# Licensed under a 3-clause BSD style license - see LICENSE.rst
import html
import logging
import subprocess
from copy import copy
from pathlib import Path
import numpy as np
from astropy import units as u
from astropy.coordinates import SkyCoord
from astropy.io import fits
import gammapy.utils.time as tu
from gammapy.utils.pbar import progress_bar
from gammapy.utils.scripts import make_path
from gammapy.utils.testing import Checker
from .hdu_index_table import HDUIndexTable
from .obs_table import ObservationTable, ObservationTableChecker
from .observations import Observation, ObservationChecker, Observations
__all__ = ["DataStore"]
ALL_IRFS = ["aeff", "edisp", "psf", "bkg", "rad_max"]
ALL_HDUS = ["events", "gti", "pointing"] + ALL_IRFS
REQUIRED_IRFS = {
"full-enclosure": {"aeff", "edisp", "psf", "bkg"},
"point-like": {"aeff", "edisp"},
"all-optional": {},
}
class MissingRequiredHDU(IOError):
pass
log = logging.getLogger(__name__)
log.setLevel(logging.INFO)
[docs]
class DataStore:
"""IACT data store.
The data selection and access happens using an observation
and an HDU index file as described at :ref:`gadf:iact-storage`.
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() #doctest: +SKIP
Data store:
HDU index table:
BASE_DIR: /Users/ASinha/Gammapy-dev/gammapy-data/hess-dl3-dr1
Rows: 630
OBS_ID: 20136 -- 47829
HDU_TYPE: ['aeff', 'bkg', 'edisp', 'events', 'gti', 'psf']
HDU_CLASS: ['aeff_2d', 'bkg_3d', 'edisp_2d', 'events', 'gti', 'psf_table']
<BLANKLINE>
<BLANKLINE>
Observation table:
Observatory name: 'N/A'
Number of observations: 105
<BLANKLINE>
For further usage example see :doc:`/tutorials/data/cta` tutorial.
"""
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)
def _repr_html_(self):
try:
return self.to_html()
except AttributeError:
return f"<pre>{html.escape(str(self))}</pre>"
@property
def obs_ids(self):
"""Return the sorted obs_ids contained in the datastore."""
return np.unique(self.hdu_table["OBS_ID"].data)
[docs]
@classmethod
def from_file(cls, filename, hdu_hdu="HDU_INDEX", hdu_obs="OBS_INDEX"):
"""Create a Datastore from a FITS file.
The FITS file must contain both index files.
Parameters
----------
filename : str or `~pathlib.Path`
FITS filename.
hdu_hdu : str or int, optional
FITS HDU name or number for the HDU index table. Default is "HDU_INDEX".
hdu_obs : str or int, optional
FITS HDU name or number for the observation index table. Default is "OBS_INDEX".
Returns
-------
data_store : `DataStore`
Data store.
"""
filename = make_path(filename)
hdu_table = HDUIndexTable.read(filename, hdu=hdu_hdu, format="fits")
obs_table = None
if hdu_obs:
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 or `~pathlib.Path`
Base directory of the data files.
hdu_table_filename : str or `~pathlib.Path`, optional
Filename of the HDU index file. May be specified either relative
to `base_dir` or as an absolute path. If None, default is "hdu-index.fits.gz".
obs_table_filename : str or `~pathlib.Path`, optional
Filename of the observation index file. May be specified either relative
to `base_dir` or as an absolute path. If None, default is obs-index.fits.gz.
Returns
-------
data_store : `DataStore`
Data store.
Examples
--------
>>> from gammapy.data import DataStore
>>> data_store = DataStore.from_dir('$GAMMAPY_DATA/hess-dl3-dr1')
"""
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
elif not obs_table_filename.exists():
raise IOError(f"File not found : {obs_table_filename}")
else:
obs_table_filename = base_dir / cls.DEFAULT_OBS_TABLE
if not hdu_table_filename.exists():
raise OSError(f"File not found: {hdu_table_filename}")
log.debug(f"Reading {hdu_table_filename}")
hdu_table = HDUIndexTable.read(hdu_table_filename, format="fits")
hdu_table.meta["BASE_DIR"] = str(base_dir)
if not obs_table_filename.exists():
log.info("Cannot find default obs-index table.")
obs_table = None
else:
log.debug(f"Reading {obs_table_filename}")
obs_table = ObservationTable.read(obs_table_filename, format="fits")
return cls(hdu_table=hdu_table, obs_table=obs_table)
[docs]
@classmethod
def from_events_files(cls, events_paths, irfs_paths=None):
"""Create from a list of event filenames.
HDU and observation index tables will be created from the EVENTS header.
IRFs are found only if you have a ``CALDB`` environment variable set,
and if the EVENTS files contain the following keys:
- ``TELESCOP`` (example: ``TELESCOP = CTA``)
- ``CALDB`` (example: ``CALDB = 1dc``)
- ``IRF`` (example: ``IRF = South_z20_50h``)
Parameters
----------
events_paths : list of str or `~pathlib.Path`
List of paths to the events files.
irfs_paths : str or `~pathlib.Path`, or list of str or list of `~pathlib.Path`, optional
Path to the IRFs file. If a list is provided it must be the same length
as `events_paths`. If None the events files have to contain CALDB and
IRF header keywords to locate the IRF files, otherwise the IRFs are
assumed to be contained in the events files.
Returns
-------
data_store : `DataStore`
Data store.
Examples
--------
This is how you can access a single event list::
>>> from gammapy.data import DataStore
>>> import os
>>> os.environ["CALDB"] = os.environ["GAMMAPY_DATA"] + "/cta-1dc/caldb"
>>> path = "$GAMMAPY_DATA/cta-1dc/data/baseline/gps/gps_baseline_110380.fits"
>>> data_store = DataStore.from_events_files([path])
>>> observations = data_store.get_observations()
You can now analyse this data as usual (see any Gammapy tutorial).
If you have multiple event files, you have to make the list. Here's an example
using ``Path.glob`` to get a list of all events files in a given folder::
>>> import os
>>> from pathlib import Path
>>> path = Path(os.environ["GAMMAPY_DATA"]) / "cta-1dc/data"
>>> paths = list(path.rglob("*.fits"))
>>> data_store = DataStore.from_events_files(paths)
>>> observations = data_store.get_observations()
>>> #Note that you have a lot of flexibility to select the observations you want,
>>> # by having a few lines of custom code to prepare ``paths``, or to select a
>>> # subset via a method on the ``data_store`` or the ``observations`` objects.
>>> # If you want to generate HDU and observation index files, write the tables to disk::
>>> data_store.hdu_table.write("hdu-index.fits.gz") # doctest: +SKIP
>>> data_store.obs_table.write("obs-index.fits.gz") # doctest: +SKIP
"""
return DataStoreMaker(events_paths, irfs_paths).run()
[docs]
def info(self, show=True):
"""Print some info."""
s = "Data store:\n"
s += self.hdu_table.summary()
s += "\n\n"
if self.obs_table:
s += self.obs_table.summary()
else:
s += "No observation index table."
if show:
print(s)
else:
return s
[docs]
def obs(self, obs_id, required_irf="full-enclosure", require_events=True):
"""Access a given `~gammapy.data.Observation`.
Parameters
----------
obs_id : int
Observation ID.
required_irf : list of str or str, optional
The list can include the following options:
* `"events"` : Events
* `"gti"` : Good time intervals
* `"aeff"` : Effective area
* `"bkg"` : Background
* `"edisp"` : Energy dispersion
* `"psf"` : Point Spread Function
* `"rad_max"` : Maximal radius
Alternatively single string can be used as shortcut:
* `"full-enclosure"` : includes `["events", "gti", "aeff", "edisp", "psf", "bkg"]`
* `"point-like"` : includes `["events", "gti", "aeff", "edisp"]`
Default is `"full-enclosure"`.
require_events : bool, optional
Require events and gti table or not. Default is True.
Returns
-------
observation : `~gammapy.data.Observation`
Observation container.
"""
if obs_id not in self.hdu_table["OBS_ID"]:
raise ValueError(f"OBS_ID = {obs_id} not in HDU index table.")
kwargs = {"obs_id": int(obs_id)}
# check for the "short forms"
if isinstance(required_irf, str):
required_irf = REQUIRED_IRFS[required_irf]
if not set(required_irf).issubset(ALL_IRFS):
difference = set(required_irf).difference(ALL_IRFS)
raise ValueError(
f"{difference} is not a valid hdu key. Choose from: {ALL_IRFS}"
)
if require_events:
required_hdus = {"events", "gti"}.union(required_irf)
else:
required_hdus = required_irf
missing_hdus = []
for hdu in ALL_HDUS:
hdu_location = self.hdu_table.hdu_location(
obs_id=obs_id,
hdu_type=hdu,
warn_missing=False,
)
if hdu_location is not None:
kwargs[hdu] = hdu_location
elif hdu in required_hdus:
missing_hdus.append(hdu)
if len(missing_hdus) > 0:
raise MissingRequiredHDU(
f"Required HDUs {missing_hdus} not found in observation {obs_id}"
)
# TODO: right now, gammapy doesn't support using the pointing table of GADF
# so we always pass the events location here to be read into a FixedPointingInfo
if "events" in kwargs:
pointing_location = copy(kwargs["events"])
pointing_location.hdu_class = "pointing"
kwargs["pointing"] = pointing_location
return Observation(**kwargs)
[docs]
def get_observations(
self,
obs_id=None,
skip_missing=False,
required_irf="full-enclosure",
require_events=True,
):
"""Generate a `~gammapy.data.Observations`.
Notes
-----
The progress bar can be displayed for this function.
Parameters
----------
obs_id : list, optional
Observation IDs.
If None, default is all observations ordered by OBS_ID are returned.
This is not necessarily the order in the ``obs_table``.
skip_missing : bool, optional
Skip missing observations. Default is False.
required_irf : list of str or str, optional
Runs will be added to the list of observations only if the
required HDUs are present. Otherwise, the given run will be skipped
The list can include the following options:
* `"events"` : Events
* `"gti"` : Good time intervals
* `"aeff"` : Effective area
* `"bkg"` : Background
* `"edisp"` : Energy dispersion
* `"psf"` : Point Spread Function
* `"rad_max"` : Maximal radius
Alternatively single string can be used as shortcut:
* `"full-enclosure"` : includes `["events", "gti", "aeff", "edisp", "psf", "bkg"]`
* `"point-like"` : includes `["events", "gti", "aeff", "edisp"]`
* `"all-optional"` : no HDUs are required, only warnings will be emitted
for missing HDUs among all possibilities.
Default is `"full-enclosure"`.
require_events : bool, optional
Require events and gti table or not. Default is True.
Returns
-------
observations : `~gammapy.data.Observations`
Container holding a list of `~gammapy.data.Observation`.
"""
if obs_id is None:
obs_id = self.obs_ids
obs_list = []
for _ in progress_bar(obs_id, desc="Obs Id"):
try:
obs = self.obs(_, required_irf, require_events)
except ValueError as err:
if skip_missing:
log.warning(f"Skipping missing obs_id: {_!r}")
continue
else:
raise err
except MissingRequiredHDU as e:
log.warning(f"Skipping run with missing HDUs; {e}")
continue
obs_list.append(obs)
log.info(f"Observations selected: {len(obs_list)} out of {len(obs_id)}.")
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 or `~pathlib.Path`
Directory for the new store.
hdu_class : list of str, optional
see :attr:`gammapy.data.HDUIndexTable.VALID_HDU_CLASS`.
verbose : bool, optional
Print copied files. Default is False.
overwrite : bool, optional
Overwrite. Default is False.
"""
outdir = make_path(outdir)
if not outdir.is_dir():
raise OSError(f"Not a directory: outdir={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]
if self.obs_table:
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"]
if verbose:
cmd += ["-v"]
if not overwrite:
cmd += ["-n"]
cmd += [str(loc.path()), str(targetdir)]
subprocess.run(cmd)
filename = outdir / self.DEFAULT_HDU_TABLE
subhdutable.write(filename, format="fits", overwrite=overwrite)
if self.obs_table:
filename = outdir / self.DEFAULT_OBS_TABLE
subobstable.write(str(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):
"""Check for the observation index table."""
yield from ObservationTableChecker(self.data_store.obs_table).run()
def check_hdu_table(self):
"""Check 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": f"HDU not found: {location_info.__dict__!r}",
}
def check_consistency(self):
"""Check consistency 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)
yield from ObservationChecker(obs).run()
class DataStoreMaker:
"""Create data store index tables.
This is a multistep process coded as a class.
Users will usually call this via `DataStore.from_events_files`.
"""
def __init__(self, events_paths, irfs_paths=None):
if isinstance(events_paths, (str, Path)):
raise TypeError("Need list of paths, not a single string or Path object.")
self.events_paths = [make_path(path) for path in events_paths]
if irfs_paths is None or isinstance(irfs_paths, (str, Path)):
self.irfs_paths = [make_path(irfs_paths)] * len(events_paths)
else:
self.irfs_paths = [make_path(path) for path in irfs_paths]
# Cache for EVENTS file header information, to avoid multiple reads
self._events_info = {}
def run(self):
"""Run all steps."""
hdu_table = self.make_hdu_table()
obs_table = self.make_obs_table()
return DataStore(hdu_table=hdu_table, obs_table=obs_table)
def get_events_info(self, events_path, irf_path=None):
"""Read events header information."""
if events_path not in self._events_info:
self._events_info[events_path] = self.read_events_info(
events_path, irf_path
)
return self._events_info[events_path]
def get_obs_info(self, events_path, irf_path=None):
"""Read events header information and add some extra information."""
# We could add or remove info here depending on what we want in the obs table
return self.get_events_info(events_path, irf_path)
@staticmethod
def read_events_info(events_path, irf_path=None):
"""Read mandatory events header information."""
log.debug(f"Reading {events_path}")
with fits.open(events_path, memmap=False) as hdu_list:
header = hdu_list["EVENTS"].header
na_int, na_str = -1, "NOT AVAILABLE"
info = {}
# Note: for some reason `header["OBS_ID"]` is sometimes `str`, maybe trailing whitespace
# mandatory header info:
info["OBS_ID"] = int(header["OBS_ID"])
info["TSTART"] = header["TSTART"] * u.s
info["TSTOP"] = header["TSTOP"] * u.s
info["ONTIME"] = header["ONTIME"] * u.s
info["LIVETIME"] = header["LIVETIME"] * u.s
info["DEADC"] = header["DEADC"]
info["TELESCOP"] = header.get("TELESCOP", na_str)
obs_mode = header.get("OBS_MODE", "POINTING")
if obs_mode == "DRIFT":
info["ALT_PNT"] = header["ALT_PNT"] * u.deg
info["AZ_PNT"] = header["AZ_PNT"] * u.deg
info["ZEN_PNT"] = 90 * u.deg - info["ALT_PNT"]
else:
info["RA_PNT"] = header["RA_PNT"] * u.deg
info["DEC_PNT"] = header["DEC_PNT"] * u.deg
# optional header info
pos = SkyCoord(info["RA_PNT"], info["DEC_PNT"], unit="deg").galactic
info["GLON_PNT"] = pos.l
info["GLAT_PNT"] = pos.b
info["DATE-OBS"] = header.get("DATE_OBS", na_str)
info["TIME-OBS"] = header.get("TIME_OBS", na_str)
info["DATE-END"] = header.get("DATE_END", na_str)
info["TIME-END"] = header.get("TIME_END", na_str)
info["N_TELS"] = header.get("N_TELS", na_int)
info["OBJECT"] = header.get("OBJECT", na_str)
# Not part of the spec, but good to know from which file the info comes
info["EVENTS_FILENAME"] = str(events_path)
info["EVENT_COUNT"] = header["NAXIS2"]
# This is the info needed to link from EVENTS to IRFs
info["CALDB"] = header.get("CALDB", na_str)
info["IRF"] = header.get("IRF", na_str)
if irf_path is not None:
info["IRF_FILENAME"] = str(irf_path)
elif info["CALDB"] != na_str and info["IRF"] != na_str:
caldb_irf = CalDBIRF.from_meta(info)
info["IRF_FILENAME"] = str(caldb_irf.file_path)
else:
info["IRF_FILENAME"] = info["EVENTS_FILENAME"]
# Mandatory fields defining the time data
for name in tu.TIME_KEYWORDS:
info[name] = header.get(name, None)
return info
def make_obs_table(self):
"""Make observation index table."""
rows = []
time_rows = []
for events_path, irf_path in zip(self.events_paths, self.irfs_paths):
row = self.get_obs_info(events_path, irf_path)
rows.append(row)
time_row = tu.extract_time_info(row)
time_rows.append(time_row)
names = list(rows[0].keys())
table = ObservationTable(rows=rows, names=names)
m = table.meta
if not tu.unique_time_info(time_rows):
raise RuntimeError(
"The time information in the EVENT header are not consistent between observations"
)
for name in tu.TIME_KEYWORDS:
m[name] = time_rows[0][name]
m["HDUCLASS"] = "GADF"
m["HDUDOC"] = "https://github.com/open-gamma-ray-astro/gamma-astro-data-formats"
m["HDUVERS"] = "0.2"
m["HDUCLAS1"] = "INDEX"
m["HDUCLAS2"] = "OBS"
return table
def make_hdu_table(self):
"""Make HDU index table."""
rows = []
for events_path, irf_path in zip(self.events_paths, self.irfs_paths):
rows.extend(self.get_hdu_table_rows(events_path, irf_path))
names = list(rows[0].keys())
# names = ['OBS_ID', 'HDU_TYPE', 'HDU_CLASS', 'FILE_DIR', 'FILE_NAME', 'HDU_NAME']
table = HDUIndexTable(rows=rows, names=names)
m = table.meta
m["HDUCLASS"] = "GADF"
m["HDUDOC"] = "https://github.com/open-gamma-ray-astro/gamma-astro-data-formats"
m["HDUVERS"] = "0.2"
m["HDUCLAS1"] = "INDEX"
m["HDUCLAS2"] = "HDU"
return table
def get_hdu_table_rows(self, events_path, irf_path=None):
"""Make HDU index table rows for one observation."""
events_info = self.get_obs_info(events_path, irf_path)
info = dict(
OBS_ID=events_info["OBS_ID"],
FILE_DIR=events_path.parent.as_posix(),
FILE_NAME=events_path.name,
)
yield dict(HDU_TYPE="events", HDU_CLASS="events", HDU_NAME="EVENTS", **info)
yield dict(HDU_TYPE="gti", HDU_CLASS="gti", HDU_NAME="GTI", **info)
irf_path = Path(events_info["IRF_FILENAME"])
info = dict(
OBS_ID=events_info["OBS_ID"],
FILE_DIR=irf_path.parent.as_posix(),
FILE_NAME=irf_path.name,
)
yield dict(
HDU_TYPE="aeff", HDU_CLASS="aeff_2d", HDU_NAME="EFFECTIVE AREA", **info
)
yield dict(
HDU_TYPE="edisp", HDU_CLASS="edisp_2d", HDU_NAME="ENERGY DISPERSION", **info
)
yield dict(
HDU_TYPE="psf",
HDU_CLASS="psf_3gauss",
HDU_NAME="POINT SPREAD FUNCTION",
**info,
)
yield dict(HDU_TYPE="bkg", HDU_CLASS="bkg_3d", HDU_NAME="BACKGROUND", **info)
class CalDBIRF:
"""Helper class to work with IRFs in CALDB format."""
def __init__(self, telescop, caldb, irf):
self.telescop = telescop
self.caldb = caldb
self.irf = irf
@classmethod
def from_meta(cls, meta):
return cls(telescop=meta["TELESCOP"], caldb=meta["CALDB"], irf=meta["IRF"])
@property
def file_dir(self):
# In CTA 1DC the header key is "CTA", but the directory is lower-case "cta"
telescop = self.telescop.lower()
return f"$CALDB/data/{telescop}/{self.caldb}/bcf/{self.irf}"
@property
def file_path(self):
return Path(f"{self.file_dir}/{self.file_name}")
@property
def file_name(self):
path = make_path(self.file_dir)
return list(path.iterdir())[0].name
