Source code for gammapy.data.data_store

# Licensed under a 3-clause BSD style license - see LICENSE.rst
from __future__ import absolute_import, division, print_function, unicode_literals
import sys
import logging
import numpy as np
from collections import OrderedDict
import subprocess
from astropy.extern.six.moves import UserList
from astropy.table import Table
from astropy.utils import lazyproperty
from astropy.units import Quantity
from astropy.time import Time
from astropy.coordinates import SkyCoord
from ..utils.scripts import make_path
from ..utils.energy import Energy
from .obs_table import ObservationTable
from .hdu_index_table import HDUIndexTable
from .utils import _earth_location_from_dict
from ..irf import EnergyDependentTablePSF, IRFStacker, PSF3D

__all__ = [
    'DataStore',
    'DataStoreObservation',
    'ObservationList',
]

log = logging.getLogger(__name__)


[docs]class DataStore(object): """IACT data store. The data selection and access happens using an observation and an HDU index file as described at :ref:`gadf:iact-storage`. See :ref:`data_store` or :gp-extra-notebook:`data_iact` for usage examples. Parameters ---------- hdu_table : `~gammapy.data.HDUIndexTable` HDU index table obs_table : `~gammapy.data.ObservationTable` Observation index table name : str Data store name Examples -------- Here's an example how to create a `DataStore` to access H.E.S.S. data: >>> from gammapy.data import DataStore >>> dir = '$GAMMAPY_EXTRA/datasets/hess-crab4-hd-hap-prod2' >>> data_store = DataStore.from_dir(dir) >>> data_store.info() """ DEFAULT_HDU_TABLE = 'hdu-index.fits.gz' """Default HDU table filename.""" DEFAULT_OBS_TABLE = 'obs-index.fits.gz' """Default observation table filename.""" DEFAULT_NAME = 'noname' """Default data store name.""" def __init__(self, hdu_table=None, obs_table=None, name=None): self.hdu_table = hdu_table self.obs_table = obs_table if name: self.name = name else: self.name = self.DEFAULT_NAME @classmethod
[docs] def from_files(cls, base_dir, hdu_table_filename=None, obs_table_filename=None, name=None): """Construct from HDU and observation index table files.""" if hdu_table_filename: log.debug('Reading {}'.format(hdu_table_filename)) hdu_table = HDUIndexTable.read(str(hdu_table_filename), format='fits') hdu_table.meta['BASE_DIR'] = base_dir else: hdu_table = None if obs_table_filename: log.debug('Reading {}'.format(str(obs_table_filename))) obs_table = ObservationTable.read(str(obs_table_filename), format='fits') else: obs_table = None return cls( hdu_table=hdu_table, obs_table=obs_table, name=name, )
@classmethod
[docs] def from_dir(cls, base_dir, name=None): """Create from a directory. This assumes that the HDU and observations index tables have the default filename. """ base_dir = make_path(base_dir) return cls.from_files( base_dir=base_dir, hdu_table_filename=base_dir / cls.DEFAULT_HDU_TABLE, obs_table_filename=base_dir / cls.DEFAULT_OBS_TABLE, name=name, )
@classmethod
[docs] def from_config(cls, config): """Create from a config dict.""" base_dir = config['base_dir'] name = config.get('name', cls.DEFAULT_NAME) hdu_table_filename = config.get('hduindx', cls.DEFAULT_HDU_TABLE) obs_table_filename = config.get('obsindx', cls.DEFAULT_OBS_TABLE) hdu_table_filename = cls._find_file(hdu_table_filename, base_dir) obs_table_filename = cls._find_file(obs_table_filename, base_dir) return cls.from_files( base_dir=base_dir, hdu_table_filename=hdu_table_filename, obs_table_filename=obs_table_filename, name=name, )
@staticmethod def _find_file(filename, dir): """Find a file at an absolute or relative location. - First tries ``Path(filename)`` - Second tries ``Path(dir) / filename`` - Raises ``OSError`` if both don't exist. """ path1 = make_path(filename) path2 = make_path(dir) / filename if path1.is_file(): filename = path1 elif path2.is_file(): filename = path2 else: raise OSError('File not found at {} or {}'.format(path1, path2)) return filename @classmethod
[docs] def from_name(cls, name): """Convenience method to look up DataStore from DataManager.""" # This import needs to be delayed to avoid a circular import # It can't be moved to the top of the file from .data_manager import DataManager dm = DataManager() return dm[name]
@classmethod
[docs] def from_all(cls, val): """Try different DataStore constructors. Currently tried (in this order) - :func:`~gammapy.data.DataStore.from_dir` - :func:`~gammapy.data.DataStore.from_name` Parameters ---------- val : str Key to construct DataStore from """ try: store = cls.from_dir(val) except OSError as e1: try: store = cls.from_name(val) except KeyError as e2: raise ValueError('Not able to contruct DataStore using key:' ' {0}.\nErrors\nfrom_dir: {1}\nfrom_name: {2}' .format(val, e1, e2)) return store
[docs] def info(self, file=None): """Print some info.""" if not file: stream = sys.stdout print(file=stream) print('Data store summary info:', file=file) print('name: {}'.format(self.name), file=file) print('', file=file) self.hdu_table.summary(file=file) print('', file=file) self.obs_table.summary(file=file)
[docs] def obs(self, obs_id): """Access a given `~gammapy.data.DataStoreObservation`. Parameters ---------- obs_id : int Observation ID. Returns ------- obs : `~gammapy.data.DataStoreObservation` Observation container """ return DataStoreObservation( obs_id=obs_id, data_store=self, )
[docs] def obs_list(self, obs_id): """Generate a `~gammapy.data.ObservationList`. Parameters ---------- obs_id : list Observation IDs. Returns ------- obs : `~gammapy.data.ObservationList` List of `~gammapy.data.DataStoreObservation` """ return ObservationList(self.obs(_) for _ in obs_id)
[docs] def load_all(self, hdu_type=None, hdu_class=None): """Load a given file type for all observations. Parameters ---------- hdu_type : str HDU type (see `~gammapy.data.HDUIndexTable.VALID_HDU_TYPE`) hdu_class : str HDU class (see `~gammapy.data.HDUIndexTable.VALID_HDU_CLASS`) Returns ------- list : python list of object Object depends on type, e.g. for `events` it is a list of `~gammapy.data.EventList`. """ obs_ids = self.obs_table['OBS_ID'] return self.load_many(obs_ids=obs_ids, hdu_type=hdu_type, hdu_class=hdu_class)
[docs] def load_many(self, obs_ids, hdu_type=None, hdu_class=None): """Load a given file type for certain observations in an observation table. Parameters ---------- obs_ids : list List of observation IDs hdu_type : str HDU type (see `~gammapy.data.HDUIndexTable.VALID_HDU_TYPE`) hdu_class : str HDU class (see `~gammapy.data.HDUIndexTable.VALID_HDU_CLASS`) Returns ------- list : list of object Object depends on type, e.g. for `events` it is a list of `~gammapy.data.EventList`. """ things = [] for obs_id in obs_ids: obs = self.obs(obs_id=obs_id) thing = obs.load(hdu_type=hdu_type, hdu_class=hdu_class) things.append(thing) return things
[docs] def check_integrity(self, logger=None): """Check integrity, i.e. whether index and observation table match. """ # Todo: This is broken - remove or fix? sane = True if logger is None: logger = logging.getLogger('default') logger.info('Checking event list files') available = self.check_available_event_lists(logger) if np.any(~available): logger.warning('Number of missing event list files: {}'.format(np.invert(available).sum())) # TODO: implement better, more complete integrity checks. return sane
[docs] def make_table_of_files(self, observation_table=None, filetypes=['events']): """Make list of files in the datastore directory. Parameters ---------- observation_table : `~gammapy.data.ObservationTable` or None Observation table (``None`` means select all observations). filetypes : list of str File types (TODO: document in a central location and reference from here). Returns ------- table : `~astropy.table.Table` Table summarising info about files. """ # TODO : remove or fix raise NotImplementedError if observation_table is None: observation_table = ObservationTable(self.obs_table) data = [] for observation in observation_table: for filetype in filetypes: row = dict() row['OBS_ID'] = observation['OBS_ID'] row['filetype'] = filetype filename = self.filename(observation['OBS_ID'], filetype=filetype, abspath=True) row['filename'] = filename data.append(row) return Table(data=data, names=['OBS_ID', 'filetype', 'filename'])
[docs] def check_available_event_lists(self, logger=None): """Check if all event lists are available. TODO: extend this function, or combine e.g. with ``make_table_of_files``. Returns ------- file_available : `~numpy.ndarray` Boolean mask which files are available. """ # TODO: This is broken. Remove (covered by HDUlocation class)? raise NotImplementedError observation_table = self.obs_table file_available = np.ones(len(observation_table), dtype='bool') for ii in range(len(observation_table)): obs_id = observation_table['OBS_ID'][ii] filename = self.filename(obs_id) if not make_path(filename).is_file(): file_available[ii] = False if logger: logger.warning('For OBS_ID = {:06d} the event list file is missing: {}' ''.format(obs_id, filename)) return file_available
[docs] def copy_obs(self, obs_id, outdir, hdu_class=None, verbose=False, clobber=False): """Create a new `~gammapy.data.DataStore` containing a subset of observations. Parameters ---------- obs_id : array-like, `~gammapy.data.ObservationTable` List of observations to copy outdir : str, Path Directory for the new store hdu_class : list of str see :attr:`gammapy.data.HDUIndexTable.VALID_HDU_CLASS` verbose : bool Print copied files clobber : bool Overwrite """ # TODO : Does rsync give any benefits here? outdir = make_path(outdir) if isinstance(obs_id, ObservationTable): obs_id = obs_id['OBS_ID'].data hdutable = self.hdu_table hdutable.add_index('OBS_ID') with hdutable.index_mode('discard_on_copy'): subhdutable = hdutable.loc[obs_id] if hdu_class is not None: subhdutable.add_index('HDU_CLASS') with subhdutable.index_mode('discard_on_copy'): subhdutable = subhdutable.loc[hdu_class] subobstable = self.obs_table.select_obs_id(obs_id) for idx in range(len(subhdutable)): # Changes to the file structure could be made here loc = subhdutable.location_info(idx) targetdir = outdir / loc.file_dir targetdir.mkdir(exist_ok=True, parents=True) cmd = ['cp', '-v'] if verbose else ['cp'] if not clobber: cmd += ['-n'] cmd += [str(loc.path()), str(targetdir)] subprocess.call(cmd) subhdutable.write(str(outdir / self.DEFAULT_HDU_TABLE), format='fits', overwrite=clobber) subobstable.write(str(outdir / self.DEFAULT_OBS_TABLE), format='fits', overwrite=clobber)
[docs] def data_summary(self, obs_id=None, summed=False): """Create a summary `~astropy.table.Table` with HDU size information. Parameters ---------- obs_id : array-like, `~gammapy.data.ObservationTable` Observations to create summary for summed : bool Add up file size over all obs """ if obs_id is None: obs_id = self.obs_table['OBS_ID'].data elif isinstance(obs_id, ObservationTable): obs_id = obs_id['OBS_ID'].data hdut = self.hdu_table hdut.add_index('OBS_ID') subhdut = hdut.loc[obs_id] subhdut_grpd = subhdut.group_by('OBS_ID') colnames = subhdut_grpd.groups[0]['HDU_CLASS'].data temp = np.zeros(len(colnames), dtype=int) rows = list() for key, group in zip(subhdut_grpd.groups.keys, subhdut_grpd.groups): # This is needed to get the column order right group.add_index('HDU_CLASS') vals = group.loc[colnames]['SIZE'].data if summed: temp = temp + vals else: rows.append(np.append(key['OBS_ID'], vals)) if summed: rows.append(temp) else: colnames = np.append(['OBS_ID'], colnames) return Table(rows=rows, names=colnames)
[docs]class DataStoreObservation(object): """IACT data store observation. See :ref:`data_store` """ def __init__(self, obs_id, data_store): # Assert that `obs_id` is available if obs_id not in data_store.obs_table['OBS_ID']: raise ValueError('OBS_ID = {} not in obs index table.'.format(obs_id)) if obs_id not in data_store.hdu_table['OBS_ID']: raise ValueError('OBS_ID = {} not in HDU index table.'.format(obs_id)) self.obs_id = obs_id self.data_store = data_store
[docs] def location(self, hdu_type=None, hdu_class=None): """HDU location object. Parameters ---------- hdu_type : str HDU type (see `~gammapy.data.HDUIndexTable.VALID_HDU_TYPE`) hdu_class : str HDU class (see `~gammapy.data.HDUIndexTable.VALID_HDU_CLASS`) Returns ------- location : `~gammapy.data.HDULocation` HDU location """ return self.data_store.hdu_table.hdu_location( obs_id=self.obs_id, hdu_type=hdu_type, hdu_class=hdu_class, )
[docs] def load(self, hdu_type=None, hdu_class=None): """Load data file as appropriate object. Parameters ---------- hdu_type : str HDU type (see `~gammapy.data.HDUIndexTable.VALID_HDU_TYPE`) hdu_class : str HDU class (see `~gammapy.data.HDUIndexTable.VALID_HDU_CLASS`) Returns ------- object : object Object depends on type, e.g. for `events` it's a `~gammapy.data.EventList`. """ location = self.location(hdu_type=hdu_type, hdu_class=hdu_class) return location.load()
@lazyproperty def events(self): """Load `gammapy.data.EventList` object (lazy property).""" return self.load(hdu_type='events') @lazyproperty def gti(self): """Load `gammapy.data.GTI` object (lazy property).""" return self.load(hdu_type='gti') @lazyproperty def aeff(self): """Load effective area object (lazy property).""" return self.load(hdu_type='aeff') @lazyproperty def edisp(self): """Load energy dispersion object (lazy property).""" return self.load(hdu_type='edisp') @lazyproperty def psf(self): """Load point spread function object (lazy property).""" return self.load(hdu_type='psf') @lazyproperty def bkg(self): """Load background object (lazy property).""" return self.load(hdu_type='bkg') # TODO: maybe the obs table row info should be put in a separate object? @lazyproperty def _obs_info(self): """Observation information.""" row = self.data_store.obs_table.select_obs_id(obs_id=self.obs_id)[0] data = OrderedDict(zip(row.colnames, row.as_void())) return data @lazyproperty def pointing_radec(self): """Pointing RA / DEC sky coordinates (`~astropy.coordinates.SkyCoord`).""" info = self._obs_info lon, lat = info['RA_PNT'], info['DEC_PNT'] return SkyCoord(lon, lat, unit='deg', frame='icrs') @lazyproperty def tstart(self): """Observation start time (`~astropy.time.Time`).""" info = self._obs_info return Time(info['TSTART'], format='mjd') @lazyproperty def tstop(self): """Observation stop time (`~astropy.time.Time`).""" info = self._obs_info return Time(info['TSTOP'], format='mjd') @lazyproperty def muoneff(self): """Observation muon efficiency.""" info = self._obs_info return info['MUONEFF'] @lazyproperty def pointing_altaz(self): """Pointing ALT / AZ sky coordinates (`~astropy.coordinates.SkyCoord`).""" info = self._obs_info alt, az = info['ALT_PNT'], info['AZ_PNT'] return SkyCoord(az, alt, unit='deg', frame='altaz') @lazyproperty def pointing_zen(self): """Pointing zenith angle sky (`~astropy.units.Quantity`).""" info = self._obs_info zen = info['ZEN_PNT'] return Quantity(zen, unit='deg') return Quantity(info['TSTART'], 'second') @lazyproperty def target_radec(self): """Target RA / DEC sky coordinates (`~astropy.coordinates.SkyCoord`).""" info = self._obs_info lon, lat = info['RA_OBJ'], info['DEC_OBJ'] return SkyCoord(lon, lat, unit='deg', frame='icrs') @lazyproperty def observatory_earth_location(self): """Observatory location (`~astropy.coordinates.EarthLocation`).""" info = self._obs_info return _earth_location_from_dict(info) @lazyproperty def observation_time_duration(self): """Observation time duration in seconds (`~astropy.units.Quantity`). The wall time, including dead-time. """ info = self._obs_info return Quantity(info['ONTIME'], 'second') @lazyproperty def observation_live_time_duration(self): """Live-time duration in seconds (`~astropy.units.Quantity`). The dead-time-corrected observation time. Computed as ``t_live = t_observation * (1 - f_dead)`` where ``f_dead`` is the dead-time fraction. """ info = self._obs_info return Quantity(info['LIVETIME'], 'second') @lazyproperty def observation_dead_time_fraction(self): """Dead-time fraction (float). Defined as dead-time over observation time. Dead-time is defined as the time during the observation where the detector didn't record events: http://en.wikipedia.org/wiki/Dead_time http://adsabs.harvard.edu/abs/2004APh....22..285F The dead-time fraction is used in the live-time computation, which in turn is used in the exposure and flux computation. """ info = self._obs_info return 1 - info['DEADC'] def __str__(self): """Generate summary info string.""" ss = 'Info for OBS_ID = {}\n'.format(self.obs_id) ss += '- Start time: {:.2f}\n'.format(self.tstart.mjd) ss += '- Pointing pos: RA {:.2f} / Dec {:.2f}\n'.format(self.pointing_radec.ra, self.pointing_radec.dec) ss += '- Observation duration: {}\n'.format(self.observation_time_duration) ss += '- Dead-time fraction: {:5.3f} %\n'.format(100 * self.observation_dead_time_fraction) # TODO: Which target was observed? # TODO: print info about available HDUs for this observation ... return ss
[docs] def peek(self): """Quick-look plots in a few panels.""" raise NotImplementedError
[docs] def make_exposure_image(self, fov, energy_range): """Make exposure image. TODO: Do we want such methods here or as standalone functions that work with obs objects? """ raise NotImplementedError
[docs] def make_psf(self, position, energy=None, rad=None): """Make energy-dependent PSF for a given source position. Parameters ---------- position : `~astropy.coordinates.SkyCoord` Position at which to compute the PSF energy : `~astropy.units.Quantity` 1-dim energy array for the output PSF. If none is given, the energy array of the PSF from the observation is used. rad : `~astropy.coordinates.Angle` 1-dim offset wrt source position array for the output PSF. If none is given, the offset array of the PSF from the observation is used. Returns ------- psf : `~gammapy.irf.EnergyDependentTablePSF` Energy dependent psf table """ offset = position.separation(self.pointing_radec) energy = energy or self.psf.to_energy_dependent_table_psf(theta=offset).energy rad = rad or self.psf.to_energy_dependent_table_psf(theta=offset).rad print(self.psf) if isinstance(self.psf, PSF3D): # PSF3D is a table PSF, so we use the native RAD binning by default # TODO: should handle this via a uniform caller API psf_value = self.psf.to_energy_dependent_table_psf(theta=offset).evaluate(energy) else: psf_value = self.psf.to_energy_dependent_table_psf(theta=offset, rad=rad).evaluate(energy) arf = self.aeff.data.evaluate(offset=offset, energy=energy) exposure = arf * self.observation_live_time_duration psf = EnergyDependentTablePSF(energy=energy, rad=rad, exposure=exposure, psf_value=psf_value) return psf
[docs]class ObservationList(UserList): """List of `~gammapy.data.DataStoreObservation`. Could be extended to hold a more generic class of observations. """ def __str__(self): s = self.__class__.__name__ + '\n' s += 'Number of observations: {}\n'.format(len(self)) for obs in self: s += str(obs) return s def make_mean_psf(self, position, energy=None, rad=None): """Compute mean energy-dependent PSF. Parameters ---------- position : `~astropy.coordinates.SkyCoord` Position at which to compute the PSF energy : `~astropy.units.Quantity` 1-dim energy array for the output PSF. If none is given, the energy array of the PSF from the first observation is used. rad : `~astropy.coordinates.Angle` 1-dim offset wrt source position array for the output PSF. If none is given, the energy array of the PSF from the first observation is used. Returns ------- psf : `~gammapy.irf.EnergyDependentTablePSF` Mean PSF """ psf = self[0].make_psf(position, energy, rad) rad = rad or psf.rad energy = energy or psf.energy exposure = psf.exposure psf_value = psf.psf_value.T * psf.exposure for obs in self[1:]: psf = obs.make_psf(position, energy, rad) exposure += psf.exposure psf_value += psf.psf_value.T * psf.exposure psf_value /= exposure psf_tot = EnergyDependentTablePSF(energy=energy, rad=rad, exposure=exposure, psf_value=psf_value.T) return psf_tot def make_mean_edisp(self, position, e_true, e_reco, low_reco_threshold=Energy(0.002, "TeV"), high_reco_threshold=Energy(150, "TeV")): """Compute mean energy dispersion. Compute the mean edisp of a set of observations j at a given position The stacking is implemented in :func:`~gammapy.irf.IRFStacker.stack_edisp` Parameters ---------- position : `~astropy.coordinates.SkyCoord` Position at which to compute the mean EDISP e_true : `~gammapy.utils.energy.EnergyBounds` True energy axis e_reco : `~gammapy.utils.energy.EnergyBounds` Reconstructed energy axis low_reco_threshold : `~gammapy.utils.energy.Energy` low energy threshold in reco energy, default 0.002 TeV high_reco_threshold : `~gammapy.utils.energy.Energy` high energy threshold in reco energy , default 150 TeV Returns ------- stacked_edisp : `~gammapy.irf.EnergyDispersion` Stacked EDISP for a set of observation """ list_aeff = [] list_edisp = [] list_livetime = [] list_low_threshold = [low_reco_threshold] * len(self) list_high_threshold = [high_reco_threshold] * len(self) for obs in self: offset = position.separation(obs.pointing_radec) list_aeff.append(obs.aeff.to_effective_area_table(offset, energy=e_true)) list_edisp.append(obs.edisp.to_energy_dispersion(offset, e_reco=e_reco, e_true=e_true)) list_livetime.append(obs.observation_live_time_duration) irf_stack = IRFStacker(list_aeff=list_aeff, list_edisp=list_edisp, list_livetime=list_livetime, list_low_threshold=list_low_threshold, list_high_threshold=list_high_threshold) irf_stack.stack_edisp() return irf_stack.stacked_edisp