diff --git a/bilby/core/sampler/emcee.py b/bilby/core/sampler/emcee.py
index b52c2bee052e10e2e144bef3f5d0aabcfff5e1ea..3117a6c7a2cdd11266bce26fda6e9b06feb9a36d 100644
--- a/bilby/core/sampler/emcee.py
+++ b/bilby/core/sampler/emcee.py
@@ -51,6 +51,11 @@ class Emcee(MCMCSampler):
use_ratio=False, plot=False, skip_import_verification=False,
pos0=None, nburn=None, burn_in_fraction=0.25, resume=True,
burn_in_act=3, **kwargs):
+ import emcee
+ if LooseVersion(emcee.__version__) > LooseVersion('2.2.1'):
+ self.prerelease = True
+ else:
+ self.prerelease = False
MCMCSampler.__init__(
self, likelihood=likelihood, priors=priors, outdir=outdir,
label=label, use_ratio=use_ratio, plot=plot,
@@ -82,7 +87,6 @@ class Emcee(MCMCSampler):
@property
def sampler_function_kwargs(self):
import emcee
-
keys = ['lnprob0', 'rstate0', 'blobs0', 'iterations', 'thin', 'storechain', 'mh_proposal']
# updated function keywords for emcee > v2.2.1
@@ -93,7 +97,7 @@ class Emcee(MCMCSampler):
function_kwargs = {key: self.kwargs[key] for key in keys if key in self.kwargs}
function_kwargs['p0'] = self.pos0
- if LooseVersion(emcee.__version__) > LooseVersion('2.2.1'):
+ if self.prerelease:
if function_kwargs['mh_proposal'] is not None:
logger.warning("The 'mh_proposal' option is no longer used "
"in emcee v{}, and will be ignored.".format(emcee.__version__))
@@ -109,8 +113,6 @@ class Emcee(MCMCSampler):
@property
def sampler_init_kwargs(self):
- import emcee
-
init_kwargs = {key: value
for key, value in self.kwargs.items()
if key not in self.sampler_function_kwargs}
@@ -122,7 +124,7 @@ class Emcee(MCMCSampler):
updatekeys = {'dim': 'ndim',
'lnpostfn': 'log_prob_fn'}
- if LooseVersion(emcee.__version__) > LooseVersion('2.2.1'):
+ if self.prerelease:
for key in updatekeys:
if key in init_kwargs:
init_kwargs[updatekeys[key]] = init_kwargs.pop(key)
@@ -193,8 +195,10 @@ class Emcee(MCMCSampler):
for sample in tqdm(sampler.sample(**self.sampler_function_kwargs),
total=self.nsteps):
- points = np.hstack([sample[0], np.array(sample[3])])
- # import IPython; IPython.embed()
+ if self.prerelease:
+ points = np.hstack([sample.coords, sample.blobs])
+ else:
+ points = np.hstack([sample[0], np.array(sample[3])])
with open(out_file, "a") as ff:
for ii, point in enumerate(points):
ff.write(template.format(ii, *point))
diff --git a/bilby/gw/detector.py b/bilby/gw/detector.py
index 6da387ab93d592bd360b06dff4028b7ebc4d5c3d..9b01722dc445c8c0c1cea58b12ead3a864045cde 100644
--- a/bilby/gw/detector.py
+++ b/bilby/gw/detector.py
@@ -147,38 +147,8 @@ class InterferometerList(list):
if utils.command_line_args.test:
return
- fig = plt.figure()
- for ii, interferometer in enumerate(self):
- ax = fig.add_subplot(len(self) // 2, 2, ii + 1)
- ax.loglog(interferometer.frequency_array,
- gwutils.asd_from_freq_series(freq_data=interferometer.frequency_domain_strain,
- df=(interferometer.frequency_array[1] -
- interferometer.frequency_array[0])),
- color='C0', label=interferometer.name)
- ax.loglog(interferometer.frequency_array,
- interferometer.amplitude_spectral_density_array,
- color='C1', lw=0.5, label=interferometer.name + ' ASD')
- ax.grid('on')
- ax.set_ylabel(r'strain [strain/$\sqrt{\rm Hz}$]')
- ax.set_xlabel(r'frequency [Hz]')
- ax.set_xlim(20, 2000)
- ax.legend(loc='best')
- if signal is not None:
- ax.loglog(self.frequency_array,
- gwutils.asd_from_freq_series(freq_data=signal,
- df=(self.frequency_array[1] -
- self.frequency_array[0])
- ),
- color='C2',
- label='Signal')
- fig.tight_layout()
- if label is None:
- fig.savefig(
- '{}/frequency_domain_data.png'.format(outdir))
- else:
- fig.savefig(
- '{}/{}_frequency_domain_data.png'.format(
- outdir, label))
+ for interferometer in self:
+ interferometer.plot_data(signal=signal, outdir=outdir, label=label)
@property
def number_of_interferometers(self):
diff --git a/bilby/gw/source.py b/bilby/gw/source.py
index 6d4071776db7f9f9f361b7eb04b8ad354ab728cf..22cc8f2353401e6258b7a79324c281331d776a00 100644
--- a/bilby/gw/source.py
+++ b/bilby/gw/source.py
@@ -4,12 +4,14 @@ import numpy as np
from ..core import utils
from ..core.utils import logger, spherical_to_cartesian
+from .conversion import transform_precessing_spins
from .utils import (lalsim_GetApproximantFromString,
lalsim_SimInspiralFD,
lalsim_SimInspiralChooseFDWaveform,
lalsim_SimInspiralWaveformParamsInsertTidalLambda1,
- lalsim_SimInspiralWaveformParamsInsertTidalLambda2)
-from .conversion import transform_precessing_spins
+ lalsim_SimInspiralWaveformParamsInsertTidalLambda2,
+ lalsim_SimIMRPhenomPCalculateModelParametersFromSourceFrame,
+ lalsim_SimIMRPhenomPFrequencySequence)
try:
import lal
@@ -402,20 +404,20 @@ def roq(frequency_array, mass_1, mass_2, luminosity_distance, a_1, tilt_1,
reference_frequency, phase)
chi_1_l, chi_2_l, chi_p, theta_jn, alpha, phase_aligned, zeta =\
- lalsim.SimIMRPhenomPCalculateModelParametersFromSourceFrame(
+ lalsim_SimIMRPhenomPCalculateModelParametersFromSourceFrame(
mass_1, mass_2, reference_frequency, phase, iota, spin_1x,
spin_1y, spin_1z, spin_2x, spin_2y, spin_2z, version)
waveform_polarizations = dict()
- h_linear_plus, h_linear_cross = lalsim.SimIMRPhenomPFrequencySequence(
+ h_linear_plus, h_linear_cross = lalsim_SimIMRPhenomPFrequencySequence(
frequency_nodes_linear, chi_1_l, chi_2_l, chi_p, theta_jn,
mass_1, mass_2, luminosity_distance,
- alpha, phase_aligned, reference_frequency, version, None)
- h_quadratic_plus, h_quadratic_cross = lalsim.SimIMRPhenomPFrequencySequence(
+ alpha, phase_aligned, reference_frequency, version)
+ h_quadratic_plus, h_quadratic_cross = lalsim_SimIMRPhenomPFrequencySequence(
frequency_nodes_quadratic, chi_1_l, chi_2_l, chi_p, theta_jn,
mass_1, mass_2, luminosity_distance,
- alpha, phase_aligned, reference_frequency, version, None)
+ alpha, phase_aligned, reference_frequency, version)
waveform_polarizations['linear'] = dict(
plus=(np.cos(2 * zeta) * h_linear_plus.data.data +
diff --git a/bilby/gw/utils.py b/bilby/gw/utils.py
index e4c2007342b9f7387d2d28d821bbecfe74558639..94c3cafb2c0cdb63a73e72f6cef8db7c9757974a 100644
--- a/bilby/gw/utils.py
+++ b/bilby/gw/utils.py
@@ -799,6 +799,33 @@ def lalsim_SimInspiralChooseFDWaveform(
waveform_dictionary, approximant)
+def lalsim_SimIMRPhenomPCalculateModelParametersFromSourceFrame(
+ mass_1, mass_2, reference_frequency, phase, iota, spin_1x,
+ spin_1y, spin_1z, spin_2x, spin_2y, spin_2z, version):
+ [mass_1, mass_2, reference_frequency, phase, iota, spin_1x,
+ spin_1y, spin_1z, spin_2x, spin_2y, spin_2z] = convert_args_list_to_float(
+ mass_1, mass_2, reference_frequency, phase, iota, spin_1x,
+ spin_1y, spin_1z, spin_2x, spin_2y, spin_2z)
+ return lalsim.SimIMRPhenomPCalculateModelParametersFromSourceFrame(
+ mass_1, mass_2, reference_frequency, phase, iota, spin_1x,
+ spin_1y, spin_1z, spin_2x, spin_2y, spin_2z, version)
+
+
+def lalsim_SimIMRPhenomPFrequencySequence(
+ frequency_nodes, chi_1_l, chi_2_l, chi_p, theta_jn,
+ mass_1, mass_2, luminosity_distance,
+ alpha, phase_aligned, reference_frequency, version):
+ [chi_1_l, chi_2_l, chi_p, theta_jn, mass_1, mass_2, luminosity_distance,
+ alpha, phase_aligned, reference_frequency] = convert_args_list_to_float(
+ chi_1_l, chi_2_l, chi_p, theta_jn, mass_1, mass_2, luminosity_distance,
+ alpha, phase_aligned, reference_frequency)
+
+ return lalsim.SimIMRPhenomPFrequencySequence(
+ frequency_nodes, chi_1_l, chi_2_l, chi_p, theta_jn, mass_1, mass_2,
+ luminosity_distance, alpha, phase_aligned, reference_frequency, version,
+ None)
+
+
def lalsim_SimInspiralWaveformParamsInsertTidalLambda1(
waveform_dictionary, lambda_1):
try:
diff --git a/test/detector_test.py b/test/detector_test.py
index 95b2f5f3247d2c604b5200c8ac0f4c82b5ebf3ef..edaa139fc74c12f694254986771decf16512ceee 100644
--- a/test/detector_test.py
+++ b/test/detector_test.py
@@ -39,7 +39,8 @@ class TestInterferometer(unittest.TestCase):
xarm_tilt=self.xarm_tilt, yarm_tilt=self.yarm_tilt)
self.ifo.strain_data.set_from_frequency_domain_strain(
np.linspace(0, 4096, 4097), sampling_frequency=4096, duration=2)
- bilby.core.utils.check_directory_exists_and_if_not_mkdir('outdir')
+ self.outdir = 'outdir'
+ bilby.core.utils.check_directory_exists_and_if_not_mkdir(self.outdir)
def tearDown(self):
del self.name
@@ -55,7 +56,7 @@ class TestInterferometer(unittest.TestCase):
del self.xarm_tilt
del self.yarm_tilt
del self.ifo
- rmtree('outdir')
+ rmtree(self.outdir)
def test_name_setting(self):
self.assertEqual(self.ifo.name, self.name)
@@ -798,7 +799,8 @@ class TestInterferometerList(unittest.TestCase):
self.ifo2.strain_data.set_from_frequency_domain_strain(
self.frequency_arrays, sampling_frequency=4096, duration=2)
self.ifo_list = bilby.gw.detector.InterferometerList([self.ifo1, self.ifo2])
- bilby.core.utils.check_directory_exists_and_if_not_mkdir('outdir')
+ self.outdir = 'outdir'
+ bilby.core.utils.check_directory_exists_and_if_not_mkdir(self.outdir)
def tearDown(self):
del self.frequency_arrays
@@ -829,7 +831,7 @@ class TestInterferometerList(unittest.TestCase):
del self.ifo1
del self.ifo2
del self.ifo_list
- rmtree('outdir')
+ rmtree(self.outdir)
def test_init_with_string(self):
with self.assertRaises(TypeError):
@@ -986,6 +988,15 @@ class TestInterferometerList(unittest.TestCase):
with self.assertRaises(TypeError):
bilby.gw.detector.InterferometerList.from_hdf5(filename)
+ def test_plot_data(self):
+ ifos = bilby.gw.detector.InterferometerList(['H1', 'L1'])
+ ifos.set_strain_data_from_power_spectral_densities(2048, 4)
+ ifos.plot_data(outdir=self.outdir)
+
+ ifos = bilby.gw.detector.InterferometerList(['H1', 'L1', 'V1'])
+ ifos.set_strain_data_from_power_spectral_densities(2048, 4)
+ ifos.plot_data(outdir=self.outdir)
+
class TestPowerSpectralDensityWithoutFiles(unittest.TestCase):
diff --git a/test/likelihood_test.py b/test/likelihood_test.py
index 595c1f9affea1e0ef62ac1373765ba767d9bd2a0..cf878ad85d4407bcceabd6a0d641cace791a34b6 100644
--- a/test/likelihood_test.py
+++ b/test/likelihood_test.py
@@ -31,6 +31,18 @@ class TestLikelihoodBase(unittest.TestCase):
def test_base_log_likelihood_ratio(self):
self.assertTrue(np.isnan(self.likelihood.log_likelihood_ratio()))
+ def test_meta_data_unset(self):
+ self.assertEqual(self.likelihood.meta_data, None)
+
+ def test_meta_data_set_fail(self):
+ with self.assertRaises(ValueError):
+ self.likelihood.meta_data = 10
+
+ def test_meta_data(self):
+ meta_data = dict(x=1, y=2)
+ self.likelihood.meta_data = meta_data
+ self.assertEqual(self.likelihood.meta_data, meta_data)
+
class TestAnalytical1DLikelihood(unittest.TestCase):
diff --git a/test/prior_test.py b/test/prior_test.py
index d8d4041de3a719e4a4238945f60e522b3a641388..4b85a66c625b43f1194fa79213278e807b65f399 100644
--- a/test/prior_test.py
+++ b/test/prior_test.py
@@ -4,7 +4,7 @@ import unittest
from mock import Mock
import numpy as np
import os
-import shutil
+import copy
from collections import OrderedDict
@@ -130,6 +130,7 @@ class TestPriorClasses(unittest.TestCase):
bilby.core.prior.Gaussian(name='test', unit='unit', mu=0, sigma=1),
bilby.core.prior.Normal(name='test', unit='unit', mu=0, sigma=1),
bilby.core.prior.PowerLaw(name='test', unit='unit', alpha=0, minimum=0, maximum=1),
+ bilby.core.prior.PowerLaw(name='test', unit='unit', alpha=-1, minimum=0.5, maximum=1),
bilby.core.prior.PowerLaw(name='test', unit='unit', alpha=2, minimum=1, maximum=1e2),
bilby.core.prior.Uniform(name='test', unit='unit', minimum=0, maximum=1),
bilby.core.prior.LogUniform(name='test', unit='unit', minimum=5e0, maximum=1e2),
@@ -205,6 +206,28 @@ class TestPriorClasses(unittest.TestCase):
outside_domain = np.linspace(prior.minimum - 1e4, prior.minimum - 1, 1000)
self.assertTrue(all(prior.prob(outside_domain) == 0))
+ def test_prob_and_ln_prob(self):
+ for prior in self.priors:
+ sample = prior.sample()
+ self.assertAlmostEqual(np.log(prior.prob(sample)), prior.ln_prob(sample), 12)
+
+ def test_log_normal_fail(self):
+ with self.assertRaises(ValueError):
+ bilby.core.prior.LogNormal(name='test', unit='unit', mu=0, sigma=-1)
+
+ def test_studentt_fail(self):
+ with self.assertRaises(ValueError):
+ bilby.core.prior.StudentT(name='test', unit='unit', df=3, mu=0, scale=-1)
+ with self.assertRaises(ValueError):
+ bilby.core.prior.StudentT(name='test', unit='unit', df=0, mu=0, scale=1)
+
+ def test_beta_fail(self):
+ with self.assertRaises(ValueError):
+ bilby.core.prior.Beta(name='test', unit='unit', alpha=-2.0, beta=2.0),
+
+ with self.assertRaises(ValueError):
+ bilby.core.prior.Beta(name='test', unit='unit', alpha=2.0, beta=-2.0),
+
def test_probability_in_domain(self):
"""Test that the prior probability is non-negative in domain of validity and zero outside."""
for prior in self.priors:
@@ -319,6 +342,15 @@ class TestPriorDict(unittest.TestCase):
del self.default_prior_file
del self.prior_set_from_file
+ def test_copy(self):
+ priors = bilby.core.prior.PriorDict(self.priors)
+ self.assertEqual(priors, priors.copy())
+
+ def test_prior_set(self):
+ priors_dict = bilby.core.prior.PriorDict(self.priors)
+ priors_set = bilby.core.prior.PriorSet(self.priors)
+ self.assertEqual(priors_dict, priors_set)
+
def test_prior_set_is_ordered_dict(self):
self.assertIsInstance(self.prior_set_from_dict, OrderedDict)