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limdauto/drf_openapi | drf_openapi/codec.py | _get_parameters | def _get_parameters(link, encoding):
"""
Generates Swagger Parameter Item object.
"""
parameters = []
properties = {}
required = []
for field in link.fields:
parser = OpenApiFieldParser(link, field)
if parser.location == 'form':
if encoding in ('multipart/form-da... | python | def _get_parameters(link, encoding):
"""
Generates Swagger Parameter Item object.
"""
parameters = []
properties = {}
required = []
for field in link.fields:
parser = OpenApiFieldParser(link, field)
if parser.location == 'form':
if encoding in ('multipart/form-da... | [
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demianbrecht/sanction | sanction/__init__.py | Client.auth_uri | def auth_uri(self, redirect_uri=None, scope=None, scope_delim=None,
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""" Builds the auth URI for the authorization endpoint
:param scope: (optional) The `scope` parameter to pass for
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fermiPy/fermipy | fermipy/diffuse/fitting.py | build_srcdict | def build_srcdict(gta, prop):
"""Build a dictionary that maps from source name to the value of a source property
Parameters
----------
gta : `fermipy.GTAnalysis`
The analysis object
prop : str
The name of the property we are mapping
Returns
-------
odict : dict
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"""Build a dictionary that maps from source name to the value of a source property
Parameters
----------
gta : `fermipy.GTAnalysis`
The analysis object
prop : str
The name of the property we are mapping
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odict : dict
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fermiPy/fermipy | fermipy/diffuse/fitting.py | get_src_names | def get_src_names(gta):
"""Build and return a list of source name
Parameters
----------
gta : `fermipy.GTAnalysis`
The analysis object
Returns
-------
l : list
Names of the source
"""
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return sorted(o) | python | def get_src_names(gta):
"""Build and return a list of source name
Parameters
----------
gta : `fermipy.GTAnalysis`
The analysis object
Returns
-------
l : list
Names of the source
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fermiPy/fermipy | fermipy/diffuse/fitting.py | set_wts_get_npred_wt | def set_wts_get_npred_wt(gta, maskname):
"""Set a weights file and get the weighted npred for all the sources
Parameters
----------
gta : `fermipy.GTAnalysis`
The analysis object
maskname : str
The path to the file with the mask
Returns
-------
odict : dict
... | python | def set_wts_get_npred_wt(gta, maskname):
"""Set a weights file and get the weighted npred for all the sources
Parameters
----------
gta : `fermipy.GTAnalysis`
The analysis object
maskname : str
The path to the file with the mask
Returns
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fermiPy/fermipy | fermipy/diffuse/fitting.py | snapshot | def snapshot(gta, plotter, key, do_weighted=True, make_plots=True):
"""Take a snapshot of the ROI
Parameters
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gta : `fermipy.GTAnalysis`
The analysis object
plotter : `fermipy.plotting.AnalysisPlotter`
The object that makes the plots
key : str
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"""Take a snapshot of the ROI
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The analysis object
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The object that makes the plots
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fermiPy/fermipy | fermipy/diffuse/fitting.py | get_unchanged | def get_unchanged(src_list, npred_dict_new,
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frac_threshold=0.9):
"""Compare two dictionarys of npreds, and get the list of sources
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Parameters
----------
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npred_dict_old,
npred_threshold=1e4,
frac_threshold=0.9):
"""Compare two dictionarys of npreds, and get the list of sources
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fermiPy/fermipy | fermipy/jobs/native_impl.py | NativeInterface.dispatch_job_hook | def dispatch_job_hook(self, link, key, job_config, logfile, stream=sys.stdout):
"""Send a single job to be executed
Parameters
----------
link : `fermipy.jobs.chain.Link`
The link used to invoke the command we are running
key : str
A string that identif... | python | def dispatch_job_hook(self, link, key, job_config, logfile, stream=sys.stdout):
"""Send a single job to be executed
Parameters
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The link used to invoke the command we are running
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fermiPy/fermipy | fermipy/logger.py | log_level | def log_level(level):
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"""This is a function that returns a python like
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fermiPy/fermipy | fermipy/logger.py | Logger.setup | def setup(config=None, logfile=None):
"""This method sets up the default configuration of the
logger. Once this method is called all subsequent instances
Logger instances will inherit this configuration."""
if config is None:
configpath = os.path.join(fermipy.PACKAGE_ROOT, ... | python | def setup(config=None, logfile=None):
"""This method sets up the default configuration of the
logger. Once this method is called all subsequent instances
Logger instances will inherit this configuration."""
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Parameters
----------
name : str
Logger name.
logfile : str
Path to the log file.
loglevel : int
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Logger name.
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Path to the log file.
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fermiPy/fermipy | fermipy/jobs/link.py | extract_arguments | def extract_arguments(args, defaults):
"""Extract a set of arguments from a large dictionary
Parameters
----------
args : dict
Dictionary with the arguments values to use
defaults : dict
Dictionary with all the argument to extract, and default values for each
Returns
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"""Extract a set of arguments from a large dictionary
Parameters
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args : dict
Dictionary with the arguments values to use
defaults : dict
Dictionary with all the argument to extract, and default values for each
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fermiPy/fermipy | fermipy/jobs/link.py | check_files | def check_files(filelist,
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Parameters
----------
filelist : list
The list of files we are checking for.
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filelist : list
The list of files we are checking for.
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fermiPy/fermipy | fermipy/jobs/link.py | add_argument | def add_argument(parser, dest, info):
""" Add an argument to an `argparse.ArgumentParser` object
Parameters
----------
parser : `argparse.ArgumentParser`
The parser in question
dest : str
The destination for the argument
info : `tuple`
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""" Add an argument to an `argparse.ArgumentParser` object
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parser : `argparse.ArgumentParser`
The parser in question
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The destination for the argument
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fermiPy/fermipy | fermipy/jobs/link.py | convert_dict_to_option_dict | def convert_dict_to_option_dict(input_dict):
"""Convert a simple key-value dictionary to a dictionary of options tuples"""
ret_dict = {}
for key, value in input_dict.items():
ret_dict[key] = convert_value_to_option_tuple(value)
return ret_dict | python | def convert_dict_to_option_dict(input_dict):
"""Convert a simple key-value dictionary to a dictionary of options tuples"""
ret_dict = {}
for key, value in input_dict.items():
ret_dict[key] = convert_value_to_option_tuple(value)
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fermiPy/fermipy | fermipy/jobs/link.py | reduce_by_keys | def reduce_by_keys(orig_dict, keys, default=None):
"""Reduce a dictionary by selecting a set of keys """
ret = {}
for key in keys:
ret[key] = orig_dict.get(key, default)
return ret | python | def reduce_by_keys(orig_dict, keys, default=None):
"""Reduce a dictionary by selecting a set of keys """
ret = {}
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"""Construct a docstring for a set of options"""
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s += "%s : %s\n %s [%s]\n" % (key, str(opt[2]),
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"""Construct a docstring for a set of options"""
s = "\nParameters\n"
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fermiPy/fermipy | fermipy/jobs/link.py | Link.register_class | def register_class(cls):
"""Regsiter this class in the `LinkFactory` """
if cls.appname in LinkFactory._class_dict:
return
LinkFactory.register(cls.appname, cls) | python | def register_class(cls):
"""Regsiter this class in the `LinkFactory` """
if cls.appname in LinkFactory._class_dict:
return
LinkFactory.register(cls.appname, cls) | [
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fermiPy/fermipy | fermipy/jobs/link.py | Link._fill_argparser | def _fill_argparser(self, parser):
"""Fill an `argparser.ArgumentParser` with the options from this chain
"""
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add_argument(parser, key, val) | python | def _fill_argparser(self, parser):
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fermiPy/fermipy | fermipy/jobs/link.py | Link._run_argparser | def _run_argparser(self, argv):
"""Initialize a link with a set of arguments using an `argparser.ArgumentParser`
"""
if self._parser is None:
raise ValueError('Link was not given a parser on initialization')
args = self._parser.parse_args(argv)
self.update_args(args._... | python | def _run_argparser(self, argv):
"""Initialize a link with a set of arguments using an `argparser.ArgumentParser`
"""
if self._parser is None:
raise ValueError('Link was not given a parser on initialization')
args = self._parser.parse_args(argv)
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fermiPy/fermipy | fermipy/jobs/link.py | Link._update_sub_file_dict | def _update_sub_file_dict(self, sub_files):
"""Update a file dict with information from self"""
sub_files.file_dict.clear()
for job_details in self.jobs.values():
if job_details.file_dict is not None:
sub_files.update(job_details.file_dict)
if job_details.... | python | def _update_sub_file_dict(self, sub_files):
"""Update a file dict with information from self"""
sub_files.file_dict.clear()
for job_details in self.jobs.values():
if job_details.file_dict is not None:
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fermiPy/fermipy | fermipy/jobs/link.py | Link._pre_run_checks | def _pre_run_checks(self, stream=sys.stdout, dry_run=False):
"""Do some checks before running 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 return False.
... | python | def _pre_run_checks(self, stream=sys.stdout, dry_run=False):
"""Do some checks before running this link
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If input files are missing this will raise `OSError` if dry_run is False
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fermiPy/fermipy | fermipy/jobs/link.py | Link._create_job_details | def _create_job_details(self, key, job_config, logfile, status):
"""Create a `JobDetails` for a single job
Parameters
----------
key : str
Key used to identify this particular job
job_config : dict
Dictionary with arguements passed to this particular jo... | python | def _create_job_details(self, key, job_config, logfile, status):
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fermiPy/fermipy | fermipy/jobs/link.py | Link._map_scratch_files | def _map_scratch_files(self, file_dict):
"""Build and return the mapping for copying files to and from scratch area"""
if self._file_stage is None:
return ({}, {})
input_files = file_dict.input_files_to_stage
output_files = file_dict.output_files_to_stage
input_file_m... | python | def _map_scratch_files(self, file_dict):
"""Build and return the mapping for copying files to and from scratch area"""
if self._file_stage is None:
return ({}, {})
input_files = file_dict.input_files_to_stage
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fermiPy/fermipy | fermipy/jobs/link.py | Link._update_file_args | def _update_file_args(self, file_mapping):
"""Adjust the arguments to deal with staging files to the scratch area"""
for key, value in self.args.items():
new_value = file_mapping.get(value, value)
if new_value != value:
self.args[key] = new_value | python | def _update_file_args(self, file_mapping):
"""Adjust the arguments to deal with staging files to the scratch area"""
for key, value in self.args.items():
new_value = file_mapping.get(value, value)
if new_value != value:
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fermiPy/fermipy | fermipy/jobs/link.py | Link._stage_input_files | def _stage_input_files(self, file_mapping, dry_run=True):
"""Stage the input files to the scratch area and adjust the arguments accordingly"""
# print ("Staging input ", file_mapping)
if self._file_stage is None:
return
self._file_stage.copy_to_scratch(file_mapping, dry_run) | python | def _stage_input_files(self, file_mapping, dry_run=True):
"""Stage the input files to the scratch area and adjust the arguments accordingly"""
# print ("Staging input ", file_mapping)
if self._file_stage is None:
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fermiPy/fermipy | fermipy/jobs/link.py | Link._stage_output_files | def _stage_output_files(self, file_mapping, dry_run=True):
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# print ("Staging output ", file_mapping)
if self._file_stage is None:
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fermiPy/fermipy | fermipy/jobs/link.py | Link._register_job | def _register_job(self, key, job_config, logfile, status):
"""Create a `JobDetails` for this link
and add it to the self.jobs dictionary.
Parameters
----------
key : str
Key used to identify this particular job
job_config : dict
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"""Create a `JobDetails` for this link
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key : str
Key used to identify this particular job
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fermiPy/fermipy | fermipy/jobs/link.py | Link._register_self | def _register_self(self, logfile, key=JobDetails.topkey, status=JobStatus.unknown):
"""Runs this link, captures output to logfile,
and records the job in self.jobs"""
fullkey = JobDetails.make_fullkey(self.full_linkname, key)
if fullkey in self.jobs:
job_details = self.jobs[f... | python | def _register_self(self, logfile, key=JobDetails.topkey, status=JobStatus.unknown):
"""Runs this link, captures output to logfile,
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fermiPy/fermipy | fermipy/jobs/link.py | Link._archive_self | def _archive_self(self, logfile, key=JobDetails.topkey, status=JobStatus.unknown):
"""Write info about a job run by this `Link` to the job archive"""
self._register_self(logfile, key, status)
if self._job_archive is None:
return
self._job_archive.register_jobs(self.get_jobs()... | python | def _archive_self(self, logfile, key=JobDetails.topkey, status=JobStatus.unknown):
"""Write info about a job run by this `Link` to the job archive"""
self._register_self(logfile, key, status)
if self._job_archive is None:
return
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fermiPy/fermipy | fermipy/jobs/link.py | Link._set_status_self | def _set_status_self(self, key=JobDetails.topkey, status=JobStatus.unknown):
"""Set the status of this job, both in self.jobs and
in the `JobArchive` if it is present. """
fullkey = JobDetails.make_fullkey(self.full_linkname, key)
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"""Set the status of this job, both in self.jobs and
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fermiPy/fermipy | fermipy/jobs/link.py | Link._write_status_to_log | def _write_status_to_log(self, return_code, stream=sys.stdout):
"""Write the status of this job to a log stream.
This is used to check on job completion."""
stream.write("Timestamp: %i\n" % get_timestamp())
if return_code == 0:
stream.write("%s\n" % self._interface.string_suc... | python | def _write_status_to_log(self, return_code, stream=sys.stdout):
"""Write the status of this job to a log stream.
This is used to check on job completion."""
stream.write("Timestamp: %i\n" % get_timestamp())
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fermiPy/fermipy | fermipy/jobs/link.py | Link.get_failed_jobs | def get_failed_jobs(self, fail_running=False, fail_pending=False):
"""Return a dictionary with the subset of jobs that are marked as failed
Parameters
----------
fail_running : `bool`
If True, consider running jobs as failed
fail_pending : `bool`
If True... | python | def get_failed_jobs(self, fail_running=False, fail_pending=False):
"""Return a dictionary with the subset of jobs that are marked as failed
Parameters
----------
fail_running : `bool`
If True, consider running jobs as failed
fail_pending : `bool`
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fermiPy/fermipy | fermipy/jobs/link.py | Link.check_job_status | def check_job_status(self, key=JobDetails.topkey,
fail_running=False,
fail_pending=False,
force_check=False):
"""Check the status of a particular job
By default this checks the status of the top-level job, but
can by mad... | python | def check_job_status(self, key=JobDetails.topkey,
fail_running=False,
fail_pending=False,
force_check=False):
"""Check the status of a particular job
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fermiPy/fermipy | fermipy/jobs/link.py | Link.check_jobs_status | def check_jobs_status(self,
fail_running=False,
fail_pending=False):
"""Check the status of all the jobs run from this link
and return a status flag that summarizes that.
Parameters
----------
fail_running : `bool`
... | python | def check_jobs_status(self,
fail_running=False,
fail_pending=False):
"""Check the status of all the jobs run from this link
and return a status flag that summarizes that.
Parameters
----------
fail_running : `bool`
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fermiPy/fermipy | fermipy/jobs/link.py | Link.check_input_files | def check_input_files(self,
return_found=True,
return_missing=True):
"""Check if input files exist.
Parameters
----------
return_found : list
A list with the paths of the files that were found.
return_missing : lis... | python | def check_input_files(self,
return_found=True,
return_missing=True):
"""Check if input files exist.
Parameters
----------
return_found : list
A list with the paths of the files that were found.
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fermiPy/fermipy | fermipy/jobs/link.py | Link.check_output_files | def check_output_files(self,
return_found=True,
return_missing=True):
"""Check if output files exist.
Parameters
----------
return_found : list
A list with the paths of the files that were found.
return_missing :... | python | def check_output_files(self,
return_found=True,
return_missing=True):
"""Check if output files exist.
Parameters
----------
return_found : list
A list with the paths of the files that were found.
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fermiPy/fermipy | fermipy/jobs/link.py | Link.missing_output_files | def missing_output_files(self):
"""Make and return a dictionary of the missing output files.
This returns a dictionary mapping
filepath to list of links that produce the file as output.
"""
missing = self.check_output_files(return_found=False)
ret_dict = {}
for m... | python | def missing_output_files(self):
"""Make and return a dictionary of the missing output files.
This returns a dictionary mapping
filepath to list of links that produce the file as output.
"""
missing = self.check_output_files(return_found=False)
ret_dict = {}
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fermiPy/fermipy | fermipy/jobs/link.py | Link.formatted_command | def formatted_command(self):
"""Build and return the formatted command for this `Link`.
This is exactly the command as called from the Unix command line.
"""
# FIXME, this isn't really great as it force you to have all the arguments
command_template = self.command_template()
... | python | def formatted_command(self):
"""Build and return the formatted command for this `Link`.
This is exactly the command as called from the Unix command line.
"""
# FIXME, this isn't really great as it force you to have all the arguments
command_template = self.command_template()
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fermiPy/fermipy | fermipy/jobs/link.py | Link.run_with_log | def run_with_log(self, dry_run=False, stage_files=True, resubmit_failed=False):
"""Runs this link with output sent to a pre-defined logfile
Parameters
-----------
dry_run : bool
Print command but do not run it.
stage_files : bool
Copy files to and from s... | python | def run_with_log(self, dry_run=False, stage_files=True, resubmit_failed=False):
"""Runs this link with output sent to a pre-defined logfile
Parameters
-----------
dry_run : bool
Print command but do not run it.
stage_files : bool
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fermiPy/fermipy | fermipy/wcs_utils.py | create_wcs | def create_wcs(skydir, coordsys='CEL', projection='AIT',
cdelt=1.0, crpix=1., naxis=2, energies=None):
"""Create a WCS object.
Parameters
----------
skydir : `~astropy.coordinates.SkyCoord`
Sky coordinate of the WCS reference point.
coordsys : str
projection : str
c... | python | def create_wcs(skydir, coordsys='CEL', projection='AIT',
cdelt=1.0, crpix=1., naxis=2, energies=None):
"""Create a WCS object.
Parameters
----------
skydir : `~astropy.coordinates.SkyCoord`
Sky coordinate of the WCS reference point.
coordsys : str
projection : str
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fermiPy/fermipy | fermipy/wcs_utils.py | wcs_add_energy_axis | def wcs_add_energy_axis(wcs, energies):
"""Copy a WCS object, and add on the energy axis.
Parameters
----------
wcs : `~astropy.wcs.WCS`
WCS
energies : array-like
Array of energies.
"""
if wcs.naxis != 2:
raise Exception(
'wcs_add_energy_axis, input WCS na... | python | def wcs_add_energy_axis(wcs, energies):
"""Copy a WCS object, and add on the energy axis.
Parameters
----------
wcs : `~astropy.wcs.WCS`
WCS
energies : array-like
Array of energies.
"""
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fermiPy/fermipy | fermipy/wcs_utils.py | sky_to_offset | def sky_to_offset(skydir, lon, lat, coordsys='CEL', projection='AIT'):
"""Convert sky coordinates to a projected offset. This function
is the inverse of offset_to_sky."""
w = create_wcs(skydir, coordsys, projection)
skycrd = np.vstack((lon, lat)).T
if len(skycrd) == 0:
return skycrd
... | python | def sky_to_offset(skydir, lon, lat, coordsys='CEL', projection='AIT'):
"""Convert sky coordinates to a projected offset. This function
is the inverse of offset_to_sky."""
w = create_wcs(skydir, coordsys, projection)
skycrd = np.vstack((lon, lat)).T
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fermiPy/fermipy | fermipy/wcs_utils.py | skydir_to_pix | def skydir_to_pix(skydir, wcs):
"""Convert skydir object to pixel coordinates.
Gracefully handles 0-d coordinate arrays.
Parameters
----------
skydir : `~astropy.coordinates.SkyCoord`
wcs : `~astropy.wcs.WCS`
Returns
-------
xp, yp : `numpy.ndarray`
The pixel coordinates
... | python | def skydir_to_pix(skydir, wcs):
"""Convert skydir object to pixel coordinates.
Gracefully handles 0-d coordinate arrays.
Parameters
----------
skydir : `~astropy.coordinates.SkyCoord`
wcs : `~astropy.wcs.WCS`
Returns
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xp, yp : `numpy.ndarray`
The pixel coordinates
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fermiPy/fermipy | fermipy/wcs_utils.py | pix_to_skydir | def pix_to_skydir(xpix, ypix, wcs):
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Always returns a celestial coordinate.
Parameters
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xpix : `numpy.ndarray`
ypix : `numpy.ndarray`
wcs : `~astropy.wcs.WCS`
"""
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xpix : `numpy.ndarray`
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wcs : `~astropy.wcs.WCS`
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fermiPy/fermipy | fermipy/wcs_utils.py | wcs_to_axes | def wcs_to_axes(w, npix):
"""Generate a sequence of bin edge vectors corresponding to the
axes of a WCS object."""
npix = npix[::-1]
x = np.linspace(-(npix[0]) / 2., (npix[0]) / 2.,
npix[0] + 1) * np.abs(w.wcs.cdelt[0])
y = np.linspace(-(npix[1]) / 2., (npix[1]) / 2.,
... | python | def wcs_to_axes(w, npix):
"""Generate a sequence of bin edge vectors corresponding to the
axes of a WCS object."""
npix = npix[::-1]
x = np.linspace(-(npix[0]) / 2., (npix[0]) / 2.,
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fermiPy/fermipy | fermipy/wcs_utils.py | get_cel_to_gal_angle | def get_cel_to_gal_angle(skydir):
"""Calculate the rotation angle in radians between the longitude
axes of a local projection in celestial and galactic coordinates.
Parameters
----------
skydir : `~astropy.coordinates.SkyCoord`
Direction of projection center.
Returns
-------
an... | python | def get_cel_to_gal_angle(skydir):
"""Calculate the rotation angle in radians between the longitude
axes of a local projection in celestial and galactic coordinates.
Parameters
----------
skydir : `~astropy.coordinates.SkyCoord`
Direction of projection center.
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fermiPy/fermipy | fermipy/wcs_utils.py | extract_mapcube_region | def extract_mapcube_region(infile, skydir, outfile, maphdu=0):
"""Extract a region out of an all-sky mapcube file.
Parameters
----------
infile : str
Path to mapcube file.
skydir : `~astropy.coordinates.SkyCoord`
"""
h = fits.open(os.path.expandvars(infile))
npix = 200
... | python | def extract_mapcube_region(infile, skydir, outfile, maphdu=0):
"""Extract a region out of an all-sky mapcube file.
Parameters
----------
infile : str
Path to mapcube file.
skydir : `~astropy.coordinates.SkyCoord`
"""
h = fits.open(os.path.expandvars(infile))
npix = 200
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fermiPy/fermipy | fermipy/diffuse/utils.py | readlines | def readlines(arg):
"""Read lines from a file into a list.
Removes whitespace and lines that start with '#'
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fin = open(arg)
lines_in = fin.readlines()
fin.close()
lines_out = []
for line in lines_in:
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if not line or line[0] == '#':
cont... | python | def readlines(arg):
"""Read lines from a file into a list.
Removes whitespace and lines that start with '#'
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fermiPy/fermipy | fermipy/diffuse/utils.py | create_inputlist | def create_inputlist(arglist):
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Recursively read all files with the extension '.lst'
"""
lines = []
if isinstance(arglist, list):
for arg in arglist:
if os.path.splitext... | python | def create_inputlist(arglist):
"""Read lines from a file and makes a list of file names.
Removes whitespace and lines that start with '#'
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lines = []
if isinstance(arglist, list):
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fermiPy/fermipy | fermipy/validate/tools.py | Validator.init | def init(self):
"""Initialize histograms."""
evclass_shape = [16, 40, 10]
evtype_shape = [16, 16, 40, 10]
evclass_psf_shape = [16, 40, 10, 100]
evtype_psf_shape = [16, 16, 40, 10, 100]
self._hists_eff = dict()
self._hists = dict(evclass_on=np.zeros(evclass_shape... | python | def init(self):
"""Initialize histograms."""
evclass_shape = [16, 40, 10]
evtype_shape = [16, 16, 40, 10]
evclass_psf_shape = [16, 40, 10, 100]
evtype_psf_shape = [16, 16, 40, 10, 100]
self._hists_eff = dict()
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fermiPy/fermipy | fermipy/validate/tools.py | Validator.create_hist | def create_hist(self, evclass, evtype, xsep, energy, ctheta,
fill_sep=False, fill_evtype=False):
"""Load into a histogram."""
nevt = len(evclass)
ebin = utils.val_to_bin(self._energy_bins, energy)
scale = self._psf_scale[ebin]
vals = [energy, ctheta]
... | python | def create_hist(self, evclass, evtype, xsep, energy, ctheta,
fill_sep=False, fill_evtype=False):
"""Load into a histogram."""
nevt = len(evclass)
ebin = utils.val_to_bin(self._energy_bins, energy)
scale = self._psf_scale[ebin]
vals = [energy, ctheta]
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fermiPy/fermipy | fermipy/validate/tools.py | Validator.calc_eff | def calc_eff(self):
"""Calculate the efficiency."""
hists = self.hists
hists_out = self._hists_eff
cth_axis_idx = dict(evclass=2, evtype=3)
for k in ['evclass', 'evtype']:
if k == 'evclass':
ns0 = hists['evclass_on'][4][None, ...]
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"""Calculate the efficiency."""
hists = self.hists
hists_out = self._hists_eff
cth_axis_idx = dict(evclass=2, evtype=3)
for k in ['evclass', 'evtype']:
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fermiPy/fermipy | fermipy/validate/tools.py | Validator.calc_containment | def calc_containment(self):
"""Calculate PSF containment."""
hists = self.hists
hists_out = self._hists_eff
quantiles = [0.34, 0.68, 0.90, 0.95]
cth_axis_idx = dict(evclass=2, evtype=3)
for k in ['evclass']: # ,'evtype']:
print(k)
non = hists['... | python | def calc_containment(self):
"""Calculate PSF containment."""
hists = self.hists
hists_out = self._hists_eff
quantiles = [0.34, 0.68, 0.90, 0.95]
cth_axis_idx = dict(evclass=2, evtype=3)
for k in ['evclass']: # ,'evtype']:
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fermiPy/fermipy | fermipy/config.py | update_from_schema | def update_from_schema(cfg, cfgin, schema):
"""Update configuration dictionary ``cfg`` with the contents of
``cfgin`` using the ``schema`` dictionary to determine the valid
input keys.
Parameters
----------
cfg : dict
Configuration dictionary to be updated.
cfgin : dict
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"""Update configuration dictionary ``cfg`` with the contents of
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----------
cfg : dict
Configuration dictionary to be updated.
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fermiPy/fermipy | fermipy/config.py | Configurable.write_config | def write_config(self, outfile):
"""Write the configuration dictionary to an output file."""
utils.write_yaml(self.config, outfile, default_flow_style=False) | python | def write_config(self, outfile):
"""Write the configuration dictionary to an output file."""
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fermiPy/fermipy | fermipy/config.py | ConfigManager.create | def create(cls, configfile):
"""Create a configuration dictionary from a yaml config file.
This function will first populate the dictionary with defaults
taken from pre-defined configuration files. The configuration
dictionary is then updated with the user-defined configuration
... | python | def create(cls, configfile):
"""Create a configuration dictionary from a yaml config file.
This function will first populate the dictionary with defaults
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fermiPy/fermipy | fermipy/merge_utils.py | update_null_primary | def update_null_primary(hdu_in, hdu=None):
""" 'Update' a null primary HDU
This actually just checks hdu exists and creates it from hdu_in if it does not.
"""
if hdu is None:
hdu = fits.PrimaryHDU(header=hdu_in.header)
else:
hdu = hdu_in
hdu.header.remove('FILENAME')
ret... | python | def update_null_primary(hdu_in, hdu=None):
""" 'Update' a null primary HDU
This actually just checks hdu exists and creates it from hdu_in if it does not.
"""
if hdu is None:
hdu = fits.PrimaryHDU(header=hdu_in.header)
else:
hdu = hdu_in
hdu.header.remove('FILENAME')
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fermiPy/fermipy | fermipy/merge_utils.py | update_primary | def update_primary(hdu_in, hdu=None):
""" 'Update' a primary HDU
This checks hdu exists and creates it from hdu_in if it does not.
If hdu does exist, this adds the data in hdu_in to hdu
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hdu = fits.PrimaryHDU(data=hdu_in.data, header=hdu_in.header)
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""" 'Update' a primary HDU
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fermiPy/fermipy | fermipy/merge_utils.py | update_image | def update_image(hdu_in, hdu=None):
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If hdu does exist, this adds the data in hdu_in to hdu
"""
if hdu is None:
hdu = fits.ImageHDU(
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""" 'Update' an image HDU
This checks hdu exists and creates it from hdu_in if it does not.
If hdu does exist, this adds the data in hdu_in to hdu
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fermiPy/fermipy | fermipy/merge_utils.py | update_ebounds | def update_ebounds(hdu_in, hdu=None):
""" 'Update' the EBOUNDS HDU
This checks hdu exists and creates it from hdu_in if it does not.
If hdu does exist, this raises an exception if it doesn not match hdu_in
"""
if hdu is None:
hdu = fits.BinTableHDU(
data=hdu_in.data, header=hdu_... | python | def update_ebounds(hdu_in, hdu=None):
""" 'Update' the EBOUNDS HDU
This checks hdu exists and creates it from hdu_in if it does not.
If hdu does exist, this raises an exception if it doesn not match hdu_in
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fermiPy/fermipy | fermipy/merge_utils.py | merge_all_gti_data | def merge_all_gti_data(datalist_in, nrows, first):
""" Merge together all the GTI data
Parameters
-------
datalist_in : list of `astropy.io.fits.BinTableHDU` data
The GTI data that is being merged
nrows : `~numpy.ndarray` of ints
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""" Merge together all the GTI data
Parameters
-------
datalist_in : list of `astropy.io.fits.BinTableHDU` data
The GTI data that is being merged
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fermiPy/fermipy | fermipy/merge_utils.py | extract_gti_data | def extract_gti_data(hdu_in):
""" Extract some GTI related data
Parameters
-------
hdu_in : `astropy.io.fits.BinTableHDU`
The GTI data
Returns
-------
data : `astropy.io.fits.BinTableHDU` data
exposure : float
Exposure value taken from FITS header
tstop : float
... | python | def extract_gti_data(hdu_in):
""" Extract some GTI related data
Parameters
-------
hdu_in : `astropy.io.fits.BinTableHDU`
The GTI data
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data : `astropy.io.fits.BinTableHDU` data
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fermiPy/fermipy | fermipy/merge_utils.py | update_hpx_skymap_allsky | def update_hpx_skymap_allsky(map_in, map_out):
""" 'Update' a HEALPix skymap
This checks map_out exists and creates it from map_in if it does not.
If map_out does exist, this adds the data in map_in to map_out
"""
if map_out is None:
in_hpx = map_in.hpx
out_hpx = HPX.create_hpx(in_h... | python | def update_hpx_skymap_allsky(map_in, map_out):
""" 'Update' a HEALPix skymap
This checks map_out exists and creates it from map_in if it does not.
If map_out does exist, this adds the data in map_in to map_out
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if map_out is None:
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fermiPy/fermipy | fermipy/merge_utils.py | merge_wcs_counts_cubes | def merge_wcs_counts_cubes(filelist):
""" Merge all the files in filelist, assuming that they WCS counts cubes
"""
out_prim = None
out_ebounds = None
datalist_gti = []
exposure_sum = 0.
nfiles = len(filelist)
ngti = np.zeros(nfiles, int)
for i, filename in enumerate(filelist):
... | python | def merge_wcs_counts_cubes(filelist):
""" Merge all the files in filelist, assuming that they WCS counts cubes
"""
out_prim = None
out_ebounds = None
datalist_gti = []
exposure_sum = 0.
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ngti = np.zeros(nfiles, int)
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fermiPy/fermipy | fermipy/merge_utils.py | merge_hpx_counts_cubes | def merge_hpx_counts_cubes(filelist):
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fermiPy/fermipy | fermipy/diffuse/gt_srcmap_partial.py | SrcmapsDiffuse_SG._write_xml | def _write_xml(xmlfile, srcs):
"""Save the ROI model as an XML """
root = ElementTree.Element('source_library')
root.set('title', 'source_library')
for src in srcs:
src.write_xml(root)
output_file = open(xmlfile, 'w')
output_file.write(utils.prettify_xml(roo... | python | def _write_xml(xmlfile, srcs):
"""Save the ROI model as an XML """
root = ElementTree.Element('source_library')
root.set('title', 'source_library')
for src in srcs:
src.write_xml(root)
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fermiPy/fermipy | fermipy/diffuse/gt_srcmap_partial.py | SrcmapsDiffuse_SG._handle_component | def _handle_component(sourcekey, comp_dict):
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if comp_dict.comp_key is None:
fullkey = sourcekey
else:
fullkey = "%s_%s" % (sourcekey, comp_dict.comp_key)
srcdict = make_sources(fullkey, comp_... | python | def _handle_component(sourcekey, comp_dict):
"""Make the source objects and write the xml for a component
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if comp_dict.comp_key is None:
fullkey = sourcekey
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fullkey = "%s_%s" % (sourcekey, comp_dict.comp_key)
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fermiPy/fermipy | fermipy/sourcefind_utils.py | find_peaks | def find_peaks(input_map, threshold, min_separation=0.5):
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`threshold` and lie a distance at least `min_separation` from another
peak of larger amplitude. The implementation of this method uses
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"""Find peaks in a 2-D map object that have amplitude larger than
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peak of larger amplitude. The implementation of this method uses
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fermiPy/fermipy | fermipy/sourcefind_utils.py | estimate_pos_and_err_parabolic | def estimate_pos_and_err_parabolic(tsvals):
"""Solve for the position and uncertainty of source in one dimension
assuming that you are near the maximum and the errors are parabolic
Parameters
----------
tsvals : `~numpy.ndarray`
The TS values at the maximum TS, and for each pixel on e... | python | def estimate_pos_and_err_parabolic(tsvals):
"""Solve for the position and uncertainty of source in one dimension
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----------
tsvals : `~numpy.ndarray`
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fermiPy/fermipy | fermipy/sourcefind_utils.py | refine_peak | def refine_peak(tsmap, pix):
"""Solve for the position and uncertainty of source assuming that you
are near the maximum and the errors are parabolic
Parameters
----------
tsmap : `~numpy.ndarray`
Array with the TS data.
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"""Solve for the position and uncertainty of source assuming that you
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tsmap : `~numpy.ndarray`
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fermiPy/fermipy | fermipy/roi_model.py | spectral_pars_from_catalog | def spectral_pars_from_catalog(cat):
"""Create spectral parameters from 3FGL catalog columns."""
spectrum_type = cat['SpectrumType']
pars = get_function_defaults(cat['SpectrumType'])
par_idxs = {k: i for i, k in
enumerate(get_function_par_names(cat['SpectrumType']))}
for k in pars:... | python | def spectral_pars_from_catalog(cat):
"""Create spectral parameters from 3FGL catalog columns."""
spectrum_type = cat['SpectrumType']
pars = get_function_defaults(cat['SpectrumType'])
par_idxs = {k: i for i, k in
enumerate(get_function_par_names(cat['SpectrumType']))}
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fermiPy/fermipy | fermipy/roi_model.py | Model.is_free | def is_free(self):
""" returns True if any of the spectral model parameters is set to free, else False
"""
return bool(np.array([int(value.get("free", False)) for key, value in self.spectral_pars.items()]).sum()) | python | def is_free(self):
""" returns True if any of the spectral model parameters is set to free, else False
"""
return bool(np.array([int(value.get("free", False)) for key, value in self.spectral_pars.items()]).sum()) | [
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fermiPy/fermipy | fermipy/roi_model.py | Source.set_position | def set_position(self, skydir):
"""
Set the position of the source.
Parameters
----------
skydir : `~astropy.coordinates.SkyCoord`
"""
if not isinstance(skydir, SkyCoord):
skydir = SkyCoord(ra=skydir[0], dec=skydir[1], unit=u.deg)
if not s... | python | def set_position(self, skydir):
"""
Set the position of the source.
Parameters
----------
skydir : `~astropy.coordinates.SkyCoord`
"""
if not isinstance(skydir, SkyCoord):
skydir = SkyCoord(ra=skydir[0], dec=skydir[1], unit=u.deg)
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fermiPy/fermipy | fermipy/roi_model.py | Source.skydir | def skydir(self):
"""Return a SkyCoord representation of the source position.
Returns
-------
skydir : `~astropy.coordinates.SkyCoord`
"""
return SkyCoord(self.radec[0] * u.deg, self.radec[1] * u.deg) | python | def skydir(self):
"""Return a SkyCoord representation of the source position.
Returns
-------
skydir : `~astropy.coordinates.SkyCoord`
"""
return SkyCoord(self.radec[0] * u.deg, self.radec[1] * u.deg) | [
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fermiPy/fermipy | fermipy/roi_model.py | Source.create_from_dict | def create_from_dict(cls, src_dict, roi_skydir=None, rescale=False):
"""Create a source object from a python dictionary.
Parameters
----------
src_dict : dict
Dictionary defining the properties of the source.
"""
src_dict = copy.deepcopy(src_dict)
src... | python | def create_from_dict(cls, src_dict, roi_skydir=None, rescale=False):
"""Create a source object from a python dictionary.
Parameters
----------
src_dict : dict
Dictionary defining the properties of the source.
"""
src_dict = copy.deepcopy(src_dict)
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fermiPy/fermipy | fermipy/roi_model.py | Source.create_from_xmlfile | def create_from_xmlfile(cls, xmlfile, extdir=None):
"""Create a Source object from an XML file.
Parameters
----------
xmlfile : str
Path to XML file.
extdir : str
Path to the extended source archive.
"""
root = ElementTree.ElementTree(fil... | python | def create_from_xmlfile(cls, xmlfile, extdir=None):
"""Create a Source object from an XML file.
Parameters
----------
xmlfile : str
Path to XML file.
extdir : str
Path to the extended source archive.
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fermiPy/fermipy | fermipy/roi_model.py | Source.write_xml | def write_xml(self, root):
"""Write this source to an XML node."""
if not self.extended:
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"""Write this source to an XML node."""
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fermiPy/fermipy | fermipy/roi_model.py | ROIModel.clear | def clear(self):
"""Clear the contents of the ROI."""
self._srcs = []
self._diffuse_srcs = []
self._src_dict = collections.defaultdict(list)
self._src_radius = [] | python | def clear(self):
"""Clear the contents of the ROI."""
self._srcs = []
self._diffuse_srcs = []
self._src_dict = collections.defaultdict(list)
self._src_radius = [] | [
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fermiPy/fermipy | fermipy/roi_model.py | ROIModel.create_source | def create_source(self, name, src_dict, build_index=True,
merge_sources=True, rescale=True):
"""Add a new source to the ROI model from a dictionary or an
existing source object.
Parameters
----------
name : str
src_dict : dict or `~fermipy.roi_mod... | python | def create_source(self, name, src_dict, build_index=True,
merge_sources=True, rescale=True):
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fermiPy/fermipy | fermipy/roi_model.py | ROIModel.load_sources | def load_sources(self, sources):
"""Delete all sources in the ROI and load the input source list."""
self.clear()
for s in sources:
if isinstance(s, dict):
s = Model.create_from_dict(s)
self.load_source(s, build_index=False)
self._build_src_inde... | python | def load_sources(self, sources):
"""Delete all sources in the ROI and load the input source list."""
self.clear()
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if isinstance(s, dict):
s = Model.create_from_dict(s)
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fermiPy/fermipy | fermipy/roi_model.py | ROIModel.load_source | def load_source(self, src, build_index=True, merge_sources=True,
**kwargs):
"""
Load a single source.
Parameters
----------
src : `~fermipy.roi_model.Source`
Source object that will be added to the ROI.
merge_sources : bool
... | python | def load_source(self, src, build_index=True, merge_sources=True,
**kwargs):
"""
Load a single source.
Parameters
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src : `~fermipy.roi_model.Source`
Source object that will be added to the ROI.
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fermiPy/fermipy | fermipy/roi_model.py | ROIModel.match_source | def match_source(self, src):
"""Look for source or sources in the model that match the
given source. Sources are matched by name and any association
columns defined in the assoc_xmatch_columns parameter.
"""
srcs = []
names = [src.name]
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"""Look for source or sources in the model that match the
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columns defined in the assoc_xmatch_columns parameter.
"""
srcs = []
names = [src.name]
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fermiPy/fermipy | fermipy/roi_model.py | ROIModel.load | def load(self, **kwargs):
"""Load both point source and diffuse components."""
coordsys = kwargs.get('coordsys', 'CEL')
extdir = kwargs.get('extdir', self.extdir)
srcname = kwargs.get('srcname', None)
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"""Load both point source and diffuse components."""
coordsys = kwargs.get('coordsys', 'CEL')
extdir = kwargs.get('extdir', self.extdir)
srcname = kwargs.get('srcname', None)
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fermiPy/fermipy | fermipy/roi_model.py | ROIModel.create_from_roi_data | def create_from_roi_data(cls, datafile):
"""Create an ROI model."""
data = np.load(datafile).flat[0]
roi = cls()
roi.load_sources(data['sources'].values())
return roi | python | def create_from_roi_data(cls, datafile):
"""Create an ROI model."""
data = np.load(datafile).flat[0]
roi = cls()
roi.load_sources(data['sources'].values())
return roi | [
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fermiPy/fermipy | fermipy/roi_model.py | ROIModel.create | def create(cls, selection, config, **kwargs):
"""Create an ROIModel instance."""
if selection['target'] is not None:
return cls.create_from_source(selection['target'],
config, **kwargs)
else:
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"""Create an ROIModel instance."""
if selection['target'] is not None:
return cls.create_from_source(selection['target'],
config, **kwargs)
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fermiPy/fermipy | fermipy/roi_model.py | ROIModel.create_from_position | def create_from_position(cls, skydir, config, **kwargs):
"""Create an ROIModel instance centered on a sky direction.
Parameters
----------
skydir : `~astropy.coordinates.SkyCoord`
Sky direction on which the ROI will be centered.
config : dict
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"""Create an ROIModel instance centered on a sky direction.
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skydir : `~astropy.coordinates.SkyCoord`
Sky direction on which the ROI will be centered.
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fermiPy/fermipy | fermipy/roi_model.py | ROIModel.create_from_source | def create_from_source(cls, name, config, **kwargs):
"""Create an ROI centered on the given source."""
coordsys = kwargs.pop('coordsys', 'CEL')
roi = cls(config, src_radius=None, src_roiwidth=None,
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src = roi.get_source_by_name(name)
re... | python | def create_from_source(cls, name, config, **kwargs):
"""Create an ROI centered on the given source."""
coordsys = kwargs.pop('coordsys', 'CEL')
roi = cls(config, src_radius=None, src_roiwidth=None,
srcname=name, **kwargs)
src = roi.get_source_by_name(name)
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fermiPy/fermipy | fermipy/roi_model.py | ROIModel.get_source_by_name | def get_source_by_name(self, name):
"""Return a single source in the ROI with the given name. The
input name string can match any of the strings in the names
property of the source object. Case and whitespace are
ignored when matching name strings. If no sources are found
or m... | python | def get_source_by_name(self, name):
"""Return a single source in the ROI with the given name. The
input name string can match any of the strings in the names
property of the source object. Case and whitespace are
ignored when matching name strings. If no sources are found
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fermiPy/fermipy | fermipy/roi_model.py | ROIModel.get_sources_by_name | def get_sources_by_name(self, name):
"""Return a list of sources in the ROI matching the given
name. The input name string can match any of the strings in
the names property of the source object. Case and whitespace
are ignored when matching name strings.
Parameters
--... | python | def get_sources_by_name(self, name):
"""Return a list of sources in the ROI matching the given
name. The input name string can match any of the strings in
the names property of the source object. Case and whitespace
are ignored when matching name strings.
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fermiPy/fermipy | fermipy/roi_model.py | ROIModel.load_fits_catalog | def load_fits_catalog(self, name, **kwargs):
"""Load sources from a FITS catalog file.
Parameters
----------
name : str
Catalog name or path to a catalog FITS file.
"""
# EAC split this function to make it easier to load an existing catalog
cat = cat... | python | def load_fits_catalog(self, name, **kwargs):
"""Load sources from a FITS catalog file.
Parameters
----------
name : str
Catalog name or path to a catalog FITS file.
"""
# EAC split this function to make it easier to load an existing catalog
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fermiPy/fermipy | fermipy/roi_model.py | ROIModel._build_src_index | def _build_src_index(self):
"""Build an indices for fast lookup of a source given its name
or coordinates."""
self._srcs = sorted(self._srcs, key=lambda t: t['offset'])
nsrc = len(self._srcs)
radec = np.zeros((2, nsrc))
for i, src in enumerate(self._srcs):
r... | python | def _build_src_index(self):
"""Build an indices for fast lookup of a source given its name
or coordinates."""
self._srcs = sorted(self._srcs, key=lambda t: t['offset'])
nsrc = len(self._srcs)
radec = np.zeros((2, nsrc))
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fermiPy/fermipy | fermipy/roi_model.py | ROIModel.write_xml | def write_xml(self, xmlfile, config=None):
"""Save the ROI model as an XML file."""
root = ElementTree.Element('source_library')
root.set('title', 'source_library')
for s in self._srcs:
s.write_xml(root)
if config is not None:
srcs = self.create_diffuse... | python | def write_xml(self, xmlfile, config=None):
"""Save the ROI model as an XML file."""
root = ElementTree.Element('source_library')
root.set('title', 'source_library')
for s in self._srcs:
s.write_xml(root)
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fermiPy/fermipy | fermipy/roi_model.py | ROIModel.create_table | def create_table(self, names=None):
"""Create an astropy Table object with the contents of the ROI model.
"""
scan_shape = (1,)
for src in self._srcs:
scan_shape = max(scan_shape, src['dloglike_scan'].shape)
tab = create_source_table(scan_shape)
for s in sel... | python | def create_table(self, names=None):
"""Create an astropy Table object with the contents of the ROI model.
"""
scan_shape = (1,)
for src in self._srcs:
scan_shape = max(scan_shape, src['dloglike_scan'].shape)
tab = create_source_table(scan_shape)
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fermiPy/fermipy | fermipy/roi_model.py | ROIModel.write_fits | def write_fits(self, fitsfile):
"""Write the ROI model to a FITS file."""
tab = self.create_table()
hdu_data = fits.table_to_hdu(tab)
hdus = [fits.PrimaryHDU(), hdu_data]
fits_utils.write_hdus(hdus, fitsfile) | python | def write_fits(self, fitsfile):
"""Write the ROI model to a FITS file."""
tab = self.create_table()
hdu_data = fits.table_to_hdu(tab)
hdus = [fits.PrimaryHDU(), hdu_data]
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fermiPy/fermipy | fermipy/roi_model.py | ROIModel.write_ds9region | def write_ds9region(self, region, *args, **kwargs):
"""Create a ds9 compatible region file from the ROI.
It calls the `to_ds9` method and write the result to the region file. Only the file name is required.
All other parameters will be forwarded to the `to_ds9` method, see the documentation of... | python | def write_ds9region(self, region, *args, **kwargs):
"""Create a ds9 compatible region file from the ROI.
It calls the `to_ds9` method and write the result to the region file. Only the file name is required.
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fermiPy/fermipy | fermipy/diffuse/catalog_src_manager.py | select_extended | def select_extended(cat_table):
"""Select only rows representing extended sources from a catalog table
"""
try:
l = [len(row.strip()) > 0 for row in cat_table['Extended_Source_Name'].data]
return np.array(l, bool)
except KeyError:
return cat_table['Extended'] | python | def select_extended(cat_table):
"""Select only rows representing extended sources from a catalog table
"""
try:
l = [len(row.strip()) > 0 for row in cat_table['Extended_Source_Name'].data]
return np.array(l, bool)
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fermiPy/fermipy | fermipy/diffuse/catalog_src_manager.py | make_mask | def make_mask(cat_table, cut):
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"""Mask a bit mask selecting the rows that pass a selection
"""
cut_var = cut['cut_var']
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fermiPy/fermipy | fermipy/diffuse/catalog_src_manager.py | select_sources | def select_sources(cat_table, cuts):
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nsrc = len(cat_table)
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"""Select only rows passing a set of cuts from catalog table
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nsrc = len(cat_table)
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"'mask_ex... | Select only rows passing a set of cuts from catalog table | [
"Select",
"only",
"rows",
"passing",
"a",
"set",
"of",
"cuts",
"from",
"catalog",
"table"
] | 9df5e7e3728307fd58c5bba36fd86783c39fbad4 | https://github.com/fermiPy/fermipy/blob/9df5e7e3728307fd58c5bba36fd86783c39fbad4/fermipy/diffuse/catalog_src_manager.py#L53-L67 | train |
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