# Licensed under a 3-clause BSD style license - see LICENSE.rst
from __future__ import absolute_import, division, print_function, unicode_literals
import logging
import subprocess
from ..utils.scripts import make_path
from ..utils.testing import Checker
from .obs_table import ObservationTable
from .hdu_index_table import HDUIndexTable
from .obs_table import ObservationTableChecker
from .observations import DataStoreObservation, Observations, ObservationChecker
__all__ = ["DataStore"]
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 :gp-extra-notebook:`cta_1dc_introduction` for usage examples.
Parameters
----------
hdu_table : `~gammapy.data.HDUIndexTable`
HDU index table
obs_table : `~gammapy.data.ObservationTable`
Observation index table
Examples
--------
Here's an example how to create a `DataStore` to access H.E.S.S. data:
>>> from gammapy.data import DataStore
>>> data_store = DataStore.from_dir('$GAMMAPY_DATA/hess-dl3-dr1')
>>> 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."""
def __init__(self, hdu_table=None, obs_table=None):
self.hdu_table = hdu_table
self.obs_table = obs_table
def __str__(self):
return self.info(show=False)
[docs] @classmethod
def from_file(cls, filename, hdu_hdu="HDU_INDEX", hdu_obs="OBS_INDEX"):
"""Create from a FITS file.
The FITS file must contain both index files.
Parameters
----------
filename : str, Path
FITS filename
hdu_hdu : str or int
FITS HDU name or number for the HDU index table
hdu_obs : str or int
FITS HDU name or number for the observation index table
"""
filename = make_path(filename)
hdu_table = HDUIndexTable.read(filename, hdu=hdu_hdu, format="fits")
obs_table = ObservationTable.read(filename, hdu=hdu_obs, format="fits")
return cls(hdu_table=hdu_table, obs_table=obs_table)
[docs] @classmethod
def from_dir(cls, base_dir, hdu_table_filename=None, obs_table_filename=None):
"""Create from a directory.
Parameters
----------
base_dir : str, Path
Base directory of the data files.
hdu_table_filename : str, Path
Filename of the HDU index file. May be specified either relative
to `base_dir` or as an absolute path. If None, the default filename
will be looked for.
obs_table_filename : str, Path
Filename of the observation index file. May be specified either relative
to `base_dir` or as an absolute path. If None, the default filename
will be looked for.
"""
base_dir = make_path(base_dir)
if hdu_table_filename:
hdu_table_filename = make_path(hdu_table_filename)
if (base_dir / hdu_table_filename).exists():
hdu_table_filename = base_dir / hdu_table_filename
else:
hdu_table_filename = base_dir / cls.DEFAULT_HDU_TABLE
if obs_table_filename:
obs_table_filename = make_path(obs_table_filename)
if (base_dir / obs_table_filename).exists():
obs_table_filename = base_dir / obs_table_filename
else:
obs_table_filename = base_dir / cls.DEFAULT_OBS_TABLE
if not hdu_table_filename.exists():
raise IOError("File not found: {}".format(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"] = str(base_dir)
if not obs_table_filename.exists():
raise IOError("File not found: {}".format(obs_table_filename))
log.debug("Reading {}".format(str(obs_table_filename)))
obs_table = ObservationTable.read(str(obs_table_filename), format="fits")
return cls(hdu_table=hdu_table, obs_table=obs_table)
[docs] @classmethod
def from_config(cls, config):
"""Create from a config dict."""
base_dir = config["base_dir"]
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,
)
@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
[docs] def info(self, show=True):
"""Print some info."""
s = "Data store:\n"
s += self.hdu_table.summary()
s += "\n\n"
s += self.obs_table.summary()
if show:
print(s)
else:
return s
[docs] def obs(self, obs_id):
"""Access a given `~gammapy.data.DataStoreObservation`.
Parameters
----------
obs_id : int
Observation ID.
Returns
-------
observation : `~gammapy.data.DataStoreObservation`
Observation container
"""
return DataStoreObservation(obs_id=int(obs_id), data_store=self)
[docs] def get_observations(self, obs_id, skip_missing=False):
"""Generate a `~gammapy.data.Observations`.
Parameters
----------
obs_id : list
Observation IDs.
skip_missing : bool, optional
Skip missing observations, default: False
Returns
-------
observations : `~gammapy.data.Observations`
Container holding a list of `~gammapy.data.DataStoreObservation`
"""
obs_list = []
for _ in obs_id:
try:
obs = self.obs(_)
except ValueError as err:
if skip_missing:
log.warning("Skipping missing obs_id: {!r}".format(_))
continue
else:
raise err
else:
obs_list.append(obs)
return Observations(obs_list)
[docs] def copy_obs(self, obs_id, outdir, hdu_class=None, verbose=False, overwrite=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
overwrite : 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 overwrite:
cmd += ["-n"]
cmd += [str(loc.path()), str(targetdir)]
subprocess.call(cmd)
filename = str(outdir / self.DEFAULT_HDU_TABLE)
subhdutable.write(filename, format="fits", overwrite=overwrite)
filename = str(outdir / self.DEFAULT_OBS_TABLE)
subobstable.write(filename, format="fits", overwrite=overwrite)
[docs] def check(self, checks="all"):
"""Check index tables and data files.
This is a generator that yields a list of dicts.
"""
checker = DataStoreChecker(self)
return checker.run(checks=checks)
class DataStoreChecker(Checker):
"""Check data store.
Checks data format and a bit about the content.
"""
CHECKS = {
"obs_table": "check_obs_table",
"hdu_table": "check_hdu_table",
"observations": "check_observations",
"consistency": "check_consistency",
}
def __init__(self, data_store):
self.data_store = data_store
def check_obs_table(self):
"""Checks for the observation index table."""
checker = ObservationTableChecker(self.data_store.obs_table)
for record in checker.run():
yield record
def check_hdu_table(self):
"""Checks for the HDU index table."""
t = self.data_store.hdu_table
m = t.meta
if m.get("HDUCLAS1", "") != "INDEX":
yield {
"level": "error",
"hdu": "hdu-index",
"msg": "Invalid header key. Must have HDUCLAS1=INDEX",
}
if m.get("HDUCLAS2", "") != "HDU":
yield {
"level": "error",
"hdu": "hdu-index",
"msg": "Invalid header key. Must have HDUCLAS2=HDU",
}
# Check that all HDU in the data files exist
for idx in range(len(t)):
location_info = t.location_info(idx)
try:
location_info.get_hdu()
except KeyError:
yield {
"level": "error",
"msg": "HDU not found: {!r}".format(location_info.__dict__),
}
def check_consistency(self):
"""Consistency checks between multiple HDUs"""
# obs and HDU index should have the same OBS_ID
obs_table_obs_id = set(self.data_store.obs_table["OBS_ID"])
hdu_table_obs_id = set(self.data_store.hdu_table["OBS_ID"])
if not obs_table_obs_id == hdu_table_obs_id:
yield {
"level": "error",
"msg": "Inconsistent OBS_ID in obs and HDU index tables",
}
# TODO: obs table and events header should have the same times
def check_observations(self):
"""Perform some sanity checks for all observations."""
for obs_id in self.data_store.obs_table["OBS_ID"]:
obs = self.data_store.obs(obs_id)
for record in ObservationChecker(obs).run():
yield record