def get_optimal_cuts(data, pred_rate=0.017, usez=False):
""" Determine rates from analytic prediction for both 0.25 and 0.40 keV
cuts, and use these to estimate an optimal H test.
"""
pi_mask = (data[2] > 25) & (data[2] < 100)
sn, sn0, hs, ph_gti, gti_rts_s, gti_len_s = make_sn(data,
mask=pi_mask,
rate=pred_rate,
usez=usez)
amax = np.argmax(sn)
pi_mask = (data[2] > 40) & (data[2] < 100)
pred_rate *= 3. / 5
sn_40, sn0_40, hs_40, ph_gti_40, gti_rts_s_40, gti_len_s_40 = make_sn(
data, mask=pi_mask, rate=pred_rate, usez=usez)
if usez:
hsig_40 = sig2sigma(chi2.sf(hs, 4))
else:
hsig_40 = local_h2sig(hs)
exposure = np.cumsum(gti_len_s)
amax_40 = np.argmax(sn_40)
# get intersection of 0.25 keV data sets and 0.4 keV data sets
rate_025_cut = gti_rts_s[amax]
rate_040_cut = gti_rts_s_40[amax_40]
mask_025 = gti_rts_s <= rate_025_cut
mask_040 = ~mask_025 & (gti_rts_s_40 < rate_040_cut)
ph1 = np.concatenate(np.asarray(ph_gti)[mask_025])
try:
ph2 = np.concatenate(np.asarray(ph_gti_40)[mask_040])
except ValueError:
ph2 = np.asarray([])
print('Found %d photons satisfying 0.25 keV cut; exposure = %.1fs' %
(len(ph1), np.sum(np.asarray(gti_len_s)[mask_025])))
print('Found %d photons satisfying 0.40 keV cut; exposure = %.1fs' %
(len(ph2), np.sum(np.asarray(gti_len_s_40)[mask_040])))
if usez:
print('Z-test 1: %.2f' % z2m(ph1, m=2)[-1])
if len(ph2) > 0:
print('Z-test 2: %.2f' % z2m(ph2, m=2)[-1])
else:
print('Z-test 2: no photons!')
print('Z-test joint: %.2f' % z2m(np.append(ph1, ph2), m=2)[-1])
else:
print('H-test 1: %.2f' % hm(ph1))
if len(ph2) > 0:
print('H-test 2: %.2f' % hm(ph2))
else:
print('H-test 2: no photons!')
print('H-test joint: %.2f' % hm(np.append(ph1, ph2)))
def prof_vs_weights(self, nbins=50, use_weights=False):
"""
Show binned profiles (and H-test values) as a function
of the minimum weight used. nbins is only for the plots.
"""
f, ax = plt.subplots(3, 3, sharex=True)
phss = self.get_event_phases()
htests = []
weights = np.linspace(0.0, 0.95, 20)
swgts = self.get_weights()
for ii, minwgt in enumerate(weights):
good = swgts > minwgt
nphotons = np.sum(good)
wgts = swgts[good] if use_weights else None
if nphotons <= 0:
hval = 0
else:
if use_weights:
hval = hmw(phss[good], weights=wgts)
else:
hval = hm(phss[good])
htests.append(hval)
if ii > 0 and ii % 2 == 0 and ii < 20:
r, c = ((ii - 2) / 2) / 3, ((ii - 2) / 2) % 3
ax[r][c].hist(
phss[good],
nbins,
range=[0, 1],
weights=wgts,
color="k",
histtype="step",
)
ax[r][c].set_title("%.1f / %.1f / %.0f" %
(minwgt, hval, nphotons),
fontsize=11)
if c == 0:
ax[r][c].set_ylabel("Htest")
if r == 2:
ax[r][c].set_xlabel("Phase")
f.suptitle(
"%s: Minwgt / H-test / Approx # events" %
self.model.PSR.value,
fontweight="bold",
)
if use_weights:
plt.savefig(self.model.PSR.value + "_profs_v_wgtcut.png")
else:
plt.savefig(self.model.PSR.value +
"_profs_v_wgtcut_unweighted.png")
plt.close()
plt.plot(weights, htests, "k")
plt.xlabel("Min Weight")
plt.ylabel("H-test")
plt.title(self.model.PSR.value)
if use_weights:
plt.savefig(self.model.PSR.value + "_htest_v_wgtcut.png")
else:
plt.savefig(self.model.PSR.value +
"_htest_v_wgtcut_unweighted.png")
plt.close()
def test_h_and_z():
phases = np.linspace(0, 1, 101)
weights = np.zeros(101)
weights[:50] = 1
ans = 0.01980198019801975
res = es.hm(phases)
assert_allclose(res, ans, atol=1.0e-7)
ans = 40.54180942257532
res = es.hmw(phases, weights)
assert_allclose(res, ans, atol=1.0e-7)
res = es.z2m(phases, m=4)
assert len(res) == 4
ans = 0.0792079207920788
assert_allclose(res[3], ans, atol=1.0e-7)
ans = 40.54180942257532
res = es.hmw(phases, weights)
assert_allclose(res, ans, atol=1.0e-7)
res = es.z2mw(phases, weights, m=4)
assert len(res) == 4
ans = 45.05833019383544
assert_allclose(res[3], ans, atol=1.0e-7)
def pulse_profile(ax, etable, args):
if (args.orb is None) or (args.par is None):
log.warning('You did not specify orbfile or parfile')
log.info('Please input files for orb and par with --orb and --par')
return
import pint
import astropy.io.fits as pyfits
import pint.toa, pint.models
from pint.plot_utils import phaseogram_binned
from pint.observatory.nicer_obs import NICERObs
from pint.eventstats import hm
### Make arguments for parfile and orbfile and only do this if both are present
log.info('Event file TELESCOPE = {0}, INSTRUMENT = {1}'.format(
etable.meta['TELESCOP'], etable.meta['INSTRUME']))
# Instantiate NICERObs once so it gets added to the observatory registry
log.info('Setting up NICER observatory')
NICERObs(name='NICER', FPorbname=args.orb, tt2tdb_mode='none')
# Read event file and return list of TOA objects
log.info('doing the load_toas thing')
#tl = load_NICER_TOAs(pulsefilename[0])
# Create TOA list
tl = []
for t in etable['T']:
tl.append(pint.toa.TOA(t, obs='NICER'))
ts = pint.toa.TOAs(toalist=tl)
ts.compute_TDBs()
ts.compute_posvels(ephem='DE421', planets=True)
log.info('Did all the stuff, now to PARFILE')
# Load PINT model objects
modelin = pint.models.get_model(args.par)
log.info(str(modelin))
# Compute phases
phss = modelin.phase(ts.table)[1]
# Strip the units, because PINT may return u.cycle
phss = np.array(phss)
# ensure all postive
phases = np.where(phss < 0.0, phss + 1.0, phss)
mjds = ts.get_mjds()
h = hm(phases)
log.info("H = {0} from {1} phases".format(h, len(phases)))
ax.hist(phases, bins=32)
ax.text(0.1, 0.1, 'H = {0:.2f}'.format(h), transform=ax.transAxes)
#np.savetxt('{0}.phases'.format(args.basename),np.transpose([etable['MET'], etable['PI'],phases]))
plot.ylabel('Counts')
plot.xlabel('Pulse Phase')
plot.title('Pulse Profile')
return
def prof_vs_weights(self, nbins=50, use_weights=False):
"""
Show binned profiles (and H-test values) as a function
of the minimum weight used. nbins is only for the plots.
"""
global ftr
f, ax = plt.subplots(3, 3, sharex=True)
phss = ftr.get_event_phases()
htests = []
weights = np.linspace(0.0, 0.95, 20)
for ii, minwgt in enumerate(weights):
good = ftr.weights > minwgt
nphotons = np.sum(good)
wgts = ftr.weights[good] if use_weights else None
if nphotons <= 0:
hval = 0
else:
if use_weights:
hval = hmw(phss[good], weights=wgts)
else:
hval = hm(phss[good])
htests.append(hval)
if ii > 0 and ii%2==0 and ii<20:
r, c = ((ii-2)/2)/3, ((ii-2)/2)%3
ax[r][c].hist(phss[good], nbins, range=[0,1],
weights=wgts, color='k',
histtype='step')
ax[r][c].set_title("%.1f / %.1f / %.0f" %
(minwgt, hval, nphotons),
fontsize=11)
if c==0: ax[r][c].set_ylabel("Htest")
if r==2: ax[r][c].set_xlabel("Phase")
f.suptitle("%s: Minwgt / H-test / Approx # events" %
self.model.PSR.value, fontweight='bold')
if use_weights:
plt.savefig(ftr.model.PSR.value+"_profs_v_wgtcut.png")
else:
plt.savefig(ftr.model.PSR.value+"_profs_v_wgtcut_unweighted.png")
plt.close()
plt.plot(weights, htests, 'k')
plt.xlabel("Min Weight")
plt.ylabel("H-test")
plt.title(self.model.PSR.value)
if use_weights:
plt.savefig(ftr.model.PSR.value+"_htest_v_wgtcut.png")
else:
plt.savefig(ftr.model.PSR.value+"_htest_v_wgtcut_unweighted.png")
plt.close()
def _hist_setup(self):
""" Setup data for chi-squared and binned likelihood."""
h = hm(self.phases)
nbins = 25
if h > 100: nbins = 50
if h > 1000: nbins = 100
ph0,ph1 = 0+self.phase_shift,1+self.phase_shift
hist = np.histogram(self.phases,bins=np.linspace(ph0,ph1,nbins))
if len(hist[0])==nbins: raise ValueError,'Histogram too old!'
x = ((hist[1][1:] + hist[1][:-1])/2.)[hist[0]>0]
counts = (hist[0][hist[0]>0]).astype(float)
y = counts / counts.sum() * nbins
yerr = counts**0.5 / counts.sum() * nbins
self.chistuff = x,y,yerr
# now set up binning for binned likelihood
nbins = self.binned_bins+1
hist = np.histogram(self.phases,bins=np.linspace(ph0,ph1,nbins))
self.counts_centers = ((hist[1][1:] + hist[1][:-1])/2.)[hist[0]>0]
self.counts = hist[0][hist[0]>0]
def _hist_setup(self):
""" Setup data for chi-squared and binned likelihood."""
h = hm(self.phases)
nbins = 25
if h > 100: nbins = 50
if h > 1000: nbins = 100
ph0, ph1 = 0 + self.phase_shift, 1 + self.phase_shift
hist = np.histogram(self.phases, bins=np.linspace(ph0, ph1, nbins))
if len(hist[0]) == nbins: raise ValueError('Histogram too old!')
x = ((hist[1][1:] + hist[1][:-1]) / 2.)[hist[0] > 0]
counts = (hist[0][hist[0] > 0]).astype(float)
y = counts / counts.sum() * nbins
yerr = counts**0.5 / counts.sum() * nbins
self.chistuff = x, y, yerr
# now set up binning for binned likelihood
nbins = self.binned_bins + 1
hist = np.histogram(self.phases, bins=np.linspace(ph0, ph1, nbins))
self.counts_centers = ((hist[1][1:] + hist[1][:-1]) / 2.)[hist[0] > 0]
self.counts = hist[0][hist[0] > 0]
def main(argv=None):
import argparse
parser = argparse.ArgumentParser(
description=
"Use PINT to compute event phases and make plots of photon event files.",
formatter_class=argparse.ArgumentDefaultsHelpFormatter,
)
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("--minMJD",
help="Minimum MJD to include in analysis",
default=None)
parser.add_argument("--plotfile",
help="Output figure file name",
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")
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(
"--log-level",
type=str,
choices=("TRACE", "DEBUG", "INFO", "WARNING", "ERROR"),
default="WARNING",
help="Logging level",
dest="loglevel",
)
# parser.add_argument("--fix",help="Apply 1.0 second offset for NICER", action='store_true', default=False)
parser.add_argument(
"--polycos",
default=False,
action="store_true",
help=
"Use polycos to calculate phases; use when working with very large event files",
)
args = parser.parse_args(argv)
log.remove()
log.add(
sys.stderr,
level=args.loglevel,
colorize=True,
format=pint.logging.format,
filter=pint.logging.LogFilter(),
)
# 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
# set MJD ranges
maxmjd = np.inf if (args.maxMJD is None) else float(args.maxMJD)
minmjd = 0.0 if (args.minMJD is None) else float(args.minMJD)
# 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"]))
telescope = hdr["TELESCOP"].lower()
# Instantiate observatory once so it gets added to the observatory registry
if args.orbfile is not None:
log.info(f"Setting up {telescope.upper()} observatory")
try:
get_satellite_observatory(telescope, args.orbfile)
except Exception:
log.error(
"The orbit file is not recognized. It is likely that this mission is not supported. "
"Please barycenter the event file using the official mission tools before processing with PINT"
)
# Read event file and return list of TOA objects, if not using polycos
if args.polycos == False:
try:
tl = load_event_TOAs(args.eventfile,
telescope,
minmjd=minmjd,
maxmjd=maxmjd)
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)
# 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.")
# Use polycos to calculate pulse phases
if args.polycos:
log.info("Using polycos to get pulse phases.")
if args.addorbphase:
raise ValueError("Cannot use orbphase with polycos.")
# Polycos parameters
segLength = 120 # in minutes
ncoeff = 10
obsfreq = 0
# Open event file and get start and end mjds
hdulist = pyfits.open(args.eventfile)
data = hdulist[1].data
mjds = read_fits_event_mjds(hdulist[1])
minmjd = min(mjds)
maxmjd = max(mjds)
# Check if event file is barycentered
if hdulist[1].header["TIMESYS"] != "TDB":
raise ValueError(
"The event file has not been barycentered. Polycos can only be used with barycentered data."
)
# Create polycos table
log.debug("Generating polycos")
telescope_n = "@"
p = polycos.Polycos()
ptable = p.generate_polycos(modelin, minmjd, maxmjd, telescope_n,
segLength, ncoeff, obsfreq)
# Calculate phases
log.debug("Evaluating polycos")
phases = p.eval_phase(mjds)
phases[phases < 0] += 1.0
h = float(hm(phases))
print("Htest : {0:.2f} ({1:.2f} sigma)".format(h, h2sig(h)))
else: # Normal mode, not polycos
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)
phases = phss.value % 1
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=int)
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 = {}
# Handle case where minMJD/maxMJD do not exceed length of events
mjds_float = read_fits_event_mjds(hdulist[1])
time_mask = np.logical_and((mjds_float > minmjd),
(mjds_float < maxmjd))
if args.polycos:
time_mask = np.logical_and((mjds_float >= minmjd),
(mjds_float <= maxmjd))
if args.addphase:
if time_mask.sum() != len(phases):
raise RuntimeError(
"Mismatch between data selection {0} and length of phase array ({1})!"
.format(time_mask.sum(), len(phases)))
data_to_add["PULSE_PHASE"] = [phases, "D"]
if args.absphase:
data_to_add["ABS_PHASE"] = [iphss, "K"]
if args.barytime:
bats = modelin.get_barycentric_toas(ts)
data_to_add["BARY_TIME"] = [bats, "D"]
if args.addorbphase:
if time_mask.sum() != len(orbphases):
raise RuntimeError(
"Mismatch between data selection ({0}) and length of orbital phase array ({1})!"
.format(time_mask.sum(), 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][time_mask] = data_to_add[key][0]
else:
# Construct and append new column, preserving HDU header and name
log.info("Adding new %s column." % key)
new_dat = np.full(time_mask.shape,
-1,
dtype=data_to_add[key][0].dtype)
new_dat[time_mask] = data_to_add[key][0]
datacol.append(
pyfits.ColDefs([
pyfits.Column(name=key,
format=data_to_add[key][1],
array=new_dat)
]))
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("--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")
parser.add_argument("--plot",help="Show phaseogram plot.", 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='none')
# 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='none')
# 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)
else:
log.error("FITS file not recognized, TELESCOPE = {0}, INSTRUMENT = {1}".format(
hdr['TELESCOP'], hdr['INSTRUME']))
sys.exit(1)
# Read in model
modelin = pint.models.get_model(args.parfile)
# Discard SS Shapiro part if specified in ephemeris and not enabled
if (not args.planets) and (
'SolarSystemShapiro' in modelin.components.keys()):
log.info(
"Removing SS Shapiro component from model (planets=False).")
components = modelin.components
components.pop('SolarSystemShapiro')
modelin.setup_components(components.values())
# 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
iphss,phss = modelin.phase(ts.table)
# 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:
tdbs = np.asarray([t.mjd for t in ts.table['tdb']])
data_to_add['BARY_TIME'] = [tdbs,'D']
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 = pyfits.ColDefs([pyfits.Column(name=key,
format=data_to_add[key][1], array=data_to_add[key][0])])
bt = pyfits.BinTableHDU.from_columns(
hdulist[1].columns + datacol, 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(
"--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")
) # TT topocentric MJDs as floats; only used to find the index of the photon time closest to the middle of the MJD range
# Compute model phase for each TOA;
phss = modelin.phase(ts, abs_phase=True)[1].value # discard units
# Note that you can compute barycentric TOAs from topocentric data, so
# just because topo is False does NOT mean that data are barycentered!
if barydata:
ph_times = ts.table["tdb"]
else:
ph_times = ts.table["mjd"]
# ensure all positive
phases = np.where(phss < 0.0, 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)
# get exposure information
try:
f = pyfits.open(args.eventname)
exposure = f[1].header["exposure"]
f.close()
except:
exposure = 0
if args.grid > 0.0:
mets = np.asarray([t.met for t in tl])
dT = args.grid
#print(ts.get_summary())
mjds = ts.get_mjds(
) # TT topocentric MJDs as floats; only used to find the index of the photon time closest to the middle of the MJD range
# Compute model phase for each TOA;
#(TODO--'tdbs' var. needs to be renamed since it's TT and not TDB for the topocentric photon times in the if block)
phss = modelin.phase(ts, abs_phase=True)[1].value # discard units
if args.topo:
tdbs = ts.table['mjd']
else:
tdbs = ts.table['tdb']
# ensure all positive
phases = np.where(phss < 0.0, 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)
# get exposure information
try:
f = pyfits.open(args.eventname)
exposure = f[1].header['exposure']
f.close()
except:
exposure = 0
def estimate_toa(mjds, phases, tdbs, topo, obs):
""" Return a pint TOA object for the provided times and phases."""
def pulse_profile(ax, etable, args):
if (args.orb is None) or (args.par is None):
log.warning('You did not specify orbfile or parfile')
log.info('Please input files for orb and par with --orb and --par')
return
import pint
import astropy.io.fits as pyfits
from astropy.time import TimeDelta
import pint.toa, pint.models
from pint.plot_utils import phaseogram_binned
from pint.observatory.nicer_obs import NICERObs
from pint.eventstats import hm
### Make arguments for parfile and orbfile and only do this if both are present
log.info('Event file TELESCOPE = {0}, INSTRUMENT = {1}'.format(
etable.meta['TELESCOP'], etable.meta['INSTRUME']))
# Instantiate NICERObs once so it gets added to the observatory registry
log.info('Setting up NICER observatory')
NICERObs(name='NICER', FPorbname=args.orb)
log.info('Reading model from PARFILE')
# Load PINT model objects
modelin = pint.models.get_model(args.par)
log.info(str(modelin))
# Read event file and return list of TOA objects
log.info('doing the load_toas thing')
#tl = load_NICER_TOAs(pulsefilename[0])
# Create TOA list
tl = []
for t in etable['T']:
tl.append(pint.toa.TOA(t, obs='NICER'))
planets = False
if 'PLANET_SHAPIRO' in modelin.params:
if modelin.PLANET_SHAPIRO.value:
planets = True
ts = pint.toa.get_TOAs_list(tl,
planets=planets,
include_bipm=False,
include_gps=False)
# No longer needed, since Feb 28 reprocessing
# log.warning('Applying -1.0s time correction to event time TOAs for pulse phase plot')
# ts.adjust_TOAs(TimeDelta(np.ones(len(ts.table))*-1.0*u.s,scale='tt'))
# Note: adjust_TOAs recomputes TDBs and posvels so no need to do again.
# ts.compute_TDBs()
# ts.compute_posvels(ephem='DE421',planets=True)
# Compute phases
phss = modelin.phase(ts, abs_phase=True)[1]
# Strip the units, because PINT may return u.cycle
phss = np.array(phss)
# ensure all postive
phases = np.where(phss < 0.0, phss + 1.0, phss)
mjds = ts.get_mjds()
h = hm(phases)
if not np.isfinite(h):
log.error("H not finite, using {0} phases!".format(len(phases)))
print("Phases from {0} to {1}\n".format(h.min(), h.max()))
else:
log.info("H = {0} from {1} phases".format(h, len(phases)))
ax.hist(phases, bins=32)
ax.text(0.1, 0.1, 'H = {0:.2f}'.format(h), transform=ax.transAxes)
#np.savetxt('{0}.phases'.format(args.basename),np.transpose([etable['MET'], etable['PI'],phases]))
plot.ylabel('Counts')
plot.xlabel('Pulse Phase')
plot.title('Pulse Profile')
return
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')
for ef in args.evfiles:
tlist = []
for fn in args.evfiles:
log.info('Reading file {0}'.format(fn))
tlist.append(Table.read(fn, hdu=1))
log.info('Concatenating files')
if len(tlist) == 1:
etable = tlist[0]
else:
etable = vstack(tlist, metadata_conflicts='silent')
del tlist
phasesinitial = etable['PULSE_PHASE']
hbest = hm(phasesinitial)
eminbest = 0.0
emaxbest = 100.0
print("Initial Htest = {0}".format(hbest))
emins = np.arange(0.4, 4.0, 0.1)
for emin in emins:
emaxs = np.arange(emin, 12.0, 0.1)
for emax in emaxs:
idx = np.where(
np.logical_and(etable['PI'] * PI_TO_KEV > emin,
etable['PI'] * PI_TO_KEV < emax))[0]
phases = etable['PULSE_PHASE'][idx]
if len(phases) == 0:
continue
h = hm(phases)
print('Ignoring file {0} with good time {1:0.2f}.'.format(
fn, good_time))
continue
tlist.append(t)
log.info('Concatenating files')
if len(tlist) == 1:
etable = tlist[0]
else:
etable = vstack(tlist, metadata_conflicts='silent')
del tlist
m = args.maxharm
ts_func = cached_zm if args.ztest else cached_hm
phasesinitial = etable['PULSE_PHASE'].astype(np.float32)
hbest = z2m(phasesinitial, m=m)[-1] if args.ztest else hm(phasesinitial, m=m)
eminbest = 0.0
emaxbest = 100.0
ts_name = "Ztest" if args.ztest else "Htest"
if args.ztest:
print("Initial {0} = {1}".format(ts_name, np.round(hbest, 3)))
else:
print("Initial {0} = {1} ({2} sigma)".format(ts_name, np.round(hbest, 3),
np.round(h2sig(hbest), 3)))
# assemble cache
cache = np.empty([m, 2, len(phasesinitial)], dtype=np.float32)
for i in xrange(m):
cache[i, 0] = np.cos(phasesinitial * (2 * np.pi * (i + 1)))
cache[i, 1] = np.sin(phasesinitial * (2 * np.pi * (i + 1)))
cached_hm._cache = cached_zm._cache = cache
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')
#print(ts.get_summary())
mjds = ts.get_mjds(
) # TT topocentric MJDs as floats; only used to find the index of the photon time closest to the middle of the MJD range
# Compute model phase for each TOA;
#(TODO--'tdbs' var. needs to be renamed since it's TT and not TDB for the topocentric photon times in the if block)
phss = modelin.phase(ts, abs_phase=True)[1].value # discard units
if args.topo:
tdbs = ts.table['mjd']
else:
tdbs = ts.table['tdb']
# ensure all positive
phases = np.where(phss < 0.0, 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)
# get exposure information
try:
f = pyfits.open(args.eventname)
exposure = f[1].header['exposure']
f.close()
except:
exposure = 0
def estimate_toa(mjds, phases, tdbs, topo, obs):
""" Return a pint TOA object for the provided times and phases."""
help="Output file for plot (type determined by extension)",
default=None)
args = parser.parse_args()
hdulist = pyfits.open(args.evtfile)
dat = hdulist[1].data
hdr = hdulist[1].header
ph = dat['PULSE_PHASE']
try:
print("Z test = {} ({} sig)".format(
z2m(ph)[-1], sig2sigma(sf_z2m(z2m(ph)[-1], lo))))
except:
pass
print("H test = {} ({} sig)".format(hm(ph), h2sig(hm(ph))))
fig, ax = plt.subplots(figsize=(8, 4.5))
h, edges = np.histogram(ph,
bins=np.linspace(0.0, 1.0, args.nbins, endpoint=True))
try:
if hdr['EXPOSURE'] > 0:
h = np.array(h,
dtype=np.float) / (np.float(hdr['EXPOSURE']) / args.nbins)
rates = True
except:
rates = False
ax.step(np.concatenate((edges[:-1], 1.0 + edges)),
np.concatenate((h, h, np.array(h[-1:]))),
where='post')