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def testIBP(): """ Plot matrices generated by an IBP, for a few different settings. """ from pybrain.tools.plotting.colormaps import ColorMap import pylab # always 50 customers n = 50 # define parameter settings ps = [(10, 0.1), (10,), (50,), (50, 0.5), ] ...
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def rel_error(model, X, Y, meanY =0): """function to compute the relative error model : trained neural network to compute the predicted data X : input data Y : reference output data meanY : the mean of the of the untreated Y """ Yhat = model.predict(X) dY = Yhat - Y axis = tuple(...
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def read_data(vocab, path): """Reads a bAbI dataset. Args: vocab (collections.defaultdict): A dictionary storing word IDs. path (str): Path to bAbI data file. Returns: list of Query of Sentence: Parsed lines. """ data = [] all_data = [] with open(path) as f: ...
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def get_dataset(cfg: DatasetConfig, shard_id: int, num_shards: int, feature_converter_cls: Type[seqio.FeatureConverter], num_epochs: Optional[int] = None, continue_from_last_checkpoint: bool = False) -> tf.data.Dataset: """Returns a datas...
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def contour_distances_2d(image1, image2, dx=1): """ Calculate contour distances between binary masks. The region of interest must be encoded by 1 Args: image1: 2D binary mask 1 image2: 2D binary mask 2 dx: physical size of a pixel (e.g. 1.8 (mm) for UKBB) Returns: mea...
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def weighted_sequence_identity(a, b, weights, gaps='y'): """Compute the sequence identity between two sequences, different positions differently The definition of sequence_identity is ambyguous as it depends on how gaps are treated, here defined by the *gaps* argument. For details and examples, see `...
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def loss_fd(batch,model,reconv_psf_image,step=0.01): """ Defines a loss respective to unit shear response Args: batch: tf batch Image stamps as ['obs_image'] and psf models as ['psf_image'] reconv_psf_image: tf tensor Synthetic reconvolution psf step: float Step size for the f...
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def batch_tokenize(sentences: List[str], tokenizer: yttm.BPE, batch_size: int = 256, bos: bool = True, eos: bool = True) -> List[List[int]]: """ Tokenize input sentences in batches. :param sentences: sentences to tokenize :param...
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def blog_index(request): """The index of all blog posts""" ctx = {} entries = Page.objects.filter(blog_entry=True).order_by( '-pinned', '-date_created') paginator = Paginator(entries, 10) page_num = request.GET.get('page') ctx['BASE_URL'] = settings.BASE_URL try: entries = ...
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def read_ini_file(file_path): """Read an ini file and return the profile data. If the profile name begins with 'profile ', remove it. Parameters ---------- - file_path - the path to the file to read Returns ------- The profile data. """ LOG.info('Reading ini file from %s', file...
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def pair_time(pos_k, pos_l, vel_k, vel_l, radius): """ pos_k, pos_l, vel_k, vel_l all have two elements as a list """ t_0=0.0 pos_x=pos_l[0]-pos_k[0] pos_y=pos_l[1]-pos_k[1] Delta_pos=np.array([pos_x, pos_y]) vel_x=vel_l[0]-vel_k[0] vel_y=vel_l[1]-vel_k[1...
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def test_systeminit(): """ Test that initializing a ``System`` class produces a list of ``Prior`` objects of the correct length when: - parallax and total mass are fixed - parallax and total mass errors are given - parallax is fixed, total mass error is given - parallax error...
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def replace_version(search_dir: Path = _DEFAULT_SEARCH_DIR, *, old: str, new: str): """Replaces the current version number with a new version number. Args: search_dir: the search directory for modules. old: the current version number. new: the new version number. Raises: Val...
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def coco_to_shapely(inpath_json: Union[Path, str], categories: List[int] = None) -> Dict: """Transforms COCO annotations to shapely geometry format. Args: inpath_json: Input filepath coco json file. categories: Categories will filter to specific categories and images that co...
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def test_ssl_configuration(): """ Given: - Kafka initialization parameters When: - Initializing KafkaCommunicator object Then: - Assert initialization is as expected. """ kafka = KafkaCommunicator(brokers='brokers', ca_cert='ca_cert', ...
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def create_activity_specific_breathing_rate_df( person_breathing_in, time, event, breathing_rate_key, rounding=5 ): """ Generate breathing rates taking into account age and activity intensity. Parameters: person_breathing_in: string E.g. "person 1" time: stri...
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def find_valid_imported_name(name): """return a name preceding an import op, or False if there isn't one""" return name.endswith(MARKER) and remove_import_op(name)
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def parseText(text1, nlp): """Run the Spacy parser on the input text that is converted to unicode.""" doc = nlp(text1) return doc
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def read_rc(rcpath): """Retrieve color values from the rc file. Arguments: rcpath (str): path to the rc file. Returns: 3-tuple of integers representing R,G,B. """ if not os.path.exists(rcpath): return None with open(rcpath) as rc: colors = [int(ln) for ln in rc....
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def load_gij_coeff_matrix(friction_coeffs_root, translation, order_g12, eps=1e-8): """ Load Fourier expansion coefficients of friction coefficients gii and gij. Represent result as a matrix (numpy.array) :param translation: means relative position of the second oscillator """ # Determine if tra...
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def view_pebbles_home(request): """Serve up the workspace, the current home page. Include global js settings""" app_config = AppConfiguration.get_config() if app_config is None: return HttpResponseRedirect(reverse('view_no_domain_config_error')) # Is this D3M Mode? If so, make sure: # ...
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def save_to_pickle(value, path, file_name): """saves a value into a pickle file""" if not os.path.exists(path): os.mkdir(path) with open(os.path.join(path, file_name), 'wb') as handle: pickle.dump(value, handle, protocol=pickle.HIGHEST_PROTOCOL)
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def multi_pretty(request): """ 批量添加(Excel文件)""" from openpyxl import load_workbook if request.method == "GET": return render(request, 'multi_pretty.html') file_object = request.FILES.get("exc") wb = load_workbook(file_object) sheet = wb.worksheets[0] for row in sheet.iter_rows(min_ro...
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def is_port_open(host, port, timeout=5): """ verifies if a port is open in a remote host :param host: IP of the remote host :type host: str :param port: port to check :type port: int :param timeout: timeout max to check :type timeout: int :return: True if the port is open :rt...
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def check_transport_reaction_gpr_presence(model): """Return the list of transport reactions that have no associated gpr.""" return [ rxn for rxn in helpers.find_transport_reactions(model) if not rxn.gene_reaction_rule ]
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def get_RSA_modulus(b, num): """ Generates a list of RSA modulus' of bit length b such that each modulus, n = pq, where p and q are both primes. :param b: bit length of the modulus :param num: number of modulus' you want :returns: a list of RSA modulus' """ p_lst = [] # genera...
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def generate_single_color_images(width, height, destination_dir): """ Generates and saves to disk about 1000 single-color rectangle-shaped images """ light_values = range(69, 231, 3) medium_values = range(46, 154, 2) dark_values = range(23, 78, 1) index = 1 # Generate light coloured images ...
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def reset_data(): """Reset the datastore to a known state, populated with test data.""" setup.reset_datastore() db.put([ Authorization.create( 'haiti', 'test_key', domain_write_permission='test.google.com'), Authorization.create( 'haiti', 'domain_test_key', ...
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def use_processors(n_processes): """ This routine finds the number of available processors in your machine """ from multiprocessing import cpu_count available_processors = cpu_count() n_processes = n_processes % (available_processors+1) if n_processes == 0: n_processes = 1 print...
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def test_gauge_absolute_negative_rate_tcp(mock_random): """TCPStatsClient.gauge works with absolute negative value and rate.""" cl = _tcp_client() _test_gauge_absolute_negative_rate(cl, 'tcp', mock_random)
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def climate_radio_thermostat_ct101_multiple_temp_units_state_fixture(): """Load the climate multiple temp units node state fixture data.""" return json.loads( load_fixture( "zwave_js/climate_radio_thermostat_ct101_multiple_temp_units_state.json" ) )
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def get_TR_and_ntpts(dtseries_path, wb_command_path): """ :param dtseries_path: String, the full path to a .dtseries.nii file :param wb_command_path: String, the full path to the wb_command executable :return: Tuple of 2 numbers, the number of timepoints and repetition time """ if not os.path.ex...
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def GetPseudoAAC1(ProteinSequence, lamda=30, weight=0.05, AAP=[]): """ ####################################################################################### Computing the first 20 of type I pseudo-amino acid compostion descriptors based on the given properties. ####################################...
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def reversedict(dct): """ Reverse the {key:val} in dct to {val:key} """ # print labelmap newmap = {} for (key, val) in dct.iteritems(): newmap[val] = key return newmap
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def createNewEnsemble(templateVars, project, targetPath, mono): """ If "localEnv" is in templateVars, clone that ensemble; otherwise create one from a template with templateVars """ # targetPath is relative to the project root from unfurl import yamlmanifest assert not os.path.isabs(targetP...
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def pi_tune(): """Attempts to automatically tune the PI loop.""" print("TO BE IMPLEMENTED") # TODO return
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def mincut_graph_tool(edges: Iterable[Sequence[np.uint64]], affs: Sequence[np.uint64], sources: Sequence[np.uint64], sinks: Sequence[np.uint64], logger: Optional[logging.Logger] = None) -> np.ndarray: """ Computes the min cut on...
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def mock_graph_literal(): """Creates a mock tree Metasyntactic variables: https://www.ietf.org/rfc/rfc3092.txt """ graph_dict = [ { "frame": {"name": "foo", "type": "function"}, "metrics": {"time (inc)": 130.0, "time": 0.0}, "children": [ { ...
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def parse_footer(fn): """ Parse the downloaded FOOTER file, which contains a header for each program and (usually) a description line. Yields either a nested 2-tuple of (header-program-name, (description-program-name, description-text)) if a description can be found, or a 1-tuple of (header-pro...
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def parse_ADD_ins(tokens): """Attempts to parse an ADD instruction.""" failure = None assert len(tokens) > 0 if tokens[0].text.upper() != 'ADD': return failure statement = Obj() statement.type = 'STATEMENT' statement.statement_type = 'INSTRUCTION' statement.instruction = 'ADD' ...
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def commonIntegerPredicate(field): """"return any integers""" return tuple(re.findall("\d+", field))
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def spatialft(image, cosine_window=True, rmdc=True): """Take the fourier transform of an image (or flow field). shift the quadrants around so that low spatial frequencies are in the center of the 2D fourier transformed image""" #raised cosyne window on image to avoid border artifacts (dim1,dim2) = ...
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def _get_instrument_parameters(ufile, filemetadata): """ Return a dictionary containing instrument parameters. """ # pulse width pulse_width = filemetadata('pulse_width') pulse_width['data'] = ufile.get_pulse_widths() / _LIGHT_SPEED # m->sec # assume that the parameters in the first ray represent...
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def get_deployment_mode(path): """ Work out the 'deployment mode' from the global attributes in a NetCDF file :param path: path to dataset :return: Mode as a value from `DeploymentModes` enumeration :raises ValueError: if mode cannot be determined or is invalid """ fname = os.path.basena...
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def split_reaction(reac): """ split a CHEMKIN reaction into reactants and products :param reac: reaction string :type reac: str :returns: reactants and products :rtype: (tuple of strings, tuple of strings) """ em_pattern = one_of_these([PAREN_PLUS_EM + STRING_END, ...
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def bond_stereo_parities(sgr): """ bond parities, as a dictionary """ return mdict.by_key_by_position(bonds(sgr), bond_keys(sgr), BND_STE_PAR_POS)
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def archive_fs(locations): """Fixture to check the BagIt file generation.""" archive_path = locations['archive'].uri fs = opener.opendir(archive_path, writeable=False, create_dir=True) yield fs for d in fs.listdir(): fs.removedir(d, force=True)
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def encode(text): """ Encode to base64 """ return [int(x) for x in text.encode('utf8')]
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def _get_ip(): """ :return: This computer's default AF_INET IP address as a string """ # find ip using answer with 75 votes # https://stackoverflow.com/questions/166506/finding-local-ip-addresses-using-pythons-stdlib ip = '' sock = socket.socket(socket.AF_INET, socket.SOCK_DGRAM) ...
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def _get_value(cav, _type): """Get value of custom attribute item""" if _type == 'Map:Person': return cav["attribute_object"]["id"] \ if cav.get("attribute_object") else None if _type == 'Checkbox': return cav["attribute_value"] == '1' return cav["attribute_value"]
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def test_post_order_with_empty_input(): """To test post_order method with an empty tree.""" tree_new = BST() with pytest.raises(TypeError) as err: tree_new.post_order_traversal(tree_new.root) assert str(err.value) == (f'There is no node to traverse.')
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def get_inference(model, vectorizer, topics, text, threshold): """ runs inference on text input paramaters ---------- model: loaded model to use to transform the input vectorizer: instance of the vectorizer e.g TfidfVectorizer(ngram_range=(2, 3)) topics: the list of topics in the model ...
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def get_message_id(update: dict, status_update: str) -> int: """функция для получения номера сообщения. Описание - функция получает номер сообщения от пользователя Parameters ---------- update : dict новое сообщение от бота status_update : str состояние сообщения, изменено или ...
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def gmm_clustering_predict(model, X): """ X is a (N, 1) array """ X = np.clip(X, -2.5, 2.5) return model.predict(X)
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def http_request(url, method='GET', timeout=2, **kwargs): """Generic task to make an http request.""" headers = kwargs.get('headers', {}) params = kwargs.get('params', {}) data = kwargs.get('data', {}) request_kwargs = {} if headers: request_kwargs['headers'] = headers if params: ...
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def start_grpc_server(server: Server): """ Start the given gRPC `server`. This does not block so, if you don't have a mainloop, this will simply finish immediatly with the thread/process. """ server.start()
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def unify_nest(args: Type[MultiNode], kwargs: Type[MultiNode], node_str, mode, axis=0, max_depth=1): """ Unify the input nested arguments, which consist of sub-arrays spread across arbitrary nodes, to unified arrays on the single target node. :param args: The nested positional arguments to unify. :...
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def ast_for_inv_exp(inv: 'Ast', ctx: 'ReferenceDict'): """ invExp ::= atomExpr (atomExpr | invTrailer)*; """ assert inv.name is UNameEnum.invExp atom_expr, *inv_trailers = inv res = ast_for_atom_expr(atom_expr, ctx) if len(inv_trailers) is 1: [each] = inv_trailers if each.n...
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def json_writer(docs, json_file_path: str, source: str = None): """Converts a collection of Spacy Doc objects to a JSON format, such that it can be used to train the Spacy NER model. (for Spacy v2) Source must be an aggregated source (defined in user_data["agg_spans"]), which will correspond to the tar...
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def euler42_(): """Solution for problem 42.""" pass
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def create_input_pipeline(files, batch_size, n_epochs, shape, crop_shape=None, crop_factor=1.0, n_threads=2): """Creates a pipefile from a list of image files. ...
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def validate_supervise(key_name: str, sup_conf: Dict, params: Dict) -> None: """ Validate the supervise config subblock to be used for ETLBlock supervise operation. Parameters ---------- key_name : The subkey that maps to this extract subblock. sup_conf : The extract sub-config dict or config['...
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def confirm_email_page(): """Returns page for users that have not confirmed their email address""" if not g.loggedIn: return redirect(url_for('general.loginPage')) next = request.args.get('next') if general_db.is_activated(g.user): if next is not '': return make_auth_to...
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def get_movie_names(url_data): """Get all the movies from the webpage""" soup = BeautifulSoup(url_data, 'html.parser') data = soup.findAll('ul', attrs={'class' : 'ctlg-holder'}) #Get all the lines from HTML that are a part of ul with class = 'ctlg-holder' movie_list = [] for div in data: ...
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def message_results(): """Shows the user their message, with the letters in sorted order.""" message = request.form.get('message') encrypted_message = sort_letters(message) return render_template('message_results.html', message=encrypted_message)
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def fsum(iterable): # real signature unknown; restored from __doc__ """ fsum(iterable) Return an accurate floating point sum of values in the iterable. Assumes IEEE-754 floating point arithmetic. """ pass
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def flatten_dict(dicts, keys): """ Input is list of dicts. This operation pulls out the key in each dict and combines the values into a new list mapped to the original key. A new dictionary is formed with these key -> list mappings. """ return { key: flatten_n([d[key] for d in dicts]) fo...
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def main( source_files: List[str], destination_file: Optional[str], fail_on_failures: bool ) -> None: """ Convert2JUnit This tool allows you to convert various reports into the JUnit format. """ report = initialize_report(destination_file, source_files) apply_source_files(report, source_fil...
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def delete_file(file_name): """ Delete a file, does nothing if file does not exist. :param file_name: file to delete .. versionadded:: 9.3.1 """ if file_name: try: os.remove(file_name) except (FileNotFoundError, PermissionError): pass
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def render_url(fullpath, notebook=False): # , prefix="files"): """Converts a path relative to the notebook (i.e. kernel) to a URL that can be served by the notebook server, by prepending the notebook directory""" if fullpath.startswith('http://'): url = fullpath else: url = (radiopad...
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def register(): """Register User route.""" email = request.form.get('email') password = request.form.get('password') new_user = User.register(email, password) if new_user: return jsonify({'message': 'Registration successful.'}), 201 return jsonify({'message': 'Invalid username or passwor...
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def route_sns_task(event, context): """ Gets SNS Message, deserialises the message, imports the function, calls the function with args """ record = event['Records'][0] message = json.loads( record['Sns']['Message'] ) return run_message(message)
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def RAND_pseudo_bytes(*args, **kwargs): # real signature unknown """ Generate n pseudo-random bytes. Return a pair (bytes, is_cryptographic). is_cryptographic is True if the bytes generated are cryptographically strong. """ pass
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def release_dp_mean_absolute_deviation(x, bounds, epsilon): """Release the dp mean absolute deviation. Assumes dataset size len(`x`) is public. Theorem 27: https://arxiv.org/pdf/2001.02285.pdf """ lower, upper = bounds sensitivity = (upper - lower) * 2. / len(x) x = np.clip(x, *bounds) ...
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def train(hparams, datas=None, scope=None): """build the train process""" # 1. create the model model_creator = select_model_creator(hparams) train_model = _mh.create_model(model_creator, hparams, 'train') # eval_model = _mh.create_model(model_creator, hparams, 'eval') # infer_model = _mh.create_model(model_cre...
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def create_test_account(test_case, username="TestUser"): """ Creates user TestUser """ test_case.client.post(reverse("users:register"), {"username": username, "password": "password", "confirm_pass...
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def get_configuration(spec_path): """Get mrunner experiment specification and gin-config overrides.""" try: with open(spec_path, 'rb') as f: specification = cloudpickle.load(f) except pickle.UnpicklingError: with open(spec_path) as f: vars_ = {'script': os.path.basena...
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def inspect_single_run(raw_df, tag): """ :param : :return: None """ df = raw_df[ (raw_df['tag'] == tag) ].copy() print(len(df)) print(df[['seed_input_graph', 'seed_embedding', 'solution_frequency']]) print(df.columns) print(len(df)) print(df.head()) for j ...
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def LoadScores(firstfile, prevfile): """Load the first and previous scores. For each peptide, compute a prize that is -log10(min p-value across all time points). Assumes the scores are p-values or equivalaent scores in (0, 1]. Do not allow null or missing scores. Return: data frame with scores a...
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def add_makeflags(job_core_count, cmd): """ Correct for multi-core if necessary (especially important in case coreCount=1 to limit parallel make). :param job_core_count: core count from the job definition (int). :param cmd: payload execution command (string). :return: updated payload execution comm...
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def process_map(file_in, validate): """Iteratively process each XML element and write to csv(s)""" with codecs.open(NODES_PATH, 'w') as nodes_file, \ codecs.open(NODE_TAGS_PATH, 'w') as nodes_tags_file, \ codecs.open(WAYS_PATH, 'w') as ways_file, \ codecs.open(WAY_NODES_PATH, 'w') as...
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def _gen_find(subseq, generator): """Returns the first position of `subseq` in the generator or -1 if there is no such position.""" if isinstance(subseq, bytes): subseq = bytearray(subseq) subseq = list(subseq) pos = 0 saved = [] for c in generator: saved.append(c) if le...
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def fnCalculate_Bistatic_RangeAndDoppler(pos_target,vel_target,pos_rx,pos_tx,wavelength): """ Calculate measurement vector consisting of bistatic range and Doppler shift for 3D bistatic case. pos_rx, pos_tx = position of Rx and Tx in [km]. pos_target = position of target in [km]. wavelength = wavele...
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def all_permits(target_dynamo_table): """ Simply return all data from DynamoDb Table :param target_dynamo_table: :return: """ response = target_dynamo_table.scan() data = response['Items'] while response.get('LastEvaluatedKey', False): response = target_dynamo_table.scan(Exclusi...
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def maximum_difference_sort_value(contributions): """ Auxiliary function to sort the contributions for the compare_plot. Returns the value of the maximum difference between values in contributions[0]. Parameters ---------- contributions: list list containing 2 elements: a Numpy....
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def load_test_val_train_files(version): """Load the test, validation and train labels and images from the data folder. Also does the basic preprocessing (converting to the right datatype, clamping and rescaling etc.) return images_train, images_validation, images_test, labels_train, labels_validati...
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def get_primer_target_sequence(id, svStartChr, svStartPos, svEndChr, svEndPos, svType, svComment, primerTargetSize, primerOffset, blastdbcmd, genomeFile): """Get the sequences in which primers will be placed""" if svType in ["del", "inv3to3", "trans3to3", "trans3to5", "snv", "invRefA", "invAltA"]: targe...
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def human_format(num): """ :param num: A number to print in a nice readable way. :return: A string representing this number in a readable way (e.g. 1000 --> 1K). """ magnitude = 0 while abs(num) >= 1000: magnitude += 1 num /= 1000.0 return '%.2f%s' % (num, ['', 'K', 'M', 'G...
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def torchserve( model_path: str, management_api: str, image: str = TORCHX_IMAGE, params: Optional[Dict[str, object]] = None, ) -> specs.AppDef: """Deploys the provided model to the given torchserve management API endpoint. >>> from torchx.components.serve import torchserve >>> torchserv...
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def ExpandRange(r,s=1): """expand 1-5 to [1..5], step by 1-10/2""" if REGEX_PATTERNS['step'].search(r): [r1,s] = r.split('/') s=int(s) else: r1 = r (start,end) = r1.split('-') return [i for i in range(int(start),int(end)+1,s)]
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def write_file_if_changed(name, data): """ Write a file if the contents have changed. Returns True if the file was written. """ if path_exists(name): old_contents = read_file(name) else: old_contents = '' if (data != old_contents): write_file(name, data) return True return False
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def _get_preprocessor_loader(plugin_name): """Get a class that loads a preprocessor class. This returns a class with a single class method, ``transform``, which, when called, finds a plugin and defers to its ``transform`` class method. This is necessary because ``convert()`` is called as a decorato...
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def preprocess_sample(data, word_dict): """ Args: data (dict) Returns: dict """ processed = {} processed['Abstract'] = [sentence_to_indices(sent, word_dict) for sent in data['Abstract'].split('$$$')] if 'Task 2' in data: processed['Label'] = label_to_onehot(data['Task...
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def read_input_file(input_file_path): """ read inputs from input_file_path :param input_file_path: :return: """ cprint('[INFO]', bc.dgreen, "read input file: {}".format(input_file_path)) with open(input_file_path, 'r') as input_file_read: dl_inputs = yaml.load(input_file_read, Loader...
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async def test_burn( async_stubbed_sender, async_stubbed_sender_token_account_pk, test_token ): # pylint: disable=redefined-outer-name """Test burning tokens.""" burn_amount = 200 expected_amount = 300 burn_resp = await test_token.burn( account=async_stubbed_sender_token_account_pk, ...
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def test_cMpc_to_z_array(): """ Test passing a comoving distance array returns a redshift array """ comoving_distance_array = np.array([0.0, 3000]) # Must return an array expected_redshift_array = np.array([0.0, 0.8479314667609102]) calculated_redshift_array = pyxcosmo.cMpc_to_z(comoving_di...
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def PWebFetch (url, args, outfile, err): """ Generic Fetch a web product Sends a http post request to url and sames response to outfile Throws exception on error * url = where the request to be sent, e.g."https://www.cv.nrao.edu/cgi-bin/postage.pl" * args = dict or argum...
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def run_client( cfg: DictConfig, comm: MPI.Comm, model: nn.Module, loss_fn: nn.Module, num_clients: int, train_data: Dataset, test_data: Dataset = Dataset(), ): """Run PPFL simulation clients, each of which updates its own local parameters of model Args: cfg (DictConfig): th...
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def task_deploy_docs() -> DoitTask: """Deploy docs to the Github `gh-pages` branch. Returns: DoitTask: doit task """ if _is_mkdocs_local(): # pragma: no cover return debug_task([ (echo, ('ERROR: Not yet configured to deploy documentation without "use_directory_urls"',)), ...
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def plugin(version: str) -> 'Plugin': """Get the application plugin.""" return XPXPlugin
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