the keys buffer.\\n if not catching_keys_data['amount']:\\n vi_buffer = \\\"\\\"\\n weechat.bar_item_update(\\\"vi_buffer\\\")\\n return weechat.WEECHAT_RC_OK_EAT\",\n \"def on_events(self, add_callback=None, set_callback=None, del_callback=None):\\n self.on_add(add_callback)\\n self.on_set(set_callback)\\n self.on_del(del_callback)\",\n \"def subscribe_callbacks(self, *args):\\n for arg in args:\\n self.callbacks.append(arg)\",\n \"def _callbackKeyButton(self, channel):\\n if self._myKey.readKeyButton(channel) == 0:\\n self.onKeyButtonDown(channel)\\n return\\n\\n if self._myKey.readKeyButton(channel) == 1:\\n self.onKeyButtonUp(channel)\\n return\",\n \"def keys():\",\n \"def _type_keys(keys):\\n FlaUIKeyboard.TypeSimultaneously(keys)\",\n \"def cb_multi_hello(self, name):\\n\\n def cb_function(event):\\n print(\\\"Hello %s!\\\"%name)\\n\\n return cb_function\",\n \"def set_callback(self, key_name, callback):\\n self.keymap[key_name] = callback\",\n \"def key_handler(self):\\n \\n self.pressed = waitKey(1) & 255 #wait for keypress for 10 ms\\n if self.pressed == 27: #exit program on 'esc'\\n print \\\"exiting...\\\"\\n self.camera.cam.release()\\n exit()\\n \\n for key in self.key_controls.keys():\\n if chr(self.pressed) == key:\\n self.key_controls[key]()\",\n \"def process_key(self, key):\\n # Global and nonmaskable callbacks are supposed to work\\n # even when the screen backlight is off\\n #\\n # First, querying global callbacks - they're more important than\\n # even the current proxy nonmaskable callbacks\\n logger.debug(\\\"Received key: {}\\\".format(key))\\n if key in self.global_keymap:\\n callback = self.global_keymap[key]\\n self.handle_callback(callback, key, type=\\\"global\\\")\\n return\\n # Now, all the callbacks are either proxy callbacks or backlight-related\\n # Saving a reference to current_proxy, in case it changes during the lookup\\n current_proxy = self.get_current_proxy()\\n if key in current_proxy.nonmaskable_keymap:\\n callback = current_proxy.nonmaskable_keymap[key]\\n self.handle_callback(callback, key, type=\\\"nonmaskable\\\", context_name=current_proxy.context_alias)\\n return\\n # Checking backlight state, turning it on if necessary\\n if callable(self.backlight_cb):\\n try:\\n # backlight_cb turns on the backligth as a side effect\\n backlight_was_off = self.backlight_cb()\\n except:\\n logger.exception(\\\"Exception while calling the backlight check callback!\\\")\\n else:\\n # If backlight was off, ignore the keypress\\n if backlight_was_off is True:\\n return\\n # Now, all the other callbacks of the proxy:\\n # Simple callbacks\\n if key in current_proxy.keymap:\\n callback = current_proxy.keymap[key]\\n self.handle_callback(callback, key, context_name=current_proxy.context_alias)\\n #Maskable callbacks\\n elif key in current_proxy.maskable_keymap:\\n callback = current_proxy.maskable_keymap[key]\\n self.handle_callback(callback, key, type=\\\"maskable\\\", context_name=current_proxy.context_alias)\\n #Keycode streaming\\n elif callable(current_proxy.streaming):\\n self.handle_callback(current_proxy.streaming, key, pass_key=True, type=\\\"streaming\\\", context_name=current_proxy.context_alias)\\n else:\\n logger.debug(\\\"Key {} has no handlers - ignored!\\\".format(key))\\n pass #No handler for the key\",\n \"def cbhandler(cls, session, cb_input):\\n commandhandler = dict()\\n commandhandler.update(dict({'sleep': cls.sleep}))\\n commandhandler.update(dict({'dupsession': cls.reinitsession}))\\n for i in range(len(cb_input)):\\n command = cb_input[i]['cmd']\\n arg = cb_input[i]['arg']\\n if command in commandhandler.keys():\\n cb_input[i]['ret'] = commandhandler[command](arg, session)\\n else:\\n print(\\\"Unknown command passed\\\", command)\\n cls.log(3, \\\"Unknown command passed\\\", command)\",\n \"def sync(self):\\n available = self.count\\n if available > 0:\\n available = available + 2\\n buf = self.read_keypad(available)\\n for raw in buf:\\n evt = KeyEvent(_seesaw_key((raw >> 2) & 0x3F), raw & 0x3)\\n if (\\n evt.number < _NEO_TRELLIS_NUM_KEYS\\n and self.callbacks[evt.number] is not None\\n ):\\n self.callbacks[evt.number](evt)\",\n \"def set_callbacks(self, **dic_functions):\\n for action in self.interface.CALLBACKS:\\n try:\\n f = dic_functions[action]\\n except KeyError:\\n pass\\n else:\\n setattr(self.interface.callbacks, action, f)\\n manquantes = [\\n a for a in self.interface.CALLBACKS if not a in dic_functions]\\n if not manquantes:\\n logging.debug(\\n f\\\"{self.__class__.__name__} : Tous les callbacks demandés sont fournis.\\\")\\n else:\\n logging.warning(\\n f\\\"{self.__class__.__name__} didn't set asked callbacks {manquantes}\\\")\",\n \"def _add_event_callback(self):\\n for gpio_channel in self.registered_gpio:\\n self.gpio_add_event_callback(gpio_channel)\",\n \"def on_key_release(self, key, callback):\\n self._key_release_mappings.setdefault(key, []).append(callback)\",\n \"def wait_for_keys(self, *keys, timeout=0, sleeptime=0):\\n if len(keys) == 1 and _is_iterable(keys[0]):\\n keys = keys[0]\\n\\n return self.listen_until_return(Handler.key_press(keys), timeout=timeout,\\n sleeptime=sleeptime)\",\n \"def _GetMacKeyBindings():\\n # A good reference for these: http://www.yellowbrain.com/stc/keymap.html\\n return [\\n # Move/select/delete by word\\n (wx.stc.STC_KEY_LEFT, wx.stc.STC_SCMOD_ALT,\\n wx.stc.STC_CMD_WORDLEFT),\\n (wx.stc.STC_KEY_RIGHT, wx.stc.STC_SCMOD_ALT,\\n wx.stc.STC_CMD_WORDRIGHT),\\n (wx.stc.STC_KEY_LEFT, ALT_SHIFT, wx.stc.STC_CMD_WORDLEFTEXTEND),\\n (wx.stc.STC_KEY_RIGHT, ALT_SHIFT, wx.stc.STC_CMD_WORDRIGHTEXTEND),\\n (wx.stc.STC_KEY_BACK, wx.stc.STC_SCMOD_ALT,\\n wx.stc.STC_CMD_DELWORDLEFT),\\n (wx.stc.STC_KEY_DELETE, wx.stc.STC_SCMOD_ALT,\\n wx.stc.STC_CMD_DELWORDRIGHT),\\n (wx.stc.STC_KEY_BACK, ALT_SHIFT, wx.stc.STC_CMD_DELWORDRIGHT),\\n (wx.stc.STC_KEY_DELETE, ALT_SHIFT, wx.stc.STC_CMD_DELWORDLEFT),\\n\\n # Move/select/delete by line\\n (wx.stc.STC_KEY_LEFT, wx.stc.STC_SCMOD_CTRL,\\n wx.stc.STC_CMD_VCHOME),\\n (wx.stc.STC_KEY_LEFT, CTRL_SHIFT, wx.stc.STC_CMD_VCHOMEEXTEND),\\n (wx.stc.STC_KEY_RIGHT, wx.stc.STC_SCMOD_CTRL,\\n wx.stc.STC_CMD_LINEEND),\\n (wx.stc.STC_KEY_RIGHT, CTRL_SHIFT, wx.stc.STC_CMD_LINEENDEXTEND),\\n (wx.stc.STC_KEY_BACK, wx.stc.STC_SCMOD_CTRL,\\n wx.stc.STC_CMD_DELLINELEFT),\\n (wx.stc.STC_KEY_DELETE, wx.stc.STC_SCMOD_CTRL,\\n wx.stc.STC_CMD_DELLINERIGHT),\\n (wx.stc.STC_KEY_BACK, CTRL_SHIFT, wx.stc.STC_CMD_DELLINERIGHT),\\n (wx.stc.STC_KEY_DELETE, CTRL_SHIFT, wx.stc.STC_CMD_DELLINELEFT),\\n\\n # By-character deletion behavior\\n (wx.stc.STC_KEY_BACK, wx.stc.STC_SCMOD_NORM,\\n wx.stc.STC_CMD_DELETEBACK),\\n (wx.stc.STC_KEY_DELETE, wx.stc.STC_SCMOD_SHIFT,\\n wx.stc.STC_CMD_DELETEBACK),\\n\\n # NOTE: The following two are a special case, since Scintilla\\n # doesn't have a forward-delete action. So here we just cancel any\\n # tip our auto-completion display, and then implement forward\\n # delete in OnKeyDown.\\n #(wx.stc.STC_KEY_DELETE, 0, wx.stc.STC_CMD_CANCEL),\\n # Disabled as it breaks some keyboard functionality\\n # NOTE: forward delete on mac is Fn+Delete and works fine\\n # (wx.stc.STC_KEY_BACK, wx.stc.STC_SCMOD_SHIFT,\\n # wx.stc.STC_CMD_CANCEL),\\n ]\",\n \"def check_events(self):\\n for event in pygame.event.get():\\n if event.type == pygame.KEYDOWN:\\n if event.key == pygame.K_ESCAPE:\\n self.menu_running = False\\n if event.key == pygame.K_RETURN:\\n self.START_KEY = True\\n if event.key == pygame.K_BACKSPACE:\\n self.BACK_KEY = True \\n if event.key == pygame.K_DOWN:\\n self.DOWN_KEY = True\\n if event.key == pygame.K_UP:\\n self.UP_KEY = True\",\n \"def cb_key_pressed(data, signal, signal_data):\\n global last_signal_time\\n last_signal_time = time.time()\\n if signal_data == \\\"\\\\x01[\\\":\\n # In 50ms, check if any other keys were pressed. If not, it's Esc!\\n weechat.hook_timer(50, 0, 1, \\\"cb_check_esc\\\",\\n \\\"{:f}\\\".format(last_signal_time))\\n return weechat.WEECHAT_RC_OK\",\n \"def event_handler(self):\\r\\n for event in pygame.event.get():\\r\\n if event.type == QUIT:\\r\\n pygame.quit()\\r\\n sys.exit()\\r\\n elif event.type == MOUSEBUTTONDOWN and event.button == LEFT_CLICK:\\r\\n self.left_mouse_down_handler(event)\\r\\n elif event.type == MOUSEBUTTONUP and event.button == LEFT_CLICK:\\r\\n self.left_mouse_up_handler(event)\\r\\n elif event.type == MOUSEBUTTONDOWN and event.button == RIGHT_CLICK:\\r\\n self.right_mouse_down_handler(event)\\r\\n elif event.type == MOUSEBUTTONUP and event.button == RIGHT_CLICK:\\r\\n self.right_mouse_up_handler(event)\\r\\n elif event.type == MOUSEMOTION:\\r\\n self.mouse_motion_handler(event)\\r\\n elif event.type == MOUSEBUTTONUP and event.button in [2, 4, 5]:\\r\\n self.shortcut_click(event)\",\n \"def keys(self, pattern=\\\"*\\\"):\\n return self._command(b'KEYS', pattern, handler=list_of_keys)\",\n \"def _handleEvents(self):\\n\\n pygame.event.pump()\\n keyboardState = pygame.key.get_pressed()\\n for key in Game.BoundControls:\\n Game.ControlState[Game.Controls[key]] = keyboardState[key]\\n if Game.ControlState[Game.Quit]:\\n self._quit()\",\n \"def slot_keypress(self, gox, (key)):\\r\\n pass\",\n \"def initActions(self):\\n\\n\\t\\t#\\n\\t\\t# this is super confusing to me, this is also defined in bToolBar\\n\\t\\t# todo: where do I define it?????\\n\\t\\t# if we define in both places,we get\\n\\t\\t# WARNING: QAction::event: Ambiguous shortcut overload: 1\\n\\t\\t'''\\n\\t\\tmyName = '1'\\n\\t\\tkeyboardAction1 = QtWidgets.QAction(myName, self)\\n\\t\\tkeyboardAction1.setShortcut('1')# or 'Ctrl+r' or '&r' for alt+r\\n\\t\\tkeyboardAction1.setToolTip('Set 1 [1]')\\n\\t\\tkeyboardAction1.triggered.connect(lambda state, myName=myName: self.myAction_callback(myName))\\n\\t\\tself.addAction(keyboardAction1)\\n\\t\\t'''\\n\\n\\t\\t#\\n\\t\\tmyName = 'Set Bad'\\n\\t\\ttoggleBadAction = QtWidgets.QAction(myName, self)\\n\\t\\ttoggleBadAction.setShortcut('b')# or 'Ctrl+r' or '&r' for alt+r\\n\\t\\ttoggleBadAction.setToolTip('Set Bad [b]')\\n\\t\\ttoggleBadAction.triggered.connect(lambda state, myName=myName: self.myAction_callback(myName))\\n\\t\\tself.addAction(toggleBadAction)\\n\\n\\t\\t#\\n\\t\\tmyName = 'Set Good'\\n\\t\\ttoggleBadAction = QtWidgets.QAction(myName, self)\\n\\t\\ttoggleBadAction.setShortcut('g')# or 'Ctrl+r' or '&r' for alt+r\\n\\t\\ttoggleBadAction.setToolTip('Set Good [g]')\\n\\t\\ttoggleBadAction.triggered.connect(lambda state, myName=myName: self.myAction_callback(myName))\\n\\t\\tself.addAction(toggleBadAction)\\n\\n\\t\\t#\\n\\t\\tmyName = 'Increase Tracing Sliding-Z'\\n\\t\\ttoggleBadAction = QtWidgets.QAction(myName, self)\\n\\t\\t#toggleBadAction.setShortcut('Shift+QtCore.Qt.Key_Plus')# or 'Ctrl+r' or '&r' for alt+r\\n\\t\\t#myKeySequence = QtGui.QKeySequence(QtCore.Qt.Key_Shift + QtCore.Qt.Key_G)\\n\\t\\tmyKeySequence = '.'\\n\\t\\ttoggleBadAction.setShortcut(myKeySequence)# or 'Ctrl+r' or '&r' for alt+r\\n\\t\\ttoggleBadAction.setToolTip('Increase Tracing Sliding-Z [.]')\\n\\t\\ttoggleBadAction.triggered.connect(lambda state, myName=myName: self.myAction_callback(myName))\\n\\t\\tself.addAction(toggleBadAction)\\n\\n\\t\\tmyName = 'Decrease Tracing Sliding-Z'\\n\\t\\ttoggleBadAction = QtWidgets.QAction(myName, self)\\n\\t\\t#toggleBadAction.setShortcut('Shift+QtCore.Qt.Key_Plus')# or 'Ctrl+r' or '&r' for alt+r\\n\\t\\t#myKeySequence = QtGui.QKeySequence(QtCore.Qt.Key_Shift + QtCore.Qt.Key_G)\\n\\t\\tmyKeySequence = ','\\n\\t\\ttoggleBadAction.setShortcut(myKeySequence)# or 'Ctrl+r' or '&r' for alt+r\\n\\t\\ttoggleBadAction.setToolTip('Decrease Tracing Sliding-Z [,]')\\n\\t\\ttoggleBadAction.triggered.connect(lambda state, myName=myName: self.myAction_callback(myName))\\n\\t\\tself.addAction(toggleBadAction)\\n\\n\\t\\t#\\n\\t\\tmyName = 'Increase Sliding-Z'\\n\\t\\ttoggleBadAction = QtWidgets.QAction(myName, self)\\n\\t\\tmyKeySequence = QtGui.QKeySequence(QtCore.Qt.Key_Greater)\\n\\t\\ttoggleBadAction.setShortcut(myKeySequence)# or 'Ctrl+r' or '&r' for alt+r\\n\\t\\ttoggleBadAction.setToolTip('Increase Tracing Sliding-Z [>]')\\n\\t\\ttoggleBadAction.triggered.connect(lambda state, myName=myName: self.myAction_callback(myName))\\n\\t\\tself.addAction(toggleBadAction)\\n\\n\\t\\tmyName = 'Decrease Sliding-Z'\\n\\t\\ttoggleBadAction = QtWidgets.QAction(myName, self)\\n\\t\\t#toggleBadAction.setShortcut('Shift+QtCore.Qt.Key_Plus')# or 'Ctrl+r' or '&r' for alt+r\\n\\t\\tmyKeySequence = QtGui.QKeySequence(QtCore.Qt.Key_Less)\\n\\t\\ttoggleBadAction.setShortcut(myKeySequence)# or 'Ctrl+r' or '&r' for alt+r\\n\\t\\ttoggleBadAction.setToolTip('Decrease Sliding-Z [<]')\\n\\t\\ttoggleBadAction.triggered.connect(lambda state, myName=myName: self.myAction_callback(myName))\\n\\t\\tself.addAction(toggleBadAction)\\n\\n\\t\\t'''\\n\\t\\tfor action in self.actions():\\n\\t\\t\\tprint(' bStackWidget action:', action, action.text(), action.shortcut().toString())\\n\\t\\t'''\\n\\t\\t#print('bScatterPlotWidget.actions():', self.actions())\",\n \"def _process_events(self, events):\\n # Seperate modifiers and keys\\n modifiers = []\\n key_act_tuples = []\\n for e in events:\\n if e == []:\\n pass\\n elif e[0] in self.modifiers:\\n modifiers.append(e[0])\\n elif e[0] in self.keys:\\n key_act_tuples.append(e)\\n else:\\n raise ValueError\\n # Create processed events\\n new_events = []\\n new_events.append((None, None, None)) # The default event\\n for key, key_act in key_act_tuples:\\n new_events.append((key, key_act, None)) # None for any modifiers\\n new_events.append((key, key_act, tuple(set(modifiers))))\\n return new_events\",\n \"def wait_for_keys_modified(self, *keys, modifiers_to_check=_mod_keys,\\n timeout=0, sleeptime=0.001):\\n\\n set_mods = pygame.key.get_mods()\\n return frozenset.union(\\n frozenset([self.wait_for_keys(*keys, timeout=timeout, sleeptime=sleeptime)]),\\n EventListener._contained_modifiers(set_mods, modifiers_to_check))\",\n \"def signal_callbacks(self):\\n for name in self.lookup_dict[self.__class__]:\\n yield name, getattr(self, name)\",\n \"def key_press_event(self, event):\\n pass\",\n \"def Handler(self, *events: str, colon: bool = False,\\n ircv3: bool = False) -> Callable:\\n ...\",\n \"def on_events(self, insert_callback=None, set_callback=None,\\n del_callback=None, reverse_callback=None, sort_callback=None):\\n self.on_insert(insert_callback)\\n self.on_set(set_callback)\\n self.on_del(del_callback)\\n self.on_reverse(reverse_callback)\\n self.on_sort(sort_callback)\",\n \"def event_loop(self):\\n for event in pg.event.get():\\n if event.type == pg.QUIT:\\n self.done = True\\n elif event.type in (pg.KEYDOWN, pg.KEYUP):\\n self.keys = pg.key.get_pressed()\",\n \"def wait_for_n_keypresses(self, key, n=1):\\n my_const = \\\"key_consumed\\\"\\n counter = 0\\n\\n def keypress_listener(e): return my_const \\\\\\n if e.type == pygame.KEYDOWN and e.key == key \\\\\\n else EventConsumerInfo.DONT_CARE\\n\\n while counter < n:\\n if self.listen(keypress_listener) == my_const:\\n counter += 1\",\n \"def _get_mods(evt):\\n mods = []\\n mods += [keys.CONTROL] if evt.ControlDown() else []\\n mods += [keys.ALT] if evt.AltDown() else []\\n mods += [keys.SHIFT] if evt.ShiftDown() else []\\n mods += [keys.META] if evt.MetaDown() else []\\n return mods\",\n \"def bind_keys_to_modes(self):\\n for i,button in enumerate(self.mode_select.buttons, 1):\\n key = getattr(pg, \\\"K_{}\\\".format(i))\\n button.bind_key(key)\",\n \"def run_callbacks(self, **kwargs):\\n for callback in self.CALLBACKS:\\n getattr(self, callback)(**kwargs)\",\n \"def _run_callback() -> None:\\n\\n if keys.ANY_KEY in self._bindings:\\n method, _ = self._bindings[keys.ANY_KEY]\\n method(self, key)\",\n \"def get_pygame_events(self):\\n for event in pygame.event.get():\\n if event.type in self.registered_pygame_handlers:\\n for handler in self.registered_pygame_handlers[event.type]:\\n\\n if (event.type == pygame.KEYDOWN or\\n event.type == pygame.KEYUP):\\n handler(event.key, event.mod)\\n else:\\n handler()\",\n \"def processKeyPressEvent(self, e):\\n event = (int(e.modifiers()),e.key())\\n# print \\\"<%x %x>\\\" % event, event\\n# def f(d, stack):\\n# for k,v in d.items():\\n# stack.append(k)\\n# if isinstance(v,dict):\\n# f(v, stack)\\n# else:\\n# for x in stack:\\n# print \\\"[%x %x]\\\" % x, x\\n# print\\n# stack.pop()\\n# stack = []\\n# f(self.AKH_keyBindings, stack)\\n\\n if event in self.AKH_keyBindingsWaiting:\\n found = self.AKH_keyBindingsWaiting[event]\\n elif event in self.AKH_keyBindings:\\n found = self.AKH_keyBindings[event]\\n else:\\n key = event[1]\\n if key!=QtCore.Qt.Key_Control and \\\\\\n key!=QtCore.Qt.Key_Alt and \\\\\\n key!=QtCore.Qt.Key_Shift:\\n self.AKH_keyBindingsWaiting = {}\\n return False\\n if type(found) == dict:\\n self.AKH_keyBindingsWaiting = found\\n else:\\n found()\\n return True\",\n \"def keypress(self, event):\\n events = {\\n '1': lambda: self.slot.set(1),\\n '2': lambda: self.slot.set(2),\\n '6': lambda: self.digits.set(6),\\n '8': lambda: self.digits.set(8),\\n }\\n try:\\n events[event.keysym]()\\n except KeyError:\\n pass\\n if event.keysym in ('1', '2', 'Return', 'Enter'):\\n self.get_totp()\\n self.root.wm_withdraw()\",\n \"def set_callbacks(self):\\n\\t\\tself.set_floor_callbacks()\\n\\t\\tself.set_button_callbacks()\\n\\t\\tself.set_stop_callback()\",\n \"def check_events(ai, var, screen, ship, shots, enemies, charges, shields, blasters, hub):\\r\\n\\tfor event in pygame.event.get():\\r\\n\\t\\tif event.type == pygame.QUIT:\\r\\n\\t\\t\\tsys.exit()\\r\\n\\t\\telif event.type == pygame.KEYDOWN:\\r\\n\\t\\t\\tkey_down(event, ai, var, screen, ship, shots, enemies, charges, shields, hub)\\r\\n\\t\\telif event.type == pygame.KEYUP:\\r\\n\\t\\t\\tkey_up(event, ai, var, screen, ship, charges, shields, blasters, hub)\",\n \"def iterkeys(self, *args, **kwargs):\\n self.__iter__(*args, **kwargs)\",\n \"def _set_keys(self, listOfKeys):\\n self._keys = listOfKeys\",\n \"def __enableControls(self):\\n for key in self._keyMap.keys():\\n self.__acceptKeyDown(key)\\n self.__acceptKeyUp(key)\",\n \"def _onkeypress(self, fun, key=None):\\n if fun is None:\\n if key is None:\\n self.cv.unbind(\\\"<KeyPress>\\\", None)\\n else:\\n self.cv.unbind(\\\"<KeyPress-%s>\\\" % key, None)\\n else:\\n def eventfun(event):\\n fun()\\n if key is None:\\n self.cv.bind(\\\"<KeyPress>\\\", eventfun)\\n else:\\n self.cv.bind(\\\"<KeyPress-%s>\\\" % key, eventfun)\",\n \"def releaseKeyButtons(self):\\n self._myKey.removeKeyButtonEvent([\\n CONFIG_KEY.BUTTON_ACT_A,\\n CONFIG_KEY.BUTTON_ACT_B,\\n CONFIG_KEY.BUTTON_JOY_UP,\\n CONFIG_KEY.BUTTON_JOY_DOWN,\\n CONFIG_KEY.BUTTON_JOY_LEFT,\\n CONFIG_KEY.BUTTON_JOY_RIGHT,\\n CONFIG_KEY.BUTTON_JOY_OK\\n ])\",\n \"def test_callback_keys(self):\\n\\n class Artist(Model):\\n pass\\n\\n assert isinstance(Artist._callbacks, dict)\\n assert 'before_save' in Artist._callbacks\\n assert 'after_save' in Artist._callbacks\\n assert 'before_delete' in Artist._callbacks\\n assert 'after_delete' in Artist._callbacks\\n assert 'after_init' in Artist._callbacks\",\n \"def handle_events(self):\\n keys = pygame.key.get_pressed()\\n if self.game_manager.game_state == GameState.Running:\\n if self.arcade:\\n self.game_manager.control_players_arcade(self.joysticks) \\n else:\\n self.game_manager.control_players(keys)\\n elif self.arcade:\\n self.ui.arcade_control(self.joysticks[1])\\n\\n\\n for event in pygame.event.get():\\n if event.type == pygame.QUIT:\\n self.game_manager.game_state = GameState.Quit \\n if self.game_manager.game_state == GameState.Finished or\\\\\\n self.game_manager.game_state == GameState.Menu :\\n if event.type == pygame.KEYDOWN and not self.arcade:\\n self.ui.control(event.key)\\n #self.start_new_game(GameMode.EatToSurvive)\",\n \"def initKeyButtons(self, mode = \\\"INT\\\"):\\n if mode.upper() == \\\"INT\\\":\\n try:\\n self._myKey.configKeyButtons(\\n enableButtons = [\\n {\\\"id\\\":CONFIG_KEY.BUTTON_ACT_A, \\\"callback\\\":self._callbackKeyButton},\\n {\\\"id\\\":CONFIG_KEY.BUTTON_ACT_B, \\\"callback\\\":self._callbackKeyButton},\\n {\\\"id\\\":CONFIG_KEY.BUTTON_JOY_UP, \\\"callback\\\":self._callbackKeyButton},\\n {\\\"id\\\":CONFIG_KEY.BUTTON_JOY_DOWN, \\\"callback\\\":self._callbackKeyButton},\\n {\\\"id\\\":CONFIG_KEY.BUTTON_JOY_LEFT, \\\"callback\\\":self._callbackKeyButton},\\n {\\\"id\\\":CONFIG_KEY.BUTTON_JOY_RIGHT, \\\"callback\\\":self._callbackKeyButton},\\n {\\\"id\\\":CONFIG_KEY.BUTTON_JOY_OK, \\\"callback\\\":self._callbackKeyButton}\\n ],\\n bounceTime = DEF_BOUNCE_TIME_SHORT_MON )\\n except:\\n pass\\n\\n if mode.upper() == \\\"QUERY\\\":\\n self._myKey.configKeyButtons([\\n {\\\"id\\\":CONFIG_KEY.BUTTON_ACT_A, \\\"callback\\\":None},\\n {\\\"id\\\":CONFIG_KEY.BUTTON_ACT_B, \\\"callback\\\":None},\\n {\\\"id\\\":CONFIG_KEY.BUTTON_JOY_OK, \\\"callback\\\":None},\\n {\\\"id\\\":CONFIG_KEY.BUTTON_JOY_UP, \\\"callback\\\":None},\\n {\\\"id\\\":CONFIG_KEY.BUTTON_JOY_DOWN, \\\"callback\\\":None},\\n {\\\"id\\\":CONFIG_KEY.BUTTON_JOY_LEFT, \\\"callback\\\":None},\\n {\\\"id\\\":CONFIG_KEY.BUTTON_JOY_RIGHT, \\\"callback\\\":None}\\n ])\",\n \"def events_delete_btns(self):\\n events = pg.event.get()\\n for btn in self.delete_btns:\\n btn.listen(events)\",\n \"def send_keys(*input_seq):\\n for chunk in input_seq:\\n if isinstance(chunk, int):\\n send_key_event(chunk)\\n yield timeout(10)\\n elif isinstance(chunk, str):\\n for c in chunk:\\n if c == \\\"\\\\n\\\":\\n send_key_event(GDK_RETURN)\\n else:\\n send_key_event(ord(c))\\n yield timeout(10)\",\n \"def init_keystrokes(self):\\n import x84.bbs.session\\n term = x84.bbs.session.getterminal()\\n self.keyset['home'].append(term.KEY_HOME)\\n self.keyset['end'].append(term.KEY_END)\\n self.keyset['pgup'].append(term.KEY_PGUP)\\n self.keyset['pgdown'].append(term.KEY_PGDOWN)\\n self.keyset['up'].append(term.KEY_UP)\\n self.keyset['down'].append(term.KEY_DOWN)\\n self.keyset['down'].append(term.KEY_ENTER)\\n self.keyset['exit'].append(term.KEY_ESCAPE)\",\n \"def keypress_handler(self, caller, event):\\n ## Handle right arrow key press\\n if event.keyval == 65363:\\n self.tetris.right()\\n\\n ## Handle left arrow key press\\n elif event.keyval == 65361:\\n self.tetris.left()\\n\\n ## Handle up arrow key press\\n elif event.keyval == 65362:\\n self.tetris.rotate()\\n\\n ## Handle down arrow key press\\n elif event.keyval == 65364:\\n self.tetris.jump()\\n\\n ## Handle spacebar or pause key press\\n elif event.keyval in (32, 65299): ## Spacebar \\n self.tetris.pause()\\n \\n ## Call redraw on game\\n self.tetris.call_redraw()\",\n \"def get_keys(self):\\n return [(['up', 'down', 'pg.up', 'pg.down'],\\n 'navigate through the fields.'),\\n (['esc'], 'backtrack to the previous pane or exit.'),\\n (['F1', '?'], 'open this pane help.')]\",\n \"def setupKeyMappings(self) :\\n\\t\\t# first create keyMap object with default values\\n\\t\\tself.keyMap = { \\\"left\\\":0, \\\"right\\\":0, \\\\\\n\\t\\t\\t\\t\\\"forward\\\":0, \\\"backward\\\":0, \\\"dash\\\":0, \\\\\\n\\t\\t\\t\\t\\\"slide-left\\\":0, \\\"slide-right\\\":0, \\\\\\n \\t\\t\\t\\t\\\"cam-up\\\":0, \\\"cam-down\\\":0, \\\\\\n\\t\\t\\t\\t\\\"cam-left\\\":0, \\\"cam-right\\\":0, \\\\\\n\\t\\t\\t\\t\\\"zoom-in\\\":0, \\\"zoom-out\\\":0, \\\\\\n\\t\\t\\t\\t\\\"reset-view\\\":0, \\\"view\\\":0}\\n\\t\\t\\n\\t\\t# now setup keyboard events that modify keyMap thru setKey\\n\\t\\tself.accept(\\\"escape\\\", sys.exit)\\n\\n\\t\\t# turn help text on/off\\n\\t\\tself.accept(\\\"h\\\", self.setKey, [\\\"help\\\",1])\\n\\t\\tself.accept(\\\"h-up\\\", self.setKey, [\\\"help\\\",0])\\n\\n\\t\\t# movement controls\\n\\t\\tself.accept(\\\"arrow_left\\\", self.setKey, [\\\"left\\\",1])\\n\\t\\tself.accept(\\\"arrow_left-up\\\", self.setKey, [\\\"left\\\",0])\\n\\t\\tself.accept(\\\"arrow_right\\\", self.setKey, [\\\"right\\\",1])\\n\\t\\tself.accept(\\\"arrow_right-up\\\", self.setKey, [\\\"right\\\",0])\\n\\n\\t\\tself.accept(\\\"arrow_up\\\", self.setKey, [\\\"forward\\\",1])\\n\\t\\tself.accept(\\\"arrow_up-up\\\", self.setKey, [\\\"forward\\\",0])\\n \\t\\tself.accept(\\\"arrow_down\\\", self.setKey, [\\\"backward\\\",1])\\n \\t\\tself.accept(\\\"arrow_down-up\\\", self.setKey, [\\\"backward\\\",0])\\n\\n \\t\\tself.accept(\\\",\\\", self.setKey, [\\\"slide-left\\\",1])\\n \\t\\tself.accept(\\\",-up\\\", self.setKey, [\\\"slide-left\\\",0])\\n \\t\\tself.accept(\\\".\\\", self.setKey, [\\\"slide-right\\\",1])\\n \\t\\tself.accept(\\\".-up\\\", self.setKey, [\\\"slide-right\\\",0])\\n\\n\\t\\tself.accept(\\\"alt-arrow_up\\\", self.setKey, [\\\"dash\\\", 1])\\n \\t\\tself.accept(\\\"alt-up\\\", self.setKey, [\\\"dash\\\", 0])\\n\\n\\t\\t# camera direction contols\\n\\t\\tself.accept(\\\"shift-arrow_up\\\", self.setKey, [\\\"cam-up\\\",1])\\n\\t\\tself.accept(\\\"shift-arrow_down\\\", self.setKey, [\\\"cam-down\\\",1])\\n\\t\\tself.accept(\\\"shift-arrow_left\\\", self.setKey, [\\\"cam-left\\\",1])\\n\\t\\tself.accept(\\\"shift-arrow_right\\\", self.setKey, [\\\"cam-right\\\",1])\\t\\n\\n\\t\\t# zoom controls\\n\\t\\tself.accept(\\\"z\\\", self.setKey, [\\\"zoom-in\\\",1])\\n\\t\\tself.accept(\\\"z-up\\\", self.setKey, [\\\"zoom-in\\\",0])\\n \\t\\tself.accept(\\\"shift-z\\\", self.setKey, [\\\"zoom-out\\\",1])\\n\\t\\tself.accept(\\\"r\\\", self.setKey, [\\\"reset-view\\\",1]) \\n\\t\\tself.accept(\\\"r-up\\\", self.setKey, [\\\"reset-view\\\",0]) \\n\\n\\t\\tself.accept(\\\"v\\\", self.setKey, [\\\"view\\\",1])\\n\\t\\tself.accept(\\\"v-up\\\", self.setKey, [\\\"view\\\",0])\",\n \"def ev_keyup(self, event: KeyUp) -> None:\",\n \"def add_callbacks(am, ifttkey, ifttevent):\\n if _debug:\\n print(\\\"add_callbacks\\\", am)\\n\\n xurl = IFTT_URL.format(ifttevent, ifttkey)\\n for c in am.mac_targets.values():\\n call_val = {\\n 'url': xurl,\\n 'id': c.name,\\n 'cur_val': -1\\n }\\n c.add_callback(iftt_callback, call_val)\",\n \"def whait_for_keys_press(prompt, key1, key2, key3, key4):\\n print(prompt)\\n while True:\\n Key_pressed = curses.wrapper(main)\\n #if Key_pressed != (-1): print(Key_pressed) # displays number of key\\n if Key_pressed == key1:\\n break\\n if Key_pressed == key2:\\n break\\n if Key_pressed == key3:\\n break \\n if Key_pressed == key4:\\n break \\n time.sleep(0.1)\\n return Key_pressed\",\n \"def addHandlers(self, handlers):\\n self._eventHandlers.update(handlers)\\n keys = self._eventHandlers.keys()\\n pygame.event.set_allowed(keys)\",\n \"def _key_press_event(self, event):\\n if event.key() == 'escape':\\n self.close()\\n\\n if event.text() == 'h':\\n self._show_help()\\n\\n if event.text() in ('=', '+', '-'):\\n self._zoom(sign=-2 * (event.text() == '-') + 1, draw=True)\\n\\n # Changing slices\\n if event.key() in (QtCore.Qt.Key_Up, QtCore.Qt.Key_Down,\\n QtCore.Qt.Key_Left, QtCore.Qt.Key_Right,\\n QtCore.Qt.Key_Comma, QtCore.Qt.Key_Period,\\n QtCore.Qt.Key_PageUp, QtCore.Qt.Key_PageDown):\\n ras = np.array(self._ras)\\n if event.key() in (QtCore.Qt.Key_Up, QtCore.Qt.Key_Down):\\n ras[2] += 2 * (event.key() == QtCore.Qt.Key_Up) - 1\\n elif event.key() in (QtCore.Qt.Key_Left, QtCore.Qt.Key_Right):\\n ras[0] += 2 * (event.key() == QtCore.Qt.Key_Right) - 1\\n else:\\n ras[1] += 2 * (event.key() == QtCore.Qt.Key_PageUp or\\n event.key() == QtCore.Qt.Key_Period) - 1\\n self._set_ras(ras)\",\n \"def keypress_signal_from_behaviors_coding_map(self, event):\\n self.keyPressEvent(event)\"\n]","isConversational":false},"negative_scores":{"kind":"list like","value":["0.68615484","0.68123263","0.6174684","0.58327556","0.58170974","0.5806323","0.5780186","0.5754679","0.5689066","0.567472","0.56471545","0.5627545","0.56092143","0.55985314","0.55752456","0.55332804","0.5533179","0.55255973","0.55047953","0.5493462","0.54629964","0.5438999","0.5435614","0.54022145","0.53903913","0.5346239","0.5340012","0.53292745","0.53189605","0.5289565","0.5281105","0.5268583","0.52638394","0.5261332","0.52379066","0.5227225","0.5216639","0.52154344","0.5201255","0.5199093","0.51939034","0.5190505","0.5190126","0.51864684","0.5186097","0.51685864","0.5168363","0.51680845","0.51674217","0.5155618","0.51531917","0.5150911","0.5150702","0.5132184","0.51316744","0.51273394","0.5122748","0.51203686","0.5109716","0.5104188","0.50999874","0.5098454","0.5093697","0.50920635","0.5089539","0.5088068","0.508622","0.5085896","0.5085848","0.5085586","0.5070626","0.50618994","0.50598824","0.5055598","0.50443614","0.50405073","0.5038618","0.50374985","0.50329345","0.5020971","0.50176966","0.5010917","0.50089437","0.49989432","0.4989582","0.49753976","0.4966583","0.49595714","0.49481958","0.4942171","0.49416938","0.49413794","0.49396148","0.49382797","0.4937199","0.49207017","0.49177969","0.4904793","0.49029312","0.49029014"],"string":"[\n \"0.68615484\",\n \"0.68123263\",\n \"0.6174684\",\n \"0.58327556\",\n \"0.58170974\",\n \"0.5806323\",\n \"0.5780186\",\n \"0.5754679\",\n \"0.5689066\",\n \"0.567472\",\n \"0.56471545\",\n \"0.5627545\",\n \"0.56092143\",\n \"0.55985314\",\n \"0.55752456\",\n \"0.55332804\",\n \"0.5533179\",\n \"0.55255973\",\n \"0.55047953\",\n \"0.5493462\",\n \"0.54629964\",\n \"0.5438999\",\n \"0.5435614\",\n \"0.54022145\",\n \"0.53903913\",\n \"0.5346239\",\n \"0.5340012\",\n \"0.53292745\",\n \"0.53189605\",\n \"0.5289565\",\n \"0.5281105\",\n \"0.5268583\",\n \"0.52638394\",\n \"0.5261332\",\n \"0.52379066\",\n \"0.5227225\",\n \"0.5216639\",\n \"0.52154344\",\n \"0.5201255\",\n \"0.5199093\",\n \"0.51939034\",\n \"0.5190505\",\n \"0.5190126\",\n \"0.51864684\",\n \"0.5186097\",\n \"0.51685864\",\n \"0.5168363\",\n \"0.51680845\",\n \"0.51674217\",\n \"0.5155618\",\n \"0.51531917\",\n \"0.5150911\",\n \"0.5150702\",\n \"0.5132184\",\n \"0.51316744\",\n \"0.51273394\",\n \"0.5122748\",\n \"0.51203686\",\n \"0.5109716\",\n \"0.5104188\",\n \"0.50999874\",\n \"0.5098454\",\n \"0.5093697\",\n \"0.50920635\",\n \"0.5089539\",\n \"0.5088068\",\n \"0.508622\",\n \"0.5085896\",\n \"0.5085848\",\n \"0.5085586\",\n \"0.5070626\",\n \"0.50618994\",\n \"0.50598824\",\n \"0.5055598\",\n \"0.50443614\",\n \"0.50405073\",\n \"0.5038618\",\n \"0.50374985\",\n \"0.50329345\",\n \"0.5020971\",\n \"0.50176966\",\n \"0.5010917\",\n \"0.50089437\",\n \"0.49989432\",\n \"0.4989582\",\n \"0.49753976\",\n \"0.4966583\",\n \"0.49595714\",\n \"0.49481958\",\n \"0.4942171\",\n \"0.49416938\",\n \"0.49413794\",\n \"0.49396148\",\n \"0.49382797\",\n \"0.4937199\",\n \"0.49207017\",\n \"0.49177969\",\n \"0.4904793\",\n \"0.49029312\",\n \"0.49029014\"\n]","isConversational":false},"document_score":{"kind":"string","value":"0.65743834"},"document_rank":{"kind":"string","value":"2"}}},{"rowIdx":16599,"cells":{"query":{"kind":"string","value":"Unsubscribe events for a callback."},"document":{"kind":"string","value":"def unsubscribe(callback):\n if callback in _subscribers:\n del _subscribers[callback]"},"metadata":{"kind":"string","value":"{\n \"objective\": {\n \"self\": [],\n \"paired\": [],\n \"triplet\": [\n [\n \"query\",\n \"document\",\n \"negatives\"\n ]\n ]\n }\n}"},"negatives":{"kind":"list like","value":["def unsubscribe(self, callback: Callable) -> None:\n self.callbacks.discard(callback)","def unsubscribe(self, event_type: typing.Type[typing.Any], callback: CallbackT[typing.Any]) -> None:","def unsubscribe_callback(self, callback, sensor):\n if sensor in self._callbacks:\n self._callbacks[sensor].remove(callback)","def unregister(self, callback):\n\t\tcallbacks = []\n\t\tfor i in range(0, len(self.callbacks)):\n\t\t\tif self.callbacks[i][0] != callback:\n\t\t\t\tcallbacks.append(self.callbacks[i])\n\t\t\t\t\n\t\tself.callbacks = callbacks\n\t\tself.events[str(callback)] = []","def unsubscribe(self, event_handler):\n pass # pragma: no cover","def unsubscribe(self, event, callback, args = None):\n if {\"event\": event, \"callback\": callback, \"args\": args, }\\\n in self.events:\n self.events.remove({\"event\": event, \"callback\": callback,\\\n \"args\": args, })\n\n return True","def unsubscribe(receiver):","def unsubscribe(receiver):","def unsubscribe(receiver):","def unsubscribe(receiver):","def unsubscribe(receiver):","def unsubscribe(self, name, callback_function):\n # Remove the callback from _callbacks.\n if self._callbacks.has_key(name):\n if callback_function in self._callbacks[name]:\n self._callbacks[name].remove(callback_function)\n if len(self._callbacks[name]) == 0:\n self._callbacks.pop(name)\n else:\n raise PresenceException('This function is not registered to receive callbacks.')\n else:\n raise PresenceException('Unknown service name. No callback handler exists.')","def unsubscribeFromEvent(eventName,subscriber):","def unregister(self, event, callback):\n if self._events_tree[event].isListed(callback):\n self._events_tree[event].remove(callback)\n self._events_cbs[event][0] = self._events_tree.getCallbacksSequence()\n else:\n self._events_cbs[event][1].remove(callback)","def remove_callback(event_name, callback):\n _callbacks.get(event_name, set()).discard(callback)","def unsubscribe(self, meta_type, callback):\n try:\n self.subscribers.get(meta_type, []).remove(callback)\n except ValueError:\n pass\n try:\n self.nackables.get(meta_type, []).remove(callback)\n except ValueError:\n pass","def unsubscribe_all_known(self):\n for key, value in self.__callbacks.items():\n self.__logger.debug(f'unsubscribe from event {key}')\n succ = self.__twitch.delete_eventsub_subscription(key)\n if not succ:\n self.__logger.warning(f'failed to unsubscribe from event {key}')\n self.__callbacks.clear()","def unregister(self, event_name, callback_func=None, identifier=None):\n if callback_func:\n self.events[event_name].remove(callback_func)\n else:\n del self.events[event_name]","def unsubscribe(self, event_type, func):\n if func in self.event_subscribers[event_type]:\n kwargs = {event_type: func}\n self.unbind(**kwargs)\n self.event_subscribers[event_type].remove(func)","def unsubscribe(observer):","def unsubscribe(observer):","def unregister_handler(self, event_type, callback):\n\n if event_type not in self._event_handlers:\n return\n if callback not in self._event_handlers[event_type]:\n return\n\n self._event_handlers[event_type].remove(callback)\n\n if not self._event_handlers[event_type]:\n del self._event_handlers[event_type]","def subscribe_off(self, callback: callable):\n topic = f\"{self._subscriber_topic}_off\"\n subscribe_topic(callback, topic)","def deregister(self):\n self.callback = None","def remove_callback(self, callback):\n if callback in self._async_callbacks:\n self._async_callbacks.remove(callback)","def unsubscribe(self):\r\n self._unregister()","def unsubscribe(self):\n pass # pragma: no cover","def unregister_signals(self):\n for _, callback in self.signal_callbacks:\n Signal.unsubscribe(self, callback)","def unregister(self, signal_id, callback):\n # if the callback was registered the remove it \n if signal_id in self.registered_callbacks:\n self.registered_callbacks[signal_id].remove(callback)","def subscribe_off(self, callback: callable):\n subscribe_topic(callback, self._off_subscriber_topic)","def remove_callback(self, callback):\n if callback in self._callbacks:\n self._callbacks.remove(callback)","def remove_notify_handler(self, callback: NotifyHandler) -> None:\n self._notify_handlers.remove(callback)","def unregister_callback(self, name):\n self._callbacks.remove(name)\n del self._cb_dict[name]\n\n self.logger.debug('Callback unregistered: %s' % name)","def remove_watch(callback: Callable[[Event], None]) -> None:\n if callback not in _event_watch_handles:\n warnings.warn(f\"{callback} is not an active event watcher, nothing was removed.\", RuntimeWarning)\n return\n handle = _event_watch_handles[callback]\n lib.SDL_DelEventWatch(lib._sdl_event_watcher, handle)\n del _event_watch_handles[callback]","def off(self, event_name, callback=None):\n if callback:\n self.factory.off(event_name, callback)\n else:\n self.factory.remove_all_listeners(event_name)","def unlisten(obj, name, func):\n _signals(obj, name).remove(func)","def _unsubscribe(self, signal):\n while signal in self._downstream:\n self._downstream.remove(signal)\n while signal in self._downstream_reconnect:\n self._downstream_reconnect.remove(signal)","def remove_callback(self, callback: Callback):\n self._callbacks.remove(callback)\n self._stage.remove_callback(callback)","def unreg_event_handler(self, callback_func, userData):\n\t\tcall_sdk_function('PrlSrv_UnregEventHandler', self.handle, callback_func, userData)","def remove_stopcallback(self, stopcallback):\n self.stopcallbacks.discard(stopcallback)","def stopCallback (self):\n GPIO.remove_event_detect (self.IRQ_PIN)\n self.hasCallback = False","def unsubscribe(self, callback_id):\n request = self.get_active_subscription(callback_id)\n request['mode'] = 'unsubscribe'\n self.subscribe_impl(callback_id, **request)","def remove_on_stop_callback(self, callback):\n self.__condition.acquire()\n try:\n if self.__is_running:\n self.__on_stop_callbacks.remove(callback)\n finally:\n self.__condition.release()","def unsubscribe(self, channel, update_handler=None):\n pass","def deregister(self, event_type, callback, details_filter=None):\n with self._lock:\n listeners = self._topics.get(event_type, [])\n for i, listener in enumerate(listeners):\n if listener.is_equivalent(callback,\n details_filter=details_filter):\n listeners.pop(i)\n return True\n return False","def unregister( key ):\n global callbacks\n del callbacks[ key ]","def _onUnsubscribe(self, client:mqtt.Client, userdata:Any, mid:int) -> None:\n\t\t# TODO doc, error check when not connected, not subscribed\n\t\tfor t in self.subscribedTopics.values():\n\t\t\tif t.mid == mid:\n\t\t\t\tdel self.subscribedTopics[t.topic]\n\t\t\t\tself.messageHandler and self.messageHandler.onUnsubscribed(self, t.topic)\n\t\t\t\tbreak","def destroy_event(self, event_type):\n for func in self.event_subscribers[event_type][:]:\n self.unsubscribe(event_type, func)\n self.unregister_event_types(event_type)","def UnsubscribeFromRedeemingQueueUpdatedEvent(self, callBackFunction):\n self.redeemingQueueUpdated.disconnect(callBackFunction)","def unregister_aggregate_handler(self, event_name, callback):\n\n raise NotImplementedError()","def unregisterEvent(eventName, publisher):","def unsubscribe_all(self):\n ids = []\n repeat = True\n cursor = None\n # get all ids\n while repeat:\n ret = self.__twitch.get_eventsub_subscriptions(after=cursor)\n for d in ret.get('data', []):\n ids.append(d.get('id'))\n cursor = ret.get('pagination', {}).get('cursor')\n repeat = cursor is not None\n for _id in ids:\n succ = self.__twitch.delete_eventsub_subscription(_id)\n if not succ:\n self.__logger.warning(f'failed to unsubscribe from event {_id}')\n self.__callbacks.clear()","def unregisterStatusListener(self, cb):\r\n self._statusListener.discard(cb)","async def unlistened(self, value=None):\n pass","def unsubscribe(cls,sender,receiver):\n cls._unsubscribe(id(sender),receiver)","def unregister_standard(self, event_name, callback):\n\n raise NotImplementedError()","def unregister(self, listener):\n for event_type in self.listeners:\n for event_listeners in self.listeners[event_type]:\n if event_listeners:\n try:\n event_listeners.remove(listener)\n logger.debug('Unregistered listener for event type \"%s\"', hr_event_type(event_type))\n except ValueError:\n pass","def _unregisterConnect(self, function):\n self._sig_connect.unsubscribe(function)","def unsubscribe(self, destination, *args, **kwargs):","def unregister(self,listener):\n\t\tif listener in self.cartesianListeners:\n\t\t\tself.cartesianListeners.remove(listener)\n\t\tif listener in self.polarListeners:\n\t\t\tself.polarListeners.remove(listener)","def remove_callback(self, chain):\n for reactor in self._reactors:\n reactor.remove_callback(chain)","def unreg_event_handler(self, callback_func, userData):\n\t\tcall_sdk_function('PrlVm_UnregEventHandler', self.handle, callback_func, userData)","def on_del(self, callback):\n self._del_callback = callback if callable(callback) else _void","def on_del(self, callback):\n self._del_callback = callback if callable(callback) else _void","def unsubscribe(self, observer):\n self._observers.remove(observer)","def UnsubscribeFromAurumBalanceChanged(self, callBackFunction):\n self.accountAurumBalanceChanged.disconnect(callBackFunction)","def remove_delegate(self, callback):\n\n if not callback in self._delegate_methods:\n return\n\n self._delegate_methods.remove(callback)","def disconnect(self, callback):\n if not callable(callback):\n raise TypeError('Cannot disconnect a non-callable from a Signal')\n conn = self._make_connection(callback)\n self._connection_dead(conn)","def unsubscribe(self, observer, name=None):\n if name is None:\n name = 'default'\n if observer in self._observers:\n del self._observers[observer][name]","def unregisterUnready(self, function):\n self._sig_unready.unsubscribe(function)","def dontNotifyOnDeath(self, cb):\r\n try:\r\n self.__cbs.remove(cb)\r\n except AttributeError:\r\n pass","def disconnect(self, handler, event=None):\n if event:\n self.event_handlers.remove(handler)\n else:\n for event in self.event_handlers:\n if hasattr(handler, event):\n self.disconnect(getattr(handler, event), event)","def remove_callback(self, chain):","def remove_callback(self, fn):\n self._callbacks.remove(fn)\n return self","def test_unsubscribe_one_listener(self):\n def listener():\n pass\n\n EVENT_MANAGER.subscribe('test_listener', listener)\n EVENT_MANAGER.unsubscribe(listener)\n self.assertNotIn(listener, EVENT_MANAGER._listeners['test_listener'])","def dontNotifyOnDeath(self, cb):\r\n try:\r\n self._cbs.remove(cb)\r\n except AttributeError:\r\n pass","def dontNotifyOnDeath(self, cb):\r\n try:\r\n self._cbs.remove(cb)\r\n except AttributeError:\r\n pass","def unsubscribe(self, inst):\r\n if inst in self._subscribers:\r\n self._subscribers.remove(inst)\r\n vprint(\"{} is unsubscribed from {}\".format(inst.name, self.name))","def unsubscribe(self, instrument_ids, exchange_id=b''):\n pass","def unregisterValueChanged(self, function):\n self._sig_value_changed.unsubscribe(function)","def unregister_url_callback(self, pattern, callback):\n if isinstance(pattern, str):\n pattern = re.compile(pattern)\n\n try:\n del self._url_callbacks[pattern]\n except KeyError:\n pass","def remove_change_callback(self, callback_function):\n if callback_function in self.changeCallbacks:\n self.changeCallbacks.remove(callback_function)","def unregisterRemoved(self, function):\n self._sig_removed.unsubscribe(function)","def unsubscribe(self, subject):\n pass","def test_unsubscribe(self):\n self.service.clientConnected()\n\n unsubscribers = []\n self.service.subscribe(u'url', 1\n ).addCallback(lambda fn: unsubscribers.append(fn))\n self.service.subscribe(u'url', 2\n ).addCallback(lambda fn: unsubscribers.append(fn))\n\n pubsubClient = self.service.pubsubClient\n self.assertIn(u'url', pubsubClient.subscriptions)\n\n unsubscribers.pop()()\n self.service.unsubscribe(u'url')\n self.assertIn(u'url', pubsubClient.subscriptions)\n\n unsubscribers.pop()()\n self.service.unsubscribe(u'url')\n self.assertNotIn(u'url', pubsubClient.subscriptions)","def unsubscribe(self, instrument_ids, exchange_id=b''):\n self.invoke_log('on_invoke_unsubscribe', instrument_ids=instrument_ids, exchange_id=exchange_id)\n if self._xapi:\n func = self._xapi.X_Unsubscribe\n func.restype = None\n func.argtypes = [c_void_p, c_void_p, c_char_p, c_char_p]\n func(self.p_fun, self.p_api, c_char_p(\n b','.join(instrument_ids) if isinstance(instrument_ids, list) else instrument_ids),\n c_char_p(exchange_id))","def unsubscribe(self, namespace, unsub_strings=None):\n req = JSONRPCRequest('unsubscribe', [namespace, unsub_strings])\n result = yield self._send(req)\n self._cache_jsonrpc_request(req)\n raise tornado.gen.Return(result)","def disconnect(\n cls,\n on_start=None,\n on_resume=None,\n on_pause=None,\n on_stop=None,\n on_save=None,\n on_reset=None,\n ):\n try:\n cls.start_callback.remove(on_start)\n except ValueError:\n pass\n\n try:\n cls.resume_callback.remove(on_resume)\n except ValueError:\n pass\n\n try:\n cls.pause_callback.remove(on_pause)\n except ValueError:\n pass\n\n try:\n cls.stop_callback.remove(on_stop)\n except ValueError:\n pass\n\n try:\n cls.save_callback.remove(on_save)\n except ValueError:\n pass\n\n try:\n cls.reset_callback.remove(on_reset)\n except ValueError:\n pass","def deleteCallbacks(self):\n if self.callbacks:\n for cb in self.callbacks:\n OpenMaya.MMessage.removeCallback(cb)\n self.callbacks.remove(cb)","def unregisterRemove(self, function):\n self._sig_remove.unsubscribe(function)","def unsubscribe_from_all(module):\n for name, signal in _signals.items():\n for receiver in list(signal.receivers.values()):\n obj = receiver()\n if obj is not None:\n if inspect.ismethod(obj):\n # find the object to which a method is bound\n self = None\n for name, value in inspect.getmembers(obj):\n if name == '__self__':\n self = value\n # if this is a method which belongs to the module\n if self is not None and self is module:\n signal.disconnect(obj)","def unregisterListener( self, listener ):\n # FIXME---! eventTypesToListeners!\n if listener in self.listeners:\n del self.listeners[ listener ]","def remove_callbacks(m_obj):\n cbs = oMa.MMessage.nodeCallbacks(m_obj)\n for cb in cbs:\n oMa.MMessage.removeCallback(cb)","def unregisterDisconnect(self, function):\n self._sig_disconnect.unsubscribe(function)","def remove_message_listener(self, callback_message):\n if callback_message in self._callback_message:\n self.callback_message.remove(callback_message)","def clear_message_listener(self):\n self.callback_message.clear()","def unregister_events( register, name, events ):\n\tgroup_name = '%(name)s_events' % locals()\n\n\tlog.info( 'Register\\'s events for %s.', name )\n\t_vim.command( 'augroup %(group_name)s' % locals() )\n\t_vim.command( 'au!' )\n\t_vim.command( 'augroup END' )\n\n\tfor e in events:\n\t\tevent, ftype, func, args = e\n\n\t\tfunc_id = '%s.%s.%s' % ( name, func.__module__, func.func_name )\n\t\tdel register[ func_id ]","def test_unsubscribe_any_listener(self):\n with self.assertRaises(AssertionError):\n EVENT_MANAGER.unsubscribe()","def unsubscribe(self):\n res = self._unsubscribe()\n if res is not None:\n self._subscribed = False\n return res","def test_unsubscribe_many_listeners(self):\n def listener():\n pass\n\n def listener1():\n pass\n\n def listener2():\n pass\n\n EVENT_MANAGER.subscribe('test_listeners', listener, listener1, listener2)\n EVENT_MANAGER.unsubscribe(listener, listener1, listener2)\n\n self.assertNotIn(listener, EVENT_MANAGER._listeners['test_listeners'])\n self.assertNotIn(listener1, EVENT_MANAGER._listeners['test_listeners'])\n self.assertNotIn(listener2, EVENT_MANAGER._listeners['test_listeners'])"],"string":"[\n \"def unsubscribe(self, callback: Callable) -> None:\\n self.callbacks.discard(callback)\",\n \"def unsubscribe(self, event_type: typing.Type[typing.Any], callback: CallbackT[typing.Any]) -> None:\",\n \"def unsubscribe_callback(self, callback, sensor):\\n if sensor in self._callbacks:\\n self._callbacks[sensor].remove(callback)\",\n \"def unregister(self, callback):\\n\\t\\tcallbacks = []\\n\\t\\tfor i in range(0, len(self.callbacks)):\\n\\t\\t\\tif self.callbacks[i][0] != callback:\\n\\t\\t\\t\\tcallbacks.append(self.callbacks[i])\\n\\t\\t\\t\\t\\n\\t\\tself.callbacks = callbacks\\n\\t\\tself.events[str(callback)] = []\",\n \"def unsubscribe(self, event_handler):\\n pass # pragma: no cover\",\n \"def unsubscribe(self, event, callback, args = None):\\n if {\\\"event\\\": event, \\\"callback\\\": callback, \\\"args\\\": args, }\\\\\\n in self.events:\\n self.events.remove({\\\"event\\\": event, \\\"callback\\\": callback,\\\\\\n \\\"args\\\": args, })\\n\\n return True\",\n \"def unsubscribe(receiver):\",\n \"def unsubscribe(receiver):\",\n \"def unsubscribe(receiver):\",\n \"def unsubscribe(receiver):\",\n \"def unsubscribe(receiver):\",\n \"def unsubscribe(self, name, callback_function):\\n # Remove the callback from _callbacks.\\n if self._callbacks.has_key(name):\\n if callback_function in self._callbacks[name]:\\n self._callbacks[name].remove(callback_function)\\n if len(self._callbacks[name]) == 0:\\n self._callbacks.pop(name)\\n else:\\n raise PresenceException('This function is not registered to receive callbacks.')\\n else:\\n raise PresenceException('Unknown service name. No callback handler exists.')\",\n \"def unsubscribeFromEvent(eventName,subscriber):\",\n \"def unregister(self, event, callback):\\n if self._events_tree[event].isListed(callback):\\n self._events_tree[event].remove(callback)\\n self._events_cbs[event][0] = self._events_tree.getCallbacksSequence()\\n else:\\n self._events_cbs[event][1].remove(callback)\",\n \"def remove_callback(event_name, callback):\\n _callbacks.get(event_name, set()).discard(callback)\",\n \"def unsubscribe(self, meta_type, callback):\\n try:\\n self.subscribers.get(meta_type, []).remove(callback)\\n except ValueError:\\n pass\\n try:\\n self.nackables.get(meta_type, []).remove(callback)\\n except ValueError:\\n pass\",\n \"def unsubscribe_all_known(self):\\n for key, value in self.__callbacks.items():\\n self.__logger.debug(f'unsubscribe from event {key}')\\n succ = self.__twitch.delete_eventsub_subscription(key)\\n if not succ:\\n self.__logger.warning(f'failed to unsubscribe from event {key}')\\n self.__callbacks.clear()\",\n \"def unregister(self, event_name, callback_func=None, identifier=None):\\n if callback_func:\\n self.events[event_name].remove(callback_func)\\n else:\\n del self.events[event_name]\",\n \"def unsubscribe(self, event_type, func):\\n if func in self.event_subscribers[event_type]:\\n kwargs = {event_type: func}\\n self.unbind(**kwargs)\\n self.event_subscribers[event_type].remove(func)\",\n \"def unsubscribe(observer):\",\n \"def unsubscribe(observer):\",\n \"def unregister_handler(self, event_type, callback):\\n\\n if event_type not in self._event_handlers:\\n return\\n if callback not in self._event_handlers[event_type]:\\n return\\n\\n self._event_handlers[event_type].remove(callback)\\n\\n if not self._event_handlers[event_type]:\\n del self._event_handlers[event_type]\",\n \"def subscribe_off(self, callback: callable):\\n topic = f\\\"{self._subscriber_topic}_off\\\"\\n subscribe_topic(callback, topic)\",\n \"def deregister(self):\\n self.callback = None\",\n \"def remove_callback(self, callback):\\n if callback in self._async_callbacks:\\n self._async_callbacks.remove(callback)\",\n \"def unsubscribe(self):\\r\\n self._unregister()\",\n \"def unsubscribe(self):\\n pass # pragma: no cover\",\n \"def unregister_signals(self):\\n for _, callback in self.signal_callbacks:\\n Signal.unsubscribe(self, callback)\",\n \"def unregister(self, signal_id, callback):\\n # if the callback was registered the remove it \\n if signal_id in self.registered_callbacks:\\n self.registered_callbacks[signal_id].remove(callback)\",\n \"def subscribe_off(self, callback: callable):\\n subscribe_topic(callback, self._off_subscriber_topic)\",\n \"def remove_callback(self, callback):\\n if callback in self._callbacks:\\n self._callbacks.remove(callback)\",\n \"def remove_notify_handler(self, callback: NotifyHandler) -> None:\\n self._notify_handlers.remove(callback)\",\n \"def unregister_callback(self, name):\\n self._callbacks.remove(name)\\n del self._cb_dict[name]\\n\\n self.logger.debug('Callback unregistered: %s' % name)\",\n \"def remove_watch(callback: Callable[[Event], None]) -> None:\\n if callback not in _event_watch_handles:\\n warnings.warn(f\\\"{callback} is not an active event watcher, nothing was removed.\\\", RuntimeWarning)\\n return\\n handle = _event_watch_handles[callback]\\n lib.SDL_DelEventWatch(lib._sdl_event_watcher, handle)\\n del _event_watch_handles[callback]\",\n \"def off(self, event_name, callback=None):\\n if callback:\\n self.factory.off(event_name, callback)\\n else:\\n self.factory.remove_all_listeners(event_name)\",\n \"def unlisten(obj, name, func):\\n _signals(obj, name).remove(func)\",\n \"def _unsubscribe(self, signal):\\n while signal in self._downstream:\\n self._downstream.remove(signal)\\n while signal in self._downstream_reconnect:\\n self._downstream_reconnect.remove(signal)\",\n \"def remove_callback(self, callback: Callback):\\n self._callbacks.remove(callback)\\n self._stage.remove_callback(callback)\",\n \"def unreg_event_handler(self, callback_func, userData):\\n\\t\\tcall_sdk_function('PrlSrv_UnregEventHandler', self.handle, callback_func, userData)\",\n \"def remove_stopcallback(self, stopcallback):\\n self.stopcallbacks.discard(stopcallback)\",\n \"def stopCallback (self):\\n GPIO.remove_event_detect (self.IRQ_PIN)\\n self.hasCallback = False\",\n \"def unsubscribe(self, callback_id):\\n request = self.get_active_subscription(callback_id)\\n request['mode'] = 'unsubscribe'\\n self.subscribe_impl(callback_id, **request)\",\n \"def remove_on_stop_callback(self, callback):\\n self.__condition.acquire()\\n try:\\n if self.__is_running:\\n self.__on_stop_callbacks.remove(callback)\\n finally:\\n self.__condition.release()\",\n \"def unsubscribe(self, channel, update_handler=None):\\n pass\",\n \"def deregister(self, event_type, callback, details_filter=None):\\n with self._lock:\\n listeners = self._topics.get(event_type, [])\\n for i, listener in enumerate(listeners):\\n if listener.is_equivalent(callback,\\n details_filter=details_filter):\\n listeners.pop(i)\\n return True\\n return False\",\n \"def unregister( key ):\\n global callbacks\\n del callbacks[ key ]\",\n \"def _onUnsubscribe(self, client:mqtt.Client, userdata:Any, mid:int) -> None:\\n\\t\\t# TODO doc, error check when not connected, not subscribed\\n\\t\\tfor t in self.subscribedTopics.values():\\n\\t\\t\\tif t.mid == mid:\\n\\t\\t\\t\\tdel self.subscribedTopics[t.topic]\\n\\t\\t\\t\\tself.messageHandler and self.messageHandler.onUnsubscribed(self, t.topic)\\n\\t\\t\\t\\tbreak\",\n \"def destroy_event(self, event_type):\\n for func in self.event_subscribers[event_type][:]:\\n self.unsubscribe(event_type, func)\\n self.unregister_event_types(event_type)\",\n \"def UnsubscribeFromRedeemingQueueUpdatedEvent(self, callBackFunction):\\n self.redeemingQueueUpdated.disconnect(callBackFunction)\",\n \"def unregister_aggregate_handler(self, event_name, callback):\\n\\n raise NotImplementedError()\",\n \"def unregisterEvent(eventName, publisher):\",\n \"def unsubscribe_all(self):\\n ids = []\\n repeat = True\\n cursor = None\\n # get all ids\\n while repeat:\\n ret = self.__twitch.get_eventsub_subscriptions(after=cursor)\\n for d in ret.get('data', []):\\n ids.append(d.get('id'))\\n cursor = ret.get('pagination', {}).get('cursor')\\n repeat = cursor is not None\\n for _id in ids:\\n succ = self.__twitch.delete_eventsub_subscription(_id)\\n if not succ:\\n self.__logger.warning(f'failed to unsubscribe from event {_id}')\\n self.__callbacks.clear()\",\n \"def unregisterStatusListener(self, cb):\\r\\n self._statusListener.discard(cb)\",\n \"async def unlistened(self, value=None):\\n pass\",\n \"def unsubscribe(cls,sender,receiver):\\n cls._unsubscribe(id(sender),receiver)\",\n \"def unregister_standard(self, event_name, callback):\\n\\n raise NotImplementedError()\",\n \"def unregister(self, listener):\\n for event_type in self.listeners:\\n for event_listeners in self.listeners[event_type]:\\n if event_listeners:\\n try:\\n event_listeners.remove(listener)\\n logger.debug('Unregistered listener for event type \\\"%s\\\"', hr_event_type(event_type))\\n except ValueError:\\n pass\",\n \"def _unregisterConnect(self, function):\\n self._sig_connect.unsubscribe(function)\",\n \"def unsubscribe(self, destination, *args, **kwargs):\",\n \"def unregister(self,listener):\\n\\t\\tif listener in self.cartesianListeners:\\n\\t\\t\\tself.cartesianListeners.remove(listener)\\n\\t\\tif listener in self.polarListeners:\\n\\t\\t\\tself.polarListeners.remove(listener)\",\n \"def remove_callback(self, chain):\\n for reactor in self._reactors:\\n reactor.remove_callback(chain)\",\n \"def unreg_event_handler(self, callback_func, userData):\\n\\t\\tcall_sdk_function('PrlVm_UnregEventHandler', self.handle, callback_func, userData)\",\n \"def on_del(self, callback):\\n self._del_callback = callback if callable(callback) else _void\",\n \"def on_del(self, callback):\\n self._del_callback = callback if callable(callback) else _void\",\n \"def unsubscribe(self, observer):\\n self._observers.remove(observer)\",\n \"def UnsubscribeFromAurumBalanceChanged(self, callBackFunction):\\n self.accountAurumBalanceChanged.disconnect(callBackFunction)\",\n \"def remove_delegate(self, callback):\\n\\n if not callback in self._delegate_methods:\\n return\\n\\n self._delegate_methods.remove(callback)\",\n \"def disconnect(self, callback):\\n if not callable(callback):\\n raise TypeError('Cannot disconnect a non-callable from a Signal')\\n conn = self._make_connection(callback)\\n self._connection_dead(conn)\",\n \"def unsubscribe(self, observer, name=None):\\n if name is None:\\n name = 'default'\\n if observer in self._observers:\\n del self._observers[observer][name]\",\n \"def unregisterUnready(self, function):\\n self._sig_unready.unsubscribe(function)\",\n \"def dontNotifyOnDeath(self, cb):\\r\\n try:\\r\\n self.__cbs.remove(cb)\\r\\n except AttributeError:\\r\\n pass\",\n \"def disconnect(self, handler, event=None):\\n if event:\\n self.event_handlers.remove(handler)\\n else:\\n for event in self.event_handlers:\\n if hasattr(handler, event):\\n self.disconnect(getattr(handler, event), event)\",\n \"def remove_callback(self, chain):\",\n \"def remove_callback(self, fn):\\n self._callbacks.remove(fn)\\n return self\",\n \"def test_unsubscribe_one_listener(self):\\n def listener():\\n pass\\n\\n EVENT_MANAGER.subscribe('test_listener', listener)\\n EVENT_MANAGER.unsubscribe(listener)\\n self.assertNotIn(listener, EVENT_MANAGER._listeners['test_listener'])\",\n \"def dontNotifyOnDeath(self, cb):\\r\\n try:\\r\\n self._cbs.remove(cb)\\r\\n except AttributeError:\\r\\n pass\",\n \"def dontNotifyOnDeath(self, cb):\\r\\n try:\\r\\n self._cbs.remove(cb)\\r\\n except AttributeError:\\r\\n pass\",\n \"def unsubscribe(self, inst):\\r\\n if inst in self._subscribers:\\r\\n self._subscribers.remove(inst)\\r\\n vprint(\\\"{} is unsubscribed from {}\\\".format(inst.name, self.name))\",\n \"def unsubscribe(self, instrument_ids, exchange_id=b''):\\n pass\",\n \"def unregisterValueChanged(self, function):\\n self._sig_value_changed.unsubscribe(function)\",\n \"def unregister_url_callback(self, pattern, callback):\\n if isinstance(pattern, str):\\n pattern = re.compile(pattern)\\n\\n try:\\n del self._url_callbacks[pattern]\\n except KeyError:\\n pass\",\n \"def remove_change_callback(self, callback_function):\\n if callback_function in self.changeCallbacks:\\n self.changeCallbacks.remove(callback_function)\",\n \"def unregisterRemoved(self, function):\\n self._sig_removed.unsubscribe(function)\",\n \"def unsubscribe(self, subject):\\n pass\",\n \"def test_unsubscribe(self):\\n self.service.clientConnected()\\n\\n unsubscribers = []\\n self.service.subscribe(u'url', 1\\n ).addCallback(lambda fn: unsubscribers.append(fn))\\n self.service.subscribe(u'url', 2\\n ).addCallback(lambda fn: unsubscribers.append(fn))\\n\\n pubsubClient = self.service.pubsubClient\\n self.assertIn(u'url', pubsubClient.subscriptions)\\n\\n unsubscribers.pop()()\\n self.service.unsubscribe(u'url')\\n self.assertIn(u'url', pubsubClient.subscriptions)\\n\\n unsubscribers.pop()()\\n self.service.unsubscribe(u'url')\\n self.assertNotIn(u'url', pubsubClient.subscriptions)\",\n \"def unsubscribe(self, instrument_ids, exchange_id=b''):\\n self.invoke_log('on_invoke_unsubscribe', instrument_ids=instrument_ids, exchange_id=exchange_id)\\n if self._xapi:\\n func = self._xapi.X_Unsubscribe\\n func.restype = None\\n func.argtypes = [c_void_p, c_void_p, c_char_p, c_char_p]\\n func(self.p_fun, self.p_api, c_char_p(\\n b','.join(instrument_ids) if isinstance(instrument_ids, list) else instrument_ids),\\n c_char_p(exchange_id))\",\n \"def unsubscribe(self, namespace, unsub_strings=None):\\n req = JSONRPCRequest('unsubscribe', [namespace, unsub_strings])\\n result = yield self._send(req)\\n self._cache_jsonrpc_request(req)\\n raise tornado.gen.Return(result)\",\n \"def disconnect(\\n cls,\\n on_start=None,\\n on_resume=None,\\n on_pause=None,\\n on_stop=None,\\n on_save=None,\\n on_reset=None,\\n ):\\n try:\\n cls.start_callback.remove(on_start)\\n except ValueError:\\n pass\\n\\n try:\\n cls.resume_callback.remove(on_resume)\\n except ValueError:\\n pass\\n\\n try:\\n cls.pause_callback.remove(on_pause)\\n except ValueError:\\n pass\\n\\n try:\\n cls.stop_callback.remove(on_stop)\\n except ValueError:\\n pass\\n\\n try:\\n cls.save_callback.remove(on_save)\\n except ValueError:\\n pass\\n\\n try:\\n cls.reset_callback.remove(on_reset)\\n except ValueError:\\n pass\",\n \"def deleteCallbacks(self):\\n if self.callbacks:\\n for cb in self.callbacks:\\n OpenMaya.MMessage.removeCallback(cb)\\n self.callbacks.remove(cb)\",\n \"def unregisterRemove(self, function):\\n self._sig_remove.unsubscribe(function)\",\n \"def unsubscribe_from_all(module):\\n for name, signal in _signals.items():\\n for receiver in list(signal.receivers.values()):\\n obj = receiver()\\n if obj is not None:\\n if inspect.ismethod(obj):\\n # find the object to which a method is bound\\n self = None\\n for name, value in inspect.getmembers(obj):\\n if name == '__self__':\\n self = value\\n # if this is a method which belongs to the module\\n if self is not None and self is module:\\n signal.disconnect(obj)\",\n \"def unregisterListener( self, listener ):\\n # FIXME---! eventTypesToListeners!\\n if listener in self.listeners:\\n del self.listeners[ listener ]\",\n \"def remove_callbacks(m_obj):\\n cbs = oMa.MMessage.nodeCallbacks(m_obj)\\n for cb in cbs:\\n oMa.MMessage.removeCallback(cb)\",\n \"def unregisterDisconnect(self, function):\\n self._sig_disconnect.unsubscribe(function)\",\n \"def remove_message_listener(self, callback_message):\\n if callback_message in self._callback_message:\\n self.callback_message.remove(callback_message)\",\n \"def clear_message_listener(self):\\n self.callback_message.clear()\",\n \"def unregister_events( register, name, events ):\\n\\tgroup_name = '%(name)s_events' % locals()\\n\\n\\tlog.info( 'Register\\\\'s events for %s.', name )\\n\\t_vim.command( 'augroup %(group_name)s' % locals() )\\n\\t_vim.command( 'au!' )\\n\\t_vim.command( 'augroup END' )\\n\\n\\tfor e in events:\\n\\t\\tevent, ftype, func, args = e\\n\\n\\t\\tfunc_id = '%s.%s.%s' % ( name, func.__module__, func.func_name )\\n\\t\\tdel register[ func_id ]\",\n \"def test_unsubscribe_any_listener(self):\\n with self.assertRaises(AssertionError):\\n EVENT_MANAGER.unsubscribe()\",\n \"def unsubscribe(self):\\n res = self._unsubscribe()\\n if res is not None:\\n self._subscribed = False\\n return res\",\n \"def test_unsubscribe_many_listeners(self):\\n def listener():\\n pass\\n\\n def listener1():\\n pass\\n\\n def listener2():\\n pass\\n\\n EVENT_MANAGER.subscribe('test_listeners', listener, listener1, listener2)\\n EVENT_MANAGER.unsubscribe(listener, listener1, listener2)\\n\\n self.assertNotIn(listener, EVENT_MANAGER._listeners['test_listeners'])\\n self.assertNotIn(listener1, EVENT_MANAGER._listeners['test_listeners'])\\n self.assertNotIn(listener2, EVENT_MANAGER._listeners['test_listeners'])\"\n]","isConversational":false},"negative_scores":{"kind":"list like","value":["0.84749424","0.8190403","0.79367375","0.7856983","0.7775709","0.7710769","0.7495644","0.7495644","0.7495644","0.7495644","0.7495644","0.74490726","0.74136734","0.73761433","0.72853684","0.72737384","0.72261065","0.72020453","0.7193984","0.71859956","0.71859956","0.7172428","0.7135467","0.71341306","0.7131223","0.70963967","0.70826983","0.70612276","0.7038875","0.70177114","0.69910765","0.69844323","0.6957236","0.68761295","0.6804721","0.6792163","0.67827386","0.67636776","0.6692595","0.6686539","0.66651136","0.66082376","0.65893185","0.6569734","0.65590644","0.6547351","0.6537352","0.6515785","0.6489424","0.6485802","0.64689875","0.6457208","0.6430993","0.6408444","0.6407529","0.6404105","0.64003193","0.6381887","0.63610107","0.633663","0.63251346","0.63136786","0.6311706","0.6311706","0.6306277","0.63019276","0.62847257","0.62637055","0.62631565","0.6224113","0.6223328","0.62088525","0.62038594","0.6196142","0.61948985","0.61816305","0.61816305","0.61783373","0.6158971","0.61585873","0.61395997","0.6130679","0.6130112","0.6101564","0.60976774","0.60719657","0.6069789","0.6027825","0.6011042","0.600976","0.60054314","0.5974822","0.5974283","0.5940549","0.59334767","0.5907541","0.5901737","0.58987284","0.58937013","0.58850986"],"string":"[\n \"0.84749424\",\n \"0.8190403\",\n \"0.79367375\",\n \"0.7856983\",\n \"0.7775709\",\n \"0.7710769\",\n \"0.7495644\",\n \"0.7495644\",\n \"0.7495644\",\n \"0.7495644\",\n \"0.7495644\",\n \"0.74490726\",\n \"0.74136734\",\n \"0.73761433\",\n \"0.72853684\",\n \"0.72737384\",\n \"0.72261065\",\n \"0.72020453\",\n \"0.7193984\",\n \"0.71859956\",\n \"0.71859956\",\n \"0.7172428\",\n \"0.7135467\",\n \"0.71341306\",\n \"0.7131223\",\n \"0.70963967\",\n \"0.70826983\",\n \"0.70612276\",\n \"0.7038875\",\n \"0.70177114\",\n \"0.69910765\",\n \"0.69844323\",\n \"0.6957236\",\n \"0.68761295\",\n \"0.6804721\",\n \"0.6792163\",\n \"0.67827386\",\n \"0.67636776\",\n \"0.6692595\",\n \"0.6686539\",\n \"0.66651136\",\n \"0.66082376\",\n \"0.65893185\",\n \"0.6569734\",\n \"0.65590644\",\n \"0.6547351\",\n \"0.6537352\",\n \"0.6515785\",\n \"0.6489424\",\n \"0.6485802\",\n \"0.64689875\",\n \"0.6457208\",\n \"0.6430993\",\n \"0.6408444\",\n \"0.6407529\",\n \"0.6404105\",\n \"0.64003193\",\n \"0.6381887\",\n \"0.63610107\",\n \"0.633663\",\n \"0.63251346\",\n \"0.63136786\",\n \"0.6311706\",\n \"0.6311706\",\n \"0.6306277\",\n \"0.63019276\",\n \"0.62847257\",\n \"0.62637055\",\n \"0.62631565\",\n \"0.6224113\",\n \"0.6223328\",\n \"0.62088525\",\n \"0.62038594\",\n \"0.6196142\",\n \"0.61948985\",\n \"0.61816305\",\n \"0.61816305\",\n \"0.61783373\",\n \"0.6158971\",\n \"0.61585873\",\n \"0.61395997\",\n \"0.6130679\",\n \"0.6130112\",\n \"0.6101564\",\n \"0.60976774\",\n \"0.60719657\",\n \"0.6069789\",\n \"0.6027825\",\n \"0.6011042\",\n \"0.600976\",\n \"0.60054314\",\n \"0.5974822\",\n \"0.5974283\",\n \"0.5940549\",\n \"0.59334767\",\n \"0.5907541\",\n \"0.5901737\",\n \"0.58987284\",\n \"0.58937013\",\n \"0.58850986\"\n]","isConversational":false},"document_score":{"kind":"string","value":"0.85581386"},"document_rank":{"kind":"string","value":"0"}}}],"truncated":false,"partial":true},"paginationData":{"pageIndex":165,"numItemsPerPage":100,"numTotalItems":95772,"offset":16500,"length":100}},"jwt":"eyJhbGciOiJFZERTQSIsImtpZCI6IjVHZDBvd0g5MTM2eDZjc1FvbE1zcktNWUZoRVFoUm5PVVVybEpjOUhaUEEifQ.eyJyZWFkIjp0cnVlLCJwZXJtaXNzaW9ucyI6eyJyZXBvLmNvbnRlbnQucmVhZCI6dHJ1ZX0sImlhdCI6MTc4NjE3NTAzNywianRpIjoiM2I5OWM1MGUtODcyMS00MGQ3LWEwOGQtM2U4MjEzZDcyZDM2Iiwic3ViIjoiL2RhdGFzZXRzL25vbWljLWFpL2Nvcm5zdGFjay1weXRob24tdjEiLCJleHAiOjE3ODYxNzg2MzcsImlzcyI6Imh0dHBzOi8vaHVnZ2luZ2ZhY2UuY28ifQ.gNUHEMJiNdtCUUTTql3bSJ1XGOVt1t3OLdt42bn-tz4EQxxMR8amkrWlqXBUp-5-TY_clDd_UgtC1IVDZU7uDQ","displayUrls":true,"splitSizeSummaries":[{"config":"default","split":"train","numRows":95772,"numBytesParquet":1928375891}]},"discussionsStats":{"closed":1,"open":1,"total":2},"fullWidth":true,"hasGatedAccess":true,"hasFullAccess":true,"isEmbedded":false,"savedQueries":{"community":[],"user":[]}}">
query stringlengths 9 3.4k | document stringlengths 9 87.4k | metadata dict | negatives listlengths 4 101 | negative_scores listlengths 4 101 | document_score stringlengths 3 10 | document_rank stringclasses 102
values |
|---|---|---|---|---|---|---|
Load all cells from a GDSII stream file in binary format. | def get_binary_cells(infile):
close = True
if hasattr(infile, "__fspath__"):
infile = open(infile.__fspath__(), "rb")
elif isinstance(infile, (basestring, Path)):
infile = open(infile, "rb")
else:
close = False
cells = {}
name = None
cell_data = None
for rec_type,... | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def load(datastream):",
"def load_rbc( fname, skiprows, nx, ny ):\n C = numpy.loadtxt( fname, skiprows=skiprows ) \n cell_frames = [ C[i].reshape(( nx,ny )) for i in range( 5000-skiprows ) ]\n return cell_frames",
"def load_binary_data(self, encoding='utf8'):\n\n # TODO use smart_open again ... | [
"0.59665906",
"0.5666531",
"0.5652383",
"0.56487894",
"0.5564757",
"0.5411691",
"0.53955466",
"0.5385155",
"0.538372",
"0.53774667",
"0.52971804",
"0.5276019",
"0.52390313",
"0.52172196",
"0.5202131",
"0.51881504",
"0.5182322",
"0.5163801",
"0.5156424",
"0.5144767",
"0.513413... | 0.61892736 | 0 |
Gets the created_on of this SubscriptionProductRetirement. The date and time when the object was created. | def created_on(self):
return self._created_on | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def created_date(self):\n return self._created_date",
"def created_date(self):\n return self._created_date",
"def date_created(self):\n return self._date_created",
"def date_created(self):\n return self._date_created",
"def date_created(self):\n return self._date_created"... | [
"0.7168697",
"0.7168697",
"0.7047112",
"0.7047112",
"0.7047112",
"0.6913553",
"0.6905717",
"0.672921",
"0.66820747",
"0.6590892",
"0.65313655",
"0.64979154",
"0.64952743",
"0.6466305",
"0.6449166",
"0.6449166",
"0.6449166",
"0.64408654",
"0.6436507",
"0.64327043",
"0.64327043... | 0.7107456 | 5 |
Sets the created_on of this SubscriptionProductRetirement. The date and time when the object was created. | def created_on(self, created_on):
self._created_on = created_on | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def created_date(self, created_date):\n self._created_date = created_date",
"def created_date(self, created_date):\n\n self._created_date = created_date",
"def created_date(self, created_date):\n\n self._created_date = created_date",
"def created_date(self, created_date):\n\n self... | [
"0.61930114",
"0.61522496",
"0.61522496",
"0.61522496",
"0.61522496",
"0.61522496",
"0.60280794",
"0.60078293",
"0.60078293",
"0.59660447",
"0.59558755",
"0.59558755",
"0.59558755",
"0.58354986",
"0.583224",
"0.58256143",
"0.58256143",
"0.5760754",
"0.5735765",
"0.56967336",
... | 0.6739802 | 6 |
Gets the id of this SubscriptionProductRetirement. A unique identifier for the object. | def id(self):
return self._id | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def product_id(self):\n return self._product_id",
"def product_id(self):\n return self._product_id",
"def product_id(self):\n return self._product_id",
"def product_id(self):\n return self._product_id",
"def product_id(self) -> pulumi.Output[str]:\n return pulumi.get(self... | [
"0.7453236",
"0.7453236",
"0.7453236",
"0.7453236",
"0.70733815",
"0.6746917",
"0.6697227",
"0.6697227",
"0.66862226",
"0.66862226",
"0.66862226",
"0.66862226",
"0.66862226",
"0.66862226",
"0.6684057",
"0.66782755",
"0.66718966",
"0.66718966",
"0.66718966",
"0.66718966",
"0.6... | 0.0 | -1 |
Sets the id of this SubscriptionProductRetirement. A unique identifier for the object. | def id(self, id):
self._id = id | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def product_id(self, product_id):\n self._product_id = product_id",
"def product_id(self, product_id):\n\n self._product_id = product_id",
"def product_id(self, product_id):\n\n self._product_id = product_id",
"def set_id(self, id):\n self.__id = id",
"def set_id(self, id_):\n\n... | [
"0.6687188",
"0.65710616",
"0.65710616",
"0.65566206",
"0.65250146",
"0.64017624",
"0.64017624",
"0.64017624",
"0.64017624",
"0.64017624",
"0.63562167",
"0.63235307",
"0.63213336",
"0.63213336",
"0.63213336",
"0.63213336",
"0.63213336",
"0.63213336",
"0.63213336",
"0.63213336",... | 0.0 | -1 |
Gets the linked_space_id of this SubscriptionProductRetirement. The ID of the space this object belongs to. | def linked_space_id(self):
return self._linked_space_id | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def get_subscription_id(self):\n return self.instance_metadata.subscription_id",
"def product_id(self):\n return self._product_id",
"def product_id(self):\n return self._product_id",
"def product_id(self):\n return self._product_id",
"def product_id(self):\n return self._... | [
"0.5639911",
"0.5487876",
"0.5487876",
"0.5487876",
"0.5487876",
"0.53018355",
"0.52775943",
"0.52646273",
"0.51881564",
"0.5121563",
"0.5112025",
"0.5101079",
"0.5073609",
"0.5073609",
"0.5073609",
"0.5073609",
"0.5073609",
"0.5073609",
"0.5060274",
"0.5060274",
"0.50597024"... | 0.7217349 | 2 |
Sets the linked_space_id of this SubscriptionProductRetirement. The ID of the space this object belongs to. | def linked_space_id(self, linked_space_id):
self._linked_space_id = linked_space_id | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def link_document_workspace_id(self, link_document_workspace_id):\n\n self._link_document_workspace_id = link_document_workspace_id",
"def link_id(self, link_id):\n\n self._link_id = link_id",
"def linked_space_id(self):\n return self._linked_space_id",
"def linked_space_id(self):\n ... | [
"0.55407226",
"0.55088866",
"0.5413146",
"0.5413146",
"0.5413146",
"0.5327779",
"0.5327779",
"0.5327779",
"0.51047593",
"0.49513242",
"0.49150938",
"0.49150938",
"0.48627087",
"0.4772015",
"0.47145233",
"0.47094992",
"0.46938464",
"0.46066585",
"0.46059442",
"0.45948213",
"0.... | 0.72988594 | 2 |
Gets the product of this SubscriptionProductRetirement. | def product(self):
return self._product | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def getProduct(self, *args):\n return _libsbml.Reaction_getProduct(self, *args)",
"def get_card_product(self):\n\n return self.card_product",
"def product(self, product_id):\r\n return products.Product(self, product_id)",
"def get(self, product_id):\n\n return product.get_single_p... | [
"0.71919554",
"0.7168041",
"0.70292336",
"0.6978669",
"0.69453955",
"0.6790158",
"0.65579",
"0.6556982",
"0.6439483",
"0.642651",
"0.642651",
"0.642651",
"0.642651",
"0.64097875",
"0.6401133",
"0.6386566",
"0.6296203",
"0.629263",
"0.62489635",
"0.6159131",
"0.6152622",
"0.... | 0.73504794 | 2 |
Sets the product of this SubscriptionProductRetirement. | def product(self, product):
self._product = product | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def product(self, product):\n self._product = product",
"def product(self, product):\n if product is None:\n raise ValueError(\"Invalid value for `product`, must not be `None`\") # noqa: E501\n\n self._product = product",
"def set_product(self, product):\n self.single_se... | [
"0.77392894",
"0.7601882",
"0.7119301",
"0.7109555",
"0.69029176",
"0.6886196",
"0.6886196",
"0.6858822",
"0.6649319",
"0.64404374",
"0.6351997",
"0.6307819",
"0.62698454",
"0.601716",
"0.6005919",
"0.59450114",
"0.59232247",
"0.5884955",
"0.58693993",
"0.5860039",
"0.5857742... | 0.78371936 | 0 |
Gets the respect_terminiation_periods_enabled of this SubscriptionProductRetirement. | def respect_terminiation_periods_enabled(self):
return self._respect_terminiation_periods_enabled | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def respect_terminiation_periods_enabled(self, respect_terminiation_periods_enabled):\n\n self._respect_terminiation_periods_enabled = respect_terminiation_periods_enabled",
"def evaluation_periods(self) -> Optional[pulumi.Input[int]]:\n return pulumi.get(self, \"evaluation_periods\")",
"def eval... | [
"0.74990064",
"0.59558636",
"0.59558636",
"0.59558636",
"0.59558636",
"0.59558636",
"0.59558636",
"0.59558636",
"0.59558636",
"0.59558636",
"0.59558636",
"0.59558636",
"0.59558636",
"0.52868",
"0.52440816",
"0.51808107",
"0.51157266",
"0.51113236",
"0.50006104",
"0.49916717",
... | 0.7897476 | 0 |
Sets the respect_terminiation_periods_enabled of this SubscriptionProductRetirement. | def respect_terminiation_periods_enabled(self, respect_terminiation_periods_enabled):
self._respect_terminiation_periods_enabled = respect_terminiation_periods_enabled | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def respect_terminiation_periods_enabled(self):\n return self._respect_terminiation_periods_enabled",
"def set_atr_periods(self, periods: int = 100):\n h, l, c_prev = self.data.High, self.data.Low, pd.Series(self.data.Close).shift(1)\n tr = np.max([h - l, (c_prev - h).abs(), (c_prev - l).abs... | [
"0.73718745",
"0.45488954",
"0.44557628",
"0.44557628",
"0.44557628",
"0.44557628",
"0.44557628",
"0.44557628",
"0.44557628",
"0.44557628",
"0.44557628",
"0.44557628",
"0.44557628",
"0.44557628",
"0.42839718",
"0.4270166",
"0.40364996",
"0.4027975",
"0.39874214",
"0.39431196",
... | 0.8498492 | 0 |
Gets the target_product of this SubscriptionProductRetirement. | def target_product(self):
return self._target_product | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def target_for_product(self, product):\n for target, products in self._products_by_target.items():\n if product in products:\n return target\n return None",
"def getTarget(self):\n return self._target",
"def getTarget(self):\n\n return self._target",
"def target_resource(self)... | [
"0.679874",
"0.65475947",
"0.65354234",
"0.6525121",
"0.6492427",
"0.6492427",
"0.6492427",
"0.638465",
"0.6314479",
"0.616897",
"0.61486644",
"0.61486644",
"0.61486644",
"0.61486644",
"0.6129035",
"0.60792124",
"0.6019437",
"0.6019437",
"0.6019437",
"0.6019437",
"0.60076684"... | 0.8075166 | 0 |
Sets the target_product of this SubscriptionProductRetirement. | def target_product(self, target_product):
self._target_product = target_product | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def target_resource(self, target_resource):\n self._target_resource = target_resource",
"def product(self, product):\n\n self._product = product",
"def product(self, product):\n\n self._product = product",
"def target_product(self):\n return self._target_product",
"def product(s... | [
"0.6490736",
"0.6366156",
"0.6366156",
"0.633028",
"0.62527555",
"0.6134227",
"0.6102009",
"0.59970754",
"0.59970754",
"0.59861636",
"0.5946594",
"0.5928907",
"0.58098286",
"0.57920307",
"0.5782366",
"0.57533026",
"0.57472503",
"0.56921405",
"0.56693083",
"0.56693083",
"0.566... | 0.84785706 | 0 |
Gets the version of this SubscriptionProductRetirement. The version is used for optimistic locking and incremented whenever the object is updated. | def version(self):
return self._version | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def product_version(self):\n return self._product_version",
"def get_product_version(self):\n\t\treturn call_sdk_function('PrlSrvInfo_GetProductVersion', self.handle)",
"def get_product_version(self):\n return self.get_attr('product_version')",
"def get_product_version(self):\n\t\treturn call_s... | [
"0.7609071",
"0.7556369",
"0.7447159",
"0.7211711",
"0.7078787",
"0.7065332",
"0.7065332",
"0.6965987",
"0.6928433",
"0.6927428",
"0.69248474",
"0.68874663",
"0.6880073",
"0.6839752",
"0.68232965",
"0.67877114",
"0.67861766",
"0.67816305",
"0.67618465",
"0.6750636",
"0.673643... | 0.67298514 | 30 |
Sets the version of this SubscriptionProductRetirement. The version is used for optimistic locking and incremented whenever the object is updated. | def version(self, version):
self._version = version | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def product_version(self, product_version):\n\n self._product_version = product_version",
"def version(self, version):\n \n self._version = version",
"def version(self, version):\n self._version = version",
"def version(self, version):\n self._version = version",
"def ver... | [
"0.7180803",
"0.6708293",
"0.6647392",
"0.6647392",
"0.6574128",
"0.6495684",
"0.64354223",
"0.64354223",
"0.6300998",
"0.62922347",
"0.6192053",
"0.6126061",
"0.60471845",
"0.60471845",
"0.60471845",
"0.60225743",
"0.5944241",
"0.59408695",
"0.59389913",
"0.5929401",
"0.5891... | 0.6649448 | 15 |
Execute each job as a multiprocessing.Process as each one should submit command by command to the global executor class | def run(self, **kwargs):
for repl in self.replicas:
self.log.info('-'*50)
self.log.info("Running %s analysis..."%repl.name)
self.__submitReplica(repl, **kwargs)
self.log.info('-'*50) | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def run_commands(self):\n processes = []\n\n i = 0\n ## get list of commands\n commands = self.get_commands()\n cnum = multiprocessing.cpu_count()\n\n while len(commands)>0:\n while len(processes)<cnum-1:\n c = commands.pop()\n i+=1... | [
"0.7240149",
"0.72245026",
"0.6674598",
"0.6623324",
"0.6486739",
"0.63962394",
"0.63046163",
"0.63006055",
"0.6284784",
"0.621504",
"0.6210209",
"0.62053984",
"0.61710286",
"0.6170014",
"0.61691916",
"0.61599463",
"0.60844254",
"0.6076164",
"0.60661584",
"0.6051776",
"0.6045... | 0.0 | -1 |
! Makes recursively all the directory in input path | def safe_mkdirs(path):
if not os.path.exists(path):
try:
os.makedirs(path)
except Exception as e:
raise IOError(
("Failed to create recursive directories: "
" {}".format(path)
)
) | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def create_path(self, path):\n path_list = path.split(\"/\")\n done_path = self.parent_folder + \"/\"\n\n for directory in path_list:\n try:\n os.mkdir(done_path + directory + \"/\")\n except FileExistsError:\n done_path += directory + \"/\""... | [
"0.6848508",
"0.6776255",
"0.6751329",
"0.67272055",
"0.66558444",
"0.66327935",
"0.6594902",
"0.64868104",
"0.64620495",
"0.64169073",
"0.6391926",
"0.63862544",
"0.6384313",
"0.63800734",
"0.6379803",
"0.63403",
"0.6321055",
"0.6309966",
"0.63069654",
"0.6300319",
"0.628608... | 0.58037275 | 67 |
! Command line parser for Utterance level classification Leave one speaker out schema pipeline | def get_args():
parser = argparse.ArgumentParser(
description='Utterance level classification Leave one '
'speaker out schema pipeline' )
parser.add_argument('-i', '--input_features_paths', nargs='+',
help='File paths of the features you want to '
... | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def main():\n parser = argparse.ArgumentParser()\n subparsers = parser.add_subparsers(dest='mode')\n\n # Add sub-parser for feature extraction\n parser_extract = subparsers.add_parser('extract')\n parser_extract.add_argument('dataset',\n choices=['training', 'validatio... | [
"0.65690255",
"0.6566645",
"0.6457948",
"0.6415648",
"0.62353814",
"0.62087375",
"0.6207265",
"0.617082",
"0.61693275",
"0.609565",
"0.60759753",
"0.60393417",
"0.60188335",
"0.5964898",
"0.591729",
"0.5908559",
"0.5883085",
"0.5858392",
"0.585827",
"0.5837335",
"0.5829505",
... | 0.0 | -1 |
Creates a module for converting to two theta | def pixels_two_theta_module(id=None, datatype=None, action=None,
version='0.0', fields=[], xtype=None, **kwargs):
icon = {
'URI': config.IMAGES + config.ANDR_FOLDER + "twotheta.png",
'image': config.IMAGES + config.ANDR_FOLDER + "twotheta_image.png",
'terminals': {
... | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def theta():\n pass",
"def theta(a, b):\n \n \n def norm_vec(x):\n norm_out = sqrt(dot(x, x))\n return norm_out\n \n theta = acos(dot(a, b) / (norm_vec(a) * norm_vec(b))) * 180 / pi\n \n print theta",
"def world_to_tanp(self, ra, dec):\n x, y = ra, dec\n retu... | [
"0.7062045",
"0.62151426",
"0.61780596",
"0.6039193",
"0.5918481",
"0.58948064",
"0.57671696",
"0.5749727",
"0.5746482",
"0.5715399",
"0.5696348",
"0.56941783",
"0.56172824",
"0.5604744",
"0.5569989",
"0.5564663",
"0.55641603",
"0.5526037",
"0.5512258",
"0.5491512",
"0.549099... | 0.6354712 | 1 |
Builds and compiles an LSTM model with the provided hyperparameters | def build_lstm_model(num_features,
embedding_size=None,
kernel_size=None,
filters=None,
pool_size=None,
lstm_output_size=None):
# Embedding
if embedding_size is None:
embedding_size = 64
# Convo... | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def build_model():\n model = Sequential()\n\n # declare the sizes of the layers (1d input and output)\n layers = [1, 50, 100, 1]\n\n # first hidden layer, using linear activation (not specified)\n model.add(LSTM(layers[1], input_shape=(None, layers[0]), return_sequences=True))\n model.add(Dropout... | [
"0.7327266",
"0.7019922",
"0.69401413",
"0.6916434",
"0.6855566",
"0.6760684",
"0.6749975",
"0.66563517",
"0.6652487",
"0.6617321",
"0.6601682",
"0.6585494",
"0.6581302",
"0.65048313",
"0.6483536",
"0.64814115",
"0.6456501",
"0.6426442",
"0.63948613",
"0.6370045",
"0.63666123... | 0.70667225 | 1 |
Builds and compiles an GRU model with the provided hyperparameters | def build_gru_model(num_features,
embedding_size=None,
kernel_size=None,
filters=None,
pool_size=None,
gru_output_size=None):
# Embedding
if embedding_size is None:
embedding_size = 64
# Convolu... | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def compile_gru_model(input_dim=101, output_dim=4563, recur_layers=3, nodes=1000,\n conv_context=11, conv_border_mode='valid', conv_stride=2,\n initialization='glorot_uniform', batch_norm=True, num_gpu=1):\n logger.info(\"Building gru model\")\n # Main acoustic input... | [
"0.73912466",
"0.66649204",
"0.6635141",
"0.6230592",
"0.6221744",
"0.61874807",
"0.61704993",
"0.61428016",
"0.6135985",
"0.61158645",
"0.6077031",
"0.6056821",
"0.60392755",
"0.60282505",
"0.5926871",
"0.5913023",
"0.5907081",
"0.5886617",
"0.58645344",
"0.58603835",
"0.584... | 0.7483657 | 0 |
Trains model on provided data. | def train_model(model, x_train, y_train, x_test, y_test,
epochs=None, batch_size=None):
# Training
if batch_size is None:
batch_size = 128
if epochs is None:
epochs = 20
print('x_train shape:', x_train.shape)
print('x_test shape:', x_test.shape)
print('Train...... | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def run(self) -> None:\n self.model = self.trainer.train_model(self.model, self.data)",
"def train(self, data):\n pass",
"def train_model(self, *args, **kwargs):\n self.model.train(self.training, *args, **kwargs)",
"def train(self):\n self.emission_model(self.train_data)\n ... | [
"0.7325476",
"0.7171853",
"0.71036",
"0.7054624",
"0.7053082",
"0.6950429",
"0.69431555",
"0.6903937",
"0.67463744",
"0.67463744",
"0.67463744",
"0.67463744",
"0.67463744",
"0.6552785",
"0.65009505",
"0.6491041",
"0.64885336",
"0.64885336",
"0.648785",
"0.64862865",
"0.648012... | 0.0 | -1 |
Evaluated model on provided testing data | def eval_model(model, x_test, y_test, batch_size=None):
if batch_size is None:
batch_size = 128
loss, acc = model.evaluate(x_test, y_test, batch_size=batch_size)
confusion_matrix_model(model, y_test, x_test)
return loss, acc | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def evaluate(self, test_data):\n result = self.model.run(test_data)\n self._save_result(result)",
"def testModel( self, classTest, classPred):",
"def test_model(predictions: np.array, configs: dict, folder_path: str, test_data_index: pd.Index,\n y_test: np.array,\n stu... | [
"0.77105874",
"0.73843247",
"0.71052754",
"0.7091229",
"0.7074009",
"0.70619357",
"0.70250666",
"0.69914263",
"0.6987785",
"0.6940113",
"0.6847204",
"0.68219995",
"0.682195",
"0.6812695",
"0.68056965",
"0.6804291",
"0.6798132",
"0.6798132",
"0.6798132",
"0.6785797",
"0.675326... | 0.0 | -1 |
Executes CLI conversion based on arguments passed through argparse | def main():
p = argparse.ArgumentParser(description='Convert images into unicode')
p.add_argument('image', metavar='<path>', type=str,
help='path to the file, use - for stdin')
p.add_argument('--no-x256', action='store_false', dest='x256', default=True,
help='prints wit... | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def main(args):\n cli = CLI()\n # Check arguments\n cli.parse_arguments(args)",
"def cli(args): # noqa; pylint: disable=unused-argument",
"def main(args):\n options = parse_cmd_parameters_(args)\n execute_(options)",
"def cli_main():\n\n\n if len(sys.argv) > 1 and sys.argv[1].endswith('.xm... | [
"0.746649",
"0.7381625",
"0.69064456",
"0.68905646",
"0.68654567",
"0.6787291",
"0.6781822",
"0.66854477",
"0.66840136",
"0.66840136",
"0.66840136",
"0.66840136",
"0.66840136",
"0.66840136",
"0.66840136",
"0.66840136",
"0.66840136",
"0.66840136",
"0.66840136",
"0.66840136",
"... | 0.0 | -1 |
Calculate the mean squared error between two images. | def mse(image_a, image_b):
# Credit Adrian Rosebrock
# https://www.pyimagesearch.com/2014/09/15/python-compare-two-images/
err = np.sum((image_a.astype("float") - image_b.astype("float")) ** 2)
err /= float(image_a.shape[0] * image_a.shape[1])
return err | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def _mean_squared_error(img1, img2):\n err = np.sum((img1.astype(\"float\") - img2.astype(\"float\")) ** 2)\n err /= float(img1.shape[0] * img1.shape[1])\n return err",
"def mse(image1: np.ndarray, image2: np.ndarray) -> np.ndarray:\n return np.sqrt(np.power((image1 - image2), 2).mean(axis=(-1, -2)))... | [
"0.8491732",
"0.796332",
"0.7908834",
"0.7711211",
"0.7675966",
"0.76289874",
"0.75710887",
"0.73973286",
"0.7323558",
"0.7070734",
"0.70387596",
"0.69253063",
"0.6891484",
"0.6875303",
"0.6873738",
"0.68721145",
"0.6867625",
"0.6805113",
"0.6760967",
"0.6729491",
"0.67219573... | 0.722647 | 9 |
Convert to numpy array as floats for use in comparisons | def standardize_format(image):
if isinstance(image, Image.Image):
new_file = BytesIO()
image.save(new_file, format='PNG')
new_file.seek(0)
return imageio.imread(new_file).astype(float)
elif isinstance(image, IOBase):
return imageio.imread(image).astype(float)
elif is... | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def solution(array):\n array1 = np.array(array)\n array2 = array1.astype(float)\n return array2",
"def make_float(array):\n finial_array = []\n\n for number in array:\n finial_array.append(float(number))\n return finial_array",
"def convertToFloatArray(booleanArray: typ... | [
"0.7205452",
"0.68435144",
"0.66298336",
"0.64569485",
"0.63817096",
"0.6317905",
"0.6316836",
"0.62721807",
"0.626991",
"0.62662345",
"0.6255745",
"0.6253336",
"0.6210134",
"0.6170176",
"0.6134217",
"0.61017036",
"0.60811114",
"0.6020606",
"0.6014738",
"0.6004565",
"0.600233... | 0.0 | -1 |
Compare two image files, can be given as Image or File objects. Comparison returns a float which indicates the relative similarity. Lower is more similar. | def compare(image_a, image_b):
image_a = standardize_format(image_a)
grayscale_image_a = to_grayscale(image_a)
image_b = standardize_format(image_b)
grayscale_image_b = to_grayscale(image_b)
err = mse(grayscale_image_a, grayscale_image_b)
return err | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def img_compare(file1, file2):\n # read image\n img1 = Image.open(file1)\n img2 = Image.open(file2)\n\n # resize \n size = 128, 128\n img1_res = img_resize(img1, size)\n img2_res = img_resize(img2, size)\n\n img1_res.save(\"img_1.thumbnail\", \"JPEG\")\n img2_res.save(\"img_2.thumbnail\"... | [
"0.7770484",
"0.755781",
"0.74901986",
"0.7209049",
"0.7027238",
"0.68469214",
"0.6797728",
"0.67634106",
"0.66868806",
"0.66799664",
"0.6614814",
"0.66090757",
"0.66017044",
"0.65690494",
"0.65652287",
"0.65169317",
"0.64967906",
"0.6491164",
"0.64799553",
"0.64664555",
"0.6... | 0.6380499 | 23 |
Converts the given image to grayscale and returns the converted image. | def to_grayscale(image):
# Credit sastanin (https://stackoverflow.com/a/3935002)
if len(image.shape) == 3:
return np.average(image, -1) # average the last axis (color channels)
else:
return image | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def convert_to_gray_scale(img):\r\n #reading image\r\n im = Image.open(\"filename\")\r\n\r\n if im.mode != \"L\":\r\n im = im.convert(\"L\")\r\n\r\n return img",
"def rgb2grayscale(image):\r\n\r\n assert image.ndim == 3 and image.shape[2] == 3\r\n\r\n gray_image = np.dot(image, [0.2989, ... | [
"0.8205708",
"0.8185807",
"0.80551726",
"0.8024271",
"0.7895879",
"0.7893156",
"0.78000677",
"0.7795188",
"0.7791997",
"0.7762031",
"0.7735562",
"0.77146196",
"0.77146196",
"0.76740164",
"0.7670393",
"0.76592916",
"0.75646484",
"0.7518474",
"0.7518474",
"0.7518474",
"0.751847... | 0.7996766 | 4 |
Create bitmap from given unicode character, return image file object. | def create_unicode_image(unicode_character):
# Check the cache
if unicode_character in unicode_cache.keys():
return unicode_cache[unicode_character]
# Initialize canvas and font parameters
# Credit: JackNova (until URL)
width = 10
height = 20
background_color=(0,0,0)
font_size=2... | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def fromascii(self, *args, **kwargs):\n return _image.image_fromascii(self, *args, **kwargs)",
"def get_tile_bitmap(self, char):\n if char == '#':\n return self.tiles[0:32, 0:32, :]\n elif char == 'b':\n return self.tiles[0:32, 128:160, :]\n elif char == 'd':\n ... | [
"0.5853663",
"0.58179283",
"0.56746536",
"0.5479672",
"0.5382288",
"0.53489006",
"0.53442067",
"0.53410566",
"0.53409886",
"0.52899945",
"0.52466315",
"0.52246463",
"0.5191945",
"0.5159506",
"0.5151667",
"0.5137356",
"0.51334125",
"0.5129038",
"0.5070787",
"0.50635946",
"0.50... | 0.777532 | 0 |
Ingest a file and slice it into 10x20 bitmaps which are compared with bitmaps of unicode charcters. The most similar character is printed with x256 color which is most like the average color for the 10x20 bitmap slice. | def print_image_as_unicode(image_file, **kwargs):
char_set = kwargs['char_set']
x256_mode = kwargs['x256']
height = 20 # height of unicode character
width = 10 # width of the unicode characters we are using
# Credit ElTero and ABM (https://stackoverflow.com/a/7051075)
if image_file == '-':
... | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def __init__(self, file_path=\"data/\", batch_size=1, img_size=[128, 2048], max_text_len=256):\r\n\r\n # filePath needs to be a folder\r\n assert file_path[-1]=='/'\r\n\r\n self.current_index = 0\r\n self.batch_size = batch_size\r\n self.img_size = img_size\r\n self.sample... | [
"0.5643496",
"0.5535181",
"0.5525569",
"0.54742545",
"0.5472219",
"0.5442176",
"0.53953683",
"0.5384109",
"0.5324327",
"0.53202426",
"0.528826",
"0.5234474",
"0.5232815",
"0.5206607",
"0.52048206",
"0.5201688",
"0.5193406",
"0.51914054",
"0.51873463",
"0.5156003",
"0.51466596... | 0.57994384 | 0 |
Returns df with dtype set for structure without any column filter. | def meta_df(self):
return NotImplemented | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def test_df_all_types():\n return pd.DataFrame({\n 'intcol': [1, 2],\n 'strcol': ['three', 'four'],\n 'floatcol': [5.0, 6.0],\n 'boolcol': [True, False],\n 'datetimecol': [\n np.datetime64('2020-01-01'), np.datetime64('2020-01-02')],\n })",
"def set_dtypes(df):... | [
"0.6611793",
"0.6518844",
"0.6439829",
"0.620935",
"0.61962974",
"0.6109263",
"0.5990738",
"0.5988264",
"0.59865373",
"0.5986267",
"0.5910748",
"0.5909542",
"0.5873334",
"0.58664733",
"0.5857477",
"0.58217114",
"0.5814661",
"0.5797066",
"0.57949156",
"0.57742786",
"0.5751437"... | 0.0 | -1 |
Fetch molecular properties from database/cache into a dask array. | def fetch_molecular_embedding(self, n_molecules: int, cache_directory: str = None):
return NotImplemented | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def to_dask(self):\n self._load_metadata()\n return self._ds",
"def to_dask(self):\n self._load_metadata()\n return self._ds",
"def getData(self, local_cache):",
"def get_dataset():\n\n return db.store.all()",
"def read_DB(self):\n mgdb = mongodata.db\n client =... | [
"0.5862701",
"0.5862701",
"0.5703025",
"0.54499245",
"0.54294366",
"0.5384057",
"0.5363727",
"0.53618395",
"0.5356752",
"0.5353922",
"0.53477436",
"0.53364336",
"0.52967966",
"0.523297",
"0.5213357",
"0.5203905",
"0.5146133",
"0.5135311",
"0.5124653",
"0.51239353",
"0.5103742... | 0.0 | -1 |
Fetch molecular properties from database for the given id. Id depends on the backend databse. For chemble DB it should be molregid. | def fetch_molecular_embedding_by_id(self, molecule_id: List):
return NotImplemented | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def read(id):\n db = core.connect()\n return db[id]",
"def get(id):\n\n result = {}\n status = 404\n print id\n # nodes=Property.query.all()\n obj = Property.query.filter_by(id=id).filter(Property.users.contains(current_user)).first()\n if obj:\n result['prop'] = obj\n statu... | [
"0.6137392",
"0.6040892",
"0.5930535",
"0.58252835",
"0.58252835",
"0.5805151",
"0.5775725",
"0.5751588",
"0.57094043",
"0.56897104",
"0.5672773",
"0.56270885",
"0.55932415",
"0.55593854",
"0.55126894",
"0.5511353",
"0.54916537",
"0.5467944",
"0.54224604",
"0.54109854",
"0.54... | 0.5316095 | 26 |
Fetch molecular details for a list of molecules. The values in the list of molecules depends on database/service used. For e.g. it could be ChemblId or molreg_id for Chemble database. | def fetch_id_from_smile(self, new_molecules: List):
return NotImplemented | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def getMoleculeData(self, moleculeChEMBLIdList):\n oD = {}\n chunkSize = 50\n try:\n for ii in range(0, len(moleculeChEMBLIdList), chunkSize):\n drug = new_client.molecule # pylint: disable=no-member\n drug.set_format(\"json\")\n mDL = d... | [
"0.68206555",
"0.60511196",
"0.5856835",
"0.58565825",
"0.5701199",
"0.56697226",
"0.5620971",
"0.5596572",
"0.5584915",
"0.55798215",
"0.54545426",
"0.5418826",
"0.53591985",
"0.5348931",
"0.53488845",
"0.5341942",
"0.5338322",
"0.530197",
"0.5297963",
"0.5284677",
"0.527967... | 0.5368393 | 12 |
Fetch molecular details for a list of molecules. The values in the list of molecules depends on database/service used. For e.g. it could be ChemblId or molreg_id for Chemble database. | def fetch_id_from_chembl(self, id: List):
return NotImplemented | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def getMoleculeData(self, moleculeChEMBLIdList):\n oD = {}\n chunkSize = 50\n try:\n for ii in range(0, len(moleculeChEMBLIdList), chunkSize):\n drug = new_client.molecule # pylint: disable=no-member\n drug.set_format(\"json\")\n mDL = d... | [
"0.68211865",
"0.6050688",
"0.58566874",
"0.58560246",
"0.570075",
"0.56694674",
"0.56206733",
"0.5596092",
"0.55844384",
"0.5577729",
"0.5454434",
"0.5418259",
"0.5366659",
"0.53580934",
"0.5348218",
"0.53474617",
"0.5341979",
"0.5338593",
"0.5302504",
"0.5297541",
"0.528347... | 0.0 | -1 |
Fit the model using x_train as training data and y_train as target values | def fit(self, x_train: np.ndarray, y_train: np.ndarray) -> None:
# Stores training data and targets for use in derived classes
self.x_train = x_train
self.y_train = y_train | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def fit(self, X, y):\n self.X_train = X\n self.y_train = y",
"def train(self, X_train, y_train):\n self.model.fit(X_train, y_train)",
"def train(self, X, y):\n self.model.fit(X, y)",
"def fit_training_data(self):\n self.model.fit(self.X_train)",
"def fit(self, X_train, y_... | [
"0.808191",
"0.7904677",
"0.7882587",
"0.78722423",
"0.78268933",
"0.7770836",
"0.7697726",
"0.7596521",
"0.7596521",
"0.7596521",
"0.75560147",
"0.7509245",
"0.74777925",
"0.74643713",
"0.7451252",
"0.7425392",
"0.7420984",
"0.74162674",
"0.74025804",
"0.7401003",
"0.7377242... | 0.73412484 | 31 |
Filter a `items` list according to a list of `queries`. Values from `items` are kept if they match at least one query. The original `items` list is untouched but the result list uses the same data (not a deep copy). If `attribute` is None, it is assumed that `items` is a list of strings to be filtered directly. If `att... | def stringfilter(items, queries, attribute=None):
result = []
if attribute is not None:
key_path = attribute.split('.')
else:
key_path = None
for item in items:
if key_path is not None:
string = _get_nested_value(item, key_path)
if not isinstance(string, ... | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def itemFilterAttr(*args, byName: Union[AnyStr, bool]=\"\", byNameString: Union[AnyStr,\n List[AnyStr], bool]=\"\", byScript: Union[AnyStr, bool]=\"\", classification:\n Union[AnyStr, bool]=\"\", dynamic: bool=True, exists: bool=True, hasCurve:\n bool=True, has... | [
"0.57204485",
"0.5617756",
"0.548573",
"0.54075944",
"0.5388926",
"0.52190524",
"0.5199355",
"0.5139567",
"0.50037485",
"0.48549065",
"0.4841358",
"0.47993222",
"0.47757334",
"0.47549915",
"0.47255918",
"0.47191286",
"0.47072586",
"0.4689648",
"0.46839404",
"0.46671137",
"0.4... | 0.68550235 | 0 |
Get value under `key_path` key in `dct` dictionary. `key_path` is a list of keys to be traversed into a potentially nested `dct` dictionary. | def _get_nested_value(dct, key_path):
key = key_path[0]
if not isinstance(dct, dict):
raise errors.AnsibleFilterError(
f"stringfilter: looking for key '{key}' "
f"but list item is not dict: {pformat(dct)}"
)
if key not in dct:
raise errors.AnsibleFilterError(
... | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def get_by_path(data: Dict[str, T], path: Sequence[str]) -> T:\n return reduce(operator.getitem, path, data)",
"def _get_by_path(dic, keys):\n assert len(keys) > 0, \"Path key can not be an empty list.\"\n\n d = dic\n for key in keys[:-1]:\n if isinstance(key, int) or key in d:\n d ... | [
"0.6952644",
"0.68554395",
"0.6719718",
"0.64265496",
"0.64265496",
"0.6403472",
"0.63947314",
"0.63453716",
"0.6322947",
"0.6304281",
"0.6285504",
"0.62721723",
"0.6161064",
"0.61594445",
"0.6127265",
"0.61137265",
"0.60990524",
"0.60921264",
"0.6087193",
"0.6030112",
"0.602... | 0.7896383 | 0 |
Perform the 2D discrete Fourier transform and extend the data with padding. | def fft_pad_data(data, mode='edge'):
n_points=int(2**(np.ceil(np.log(np.max(data.shape))/np.log(2))))
nx, ny = data.shape
padx = int((n_points - nx)/2)
pady = int((n_points - ny)/2)
padded_data = np.pad(data, ((padx, padx), (pady, pady)),mode)
mask = np.zeros_like(padded_data,... | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def fourier_transform2d(self):\n\n zerofill = np.zeros(1024 * np.array([1,1])) #so it will always be square\n zerofill[:len(self.windowed), :len(self.windowed)] = self.windowed\n transform = np.fft.fft2(zerofill)\n transform = np.fft.fftshift(transform) # shift center to... | [
"0.65467256",
"0.6410407",
"0.6086163",
"0.59369767",
"0.5931539",
"0.5929195",
"0.5889854",
"0.5879024",
"0.58667964",
"0.58256716",
"0.5793475",
"0.57264745",
"0.5614827",
"0.5607132",
"0.5590157",
"0.5572319",
"0.55702704",
"0.5560839",
"0.5545364",
"0.55280906",
"0.550855... | 0.5950112 | 3 |
Designs a lowpass 2D Butterworth filter. Modified from Peirce JW (2009) Generating stimuli for neuroscience using | def butter2d_lp(shape, f, n):
rows, cols = shape
x = np.linspace(-0.5, 0.5, cols)
y = np.linspace(-0.5, 0.5, rows)
radius = np.sqrt((x**2)[np.newaxis] + (y**2)[:, np.newaxis])
filt = 1 / (1.0 + (radius / f)**(2*n))
return (filt) | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def get_butterworth_low_pass_filter(shape, cutoff, order):\n \n \n print(\"butterworth_low_pass_filter = \")\n print(\"cutoff: \",cutoff)\n print(\"order: \",order)\n filter = np.zeros(shape)\n for i in range(shape[0]):\n for j in range(shape[1]):\n D = np.sqrt((i - (shape[0]... | [
"0.67872274",
"0.66857934",
"0.64890873",
"0.6436643",
"0.63463753",
"0.6341585",
"0.63169885",
"0.63033724",
"0.6281029",
"0.6272661",
"0.62672955",
"0.62393",
"0.62285304",
"0.61405635",
"0.6119317",
"0.6114302",
"0.6098206",
"0.6097736",
"0.6076158",
"0.6067853",
"0.604568... | 0.6352877 | 4 |
Plot the data in DWT domain | def plot_wav(decomp):
plt.figure(figsize=(10,10))
gs = GridSpec(4, 4)
ax = plt.subplot(gs[0, 0])
plt.imshow(decomp[0])
plt.xticks([])
plt.yticks([])
ax = plt.subplot(gs[1,0])
plt.imshow(decomp[1][0])
plt.xticks([])
plt.yticks([])
ax = plt.subplot(gs[0, 1])... | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def plot_data(self):",
"def dplot(self):\n\n try:\n import matplotlib.pyplot as plt\n except ImportError:\n from sys import stderr\n print(\"ERROR: matplotlib.pyplot not found, matplotlib must be installed to use this function\", file=stderr)\n raise\n\n ... | [
"0.7187857",
"0.6936303",
"0.66426486",
"0.65928483",
"0.6591709",
"0.64936006",
"0.64238495",
"0.63904613",
"0.63418317",
"0.63384956",
"0.630438",
"0.6246254",
"0.62004626",
"0.6199328",
"0.618154",
"0.61802506",
"0.6109246",
"0.6105832",
"0.61016023",
"0.6097523",
"0.60812... | 0.0 | -1 |
The constructor takes a coarse timestepper and an order of approximation | def __init__(self,diff,boxtimestepper,gaptoothStep,maxDeriv):
self.boxts=boxtimestepper
self.delta_t=gaptoothStep
macro.fd.fd_estimator.FDEstimator.__init__(self,diff,maxDeriv) | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def __init__(self,\n time_step: float,\n acceleration: Callable[[float], float],\n initial_value: float = 0.0,\n initial_velocity: float = 0.0,\n num_steps: int = 50,\n collected_data: Iterable[Dict[str, float]] = [],\n... | [
"0.5920452",
"0.57915515",
"0.5682523",
"0.5663074",
"0.56580824",
"0.5614911",
"0.555747",
"0.552551",
"0.5491382",
"0.5489133",
"0.5476062",
"0.54720134",
"0.546864",
"0.54354644",
"0.54314643",
"0.54314643",
"0.53980315",
"0.53959155",
"0.53954285",
"0.5391545",
"0.5379088... | 0.5623274 | 5 |
Tests whether the trace for step methods is exactly the same as on master. Code changes that effect how random numbers are drawn may change this, and require `master_samples` to be updated, but such changes should be noted and justified in the commit. This method may also be used to benchmark step methods across commit... | def check_trace(self, step_method):
n_steps = 100
with Model():
x = Normal('x', mu=0, sd=1)
if step_method.__name__ == 'SMC':
Deterministic('like', - 0.5 * tt.log(2 * np.pi) - 0.5 * x.T.dot(x))
trace = smc.ATMIP_sample(n_steps=n_steps, step=step_me... | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def TestOneStep(self):\n pass",
"def test_changes(monkeypatch, local):\n monkeypatch.setenv('LANG', 'en_US.UTF-8')\n monkeypatch.setenv('TRAVIS_BUILD_ID', '12345')\n monkeypatch.setenv('TRAVIS_BRANCH', 'master')\n old_sha = pytest.run(local, ['git', 'rev-parse', 'HEAD']).strip()\n local.ens... | [
"0.5406668",
"0.5375",
"0.53389776",
"0.5314626",
"0.52967477",
"0.5258354",
"0.52216065",
"0.52073497",
"0.51792115",
"0.51779264",
"0.51701105",
"0.5160602",
"0.5152976",
"0.51241815",
"0.50939167",
"0.50733656",
"0.50511485",
"0.5043404",
"0.50413126",
"0.50389934",
"0.503... | 0.549506 | 0 |
Test that samplers correctly create nonblocked compound steps. | def test_non_blocked(self):
_, model = simple_2model()
with model:
for sampler in self.samplers:
assert isinstance(sampler(blocked=False), CompoundStep) | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def test_block_extra_batch(self):\n pass",
"def test_block_bad_batch(self):\n pass",
"def test_validation_correct_samplers():\n samplers = [\n {'type': 'MultiStateSampler', 'locality': 3},\n {'type': 'ReplicaExchangeSampler'},\n # MCMCMove 'single' is defined in get_templa... | [
"0.66656935",
"0.6592942",
"0.64613193",
"0.64177775",
"0.6116642",
"0.6095393",
"0.6079921",
"0.6000796",
"0.5993817",
"0.59393144",
"0.5934992",
"0.57287186",
"0.5716562",
"0.57142526",
"0.57003576",
"0.56979024",
"0.5697373",
"0.5691124",
"0.567336",
"0.5657544",
"0.565397... | 0.79553413 | 0 |
Test bernoulli distribution is assigned binary gibbs metropolis method | def test_bernoulli(self):
with Model() as model:
Bernoulli('x', 0.5)
steps = assign_step_methods(model, [])
assert isinstance(steps, BinaryGibbsMetropolis) | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def bernoulli(p):\n bern = rn.binomial(1,p)\n return bern",
"def bernoulli(p):\r\n if np.random.random() < p:\r\n return 0\r\n else:\r\n return 1",
"def bernoulli_num(n):\n return mp.bernoulli(n)",
"def bernoulli(n):\n\n x, res, s, c = Rat(0), Rat(0), Rat(0), Rat(-1)\n for ... | [
"0.7547345",
"0.7430234",
"0.737914",
"0.7260277",
"0.7170436",
"0.70253694",
"0.6839243",
"0.67702055",
"0.653989",
"0.6529904",
"0.6523155",
"0.64852256",
"0.648092",
"0.6472643",
"0.6457794",
"0.64568967",
"0.64539707",
"0.6446213",
"0.63996285",
"0.63980657",
"0.6349709",... | 0.77244 | 0 |
Test normal distribution is assigned NUTS method | def test_normal(self):
with Model() as model:
Normal('x', 0, 1)
steps = assign_step_methods(model, [])
assert isinstance(steps, NUTS) | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def test_2_normal(self):\n print(\"test 2: normal distributions\")\n\n mean = self.means[0]\n dispersion = self.dispersions[0]\n\n for i, x in enumerate(self.X):\n print(i+1, normal(x, mean, dispersion), sep=' : ')",
"def test_normdistcreation():\n test_array = np.vstack... | [
"0.7466253",
"0.69424164",
"0.67911315",
"0.6775584",
"0.67698973",
"0.6682361",
"0.65429854",
"0.6531256",
"0.649198",
"0.6416713",
"0.640294",
"0.6401808",
"0.6341993",
"0.63400614",
"0.6283304",
"0.6281596",
"0.6272235",
"0.6225952",
"0.6208192",
"0.6189331",
"0.61540663",... | 0.67004794 | 5 |
Test categorical distribution is assigned categorical gibbs metropolis method | def test_categorical(self):
with Model() as model:
Categorical('x', np.array([0.25, 0.75]))
steps = assign_step_methods(model, [])
assert isinstance(steps, BinaryGibbsMetropolis)
with Model() as model:
Categorical('y', np.array([0.25, 0.70, 0.05]))
... | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def test_Bernoulli_NB_estimators():",
"def gibbs_sample(self):\n # Initialize the initial state of Markov Chain.\n self.initialize()\n # Gibbs Sampling.\n for iteration_index in range(0, self.iteration_number, 1):\n for m in range(0,self.document_number,1):\n ... | [
"0.6492466",
"0.6474214",
"0.642306",
"0.62708336",
"0.6208008",
"0.618504",
"0.61007977",
"0.59815496",
"0.59573436",
"0.59539115",
"0.59391415",
"0.5922018",
"0.59049296",
"0.58518004",
"0.58390254",
"0.5831838",
"0.58220774",
"0.5815369",
"0.5810455",
"0.5798642",
"0.57903... | 0.6250971 | 4 |
Test binomial distribution is assigned metropolis method. | def test_binomial(self):
with Model() as model:
Binomial('x', 10, 0.5)
steps = assign_step_methods(model, [])
assert isinstance(steps, Metropolis) | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def test_bernoulli(self):\n with Model() as model:\n Bernoulli('x', 0.5)\n steps = assign_step_methods(model, [])\n assert isinstance(steps, BinaryGibbsMetropolis)",
"def test_multinomial(self):\r\n # Check over two calls to see if the random state is correctly updated.... | [
"0.69088066",
"0.6723618",
"0.66573316",
"0.6643335",
"0.6618572",
"0.6482851",
"0.6428169",
"0.6424013",
"0.6345978",
"0.62615824",
"0.6225464",
"0.61995316",
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"0.60746217",
"0.6054197",
"0.6051179",
"0.60234743",
"0.60210484",
"0.60168356",
"0.5997... | 0.76352745 | 0 |
Ensure that, for the given service, the video_id is valid. | def clean_video_id(self):
failed = False
d = self.cleaned_data
service = d.get('service')
# Get the video id and clear whitespace on either side.
video_id = d.get('video_id', '').strip()
# Validate using YouTube's API:
if service == 'youtube':
url = (... | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def allow_video(self, video_id):\n print(\"allow_video needs implementation\")",
"def allow_video(self, video_id):\n print(\"allow_video needs implementation\")",
"def allow_video(self, video_id):\n print(\"allow_video needs implementation\")",
"def allow_video(self, video_id):\n ... | [
"0.60907304",
"0.60907304",
"0.60907304",
"0.60907304",
"0.6068158",
"0.5851678",
"0.57884514",
"0.56182677",
"0.5566757",
"0.55377215",
"0.5534833",
"0.5517205",
"0.5513362",
"0.5502711",
"0.5484015",
"0.54670113",
"0.54354274",
"0.54342276",
"0.53538764",
"0.53443223",
"0.5... | 0.7674897 | 0 |
Computes coverage rate for `y_pred`. | def coverage(y_true, y_pred):
m = tf.shape(y_pred)[1] - tf.constant(1, dtype=tf.int32)
n_samples = tf.cast(tf.shape(y_pred)[0], tf.float32)
n_abstain = tf.reduce_sum(
tf.where(tf.argmax(y_pred, axis=1, output_type=tf.int32) == m, 1.0, 0.0)
)
return tf.constant(1.0) - n_abstain / n_samples | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def hit_rate(y_true, y_pred, spu=None):\n mask = y_pred.astype(bool)\n y_true_in_pred = y_true[mask]\n return y_true_in_pred.sum()/y_true.sum()",
"def recall_score(y_true, y_pred):\n return ((y_true == 1) * (y_pred == 1)).sum() / (y_true == 1).sum()",
"def ari(y_pred, y_true):\n return metrics.a... | [
"0.71039015",
"0.70715314",
"0.6947408",
"0.6926472",
"0.68919915",
"0.6836527",
"0.6757787",
"0.6753589",
"0.67308986",
"0.67180943",
"0.66951615",
"0.66951615",
"0.66951615",
"0.66951615",
"0.66951615",
"0.66951615",
"0.66951615",
"0.66951615",
"0.66951615",
"0.66951615",
"... | 0.75946474 | 0 |
Get a User based on email address. | def show(self, email):
return User.query.filter_by(email=email).first() | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def user(email):\r\n return User.objects.get(email=email)",
"def get_user_by_email(email):\n\n return User.query.filter(User.email == email).first()",
"def get_user_by_email(email):\n\n return User.query.filter(User.email == email).first()",
"def get_by_email(self, email):\n user = (\n ... | [
"0.85743433",
"0.8544356",
"0.8544356",
"0.84845865",
"0.8470432",
"0.8443715",
"0.8424075",
"0.83887917",
"0.8271503",
"0.8270463",
"0.8237727",
"0.82315016",
"0.81901556",
"0.8184349",
"0.81050164",
"0.80862194",
"0.8068554",
"0.8065875",
"0.80543447",
"0.8032841",
"0.80034... | 0.73686725 | 36 |
Get Product based on name. | def show(self, title):
return Product.query.filter_by(title=title).first() | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def get_product(cls, product_id):\n return Product.query.get(product_id)",
"def get_products_by_name(name: str = '') -> List[Product]:\n products = []\n for p in get_market().products.values():\n if not name or p.name == name:\n products.append(p)\n return products",
"def sear... | [
"0.7238149",
"0.7212795",
"0.72054875",
"0.71924907",
"0.71586484",
"0.7007384",
"0.6974032",
"0.68805",
"0.6826333",
"0.68231606",
"0.67831254",
"0.6731516",
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"0.66819346",
"0.66207284",
"0.6595219",
"0.65523624",
"0.65501523",
"0.6533631",
"0.65288424",
"0.6504... | 0.5911903 | 74 |
View products in Cart. | def index(self, user):
cart_products = CartProduct.index(user)
CartProductsView.index(cart_products) | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def products(request):\n\n if not request.user.is_superuser:\n messages.error(request, 'Sorry, only store owners can do that.')\n return redirect(reverse('home'))\n\n products = Product.objects.all()\n template = \"auctionsmng/products.html\"\n\n context = {\n 'products': products\... | [
"0.7544936",
"0.74219257",
"0.72852266",
"0.7261602",
"0.72421676",
"0.7014876",
"0.70145303",
"0.70145303",
"0.7007686",
"0.6988518",
"0.6979214",
"0.6970391",
"0.69648755",
"0.69648755",
"0.69648755",
"0.69543886",
"0.69423074",
"0.6799814",
"0.6670603",
"0.6653604",
"0.658... | 0.77032435 | 0 |
Add Product to Cart. | def create(self, user, product, quantity):
cart_product = CartProduct.create(user, product, quantity)
CartProductsView.create(cart_product) | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def add(self, product, product_qty):\n product_id = str(product.id)\n if product_id in self.cart:\n self.cart[product_id][\"qty\"] = product_qty\n else:\n self.cart[product_id] = {'price': str(product.price), 'qty':int(product_qty)}\n self.save()",
"def cart_add(... | [
"0.8279945",
"0.8130827",
"0.8084389",
"0.80390966",
"0.7810375",
"0.7795158",
"0.77597386",
"0.7748757",
"0.7740242",
"0.7729689",
"0.76999176",
"0.766027",
"0.7653296",
"0.7621587",
"0.7587989",
"0.7569859",
"0.74912816",
"0.7433777",
"0.7431253",
"0.7365529",
"0.7344932",
... | 0.7053575 | 29 |
Delete Product from Cart. | def delete(self, user, product):
cart_product = CartProduct.delete(user, product)
CartProductsView.delete(cart_product) | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def delete(self, product):\n product_id = str(product)\n if product_id in self.cart:\n del self.cart[product_id]\n self.save()",
"def cart_remove(request, product_id):\n cart = Cart(request)\n product = get_object_or_404(Product, id=product_id)\n cart.remove(product)\n ... | [
"0.8534601",
"0.8041614",
"0.79457",
"0.770682",
"0.7690166",
"0.7668008",
"0.76628315",
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"0.7338678",
"0.73137146",
"0.7273116",
"0.7239314",
"0.7206781",
"0.7196743",
... | 0.81086886 | 1 |
Update product quantity in cart. | def update(self, user, product, quantity):
cart_product = CartProduct.update(user, product, quantity)
CartProductsView.update(cart_product) | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def update(self, product, qty):\n product_id = str(product)\n if product_id in self.cart:\n self.cart[product_id]['qty'] = qty\n self.save()",
"def update(self, product, qty):\n product_id = str(product)\n if product_id in self.basket:\n self.basket[produc... | [
"0.827262",
"0.79062",
"0.75526017",
"0.7427123",
"0.7330307",
"0.7124662",
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"0.6850595",
"0.67024165",
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"0.66433424",
"0.66109204",
"0.65673107",
"0.65499806",
"0.65499806",
"0.65499806",
"0.6549980... | 0.78177625 | 2 |
Get completed orders for a user. | def show_completed(self, user):
orders = CartProduct.show_completed(user)
CartProductsView.show_completed(orders) | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def get_one_user_orders(self,user_id):\n\n sql = \"SELECT * FROM parcel_orders WHERE user_id='{}'\".format(user_id)\n self.db_object.cursor.execute(sql)\n placed_orders = self.db_object.cursor.fetchall()\n return placed_orders",
"def get_completed_user_requests(self):\n user_re... | [
"0.6891886",
"0.6568276",
"0.64125514",
"0.6124557",
"0.57911223",
"0.56917673",
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"0.539336",
"0.53909403",
"0.53864336",
"0.5384064",
"0.53825545",
"0.5372619... | 0.6389238 | 3 |
Yield the classes in module ``mod`` that inherit from ``cls`` | def get_subclasses(mod, cls):
for name, obj in inspect.getmembers(mod):
if hasattr(obj, "__bases__") and cls in obj.__bases__:
yield obj | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def _classes_(cls):\n for base_cls in cls.__bases__:\n # Avoid infinite loop\n if base_cls == Sandbox:\n continue\n\n yield base_cls",
"def _classesToCheck(self, cls):\r\n yield cls\r\n yield from inspect.getmro(cls)",
"def get_all_classes_de... | [
"0.7661169",
"0.75540936",
"0.74157786",
"0.74068946",
"0.71664065",
"0.7122239",
"0.70386964",
"0.68738073",
"0.6851402",
"0.6728931",
"0.66658",
"0.66300493",
"0.6608214",
"0.65761477",
"0.65552634",
"0.65492725",
"0.65423816",
"0.65163565",
"0.647793",
"0.64746547",
"0.644... | 0.80770713 | 0 |
Define the class balanced cross entropy loss to train the network | def class_balanced_cross_entropy_loss(output, label, size_average=True, batch_average=True, void_pixels=None):
assert(output.size() == label.size())
labels = torch.ge(label, 0.5).float()
num_labels_pos = torch.sum(labels)
num_labels_neg = torch.sum(1.0 - labels)
num_total = num_labels_pos + num... | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def setup_loss(self):\n self.loss = nn.CrossEntropyLoss(weight = self.to_device(self.datasetManager.class_weights))\n #self.loss = nn.CrossEntropyLoss()",
"def cross_entropy_loss():\n return nn.CrossEntropyLoss()",
"def _classification_loss(self, logits, labels, num_classes):\n labels = tf.... | [
"0.7614162",
"0.72006047",
"0.7150641",
"0.71390414",
"0.70425236",
"0.69947386",
"0.6988147",
"0.69880617",
"0.69836",
"0.6958063",
"0.69394386",
"0.69217324",
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"0.69120765",
"0.69120765",
"0.6910133",
"0.6886472",
"0.67843294",
"0.67344993",
"0.671... | 0.61960006 | 96 |
A main function to run the simulation | def Main():
numberOfPopulation = 350
numberOfDays = 60
simulation = Simulation(Covid19(), numberOfPopulation, numberOfDays, "Covid 19 Simulation")
simulation.run()
simulation = Simulation(Ebola(), numberOfPopulation, numberOfDays, "Ebola Simulation")
simulation.run() | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def Main():\n EnigmaSim = simulation() #Creates the simulation object\n EnigmaSim.Run() #Runs the simulation",
"def main():\n run_simulation(spectral=False, ml=False, num_procs=1)\n run_simulation(spectral=True, ml=False, num_procs=1)\n run_simulation(spectral=False, ml=True, num_procs=1)\n run... | [
"0.82430094",
"0.80094373",
"0.770448",
"0.7694861",
"0.7663943",
"0.7658844",
"0.7653654",
"0.76189035",
"0.76126456",
"0.74813896",
"0.74432015",
"0.73796666",
"0.73725206",
"0.7330815",
"0.7320483",
"0.73116446",
"0.72484505",
"0.7242806",
"0.7231775",
"0.7191046",
"0.7118... | 0.8399111 | 0 |
runs the network to get the reading of the nodes | def update_all_readings(self):
# update the reading of all nodes
for node_name in self.nodes:
# update the readings of all nodes
self.nodes[node_name].reading()
# once all nodes have updated, they can be stabilized
for node_name in self.nodes:
self... | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def run(self):\n\t\tself._run_neural_network()\n\t\tself._run_webots()\n\n\t\t# We first wait for webots inputs\n\t\twebotsTurn = True\n\t\tneuralNetworkTurn = False\n\t\twhile True:\n\t\t\tif webotsTurn:\n\t\t\t\tprint \"reading data from webots:\"\n\t\t\t\twbtData = self._wbt_read_data()\n\t\t\t\tprint \"sending... | [
"0.67898077",
"0.63943046",
"0.6293423",
"0.6178959",
"0.61693454",
"0.6072311",
"0.60665065",
"0.59855515",
"0.5962578",
"0.592378",
"0.592378",
"0.5919859",
"0.59175384",
"0.58729637",
"0.58661026",
"0.58609766",
"0.5849859",
"0.58277494",
"0.5815831",
"0.5813402",
"0.58080... | 0.5388483 | 76 |
Uses the readings from all nodes to report the mean and standard deviation of all nodes | def get_network_reading(self):
# update the readings for all nodes
self.update_all_readings()
# get the current readings from all nodes
node_readings = []
for node_name in self.nodes:
node_readings.append(self.nodes[node_name].stable_reading)
node_readings... | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def compute_training_stats():\n means, stds = [], []\n data = SUNRGBDTrainDataset(True)\n for i in range(len(data)):\n print(i)\n img, _ = data[i]\n std, mean = t.std_mean(input=img, dim=(1, 2))\n means.append(mean)\n stds.append(std)\n means = t.sum(t.vstack(means), ... | [
"0.6639394",
"0.6492293",
"0.6476488",
"0.6289496",
"0.6249173",
"0.61678153",
"0.61512434",
"0.6148738",
"0.61152846",
"0.6097314",
"0.60312355",
"0.60029006",
"0.5964977",
"0.5934712",
"0.5916757",
"0.59007215",
"0.5894467",
"0.58875763",
"0.5869987",
"0.58500725",
"0.58438... | 0.6637554 | 1 |
Generator that returns the names of all nodes in the network | def node_names(self):
for node_name in self.nodes.keys():
yield node_name | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def all_nodes_as_iterable(self, include_metadata: bool = False) -> Generator:\n if include_metadata:\n return [\n (self._names.get_name(i), self._meta.get_node(self._names.get_name(i)))\n for i in self._nk_graph.iterNodes()\n ]\n return [self._names... | [
"0.72962666",
"0.71726984",
"0.7021836",
"0.6995421",
"0.6957169",
"0.68337035",
"0.67822737",
"0.6635629",
"0.66200304",
"0.6613424",
"0.66128385",
"0.6590175",
"0.6584443",
"0.6574914",
"0.6530787",
"0.6516793",
"0.6490995",
"0.64839625",
"0.6473152",
"0.6454208",
"0.642815... | 0.80899006 | 0 |
gets average position of all nodes in the network | def get_network_average_position(self):
# the total number of nodes in the network
num_nodes = self.total_nodes()
# get the location of all nodes
all_nodes = np.empty((num_nodes, R_space))
for index, item in enumerate(self.nodes.values()):
all_nodes[index] = item.ge... | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def mean_average_position():\n pass",
"def streets_per_node_avg(G):\n spn_vals = streets_per_node(G).values()\n return sum(spn_vals) / len(G.nodes)",
"def average_distance(self):\r\n total = 0\r\n edges = 0\r\n for code, _list in self.edges.items():\r\n for edge in _lis... | [
"0.71411693",
"0.6822021",
"0.6471728",
"0.6465491",
"0.63243866",
"0.6256085",
"0.62065727",
"0.592237",
"0.58896816",
"0.5823813",
"0.5820218",
"0.57679445",
"0.5765885",
"0.57562655",
"0.57562655",
"0.57562655",
"0.57562655",
"0.57562655",
"0.57481986",
"0.5742098",
"0.573... | 0.84714663 | 0 |
Makes an undirected graph from the nodes and their neighbors | def make_graph(self):
# update the neighbors in the graph
self.update_neighbors()
# Go through each node and get their neighbors
self.edges = []
for node_name in self.nodes:
# get the neighbors
node_neighbors = self.nodes[node_name].neighbors
... | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def to_undirected_graph(self):\n visited = set() \n G = Graph.Graph()\n \n for node in self.node_set:\n \n if node not in visited:\n visited.add(node)\n for i in self.suffix[node]:\n G.add_edge(node, i)\n ... | [
"0.75638914",
"0.7205912",
"0.71880054",
"0.7131666",
"0.71072274",
"0.6858183",
"0.6852115",
"0.68332267",
"0.6815476",
"0.6774215",
"0.67656296",
"0.6728196",
"0.67220825",
"0.6714339",
"0.6708744",
"0.6696275",
"0.66795415",
"0.667814",
"0.6614417",
"0.65941584",
"0.657723... | 0.6932689 | 5 |
checks to make sure that the network is connected | def check_connected(self, update=True):
# update if needed
if update:
self.update_neighbors()
# go through each node checking that each degree id greater than 0
for node in self.nodes:
# only one node needs to be disconnected to fail
if len(self.nod... | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def isConnected():",
"def status_check(self):\n try:\n client = self.connect()\n client.sys.is_initialized() # make an actual network connection\n return True\n except:\n return False",
"def __CheckConnectStatus(self):\r\n if not self.tn:\r\n ... | [
"0.81566215",
"0.79727143",
"0.7940008",
"0.78969526",
"0.7855953",
"0.77820456",
"0.7739617",
"0.7734968",
"0.76910055",
"0.7622621",
"0.76209754",
"0.7618871",
"0.75643706",
"0.75183284",
"0.75183284",
"0.7486937",
"0.74535733",
"0.7438523",
"0.74041045",
"0.74012107",
"0.7... | 0.0 | -1 |
get the nodes with the lowest and highest number of neighbors | def get_interest_nodes(self):
# go through each node in the network to find the min and max degrees
max_value = 0
min_value = len(self.nodes)
for name in self.nodes:
# check for new max
if self.nodes[name].get_degree() >= max_value:
max_value = s... | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def get_neighbours(self):\n return []",
"def neighbours(self):\n return [x.node for x in self.edges]",
"def neighbors((min_i, min_j), (max_i, max_j), (i, j)):\n if j + 1 <= max_j:\n yield (i, j + 1)\n if j - 1 >= min_j:\n yield (i, j - 1)\n if i + 1 <= max_i:\n y... | [
"0.7004768",
"0.6752797",
"0.67516655",
"0.6725832",
"0.6695274",
"0.66674364",
"0.66209084",
"0.65983164",
"0.6586327",
"0.6554205",
"0.6553236",
"0.6543602",
"0.6524486",
"0.64795715",
"0.64779377",
"0.6466439",
"0.6460438",
"0.6440627",
"0.6440627",
"0.6440627",
"0.6440627... | 0.6979103 | 1 |
Implement the linear part of a layer's forward propagation. | def linear_forward(A, W, b):
### START CODE HERE ### (≈ 1 line of code)
Z = np.dot( W, A ) + b
### END CODE HERE ###
assert(Z.shape == (W.shape[0], A.shape[1]))
cache = (A, W, b)
return Z, cache | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def forward(cls, linear_out):\n raise Exception(\"Unimplemented\")",
"def linear_activation_forward(A_prev, W, b, activation):\n pass",
"def forward(self, x: torch.Tensor):\n x = self.linear1(x)\n x = torch.relu(x)\n x = self.linear2(x)\n x = self.dropout(x)\n retur... | [
"0.7179928",
"0.7058336",
"0.70316356",
"0.7029865",
"0.70107585",
"0.69642836",
"0.6961805",
"0.69575894",
"0.69349027",
"0.6863985",
"0.6854632",
"0.6827189",
"0.68195087",
"0.67894167",
"0.6750277",
"0.6749512",
"0.67359066",
"0.6712237",
"0.67030334",
"0.67017424",
"0.669... | 0.6471803 | 56 |
Implement the cost function defined by equation (7). | def compute_cost(AL, Y):
m = Y.shape[1]
# Compute loss from aL and y.
### START CODE HERE ### (≈ 1 lines of code)
cost = - ( np.sum( np.multiply( Y, np.log(AL)) + np.multiply( (1 - Y), np.log(1 - AL))))/Y.shape[1]
### END CODE HERE ###
cost = np.squeeze(cost) # To make sure your ... | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def costFun(self, S, x):",
"def cost(self) -> float:",
"def compute_cost(AL, Y):\n pass",
"def compute_cost(AL, Y):\n pass",
"def calcCostFun(self):\n\n self.start()\n F, K = self.model()\n \n return self.costFunction",
"def eval_cost(self, params, **kwargs):\n ... | [
"0.73584634",
"0.73044",
"0.72563547",
"0.71911925",
"0.7163819",
"0.70149416",
"0.6912114",
"0.6843692",
"0.67893624",
"0.6733327",
"0.6731844",
"0.6674887",
"0.6673156",
"0.6651433",
"0.6609615",
"0.66076875",
"0.660437",
"0.6591419",
"0.6590477",
"0.6567088",
"0.65483785",... | 0.0 | -1 |
Recibe el numero de segmentos y el valor de W Esta es la funcion de sumatoria para los numeros Impares Regresa el total de la sumatoria | def sumaImpar(self,numSeg,w):
total=0
for i in range(1,numSeg,2):
total+=4*self.F(i*w)
return total | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def sumaPar(self,numSeg,w):\n total=0\n for i in range(2,numSeg-1,2):\n total+=2*self.F(i*w)\n return total",
"def som(getallenlijst):\r\n total = sum(getallenlijst)\r\n return total",
"def patrimony_total(self):\n pass",
"def P(self,numSeg):\n w=self.x/num... | [
"0.6964878",
"0.6134664",
"0.594122",
"0.5869036",
"0.5832696",
"0.58005255",
"0.5768656",
"0.57542235",
"0.57383496",
"0.5733486",
"0.5723789",
"0.5633767",
"0.5631011",
"0.5616186",
"0.5609557",
"0.5607594",
"0.56038254",
"0.5596513",
"0.5594047",
"0.5584726",
"0.55708295",... | 0.6899784 | 1 |
Recibe el numero de segmentos y el valor de W Esta es la funcion de sumatoria para los numeros Pares Regresa el total de la sumatoria | def sumaPar(self,numSeg,w):
total=0
for i in range(2,numSeg-1,2):
total+=2*self.F(i*w)
return total | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def som(getallenlijst):\r\n total = sum(getallenlijst)\r\n return total",
"def patrimony_total(self):\n pass",
"def sumaImpar(self,numSeg,w):\n total=0\n for i in range(1,numSeg,2):\n total+=4*self.F(i*w)\n return total",
"def n_suma(a1,nr_wyrazu,r):\n return (... | [
"0.63764817",
"0.6370845",
"0.6358655",
"0.6194959",
"0.6053004",
"0.5966047",
"0.59162605",
"0.5848194",
"0.5827601",
"0.57799345",
"0.5768629",
"0.5754656",
"0.5723134",
"0.57056737",
"0.5684519",
"0.56820756",
"0.56553745",
"0.56527156",
"0.5647538",
"0.56249356",
"0.56219... | 0.72560215 | 0 |
Recibe el numero de segmentos, utiliza la x de la clase y tambien el dof Evalua la regla de Simpson Regresa el calulo | def P(self,numSeg):
w=self.x/numSeg
return (w/3)*(self.F(0)+self.sumaImpar(numSeg,w)+self.sumaPar(numSeg,w)+self.F(self.x)) | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def schaffern1fcn(x: np.ndarray) -> np.ndarray:\n if x.shape[1] != 2:\n raise ValueError(\n \"Schaffer function N. 1 is defined only on a 2D space.\"\n )\n X = x[:, 0]\n Y = x[:, 1]\n\n numeratorcomp = (np.sin((X**2 + Y**2) ** 2) ** 2) - 0.5\n denominatorcomp = (1 + 0.001 * ... | [
"0.603575",
"0.59524214",
"0.58458906",
"0.57840693",
"0.57768226",
"0.5736538",
"0.5676084",
"0.562847",
"0.5549627",
"0.5509658",
"0.5484242",
"0.5461846",
"0.5453628",
"0.5446418",
"0.53927326",
"0.5381252",
"0.53637886",
"0.53617305",
"0.53459823",
"0.53459823",
"0.534225... | 0.5704941 | 6 |
Esta funcion rescibe dos valores de P Evalua de forma booleana si el valor de la resta es menor que 0.00001 | def checarPs(self,p1,p2):
return abs(p1-p2) < 0.00001 | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def check_for_float(check):",
"def test_correct_p_values_no_change(self):\r\n exp = [None, 0.008]\r\n obs = self.mc._correct_p_values([None, 0.008])\r\n self.assertEqual(obs, exp)\r\n exp = [0.007]\r\n obs = self.mc._correct_p_values([0.007])\r\n assert_almost_equal(obs,... | [
"0.6126959",
"0.6091934",
"0.6083219",
"0.6069677",
"0.60691434",
"0.59945536",
"0.59785897",
"0.595968",
"0.59528214",
"0.59318626",
"0.5901813",
"0.5901813",
"0.5889509",
"0.5824826",
"0.5815684",
"0.57984555",
"0.5797382",
"0.57892585",
"0.5786633",
"0.5771933",
"0.5760534... | 0.0 | -1 |
Esta funcion es el constructor de la clase | def __init__(self,x,dof):
self.x=x
self.dof=dof
numSeg=10
p1=self.P(numSeg)
p2=0
while True:
numSeg*=2
p2=self.P(numSeg)
if self.checarPs(p1,p2):
break
else:
p1=p2
print(round(p2,5)) | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def __init__(self, constructor_fn=None):",
"def __init__(self, constructor_fn=None):",
"def __init__ (self) :",
"def __init__(__self__):\n pass",
"def __init__(__self__):\n pass",
"def __init__(__self__):\n pass",
"def __init__(__self__):\n pass",
"def __init__(__self__):\... | [
"0.7876094",
"0.7876094",
"0.76834565",
"0.7615697",
"0.7615697",
"0.7615697",
"0.7615697",
"0.7615697",
"0.7615697",
"0.7615697",
"0.7615697",
"0.7615697",
"0.7615697",
"0.76075494",
"0.75988233",
"0.7574014",
"0.7574014",
"0.754344",
"0.75391805",
"0.7525598",
"0.7525598",
... | 0.0 | -1 |
Return a decorator which will parse a gerber file before running the test. | def use_file(filename):
def decorator(test_method):
""" Add params to decorator function. """
@wraps(test_method)
def wrapper(self):
""" Parse file then run test. """
parser = Gerber(ignore_unknown=False)
self.design = parser.parse(path.join(DIR, filenam... | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def decorator(test_method):\n\n @wraps(test_method)\n def wrapper(self):\n \"\"\" Parse file then run test. \"\"\"\n parser = Gerber(ignore_unknown=False)\n self.design = parser.parse(path.join(DIR, filename))\n test_method(self)\n\n return wrapper",... | [
"0.7448634",
"0.71167976",
"0.59627867",
"0.59301746",
"0.5918239",
"0.59080213",
"0.58810973",
"0.57334006",
"0.56384057",
"0.5625038",
"0.55969214",
"0.55764806",
"0.5508951",
"0.550502",
"0.5491165",
"0.5372833",
"0.53668374",
"0.53651786",
"0.53651786",
"0.52833706",
"0.5... | 0.7256232 | 1 |
Add params to decorator function. | def decorator(test_method):
@wraps(test_method)
def wrapper(self):
""" Parse file then run test. """
parser = Gerber(ignore_unknown=False)
self.design = parser.parse(path.join(DIR, filename))
test_method(self)
return wrapper | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def param(*args, **kwargs):\n p = Param(*args, **kwargs)\n\n def decorator(func):\n func.param = p\n return func\n\n return decorator",
"def params(funcarglist):\n def wrapper(function):\n function.funcarglist = funcarglist\n return function\n return wrapper",
"def _u... | [
"0.6966783",
"0.68387944",
"0.6661411",
"0.65097076",
"0.64938056",
"0.64089364",
"0.637854",
"0.635611",
"0.6307712",
"0.6263976",
"0.62250924",
"0.61494106",
"0.6050514",
"0.59442437",
"0.59440565",
"0.59188884",
"0.58860785",
"0.58772427",
"0.5874225",
"0.5865413",
"0.5854... | 0.0 | -1 |
Parse file then run test. | def wrapper(self):
parser = Gerber(ignore_unknown=False)
self.design = parser.parse(path.join(DIR, filename))
test_method(self) | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def test_parse(self): \n\n results = self.parser.parse()\n self.assertEqual(results, test_case_data['parse_output'])",
"def main():\n parse_file(sys.argv[1])",
"def test_parse_file(self, tmpdir):\n filename = tmpdir.join(\"test.xbb\")\n\n with open(filename, \"w\") as f:\n ... | [
"0.72975254",
"0.72955656",
"0.68624204",
"0.6839642",
"0.68134034",
"0.6797835",
"0.6793306",
"0.67111844",
"0.6621141",
"0.66025037",
"0.66010785",
"0.65545213",
"0.6546812",
"0.65328765",
"0.65042335",
"0.6461551",
"0.64531183",
"0.6451311",
"0.64335024",
"0.6405252",
"0.6... | 0.58652794 | 58 |
Setup the test case. | def setUp(self):
self.design = None | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def setUp(self):\n MainTests.setUp(self)",
"def setUp(self):\n logging.debug('setting up')",
"def setUp(self):\n logging.debug('setting up')",
"def setUp(self):\n \n pass",
"def setUp(self):\n\n self._set_up()",
"def setUp(self):\n test_env_setup()",
"de... | [
"0.8319253",
"0.8303649",
"0.8303649",
"0.82346183",
"0.8222515",
"0.8190009",
"0.8142373",
"0.8142373",
"0.81257635",
"0.8111714",
"0.810949",
"0.8089887",
"0.8089887",
"0.8089887",
"0.8089887",
"0.8089887",
"0.8089887",
"0.8089887",
"0.8089887",
"0.8089887",
"0.8089887",
... | 0.0 | -1 |
Create an empty gerber parser. | def test_create_new_gerber_parser(self):
parser = Gerber()
assert parser != None | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def create_parser():\n pass",
"def _make_parser(self):\n return DefusedExpatParser()",
"def __init__(self, parser=None):",
"def __init__(self):\n print \"You asked for a Parser!\"",
"def __parser__(self):\n return self",
"def __init__(self, parser: Any = None):",
"def test_gen_p... | [
"0.70855314",
"0.686953",
"0.63831055",
"0.6263777",
"0.61320263",
"0.6107546",
"0.60626626",
"0.6037953",
"0.59399813",
"0.5923526",
"0.5910576",
"0.5903135",
"0.5893762",
"0.58550376",
"0.57761353",
"0.5761796",
"0.5757238",
"0.5713794",
"0.5700876",
"0.56808746",
"0.567541... | 0.7622803 | 0 |
Parse a simple, correct gerber file. | def test_simple(self):
image = self.design.layout.layers[0].images[0]
assert len(image.traces) == 2 | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def parse(self, infile):\r\n raise NotImplementedError()",
"def main():\n parse_file(sys.argv[1])",
"def _parse(self, infile):\n raise NotImplementedError()",
"def parse_data(fp):\n pass",
"def parse(self, filename):\n try:\n if 't' in self.FILE_OPEN_MODE:\n ... | [
"0.6448221",
"0.62971914",
"0.6292576",
"0.6234875",
"0.62203777",
"0.60354435",
"0.5979849",
"0.5967455",
"0.58838326",
"0.58157027",
"0.58120286",
"0.56847286",
"0.56830376",
"0.5674723",
"0.5657585",
"0.561286",
"0.55799603",
"0.557439",
"0.5564147",
"0.5547885",
"0.554700... | 0.0 | -1 |
Parse some connected arcs and lines gerber. | def test_arcs(self):
image = self.design.layout.layers[0].images[0]
assert len(image.traces) == 2 | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def parse_lats(lines):\n class Parser:\n def __init__(self):\n self.state = 'get_utt_id'\n self.utt_id = ''\n self.out = {}\n\n def is_line_utt_id(self, splited_line):\n return len(splited_line) == 1\n\n def new_utt(self, splited_line):\n ... | [
"0.654071",
"0.5878847",
"0.5738166",
"0.57329017",
"0.57178354",
"0.56650144",
"0.563962",
"0.56280166",
"0.553405",
"0.553402",
"0.55142915",
"0.54828024",
"0.5479437",
"0.54232544",
"0.54089653",
"0.5399194",
"0.5396662",
"0.53636837",
"0.53310245",
"0.53172666",
"0.531521... | 0.0 | -1 |
Parse outline fills gerber. | def test_outline_fills(self):
image = self.design.layout.layers[0].images[0]
assert len(image.fills) == 2 | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def GetLinePostProcess(self):\r\n retline = None\r\n outline = None\r\n try:\r\n retline= str(self.file.readline())\r\n except IOError:\r\n self.tracking.SetError(type(self).__name__, sys._getframe().f_code.co_name, \"cannot read a line from\" )\r\n finally... | [
"0.54550266",
"0.53504366",
"0.5275898",
"0.5209391",
"0.5129223",
"0.5023708",
"0.49978548",
"0.49913824",
"0.49811244",
"0.49447837",
"0.49260226",
"0.4864756",
"0.48543087",
"0.48436245",
"0.48063695",
"0.470252",
"0.46995398",
"0.4677932",
"0.46646264",
"0.46302944",
"0.4... | 0.5327663 | 2 |
Parse a smear gerber. | def test_smear(self):
image = self.design.layout.layers[0].images[0]
assert len(image.smears) == 1 | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def parse(self):",
"def parse(self):\n pass",
"def parse(self):\n pass",
"def parse(self):\n pass",
"def parse(self):\n pass",
"def _parse(self):\n pass",
"def parse(self) -> None:\n pass",
"def parse(cls, s):\n raise NotImplementedError",
"def parse... | [
"0.6050831",
"0.59192437",
"0.59192437",
"0.59192437",
"0.59192437",
"0.58157104",
"0.5804667",
"0.5667438",
"0.56673455",
"0.5582821",
"0.553624",
"0.5477379",
"0.5466349",
"0.5438679",
"0.5426614",
"0.5339378",
"0.5334901",
"0.53278166",
"0.52798384",
"0.5264409",
"0.525246... | 0.0 | -1 |
Parse aperture macros gerber. | def test_complex(self):
image = self.design.layout.layers[0].images[2]
assert len(image.shape_instances) == 3 | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def __parse_macro(self, buffer):\n\t\t\n\t\t# Parse an optional id\n\t\tspell = self.__read_number(buffer)\n\t\t\n\t\t##\n\t\t# FIXME technically, the effects do not exist, as\n\t\t# WoW parses the identifier alphanumerically\n\t\t# Do we really want that? It's easier to go back.\n\t\t\n\t\t# Parse an alphabetic i... | [
"0.58941257",
"0.5843007",
"0.5546842",
"0.53140604",
"0.5287681",
"0.5214822",
"0.5029532",
"0.49508327",
"0.49250644",
"0.49058402",
"0.49010736",
"0.4891424",
"0.48260668",
"0.48217857",
"0.48092648",
"0.48078823",
"0.48026338",
"0.48020837",
"0.4797323",
"0.47908527",
"0.... | 0.0 | -1 |
Parse a batch of gerber files in a zip file. | def test_zip_batch(self):
assert self.design.layout.layers[0].name == 'top' | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def _add_tag_files(\n zip_file, dir_name, payload_info_list, payload_byte_count, payload_file_count\n):\n tag_info_list = []\n _add_tag_file(zip_file, dir_name, tag_info_list, _gen_bagit_text_file_tup())\n _add_tag_file(\n zip_file,\n dir_name,\n tag_info_list,\n _gen_bag_in... | [
"0.635105",
"0.62073517",
"0.61985546",
"0.6158757",
"0.59900516",
"0.58955044",
"0.58135545",
"0.58013874",
"0.57838947",
"0.56704354",
"0.5652113",
"0.5610305",
"0.55248296",
"0.551513",
"0.5497405",
"0.549419",
"0.5461678",
"0.5454392",
"0.5449247",
"0.541069",
"0.54071915... | 0.0 | -1 |
Parse a batch of gerber files in a bz2 tarball. | def test_bz_batch(self):
assert self.design.layout.layers[0].name == 'top' | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def extract_bz2(tar_bz_f, calc_type):\n \n # we give the gaussian calculator a label that includes the directory the\n # log file is contained in, this does not affect the parsing process but\n # generate a warning as it is not an expected form for the label. To avoid\n # the profusion of warning me... | [
"0.62602454",
"0.57246566",
"0.56907696",
"0.56726176",
"0.550637",
"0.5499982",
"0.54376435",
"0.542693",
"0.54081875",
"0.5403217",
"0.53807425",
"0.5374287",
"0.53654516",
"0.53579986",
"0.53536445",
"0.5324675",
"0.53113073",
"0.5298232",
"0.52399564",
"0.5238451",
"0.522... | 0.0 | -1 |
Parse a batch of gerber files in a gz tarball. | def test_gz_batch(self):
assert self.design.layout.layers[0].name == 'top' | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def parse_gzipped_directory(input_dir, start_date, end_date, infos, backup_stamps):\n try:\n file_names = sorted(os.listdir(input_dir)) \n for file_name in file_names:\n if file_name.endswith(\".manifest.gz\") or file_name.endswith(\".manifest\"):\n ... | [
"0.62771606",
"0.5906162",
"0.580242",
"0.57709885",
"0.567405",
"0.5659064",
"0.56499046",
"0.5587792",
"0.5565765",
"0.55654675",
"0.5555699",
"0.5538824",
"0.5521462",
"0.548998",
"0.54764485",
"0.54678583",
"0.54415685",
"0.5418712",
"0.5413513",
"0.54120094",
"0.54090226... | 0.0 | -1 |
The Modifier can evaluate expressions correctly. | def test_modifier(self):
modif = Modifier('1.2')
self.assertEqual(modif.evaluate({}), 1.2)
modif = Modifier('$1')
self.assertEqual(modif.evaluate({1:3.2}), 3.2)
modif = Modifier('1+1')
self.assertEqual(modif.evaluate({}), 2)
modif = Modifier('3-1.5')
self.... | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def _should_eval(self):\n return False",
"def evaluate(compiled_expression):",
"def evaluate(self):\n pass",
"def evaluate(self):\n pass",
"def eval(self):\n pass",
"def eval(self):\n pass",
"def eval(self):\n pass",
"def evaluate(self) :\n pass",
"d... | [
"0.6572281",
"0.6568479",
"0.65574527",
"0.65574527",
"0.64303815",
"0.64303815",
"0.64303815",
"0.6407245",
"0.6345367",
"0.62577146",
"0.6183484",
"0.61799407",
"0.61565596",
"0.6149802",
"0.61396885",
"0.6117585",
"0.6077628",
"0.60701233",
"0.6039489",
"0.60292995",
"0.60... | 0.71497124 | 0 |
Trap param outside of gerber param block. | def test_missing_delim(self): | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def prepost_hook_too_many_parameters(self, param) -> None:\n pass",
"def _handleInput(self, paramInput):\n pass",
"def paramValueChanged(self, param):\n if self._printSWAP == True:\n print param.name + \" in address \" + str(param.getRegAddress()) + \" changed to \" + param.getValue... | [
"0.6485111",
"0.6299571",
"0.5991846",
"0.590375",
"0.58012176",
"0.5784556",
"0.5730866",
"0.5685745",
"0.5592114",
"0.5574099",
"0.5539806",
"0.55120116",
"0.55019736",
"0.54560244",
"0.5417562",
"0.5411254",
"0.5411254",
"0.5411254",
"0.5406385",
"0.537721",
"0.53710365",
... | 0.0 | -1 |
Trap coord preceding gerber format spec. | def test_coord_preceding_fs(self): | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def trace(self, coord01: np.ndarray) -> np.ndarray:\n rect = self.clip_rect()\n return (rect.position + coord01 * rect.size).astype(np.int)",
"def frac11(self,lx,ly,lz):\n return str(self.coord[0]/lx*2)+'\\t'+str(self.coord[1]/ly*2)+'\\t'+str(self.coord[2]/lz*2)",
"def _format_point(self, ... | [
"0.52641153",
"0.5259147",
"0.5174216",
"0.5166887",
"0.5154606",
"0.514098",
"0.51310825",
"0.51202244",
"0.51102793",
"0.5103446",
"0.50844723",
"0.5079553",
"0.507823",
"0.50599504",
"0.5053271",
"0.5025921",
"0.5018617",
"0.4984303",
"0.49542806",
"0.4949716",
"0.49197924... | 0.61945975 | 0 |
Trap coord inside gerber param block. | def test_data_in_param(self): | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def xy(self):\n ...",
"def paramValueChanged(self, param):\n if self._printSWAP == True:\n print param.name + \" in address \" + str(param.getRegAddress()) + \" changed to \" + param.getValueInAscii()",
"def modifyPoint(self, *args, **kwargs):\n ...",
"def set_coord(self, l, s... | [
"0.56467545",
"0.553417",
"0.53961",
"0.5391049",
"0.5386599",
"0.5367348",
"0.53164357",
"0.5312498",
"0.53037393",
"0.5255599",
"0.5255599",
"0.5255599",
"0.5255599",
"0.5255599",
"0.5255599",
"0.5255599",
"0.5255599",
"0.5255599",
"0.5255599",
"0.5255599",
"0.5238645",
"... | 0.0 | -1 |
Trap coord with 'Y' before 'X' gerber. | def test_y_before_x(self): | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def _coord(self, x, y):\n gridEdge = 7 # originally 5\n y = gridEdge - y\n cx = 100 * (x - 1) + 50\n cy = 100 * (y - 1) + 50\n r = 20\n return (cx - r, cy - r, cx + r, cy + r)",
"def _transform_point(self, x, y):\n return (x, y)",
"def set_position(sel... | [
"0.6347154",
"0.615938",
"0.59551126",
"0.594736",
"0.5881816",
"0.5860635",
"0.5815088",
"0.57782364",
"0.5747512",
"0.57448643",
"0.57318264",
"0.57293063",
"0.57039654",
"0.5697053",
"0.5697053",
"0.56909347",
"0.5679062",
"0.5646204",
"0.5643103",
"0.5624204",
"0.561082",... | 0.5459573 | 44 |
Trap data following M02 block gerber. | def test_trailing_data(self): | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def _data_move_out_mc_on_h():\n\n pass",
"def onBlock(self, data) :\n pass",
"def readBumper(self, msg):\n #\n # if(msg.state==1):#the bumper is pressed\n self.executeTrajectory()",
"def _handle_MonitorData (self, event, packet, reverse):\n pass",
"def handleModuleMessage(s... | [
"0.56816924",
"0.55445737",
"0.5298501",
"0.52529526",
"0.5242817",
"0.5230332",
"0.52025527",
"0.51271504",
"0.5111258",
"0.50924855",
"0.50700384",
"0.5046472",
"0.5040559",
"0.5023257",
"0.5019368",
"0.49901193",
"0.49784297",
"0.49663934",
"0.49618027",
"0.4956633",
"0.49... | 0.0 | -1 |
Trap file with no M02 block gerber. | def test_no_eof(self): | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def cleanupV032backup(self):\n doCleanup = False\n if (os.path.isfile(self.MAPSTUDIO + 'm10_00_00_00.msb.bak')):\n self.msbio.open(self.MAPSTUDIO + 'm10_00_00_00.msb.bak')\n if (len(self.msbio.models.rows) >= 373):\n doCleanup = True\n\n if (doCleanup):\n ... | [
"0.5411359",
"0.53538233",
"0.53510696",
"0.5252125",
"0.51773673",
"0.5137562",
"0.5103627",
"0.509049",
"0.50799817",
"0.50792575",
"0.5078129",
"0.5071632",
"0.50331587",
"0.5031816",
"0.50235265",
"0.5013143",
"0.50088",
"0.50076556",
"0.50074273",
"0.50043285",
"0.499754... | 0.0 | -1 |
Trap offspec data in gerber file. | def test_alien_data(self): | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def add_fault_rupture_from_file(self, fault_filename):\n self.fault.add_patches_from_file(fault_filename) \n self.irst = 214",
"def test_fake_file(self):\n fits_file = os.path.join(self.datadir, 'monol_test_fake.evt')\n hen.fake.main(['-o', fits_file, '--instrument', 'FPMB'])\n... | [
"0.55719537",
"0.5494891",
"0.51716053",
"0.51296675",
"0.5104879",
"0.5093885",
"0.50897896",
"0.50862515",
"0.5061046",
"0.50539726",
"0.5030481",
"0.5016976",
"0.50007325",
"0.4999721",
"0.49765038",
"0.4970551",
"0.4964387",
"0.4937533",
"0.4932086",
"0.49242124",
"0.4913... | 0.0 | -1 |
Trap long arc in single quadrant mode. | def test_single_quadrant(self): | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def place_rebar_long_torsion(as_tl_req, d):\r\n \"\"\"as_tl_req - area of longitudinal reinforcement required for torsion\"\"\"\r\n \"\"\"d - preferred diameter (this is initially the flexural rebar diameter. If not enough, chose one diameter above\"\"\"\r\n \"\"\"returns a list with [n, d] where n is num... | [
"0.51212114",
"0.503686",
"0.500466",
"0.49968642",
"0.49456814",
"0.4928112",
"0.4917071",
"0.48972583",
"0.48096138",
"0.48058507",
"0.47610927",
"0.4761016",
"0.47439614",
"0.47282705",
"0.47250915",
"0.47182012",
"0.47141975",
"0.47103226",
"0.47048694",
"0.47028008",
"0.... | 0.46925488 | 21 |
Trap unsuccessful outline fill closure. | def test_open_fill(self): | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def end_fill():\n turtleTmp.end_fill()",
"def test_outline_fills(self):\n image = self.design.layout.layers[0].images[0]\n assert len(image.fills) == 2",
"def fillbox(self,event=None):\n \n pass",
"def update_fill(self, event):\r\n\r\n if event.type == 'FILL':\r\n ... | [
"0.5995263",
"0.5990204",
"0.5509914",
"0.5184432",
"0.51762307",
"0.51762307",
"0.514419",
"0.51174825",
"0.50964",
"0.50798017",
"0.50475687",
"0.50426537",
"0.5025028",
"0.49561536",
"0.4947993",
"0.49472082",
"0.4876335",
"0.484599",
"0.48382837",
"0.48201862",
"0.4810579... | 0.0 | -1 |
Trap nonlinear smear gerber. | def test_arc_smear(self): | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def post_process_trap(): \n #################### 0) assign internal values #################### \n from project_parameters import trapType,debug,trapFile,name,driveAmplitude,driveFrequency,Omega,dcplot,weightElectrodes,coefs,ax,az,phi,save,scale\n #from all_functions import find_saddle,plot_potential,dc_p... | [
"0.54921705",
"0.52793443",
"0.52202374",
"0.521817",
"0.5195716",
"0.51095015",
"0.51095015",
"0.50273573",
"0.49843332",
"0.4955213",
"0.4955092",
"0.49494436",
"0.49199587",
"0.4883605",
"0.48833477",
"0.48775414",
"0.48286638",
"0.4825539",
"0.48209244",
"0.48204193",
"0.... | 0.0 | -1 |
Subscibe a set of event keys for a callback. | def subscribe(callback, keys):
assert type(keys) in (set, list, tuple)
_subscribers[callback] = keys | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def _handle_key_event(self, key, modifiers, mapping):\n if key in mapping:\n for callback in mapping[key]:\n callback()",
"def make_keyhandler(events):\n def handler(key):\n for k in events:\n if key == simplegui.KEY_MAP[k]:\n events[k]()\n ... | [
"0.68615484",
"0.68123263",
"0.6174684",
"0.58327556",
"0.58170974",
"0.5806323",
"0.5780186",
"0.5754679",
"0.5689066",
"0.567472",
"0.56471545",
"0.5627545",
"0.56092143",
"0.55985314",
"0.55752456",
"0.55332804",
"0.5533179",
"0.55255973",
"0.55047953",
"0.5493462",
"0.546... | 0.65743834 | 2 |
Unsubscribe events for a callback. | def unsubscribe(callback):
if callback in _subscribers:
del _subscribers[callback] | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def unsubscribe(self, callback: Callable) -> None:\n self.callbacks.discard(callback)",
"def unsubscribe(self, event_type: typing.Type[typing.Any], callback: CallbackT[typing.Any]) -> None:",
"def unsubscribe_callback(self, callback, sensor):\n if sensor in self._callbacks:\n self._cal... | [
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"0.7856983",
"0.7775709",
"0.7710769",
"0.7495644",
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"0.7495644",
"0.7495644",
"0.7495644",
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"0.74136734",
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"0.72853684",
"0.72737384",
"0.72261065",
"0.72020453",
"0.7193984",
"0.71859956",
"0.718... | 0.85581386 | 0 |
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