# 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 namedtuple
import numpy as np
from astropy.units import Quantity, Unit
from astropy.coordinates import SkyCoord, Angle, AltAz
from astropy.coordinates.angle_utilities import angular_separation
from astropy.table import Table
from astropy.table import vstack as vstack_tables
from ..utils.energy import EnergyBounds
from ..utils.fits import earth_location_from_dict
from ..utils.scripts import make_path
from ..utils.time import time_ref_from_dict
from ..utils.testing import Checker
__all__ = ["EventListBase", "EventList", "EventListLAT"]
log = logging.getLogger(__name__)
[docs]class EventListBase(object):
"""Event list.
This class represents the base for two different event lists:
- EventList: targeted for IACT event lists
- EventListLAT: targeted for Fermi-LAT event lists
Event list data is stored in ``table`` (`~astropy.table.Table`) data member.
The most important reconstructed event parameters
are available as the following columns:
- ``TIME`` - Mission elapsed time (sec)
- ``RA``, ``DEC`` - ICRS system position (deg)
- ``ENERGY`` - Energy (usually MeV for Fermi and TeV for IACTs)
Other optional (columns) that are sometimes useful for high-level analysis:
- ``GLON``, ``GLAT`` - Galactic coordinates (deg)
- ``DETX``, ``DETY`` - Field of view coordinates (deg)
Note that when reading data for analysis you shouldn't use those
values directly, but access them via properties which create objects
of the appropriate class:
- `time` for ``TIME``
- `radec` for ``RA``, ``DEC``
- `energy` for ``ENERGY``
- `galactic` for ``GLON``, ``GLAT``
Parameters
----------
table : `~astropy.table.Table`
Event list table
"""
def __init__(self, table):
# TODO: remove this temp fix once we drop support for `hess-hd-hap-prod2`
# There the unit wasn't set correctly in the FITS table, so this hack is needed.
if "ENERGY" in table.colnames:
if not table["ENERGY"].unit:
table["ENERGY"].unit = "TeV"
self.table = table
[docs] @classmethod
def read(cls, filename, **kwargs):
"""Read from FITS file.
Format specification: :ref:`gadf:iact-events`
Parameters
----------
filename : `~gammapy.extern.pathlib.Path`, str
Filename
"""
filename = make_path(filename)
kwargs.setdefault("hdu", "EVENTS")
table = Table.read(str(filename), **kwargs)
return cls(table=table)
[docs] @classmethod
def stack(cls, event_lists, **kwargs):
"""Stack (concatenate) list of event lists.
Calls `~astropy.table.vstack`.
Parameters
----------
event_lists : list
list of `~gammapy.data.EventList` to stack
"""
tables = [_.table for _ in event_lists]
stacked_table = vstack_tables(tables, **kwargs)
return cls(stacked_table)
def __str__(self):
ss = (
"EventList info:\n"
+ "- Number of events: {}\n".format(len(self.table))
+ "- Median energy: {:.3g} {}\n".format(
np.median(self.energy.value), self.energy.unit
)
)
if "OBS_ID" in self.table.meta:
ss += "- OBS_ID = {}".format(self.table.meta["OBS_ID"])
# TODO: add time, RA, DEC and if present GLON, GLAT info ...
if "AZ" in self.table.colnames:
# TODO: azimuth should be circular median
ss += "- Median azimuth: {}\n".format(np.median(self.table["AZ"]))
if "ALT" in self.table.colnames:
ss += "- Median altitude: {}\n".format(np.median(self.table["ALT"]))
return ss
@property
def time_ref(self):
"""Time reference (`~astropy.time.Time`)"""
return time_ref_from_dict(self.table.meta)
@property
def time(self):
"""Event times (`~astropy.time.Time`).
Notes
-----
Times are automatically converted to 64-bit floats.
With 32-bit floats times will be incorrect by a few seconds
when e.g. adding them to the reference time.
"""
met = Quantity(self.table["TIME"].astype("float64"), "second")
return self.time_ref + met
@property
def observation_time_start(self):
"""Observation start time (`~astropy.time.Time`)."""
return self.time_ref + Quantity(self.table.meta["TSTART"], "second")
@property
def observation_time_end(self):
"""Observation stop time (`~astropy.time.Time`)."""
return self.time_ref + Quantity(self.table.meta["TSTOP"], "second")
@property
def radec(self):
"""Event RA / DEC sky coordinates (`~astropy.coordinates.SkyCoord`).
"""
lon, lat = self.table["RA"], self.table["DEC"]
return SkyCoord(lon, lat, unit="deg", frame="icrs")
@property
def galactic(self):
"""Event Galactic sky coordinates (`~astropy.coordinates.SkyCoord`).
Always computed from RA / DEC using Astropy.
"""
return self.radec.galactic
@property
def observation_live_time_duration(self):
"""Live-time duration in seconds (`~astropy.units.Quantity`).
The dead-time-corrected observation time.
- In Fermi-LAT it is automatically provided in the header of the event list.
- In IACTs is computed as ``t_live = t_observation * (1 - f_dead)``
where ``f_dead`` is the dead-time fraction.
"""
return Quantity(self.table.meta["LIVETIME"], "second")
@property
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:
https://en.wikipedia.org/wiki/Dead_time
https://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.
"""
return 1 - self.table.meta["DEADC"]
@property
def pointing_radec(self):
"""Pointing RA / DEC sky coordinates (`~astropy.coordinates.SkyCoord`)."""
info = self.table.meta
lon, lat = info["RA_PNT"], info["DEC_PNT"]
return SkyCoord(lon, lat, unit="deg", frame="icrs")
@property
def offset(self):
"""Event offset from the array pointing position (`~astropy.coordinates.Angle`)."""
position = self.radec
center = self.pointing_radec
offset = center.separation(position)
return Angle(offset, unit="deg")
@property
def energy(self):
"""Event energies (`~astropy.units.Quantity`)."""
return self.table["ENERGY"].quantity
[docs] def select_row_subset(self, row_specifier):
"""Select table row subset.
Parameters
----------
row_specifier : slice, int, or array of ints
Specification for rows to select,
passed on to ``self.table[row_specifier]``.
Returns
-------
event_list : `EventList`
New event list with table row subset selected
Examples
--------
Use a boolean mask as ``row_specifier``:
mask = events.table['FOO'] > 42
events2 = events.select_row_subset(mask)
Use row index array as ``row_specifier``:
idx = np.where(events.table['FOO'] > 42)[0]
events2 = events.select_row_subset(idx)
"""
table = self.table[row_specifier]
return self.__class__(table=table)
[docs] def select_energy(self, energy_band):
"""Select events in energy band.
Parameters
----------
energy_band : `~astropy.units.Quantity`
Energy band ``[energy_min, energy_max)``
Returns
-------
event_list : `EventList`
Copy of event list with selection applied.
Examples
--------
>>> from astropy.units import Quantity
>>> from gammapy.data import EventList
>>> event_list = EventList.read('events.fits')
>>> energy_band = Quantity([1, 20], 'TeV')
>>> event_list = event_list.select_energy()
"""
energy = self.energy
mask = energy_band[0] <= energy
mask &= energy < energy_band[1]
return self.select_row_subset(mask)
[docs] def select_time(self, time_interval):
"""Select events in time interval.
"""
time = self.time
mask = time_interval[0] <= time
mask &= time < time_interval[1]
return self.select_row_subset(mask)
[docs] def select_sky_cone(self, center, radius):
"""Select events in sky circle.
Parameters
----------
center : `~astropy.coordinates.SkyCoord`
Sky circle center
radius : `~astropy.coordinates.Angle`
Sky circle radius
Returns
-------
event_list : `EventList`
Copy of event list with selection applied.
"""
position = self.radec
separation = center.separation(position)
mask = separation < radius
return self.select_row_subset(mask)
[docs] def select_sky_ring(self, center, inner_radius, outer_radius):
"""Select events in ring region on the sky.
Parameters
----------
center : `~astropy.coordinates.SkyCoord`
Sky ring center
inner_radius, outer_radius : `~astropy.coordinates.Angle`
Sky ring inner and outer radius
Returns
-------
event_list : `EventList`
Copy of event list with selection applied.
"""
position = self.radec
separation = center.separation(position)
mask1 = inner_radius < separation
mask2 = separation < outer_radius
mask = mask1 * mask2
return self.select_row_subset(mask)
[docs] def select_sky_box(self, lon_lim, lat_lim, frame="icrs"):
"""Select events in sky box.
TODO: move `gammapy.catalog.select_sky_box` to gammapy.utils.
"""
from ..catalog import select_sky_box
selected = select_sky_box(self.table, lon_lim, lat_lim, frame)
return self.__class__(selected)
[docs] def select_circular_region(self, region):
"""Select events in circular regions.
TODO: Extend to support generic regions
Parameters
----------
region : `~regions.CircleSkyRegion` or list of `~regions.CircleSkyRegion`
(List of) sky region(s)
Returns
-------
event_list : `EventList`
Copy of event list with selection applied.
"""
if not isinstance(region, list):
region = list([region])
mask = self.filter_circular_region(region)
return self.select_row_subset(mask)
[docs] def filter_circular_region(self, region):
"""Create selection mask for event in given circular regions.
TODO: Extend to support generic regions
Parameters
----------
region : list of `~regions.SkyRegion`
List of sky regions
Returns
-------
index_array : `numpy.ndarray`
Index array of selected events
"""
position = self.radec
mask = np.array([], dtype=int)
for reg in region:
separation = reg.center.separation(position)
temp = np.where(separation < reg.radius)[0]
mask = np.union1d(mask, temp)
return mask
def _default_plot_ebounds(self):
energy = self.energy
return EnergyBounds.equal_log_spacing(energy.min(), energy.max(), 50)
def _counts_spectrum(self, ebounds):
from ..spectrum import CountsSpectrum
if not ebounds:
ebounds = self._default_plot_ebounds()
spec = CountsSpectrum(energy_lo=ebounds[:-1], energy_hi=ebounds[1:])
spec.fill(self.energy)
return spec
[docs] def plot_energy(self, ax=None, ebounds=None, **kwargs):
"""Plot counts as a function of energy."""
spec = self._counts_spectrum(ebounds)
ax = spec.plot(ax=ax, **kwargs)
return ax
[docs] def plot_time(self, ax=None):
"""Plots an event rate time curve.
Parameters
----------
ax : `~matplotlib.axes.Axes` or None
Axes
Returns
-------
ax : `~matplotlib.axes.Axes`
Axes
"""
import matplotlib.pyplot as plt
ax = plt.gca() if ax is None else ax
# Note the events are not necessarily in time order
time = self.table["TIME"]
time = time - np.min(time)
ax.set_xlabel("Time (sec)")
ax.set_ylabel("Counts")
y, x_edges = np.histogram(time, bins=30)
# x = (x_edges[1:] + x_edges[:-1]) / 2
xerr = np.diff(x_edges) / 2
x = x_edges[:-1] + xerr
yerr = np.sqrt(y)
ax.errorbar(x=x, y=y, xerr=xerr, yerr=yerr, fmt="none")
return ax
[docs] def plot_offset2_distribution(self, ax=None, center=None, **kwargs):
"""Plot offset^2 distribution of the events.
The distribution shown in this plot is for this quantity::
offset = center.separation(events.radec).deg
offset2 = offset ** 2
Note that this method is just for a quicklook plot.
If you want to do computations with the offset or offset^2 values, you can
use the line above. As an example, here's how to compute the 68% event
containment radius using `numpy.percentile`::
import numpy as np
r68 = np.percentile(offset, q=68)
Parameters
----------
ax : `~matplotlib.axes.Axes` (optional)
Axes
center : `astropy.coordinates.SkyCoord`
Center position for the offset^2 distribution.
Default is the observation pointing position.
**kwargs :
Extra keyword arguments are passed to `matplotlib.pyplot.hist`.
Returns
-------
ax : `~matplotlib.axes.Axes`
Axes
Examples
--------
Load an example event list:
>>> from gammapy.data import EventList
>>> events = EventList.read('$GAMMAPY_DATA/hess-dl3-dr1/data/hess_dl3_dr1_obs_id_023523.fits.gz')
Plot the offset^2 distribution wrt. the observation pointing position
(this is a commonly used plot to check the background spatial distribution):
>>> events.plot_offset2_distribution()
Plot the offset^2 distribution wrt. the Crab pulsar position
(this is commonly used to check both the gamma-ray signal and the background spatial distribution):
>>> import numpy as np
>>> from astropy.coordinates import SkyCoord
>>> center = SkyCoord(83.63307, 22.01449, unit='deg')
>>> bins = np.linspace(start=0, stop=0.3 ** 2, num=30)
>>> events.plot_offset2_distribution(center=center, bins=bins)
Note how we passed the ``bins`` option of `matplotlib.pyplot.hist` to control the histogram binning,
in this case 30 bins ranging from 0 to (0.3 deg)^2.
"""
import matplotlib.pyplot as plt
ax = plt.gca() if ax is None else ax
if center is None:
center = self.pointing_radec
offset2 = center.separation(self.radec).deg ** 2
ax.hist(offset2, **kwargs)
ax.set_xlabel("Offset^2 (deg^2)")
ax.set_ylabel("Counts")
return ax
[docs] def plot_energy_offset(self, ax=None):
"""Plot counts histogram with energy and offset axes."""
import matplotlib.pyplot as plt
from matplotlib.colors import LogNorm
ax = plt.gca() if ax is None else ax
energy_bounds = self._default_plot_ebounds()
offset_bounds = np.linspace(0, 4, 30)
counts = np.histogram2d(
x=self.energy, y=self.offset, bins=(energy_bounds, offset_bounds)
)[0]
ax.pcolormesh(energy_bounds, offset_bounds, counts.T, norm=LogNorm())
ax.set_xscale("log")
ax.set_xlabel("Energy (TeV)")
ax.set_ylabel("Offset (deg)")
[docs] def check(self, checks="all"):
"""Run checks.
This is a generator that yields a list of dicts.
"""
checker = EventListChecker(self)
return checker.run(checks=checks)
[docs]class EventList(EventListBase):
"""Event list for IACT dataset
Data format specification: :ref:`gadf:iact-events`
For further information, see the base class: `~gammapy.data.EventListBase`.
Parameters
----------
table : `~astropy.table.Table`
Event list table
Examples
--------
To load an example H.E.S.S. event list:
>>> from gammapy.data import EventList
>>> filename = '$GAMMAPY_DATA/hess-dl3-dr1/data/hess_dl3_dr1_obs_id_023523.fits.gz'
>>> events = EventList.read(filename)
"""
@property
def observatory_earth_location(self):
"""Observatory location (`~astropy.coordinates.EarthLocation`)."""
return earth_location_from_dict(self.table.meta)
@property
def observation_time_duration(self):
"""Observation time duration in seconds (`~astropy.units.Quantity`).
This is a keyword related to IACTs
The wall time, including dead-time.
"""
return Quantity(self.table.meta["ONTIME"], "second")
@property
def observation_dead_time_fraction(self):
"""Dead-time fraction (float).
This is a keyword related to IACTs
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.
"""
return 1 - self.table.meta["DEADC"]
@property
def altaz_frame(self):
"""ALT / AZ frame (`~astropy.coordinates.AltAz`)."""
return AltAz(obstime=self.time, location=self.observatory_earth_location)
@property
def altaz(self):
"""ALT / AZ position computed from RA / DEC (`~astropy.coordinates.SkyCoord`)"""
return self.radec.transform_to(self.altaz_frame)
@property
def altaz_from_table(self):
"""ALT / AZ position from table (`~astropy.coordinates.SkyCoord`)"""
lon = self.table["AZ"]
lat = self.table["ALT"]
return SkyCoord(lon, lat, unit="deg", frame=self.altaz_frame)
@property
def pointing_radec(self):
"""Pointing RA / DEC sky coordinates (`~astropy.coordinates.SkyCoord`)."""
info = self.table.meta
lon, lat = info["RA_PNT"], info["DEC_PNT"]
return SkyCoord(lon, lat, unit="deg", frame="icrs")
@property
def offset(self):
"""Event offset from the array pointing position (`~astropy.coordinates.Angle`)."""
position = self.radec
center = self.pointing_radec
offset = center.separation(position)
return Angle(offset, unit="deg")
[docs] def select_offset(self, offset_band):
"""Select events in offset band.
Parameters
----------
offset_band : `~astropy.coordinates.Angle`
offset band ``[offset_min, offset_max)``
Returns
-------
event_list : `EventList`
Copy of event list with selection applied.
"""
offset = self.offset
mask = offset_band[0] <= offset
mask &= offset < offset_band[1]
return self.select_row_subset(mask)
[docs] def peek(self):
"""Quick look plots."""
import matplotlib.pyplot as plt
fig, axes = plt.subplots(nrows=2, ncols=3, figsize=(12, 8))
self.plot_energy(ax=axes[0, 0])
bins = np.linspace(start=0, stop=4 ** 2, num=30)
self.plot_offset2_distribution(ax=axes[0, 1], bins=bins)
self.plot_time(ax=axes[0, 2])
axes[1, 0].axis("off")
m = self._counts_image()
ax = plt.subplot(2, 3, 4, projection=m.geom.wcs)
m.plot(ax=ax, stretch="sqrt")
self.plot_energy_offset(ax=axes[1, 1])
self._plot_text_summary(ax=axes[1, 2])
plt.tight_layout()
def _plot_text_summary(self, ax):
ax.axis("off")
txt = str(self)
ax.text(0, 1, txt, fontsize=12, verticalalignment="top")
def _counts_image(self):
from ..maps import WcsNDMap
opts = {
"width": (7, 7),
"binsz": 0.1,
"proj": "TAN",
"coordsys": "GAL",
"skydir": self.pointing_radec,
}
m = WcsNDMap.create(**opts)
m.fill_by_coord(self.radec)
m = m.smooth(width=1)
return m
[docs] def plot_image(self):
"""Quick look counts map sky plot."""
m = self._counts_image()
m.plot(stretch="sqrt")
[docs]class EventListLAT(EventListBase):
"""Event list for Fermi-LAT dataset
Fermi-LAT data products
https://fermi.gsfc.nasa.gov/ssc/data/analysis/documentation/Cicerone/Cicerone_Data/LAT_DP.html
Data format specification (columns)
https://fermi.gsfc.nasa.gov/ssc/data/analysis/documentation/Cicerone/Cicerone_Data/LAT_Data_Columns.html
For further information, see the base class: `~gammapy.data.EventListBase`.
Parameters
----------
table : `~astropy.table.Table`
Event list table
Examples
--------
To load an example Fermi-LAT event list (the one corresponding to the 2FHL catalog dataset):
>>> from gammapy.data import EventListLAT
>>> filename = '$GAMMAPY_DATA/fermi_2fhl/2fhl_events.fits.gz'
>>> events = EventListLAT.read(filename)
"""
[docs] def plot_image(self):
"""Quick look counts map sky plot."""
from ..maps import WcsNDMap
m = WcsNDMap.create(npix=(360, 180), binsz=1.0, proj="AIT", coordsys="GAL")
m.fill_by_coord(self.radec)
m.plot(stretch="sqrt")
class EventListChecker(Checker):
"""Event list checker.
Data format specification: ref:`gadf:iact-events`
Parameters
----------
event_list : `~gammapy.data.EventList`
Event list
"""
CHECKS = {
"meta": "check_meta",
"columns": "check_columns",
"times": "check_times",
"coordinates_galactic": "check_coordinates_galactic",
"coordinates_altaz": "check_coordinates_altaz",
}
accuracy = {"angle": Angle("1 arcsec"), "time": Quantity(1, "microsecond")}
# https://gamma-astro-data-formats.readthedocs.io/en/latest/events/events.html#mandatory-header-keywords
meta_required = [
"HDUCLASS",
"HDUDOC",
"HDUVERS",
"HDUCLAS1",
"OBS_ID",
"TSTART",
"TSTOP",
"ONTIME",
"LIVETIME",
"DEADC",
"RA_PNT",
"DEC_PNT",
# TODO: what to do about these?
# They are currently listed as required in the spec,
# but I think we should just require ICRS and those
# are irrelevant, should not be used.
# 'RADECSYS',
# 'EQUINOX',
"ORIGIN",
"TELESCOP",
"INSTRUME",
"CREATOR",
# https://gamma-astro-data-formats.readthedocs.io/en/latest/general/time.html#time-formats
"MJDREFI",
"MJDREFF",
"TIMEUNIT",
"TIMESYS",
"TIMEREF",
# https://gamma-astro-data-formats.readthedocs.io/en/latest/general/coordinates.html#coords-location
"GEOLON",
"GEOLAT",
"ALTITUDE",
]
_col = namedtuple("col", ["name", "unit"])
columns_required = [
_col(name="EVENT_ID", unit=""),
_col(name="TIME", unit="s"),
_col(name="RA", unit="deg"),
_col(name="DEC", unit="deg"),
_col(name="ENERGY", unit="TeV"),
]
def __init__(self, event_list):
self.event_list = event_list
def _record(self, level="info", msg=None):
obs_id = self.event_list.table.meta["OBS_ID"]
return {"level": level, "obs_id": obs_id, "msg": msg}
def check_meta(self):
meta_missing = sorted(set(self.meta_required) - set(self.event_list.table.meta))
if meta_missing:
yield self._record(
level="error", msg="Missing meta keys: {!r}".format(meta_missing)
)
def check_columns(self):
t = self.event_list.table
if len(t) == 0:
yield self._record(level="error", msg="Events table has zero rows")
for name, unit in self.columns_required:
if name not in t.colnames:
yield self._record(
level="error", msg="Missing table column: {!r}".format(name)
)
else:
if Unit(unit) != (t[name].unit or ""):
yield self._record(
level="error", msg="Invalid unit for column: {!r}".format(name)
)
def check_times(self):
dt = (self.event_list.time - self.event_list.observation_time_start).sec
if dt.min() < self.accuracy["time"].to("s").value:
yield self._record(level="error", msg="Event times before obs start time")
dt = (self.event_list.time - self.event_list.observation_time_end).sec
if dt.max() > self.accuracy["time"].to("s").value:
yield self._record(level="error", msg="Event times after the obs end time")
if np.min(np.diff(dt)) <= 0:
yield self._record(level="error", msg="Events are not time-ordered.")
def check_coordinates_galactic(self):
"""Check if RA / DEC matches GLON / GLAT."""
t = self.event_list.table
if "GLON" not in t.colnames:
return
galactic = SkyCoord(t["GLON"], t["GLAT"], unit="deg", frame="galactic")
separation = self.event_list.radec.separation(galactic).to("arcsec")
if separation.max() > self.accuracy["angle"]:
yield self._record(
level="error", msg="GLON / GLAT not consistent with RA / DEC"
)
def check_coordinates_altaz(self):
"""Check if ALT / AZ matches RA / DEC."""
t = self.event_list.table
if "AZ" not in t.colnames:
return
altaz_astropy = self.event_list.altaz
separation = angular_separation(
altaz_astropy.data.lon,
altaz_astropy.data.lat,
t["AZ"].quantity,
t["ALT"].quantity,
)
if separation.max() > self.accuracy["angle"]:
yield self._record(
level="error", msg="ALT / AZ not consistent with RA / DEC"
)