code string | signature string | docstring string | loss_without_docstring float64 | loss_with_docstring float64 | factor float64 |
|---|---|---|---|---|---|
profile_path = os.path.join(basedir, "profile_%s.yaml" % profile_name)
profile_config = load_yaml(profile_path)
src_name = profile_config['name']
profile_dict = profile_config['source_model']
return profile_name, src_name, profile_dict | def build_profile_dict(basedir, profile_name) | Get the name and source dictionary for the test source.
Parameters
----------
basedir : str
Path to the analysis directory
profile_name : str
Key for the spatial from of the target
Returns
-------
profile_name : str
Name of for this particular... | 3.044314 | 2.874646 | 1.059022 |
if DEFAULT_JOB_TYPE == 'slac':
from fermipy.jobs.slac_impl import get_slac_default_args
return get_slac_default_args(job_time)
elif DEFAULT_JOB_TYPE == 'native':
from fermipy.jobs.native_impl import get_native_default_args
return get_native_default_args()
return None | def get_batch_job_args(job_time=1500) | Get the correct set of batch jobs arguments.
Parameters
----------
job_time : int
Expected max length of the job, in seconds.
This is used to select the batch queue and set the
job_check_sleep parameter that sets how often
we check for job completion.
Returns
-----... | 2.993553 | 3.465114 | 0.863912 |
batch_job_args = get_batch_job_args(job_time)
if DEFAULT_JOB_TYPE == 'slac':
from fermipy.jobs.slac_impl import SlacInterface
return SlacInterface(**batch_job_args)
elif DEFAULT_JOB_TYPE == 'native':
from fermipy.jobs.native_impl import NativeInterface
return NativeInte... | def get_batch_job_interface(job_time=1500) | Create a batch job interface object.
Parameters
----------
job_time : int
Expected max length of the job, in seconds.
This is used to select the batch queue and set the
job_check_sleep parameter that sets how often
we check for job completion.
Returns
-------
j... | 2.987807 | 3.669775 | 0.814166 |
import sys
import argparse
# Argument defintion
usage = "usage: %(prog)s [options]"
description = "Collect all the new source"
parser = argparse.ArgumentParser(usage, description=__abstract__)
parser.add_argument("-i", "--input", type=argparse.FileType('r'), required=True,
... | def main() | if args.ebin == "ALL":
wcsproj = hpxmap.geom.make_wcs(
naxis=2, proj='MOL', energies=None, oversample=2)
mapping = HpxToWcsMapping(hpxmap.hpx, wcsproj)
for i, data in enumerate(hpxmap.counts):
ip = ImagePlotter(data=data, proj=hpxmap.hpx, mapping=mapping)
fig... | 2.602846 | 2.308156 | 1.127673 |
CopyBaseROI.register_class()
CopyBaseROI_SG.register_class()
SimulateROI.register_class()
SimulateROI_SG.register_class()
RandomDirGen.register_class()
RandomDirGen_SG.register_class() | def register_classes() | Register these classes with the `LinkFactory` | 4.99781 | 5.197032 | 0.961666 |
for pattern in copyfiles:
glob_path = os.path.join(orig_dir, pattern)
files = glob.glob(glob_path)
for ff in files:
f = os.path.basename(ff)
orig_path = os.path.join(orig_dir, f)
dest_path = os.path.join(dest_dir, f)
... | def copy_analysis_files(cls, orig_dir, dest_dir, copyfiles) | Copy a list of files from orig_dir to dest_dir | 1.903398 | 1.924474 | 0.989049 |
try:
os.makedirs(dest_dir)
except OSError:
pass
copyfiles = ['%s.fits' % roi_baseline,
'%s.npy' % roi_baseline,
'%s_*.xml' % roi_baseline] + cls.copyfiles
if isinstance(extracopy, list):
copyfiles += ... | def copy_target_dir(cls, orig_dir, dest_dir, roi_baseline, extracopy) | Create and populate directoris for target analysis | 3.188967 | 3.308626 | 0.963834 |
args = self._parser.parse_args(argv)
name_keys = dict(target_type=args.ttype,
target_name=args.target,
sim_name=args.sim,
fullpath=True)
orig_dir = NAME_FACTORY.targetdir(**name_keys)
dest_dir = NAME_FA... | def run_analysis(self, argv) | Run this analysis | 6.321289 | 6.328536 | 0.998855 |
job_configs = {}
ttype = args['ttype']
(sim_targets_yaml, sim) = NAME_FACTORY.resolve_targetfile(args)
targets = load_yaml(sim_targets_yaml)
base_config = dict(ttype=ttype,
roi_baseline=args['roi_baseline'],
extraco... | def build_job_configs(self, args) | Hook to build job configurations | 4.278306 | 4.268262 | 1.002353 |
binning = config['binning']
binsz = binning['binsz']
coordsys = binning.get('coordsys', 'GAL')
roiwidth = binning['roiwidth']
proj = binning.get('proj', 'AIT')
ra = config['selection']['ra']
dec = config['selection']['dec']
npix = int(np.round(ro... | def _make_wcsgeom_from_config(config) | Build a `WCS.Geom` object from a fermipy coniguration file | 2.728108 | 2.67766 | 1.01884 |
step_x = rand_config['step_x']
step_y = rand_config['step_y']
max_x = rand_config['max_x']
max_y = rand_config['max_y']
seed = rand_config['seed']
nsims = rand_config['nsims']
cdelt = wcsgeom.wcs.wcs.cdelt
pixstep_x = step_x / cdelt[0]
pi... | def _build_skydir_dict(wcsgeom, rand_config) | Build a dictionary of random directions | 2.149304 | 2.112373 | 1.017483 |
args = self._parser.parse_args(argv)
if is_null(args.config):
raise ValueError("Config yaml file must be specified")
if is_null(args.rand_config):
raise ValueError(
"Random direction config yaml file must be specified")
config = load_yaml... | def run_analysis(self, argv) | Run this analysis | 3.752805 | 3.740568 | 1.003272 |
workdir = os.path.dirname(config_path)
new_config_path = config_path.replace('.yaml', '_%06i.yaml' % seed)
config = load_yaml(config_path)
comps = config.get('components', [config])
for i, comp in enumerate(comps):
comp_name = "%02i" % i
if 'gtlik... | def _clone_config_and_srcmaps(config_path, seed) | Clone the configuration | 2.200399 | 2.20903 | 0.996093 |
gta.load_roi('sim_baseline_%06i.npy' % current_seed)
gta.set_random_seed(seed)
gta.simulate_roi()
if injected_name:
gta.zero_source(injected_name)
gta.optimize()
gta.find_sources(sqrt_ts_threshold=5.0, search_skydir=gta.roi.skydir,
... | def _run_simulation(gta, roi_baseline,
injected_name, test_sources, current_seed, seed, non_null_src) | Simulate a realization of this analysis | 4.171017 | 4.195541 | 0.994155 |
args = self._parser.parse_args(argv)
if not HAVE_ST:
raise RuntimeError(
"Trying to run fermipy analysis, but don't have ST")
workdir = os.path.dirname(args.config)
_config_file = self._clone_config_and_srcmaps(args.config, args.seed)
gta =... | def run_analysis(self, argv) | Run this analysis | 4.035884 | 4.036464 | 0.999856 |
job_configs = {}
ttype = args['ttype']
(targets_yaml, sim) = NAME_FACTORY.resolve_targetfile(args)
if targets_yaml is None:
return job_configs
config_yaml = 'config.yaml'
config_override = args.get('config')
if is_not_null(config_override):
... | def build_job_configs(self, args) | Hook to build job configurations | 3.756018 | 3.742922 | 1.003499 |
job_configs = {}
ttype = args['ttype']
(targets_yaml, sim) = NAME_FACTORY.resolve_targetfile(args)
if targets_yaml is None:
return job_configs
config_yaml = 'config.yaml'
config_override = args.get('config')
if is_not_null(config_override):
... | def build_job_configs(self, args) | Hook to build job configurations | 3.120001 | 3.123372 | 0.998921 |
ignore = ['pow', 'log10', 'sqrt', 'max']
branches = []
for k, v in aliases.items():
tokens = re.sub('[\(\)\+\*\/\,\=\<\>\&\!\-\|]', ' ', v).split()
for t in tokens:
if bool(re.search(r'^\d', t)) or len(t) <= 3:
continue
if bool(re.search(r'[a... | def get_branches(aliases) | Get unique branch names from an alias dictionary. | 3.976238 | 3.7925 | 1.048448 |
if re.search('.root?', txt) is not None:
c = ROOT.TChain(chain.GetName())
c.SetDirectory(0)
c.Add(txt)
friend_chains.append(c)
chain.AddFriend(c, rand_str())
return
files = np.loadtxt(txt, unpack=True, dtype='str')
if files.ndim == 0:
files = np... | def load_friend_chains(chain, friend_chains, txt, nfiles=None) | Load a list of trees from a file and add them as friends to the
chain. | 2.626627 | 2.574609 | 1.020204 |
from fermipy import utils
ebins = None
if 'ENERGIES' in hdulist:
hdu = hdulist['ENERGIES']
ectr = hdu.data.field(hdu.columns[0].name)
ebins = np.exp(utils.center_to_edge(np.log(ectr)))
elif 'EBOUNDS' in hdulist:
hdu = hdulist['EBOUNDS']
emin = hdu.data.field(... | def find_and_read_ebins(hdulist) | Reads and returns the energy bin edges.
This works for both the CASE where the energies are in the ENERGIES HDU
and the case where they are in the EBOUND HDU | 2.408362 | 2.411111 | 0.99886 |
nebins = len(hdu.data)
ebin_edges = np.ndarray((nebins + 1))
try:
ebin_edges[0:-1] = np.log10(hdu.data.field("E_MIN")) - 3.
ebin_edges[-1] = np.log10(hdu.data.field("E_MAX")[-1]) - 3.
except KeyError:
ebin_edges[0:-1] = np.log10(hdu.data.field("energy_MIN"))
ebin_edg... | def read_energy_bounds(hdu) | Reads and returns the energy bin edges from a FITs HDU | 2.071126 | 2.022384 | 1.024101 |
ebins = read_energy_bounds(hdu)
fluxes = np.ndarray((len(ebins)))
try:
fluxes[0:-1] = hdu.data.field("E_MIN_FL")
fluxes[-1] = hdu.data.field("E_MAX_FL")[-1]
npreds = hdu.data.field("NPRED")
except:
fluxes = np.ones((len(ebins)))
npreds = np.ones((len(ebins)))... | def read_spectral_data(hdu) | Reads and returns the energy bin edges, fluxes and npreds from
a FITs HDU | 2.929882 | 2.494006 | 1.174769 |
cols = [fits.Column("Energy", "D", unit='MeV', array=energy_vals)]
hdu = fits.BinTableHDU.from_columns(cols, name=extname)
return hdu | def make_energies_hdu(energy_vals, extname="ENERGIES") | Builds and returns a FITs HDU with the energy values
extname : The HDU extension name | 2.598012 | 3.251746 | 0.798959 |
f = fits.open(fitsfile)
nhdu = len(f)
# Try and get the energy bounds
try:
ebins = find_and_read_ebins(f)
except:
ebins = None
if extname is None:
# If there is an image in the Primary HDU we can return a WCS-based
# projection
if f[0].header['NAXIS'... | def read_projection_from_fits(fitsfile, extname=None) | Load a WCS or HPX projection. | 2.204365 | 2.12091 | 1.039348 |
outhdulist = [fits.PrimaryHDU()]
rmlist = []
for i, table in enumerate(tablelist):
ft_name = "%s._%i" % (filepath, i)
rmlist.append(ft_name)
try:
os.unlink(ft_name)
except:
pass
table.write(ft_name, format="fits")
ft_in = fits.open... | def write_tables_to_fits(filepath, tablelist, clobber=False,
namelist=None, cardslist=None, hdu_list=None) | Write some astropy.table.Table objects to a single fits file | 2.163943 | 2.189069 | 0.988522 |
options_str = []
for i, (k, v) in enumerate(sorted(options_dict.items())):
option_str = ''
if i == 0:
option_str += '%s : %s\n' % (k, v[2].__name__)
else:
option_str += ' ' * 8 + '%s : %s\n' % (k, v[2].__name__)
option_doc = v[1]
option_doc... | def update_docstring(docstring, options_dict) | Update a method docstring by inserting option docstrings defined in
the options dictionary. The input docstring should define `{options}`
at the location where the options docstring block should be inserted.
Parameters
----------
docstring : str
Existing method docstring.
options_dict... | 2.240639 | 2.236698 | 1.001762 |
islice = slice(imin, imax)
o = np.zeros(m[islice, ...].shape)
ix = int(cpix[0])
iy = int(cpix[1])
# Loop over energy
for i in range(m[islice, ...].shape[0]):
ks = k[islice, ...][i, ...]
ms = m[islice, ...][i, ...]
mx = ks[ix, :] > ks[ix, iy] * threshold
m... | def convolve_map(m, k, cpix, threshold=0.001, imin=0, imax=None, wmap=None) | Perform an energy-dependent convolution on a sequence of 2-D spatial maps.
Parameters
----------
m : `~numpy.ndarray`
3-D map containing a sequence of 2-D spatial maps. First
dimension should be energy.
k : `~numpy.ndarray`
3-D map containing a sequence of convolution kernels (P... | 2.457592 | 2.389348 | 1.028562 |
islice = slice(imin, imax)
o = np.zeros(m.data.shape)
nside = m.geom.nside
nest = m.geom.nest
# Loop over energy
for i, ms in enumerate(m.data[islice, ...]):
sigma = sigmas[islice][i]
# Need to be in RING scheme
if nest:
ms = hp.pixelfunc.reorder(ms, n... | def convolve_map_hpx_gauss(m, sigmas, imin=0, imax=None, wmap=None) | Perform an energy-dependent convolution on a sequence of 2-D spatial maps.
Parameters
----------
m : `HpxMap`
2-D map containing a sequence of 1-D HEALPix maps. First
dimension should be energy.
sigmas : `~numpy.ndarray`
1-D map containing a sequence gaussian widths for smoothin... | 2.889936 | 2.938101 | 0.983607 |
sm = []
zs = 0
for c in gta.components:
z = c.model_counts_map(name).data.astype('float')
if kernel is not None:
shape = (z.shape[0],) + kernel.shape
z = np.apply_over_axes(np.sum, z, axes=[1, 2]) * np.ones(
shape) * kernel[np.newaxis, :, :]
... | def get_source_kernel(gta, name, kernel=None) | Get the PDF for the given source. | 3.271206 | 3.233515 | 1.011656 |
timer = Timer.create(start=True)
self.logger.info('Generating residual maps')
schema = ConfigSchema(self.defaults['residmap'])
config = schema.create_config(self.config['residmap'], **kwargs)
# Defining default properties of test source model
config['model'].s... | def residmap(self, prefix='', **kwargs) | Generate 2-D spatial residual maps using the current ROI
model and the convolution kernel defined with the `model`
argument.
Parameters
----------
prefix : str
String that will be prefixed to the output residual map files.
{options}
Returns
... | 4.726853 | 4.637395 | 1.019291 |
if appname in LinkFactory._class_dict:
return LinkFactory._class_dict[appname].create(**kwargs)
else:
raise KeyError(
"Could not create object associated to app %s" % appname) | def create(appname, **kwargs) | Create a `Link` of a particular class, using the kwargs as options | 5.646931 | 4.785776 | 1.179941 |
comp_file = args.get('comp', None)
datafile = args.get('data', None)
if is_null(comp_file):
return
if is_null(datafile):
return
NAME_FACTORY.update_base_dict(datafile)
outdir = args.get('outdir', None)
outkey = args.get('outkey',... | def _map_arguments(self, args) | Map from the top-level arguments to the arguments provided to
the indiviudal links | 2.785696 | 2.73806 | 1.017398 |
data = args.get('data')
comp = args.get('comp')
ft1file = args.get('ft1file')
scratch = args.get('scratch', None)
dry_run = args.get('dry_run', None)
self._set_link('split-and-bin', SplitAndBin_SG,
comp=comp, data=data,
... | def _map_arguments(self, args) | Map from the top-level arguments to the arguments provided to
the indiviudal links | 4.044626 | 3.979566 | 1.016348 |
for k, v in aDict.items():
if v is None:
aDict[k] = 'none' | def _replace_none(self, aDict) | Replace all None values in a dict with 'none' | 2.684974 | 2.081424 | 1.28997 |
dsval = kwargs.get('dataset', self.dataset(**kwargs))
tokens = dsval.split('_')
irf_name = "%s_%s_%s" % (DATASET_DICTIONARY['%s_%s' % (tokens[0], tokens[1])],
EVCLASS_NAME_DICTIONARY[tokens[3]],
kwargs.get('irf_ver'))
... | def irfs(self, **kwargs) | Get the name of IFRs associted with a particular dataset | 6.592806 | 6.014093 | 1.096226 |
kwargs_copy = self.base_dict.copy()
kwargs_copy.update(**kwargs)
self._replace_none(kwargs_copy)
try:
return NameFactory.dataset_format.format(**kwargs_copy)
except KeyError:
return None | def dataset(self, **kwargs) | Return a key that specifies the data selection | 5.83026 | 5.452371 | 1.069307 |
kwargs_copy = self.base_dict.copy()
kwargs_copy.update(**kwargs)
self._replace_none(kwargs_copy)
try:
return NameFactory.component_format.format(**kwargs_copy)
except KeyError:
return None | def component(self, **kwargs) | Return a key that specifies data the sub-selection | 6.21059 | 6.074118 | 1.022468 |
kwargs_copy = self.base_dict.copy()
kwargs_copy.update(**kwargs)
self._replace_none(kwargs_copy)
try:
return NameFactory.sourcekey_format.format(**kwargs_copy)
except KeyError:
return None | def sourcekey(self, **kwargs) | Return a key that specifies the name and version of a source or component | 5.680584 | 5.583528 | 1.017383 |
kwargs_copy = self.base_dict.copy()
kwargs_copy.update(**kwargs)
self._replace_none(kwargs_copy)
try:
return NameFactory.galprop_ringkey_format.format(**kwargs_copy)
except KeyError:
return None | def galprop_ringkey(self, **kwargs) | return the sourcekey for galprop input maps : specifies the component and ring | 5.410459 | 5.295857 | 1.02164 |
kwargs_copy = self.base_dict.copy()
kwargs_copy.update(**kwargs)
self._replace_none(kwargs_copy)
try:
return NameFactory.galprop_sourcekey_format.format(**kwargs_copy)
except KeyError:
return None | def galprop_sourcekey(self, **kwargs) | return the sourcekey for merged galprop maps :
specifies the merged component and merging scheme | 5.273317 | 5.309855 | 0.993119 |
kwargs_copy = self.base_dict.copy()
kwargs_copy.update(**kwargs)
self._replace_none(kwargs_copy)
try:
return NameFactory.merged_sourcekey_format.format(**kwargs_copy)
except KeyError:
return None | def merged_sourcekey(self, **kwargs) | return the sourcekey for merged sets of point sources :
specifies the catalog and merging rule | 5.319647 | 5.487777 | 0.969363 |
kwargs_copy = self.base_dict.copy()
kwargs_copy.update(**kwargs)
self._replace_none(kwargs_copy)
localpath = NameFactory.galprop_gasmap_format.format(**kwargs_copy)
if kwargs.get('fullpath', False):
return self.fullpath(localpath=localpath)
re... | def galprop_gasmap(self, **kwargs) | return the file name for Galprop input gasmaps | 5.438329 | 5.165104 | 1.052898 |
kwargs_copy = self.base_dict.copy()
kwargs_copy.update(**kwargs)
self._replace_none(kwargs_copy)
localpath = NameFactory.merged_gasmap_format.format(**kwargs_copy)
if kwargs.get('fullpath', False):
return self.fullpath(localpath=localpath)
ret... | def merged_gasmap(self, **kwargs) | return the file name for Galprop merged gasmaps | 5.56413 | 5.225203 | 1.064864 |
kwargs_copy = self.base_dict.copy()
kwargs_copy.update(**kwargs)
self._replace_none(kwargs_copy)
localpath = NameFactory.diffuse_template_format.format(**kwargs_copy)
if kwargs.get('fullpath', False):
return self.fullpath(localpath=localpath)
... | def diffuse_template(self, **kwargs) | return the file name for other diffuse map templates | 5.58671 | 5.334046 | 1.047368 |
kwargs_copy = self.base_dict.copy()
kwargs_copy.update(**kwargs)
localpath = NameFactory.spectral_template_format.format(**kwargs_copy)
if kwargs.get('fullpath', False):
return self.fullpath(localpath=localpath)
return localpath | def spectral_template(self, **kwargs) | return the file name for spectral templates | 5.428024 | 4.853129 | 1.118459 |
kwargs_copy = self.base_dict.copy()
kwargs_copy.update(**kwargs)
localpath = NameFactory.srcmdl_xml_format.format(**kwargs_copy)
if kwargs.get('fullpath', False):
return self.fullpath(localpath=localpath)
return localpath | def srcmdl_xml(self, **kwargs) | return the file name for source model xml files | 5.015269 | 4.749602 | 1.055935 |
kwargs_copy = self.base_dict.copy()
kwargs_copy.update(**kwargs)
self._replace_none(kwargs_copy)
localpath = NameFactory.nested_srcmdl_xml_format.format(**kwargs_copy)
if kwargs.get('fullpath', False):
return self.fullpath(localpath=localpath)
... | def nested_srcmdl_xml(self, **kwargs) | return the file name for source model xml files of nested sources | 5.12751 | 4.868155 | 1.053276 |
kwargs_copy = self.base_dict.copy()
kwargs_copy.update(**kwargs)
kwargs_copy['dataset'] = kwargs.get('dataset', self.dataset(**kwargs))
self._replace_none(kwargs_copy)
localpath = NameFactory.ft1file_format.format(**kwargs_copy)
if kwargs.get('fullpath', ... | def ft1file(self, **kwargs) | return the name of the input ft1 file list | 4.99646 | 4.904219 | 1.018809 |
kwargs_copy = self.base_dict.copy()
kwargs_copy.update(**kwargs)
kwargs_copy['data_time'] = kwargs.get(
'data_time', self.dataset(**kwargs))
self._replace_none(kwargs_copy)
localpath = NameFactory.ft2file_format.format(**kwargs_copy)
if kwargs... | def ft2file(self, **kwargs) | return the name of the input ft2 file list | 5.649732 | 5.558366 | 1.016437 |
kwargs_copy = self.base_dict.copy()
kwargs_copy.update(**kwargs)
kwargs_copy['dataset'] = kwargs.get('dataset', self.dataset(**kwargs))
localpath = NameFactory.ltcube_format.format(**kwargs_copy)
if kwargs.get('fullpath', False):
return self.fullpath(localpat... | def ltcube(self, **kwargs) | return the name of a livetime cube file | 5.217741 | 4.778446 | 1.091932 |
kwargs_copy = self.base_dict.copy()
kwargs_copy.update(**kwargs)
kwargs_copy['dataset'] = kwargs.get('dataset', self.dataset(**kwargs))
kwargs_copy['component'] = kwargs.get(
'component', self.component(**kwargs))
self._replace_none(kwargs_copy)
... | def select(self, **kwargs) | return the name of a selected events ft1file | 4.629521 | 4.539134 | 1.019913 |
kwargs_copy = self.base_dict.copy()
kwargs_copy.update(**kwargs)
kwargs_copy['dataset'] = kwargs.get('dataset', self.dataset(**kwargs))
kwargs_copy['component'] = kwargs.get(
'component', self.component(**kwargs))
self._replace_none(kwargs_copy)
... | def mktime(self, **kwargs) | return the name of a selected events ft1file | 4.643551 | 4.502839 | 1.03125 |
kwargs_copy = self.base_dict.copy()
kwargs_copy.update(**kwargs)
kwargs_copy['dataset'] = kwargs.get('dataset', self.dataset(**kwargs))
kwargs_copy['component'] = kwargs.get(
'component', self.component(**kwargs))
localpath = NameFactory.ccube_format.format(*... | def ccube(self, **kwargs) | return the name of a counts cube file | 4.166788 | 3.936048 | 1.058622 |
kwargs_copy = self.base_dict.copy()
kwargs_copy.update(**kwargs)
kwargs_copy['dataset'] = kwargs.get('dataset', self.dataset(**kwargs))
kwargs_copy['component'] = kwargs.get(
'component', self.component(**kwargs))
self._replace_none(kwargs_copy)
... | def bexpcube(self, **kwargs) | return the name of a binned exposure cube file | 4.479274 | 4.284448 | 1.045473 |
kwargs_copy = self.base_dict.copy()
kwargs_copy.update(**kwargs)
kwargs_copy['dataset'] = kwargs.get('dataset', self.dataset(**kwargs))
kwargs_copy['component'] = kwargs.get(
'component', self.component(**kwargs))
self._replace_none(kwargs_copy)
... | def srcmaps(self, **kwargs) | return the name of a source map file | 4.433913 | 4.416672 | 1.003904 |
kwargs_copy = self.base_dict.copy()
kwargs_copy.update(**kwargs)
kwargs_copy['dataset'] = kwargs.get('dataset', self.dataset(**kwargs))
kwargs_copy['component'] = kwargs.get(
'component', self.component(**kwargs))
self._replace_none(kwargs_copy)
... | def mcube(self, **kwargs) | return the name of a model cube file | 4.437266 | 4.305578 | 1.030585 |
kwargs_copy = self.base_dict.copy()
kwargs_copy.update(**kwargs)
kwargs_copy['dataset'] = kwargs.get('dataset', self.dataset(**kwargs))
self._replace_none(kwargs_copy)
localpath = NameFactory.ltcubesun_format.format(**kwargs_copy)
if kwargs.get('fullpath'... | def ltcube_sun(self, **kwargs) | return the name of a livetime cube file | 6.012344 | 5.574208 | 1.078601 |
kwargs_copy = self.base_dict.copy()
kwargs_copy.update(**kwargs)
kwargs_copy['dataset'] = kwargs.get('dataset', self.dataset(**kwargs))
self._replace_none(kwargs_copy)
localpath = NameFactory.ltcubemoon_format.format(**kwargs_copy)
if kwargs.get('fullpath... | def ltcube_moon(self, **kwargs) | return the name of a livetime cube file | 6.091589 | 5.725101 | 1.064014 |
kwargs_copy = self.base_dict.copy()
kwargs_copy.update(**kwargs)
kwargs_copy['dataset'] = kwargs.get('dataset', self.dataset(**kwargs))
kwargs_copy['component'] = kwargs.get(
'component', self.component(**kwargs))
self._replace_none(kwargs_copy)
... | def bexpcube_sun(self, **kwargs) | return the name of a binned exposure cube file | 4.884633 | 4.645716 | 1.051427 |
kwargs_copy = self.base_dict.copy()
kwargs_copy.update(**kwargs)
kwargs_copy['dataset'] = kwargs.get('dataset', self.dataset(**kwargs))
kwargs_copy['component'] = kwargs.get(
'component', self.component(**kwargs))
self._replace_none(kwargs_copy)
... | def bexpcube_moon(self, **kwargs) | return the name of a binned exposure cube file | 5.045954 | 4.878186 | 1.034391 |
kwargs_copy = self.base_dict.copy()
kwargs_copy.update(**kwargs)
self._replace_none(kwargs_copy)
localpath = NameFactory.angprofile_format.format(**kwargs_copy)
if kwargs.get('fullpath', False):
return self.fullpath(localpath=localpath)
return... | def angprofile(self, **kwargs) | return the file name for sun or moon angular profiles | 5.778082 | 5.373333 | 1.075326 |
kwargs_copy = self.base_dict.copy()
kwargs_copy.update(**kwargs)
kwargs_copy['dataset'] = kwargs.get('dataset', self.dataset(**kwargs))
kwargs_copy['component'] = kwargs.get(
'component', self.component(**kwargs))
self._replace_none(kwargs_copy)
... | def template_sunmoon(self, **kwargs) | return the file name for sun or moon template files | 4.807616 | 4.735126 | 1.015309 |
kwargs_copy = self.base_dict.copy()
kwargs_copy.update(**kwargs)
kwargs_copy['dataset'] = kwargs.get('dataset', self.dataset(**kwargs))
kwargs_copy['component'] = kwargs.get(
'component', self.component(**kwargs))
localpath = NameFactory.residual_cr_format.fo... | def residual_cr(self, **kwargs) | Return the name of the residual CR analysis output files | 4.449659 | 4.090839 | 1.087713 |
kwargs_copy = self.base_dict.copy()
kwargs_copy.update(**kwargs)
self._replace_none(kwargs_copy)
localpath = NameFactory.galprop_rings_yaml_format.format(**kwargs_copy)
if kwargs.get('fullpath', False):
return self.fullpath(localpath=localpath)
... | def galprop_rings_yaml(self, **kwargs) | return the name of a galprop rings merging yaml file | 5.171557 | 5.029419 | 1.028261 |
kwargs_copy = self.base_dict.copy()
kwargs_copy.update(**kwargs)
self._replace_none(kwargs_copy)
localpath = NameFactory.catalog_split_yaml_format.format(**kwargs_copy)
if kwargs.get('fullpath', False):
return self.fullpath(localpath=localpath)
... | def catalog_split_yaml(self, **kwargs) | return the name of a catalog split yaml file | 5.189786 | 4.87978 | 1.063529 |
kwargs_copy = self.base_dict.copy()
kwargs_copy.update(**kwargs)
self._replace_none(kwargs_copy)
localpath = NameFactory.model_yaml_format.format(**kwargs_copy)
if kwargs.get('fullpath', False):
return self.fullpath(localpath=localpath)
return... | def model_yaml(self, **kwargs) | return the name of a model yaml file | 5.518291 | 5.156744 | 1.070111 |
kwargs_copy = self.base_dict.copy()
kwargs_copy.update(**kwargs)
kwargs_copy['dataset'] = kwargs.get('dataset', self.dataset(**kwargs))
kwargs_copy['component'] = kwargs.get(
'component', self.component(**kwargs))
self._replace_none(kwargs_copy)
... | def merged_srcmaps(self, **kwargs) | return the name of a source map file | 4.501946 | 4.446039 | 1.012575 |
kwargs_copy = self.base_dict.copy()
kwargs_copy.update(**kwargs)
self._replace_none(kwargs_copy)
localpath = NameFactory.master_srcmdl_xml_format.format(**kwargs_copy)
if kwargs.get('fullpath', False):
return self.fullpath(localpath=localpath)
... | def master_srcmdl_xml(self, **kwargs) | return the name of a source model file | 5.091492 | 5.12796 | 0.992888 |
kwargs_copy = self.base_dict.copy()
kwargs_copy.update(**kwargs)
kwargs_copy['dataset'] = kwargs.get('dataset', self.dataset(**kwargs))
kwargs_copy['component'] = kwargs.get(
'component', self.component(**kwargs))
self._replace_none(kwargs_copy)
... | def comp_srcmdl_xml(self, **kwargs) | return the name of a source model file | 4.257224 | 4.194346 | 1.014991 |
kwargs_copy = self.base_dict.copy()
kwargs_copy.update(**kwargs)
self._replace_none(kwargs_copy)
return NameFactory.fullpath_format.format(**kwargs_copy) | def fullpath(self, **kwargs) | Return a full path name for a given file | 6.481748 | 6.190708 | 1.047012 |
kwargs_copy = self.base_dict.copy()
kwargs_copy.update(**kwargs)
kwargs_copy['dataset'] = kwargs.get('dataset', self.dataset(**kwargs))
kwargs_copy['component'] = kwargs.get(
'component', self.component(**kwargs))
self._replace_none(kwargs_copy)
... | def generic(self, input_string, **kwargs) | return a generic filename for a given dataset and component | 3.833001 | 3.298757 | 1.161953 |
out_dict = dict(ft1file=self.ft1file(**kwargs),
ltcube=self.ltcube(**kwargs),
ccube=self.ccube(**kwargs),
bexpcube=self.bexpcube(**kwargs),
srcmaps=self.srcmaps(**kwargs),
mcube=self.... | def make_filenames(self, **kwargs) | Make a dictionary of filenames for various types | 4.153132 | 4.191762 | 0.990784 |
data = args.get('data')
comp = args.get('comp')
library = args.get('library')
dry_run = args.get('dry_run', False)
self._set_link('sum-rings', SumRings_SG,
library=library,
outdir=args['outdir'],
dry_r... | def _map_arguments(self, args) | Map from the top-level arguments to the arguments provided to
the indiviudal links | 4.146354 | 3.976834 | 1.042627 |
data = args.get('data')
comp = args.get('comp')
library = args.get('library')
dry_run = args.get('dry_run', False)
self._set_link('srcmaps-catalog', SrcmapsCatalog_SG,
comp=comp, data=data,
library=library,
... | def _map_arguments(self, args) | Map from the top-level arguments to the arguments provided to
the indiviudal links | 3.333812 | 3.259785 | 1.022709 |
config_yaml = args['config']
config_dict = load_yaml(config_yaml)
dry_run = args.get('dry_run', False)
data = config_dict.get('data')
comp = config_dict.get('comp')
library = config_dict.get('library')
models = config_dict.get('models')
scratch ... | def _map_arguments(self, args) | Map from the top-level arguments to the arguments provided to
the indiviudal links | 3.064277 | 3.05764 | 1.002171 |
if fn is None:
fn = pyLike.SourceFactory_funcFactory().create(str(spectrum_type))
if spectrum_type == 'PiecewisePowerLaw':
build_piecewise_powerlaw(fn, spectral_pars)
for k, v in spectral_pars.items():
v.setdefault('scale', 1.0)
v.setdefault('min', v['value']... | def create_spectrum_from_dict(spectrum_type, spectral_pars, fn=None) | Create a Function object from a parameter dictionary.
Parameters
----------
spectrum_type : str
String identifying the spectrum type (e.g. PowerLaw).
spectral_pars : dict
Dictionary of spectral parameters. | 3.191875 | 3.170016 | 1.006895 |
parameters = pyLike.ParameterVector()
spectrum.getParams(parameters)
d = dict(spectrum_type=spectrum.genericName())
for p in parameters:
pname = p.getName()
pval = p.getTrueValue()
perr = abs(p.error() * p.getScale()) if p.isFree() else np.nan
d[pname] = np.array([p... | def gtlike_spectrum_to_dict(spectrum) | Convert a pyLikelihood object to a python dictionary which can
be easily saved to a file. | 5.139487 | 5.065882 | 1.01453 |
parameters = pyLike.ParameterVector()
spectrum.getParams(parameters)
npar = max(parameters.size(), 10)
o = {'param_names': np.zeros(npar, dtype='S32'),
'param_values': np.empty(npar, dtype=float) * np.nan,
'param_errors': np.empty(npar, dtype=float) * np.nan,
}
fo... | def gtlike_spectrum_to_vectors(spectrum) | Convert a pyLikelihood object to a python dictionary which can
be easily saved to a file. | 2.981294 | 2.837317 | 1.050744 |
pars = []
par_names = pyLike.StringVector()
fn.getParamNames(par_names)
for pname in par_names:
par = fn.getParam(pname)
bounds = par.getBounds()
perr = par.error() if par.isFree() else np.nan
pars += [dict(name=pname,
value=par.getValue(),
... | def get_function_pars(fn) | Extract the parameters of a pyLikelihood function object
(value, scale, bounds).
Parameters
----------
fn : pyLikelihood.Function
Returns
-------
pars : list | 3.319301 | 3.377923 | 0.982646 |
npar = len(like.params())
vals = np.ones(npar)
errs = np.ones(npar)
has_prior = np.array([False] * npar)
for i, p in enumerate(like.params()):
prior = like[i].log_prior()
if prior is None:
continue
par_names = pyLike.StringVector()
prior.getPara... | def get_priors(like) | Extract priors from a likelihood object. | 2.907206 | 2.841166 | 1.023244 |
fnmap = src.getSrcFuncs()
keys = fnmap.keys()
if 'Position' in keys:
ppars = get_function_pars(src.getSrcFuncs()[str('Position')])
elif 'SpatialDist' in keys:
ppars = get_function_pars(src.getSrcFuncs()[str('SpatialDist')])
else:
raise Exception('Failed to extract spa... | def get_source_pars(src) | Extract the parameters associated with a pyLikelihood Source object. | 3.393913 | 3.211129 | 1.056922 |
nF = 0
pars = self.params()
for par in pars:
if par.isFree():
nF += 1
return nF | def nFreeParams(self) | Count the number of free parameters in the active model. | 3.343074 | 3.015517 | 1.108624 |
saved_state = LikelihoodState(self)
if verbosity > 0:
print("*** Start Ts_dl ***")
source_attributes = self.getExtraSourceAttributes()
self.logLike.syncParams()
src = self.logLike.getSource(srcName)
self._ts_src = src
freeParams = pyLike.Doub... | def Ts2(self, srcName, reoptimize=False, approx=True,
tol=None, MaxIterations=10, verbosity=0) | Computes the TS value for a source indicated by "srcName."
If "reoptimize=True" is selected this function will reoptimize
the model up to "MaxIterations" given the tolerance "tol"
(default is the tolerance selected for the overall fit). If
"appox=True" is selected (the default) it will... | 4.009394 | 3.96013 | 1.01244 |
logfile = job_config.get('logfile', "%s_%s_%s.log" %
(cls.default_prefix_logfile, linkname, key))
job_config['logfile'] = logfile | def _make_scatter_logfile_name(cls, key, linkname, job_config) | Hook to inster the name of a logfile into the input config | 4.577169 | 3.998481 | 1.144727 |
linkname = kwargs.setdefault('linkname', cls.clientclass.linkname_default)
# Don't use setdefault b/c we don't want to build a JobArchive
# Unless it is needed
job_archive = kwargs.get('job_archive', None)
if job_archive is None:
job_archive = JobArchive.buil... | def create(cls, **kwargs) | Build and return a `ScatterGather` object | 4.899405 | 4.768774 | 1.027393 |
self.files.file_dict.clear()
self.sub_files.file_dict.clear()
self.files.latch_file_info(self.args)
self._scatter_link._update_sub_file_dict(self.sub_files) | def _latch_file_info(self) | Internal function to update the dictionaries
keeping track of input and output files | 7.666488 | 6.252975 | 1.226054 |
status_vect = JobStatusVector()
for job_key, job_details in link.jobs.items():
# if job_details.status == JobStatus.failed:
# failed = True
# continue
# elif job_details.status == JobStatus.done:
# continue
if job... | def _check_link_completion(self, link, fail_pending=False, fail_running=False) | Internal function to check the completion of all the dispatched jobs
Returns
-------
status_vect : `JobStatusVector`
Vector that summarize the number of jobs in various states. | 3.027832 | 2.704639 | 1.119496 |
if self.args['dry_run']:
status = JobStatus.unknown
else:
status = JobStatus.not_ready
base_config = self.scatter_link.args
for jobkey, job_config in sorted(self._job_configs.items()):
full_job_config = base_config.copy()
full_jo... | def _build_job_dict(self) | Build a dictionary of `JobDetails` objects for the internal `Link` | 5.328337 | 5.134775 | 1.037696 |
if resubmit_failed:
self.args['action'] = 'resubmit'
argv = self._make_argv()
if dry_run:
argv.append('--dry_run')
self._invoke(argv, stream, resubmit_failed=resubmit_failed) | def _run_link(self, stream=sys.stdout, dry_run=False,
stage_files=True, resubmit_failed=False) | Internal function that actually runs this link.
This checks if input and output files are present.
If input files are missing this will raise `OSError` if dry_run is False
If all output files are present this will skip execution.
Parameters
-----------
stream : `file`
... | 3.653907 | 4.546087 | 0.803748 |
args = self._run_argparser(argv)
if args.action not in ACTIONS:
sys.stderr.write(
"Unrecognized action %s, options are %s\n" % (args.action, ACTIONS))
if args.action == 'skip':
return JobStatus.no_job
elif args.action in ['run', 'resubmi... | def _invoke(self, argv, stream=sys.stdout, resubmit_failed=False) | Invoke this object to preform a particular action
Parameters
----------
argv : list
List of command line arguments, passed to helper classes
stream : `file`
Stream that this function will print to,
must have 'write' function.
resubmit_faile... | 3.162926 | 2.92626 | 1.080876 |
self.args = extract_arguments(override_args, self.args)
self._job_configs = self.build_job_configs(self.args)
if not self._scatter_link.jobs:
self._build_job_dict()
self._latch_file_info() | def update_args(self, override_args) | Update the arguments used to invoke the application
Note that this will also update the dictionary of input and output files
Parameters
----------
override_args : dict
dictionary of arguments to override the current values | 9.182618 | 10.194831 | 0.900713 |
if recursive:
self._scatter_link.clear_jobs(recursive)
self.jobs.clear() | def clear_jobs(self, recursive=True) | Clear the self.jobs dictionary that contains information
about jobs associated with this `ScatterGather`
If recursive is True this will include jobs from all internal `Link` | 11.184148 | 9.5645 | 1.16934 |
if recursive:
ret_dict = self.jobs.copy()
ret_dict.update(self._scatter_link.get_jobs(recursive))
return ret_dict
return self.jobs | def get_jobs(self, recursive=True) | Return a dictionary with all the jobs
If recursive is True this will include jobs from all internal `Link` | 5.430427 | 5.18699 | 1.046932 |
running = True
first = True
if not check_once:
if stream != sys.stdout:
sys.stdout.write('Checking status (%is): ' %
self.args['job_check_sleep'])
sys.stdout.flush()
status_vect = JobStatusVector()
... | def check_status(self, stream=sys.stdout,
check_once=False,
fail_pending=False, fail_running=False,
no_wait=False, do_print=True,
write_status=False) | Loop to check on the status of all the jobs in job dict.
Parameters
-----------
stream : `file`
Stream that this function will print to,
Must have 'write' function.
check_once : bool
Check status once and exit loop.
fail_pending : `bool`
... | 2.901278 | 2.835777 | 1.023098 |
self._build_job_dict()
self._interface._dry_run = self.args['dry_run']
scatter_status = self._interface.submit_jobs(self.scatter_link,
job_archive=self._job_archive,
stream=stream)... | def run_jobs(self, stream=sys.stdout, resubmit_failed=False) | Function to dipatch jobs and collect results
Parameters
-----------
stream : `file`
Stream that this function will print to,
Must have 'write' function.
resubmit_failed : bool
Resubmit failed jobs.
Returns
-------
status_vect... | 4.76973 | 4.660319 | 1.023477 |
self._build_job_dict()
status_vect = self.check_status(stream, check_once=True, fail_pending=True,
fail_running=fail_running)
status = status_vect.get_status()
if status == JobStatus.done:
return status
failed_jobs = s... | def resubmit(self, stream=sys.stdout, fail_running=False, resubmit_failed=False) | Function to resubmit failed jobs and collect results
Parameters
-----------
stream : `file`
Stream that this function will print to,
Must have 'write' function.
fail_running : `bool`
If True, consider running jobs as failed
resubmit_failed :... | 3.536144 | 3.559484 | 0.993443 |
self._interface.clean_jobs(self.scatter_link,
clean_all=recursive) | def clean_jobs(self, recursive=False) | Clean up all the jobs associated with this object.
If recursive is True this also clean jobs dispatch by this
object. | 28.784554 | 28.237968 | 1.019356 |
Link.print_summary(self, stream, indent, recurse_level)
if recurse_level > 0:
recurse_level -= 1
indent += " "
stream.write("\n")
self._scatter_link.print_summary(stream, indent, recurse_level) | def print_summary(self, stream=sys.stdout, indent="", recurse_level=2) | Print a summary of the activity done by this `Link`.
Parameters
----------
stream : `file`
Stream to print to
indent : str
Indentation at start of line
recurse_level : int
Number of recursion levels to print | 3.39113 | 3.460793 | 0.979871 |
if job_stats is None:
job_stats = JobStatusVector()
job_det_list = []
job_det_list += self._scatter_link.jobs.values()
for job_dets in job_det_list:
if job_dets.status == JobStatus.no_job:
continue
job_... | def print_update(self, stream=sys.stdout, job_stats=None) | Print an update about the current number of jobs running | 2.506565 | 2.480028 | 1.0107 |
for job_key, job_details in sorted(self.scatter_link.jobs.items()):
if job_details.status == JobStatus.failed:
stream.write("Failed job %s\n log = %s\n" %
(job_key, job_details.logfile)) | def print_failed(self, stream=sys.stderr) | Print list of the failed jobs | 5.89813 | 5.21576 | 1.130829 |
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