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fermiPy/fermipy | fermipy/tsmap.py | TSMapGenerator.tsmap | def tsmap(self, prefix='', **kwargs):
"""Generate a spatial TS map for a source component with
properties defined by the `model` argument. The TS map will
have the same geometry as the ROI. The output of this method
is a dictionary containing `~fermipy.skymap.Map` objects with
... | python | def tsmap(self, prefix='', **kwargs):
"""Generate a spatial TS map for a source component with
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fermiPy/fermipy | fermipy/tsmap.py | TSMapGenerator._make_tsmap_fast | def _make_tsmap_fast(self, prefix, **kwargs):
"""
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fermiPy/fermipy | fermipy/tsmap.py | TSCubeGenerator.tscube | def tscube(self, prefix='', **kwargs):
"""Generate a spatial TS map for a source component with
properties defined by the `model` argument. This method uses
the `gttscube` ST application for source fitting and will
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the... | python | def tscube(self, prefix='', **kwargs):
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fermiPy/fermipy | fermipy/irfs.py | compute_ps_counts | def compute_ps_counts(ebins, exp, psf, bkg, fn, egy_dim=0, spatial_model='PointSource',
spatial_size=1E-3):
"""Calculate the observed signal and background counts given models
for the exposure, background intensity, PSF, and source flux.
Parameters
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ebins : `~numpy.n... | python | def compute_ps_counts(ebins, exp, psf, bkg, fn, egy_dim=0, spatial_model='PointSource',
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fermiPy/fermipy | fermipy/irfs.py | compute_norm | def compute_norm(sig, bkg, ts_thresh, min_counts, sum_axes=None, bkg_fit=None,
rebin_axes=None):
"""Solve for the normalization of the signal distribution at which the
detection test statistic (twice delta-loglikelihood ratio) is >=
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fermiPy/fermipy | fermipy/irfs.py | create_psf | def create_psf(event_class, event_type, dtheta, egy, cth):
"""Create an array of PSF response values versus energy and
inclination angle.
Parameters
----------
egy : `~numpy.ndarray`
Energy in MeV.
cth : `~numpy.ndarray`
Cosine of the incidence angle.
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egy : `~numpy.ndarray`
Energy in MeV.
cth : `~numpy.ndarray`
Cosine of the incidence angle.
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fermiPy/fermipy | fermipy/irfs.py | create_edisp | def create_edisp(event_class, event_type, erec, egy, cth):
"""Create an array of energy response values versus energy and
inclination angle.
Parameters
----------
egy : `~numpy.ndarray`
Energy in MeV.
cth : `~numpy.ndarray`
Cosine of the incidence angle.
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Energy in MeV.
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Cosine of the incidence angle.
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fermiPy/fermipy | fermipy/irfs.py | create_aeff | def create_aeff(event_class, event_type, egy, cth):
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Parameters
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fermiPy/fermipy | fermipy/irfs.py | calc_exp | def calc_exp(skydir, ltc, event_class, event_types,
egy, cth_bins, npts=None):
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fermiPy/fermipy | fermipy/irfs.py | create_avg_rsp | def create_avg_rsp(rsp_fn, skydir, ltc, event_class, event_types, x,
egy, cth_bins, npts=None):
"""Calculate the weighted response function.
"""
if npts is None:
npts = int(np.ceil(np.max(cth_bins[1:] - cth_bins[:-1]) / 0.05))
wrsp = np.zeros((len(x), len(egy), len(cth_bins) ... | python | def create_avg_rsp(rsp_fn, skydir, ltc, event_class, event_types, x,
egy, cth_bins, npts=None):
"""Calculate the weighted response function.
"""
if npts is None:
npts = int(np.ceil(np.max(cth_bins[1:] - cth_bins[:-1]) / 0.05))
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fermiPy/fermipy | fermipy/irfs.py | create_avg_psf | def create_avg_psf(skydir, ltc, event_class, event_types, dtheta,
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Energies in MeV.
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fermiPy/fermipy | fermipy/irfs.py | create_avg_edisp | def create_avg_edisp(skydir, ltc, event_class, event_types, erec,
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True energies in MeV.
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fermiPy/fermipy | fermipy/irfs.py | create_wtd_psf | def create_wtd_psf(skydir, ltc, event_class, event_types, dtheta,
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fermiPy/fermipy | fermipy/irfs.py | calc_drm | def calc_drm(skydir, ltc, event_class, event_types,
egy_bins, cth_bins, nbin=64):
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npts = int(np.ceil(128. / bins_per_dec(egy_bins)))
egy_bins = np.exp(utils.split_bin_edges(np.log(egy_bins), npts))
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egy_bins, cth_bins, nbin=64):
"""Calculate the detector response matrix."""
npts = int(np.ceil(128. / bins_per_dec(egy_bins)))
egy_bins = np.exp(utils.split_bin_edges(np.log(egy_bins), npts))
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fermiPy/fermipy | fermipy/irfs.py | calc_counts | def calc_counts(skydir, ltc, event_class, event_types,
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fermiPy/fermipy | fermipy/irfs.py | calc_counts_edisp | def calc_counts_edisp(skydir, ltc, event_class, event_types,
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fermiPy/fermipy | fermipy/irfs.py | calc_wtd_exp | def calc_wtd_exp(skydir, ltc, event_class, event_types,
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"""Calculate the effective exposure.
Parameters
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skydir : `~astropy.coordinates.SkyCoord`
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nbin : int
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fermiPy/fermipy | fermipy/irfs.py | ExposureMap.create | def create(cls, ltc, event_class, event_types, ebins):
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generate an exposure map with the same geometry as the
livetime cube (nside, etc.).
Parameters
----------
ltc : `~fermipy.irfs.LTCube`
Liv... | python | def create(cls, ltc, event_class, event_types, ebins):
"""Create an exposure map from a livetime cube. This method will
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fermiPy/fermipy | fermipy/irfs.py | PSFModel.eval | def eval(self, ebin, dtheta, scale_fn=None):
"""Evaluate the PSF at the given energy bin index.
Parameters
----------
ebin : int
Index of energy bin.
dtheta : array_like
Array of angular separations in degrees.
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... | python | def eval(self, ebin, dtheta, scale_fn=None):
"""Evaluate the PSF at the given energy bin index.
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ebin : int
Index of energy bin.
dtheta : array_like
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fermiPy/fermipy | fermipy/irfs.py | PSFModel.interp | def interp(self, energies, dtheta, scale_fn=None):
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Parameters
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energies : array_like
Array of energies in MeV.
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fermiPy/fermipy | fermipy/irfs.py | PSFModel.interp_bin | def interp_bin(self, egy_bins, dtheta, scale_fn=None):
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Energy bin edges in MeV.
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fermiPy/fermipy | fermipy/irfs.py | PSFModel.containment_angle | def containment_angle(self, energies=None, fraction=0.68, scale_fn=None):
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if energies is None:
energies = self.energies
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fermiPy/fermipy | fermipy/irfs.py | PSFModel.containment_angle_bin | def containment_angle_bin(self, egy_bins, fraction=0.68, scale_fn=None):
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fermiPy/fermipy | fermipy/irfs.py | PSFModel.create | def create(cls, skydir, ltc, event_class, event_types, energies, cth_bins=None,
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fermiPy/fermipy | fermipy/jobs/sys_interface.py | remove_file | def remove_file(filepath, dry_run=False):
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fermiPy/fermipy | fermipy/jobs/sys_interface.py | clean_job | def clean_job(logfile, outfiles, dry_run=False):
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remove_file(logfile, dry_run)
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fermiPy/fermipy | fermipy/jobs/sys_interface.py | check_log | def check_log(logfile, exited='Exited with exit code',
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fermiPy/fermipy | fermipy/jobs/sys_interface.py | SysInterface.check_job | def check_job(cls, job_details):
""" Check the status of a specfic job """
return check_log(job_details.logfile, cls.string_exited, cls.string_successful) | python | def check_job(cls, job_details):
""" Check the status of a specfic job """
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fermiPy/fermipy | fermipy/jobs/sys_interface.py | SysInterface.submit_jobs | def submit_jobs(self, link, job_dict=None, job_archive=None, stream=sys.stdout):
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If job_dict is None, the job_dict will be take from link.jobs
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failed = False
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If job_dict is None, the job_dict will be take from link.jobs
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fermiPy/fermipy | fermipy/jobs/sys_interface.py | SysInterface.clean_jobs | def clean_jobs(self, link, job_dict=None, clean_all=False):
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Returns a `JobStatus` enum
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failed = False
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job_dict = link.jobs
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failed = False
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fermiPy/fermipy | fermipy/model_utils.py | get_function_spec | def get_function_spec(name):
"""Return a dictionary with the specification of a function:
parameter names and defaults (value, bounds, scale, etc.).
Returns
-------
par_names : list
List of parameter names for this function.
norm_par : str
Name of normalization parameter.
... | python | def get_function_spec(name):
"""Return a dictionary with the specification of a function:
parameter names and defaults (value, bounds, scale, etc.).
Returns
-------
par_names : list
List of parameter names for this function.
norm_par : str
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fermiPy/fermipy | fermipy/model_utils.py | get_spatial_type | def get_spatial_type(spatial_model):
"""Translate a spatial model string to a spatial type."""
if spatial_model in ['SkyDirFunction', 'PointSource',
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return 'SkyDirFunction'
elif spatial_model in ['SpatialMap']:
return 'SpatialMap'
elif spatial_model... | python | def get_spatial_type(spatial_model):
"""Translate a spatial model string to a spatial type."""
if spatial_model in ['SkyDirFunction', 'PointSource',
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return 'SkyDirFunction'
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fermiPy/fermipy | fermipy/model_utils.py | create_pars_from_dict | def create_pars_from_dict(name, pars_dict, rescale=True, update_bounds=False):
"""Create a dictionary for the parameters of a function.
Parameters
----------
name : str
Name of the function.
pars_dict : dict
Existing parameter dict that will be merged with the
default d... | python | def create_pars_from_dict(name, pars_dict, rescale=True, update_bounds=False):
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Parameters
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name : str
Name of the function.
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fermiPy/fermipy | fermipy/model_utils.py | make_parameter_dict | def make_parameter_dict(pdict, fixed_par=False, rescale=True,
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Update a parameter dictionary. This function will automatically
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fermiPy/fermipy | fermipy/model_utils.py | cast_pars_dict | def cast_pars_dict(pars_dict):
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fermiPy/fermipy | fermipy/scripts/gather_srcmaps.py | do_gather | def do_gather(flist):
""" Gather all the HDUs from a list of files"""
hlist = []
nskip = 3
for fname in flist:
fin = fits.open(fname)
if len(hlist) == 0:
if fin[1].name == 'SKYMAP':
nskip = 4
start = 0
else:
start = nskip
... | python | def do_gather(flist):
""" Gather all the HDUs from a list of files"""
hlist = []
nskip = 3
for fname in flist:
fin = fits.open(fname)
if len(hlist) == 0:
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fermiPy/fermipy | fermipy/scripts/gather_srcmaps.py | main | def main():
""" Main function for command line usage """
usage = "usage: %(prog)s [options] "
description = "Gather source maps from Fermi-LAT files."
parser = argparse.ArgumentParser(usage=usage, description=description)
parser.add_argument('-o', '--output', default=None, type=str,
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""" Main function for command line usage """
usage = "usage: %(prog)s [options] "
description = "Gather source maps from Fermi-LAT files."
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fermiPy/fermipy | fermipy/jobs/job_archive.py | main_browse | def main_browse():
"""Entry point for command line use for browsing a JobArchive """
parser = argparse.ArgumentParser(usage="job_archive.py [options]",
description="Browse a job archive")
parser.add_argument('--jobs', action='store', dest='job_archive_table',
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"""Entry point for command line use for browsing a JobArchive """
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fermiPy/fermipy | fermipy/jobs/job_archive.py | JobStatusVector.n_waiting | def n_waiting(self):
"""Return the number of jobs in various waiting states"""
return self._counters[JobStatus.no_job] +\
self._counters[JobStatus.unknown] +\
self._counters[JobStatus.not_ready] +\
self._counters[JobStatus.ready] | python | def n_waiting(self):
"""Return the number of jobs in various waiting states"""
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"""Return the number of failed jobs"""
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fermiPy/fermipy | fermipy/jobs/job_archive.py | JobStatusVector.get_status | def get_status(self):
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fermiPy/fermipy | fermipy/jobs/job_archive.py | JobDetails.make_tables | def make_tables(job_dict):
"""Build and return an `astropy.table.Table' to store `JobDetails`"""
col_dbkey = Column(name='dbkey', dtype=int)
col_jobname = Column(name='jobname', dtype='S64')
col_jobkey = Column(name='jobkey', dtype='S64')
col_appname = Column(name='appname', dtyp... | python | def make_tables(job_dict):
"""Build and return an `astropy.table.Table' to store `JobDetails`"""
col_dbkey = Column(name='dbkey', dtype=int)
col_jobname = Column(name='jobname', dtype='S64')
col_jobkey = Column(name='jobkey', dtype='S64')
col_appname = Column(name='appname', dtyp... | [
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fermiPy/fermipy | fermipy/jobs/job_archive.py | JobDetails.get_file_ids | def get_file_ids(self, file_archive, creator=None, status=FileStatus.no_file):
"""Fill the file id arrays from the file lists
Parameters
----------
file_archive : `FileArchive`
Used to look up file ids
creator : int
A unique key for the job that created... | python | def get_file_ids(self, file_archive, creator=None, status=FileStatus.no_file):
"""Fill the file id arrays from the file lists
Parameters
----------
file_archive : `FileArchive`
Used to look up file ids
creator : int
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fermiPy/fermipy | fermipy/jobs/job_archive.py | JobDetails.get_file_paths | def get_file_paths(self, file_archive, file_id_array):
"""Get the full paths of the files used by this object from the the id arrays
Parameters
----------
file_archive : `FileArchive`
Used to look up file ids
file_id_array : `numpy.array`
Array that rema... | python | def get_file_paths(self, file_archive, file_id_array):
"""Get the full paths of the files used by this object from the the id arrays
Parameters
----------
file_archive : `FileArchive`
Used to look up file ids
file_id_array : `numpy.array`
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fermiPy/fermipy | fermipy/jobs/job_archive.py | JobDetails._fill_array_from_list | def _fill_array_from_list(the_list, the_array):
"""Fill an `array` from a `list`"""
for i, val in enumerate(the_list):
the_array[i] = val
return the_array | python | def _fill_array_from_list(the_list, the_array):
"""Fill an `array` from a `list`"""
for i, val in enumerate(the_list):
the_array[i] = val
return the_array | [
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fermiPy/fermipy | fermipy/jobs/job_archive.py | JobDetails.make_dict | def make_dict(cls, table):
"""Build a dictionary map int to `JobDetails` from an `astropy.table.Table`"""
ret_dict = {}
for row in table:
job_details = cls.create_from_row(row)
ret_dict[job_details.dbkey] = job_details
return ret_dict | python | def make_dict(cls, table):
"""Build a dictionary map int to `JobDetails` from an `astropy.table.Table`"""
ret_dict = {}
for row in table:
job_details = cls.create_from_row(row)
ret_dict[job_details.dbkey] = job_details
return ret_dict | [
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fermiPy/fermipy | fermipy/jobs/job_archive.py | JobDetails.create_from_row | def create_from_row(cls, table_row):
"""Create a `JobDetails` from an `astropy.table.row.Row` """
kwargs = {}
for key in table_row.colnames:
kwargs[key] = table_row[key]
infile_refs = kwargs.pop('infile_refs')
outfile_refs = kwargs.pop('outfile_refs')
rmfile_... | python | def create_from_row(cls, table_row):
"""Create a `JobDetails` from an `astropy.table.row.Row` """
kwargs = {}
for key in table_row.colnames:
kwargs[key] = table_row[key]
infile_refs = kwargs.pop('infile_refs')
outfile_refs = kwargs.pop('outfile_refs')
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fermiPy/fermipy | fermipy/jobs/job_archive.py | JobDetails.append_to_tables | def append_to_tables(self, table, table_ids):
"""Add this instance as a row on a `astropy.table.Table` """
infile_refs = np.zeros((2), int)
outfile_refs = np.zeros((2), int)
rmfile_refs = np.zeros((2), int)
intfile_refs = np.zeros((2), int)
f_ptr = len(table_ids['file_id'... | python | def append_to_tables(self, table, table_ids):
"""Add this instance as a row on a `astropy.table.Table` """
infile_refs = np.zeros((2), int)
outfile_refs = np.zeros((2), int)
rmfile_refs = np.zeros((2), int)
intfile_refs = np.zeros((2), int)
f_ptr = len(table_ids['file_id'... | [
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fermiPy/fermipy | fermipy/jobs/job_archive.py | JobDetails.update_table_row | def update_table_row(self, table, row_idx):
"""Add this instance as a row on a `astropy.table.Table` """
try:
table[row_idx]['timestamp'] = self.timestamp
table[row_idx]['status'] = self.status
except IndexError:
print("Index error", len(table), row_idx) | python | def update_table_row(self, table, row_idx):
"""Add this instance as a row on a `astropy.table.Table` """
try:
table[row_idx]['timestamp'] = self.timestamp
table[row_idx]['status'] = self.status
except IndexError:
print("Index error", len(table), row_idx) | [
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fermiPy/fermipy | fermipy/jobs/job_archive.py | JobDetails.check_status_logfile | def check_status_logfile(self, checker_func):
"""Check on the status of this particular job using the logfile"""
self.status = checker_func(self.logfile)
return self.status | python | def check_status_logfile(self, checker_func):
"""Check on the status of this particular job using the logfile"""
self.status = checker_func(self.logfile)
return self.status | [
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fermiPy/fermipy | fermipy/jobs/job_archive.py | JobArchive._fill_cache | def _fill_cache(self):
"""Fill the cache from the `astropy.table.Table`"""
for irow in range(len(self._table)):
job_details = self.make_job_details(irow)
self._cache[job_details.fullkey] = job_details | python | def _fill_cache(self):
"""Fill the cache from the `astropy.table.Table`"""
for irow in range(len(self._table)):
job_details = self.make_job_details(irow)
self._cache[job_details.fullkey] = job_details | [
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fermiPy/fermipy | fermipy/jobs/job_archive.py | JobArchive._read_table_file | def _read_table_file(self, table_file):
"""Read an `astropy.table.Table` from table_file to set up the `JobArchive`"""
self._table_file = table_file
if os.path.exists(self._table_file):
self._table = Table.read(self._table_file, hdu='JOB_ARCHIVE')
self._table_ids = Table.... | python | def _read_table_file(self, table_file):
"""Read an `astropy.table.Table` from table_file to set up the `JobArchive`"""
self._table_file = table_file
if os.path.exists(self._table_file):
self._table = Table.read(self._table_file, hdu='JOB_ARCHIVE')
self._table_ids = Table.... | [
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fermiPy/fermipy | fermipy/jobs/job_archive.py | JobArchive.make_job_details | def make_job_details(self, row_idx):
"""Create a `JobDetails` from an `astropy.table.row.Row` """
row = self._table[row_idx]
job_details = JobDetails.create_from_row(row)
job_details.get_file_paths(self._file_archive, self._table_id_array)
self._cache[job_details.fullkey] = job_d... | python | def make_job_details(self, row_idx):
"""Create a `JobDetails` from an `astropy.table.row.Row` """
row = self._table[row_idx]
job_details = JobDetails.create_from_row(row)
job_details.get_file_paths(self._file_archive, self._table_id_array)
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fermiPy/fermipy | fermipy/jobs/job_archive.py | JobArchive.get_details | def get_details(self, jobname, jobkey):
"""Get the `JobDetails` associated to a particular job instance"""
fullkey = JobDetails.make_fullkey(jobname, jobkey)
return self._cache[fullkey] | python | def get_details(self, jobname, jobkey):
"""Get the `JobDetails` associated to a particular job instance"""
fullkey = JobDetails.make_fullkey(jobname, jobkey)
return self._cache[fullkey] | [
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fermiPy/fermipy | fermipy/jobs/job_archive.py | JobArchive.register_job | def register_job(self, job_details):
"""Register a job in this `JobArchive` """
# check to see if the job already exists
try:
job_details_old = self.get_details(job_details.jobname,
job_details.jobkey)
if job_details_old.stat... | python | def register_job(self, job_details):
"""Register a job in this `JobArchive` """
# check to see if the job already exists
try:
job_details_old = self.get_details(job_details.jobname,
job_details.jobkey)
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fermiPy/fermipy | fermipy/jobs/job_archive.py | JobArchive.register_jobs | def register_jobs(self, job_dict):
"""Register a bunch of jobs in this archive"""
njobs = len(job_dict)
sys.stdout.write("Registering %i total jobs: " % njobs)
for i, job_details in enumerate(job_dict.values()):
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sys.stdout.write('.')
... | python | def register_jobs(self, job_dict):
"""Register a bunch of jobs in this archive"""
njobs = len(job_dict)
sys.stdout.write("Registering %i total jobs: " % njobs)
for i, job_details in enumerate(job_dict.values()):
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fermiPy/fermipy | fermipy/jobs/job_archive.py | JobArchive.register_job_from_link | def register_job_from_link(self, link, key, **kwargs):
"""Register a job in the `JobArchive` from a `Link` object """
job_config = kwargs.get('job_config', None)
if job_config is None:
job_config = link.args
status = kwargs.get('status', JobStatus.unknown)
job_details... | python | def register_job_from_link(self, link, key, **kwargs):
"""Register a job in the `JobArchive` from a `Link` object """
job_config = kwargs.get('job_config', None)
if job_config is None:
job_config = link.args
status = kwargs.get('status', JobStatus.unknown)
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fermiPy/fermipy | fermipy/jobs/job_archive.py | JobArchive.update_job | def update_job(self, job_details):
"""Update a job in the `JobArchive` """
other = self.get_details(job_details.jobname,
job_details.jobkey)
other.timestamp = job_details.timestamp
other.status = job_details.status
other.update_table_row(self._tab... | python | def update_job(self, job_details):
"""Update a job in the `JobArchive` """
other = self.get_details(job_details.jobname,
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other.timestamp = job_details.timestamp
other.status = job_details.status
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fermiPy/fermipy | fermipy/jobs/job_archive.py | JobArchive.remove_jobs | def remove_jobs(self, mask):
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jobkey = self.table[mask]['jobkey']
self.table[mask]['status'] = JobStatus.removed
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"""Mark all jobs that match a mask as 'removed' """
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fermiPy/fermipy | fermipy/jobs/job_archive.py | JobArchive.build_temp_job_archive | def build_temp_job_archive(cls):
"""Build and return a `JobArchive` using defualt locations of
persistent files. """
try:
os.unlink('job_archive_temp.fits')
os.unlink('file_archive_temp.fits')
except OSError:
pass
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"""Build and return a `JobArchive` using defualt locations of
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try:
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fermiPy/fermipy | fermipy/jobs/job_archive.py | JobArchive.write_table_file | def write_table_file(self, job_table_file=None, file_table_file=None):
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raise RuntimeError("No table to write")
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raise RuntimeError("No ID table to write")
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raise RuntimeError("No table to write")
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fermiPy/fermipy | fermipy/jobs/job_archive.py | JobArchive.update_job_status | def update_job_status(self, checker_func):
"""Update the status of all the jobs in the archive"""
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"""Update the status of all the jobs in the archive"""
njobs = len(self.cache.keys())
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fermiPy/fermipy | fermipy/timing.py | Timer.elapsed_time | def elapsed_time(self):
"""Get the elapsed time."""
# Timer is running
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else:
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"""Get the elapsed time."""
# Timer is running
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fermiPy/fermipy | fermipy/timing.py | Timer.stop | def stop(self):
"""Stop the timer."""
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self._t0 = None | python | def stop(self):
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fermiPy/fermipy | fermipy/diffuse/source_factory.py | make_spatialmap_source | def make_spatialmap_source(name, Spatial_Filename, spectrum):
"""Construct and return a `fermipy.roi_model.Source` object
"""
data = dict(Spatial_Filename=Spatial_Filename,
ra=0.0, dec=0.0,
SpatialType='SpatialMap',
Source_Name=name)
if spectrum is not No... | python | def make_spatialmap_source(name, Spatial_Filename, spectrum):
"""Construct and return a `fermipy.roi_model.Source` object
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data = dict(Spatial_Filename=Spatial_Filename,
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fermiPy/fermipy | fermipy/diffuse/source_factory.py | make_mapcube_source | def make_mapcube_source(name, Spatial_Filename, spectrum):
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data = dict(Spatial_Filename=Spatial_Filename)
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data = dict(Spatial_Filename=Spatial_Filename)
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fermiPy/fermipy | fermipy/diffuse/source_factory.py | make_isotropic_source | def make_isotropic_source(name, Spectrum_Filename, spectrum):
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data = dict(Spectrum_Filename=Spectrum_Filename)
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fermiPy/fermipy | fermipy/diffuse/source_factory.py | make_composite_source | def make_composite_source(name, spectrum):
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"""Construct and return a `fermipy.roi_model.CompositeSource` object
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fermiPy/fermipy | fermipy/diffuse/source_factory.py | make_catalog_sources | def make_catalog_sources(catalog_roi_model, source_names):
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Parameters
----------
catalog_roi_model : dict or `fermipy.roi_model.ROIModel`
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source_names : list
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fermiPy/fermipy | fermipy/diffuse/source_factory.py | make_sources | def make_sources(comp_key, comp_dict):
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Parameters
----------
comp_key : str
Key used to access sources
comp_dict : dict
Information used to build sources
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comp_key : str
Key used to access sources
comp_dict : dict
Information used to build sources
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fermiPy/fermipy | fermipy/diffuse/source_factory.py | SourceFactory.add_sources | def add_sources(self, source_info_dict):
"""Add all of the sources in source_info_dict to this factory
"""
self._source_info_dict.update(source_info_dict)
for key, value in source_info_dict.items():
self._sources.update(make_sources(key, value)) | python | def add_sources(self, source_info_dict):
"""Add all of the sources in source_info_dict to this factory
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self._source_info_dict.update(source_info_dict)
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fermiPy/fermipy | fermipy/diffuse/source_factory.py | SourceFactory.build_catalog | def build_catalog(**kwargs):
"""Build a `fermipy.catalog.Catalog` object
Parameters
----------
catalog_type : str
Specifies catalog type, options include 2FHL | 3FGL | 4FGLP
catalog_file : str
FITS file with catalog tables
catalog_extdir : str
... | python | def build_catalog(**kwargs):
"""Build a `fermipy.catalog.Catalog` object
Parameters
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catalog_type : str
Specifies catalog type, options include 2FHL | 3FGL | 4FGLP
catalog_file : str
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fermiPy/fermipy | fermipy/diffuse/source_factory.py | SourceFactory.make_fermipy_roi_model_from_catalogs | def make_fermipy_roi_model_from_catalogs(cataloglist):
"""Build and return a `fermipy.roi_model.ROIModel object from
a list of fermipy.catalog.Catalog` objects
"""
data = dict(catalogs=cataloglist,
src_roiwidth=360.)
return roi_model.ROIModel(data, skydir=SkyC... | python | def make_fermipy_roi_model_from_catalogs(cataloglist):
"""Build and return a `fermipy.roi_model.ROIModel object from
a list of fermipy.catalog.Catalog` objects
"""
data = dict(catalogs=cataloglist,
src_roiwidth=360.)
return roi_model.ROIModel(data, skydir=SkyC... | [
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fermiPy/fermipy | fermipy/diffuse/source_factory.py | SourceFactory.make_roi | def make_roi(cls, sources=None):
"""Build and return a `fermipy.roi_model.ROIModel` object from
a dict with information about the sources
"""
if sources is None:
sources = {}
src_fact = cls()
src_fact.add_sources(sources)
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"""Build and return a `fermipy.roi_model.ROIModel` object from
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"""
if sources is None:
sources = {}
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fermiPy/fermipy | fermipy/diffuse/source_factory.py | SourceFactory.copy_selected_sources | def copy_selected_sources(cls, roi, source_names):
"""Build and return a `fermipy.roi_model.ROIModel` object
by copying selected sources from another such object
"""
roi_new = cls.make_roi()
for source_name in source_names:
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src_cp = roi.copy_sourc... | python | def copy_selected_sources(cls, roi, source_names):
"""Build and return a `fermipy.roi_model.ROIModel` object
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"""
roi_new = cls.make_roi()
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fermiPy/fermipy | fermipy/diffuse/timefilter.py | MktimeFilterDict.build_from_yamlfile | def build_from_yamlfile(yamlfile):
""" Build a list of components from a yaml file
"""
d = yaml.load(open(yamlfile))
return MktimeFilterDict(d['aliases'], d['selections']) | python | def build_from_yamlfile(yamlfile):
""" Build a list of components from a yaml file
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d = yaml.load(open(yamlfile))
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fermiPy/fermipy | fermipy/jobs/target_extension.py | AnalyzeExtension.run_analysis | def run_analysis(self, argv):
"""Run this analysis"""
args = self._parser.parse_args(argv)
if not HAVE_ST:
raise RuntimeError(
"Trying to run fermipy analysis, but don't have ST")
if is_not_null(args.roi_baseline):
gta = GTAnalysis.create(args.ro... | python | def run_analysis(self, argv):
"""Run this analysis"""
args = self._parser.parse_args(argv)
if not HAVE_ST:
raise RuntimeError(
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fermiPy/fermipy | fermipy/scripts/dispatch.py | collect_jobs | def collect_jobs(dirs, runscript, overwrite=False, max_job_age=90):
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jobs = []
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"""Construct a list of job dictionaries."""
jobs = []
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fermiPy/fermipy | fermipy/srcmap_utils.py | make_srcmap_old | def make_srcmap_old(psf, spatial_model, sigma, npix=500, xpix=0.0, ypix=0.0,
cdelt=0.01, rebin=1, psf_scale_fn=None):
"""Compute the source map for a given spatial model.
Parameters
----------
psf : `~fermipy.irfs.PSFModel`
spatial_model : str
Spatial model.
sigma : ... | python | def make_srcmap_old(psf, spatial_model, sigma, npix=500, xpix=0.0, ypix=0.0,
cdelt=0.01, rebin=1, psf_scale_fn=None):
"""Compute the source map for a given spatial model.
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----------
psf : `~fermipy.irfs.PSFModel`
spatial_model : str
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fermiPy/fermipy | fermipy/srcmap_utils.py | make_srcmap | def make_srcmap(psf, exp, spatial_model, sigma, npix=500, xpix=0.0, ypix=0.0,
cdelt=0.01, psf_scale_fn=None, klims=None, sparse=False):
"""Compute the source map for a given spatial model.
Parameters
----------
psf : `~fermipy.irfs.PSFModel`
exp : `~numpy.ndarray`
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cdelt=0.01, psf_scale_fn=None, klims=None, sparse=False):
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fermiPy/fermipy | fermipy/srcmap_utils.py | delete_source_map | def delete_source_map(srcmap_file, names, logger=None):
"""Delete a map from a binned analysis source map file if it exists.
Parameters
----------
srcmap_file : str
Path to the source map file.
names : list
List of HDU keys of source maps to be deleted.
"""
with fits.open(sr... | python | def delete_source_map(srcmap_file, names, logger=None):
"""Delete a map from a binned analysis source map file if it exists.
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----------
srcmap_file : str
Path to the source map file.
names : list
List of HDU keys of source maps to be deleted.
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fermiPy/fermipy | fermipy/srcmap_utils.py | MapInterpolator.get_offsets | def get_offsets(self, pix):
"""Get offset of the first pixel in each dimension in the
global coordinate system.
Parameters
----------
pix : `~numpy.ndarray`
Pixel coordinates in global coordinate system.
"""
idx = []
for i in range(self.ndim)... | python | def get_offsets(self, pix):
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pix : `~numpy.ndarray`
Pixel coordinates in global coordinate system.
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fermiPy/fermipy | fermipy/srcmap_utils.py | MapInterpolator.shift_to_coords | def shift_to_coords(self, pix, fill_value=np.nan):
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pix_offset = self.get_offsets(pix)
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x = self.rebin * (pix[i] - pix_off... | python | def shift_to_coords(self, pix, fill_value=np.nan):
"""Create a new map that is shifted to the pixel coordinates
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pix_offset = self.get_offsets(pix)
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fermiPy/fermipy | fermipy/srcmap_utils.py | SourceMapCache.create_map | def create_map(self, pix):
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----------
pix : `~numpy.ndarray`
Reference pixel of new map.
Returns
-------
out_map : `~numpy.ndarray`
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pix : `~numpy.ndarray`
Reference pixel of new map.
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fermiPy/fermipy | fermipy/version.py | render_pep440 | def render_pep440(vcs):
"""Convert git release tag into a form that is PEP440 compliant."""
if vcs is None:
return None
tags = vcs.split('-')
# Bare version number
if len(tags) == 1:
return tags[0]
else:
return tags[0] + '+' + '.'.join(tags[1:]) | python | def render_pep440(vcs):
"""Convert git release tag into a form that is PEP440 compliant."""
if vcs is None:
return None
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# Bare version number
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fermiPy/fermipy | fermipy/version.py | read_release_version | def read_release_version():
"""Read the release version from ``_version.py``."""
import re
dirname = os.path.abspath(os.path.dirname(__file__))
try:
f = open(os.path.join(dirname, "_version.py"), "rt")
for line in f.readlines():
m = re.match("__version__ = '([^']+)'", line)... | python | def read_release_version():
"""Read the release version from ``_version.py``."""
import re
dirname = os.path.abspath(os.path.dirname(__file__))
try:
f = open(os.path.join(dirname, "_version.py"), "rt")
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fermiPy/fermipy | fermipy/version.py | write_release_version | def write_release_version(version):
"""Write the release version to ``_version.py``."""
dirname = os.path.abspath(os.path.dirname(__file__))
f = open(os.path.join(dirname, "_version.py"), "wt")
f.write("__version__ = '%s'\n" % version)
f.close() | python | def write_release_version(version):
"""Write the release version to ``_version.py``."""
dirname = os.path.abspath(os.path.dirname(__file__))
f = open(os.path.join(dirname, "_version.py"), "wt")
f.write("__version__ = '%s'\n" % version)
f.close() | [
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fermiPy/fermipy | fermipy/diffuse/gt_split_and_mktime.py | make_full_path | def make_full_path(basedir, outkey, origname):
"""Make a full file path by combining tokens
Parameters
-----------
basedir : str
The top level output area
outkey : str
The key for the particular instance of the analysis
origname : str
Template for the output file name... | python | def make_full_path(basedir, outkey, origname):
"""Make a full file path by combining tokens
Parameters
-----------
basedir : str
The top level output area
outkey : str
The key for the particular instance of the analysis
origname : str
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fermiPy/fermipy | fermipy/diffuse/gt_split_and_mktime.py | SplitAndMktime._map_arguments | def _map_arguments(self, args):
"""Map from the top-level arguments to the arguments provided to
the indiviudal links """
comp_file = args.get('comp', None)
datafile = args.get('data', None)
if is_null(comp_file):
return
if is_null(datafile):
retur... | python | def _map_arguments(self, args):
"""Map from the top-level arguments to the arguments provided to
the indiviudal links """
comp_file = args.get('comp', None)
datafile = args.get('data', None)
if is_null(comp_file):
return
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fermiPy/fermipy | fermipy/diffuse/gt_split_and_mktime.py | SplitAndMktime_SG.build_job_configs | def build_job_configs(self, args):
"""Hook to build job configurations
"""
job_configs = {}
comp_file = args.get('comp', None)
if comp_file is not None:
comp_dict = yaml.safe_load(open(comp_file))
coordsys = comp_dict.pop('coordsys')
for v in ... | python | def build_job_configs(self, args):
"""Hook to build job configurations
"""
job_configs = {}
comp_file = args.get('comp', None)
if comp_file is not None:
comp_dict = yaml.safe_load(open(comp_file))
coordsys = comp_dict.pop('coordsys')
for v in ... | [
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fermiPy/fermipy | fermipy/diffuse/gt_split_and_mktime.py | SplitAndMktimeChain._map_arguments | def _map_arguments(self, args):
"""Map from the top-level arguments to the arguments provided to
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data = args.get('data')
comp = args.get('comp')
ft1file = args.get('ft1file')
ft2file = args.get('ft2file')
scratch = args.get('scratch', None... | python | def _map_arguments(self, args):
"""Map from the top-level arguments to the arguments provided to
the indiviudal links """
data = args.get('data')
comp = args.get('comp')
ft1file = args.get('ft1file')
ft2file = args.get('ft2file')
scratch = args.get('scratch', None... | [
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fermiPy/fermipy | fermipy/utils.py | init_matplotlib_backend | def init_matplotlib_backend(backend=None):
"""This function initializes the matplotlib backend. When no
DISPLAY is available the backend is automatically set to 'Agg'.
Parameters
----------
backend : str
matplotlib backend name.
"""
import matplotlib
try:
os.environ['D... | python | def init_matplotlib_backend(backend=None):
"""This function initializes the matplotlib backend. When no
DISPLAY is available the backend is automatically set to 'Agg'.
Parameters
----------
backend : str
matplotlib backend name.
"""
import matplotlib
try:
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fermiPy/fermipy | fermipy/utils.py | load_data | def load_data(infile, workdir=None):
"""Load python data structure from either a YAML or numpy file. """
infile = resolve_path(infile, workdir=workdir)
infile, ext = os.path.splitext(infile)
if os.path.isfile(infile + '.npy'):
infile += '.npy'
elif os.path.isfile(infile + '.yaml'):
... | python | def load_data(infile, workdir=None):
"""Load python data structure from either a YAML or numpy file. """
infile = resolve_path(infile, workdir=workdir)
infile, ext = os.path.splitext(infile)
if os.path.isfile(infile + '.npy'):
infile += '.npy'
elif os.path.isfile(infile + '.yaml'):
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fermiPy/fermipy | fermipy/utils.py | resolve_file_path_list | def resolve_file_path_list(pathlist, workdir, prefix='',
randomize=False):
"""Resolve the path of each file name in the file ``pathlist`` and
write the updated paths to a new file.
"""
files = []
with open(pathlist, 'r') as f:
files = [line.strip() for line in f]
... | python | def resolve_file_path_list(pathlist, workdir, prefix='',
randomize=False):
"""Resolve the path of each file name in the file ``pathlist`` and
write the updated paths to a new file.
"""
files = []
with open(pathlist, 'r') as f:
files = [line.strip() for line in f]
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fermiPy/fermipy | fermipy/utils.py | collect_dirs | def collect_dirs(path, max_depth=1, followlinks=True):
"""Recursively find directories under the given path."""
if not os.path.isdir(path):
return []
o = [path]
if max_depth == 0:
return o
for subdir in os.listdir(path):
subdir = os.path.join(path, subdir)
if no... | python | def collect_dirs(path, max_depth=1, followlinks=True):
"""Recursively find directories under the given path."""
if not os.path.isdir(path):
return []
o = [path]
if max_depth == 0:
return o
for subdir in os.listdir(path):
subdir = os.path.join(path, subdir)
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fermiPy/fermipy | fermipy/utils.py | match_regex_list | def match_regex_list(patterns, string):
"""Perform a regex match of a string against a list of patterns.
Returns true if the string matches at least one pattern in the
list."""
for p in patterns:
if re.findall(p, string):
return True
return False | python | def match_regex_list(patterns, string):
"""Perform a regex match of a string against a list of patterns.
Returns true if the string matches at least one pattern in the
list."""
for p in patterns:
if re.findall(p, string):
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fermiPy/fermipy | fermipy/utils.py | find_rows_by_string | def find_rows_by_string(tab, names, colnames=['assoc']):
"""Find the rows in a table ``tab`` that match at least one of the
strings in ``names``. This method ignores whitespace and case
when matching strings.
Parameters
----------
tab : `astropy.table.Table`
Table that will be searched.... | python | def find_rows_by_string(tab, names, colnames=['assoc']):
"""Find the rows in a table ``tab`` that match at least one of the
strings in ``names``. This method ignores whitespace and case
when matching strings.
Parameters
----------
tab : `astropy.table.Table`
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