def read_NuSTAR(self, ft1_file):
# Read in model
self.modelin = pint.models.get_model(self.args.par)
# Extract target coordinates
self.t_coord = SkyCoord(self.modelin.RAJ.quantity,
self.modelin.DECJ.quantity,
frame="icrs")
# Read in Fermi data
self.data_NuSTAR = load_NuSTAR_TOAs(ft1_file)
self.weights_NuSTAR = np.ones(len(self.data_NuSTAR))
)
raise
elif hdr['TELESCOP'] == 'XTE':
# Instantiate RXTEObs once so it gets added to the observatory registry
if args.orbfile is not None:
# Determine what observatory type is.
log.info('Setting up RXTE observatory')
obs = RXTEObs(name='RXTE', FPorbname=args.orbfile)
# Read event file and return list of TOA objects
tl = load_RXTE_TOAs(args.eventname)
elif hdr['TELESCOP'].startswith('XMM'):
# Not loading orbit file here, since that is not yet supported.
tl = load_XMM_TOAs(args.eventname)
elif hdr['TELESCOP'].startswith('NuSTAR'):
# Not loading orbit file here, since that is not yet supported.
tl = load_NuSTAR_TOAs(args.eventname)
f = pyfits.open(args.eventname)
mets = f['events'].data.field('time')
f.close()
for t, met in zip(tl, mets):
t.met = met
else:
log.error(
"FITS file not recognized, TELESCOPE = {0}, INSTRUMENT = {1}".format(
hdr['TELESCOP'], hdr['INSTRUME']))
sys.exit(1)
if args.topo: #for writing UTC topo toas
SpacecraftObs(name='spacecraft')
if not args.topo and (args.orbfile is None):
def main(argv=None):
import argparse
parser = argparse.ArgumentParser(
description=
"Use PINT to compute event phases and make plots of photon event files."
)
parser.add_argument(
"eventfile",
help=
"Photon event FITS file name (e.g. from NICER, RXTE, XMM, Chandra).",
)
parser.add_argument("parfile", help="par file to construct model from")
parser.add_argument("--orbfile", help="Name of orbit file", default=None)
parser.add_argument("--maxMJD",
help="Maximum MJD to include in analysis",
default=None)
parser.add_argument("--plotfile",
help="Output figure file name (default=None)",
default=None)
parser.add_argument(
"--addphase",
help="Write FITS file with added phase column",
default=False,
action="store_true",
)
parser.add_argument(
"--addorbphase",
help="Write FITS file with added orbital phase column",
default=False,
action="store_true",
)
parser.add_argument(
"--absphase",
help="Write FITS file with integral portion of pulse phase (ABS_PHASE)",
default=False,
action="store_true",
)
parser.add_argument(
"--barytime",
help=
"Write FITS file with a column containing the barycentric time as double precision MJD.",
default=False,
action="store_true",
)
parser.add_argument(
"--outfile",
help="Output FITS file name (default=same as eventfile)",
default=None,
)
parser.add_argument("--ephem",
help="Planetary ephemeris to use (default=DE421)",
default="DE421")
parser.add_argument(
"--tdbmethod",
help="Method for computing TT to TDB (default=astropy)",
default="default",
)
parser.add_argument("--plot",
help="Show phaseogram plot.",
action="store_true",
default=False)
parser.add_argument(
"--use_gps",
default=False,
action="store_true",
help="Apply GPS to UTC clock corrections",
)
parser.add_argument(
"--use_bipm",
default=False,
action="store_true",
help="Use TT(BIPM) instead of TT(TAI)",
)
# parser.add_argument("--fix",help="Apply 1.0 second offset for NICER", action='store_true', default=False)
args = parser.parse_args(argv)
# If outfile is specified, that implies addphase
if args.outfile is not None:
args.addphase = True
# If plotfile is specified, that implies plot
if args.plotfile is not None:
args.plot = True
# Read event file header to figure out what instrument is is from
hdr = pyfits.getheader(args.eventfile, ext=1)
log.info("Event file TELESCOPE = {0}, INSTRUMENT = {1}".format(
hdr["TELESCOP"], hdr["INSTRUME"]))
if hdr["TELESCOP"] == "NICER":
# Instantiate NICERObs once so it gets added to the observatory registry
if args.orbfile is not None:
log.info("Setting up NICER observatory")
NICERObs(name="NICER", FPorbname=args.orbfile, tt2tdb_mode="pint")
# Read event file and return list of TOA objects
try:
tl = load_NICER_TOAs(args.eventfile)
except KeyError:
log.error(
"Observatory not recognized. This probably means you need to provide an orbit file or barycenter the event file."
)
sys.exit(1)
elif hdr["TELESCOP"] == "XTE":
# Instantiate RXTEObs once so it gets added to the observatory registry
if args.orbfile is not None:
# Determine what observatory type is.
log.info("Setting up RXTE observatory")
RXTEObs(name="RXTE", FPorbname=args.orbfile, tt2tdb_mode="pint")
# Read event file and return list of TOA objects
tl = load_RXTE_TOAs(args.eventfile)
elif hdr["TELESCOP"].startswith("XMM"):
# Not loading orbit file here, since that is not yet supported.
tl = load_XMM_TOAs(args.eventfile)
elif hdr["TELESCOP"].lower().startswith("nustar"):
if args.orbfile is not None:
log.info("Setting up NuSTAR observatory")
NuSTARObs(name="NuSTAR",
FPorbname=args.orbfile,
tt2tdb_mode="pint")
tl = load_NuSTAR_TOAs(args.eventfile)
else:
log.error(
"FITS file not recognized, TELESCOPE = {0}, INSTRUMENT = {1}".
format(hdr["TELESCOP"], hdr["INSTRUME"]))
sys.exit(1)
# Now convert to TOAs object and compute TDBs and posvels
if len(tl) == 0:
log.error("No TOAs, exiting!")
sys.exit(0)
# Read in model
modelin = pint.models.get_model(args.parfile)
use_planets = False
if "PLANET_SHAPIRO" in modelin.params:
if modelin.PLANET_SHAPIRO.value:
use_planets = True
if "AbsPhase" not in modelin.components:
log.error(
"TimingModel does not include AbsPhase component, which is required "
"for computing phases. Make sure you have TZR* parameters in your par file!"
)
raise ValueError("Model missing AbsPhase component.")
if args.addorbphase and (not hasattr(modelin, "binary_model_name")):
log.error(
"TimingModel does not include a binary model, which is required for "
"computing orbital phases. Make sure you have BINARY and associated "
"model parameters in your par file!")
raise ValueError("Model missing BINARY component.")
# Discard events outside of MJD range
if args.maxMJD is not None:
tlnew = []
print("pre len : ", len(tl))
maxT = Time(float(args.maxMJD), format="mjd")
print("maxT : ", maxT)
for tt in tl:
if tt.mjd < maxT:
tlnew.append(tt)
tl = tlnew
print("post len : ", len(tlnew))
ts = toa.get_TOAs_list(
tl,
ephem=args.ephem,
include_bipm=args.use_bipm,
include_gps=args.use_gps,
planets=use_planets,
tdb_method=args.tdbmethod,
)
ts.filename = args.eventfile
# if args.fix:
# ts.adjust_TOAs(TimeDelta(np.ones(len(ts.table))*-1.0*u.s,scale='tt'))
print(ts.get_summary())
mjds = ts.get_mjds()
print(mjds.min(), mjds.max())
# Compute model phase for each TOA
iphss, phss = modelin.phase(ts, abs_phase=True)
# ensure all postive
negmask = phss < 0.0
phases = np.where(negmask, phss + 1.0, phss)
h = float(hm(phases))
print("Htest : {0:.2f} ({1:.2f} sigma)".format(h, h2sig(h)))
if args.plot:
phaseogram_binned(mjds, phases, bins=100, plotfile=args.plotfile)
# Compute orbital phases for each photon TOA
if args.addorbphase:
delay = modelin.delay(ts)
orbits = modelin.binary_instance.orbits()
# These lines are already in orbits.orbit_phase() in binary_orbits.py.
# What is the correct syntax is to call this function here?
norbits = np.array(np.floor(orbits), dtype=np.long)
orbphases = orbits - norbits # fractional phase
if args.addphase or args.addorbphase:
# Read input FITS file (again).
# If overwriting, open in 'update' mode
if args.outfile is None:
hdulist = pyfits.open(args.eventfile, mode="update")
else:
hdulist = pyfits.open(args.eventfile)
datacol = []
data_to_add = {}
if args.addphase:
if len(hdulist[1].data) != len(phases):
raise RuntimeError(
"Mismatch between length of FITS table ({0}) and length of phase array ({1})!"
.format(len(hdulist[1].data), len(phases)))
data_to_add["PULSE_PHASE"] = [phases, "D"]
if args.absphase:
data_to_add["ABS_PHASE"] = [iphss - negmask, "K"]
if args.barytime:
bats = modelin.get_barycentric_toas(ts)
data_to_add["BARY_TIME"] = [bats, "D"]
if args.addorbphase:
if len(hdulist[1].data) != len(orbphases):
raise RuntimeError(
"Mismatch between length of FITS table ({0}) and length of orbital phase array ({1})!"
.format(len(hdulist[1].data), len(orbphases)))
data_to_add["ORBIT_PHASE"] = [orbphases, "D"]
# End if args.addorbphase
for key in data_to_add.keys():
if key in hdulist[1].columns.names:
log.info("Found existing %s column, overwriting..." % key)
# Overwrite values in existing Column
hdulist[1].data[key] = data_to_add[key][0]
else:
# Construct and append new column, preserving HDU header and name
log.info("Adding new %s column." % key)
datacol.append(
pyfits.ColDefs([
pyfits.Column(
name=key,
format=data_to_add[key][1],
array=data_to_add[key][0],
)
]))
if len(datacol) > 0:
cols = hdulist[1].columns
for c in datacol:
cols = cols + c
bt = pyfits.BinTableHDU.from_columns(cols,
header=hdulist[1].header,
name=hdulist[1].name)
hdulist[1] = bt
if args.outfile is None:
# Overwrite the existing file
log.info("Overwriting existing FITS file " + args.eventfile)
hdulist.flush(verbose=True, output_verify="warn")
else:
# Write to new output file
log.info("Writing output FITS file " + args.outfile)
hdulist.writeto(args.outfile,
overwrite=True,
checksum=True,
output_verify="warn")
def main(argv=None):
import argparse
parser = argparse.ArgumentParser(
description=
"Use PINT to compute event phases and make plots of photon event files."
)
parser.add_argument(
"eventfile",
help=
"Photon event FITS file name (e.g. from NICER, RXTE, XMM, Chandra).")
parser.add_argument("parfile", help="par file to construct model from")
parser.add_argument("--orbfile", help="Name of orbit file", default=None)
parser.add_argument("--maxMJD",
help="Maximum MJD to include in analysis",
default=None)
parser.add_argument("--plotfile",
help="Output figure file name (default=None)",
default=None)
parser.add_argument("--addphase",
help="Write FITS file with added phase column",
default=False,
action='store_true')
parser.add_argument(
"--absphase",
help="Write FITS file with integral portion of pulse phase (ABS_PHASE)",
default=False,
action='store_true')
parser.add_argument(
"--barytime",
help=
"Write FITS file with a column containing the barycentric time as double precision MJD.",
default=False,
action='store_true')
parser.add_argument(
"--outfile",
help="Output FITS file name (default=same as eventfile)",
default=None)
parser.add_argument("--ephem",
help="Planetary ephemeris to use (default=DE421)",
default="DE421")
parser.add_argument(
'--tdbmethod',
help="Method for computing TT to TDB (default=astropy)",
default="default")
parser.add_argument("--plot",
help="Show phaseogram plot.",
action='store_true',
default=False)
parser.add_argument("--use_gps",
default=False,
action='store_true',
help="Apply GPS to UTC clock corrections")
parser.add_argument("--use_bipm",
default=False,
action='store_true',
help="Use TT(BIPM) instead of TT(TAI)")
# parser.add_argument("--fix",help="Apply 1.0 second offset for NICER", action='store_true', default=False)
args = parser.parse_args(argv)
# If outfile is specified, that implies addphase
if args.outfile is not None:
args.addphase = True
# If plotfile is specified, that implies plot
if args.plotfile is not None:
args.plot = True
# Read event file header to figure out what instrument is is from
hdr = pyfits.getheader(args.eventfile, ext=1)
log.info('Event file TELESCOPE = {0}, INSTRUMENT = {1}'.format(
hdr['TELESCOP'], hdr['INSTRUME']))
if hdr['TELESCOP'] == 'NICER':
# Instantiate NICERObs once so it gets added to the observatory registry
if args.orbfile is not None:
log.info('Setting up NICER observatory')
NICERObs(name='NICER', FPorbname=args.orbfile, tt2tdb_mode='pint')
# Read event file and return list of TOA objects
try:
tl = load_NICER_TOAs(args.eventfile)
except KeyError:
log.error(
"Observatory not recognized. This probably means you need to provide an orbit file or barycenter the event file."
)
sys.exit(1)
elif hdr['TELESCOP'] == 'XTE':
# Instantiate RXTEObs once so it gets added to the observatory registry
if args.orbfile is not None:
# Determine what observatory type is.
log.info('Setting up RXTE observatory')
RXTEObs(name='RXTE', FPorbname=args.orbfile, tt2tdb_mode='pint')
# Read event file and return list of TOA objects
tl = load_RXTE_TOAs(args.eventfile)
elif hdr['TELESCOP'].startswith('XMM'):
# Not loading orbit file here, since that is not yet supported.
tl = load_XMM_TOAs(args.eventfile)
elif hdr['TELESCOP'].startswith('NuSTAR'):
# Not loading orbit file here, since that is not yet supported.
tl = load_NuSTAR_TOAs(args.eventfile)
else:
log.error(
"FITS file not recognized, TELESCOPE = {0}, INSTRUMENT = {1}".
format(hdr['TELESCOP'], hdr['INSTRUME']))
sys.exit(1)
# Now convert to TOAs object and compute TDBs and posvels
if len(tl) == 0:
log.error("No TOAs, exiting!")
sys.exit(0)
# Read in model
modelin = pint.models.get_model(args.parfile)
use_planets = False
if 'PLANET_SHAPIRO' in modelin.params:
if modelin.PLANET_SHAPIRO.value:
use_planets = True
# Discard events outside of MJD range
if args.maxMJD is not None:
tlnew = []
print("pre len : ", len(tl))
maxT = Time(float(args.maxMJD), format='mjd')
print("maxT : ", maxT)
for tt in tl:
if tt.mjd < maxT:
tlnew.append(tt)
tl = tlnew
print("post len : ", len(tlnew))
ts = toa.get_TOAs_list(tl,
ephem=args.ephem,
include_bipm=args.use_bipm,
include_gps=args.use_gps,
planets=use_planets,
tdb_method=args.tdbmethod)
ts.filename = args.eventfile
# if args.fix:
# ts.adjust_TOAs(TimeDelta(np.ones(len(ts.table))*-1.0*u.s,scale='tt'))
print(ts.get_summary())
mjds = ts.get_mjds()
print(mjds.min(), mjds.max())
# Compute model phase for each TOA
iphss, phss = modelin.phase(ts, abs_phase=True)
# ensure all postive
negmask = phss < 0.0 * u.cycle
phases = np.where(negmask, phss + 1.0 * u.cycle, phss)
h = float(hm(phases))
print("Htest : {0:.2f} ({1:.2f} sigma)".format(h, h2sig(h)))
if args.plot:
phaseogram_binned(mjds, phases, bins=100, plotfile=args.plotfile)
if args.addphase:
# Read input FITS file (again).
# If overwriting, open in 'update' mode
if args.outfile is None:
hdulist = pyfits.open(args.eventfile, mode='update')
else:
hdulist = pyfits.open(args.eventfile)
if len(hdulist[1].data) != len(phases):
raise RuntimeError(
'Mismatch between length of FITS table ({0}) and length of phase array ({1})!'
.format(len(hdulist[1].data), len(phases)))
data_to_add = {'PULSE_PHASE': [phases, 'D']}
if args.absphase:
data_to_add['ABS_PHASE'] = [iphss - negmask * u.cycle, 'K']
if args.barytime:
bats = modelin.get_barycentric_toas(ts)
data_to_add['BARY_TIME'] = [bats, 'D']
datacol = []
for key in data_to_add.keys():
if key in hdulist[1].columns.names:
log.info('Found existing %s column, overwriting...' % key)
# Overwrite values in existing Column
hdulist[1].data[key] = data_to_add[key][0]
else:
# Construct and append new column, preserving HDU header and name
log.info('Adding new %s column.' % key)
datacol.append(
pyfits.ColDefs([
pyfits.Column(name=key,
format=data_to_add[key][1],
array=data_to_add[key][0])
]))
if len(datacol) > 0:
cols = hdulist[1].columns
for c in datacol:
cols = cols + c
bt = pyfits.BinTableHDU.from_columns(cols,
header=hdulist[1].header,
name=hdulist[1].name)
hdulist[1] = bt
if args.outfile is None:
# Overwrite the existing file
log.info('Overwriting existing FITS file ' + args.eventfile)
hdulist.flush(verbose=True, output_verify='warn')
else:
# Write to new output file
log.info('Writing output FITS file ' + args.outfile)
hdulist.writeto(args.outfile,
overwrite=True,
checksum=True,
output_verify='warn')
def main(argv=None):
import argparse
parser = argparse.ArgumentParser(description="Use PINT to compute event phases and make plots of photon event files.")
parser.add_argument("eventfile",help="Photon event FITS file name (e.g. from NICER, RXTE, XMM, Chandra).")
parser.add_argument("parfile",help="par file to construct model from")
parser.add_argument("--orbfile",help="Name of orbit file", default=None)
parser.add_argument("--maxMJD",help="Maximum MJD to include in analysis", default=None)
parser.add_argument("--plotfile",help="Output figure file name (default=None)", default=None)
parser.add_argument("--addphase",help="Write FITS file with added phase column",default=False,action='store_true')
parser.add_argument("--absphase",help="Write FITS file with integral portion of pulse phase (ABS_PHASE)",default=False,action='store_true')
parser.add_argument("--barytime",help="Write FITS file with a column containing the barycentric time as double precision MJD.",default=False,action='store_true')
parser.add_argument("--outfile",help="Output FITS file name (default=same as eventfile)", default=None)
parser.add_argument("--ephem",help="Planetary ephemeris to use (default=DE421)", default="DE421")
parser.add_argument('--tdbmethod',help="Method for computing TT to TDB (default=astropy)", default="default")
parser.add_argument("--plot",help="Show phaseogram plot.", action='store_true', default=False)
parser.add_argument("--use_gps",default=False,action='store_true',help="Apply GPS to UTC clock corrections")
parser.add_argument("--use_bipm",default=False,action='store_true',help="Use TT(BIPM) instead of TT(TAI)")
# parser.add_argument("--fix",help="Apply 1.0 second offset for NICER", action='store_true', default=False)
args = parser.parse_args(argv)
# If outfile is specified, that implies addphase
if args.outfile is not None:
args.addphase = True
# If plotfile is specified, that implies plot
if args.plotfile is not None:
args.plot = True
# Read event file header to figure out what instrument is is from
hdr = pyfits.getheader(args.eventfile,ext=1)
log.info('Event file TELESCOPE = {0}, INSTRUMENT = {1}'.format(hdr['TELESCOP'],
hdr['INSTRUME']))
if hdr['TELESCOP'] == 'NICER':
# Instantiate NICERObs once so it gets added to the observatory registry
if args.orbfile is not None:
log.info('Setting up NICER observatory')
NICERObs(name='NICER',FPorbname=args.orbfile,tt2tdb_mode='pint')
# Read event file and return list of TOA objects
try:
tl = load_NICER_TOAs(args.eventfile)
except KeyError:
log.error("Observatory not recognized. This probably means you need to provide an orbit file or barycenter the event file.")
sys.exit(1)
elif hdr['TELESCOP'] == 'XTE':
# Instantiate RXTEObs once so it gets added to the observatory registry
if args.orbfile is not None:
# Determine what observatory type is.
log.info('Setting up RXTE observatory')
RXTEObs(name='RXTE',FPorbname=args.orbfile,tt2tdb_mode='pint')
# Read event file and return list of TOA objects
tl = load_RXTE_TOAs(args.eventfile)
elif hdr['TELESCOP'].startswith('XMM'):
# Not loading orbit file here, since that is not yet supported.
tl = load_XMM_TOAs(args.eventfile)
elif hdr['TELESCOP'].lower().startswith('nustar'):
if args.orbfile is not None:
log.info('Setting up NuSTAR observatory')
NuSTARObs(name='NuSTAR',FPorbname=args.orbfile, tt2tdb_mode='pint')
tl = load_NuSTAR_TOAs(args.eventfile)
else:
log.error("FITS file not recognized, TELESCOPE = {0}, INSTRUMENT = {1}".format(
hdr['TELESCOP'], hdr['INSTRUME']))
sys.exit(1)
# Now convert to TOAs object and compute TDBs and posvels
if len(tl) == 0:
log.error("No TOAs, exiting!")
sys.exit(0)
# Read in model
modelin = pint.models.get_model(args.parfile)
use_planets=False
if 'PLANET_SHAPIRO' in modelin.params:
if modelin.PLANET_SHAPIRO.value:
use_planets=True
# Discard events outside of MJD range
if args.maxMJD is not None:
tlnew = []
print("pre len : ",len(tl))
maxT = Time(float(args.maxMJD),format='mjd')
print("maxT : ",maxT)
for tt in tl:
if tt.mjd < maxT:
tlnew.append(tt)
tl=tlnew
print("post len : ",len(tlnew))
ts = toa.get_TOAs_list(tl, ephem=args.ephem, include_bipm=args.use_bipm,
include_gps=args.use_gps, planets=use_planets, tdb_method=args.tdbmethod)
ts.filename = args.eventfile
# if args.fix:
# ts.adjust_TOAs(TimeDelta(np.ones(len(ts.table))*-1.0*u.s,scale='tt'))
print(ts.get_summary())
mjds = ts.get_mjds()
print(mjds.min(),mjds.max())
# Compute model phase for each TOA
iphss,phss = modelin.phase(ts,abs_phase=True)
# ensure all postive
negmask = phss < 0.0 * u.cycle
phases = np.where(negmask, phss + 1.0 * u.cycle, phss)
h = float(hm(phases))
print("Htest : {0:.2f} ({1:.2f} sigma)".format(h,h2sig(h)))
if args.plot:
phaseogram_binned(mjds,phases,bins=100,plotfile = args.plotfile)
if args.addphase:
# Read input FITS file (again).
# If overwriting, open in 'update' mode
if args.outfile is None:
hdulist = pyfits.open(args.eventfile,mode='update')
else:
hdulist = pyfits.open(args.eventfile)
if len(hdulist[1].data) != len(phases):
raise RuntimeError('Mismatch between length of FITS table ({0}) and length of phase array ({1})!'.format(len(hdulist[1].data),len(phases)))
data_to_add = {'PULSE_PHASE':[phases,'D']}
if args.absphase:
data_to_add['ABS_PHASE'] = [iphss-negmask*u.cycle,'K']
if args.barytime:
bats = modelin.get_barycentric_toas(ts)
data_to_add['BARY_TIME'] = [bats,'D']
datacol = []
for key in data_to_add.keys():
if key in hdulist[1].columns.names:
log.info('Found existing %s column, overwriting...'%key)
# Overwrite values in existing Column
hdulist[1].data[key] = data_to_add[key][0]
else:
# Construct and append new column, preserving HDU header and name
log.info('Adding new %s column.'%key)
datacol.append(pyfits.ColDefs([pyfits.Column(name=key,
format=data_to_add[key][1], array=data_to_add[key][0])]))
if len(datacol)>0:
cols = hdulist[1].columns
for c in datacol:
cols = cols + c
bt = pyfits.BinTableHDU.from_columns(cols, header=hdulist[1].header,
name=hdulist[1].name)
hdulist[1] = bt
if args.outfile is None:
# Overwrite the existing file
log.info('Overwriting existing FITS file '+args.eventfile)
hdulist.flush(verbose=True, output_verify='warn')
else:
# Write to new output file
log.info('Writing output FITS file '+args.outfile)
hdulist.writeto(args.outfile,overwrite=True, checksum=True, output_verify='warn')
