def load_events(fname):
"""Load events from a file."""
if get_file_format(fname) == 'pickle':
out = _load_data_pickle(fname)
elif get_file_format(fname) == 'nc':
out = _load_data_nc(fname)
eventlist = EventList()
eventlist.time = out['time']
eventlist.gti = out['gti']
eventlist.pi = out['pi']
eventlist.mjdref = out['mjdref']
if 'instr' in list(out.keys()):
eventlist.instr = out["instr"]
if 'energy' in list(out.keys()):
eventlist.energy = out["energy"]
if 'header' in list(out.keys()):
eventlist.header = out["header"]
return eventlist
def test_get_eventlist_dataset_from_stingray_Eventlist(capsys):
from stingray.events import EventList
from astropy.io.fits import Header
ev = EventList(time=[0, 1],
pi=[2, 2],
energy=[3., 4.],
gti=np.array([[-0.5, 1.5]]))
ds = get_eventlist_dataset_from_stingray_Eventlist(ev)
out, err = capsys.readouterr()
print("Out:", out)
print("Err:", err)
assert "Event list has no header" in err
header = Header()
header["Bu"] = "Bu"
ev.header = header.tostring()
ds = get_eventlist_dataset_from_stingray_Eventlist(ev)
assert np.allclose(ds.tables["EVENTS"].columns["TIME"].values, ev.time)
assert np.allclose(ds.tables["EVENTS"].columns["ENERGY"].values, ev.energy)
assert np.allclose(ds.tables["EVENTS"].columns["PI"].values, ev.pi)
def test_get_eventlist_dataset_from_stingray_Eventlist(capsys):
from stingray.events import EventList
from astropy.io.fits import Header
ev = EventList(time=[0, 1], pi=[2, 2], energy=[3., 4.],
gti=np.array([[-0.5, 1.5]]))
ds = get_eventlist_dataset_from_stingray_Eventlist(ev)
out, err = capsys.readouterr()
print("Out:", out)
print("Err:", err)
if err:
assert "Event list has no header" in err
header = Header()
header["Bu"] = "Bu"
ev.header = header.tostring()
ds = get_eventlist_dataset_from_stingray_Eventlist(ev)
assert np.allclose(ds.tables["EVENTS"].columns["TIME"].values, ev.time)
if "ENERGY" in ds.tables["EVENTS"].columns:
assert np.allclose(ds.tables["EVENTS"].columns["ENERGY"].values, ev.energy)
assert np.allclose(ds.tables["EVENTS"].columns["PI"].values, ev.pi)
def treat_event_file(filename,
noclobber=False,
gti_split=False,
min_length=4,
gtistring=None,
length_split=None):
"""Read data from an event file, with no external GTI information.
Parameters
----------
filename : str
Other Parameters
----------------
noclobber: bool
if a file is present, do not overwrite it
gtistring: str
comma-separated set of GTI strings to consider
gti_split: bool
split the file in multiple chunks, containing one GTI each
length_split: float, default None
split the file in multiple chunks, with approximately this length
min_length: float
minimum length of GTIs accepted (only if gti_split is True or
length_split is not None)
"""
gtistring = assign_value_if_none(gtistring, 'GTI,STDGTI')
logging.info('Opening %s' % filename)
instr = read_header_key(filename, 'INSTRUME')
mission = read_header_key(filename, 'TELESCOP')
data = load_events_and_gtis(filename, gtistring=gtistring)
events = data.ev_list
gtis = events.gti
detector_id = data.detector_id
if detector_id is not None:
detectors = np.array(list(set(detector_id)))
else:
detectors = [None]
outfile_root = \
hen_root(filename) + '_' + mission.lower() + '_' + instr.lower()
for d in detectors:
if d is not None:
good_det = d == data.detector_id
outroot_local = \
'{0}_det{1:02d}'.format(outfile_root, d)
else:
good_det = np.ones_like(events.time, dtype=bool)
outroot_local = outfile_root
outfile = outroot_local + '_ev' + HEN_FILE_EXTENSION
if noclobber and os.path.exists(outfile) and (not (gti_split
or length_split)):
warnings.warn(
'{0} exists and using noclobber. Skipping'.format(outfile))
return
if gti_split or (length_split is not None):
lengths = np.array([g1 - g0 for (g0, g1) in gtis])
gtis = gtis[lengths >= min_length]
if length_split:
gti0 = np.arange(gtis[0, 0], gtis[-1, 1], length_split)
gti1 = gti0 + length_split
gti_chunks = np.array([[g0, g1]
for (g0, g1) in zip(gti0, gti1)])
label = 'chunk'
else:
gti_chunks = gtis
label = 'gti'
for ig, g in enumerate(gti_chunks):
outfile_local = \
'{0}_{1}{2:03d}_ev'.format(outroot_local, label,
ig) + HEN_FILE_EXTENSION
good_gtis = cross_two_gtis([g], gtis)
if noclobber and os.path.exists(outfile_local):
warnings.warn('{0} exists, '.format(outfile_local) +
'and noclobber option used. Skipping')
return
good = np.logical_and(events.time >= g[0], events.time < g[1])
all_good = good_det & good
if len(events.time[all_good]) < 1:
continue
events_filt = EventList(events.time[all_good],
pi=events.pi[all_good],
gti=good_gtis,
mjdref=events.mjdref)
events_filt.instr = events.instr
events_filt.header = events.header
save_events(events_filt, outfile_local)
pass
else:
events_filt = EventList(events.time[good_det],
pi=events.pi[good_det],
gti=events.gti,
mjdref=events.mjdref)
events_filt.instr = events.instr
events_filt.header = events.header
save_events(events_filt, outfile)
def treat_event_file(filename,
noclobber=False,
gti_split=False,
min_length=4,
gtistring=None):
"""Read data from an event file, with no external GTI information.
Parameters
----------
filename : str
Other Parameters
----------------
noclobber: bool
if a file is present, do not overwrite it
gtistring: str
comma-separated set of GTI strings to consider
gti_split: bool
split the file in multiple chunks, containing one GTI each
min_length: float
minimum length of GTIs accepted (only if gti_split is True)
"""
gtistring = assign_value_if_none(gtistring, 'GTI,STDGTI')
logging.info('Opening %s' % filename)
instr = read_header_key(filename, 'INSTRUME')
mission = read_header_key(filename, 'TELESCOP')
data = load_events_and_gtis(filename, gtistring=gtistring)
events = data.ev_list
gtis = events.gti
detector_id = data.detector_id
if detector_id is not None:
detectors = list(set(detector_id))
else:
detectors = [None]
outfile_root = \
hen_root(filename) + '_' + mission.lower() + '_' + instr.lower()
for d in detectors:
if d is not None:
good_det = data.detector_id
outroot_local = \
'{0}_det{1:02d}'.format(outfile_root, d)
else:
good_det = np.ones_like(events.time, dtype=bool)
outroot_local = outfile_root
outfile = outroot_local + '_ev' + HEN_FILE_EXTENSION
if noclobber and os.path.exists(outfile) and (not gti_split):
warnings.warn(
'{0} exists, and noclobber option used. Skipping'.format(
outfile))
return
if gti_split:
for ig, g in enumerate(gtis):
length = g[1] - g[0]
if length < min_length:
print("GTI shorter than {} s; skipping".format(min_length))
continue
outfile_local = \
'{0}_gti{1}_ev'.format(outroot_local,
ig) + HEN_FILE_EXTENSION
if noclobber and os.path.exists(outfile_local):
warnings.warn('{0} exists, '.format(outfile_local) +
'and noclobber option used. Skipping')
return
good = np.logical_and(events.time >= g[0], events.time < g[1])
all_good = good_det & good
events_filt = EventList(events.time[all_good],
pi=events.pi[all_good],
gti=np.array([g], dtype=np.longdouble),
mjdref=events.mjdref)
events_filt.instr = events.instr
events_filt.header = events.header
save_events(events_filt, outfile_local)
pass
else:
events_filt = EventList(events.time[good_det],
pi=events.pi[good_det],
gti=events.gti,
mjdref=events.mjdref)
events_filt.instr = events.instr
events_filt.header = events.header
save_events(events_filt, outfile)
