Source code for gammapy.spectrum.extract
# Licensed under a 3-clause BSD style license - see LICENSE.rst
from __future__ import absolute_import, division, print_function, unicode_literals
import logging
from collections import OrderedDict
import numpy as np
from regions import CircleSkyRegion
import astropy.units as u
from . import PHACountsSpectrum
from . import SpectrumObservation, SpectrumObservationList
from ..utils.scripts import make_path
from ..irf import PSF3D
__all__ = [
'SpectrumExtraction',
]
log = logging.getLogger(__name__)
[docs]class SpectrumExtraction(object):
"""Creating input data to 1D spectrum fitting.
This class is responsible for extracting a
`~gammapy.spectrum.SpectrumObservation` from a
`~gammapy.data.DataStoreObservation`. The background estimation is done
beforehand, using e.g. the
`~gammapy.background.ReflectedRegionsBackgroundEstimator`. For point
sources analyzed with 'full containment' IRFs, a correction for PSF
leakage out of the circular ON region can be applied.
For more info see :ref:`spectral_fitting`.
For a usage example see :gp-extra-notebook:`spectrum_analysis`
Parameters
----------
obs_list : `~gammapy.data.ObservationList`
Observations to process
bkg_estimate : `~gammapy.background.BackgroundEstimate`
Background estimate, e.g. of
`~gammapy.background.ReflectedRegionsBackgroundEstimator`
e_reco : `~astropy.units.Quantity`, optional
Reconstructed energy binning
e_true : `~astropy.units.Quantity`, optional
True energy binning
containment_correction : bool
Apply containment correction for point sources and circular on regions.
max_alpha : float
Maximum alpha value to accept, if the background was estimated using
reflected regions this is 1 / minimum number of regions.
use_recommended_erange : bool
Extract spectrum only within the recommended valid energy range of the
effective area table (default is True).
"""
DEFAULT_TRUE_ENERGY = np.logspace(-2, 2.5, 109) * u.TeV
"""True energy axis to be used if not specified otherwise"""
DEFAULT_RECO_ENERGY = np.logspace(-2, 2, 73) * u.TeV
"""Reconstruced energy axis to be used if not specified otherwise"""
def __init__(self, obs_list, bkg_estimate, e_reco=None, e_true=None,
containment_correction=False, max_alpha=1, use_recommended_erange=True):
self.obs_list = obs_list
self.bkg_estimate = bkg_estimate
self.e_reco = e_reco or self.DEFAULT_RECO_ENERGY
self.e_true = e_true or self.DEFAULT_TRUE_ENERGY
self.containment_correction = containment_correction
self.max_alpha = max_alpha
self.use_recommended_erange = use_recommended_erange
self.observations = SpectrumObservationList()
[docs] def run(self, outdir=None, use_sherpa=False):
"""Run all steps.
Parameters
----------
outdir : Path, str
directory to write results files to (if given)
use_sherpa : bool, optional
Write Sherpa compliant files, default: False
"""
log.info('Running {}'.format(self))
for obs, bkg in zip(self.obs_list, self.bkg_estimate):
if not self._alpha_ok(obs, bkg):
continue
self.observations.append(self.process(obs, bkg))
if outdir is not None:
self.write(outdir, use_sherpa=use_sherpa)
def _alpha_ok(self, obs, bkg):
"""Check if observation fulfills alpha criterion"""
condition = bkg.a_off == 0 or bkg.a_on / bkg.a_off > self.max_alpha
if condition:
msg = 'Skipping because {} / {} > {}'
log.info(msg.format(bkg.a_on, bkg.a_off, self.max_alpha))
return False
else:
return True
[docs] def process(self, obs, bkg):
"""Process one observation.
Parameters
----------
obs : `~gammapy.data.DataStoreObservation`
Observation
bkg : `~gammapy.background.BackgroundEstimate`
Background estimate
Returns
-------
spectrum_observation : `~gammapy.spectrum.SpectrumObservation`
Spectrum observation
"""
log.info('Process observation\n {}'.format(obs))
self.make_empty_vectors(obs, bkg)
self.extract_counts(bkg)
self.extract_irfs(obs)
if self.containment_correction:
self.apply_containment_correction(obs, bkg)
spectrum_observation = SpectrumObservation(
on_vector=self._on_vector,
aeff=self._aeff,
off_vector=self._off_vector,
edisp=self._edisp,
)
if self.use_recommended_erange:
try:
spectrum_observation.hi_threshold = obs.aeff.high_threshold
spectrum_observation.lo_threshold = obs.aeff.low_threshold
except KeyError:
log.warning('No thresholds defined for obs {}'.format(obs))
return spectrum_observation
[docs] def make_empty_vectors(self, obs, bkg):
"""Create empty vectors.
This method copies over all meta info and sets up the energy binning.
Parameters
----------
obs : `~gammapy.data.DataStoreObservation`
Observation
bkg : `~gammapy.background.BackgroundEstimate`
Background estimate
"""
log.info('Update observation meta info')
# Copy over existing meta information
meta = OrderedDict(obs.obs_info)
offset = obs.pointing_radec.separation(bkg.on_region.center)
log.info('Offset : {}\n'.format(offset))
meta['OFFSET'] = offset.deg
# LIVETIME is called EXPOSURE in the OGIP standard
meta['EXPOSURE'] = meta.pop('LIVETIME')
self._on_vector = PHACountsSpectrum(
energy_lo=self.e_reco[:-1],
energy_hi=self.e_reco[1:],
backscal=bkg.a_on,
meta=meta, )
self._off_vector = self._on_vector.copy()
self._off_vector.is_bkg = True
self._off_vector.backscal = bkg.a_off
[docs] def extract_counts(self, bkg):
"""Fill on and off vector for one observation.
Parameters
----------
bkg : `~gammapy.background.BackgroundEstimate`
Background estimate
"""
log.info('Fill events')
self._on_vector.fill(bkg.on_events)
self._off_vector.fill(bkg.off_events)
[docs] def extract_irfs(self, obs):
"""Extract IRFs.
Parameters
----------
obs : `~gammapy.data.DataStoreObservation`
Observation
"""
log.info('Extract IRFs')
offset = self._on_vector.offset
self._aeff = obs.aeff.to_effective_area_table(offset, energy=self.e_true)
self._edisp = obs.edisp.to_energy_dispersion(
offset, e_reco=self.e_reco, e_true=self.e_true)
[docs] def apply_containment_correction(self, obs, bkg):
"""Apply PSF containment correction.
Parameters
----------
obs : `~gammapy.data.DataStoreObservation`
observation
bkg : `~gammapy.background.BackgroundEstimate`
background esimate
"""
# TODO: This should be split out into a separate class
if not isinstance(bkg.on_region, CircleSkyRegion):
raise TypeError("Incorrect region type for containment correction."
" Should be CircleSkyRegion.")
log.info('Apply containment correction')
# First need psf
angles = np.linspace(0., 1.5, 150) * u.deg
offset = self._on_vector.offset
if isinstance(obs.psf, PSF3D):
psf = obs.psf.to_energy_dependent_table_psf(theta=offset)
else:
psf = obs.psf.to_energy_dependent_table_psf(offset, angles)
center_energies = self._on_vector.energy.nodes
areascal = []
for index, energy in enumerate(center_energies):
try:
correction = psf.integral(energy,
0. * u.deg,
bkg.on_region.radius)
except:
msg = 'Containment correction failed for bin {}, energy {}.'
log.warning(msg.format(index, energy))
correction = 1
finally:
areascal.append(correction)
self._on_vector.areascal = areascal
self._off_vector.areascal = areascal
[docs] def compute_energy_threshold(self, **kwargs):
"""Compute and set the safe energy threshold for all observations.
See `SpectrumObservation.compute_energy_threshold` for full
documentation about the options.
"""
for obs in self.observations:
obs.compute_energy_threshold(**kwargs)
[docs] def write(self, outdir, ogipdir='ogip_data', use_sherpa=False):
"""Write results to disk.
Parameters
----------
outdir : `~gammapy.extern.pathlib.Path`
Output folder
ogipdir : str, optional
Folder name for OGIP data, default: 'ogip_data'
use_sherpa : bool, optional
Write Sherpa compliant files, default: False
"""
outdir = make_path(outdir)
log.info("Writing OGIP files to {}".format(outdir / ogipdir))
outdir.mkdir(exist_ok=True, parents=True)
self.observations.write(outdir / ogipdir, use_sherpa=use_sherpa)
# TODO : add more debug plots etc. here