def test_set_params(lines, param, value):
model = get_model(io.StringIO("\n".join([par_base] + lines)))
with pytest.raises(KeyError) as e:
model[param].value = value
str(e.value).index(param) # raise exception if not found
with pytest.raises(AttributeError) as e:
getattr(model, param).value = value
str(e.value).index(param) # raise exception if not found
def test_change_dmepoch():
parfile = os.path.join(datadir, "J2229+2643_dm1.par")
model = models.get_model(parfile)
t0 = Time(56000, scale="tdb", format="mjd")
epoch_diff = (t0.mjd_long - model.DMEPOCH.quantity.mjd_long) * u.day
DM_at_t0 = model.DM.quantity + model.DM1.quantity * epoch_diff.to(u.s)
model.change_dmepoch(t0)
assert np.abs(model.DM.quantity - DM_at_t0) < 1e-8 * u.pc / u.cm ** 3
def test_copy_model_object(self):
model = get_model("J1614-2230_NANOGrav_12yv3.wb.gls.par")
model_copy = copy.deepcopy(model)
assert sys.getsizeof(model) == sys.getsizeof(model_copy)
assert id(model) != id(model_copy)
assert len(model.params) == len(model_copy.params)
assert list(model.components.keys()) == list(model_copy.components.keys())
def get_pint_models(psr_name, psr_file_path):
"""Function that returns pint model given a specific pulsar"""
# will need to add section for J1713 T2 file. gls is not file wanted for this specfic pulsar.
model_name = "{0}{1}_NANOGrav_11yv1.gls.par".format(
psr_file_path, psr_name)
par_model = models.get_model(model_name)
return par_model
def test_dm_barycentered():
model = get_model(io.StringIO(par_base))
toas = make_fake_toas(57000, 57900, 10, model, obs="@", freq=np.inf)
model.free_params = ["F0", "DM"]
fitter = pint.fitter.WLSFitter(toas, model)
with pytest.warns(pint.fitter.DegeneracyWarning,
match=".*degeneracy.*DM.*"):
fitter.fit_toas()
def test_A1DOT():
"""Should get changed to XDOT for TEMPO/TEMPO2"""
m = get_model(os.path.join(datadir, "J1600-3053_test.par"))
assert (("A1DOT" in m.as_parfile()) and not ("XDOT" in m.as_parfile())
and not ("A1DOT" in m.as_parfile(format="tempo"))
and ("XDOT" in m.as_parfile(format="tempo"))
and not ("A1DOT" in m.as_parfile(format="tempo2"))
and ("XDOT" in m.as_parfile(format="tempo2")))
def test_MODE1():
"""Should start TEMPO2"""
m = get_model(os.path.join(datadir, "B1855+09_NANOGrav_dfg+12_TAI.par"))
assert (not (m.as_parfile(include_info=False).startswith("MODE 1"))
and not (m.as_parfile(include_info=False,
format="tempo").startswith("MODE 1"))
and (m.as_parfile(include_info=False,
format="tempo2").startswith("MODE 1")))
def test_DMDATA_N():
"""Should be an integer for TEMPO/TEMPO2"""
m = get_model(os.path.join(datadir, "J0030+0451_post.par"))
for l in m.as_parfile(format="tempo").split("\n"):
if "DMDATA" in l:
# this should be a 0
dmdata = int(l.split()[-1])
assert dmdata == 0
def setUpClass(self):
self.parfileJ1853 = "J1853+1303_NANOGrav_11yv0.gls.par"
self.timfileJ1853 = "J1853+1303_NANOGrav_11yv0.tim"
self.toasJ1853 = toa.get_TOAs(self.timfileJ1853,
ephem="DE421",
planets=False)
self.modelJ1853 = model.get_model(self.parfileJ1853)
self.ltres, self.ltbindelay = np.genfromtxt(self.parfileJ1853 + \
'.tempo2_test',skip_header=1, unpack=True)
self.parfileJ0613 = "J0613-0200_NANOGrav_9yv1_ELL1H.gls.par"
self.timfileJ0613 = "J0613-0200_NANOGrav_9yv1.tim"
self.modelJ0613 = model.get_model(self.parfileJ0613)
self.toasJ0613 = toa.get_TOAs(self.timfileJ0613,
ephem="DE421",
planets=False)
self.parfileJ0613_STIG = "J0613-0200_NANOGrav_9yv1_ELL1H_STIG.gls.par"
self.modelJ0613_STIG = model.get_model(self.parfileJ0613_STIG)
def test_unset_other_epochs_dm1(caplog):
caplog.set_level(logging.WARNING)
with warnings.catch_warnings():
warnings.simplefilter("error")
m = models.get_model(io.StringIO("\n".join([test_par, "DM1 1e-10"])))
assert m.PEPOCH.quantity is not None
assert m.DMEPOCH.quantity == m.PEPOCH.quantity
assert m.POSEPOCH.quantity is None
assert not caplog.records
def test_solar_wind_delays_positive():
model = get_model(StringIO("\n".join([par, "NE_SW 1"])))
toas = make_fake_toas_uniform(54000,
54000 + year,
13,
model=model,
obs="gbt")
assert np.all(
model.components["SolarWindDispersion"].solar_wind_dm(toas) > 0)
def test_merge_indices():
m = get_model(StringIO(simplepar))
fakes = [
toa.make_fake_toas(55000, 55500, 5, model=m, obs="ao"),
toa.make_fake_toas(56000, 56500, 10, model=m, obs="gbt"),
toa.make_fake_toas(57000, 57500, 15, model=m, obs="@"),
]
toas = toa.merge_TOAs(fakes)
assert len(set(toas.table["index"])) == len(toas)
def test_unused_noise_model_parameter(param, value):
model = get_model(io.StringIO("\n".join([par_base, f"{param} TEL ao {value}"])))
toas = make_fake_toas_uniform(
58000, 58900, 10, model, obs="barycenter", freq=np.inf
)
model.free_params = ["F0"]
fitter = pint.fitter.GLSFitter(toas, model)
with pytest.warns(UserWarning, match=param):
fitter.fit_toas()
def test_H3_and_H4_non_zero(toasJ0613):
"""Testing if the different H3, H4 combination breaks the fitting. the
fitting result will not be checked here.
"""
simple_model = get_model(StringIO(simple_par))
test_toas = toasJ0613[::20]
f = ff.WLSFitter(test_toas, simple_model)
f.fit_toas()
def test_unset_other_epochs(caplog, par):
caplog.set_level(logging.WARNING)
with warnings.catch_warnings():
warnings.simplefilter("error")
m = models.get_model(io.StringIO(par))
assert m.PEPOCH.quantity is not None
assert m.DMEPOCH.quantity is None
assert m.POSEPOCH.quantity is None
assert not caplog.records
def test_zero_H4(toasJ0613):
H4_zero_model = get_model(StringIO(simple_par))
H4_zero_model.H4.value = 0.0
H4_zero_model.H4.frozen = False
assert H4_zero_model.H3.value != 0.0
H4_zero_model.H3.frozen = False
test_toas = toasJ0613[::20]
f = ff.WLSFitter(test_toas, H4_zero_model)
f.fit_toas()
def test_zero_H3(toasJ0613):
H3_zero_model = get_model(StringIO(simple_par))
H3_zero_model.H3.value = 0.0
H3_zero_model.H3.frozen = False
assert H3_zero_model.H4.value != 0.0
H3_zero_model.H4.frozen = False
test_toas = toasJ0613[::20]
with pytest.raises(ValueError):
ff.WLSFitter(test_toas, H3_zero_model)
def _gen_polyco(self, parfile, MJD_start, segLength = 60.0, ncoeff = 15, \
maxha=12.0, method="TEMPO", numNodes=20, usePINT = True):
"""
This will be a convenience function to generate polycos and subsequent parameters to replace the values in a
PSRFITS file header. The default way to do this will be to use PINT (usePINT = True), with other methods
currently unsupported. The input values are:
parfile [string] : path to par file used to generate the polycos. The observing frequency, and observatory will
come from the par file
MJD_start [float] : Start MJD of the polyco. Should start no later than the beginning of the observation
segLength [float] : Length in minutes of the range covered by the polycos generated. Default is 60 minutes
ncoeff [int] : number of polyco coeffeicients to generate. Default is 15, the same as in the PSRFITS file
maxha [float] : max hour angle needed by PINT. Default is 12.0
method [string] : Method PINT uses to generate the polyco. Currently only TEMPO is supported.
numNodes [int] : Number of nodes PINT will use to fit the polycos. Must be larger than ncoeff
usePINT [bool] : Method used to generate polycos. Currently only PINT is supported.
"""
if usePINT:
# Define dictionary to put parameters into
polyco_dict = {'NSPAN': segLength, 'NCOEF': ncoeff}
# load parfile to PINT model object
m = models.get_model(parfile)
# Determine MJD_end based on segLength
MJD_end = MJD_start + np.double(
make_quant(segLength, 'min').to('day').value) # MJD
# Determine obseratory and observing frequency
obsFreq = m.TZRFRQ.value # in MHz
polyco_dict['REF_FREQ'] = obsFreq
obs = m.TZRSITE.value # string
polyco_dict['NSITE'] = obs.encode(
'utf-8') # observatory code needs to be in binary
# Get pulsar frequency
polyco_dict['REF_F0'] = m.F0.value
# get the polycos
pcs = polycos.Polycos()
pcs.generate_polycos(m, MJD_start, MJD_end, obs, segLength, ncoeff, obsFreq, maxha=12.0, method="TEMPO", \
numNodes=20)
coeffs = pcs.polycoTable['entry'][-1].coeffs
polyco_dict['COEFF'] = coeffs
# Now we need to determine the reference MJD, and phase
REF_MJD = np.double(pcs.polycoTable['tmid'][-1])
polyco_dict['REF_MJD'] = REF_MJD
# Now find the phase difference
tmid_toa = toa.get_TOAs_list(
[toa.TOA(REF_MJD, obs=obs, freq=obsFreq)])
ref_phase = m.phase(tmid_toa)
# Need to force positive value
if ref_phase.frac.value[0] < 0.0:
ref_frac_phase = 1.0 - abs(ref_phase.frac.value[0])
else:
ref_frac_phase = ref_phase.frac.value[0]
polyco_dict['REF_PHS'] = ref_frac_phase
return polyco_dict
else:
print("Only PINT is currently supported for generating polycos")
raise NotImplementedError()
def test_merge_indices():
m = get_model(StringIO(simplepar))
fakes = [
toa.make_fake_toas(55000, 55500, 5, model=m, obs="ao"),
toa.make_fake_toas(56000, 56500, 10, model=m, obs="gbt"),
toa.make_fake_toas(57000, 57500, 15, model=m, obs="@"),
]
toas = toa.merge_TOAs(fakes)
check_indices_contiguous(toas)
def test_renumber_subset():
m = get_model(StringIO(simplepar))
toas = toa.make_fake_toas(55000, 55500, 10, model=m, obs="ao")
sub = toas[1:-1]
assert 0 not in sub.table["index"]
sub.renumber()
assert np.all(sub.table["index"] == np.arange(len(sub)))
def test_STIGMA():
"""Should get changed to VARSIGMA for TEMPO/TEMPO2"""
m = get_model(
os.path.join(datadir, "J0613-0200_NANOGrav_9yv1_ELL1H_STIG.gls.par"))
assert (("STIGMA" in m.as_parfile()) and not ("VARSIGMA" in m.as_parfile())
and not ("STIGMA" in m.as_parfile(format="tempo"))
and ("VARSIGMA" in m.as_parfile(format="tempo"))
and not ("STIGMA" in m.as_parfile(format="tempo2"))
and ("VARSIGMA" in m.as_parfile(format="tempo2")))
def setup(self):
self.model = get_model("J1614-2230_NANOGrav_12yv3.wb.gls.par")
self.toas = get_TOAs(
"J1614-2230_NANOGrav_12yv3.wb.tim", ephem="DE436", bipm_version="BIPM2015"
)
self.fit_data_name = ["toa", "dm"]
self.fit_params_lite = ["F0", "F1", "ELONG", "ELAT", "DMJUMP1", "DMX_0022"]
self.tempo_res = np.genfromtxt(
"J1614-2230_NANOGrav_12yv3.wb.tempo_test", comments="#"
)
def setup(self):
self.model = get_model("J1614-2230_NANOGrav_12yv3.wb.gls.par")
self.toas = get_TOAs("J1614-2230_NANOGrav_12yv3.wb.tim")
toa_backends, valid_flags = self.toas.get_flag_value("fe")
self.toa_backends = np.array(toa_backends)
self.dm_jump_params = [
getattr(self.model, x)
for x in self.model.params
if (x.startswith("DMJUMP"))
]
def test_no_H3_H4(toasJ0613):
"""Test no H3 and H4 in model."""
no_H3_H4 = simple_par.replace("H4 2.0262048E-7 1 1.1276173E-7", "")
no_H3_H4 = no_H3_H4.replace("H3 2.7507208E-7 1 1.5114416E-7", "")
no_H3_H4_model = get_model(StringIO(no_H3_H4))
assert no_H3_H4_model.H3.value is None
assert no_H3_H4_model.H4.value is None
test_toas = toasJ0613[::20]
f = ff.WLSFitter(test_toas, no_H3_H4_model)
f.fit_toas()
def main(argv=None):
parser = argparse.ArgumentParser(
description="PINT tool for command-line parfile format conversions",
formatter_class=argparse.ArgumentDefaultsHelpFormatter,
)
parser.add_argument("input", help="Input parfile", type=str)
parser.add_argument(
"-f",
"--format",
help=("Format for output"),
choices=_parfile_formats,
default="pint",
)
parser.add_argument(
"-o",
"--out",
help=("Output filename [default=stdout]"),
default=None,
)
parser.add_argument(
"--log-level",
type=str,
choices=("TRACE", "DEBUG", "INFO", "WARNING", "ERROR"),
default="WARNING",
help="Logging level",
dest="loglevel",
)
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 not os.path.exists(args.input):
log.error(f"Cannot open '{args.input}' for reading")
return
log.info(f"Reading '{args.input}'")
model = get_model(args.input)
output = model.as_parfile(format=args.format)
if args.out is None:
# just output to STDOUT
print(output)
else:
with open(args.out, "w") as outfile:
outfile.write(output)
log.info(f"Wrote to '{args.out}'")
return
def test_wave():
parfile = 'J1513-5908_PKS_alldata_white.par'
timfile = 'J1744-1134.Rcvr1_2.GASP.8y.x.tim'
t = toa.get_TOAs(timfile, usepickle=False)
m = tm.get_model(parfile)
log.info("model.as_parfile():\n%s"%m.as_parfile())
print(m.as_parfile())
print(m)
print(m.delay(t))
def test_zero_H3_H4_fit_H3(toasJ0613):
H3H4_zero2_model = get_model(StringIO(simple_par))
H3H4_zero2_model.H3.value = 0.0
H3H4_zero2_model.H3.frozen = False
H3H4_zero2_model.H4.value = 0.0
H3H4_zero2_model.H4.frozen = True
test_toas = toasJ0613[::20]
f = ff.WLSFitter(test_toas, H3H4_zero2_model)
# This should work
f.fit_toas()
assert f.model.H3.value > 0.0
def test_ECL():
"""Should be only IERS2003 for TEMPO2"""
m = get_model(os.path.join(datadir, "J0613-0200_NANOGrav_9yv1.gls.par"))
for l in m.as_parfile().split("\n"):
if "ECL" in l:
assert l.split()[-1] == "IERS2010"
for l in m.as_parfile(format="tempo").split("\n"):
if "ECL" in l:
assert l.split()[-1] == "IERS2010"
for l in m.as_parfile(format="tempo2").split("\n"):
if "ECL" in l:
assert l.split()[-1] == "IERS2003"
def test_T2CMETHOD():
"""Should be commented out in TEMPO2"""
m = get_model(os.path.join(datadir, "B1855+09_NANOGrav_dfg+12_TAI.par"))
for l in m.as_parfile().split("\n"):
if "T2CMETHOD" in l:
assert not (l.startswith("#"))
for l in m.as_parfile(format="tempo").split("\n"):
if "T2CMETHOD" in l:
assert not (l.startswith("#"))
for l in m.as_parfile(format="tempo2").split("\n"):
if "T2CMETHOD" in l:
assert l.startswith("#")
def setUpClass(cls):
os.chdir(datadir)
cls.parfileJ1853 = "J1853+1303_NANOGrav_11yv0.gls.par"
cls.timfileJ1853 = "J1853+1303_NANOGrav_11yv0.tim"
cls.toasJ1853 = toa.get_TOAs(cls.timfileJ1853,
ephem="DE421",
planets=False)
cls.modelJ1853 = model.get_model(cls.parfileJ1853)
cls.ltres, cls.ltbindelay = np.genfromtxt(cls.parfileJ1853 +
".tempo2_test",
skip_header=1,
unpack=True)
cls.parfileJ0613 = "J0613-0200_NANOGrav_9yv1_ELL1H.gls.par"
cls.timfileJ0613 = "J0613-0200_NANOGrav_9yv1.tim"
cls.modelJ0613 = model.get_model(cls.parfileJ0613)
cls.toasJ0613 = toa.get_TOAs(cls.timfileJ0613,
ephem="DE421",
planets=False)
cls.parfileJ0613_STIG = "J0613-0200_NANOGrav_9yv1_ELL1H_STIG.gls.par"
cls.modelJ0613_STIG = model.get_model(cls.parfileJ0613_STIG)
def get_orbital_correction_from_ephemeris_file(mjdstart, mjdstop, parfile,
ntimes=1000, ephem="DE405",
return_pint_model=False):
"""Get a correction for orbital motion from pulsar parameter file.
Parameters
----------
mjdstart, mjdstop : float
Start and end of the time interval where we want the orbital solution
parfile : str
Any parameter file understood by PINT (Tempo or Tempo2 format)
Other parameters
----------------
ntimes : int
Number of time intervals to use for interpolation. Default 1000
Returns
-------
correction_sec : function
Function that accepts in input an array of times in seconds and a
floating-point MJDref value, and returns the deorbited times
correction_mjd : function
Function that accepts times in MJDs and returns the deorbited times.
"""
from scipy.interpolate import interp1d
from astropy import units
simon("Assuming events are already referred to the solar system "
"barycenter (timescale is TDB)")
if not HAS_PINT:
raise ImportError("You need the optional dependency PINT to use this "
"functionality: github.com/nanograv/pint")
mjds = np.linspace(mjdstart, mjdstop, ntimes)
toalist = _load_and_prepare_TOAs(mjds, ephem=ephem)
m = get_model(parfile)
delays = m.delay(toalist)
correction_mjd = \
interp1d(mjds,
(toalist.table['tdbld'] * units.d - delays).to(units.d).value)
def correction_sec(times, mjdref):
deorb_mjds = correction_mjd(times / 86400 + mjdref)
return np.array((deorb_mjds - mjdref) * 86400)
retvals = [correction_sec, correction_mjd]
if return_pint_model:
retvals.append(m)
return retvals
def loadparfile(self, parfile):
"""
Load a parfile with pint
:param parfile:
Name of the parfile
"""
self.model = pm.get_model(parfile)
log.info("model.as_parfile():\n%s"%self.model.as_parfile())
try:
self.planets = self.model.PLANET_SHAPIRO.value
except AttributeError:
self.planets = False
self._readparams()
def __init__(self, parfile=None, timfile=None, testpulsar=False):
"""
Initialize the pulsar object
@param parfile: Filename of par file
@param timfile: Filename of tim file
@param testpulsar: If true, load J1744 test pulsar
"""
super(PPulsar, self).__init__()
# Create a timing-model
self._interface = "pint"
#m = pm.StandardTimingModel()
#m = pm.DDTimingModel()
if testpulsar:
# Write a test-pulsar, and open that for testing
parfilename = tempfile.mktemp()
timfilename = tempfile.mktemp()
parfile = open(parfilename, 'w')
timfile = open(timfilename, 'w')
parfile.write(J1744_parfile_basic)
timfile.write(J1744_timfile)
parfile.close()
timfile.close()
elif parfile is not None and timfile is not None:
parfilename = parfile
timfilename = timfile
else:
raise ValueError("No valid pulsar to load")
# We have a par/tim file. Read them in!
m = pm.get_model(parfilename)
#m.read_parfile(parfilename)
print("model.as_parfile():")
print(m.as_parfile())
try:
planet_ephems = m.PLANET_SHAPIRO.value
except AttributeError:
planet_ephems = False
#t0 = time.time()
t = toa.get_TOAs(timfilename)
#time_toa = time.time() - t0
t.print_summary()
#sys.stderr.write("Read/corrected TOAs in %.3f sec\n" % time_toa)
self._mjds = t.get_mjds()
#d_tdbs = np.array([x.tdb.delta_tdb_tt for x in t.table['mjd']])
self._toaerrs = t.get_errors()
resids = np.zeros_like(self._mjds)
#ss_roemer = np.zeros_like(self._mjds)
#ss_shapiro = np.zeros_like(self._mjds)
#sys.stderr.write("Computing residuals...\n")
#t0 = time.time()
phases = m.phase(t.table)
resids = phases.frac
#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:
self._resids_us = resids / float(m.F0.value) * 1e6
sys.stderr.write("RMS PINT residuals are %.3f us\n" % self._resids_us.std())
# Create a dictionary of the fitting parameters
self.pardict = OrderedDict()
self.pardict['START'] = tempopar('START')
self.pardict['FINISH'] = tempopar('FINISH')
self.pardict['RAJ'] = tempopar('RAJ')
self.pardict['DECJ'] = tempopar('DECJ')
self.pardict['PMRA'] = tempopar('PMRA')
self.pardict['PMDEC'] = tempopar('PMDEC')
self.pardict['F0'] = tempopar('F0')
self.pardict['F1'] = tempopar('F1')
if testpulsar:
os.remove(parfilename)
os.remove(timfilename)
#! /usr/bin/env python
import sys,os
import pint.models as tm
from pinttestdata import testdir, datadir
datadir = os.path.join(testdir,'datafile')
parfile = os.path.join(datadir,'J1744-1134.basic.par')
m = tm.get_model(parfile)
print("model.param_help():")
m.param_help()
print()
print("calling model.read_parfile():")
m.read_parfile(parfile)
print()
print("print model:")
print(m)
print()
print("model.as_parfile():")
print(m.as_parfile())
print()
import pint.models as tm
from pint.phase import Phase
from pint import toa
from pint import fitter
#import matplotlib
#matplotlib.use('TKAgg')
import matplotlib.pyplot as plt
import numpy
from pinttestdata import testdir, datadir
# Get model
m = tm.get_model(os.path.join(datadir,'NGC6440E.par'))
# Get TOAs
t = toa.TOAs(os.path.join(datadir,'NGC6440E.tim'))
t.apply_clock_corrections(include_bipm=False)
t.compute_TDBs()
try:
planet_ephems = m.PLANET_SHAPIRO.value
except AttributeError:
planet_ephems = False
t.compute_posvels(planets=planet_ephems)
f=fitter.WlsFitter(toas=t,model=m)
# Print initial chi2
print('chi^2 is initially %0.2f' % f.resids.chi2)