def get_tempo2_result(parfile, timfile, general2=None):
"""This function is to get the results from tempo and write them to a file.
Parameter
---------
parfile : str
The file to read parameters.
timfile : str
The file to read toas.
general2 : list/ None
The values required from tempo2 general2 plugin.
Return
----------
A file named as parfile name ends with '.tempo2_test' stored residuals in the
first column, binary delay in the second column and general2 results if
general2 are provided.
"""
if not has_tempo2_utils:
raise ImportError(
"To get tempo2 general2 results, tempo2_utils are"
" required. See page"
" https://github.com/demorest/tempo_utils"
)
residuals = t2u.general2(parfile, timfile, ["pre"])["pre"]
outfile = parfile + ".tempo2_test"
f = open(outfile, "w")
outstr = "residuals "
if general2 is not None and general2 != []:
tempo2_vals = t2u.general2(parfile, timfile, general2)
for keys in general2:
outstr += keys + " "
outstr += "\n"
f.write(outstr)
for ii in range(len(residuals)):
outstr = longdouble2str(residuals[ii]) + " "
if general2 is not None:
for keys in general2:
outstr += longdouble2str(tempo2_vals[keys][ii]) + " "
outstr += "\n"
f.write(outstr)
f.close()
def get_tempo2_result(parfile, timfile, general2=None):
"""This function is to get the results from tempo and write them to a file.
Parameter
---------
parfile : str
The file to read parameters.
timfile : str
The file to read toas.
general2 : list/ None
The values required from tempo2 general2 plugin.
Return
----------
A file named as parfile name ends with '.tempo2_test' stored residuals in the
first column, binary delay in the second column and general2 results if
general2 are provided.
"""
if not has_tempo2_utils:
raise ImportError("To get tempo2 general2 results, tempo2_utils are"
" required. See page"
" https://github.com/demorest/tempo_utils")
residuals = t2u.general2(parfile, timfile, ['pre'])['pre']
outfile = parfile + '.tempo2_test'
f = open(outfile, 'w')
outstr = 'residuals '
if general2 is not None and general2 != []:
tempo2_vals = t2u.general2(parfile, timfile, general2)
for keys in general2:
outstr += keys+' '
outstr += '\n'
f.write(outstr)
for ii in range(len(residuals)):
outstr = longdouble2string(residuals[ii]) +' '
if general2 is not None:
for keys in general2:
outstr += longdouble2string(tempo2_vals[keys][ii])+' '
outstr += '\n'
f.write(outstr)
f.close()
def get_tempo2_result(parfile, timfile, general2=None):
"""This function is to get the results from tempo and write them to a file.
Parameter
---------
parfile : str
The file to read parameters.
timfile : str
The file to read toas.
general2 : list/ None
The values required from tempo2 general2 plugin.
Return
----------
A file named as parfile name ends with '.tempo2_test' stored residuals in the
first column, binary delay in the second column and general2 results if
general2 are provided.
"""
psr = lt.tempopulsar(parfile, timfile)
residuals = psr.residuals()
binary_delay = psr.binarydelay()
outfile = parfile + '.tempo2_test'
f = open(outfile, 'w')
outstr = 'residuals BinaryDelay '
if general2 is not None and general2 != []:
if not has_tempo2_utils:
raise ImportError("To get tempo2 general2 results, tempo2_utils are"
" required. See page"
" https://github.com/demorest/tempo_utils")
else:
tempo2_vals = t2u.general2(parfile, timfile, general2)
for keys in general2:
outstr += keys+' '
outstr += '\n'
f.write(outstr)
for ii in range(len(residuals)):
outstr = longdouble2string(residuals[ii]) + ' ' +longdouble2string(binary_delay[ii]) +' '
if general2 is not None:
for keys in general2:
outstr += longdouble2string(tempo2_vals[keys][ii])+' '
outstr += '\n'
f.write(outstr)
f.close()
import matplotlib.pyplot as plt
import tempo2_utils
import astropy.units as u
from pint.residuals import resids
import numpy as np
import os, unittest
import tempo2_utils
# Using Nanograv data B1855
datadir = '../tests/datafile'
parfile = os.path.join(datadir, 'B1855+09_NANOGrav_dfg+12_TAI_FB90.par')
timfile = os.path.join(datadir, 'B1855+09_NANOGrav_dfg+12.tim')
# libstempo calculation
print "tempo2 calculation"
tempo2_vals = tempo2_utils.general2(parfile, timfile, ['pre'])
# Build PINT model
print "PINT calculation"
mdd = mb.get_model(parfile)
# Get toas to pint
toas = toa.get_TOAs(timfile, planets=False, ephem='DE405')
tt = toas.table
# Get residuals
t2_resids = tempo2_vals['pre']
presids_us = resids(toas, mdd).time_resids
# Plot residuals
plt.errorbar(toas.get_mjds(high_precision=False),
presids_us.value,
toas.get_errors(),
fmt='x')
plt.title("%s Pre-Fit Timing Residuals" % mdd.PSR.value)
try:
import tempo2_utils
except ImportError:
log.error(
"This example requires tempo_utils, download from: https://github.com/demorest/tempo_utils and 'pip install .'"
)
raise
# Using Nanograv data J0623-0200
datadir = "../../tests/datafile"
parfile = os.path.join(datadir, "J0613-0200_NANOGrav_dfg+12_TAI_FB90.par")
timfile = os.path.join(datadir, "J0613-0200_NANOGrav_dfg+12.tim")
# libstempo calculation
print("tempo2 calculation")
tempo2_vals = tempo2_utils.general2(parfile, timfile, ["pre"])
# Build PINT model
print("PINT calculation")
m = mb.get_model(parfile)
# Get toas to pint
toas = toa.get_TOAs(timfile, planets=False, ephem="DE405", include_bipm=False)
t2_resids = tempo2_vals["pre"]
presids_us = resids(toas, m).time_resids.to(u.us)
# Plot residuals
plt.errorbar(toas.get_mjds().value,
presids_us.value,
toas.get_errors().value,
fmt="x")
plt.title("%s Pre-Fit Timing Residuals" % m.PSR.value)
plt.xlabel("MJD")
for ii, tt in enumerate(t.table):
p = m.phase(tt)
resids[ii] = p.frac
ss_roemer[ii] = m.solar_system_geometric_delay(tt)
ss_shapiro[ii] = m.solar_system_shapiro_delay(tt)
time_phase = time.time() - t0
sys.stderr.write("Computed phases in %.3f sec\n" % time_phase)
# resids in (approximate) us:
resids_us = resids / float(m.F0.value) * 1e6
sys.stderr.write("RMS PINT residuals are %.3f us\n" % resids_us.std())
# Get some general2 stuff
tempo2_vals = tempo2_utils.general2(parfile, timfile,
['tt2tb', 'roemer', 'post_phase',
'shapiro', 'shapiroJ'])
t2_resids = tempo2_vals['post_phase'] / float(m.F0.value) * 1e6
diff_t2 = resids_us - t2_resids
diff_t2 -= diff_t2.mean()
# run tempo1 also, if the tempo_utils module is available
try:
import tempo_utils
t1_toas = tempo_utils.read_toa_file(timfile)
tempo_utils.run_tempo(t1_toas, t1_parfile)
t1_resids = t1_toas.get_resids(units='phase') / float(m.F0.value) * 1e6
diff_t1 = resids_us - t1_resids
diff_t1 -= diff_t1.mean()
diff_t2_t1 = t2_resids - t1_resids
import matplotlib.pyplot as plt
import tempo2_utils
import astropy.units as u
from pint.residuals import resids
import numpy as np
import os, unittest
import tempo2_utils
# Using Nanograv data B1855
datadir = '../tests/datafile'
parfile = os.path.join(datadir, 'B1855+09_NANOGrav_dfg+12_TAI_FB90.par')
timfile = os.path.join(datadir, 'B1855+09_NANOGrav_dfg+12.tim')
# libstempo calculation
print "tempo2 calculation"
tempo2_vals = tempo2_utils.general2(parfile, timfile,['pre'])
# Build PINT model
print "PINT calculation"
mdd = mb.get_model(parfile)
# Get toas to pint
toas = toa.get_TOAs(timfile, planets=False, ephem='DE405')
tt = toas.table
# Get residuals
t2_resids = tempo2_vals['pre']
presids_us = resids(toas, mdd).time_resids
# Plot residuals
plt.errorbar(toas.get_mjds(high_precision=False), presids_us.value,
toas.get_errors(), fmt='x')
plt.title("%s Pre-Fit Timing Residuals" % mdd.PSR.value)
plt.xlabel('MJD')
plt.ylabel('Residual (us)')
datapath = os.path.join(os.environ['PINT'],'tests','datafile')
# Using Nanograv data B1855
parfile = os.path.join(datapath, 'B1855+09_NANOGrav_dfg+12_modified.par')
timfile = os.path.join(datapath, 'B1855+09_NANOGrav_dfg+12.tim')
# libstempo calculation
print "libstempo calculation"
psr = lt.tempopulsar(parfile, timfile)
# Build PINT model
print "PINT calculation"
mdd = mb.get_model(parfile)
# Get toas to pint
toas = toa.get_TOAs(timfile, planets=True)
tt = toas.table
# Run tempo2 general2 pluging
tempo2_vals = tempo2_utils.general2(parfile, timfile,
['tt2tb', 'roemer', 'post_phase',
'shapiro', 'shapiroJ','bat','clock0',
'clock1','clock2','clock3','clock4','sat',
'tropo'])
# compute residules
t2_resids = tempo2_vals['post_phase'] / float(mdd.F0.value) * 1e6 * u.us
presids_us = resids(toas, mdd).time_resids.to(u.us)
toas = psr.toas()
toas.sort()
plt.plot(toas,presids_us-t2_resids)
plt.xlabel('Mjd (DAY)')
plt.ylabel('residule (us)')
plt.title('Residule difference between PINT and tempo2')
plt.show()
for ii, tt in enumerate(t.table):
p = m.phase(tt)
resids[ii] = p.frac
ss_roemer[ii] = m.solar_system_geometric_delay(tt)
ss_shapiro[ii] = m.solar_system_shapiro_delay(tt)
time_phase = time.time() - t0
sys.stderr.write("Computed phases in %.3f sec\n" % time_phase)
# resids in (approximate) us:
resids_us = resids / float(m.F0.value) * 1e6
sys.stderr.write("RMS PINT residuals are %.3f us\n" % resids_us.std())
# Get some general2 stuff
tempo2_vals = tempo2_utils.general2(
parfile, timfile,
['tt2tb', 'roemer', 'post_phase', 'shapiro', 'shapiroJ'])
t2_resids = tempo2_vals['post_phase'] / float(m.F0.value) * 1e6
diff_t2 = resids_us - t2_resids
diff_t2 -= diff_t2.mean()
# run tempo1 also, if the tempo_utils module is available
try:
import tempo_utils
t1_toas = tempo_utils.read_toa_file(timfile)
tempo_utils.run_tempo(t1_toas, t1_parfile)
t1_resids = t1_toas.get_resids(units='phase') / float(m.F0.value) * 1e6
diff_t1 = resids_us - t1_resids
diff_t1 -= diff_t1.mean()
diff_t2_t1 = t2_resids - t1_resids