def test_pickle_multiple(tmpdir):
m = get_model(StringIO(simplepar))
fakes = [
toa.make_fake_toas(55000, 55500, 10, model=m, obs="ao"),
toa.make_fake_toas(56000, 56500, 10, model=m, obs="gbt"),
toa.make_fake_toas(57000, 57500, 10, model=m, obs="@"),
]
filenames = [
os.path.join(tmpdir, f"t{i+1}.tim") for i in range(len(fakes))
]
picklefilename = os.path.join(tmpdir, "t.pickle.gz")
for t, f in zip(fakes, filenames):
t.write_TOA_file(f, format="tempo2")
toa.get_TOAs(filenames,
model=m,
usepickle=True,
picklefilename=picklefilename)
assert os.path.exists(picklefilename)
assert toa.get_TOAs(filenames,
model=m,
usepickle=True,
picklefilename=picklefilename).was_pickled
with open(filenames[-1], "at") as f:
f.write("\n")
assert not toa.get_TOAs(
filenames, model=m, usepickle=True,
picklefilename=picklefilename).was_pickled
def model_eccentric_toas_wb():
g = np.random.default_rng(0)
model_eccentric = get_model(
io.StringIO("\n".join([par_eccentric, "ECORR tel @ 2"])))
toas = merge_TOAs([
make_fake_toas(
57000,
57001,
20,
model_eccentric,
freq=1000,
obs="@",
dm=10 * u.pc / u.cm**3,
),
make_fake_toas(
57000,
57001,
20,
model_eccentric,
freq=2000,
obs="@",
dm=10 * u.pc / u.cm**3,
),
])
toas.adjust_TOAs(
TimeDelta(g.standard_normal(len(toas)) * toas.table["error"]))
return model_eccentric, toas
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_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_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="@"),
]
fakes_excised = [f[1:-1] for f in fakes]
toas = toa.merge_TOAs(fakes)
toas_excised = toa.merge_TOAs(fakes_excised)
for i in range(len(toas_excised)):
ix = toas_excised.table["index"][i]
match = toas.table[toas.table["index"] == ix]
assert len(match) == 1
assert match[0]["tdbld"] == toas_excised.table["tdbld"][i]
def test_ftest_wb():
"""Test for wideband fitter class F-test."""
wb_m = tm.get_model(os.path.join(datadir, "J0023+0923_ell1_simple.par"))
wb_t = toa.make_fake_toas(
56000.0, 56001.0, 10, wb_m, freq=1400.0, obs="GBT", dm=wb_m.DM.value
)
wb_f = fitter.WidebandTOAFitter(wb_t, wb_m)
wb_f.fit_toas()
# Parallax
PX = param.floatParameter(
parameter_type="float", name="PX", value=0.0, units=u.mas, frozen=False
)
PX_Component = "AstrometryEcliptic"
# A1DOT
A1DOT = param.floatParameter(
parameter_type="float",
name="A1DOT",
value=0.0,
units=ls / u.second,
frozen=False,
)
A1DOT_Component = "BinaryELL1"
# Test adding A1DOT
Ftest_dict = wb_f.ftest(A1DOT, A1DOT_Component, remove=False, full_output=True)
assert isinstance(Ftest_dict["ft"], float) or isinstance(Ftest_dict["ft"], bool)
# Test removing parallax
Ftest_dict = wb_f.ftest(PX, PX_Component, remove=True, full_output=True)
assert isinstance(Ftest_dict["ft"], float) or isinstance(Ftest_dict["ft"], bool)
def test_ftest_nb():
"""Test for narrowband fitter class F-test."""
m = tm.get_model(os.path.join(datadir, "J0023+0923_ell1_simple.par"))
t = toa.make_fake_toas(56000.0, 56001.0, 10, m, freq=1400.0, obs="AO")
f = fitter.WLSFitter(toas=t, model=m)
f.fit_toas()
# Test adding parameters
F2 = param.prefixParameter(
parameter_type="float",
name="F2",
value=0.0,
units=u.Hz / u.s / u.s,
frozen=False,
)
ft = f.ftest(F2, "Spindown", remove=False)
assert isinstance(ft["ft"], float) or isinstance(ft["ft"], bool)
# Test return the full output
Ftest_dict = f.ftest(F2, "Spindown", remove=False, full_output=True)
assert isinstance(Ftest_dict["ft"], float) or isinstance(Ftest_dict["ft"], bool)
# Test removing parameter
F1 = param.prefixParameter(
parameter_type="float", name="F1", value=0.0, units=u.Hz / u.s, frozen=False
)
ft = f.ftest(F1, "Spindown", remove=True)
assert isinstance(ft["ft"], float) or isinstance(ft["ft"], bool)
Ftest_dict = f.ftest(F1, "Spindown", remove=True, full_output=True)
assert isinstance(Ftest_dict["ft"], float) or isinstance(Ftest_dict["ft"], bool)
def test_dmx_barycentered(Fitter):
model = get_model(
io.StringIO(
"\n".join(
[
par_base,
"DMX 15",
"DMX_0001 16",
"DMXR1_0001 58000",
"DMXR2_0001 59000",
]
)
)
)
toas = make_fake_toas(58000, 58900, 10, model, obs="@", freq=np.inf)
model.free_params = ["F0", "DM", "DMX_0001"]
fitter = Fitter(toas, model)
with pytest.warns(pint.fitter.DegeneracyWarning, match=r".*degeneracy.*DM\b"):
fitter.fit_toas()
for p in fitter.model.free_params:
assert not np.isnan(fitter.model[p].value)
fitter = Fitter(toas, model)
with pytest.warns(pint.fitter.DegeneracyWarning, match=r".*degeneracy.*DMX_0001\b"):
fitter.fit_toas()
for p in fitter.model.free_params:
assert not np.isnan(fitter.model[p].value)
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_unused_noise_model_parameter(param, value):
model = get_model(io.StringIO("\n".join([par_base, f"{param} TEL ao {value}"])))
toas = make_fake_toas(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_update_model(Fitter):
model = get_model(
io.StringIO("\n".join([par_base, "JUMP TEL barycenter 0"])))
model.INFO.value = "-f"
model.ECL.value = "IERS2010"
model.TIMEEPH.value = "FB90"
model.T2CMETHOD.value = "IERS2000B"
toas = make_fake_toas(58000,
59000,
10,
model,
obs="barycenter",
freq=np.inf)
fitter = Fitter(toas, model)
fitter.fit_toas()
par_out = fitter.model.as_parfile()
assert re.search(r"CLOCK *TT\(TAI\)", par_out)
assert re.search(r"TIMEEPH *FB90", par_out)
assert re.search(r"T2CMETHOD *IERS2000B", par_out)
assert re.search(r"NE_SW *0.0", par_out)
assert re.search(r"ECL *IERS2010", par_out)
assert re.search(r"DILATEFREQ *N", par_out)
assert re.search(r"INFO *-f", par_out)
assert re.search(r"NTOA *10.0", par_out)
assert re.search(r"CHI2 *\d+.\d+", par_out)
assert re.search(r"EPHEM *DE421", par_out)
assert re.search(r"DMDATA *0.0", par_out)
assert re.search(r"START *58000.0", par_out)
assert re.search(r"FINISH *59000.0", par_out)
def test_jump_everything_wideband():
model = get_model(
io.StringIO("\n".join([par_base, "JUMP TEL barycenter 0"])))
toas = make_fake_toas(58000,
58900,
10,
model,
obs="barycenter",
freq=np.inf)
for f in toas.table["flags"]:
f["pp_dm"] = 15.0
f["pp_dme"] = 1e-4
model.free_params = ["JUMP1", "F0", "DM"]
fitter = pint.fitter.WidebandTOAFitter(toas, model)
with pytest.warns(pint.fitter.DegeneracyWarning,
match=r".*degeneracy.*Offset\b"):
fitter.fit_toas(threshold=1e-14)
for p in fitter.model.free_params:
assert not np.isnan(fitter.model[p].value)
fitter = pint.fitter.WidebandTOAFitter(toas, model)
with pytest.warns(pint.fitter.DegeneracyWarning,
match=r".*degeneracy.*JUMP1\b"):
fitter.fit_toas(threshold=1e-14)
for p in fitter.model.free_params:
assert not np.isnan(fitter.model[p].value)
def test_parameter_overrides_model(model):
t = make_fake_toas(56000, 59000, 10, model, obs="@")
t.table["error"] = 1 * u.us
delta_f = (1 / (t.last_MJD - t.first_MJD)).to(u.Hz)
m_2 = deepcopy(model)
m_2.F0.quantity += 2 * delta_f
m_2.TRACK.value = "-2"
r = Residuals(t, m_2)
assert np.amax(r.phase_resids) - np.amin(r.phase_resids) > 1
r = Residuals(t, m_2, track_mode="nearest")
assert np.amax(r.phase_resids) - np.amin(r.phase_resids) <= 1
r = Residuals(t, m_2, track_mode="use_pulse_numbers")
assert np.amax(r.phase_resids) - np.amin(r.phase_resids) > 1
m_2.TRACK.value = "0"
r = Residuals(t, m_2)
assert np.amax(r.phase_resids) - np.amin(r.phase_resids) <= 1
r = Residuals(t, m_2, track_mode="nearest")
assert np.amax(r.phase_resids) - np.amin(r.phase_resids) <= 1
r = Residuals(t, m_2, track_mode="use_pulse_numbers")
assert np.amax(r.phase_resids) - np.amin(r.phase_resids) > 1
def test_random_models():
# Get model and TOAs
m, t = get_model_and_toas(
os.path.join(datadir, "NGC6440E.par"), os.path.join(datadir, "NGC6440E.tim")
)
f = fitter.WLSFitter(toas=t, model=m)
# Do a 4-parameter fit
f.model.free_params = ("F0", "F1", "RAJ", "DECJ")
f.fit_toas()
# this contains TOAs up through 54200
# make new ones starting there
tnew = toa.make_fake_toas(54200, 59000, 59000 - 54200, f.model)
dphase, mrand = utils.calculate_random_models(f, tnew, Nmodels=100)
# this is a bit stochastic, but I see typically < 0.14 cycles
# for the uncertainty at 59000
assert np.all(dphase.std(axis=0) < 0.2)
# redo it with only F0 free
dphase_F, mrand_F = utils.calculate_random_models(
f, tnew, Nmodels=100, params=["F0"]
)
# this should be less than the fully free version
assert dphase_F.std(axis=0).max() < dphase.std(axis=0).max()
def test_load_multiple(tmpdir):
m = get_model(StringIO(simplepar))
fakes = [
toa.make_fake_toas(55000, 55500, 10, model=m, obs="ao"),
toa.make_fake_toas(56000, 56500, 10, model=m, obs="gbt"),
toa.make_fake_toas(57000, 57500, 10, model=m, obs="@"),
]
filenames = [os.path.join(tmpdir, f"t{i+1}.tim") for i in range(len(fakes))]
for t, f in zip(fakes, filenames):
t.write_TOA_file(f, format="tempo2")
merged = toa.merge_TOAs([toa.get_TOAs(f, model=m) for f in filenames])
assert merged == toa.get_TOAs(filenames, model=m)
def wb():
m = get_model(join(datadir, "NGC6440E.par"))
t = make_fake_toas(55000, 58000, 20, model=m, freq=1400 * u.MHz, dm=10 * pint.dmu)
wb = WidebandTOAFitter(t, m)
wb.fit_toas()
return wb
def test_renumber_subset_reordered():
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="@"),
]
fakes_excised = [f[1:-1] for f in fakes]
toas_excised = toa.merge_TOAs(fakes_excised)
assert 0 not in toas_excised.table["index"]
toas_excised.renumber()
assert set(toas_excised.table["index"]) == set(range(len(toas_excised)))
toas_excised.renumber(index_order=False)
assert np.all(toas_excised.table["index"] == np.arange(len(toas_excised)))
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_tim_writing_order():
m = get_model(StringIO(simplepar))
fakes = [
toa.make_fake_toas(55000, 56000, 5, model=m, obs="ao"),
toa.make_fake_toas(55000, 56000, 5, model=m, obs="gbt"),
toa.make_fake_toas(55000, 56000, 5, model=m, obs="@"),
]
toas = toa.merge_TOAs(fakes)
toas.table["index"][np.argsort(toas.table["tdbld"])] = np.arange(len(toas))
o = StringIO()
toas.write_TOA_file(o, order_by_index=False)
obs = [ln.split()[4] for ln in o.getvalue().split("\n")[1:] if ln]
assert obs[0] == obs[1] == obs[2] == obs[3]
o = StringIO()
toas.write_TOA_file(o, order_by_index=True)
obs = [ln.split()[4] for ln in o.getvalue().split("\n")[1:] if ln]
assert obs[0] == obs[3] == obs[6] == obs[9]
assert obs[0] != obs[1]
def test_renumber_order():
m = get_model(StringIO(simplepar))
toas = toa.make_fake_toas(55000, 55500, 10, model=m, obs="ao")
rev = toas[::-1]
assert np.all(rev.table["index"] == np.arange(len(rev))[::-1])
rev.renumber()
assert np.all(rev.table["index"] == np.arange(len(rev))[::-1])
rev.renumber(index_order=False)
assert np.all(rev.table["index"] == np.arange(len(rev)))
rev = toas[::-1]
rev.renumber(index_order=True)
assert np.all(rev.table["index"] == np.arange(len(rev))[::-1])
def test_jump_no_toas():
model = get_model(io.StringIO("\n".join([par_base, "JUMP -fe L_wide 0"])))
toas = make_fake_toas(57000, 57900, 10, model)
assert len(model.JUMP1.select_toa_mask(toas)) == 0
model.JUMP1.frozen = True
model.validate_toas(toas)
model.JUMP1.frozen = False
with pytest.raises(ValueError):
model.validate_toas(toas)
model.JUMP1.frozen = False
fitter = pint.fitter.WLSFitter(toas, model)
with pytest.raises(ValueError):
fitter.fit_toas()
def test_get_highest_density_range(ndays):
par_base = """
PSR J1234+5678
F0 1 0
ELAT 0 0
ELONG 0 0
PEPOCH 57000
DM 10 0
SOLARN0 0
"""
model = get_model(io.StringIO(par_base))
toas_1 = toa.make_fake_toas(57000, 58000, 1000, model, obs="@")
toas_2 = toa.make_fake_toas(57500, 57500 + ndays.value, 100, model, obs="@")
merged = toa.merge_TOAs([toas_1, toas_2])
if ndays == 7 * u.d:
x1 = merged.get_highest_density_range()
x2 = merged.get_highest_density_range(ndays)
assert abs(x2[0].value - 57500) <= 1e-5
assert abs(x2[1].value - (57500 + ndays.value)) <= 1e-5
if ndays == 7 * u.d:
assert abs(x2[0].value - x1[0].value) <= 1e-5
assert abs(x2[1].value - x1[1].value) <= 1e-5
def test_jump_everything(Fitter):
model = get_model(io.StringIO("\n".join([par_base, "JUMP TEL barycenter 0"])))
toas = make_fake_toas(58000, 58900, 10, model, obs="barycenter", freq=np.inf)
model.free_params = ["JUMP1", "F0"]
fitter = Fitter(toas, model)
with pytest.warns(pint.fitter.DegeneracyWarning, match=r".*degeneracy.*Offset\b"):
fitter.fit_toas(threshold=1e-14)
for p in fitter.model.free_params:
assert not np.isnan(fitter.model[p].value)
fitter = Fitter(toas, model)
with pytest.warns(pint.fitter.DegeneracyWarning, match=r".*degeneracy.*JUMP1\b"):
fitter.fit_toas(threshold=1e-14)
for p in fitter.model.free_params:
assert not np.isnan(fitter.model[p].value)
def model_eccentric_toas():
g = np.random.default_rng(0)
model_eccentric = get_model(io.StringIO(par_eccentric))
toas = make_fake_toas(57000,
57001,
20,
model_eccentric,
freq=1400,
obs="@")
toas.adjust_TOAs(
TimeDelta(g.standard_normal(len(toas)) * toas.table["error"]))
return model_eccentric, toas
def test_residuals_wls_chi2():
model = get_model(
StringIO("""
PSRJ J1234+5678
ELAT 0
ELONG 0
DM 10
F0 1
PEPOCH 58000
"""))
toas = make_fake_toas(57000, 59000, 20, model=model, error=1 * u.us)
np.random.seed(0)
toas.adjust_TOAs(TimeDelta(np.random.randn(len(toas)) * u.us))
r = Residuals(toas, model)
f = WLSFitter(toas, model)
assert f.fit_toas() == r.chi2
def test_dmx_no_toas():
model = get_model(
io.StringIO("\n".join([
par_base,
"DMX 15",
"DMX_0001 16 1",
"DMXR1_0001 58000",
"DMXR2_0001 59000",
])))
toas = make_fake_toas(57000, 57900, 10, model)
with pytest.raises(MissingTOAs) as e:
model.validate_toas(toas)
assert e.value.parameter_names == ["DMX_0001"]
fitter = pint.fitter.WLSFitter(toas, model)
with pytest.raises(MissingTOAs):
fitter.fit_toas()
def test_sun_angle_ecliptic(frac):
model = get_model(StringIO(par))
toas = make_fake_toas(march_equinox,
march_equinox + 2 * year,
10,
model=model,
obs="gbt")
# Sun longitude, from Astronomical Almanac
sun_n = toas.get_mjds().value - 51544.5
sun_L = 280.460 + 0.9856474 * sun_n
sun_g = 357.528 + 0.9856003 * sun_n
sun_longitude = (sun_L + 1.915 * np.sin(np.deg2rad(sun_g)) +
0.020 * np.sin(2 * np.deg2rad(sun_g)))
sun_longitude = (sun_longitude + 180) % 360 - 180
angles = np.rad2deg(model.sun_angle(toas).value)
assert_allclose(angles, np.abs(sun_longitude), atol=1)
def test_residuals_scaled_uncertainties():
model = get_model(
StringIO("""
PSRJ J1234+5678
ELAT 0
ELONG 0
DM 10
F0 1
PEPOCH 58000
EFAC mjd 57000 58000 2
"""))
toas = make_fake_toas(57000, 59000, 20, model=model, error=1 * u.us)
r = Residuals(toas, model)
e = r.get_data_error(scaled=True)
assert np.all(e != 0)
assert 0 < np.sum(e > 1.5 * u.us) < len(toas)
with pytest.raises(ValueError):
model.as_parfile().index("EQUAD")
def wideband_fake():
model = get_model(
StringIO("""
PSRJ J1234+5678
ELAT 0
ELONG 0
DM 10
F0 1
PEPOCH 58000
ECORR mjd 57000 58000 2
"""))
toas = make_fake_toas(57000, 59000, 40, model=model, error=1 * u.us, dm=10)
toas.compute_pulse_numbers(model)
np.random.seed(0)
toas.adjust_TOAs(TimeDelta(np.random.randn(len(toas)) * u.us))
for f in toas.table["flags"]:
f["pp_dm"] += np.random.randn() * f["pp_dme"]
return toas, model
def test_gls_chi2_full_cov():
model = get_model(
StringIO("""
PSRJ J1234+5678
ELAT 0
ELONG 0
DM 10
F0 1
PEPOCH 58000
TNRedAmp -14.227505410948254
TNRedGam 4.91353
TNRedC 45
"""))
model.free_params = ["ELAT", "ELONG"]
toas = make_fake_toas(57000, 59000, 100, model=model, error=1 * u.us)
np.random.seed(0)
toas.adjust_TOAs(TimeDelta(np.random.randn(len(toas)) * u.us))
r = Residuals(toas, model)
assert_allclose(r.calc_chi2(full_cov=True), r.calc_chi2(full_cov=False))