def phaseogram(self, weights=None, bins=100, rotate=0.0, size=5,
alpha=0.25, plotfile=None):
"""
Make a nice 2-panel phaseogram for the current model
"""
mjds = self.toas.table['tdbld'].quantity
phss = self.get_event_phases()
plot_utils.phaseogram(mjds, phss, weights=self.weights, bins=bins,
rotate=rotate, size=size, alpha=alpha, plotfile=plotfile)
def phaseogram(self, bins=100, rotate=0.0, size=5,
alpha=0.25, file=False):
"""
Make a nice 2-panel phaseogram for the current model
"""
mjds = self.toas.table['tdbld'].astype(np.float64)
phss = self.get_event_phases()
plot_utils.phaseogram(mjds, phss, weights=self.weights, bins=bins,
rotate=rotate, size=size, alpha=alpha, file=file)
def phaseogram(self, weights=None, bins=100, rotate=0.0, size=5,
alpha=0.25, plotfile=None):
"""
Make a nice 2-panel phaseogram for the current model
"""
mjds = self.toas.table['tdbld'].quantity
phss = self.get_event_phases()
plot_utils.phaseogram(mjds, phss, weights=self.get_weights(), bins=bins,
rotate=rotate, size=size, alpha=alpha, plotfile=plotfile)
def phaseogram(self, bins=100, rotate=0.0, size=5,
alpha=0.25, file=False):
"""
Make a nice 2-panel phaseogram for the current model
"""
mjds = self.toas.table['tdbld'].astype(np.float64)
phss = self.get_event_phases()
plot_utils.phaseogram(mjds, phss, weights=self.weights, bins=bins,
rotate=rotate, size=size, alpha=alpha, file=file)
def plot(self):
iphss, phss = self.modelin.phase(self.toas) # , abs_phase=True)
# Ensure all postive
phases = np.where(phss < 0.0 * u.cycle, phss + 1.0 * u.cycle, phss)
# Pull out the first H-Test
htest = hmw(phases, np.array(self.toas.get_flag_value('weights')))
print(htest)
phaseogram(self.toas.get_mjds(),
phases,
weights=np.array(self.toas.get_flag_value('weights')))
def main(argv=None):
parser = argparse.ArgumentParser(
description=
"Use PINT to compute H-test and plot Phaseogram from a Fermi FT1 event file."
)
parser.add_argument("eventfile", help="Fermi event FITS file name.")
parser.add_argument("parfile", help="par file to construct model from")
parser.add_argument(
"weightcol",
help="Column name for event weights (or 'CALC' to compute them)")
parser.add_argument("--ft2", help="Path to FT2 file.", default=None)
parser.add_argument(
"--addphase",
help="Write FT1 file with added phase column",
default=False,
action="store_true",
)
parser.add_argument("--plot",
help="Show phaseogram plot.",
action="store_true",
default=False)
parser.add_argument("--plotfile",
help="Output figure file name (default=None)",
default=None)
parser.add_argument("--maxMJD",
help="Maximum MJD to include in analysis",
default=None)
parser.add_argument(
"--outfile",
help="Output figure file name (default is to overwrite input file)",
default=None,
)
parser.add_argument(
"--planets",
help="Use planetary Shapiro delay in calculations (default=False)",
default=False,
action="store_true",
)
parser.add_argument("--ephem",
help="Planetary ephemeris to use (default=DE421)",
default="DE421")
args = parser.parse_args(argv)
# If outfile is specified, that implies addphase
if args.outfile is not None:
args.addphase = True
# Read in model
modelin = pint.models.get_model(args.parfile)
if "ELONG" in modelin.params:
tc = SkyCoord(
modelin.ELONG.quantity,
modelin.ELAT.quantity,
frame="barycentrictrueecliptic",
)
else:
tc = SkyCoord(modelin.RAJ.quantity,
modelin.DECJ.quantity,
frame="icrs")
if args.ft2 is not None:
# Instantiate FermiObs once so it gets added to the observatory registry
FermiObs(name="Fermi", ft2name=args.ft2)
# Read event file and return list of TOA objects
tl = load_Fermi_TOAs(args.eventfile,
weightcolumn=args.weightcol,
targetcoord=tc)
# 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))
# Now convert to TOAs object and compute TDBs and posvels
# For Fermi, we are not including GPS or TT(BIPM) corrections
ts = toa.get_TOAs_list(
tl,
include_gps=False,
include_bipm=False,
planets=args.planets,
ephem=args.ephem,
)
ts.filename = args.eventfile
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
phases = np.where(phss < 0.0 * u.cycle, phss + 1.0 * u.cycle, phss)
mjds = ts.get_mjds()
weights = np.array([w["weight"] for w in ts.table["flags"]])
h = float(hmw(phases, weights))
print("Htest : {0:.2f} ({1:.2f} sigma)".format(h, h2sig(h)))
if args.plot:
log.info("Making phaseogram plot with {0} photons".format(len(mjds)))
phaseogram(mjds, phases, weights, 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)
event_hdu = hdulist[1]
event_hdr = event_hdu.header
event_dat = event_hdu.data
if len(event_dat) != len(phases):
raise RuntimeError(
"Mismatch between length of FITS table ({0}) and length of phase array ({1})!"
.format(len(event_dat), len(phases)))
if "PULSE_PHASE" in event_hdu.columns.names:
log.info("Found existing PULSE_PHASE column, overwriting...")
# Overwrite values in existing Column
event_dat["PULSE_PHASE"] = phases
else:
# Construct and append new column, preserving HDU header and name
log.info("Adding new PULSE_PHASE column.")
phasecol = pyfits.ColDefs(
[pyfits.Column(name="PULSE_PHASE", format="D", array=phases)])
bt = pyfits.BinTableHDU.from_columns(event_hdu.columns + phasecol,
header=event_hdr,
name=event_hdu.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")
return 0
def main(argv=None):
parser = argparse.ArgumentParser(
description=
"Use PINT to compute H-test and plot Phaseogram from a Fermi FT1 event file."
)
parser.add_argument("eventfile", help="Fermi event FITS file name.")
parser.add_argument("parfile", help="par file to construct model from")
parser.add_argument(
"weightcol",
help="Column name for event weights (or 'CALC' to compute them)")
parser.add_argument("--ft2", help="Path to FT2 file.", default=None)
parser.add_argument(
"--addphase",
help="Write FT1 file with added phase column",
default=False,
action="store_true",
)
parser.add_argument("--plot",
help="Show phaseogram plot.",
action="store_true",
default=False)
parser.add_argument("--plotfile",
help="Output figure file name (default=None)",
default=None)
parser.add_argument("--maxMJD",
help="Maximum MJD to include in analysis",
default=None)
parser.add_argument("--minMJD",
help="Minimum MJD to include in analysis",
default=None)
parser.add_argument(
"--outfile",
help="Output figure file name (default is to overwrite input file)",
default=None,
)
parser.add_argument(
"--planets",
help="Use planetary Shapiro delay in calculations (default=False)",
default=False,
action="store_true",
)
parser.add_argument("--ephem",
help="Planetary ephemeris to use (default=DE421)",
default="DE421")
args = parser.parse_args(argv)
# If outfile is specified, that implies addphase
if args.outfile is not None:
args.addphase = True
# Read in model
modelin = pint.models.get_model(args.parfile)
if "ELONG" in modelin.params:
tc = SkyCoord(
modelin.ELONG.quantity,
modelin.ELAT.quantity,
frame="barycentrictrueecliptic",
)
else:
tc = SkyCoord(modelin.RAJ.quantity,
modelin.DECJ.quantity,
frame="icrs")
if args.ft2 is not None:
# Instantiate Fermi observatory once so it gets added to the observatory registry
get_satellite_observatory("Fermi", args.ft2)
# Read event file and return list of TOA objects
maxmjd = np.inf if (args.maxMJD is None) else float(args.maxMJD)
minmjd = 0.0 if (args.minMJD is None) else float(args.minMJD)
tl = load_Fermi_TOAs(
args.eventfile,
maxmjd=maxmjd,
minmjd=minmjd,
weightcolumn=args.weightcol,
targetcoord=tc,
)
# Now convert to TOAs object and compute TDBs and posvels
# For Fermi, we are not including GPS or TT(BIPM) corrections
ts = toa.get_TOAs_list(
tl,
include_gps=False,
include_bipm=False,
planets=args.planets,
ephem=args.ephem,
)
ts.filename = args.eventfile
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)
phss %= 1
phases = phss.value
mjds = ts.get_mjds()
weights = np.array([w["weight"] for w in ts.table["flags"]])
h = float(hmw(phases, weights))
print("Htest : {0:.2f} ({1:.2f} sigma)".format(h, h2sig(h)))
if args.plot:
log.info("Making phaseogram plot with {0} photons".format(len(mjds)))
phaseogram(mjds, phases, weights, 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)
event_hdu = hdulist[1]
event_hdr = event_hdu.header
event_dat = event_hdu.data
event_mjds = read_fits_event_mjds_tuples(event_hdu)
mjds_float = np.asarray([r[0] + r[1] for r in event_mjds])
time_mask = np.logical_and((mjds_float > minmjd),
(mjds_float < maxmjd))
new_phases = np.full(len(event_dat), -1, dtype=float)
new_phases[time_mask] = phases
if "PULSE_PHASE" in event_hdu.columns.names:
log.info("Found existing PULSE_PHASE column, overwriting...")
# Overwrite values in existing Column
event_dat["PULSE_PHASE"] = new_phases
else:
# Construct and append new column, preserving HDU header and name
log.info("Adding new PULSE_PHASE column.")
phasecol = pyfits.ColDefs([
pyfits.Column(name="PULSE_PHASE", format="D", array=new_phases)
])
bt = pyfits.BinTableHDU.from_columns(event_hdu.columns + phasecol,
header=event_hdr,
name=event_hdu.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")
return 0
def main(argv=None):
parser = argparse.ArgumentParser(description="Use PINT to compute H-test and plot Phaseogram from a Fermi FT1 event file.")
parser.add_argument("eventfile",help="Fermi event FITS file name.")
parser.add_argument("parfile",help="par file to construct model from")
parser.add_argument("weightcol",help="Column name for event weights (or 'CALC' to compute them)")
parser.add_argument("--ft2",help="Path to FT2 file.",default=None)
parser.add_argument("--addphase",help="Write FT1 file with added phase column",
default=False,action='store_true')
parser.add_argument("--plot",help="Show phaseogram plot.", action='store_true', default=False)
parser.add_argument("--plotfile",help="Output figure file name (default=None)", default=None)
parser.add_argument("--maxMJD",help="Maximum MJD to include in analysis", default=None)
parser.add_argument("--outfile",help="Output figure file name (default is to overwrite input file)", default=None)
parser.add_argument("--planets",help="Use planetary Shapiro delay in calculations (default=False)", default=False, action="store_true")
parser.add_argument("--ephem",help="Planetary ephemeris to use (default=DE421)", default="DE421")
args = parser.parse_args(argv)
# If outfile is specified, that implies addphase
if args.outfile is not None:
args.addphase = True
# Read in model
modelin = pint.models.get_model(args.parfile)
if 'ELONG' in modelin.params:
tc = SkyCoord(modelin.ELONG.quantity,modelin.ELAT.quantity,
frame='barycentrictrueecliptic')
else:
tc = SkyCoord(modelin.RAJ.quantity,modelin.DECJ.quantity,frame='icrs')
if args.ft2 is not None:
# Instantiate FermiObs once so it gets added to the observatory registry
FermiObs(name='Fermi',ft2name=args.ft2)
# Read event file and return list of TOA objects
tl = load_Fermi_TOAs(args.eventfile, weightcolumn=args.weightcol,
targetcoord=tc)
# 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))
# Now convert to TOAs object and compute TDBs and posvels
# For Fermi, we are not including GPS or TT(BIPM) corrections
ts = toa.get_TOAs_list(tl,include_gps=False,include_bipm=False,planets=args.planets,ephem=args.ephem)
ts.filename = args.eventfile
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
phases = np.where(phss < 0.0 * u.cycle, phss + 1.0 * u.cycle, phss)
mjds = ts.get_mjds()
weights = np.array([w['weight'] for w in ts.table['flags']])
h = float(hmw(phases,weights))
print("Htest : {0:.2f} ({1:.2f} sigma)".format(h,h2sig(h)))
if args.plot:
log.info("Making phaseogram plot with {0} photons".format(len(mjds)))
phaseogram(mjds,phases,weights,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)
event_hdu = hdulist[1]
event_hdr=event_hdu.header
event_dat=event_hdu.data
if len(event_dat) != len(phases):
raise RuntimeError('Mismatch between length of FITS table ({0}) and length of phase array ({1})!'.format(len(event_dat),len(phases)))
if 'PULSE_PHASE' in event_hdu.columns.names:
log.info('Found existing PULSE_PHASE column, overwriting...')
# Overwrite values in existing Column
event_dat['PULSE_PHASE'] = phases
else:
# Construct and append new column, preserving HDU header and name
log.info('Adding new PULSE_PHASE column.')
phasecol = pyfits.ColDefs([pyfits.Column(name='PULSE_PHASE', format='D',
array=phases)])
bt = pyfits.BinTableHDU.from_columns( event_hdu.columns + phasecol,
header=event_hdr,name=event_hdu.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')
return 0
def main(argv=None):
parser = argparse.ArgumentParser(
description=
"Use PINT to compute H-test and plot Phaseogram from a POLAR event file."
)
parser.add_argument("eventfile", help="Polar event root file name.")
parser.add_argument("parfile", help="par file to construct model from")
parser.add_argument("--wei",
help="Branch name for event weights",
default="")
parser.add_argument("--eng",
help="Path to ENG file.",
default="$POLAR_AUX/Alleng.root")
parser.add_argument("--addphase",
help="Add phase tree Friend",
default=False,
action='store_true')
parser.add_argument("--plot",
help="Show phaseogram plot.",
action='store_true',
default=False)
parser.add_argument("--plotfile",
help="Output figure file name (default=None)",
default=None)
parser.add_argument("--maxMJD",
help="Maximum MJD to include in analysis",
default=None)
parser.add_argument(
"--planets",
help="Use planetary Shapiro delay in calculations (default=False)",
default=False,
action="store_true")
parser.add_argument("--ephem",
help="Planetary ephemeris to use (default=DE421)",
default="DE421")
args = parser.parse_args(argv)
# Read in model
modelin = pint.models.get_model(args.parfile)
if 'ELONG' in modelin.params:
tc = SkyCoord(modelin.ELONG.quantity,
modelin.ELAT.quantity,
frame='barycentrictrueecliptic')
else:
tc = SkyCoord(modelin.RAJ.quantity,
modelin.DECJ.quantity,
frame='icrs')
if args.eng is not None:
# Instantiate PolarObs once so it gets added to the observatory registry
PolarObs(name='Polar', engname=args.eng)
# Read event file and return list of TOA objects
tl = load_Polar_TOAs(args.eventfile, weightcolumn=args.wei)
# 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))
# Now convert to TOAs object and compute TDBs and posvels
ts = toa.TOAs(toalist=tl)
ts.filename = args.eventfile
ts.compute_TDBs()
ts.compute_posvels(ephem=args.ephem, planets=args.planets)
print(ts.get_summary())
mjds = ts.get_mjds()
print(mjds.min(), mjds.max())
# Compute model phase for each TOA
phss = modelin.phase(ts.table)[1]
# ensure all postive
phases = np.where(phss < 0.0 * u.cycle, phss + 1.0 * u.cycle, phss)
mjds = ts.get_mjds()
weights = np.array([1] * len(mjds))
h = float(hmw(phases, weights))
print("Htest : {0:.2f} ({1:.2f} sigma)".format(h, h2sig(h)))
if args.plot:
log.info("Making phaseogram plot with {0} photons".format(len(mjds)))
phaseogram(mjds, phases, weights, bins=100, plotfile=args.plotfile)
if args.addphase:
if len(event_dat) != len(phases):
raise RuntimeError(
'Mismatch between length of ROOT tree ({0}) and length of phase array ({1})!'
.format(len(event_dat), len(phases)))
return 0
