Minor modifications to script. (6f481108) · Commits · Daniel Williams / weichangfeng-guo-encounters

2021_07/PE.py

+48 −44

Original line number	Diff line number	Diff line
		#!/usr/bin/env python
		"""
		Tutorial to demonstrate running parameter estimation on a reduced parameter
		space for an injected signal.

		This example estimates the masses using a uniform prior in both component masses
		and distance using a uniform in comoving volume prior on luminosity distance
		between luminosity distances of 100Mpc and 5Gpc, the cosmology is Planck15.
		Test run to try and debug Weichangfeng's code.
		"""

		import numpy as np
		import bilby

		# Set the duration and sampling frequency of the data segment that we're
		# going to inject the signal into
		duration = 1.
		sampling_frequency = 256.

		duration = 4
		sampling_frequency = 2048
		ref_geocent_time = 1126259642.5

		# Specify the output directory and the name of the simulation.
		outdir = 'outdir_15p'
		label = 'bbh_in_bilby_and_vitamin_0629'
		@@ -24,16 +19,25 @@ bilby.core.utils.setup_logger(outdir=outdir, label=label)
		# Set up a random seed for result reproducibility. This is optional!
		np.random.seed(88170235)

		# We are going to inject a binary black hole waveform. We first establish a
		# dictionary of parameters that includes all of the different waveform
		# parameters, including masses of the two black holes (mass_1, mass_2),
		# spins of both black holes (a, tilt, phi), etc.
		# INJECTION PARAMETERS

		injection_parameters = dict(
		mass_1=81.9, mass_2=70.91, a_1=0., a_2=0., tilt_1=0., tilt_2=0.,
		phi_12=0., phi_jl=0., luminosity_distance=1400, theta_jn=1.51, psi=1.54,
		phase=0., geocent_time=1126259642.5+0.22, ra=3.69, dec=-0.94)
		# Fixed arguments passed into the source model
		mass_1=81.9,
		mass_2=70.91,
		a_1=0.,
		a_2=0.,
		tilt_1=0.,
		tilt_2=0.,
		phi_12=0.,
		phi_jl=0.,
		luminosity_distance=1400,
		theta_jn=1.51,
		psi=1.54,
		phase=0.,
		geocent_time=ref_geocent_time,
		ra=3.69,
		dec=-0.94)

		waveform_arguments = dict(waveform_approximant='IMRPhenomPv2',
		reference_frequency=20., minimum_frequency=20.)

		@@ -45,40 +49,35 @@ waveform_generator = bilby.gw.WaveformGenerator(
		waveform_arguments=waveform_arguments,
		start_time=ref_geocent_time - 0.5)

		# Set up interferometers. In this case we'll use two interferometers
		# (LIGO-Hanford (H1), LIGO-Livingston (L1). These default to their design
		# sensitivity
		# Set-up a three-IFO arrangement for injection
		ifos = bilby.gw.detector.InterferometerList(['H1', 'L1', 'V1'])

		ifos.set_strain_data_from_power_spectral_densities(
		sampling_frequency=sampling_frequency, duration=duration,
		start_time=ref_geocent_time - 0.5)
		sampling_frequency=sampling_frequency,
		duration=duration,
		start_time=ref_geocent_time-3.0)


		ifos.inject_signal(waveform_generator=waveform_generator,
		parameters=injection_parameters)

		# Set up a PriorDict, which inherits from dict.
		# By default we will sample all terms in the signal models. However, this will
		# take a long time for the calculation, so for this example we will set almost
		# all of the priors to be equall to their injected values. This implies the
		# prior is a delta function at the true, injected value. In reality, the
		# sampler implementation is smart enough to not sample any parameter that has
		# a delta-function prior.
		# The above list does not include mass_1, mass_2, theta_jn and luminosity
		# distance, which means those are the parameters that will be included in the
		# sampler. If we do nothing, then the default priors get used.
		priors = bilby.gw.prior.BBHPriorDict()
		# PRIORS
		# use the aligned spin prior see https://lscsoft.docs.ligo.org/bilby/gw_prior.html
		priors = bilby.gw.prior.BBHPriorDict("/home/daniel/.virtualenvs/gaston/sandbox/local/lib/python3.7/site-packages/bilby/gw/prior_files/aligned_spins_bbh.prior")
		priors.pop('chirp_mass')
		priors.pop('mass_ratio')

		priors['mass_1'] = bilby.core.prior.Uniform(name='mass_1', minimum=30, maximum=160, unit='$M_{\\odot}$')
		priors['mass_2'] = bilby.core.prior.Uniform(name='mass_2', minimum=30, maximum=160, unit='$M_{\\odot}$')
		priors['luminosity_distance'] = bilby.core.prior.Uniform(name='luminosity_distance', minimum=1000, maximum=3000, unit='$Mpc_{\\odot}$')
		priors['psi'] = bilby.core.prior.Uniform(name='psi', minimum=0.0, maximum=np.pi, boundary='periodic')
		for key in ['a_1', 'a_2', 'tilt_1', 'tilt_2', 'phi_12', 'phi_jl']:
		priors[key] = 0.0
		priors['mass_1'] = bilby.core.prior.Uniform(name='mass_1', minimum=60, maximum=90, unit='$M_{\\odot}$')
		priors['mass_2'] = bilby.core.prior.Uniform(name='mass_2', minimum=60, maximum=90, unit='$M_{\\odot}$')


		priors['luminosity_distance'] = bilby.core.prior.Uniform(name='luminosity_distance', minimum=1300, maximum=1600, unit='$Mpc_{\\odot}$')
		#priors['psi'] = bilby.core.prior.Uniform(name='psi', minimum=0.0, maximum=np.pi, boundary='periodic')


		priors['geocent_time'] = bilby.core.prior.Uniform(
		minimum=ref_geocent_time + 0.15,
		maximum=ref_geocent_time + 0.35,
		minimum=ref_geocent_time-1,
		maximum=ref_geocent_time+1,
		name='geocent_time', latex_label='$t_c$', unit='$s$')


		@@ -89,8 +88,13 @@ likelihood = bilby.gw.GravitationalWaveTransient(

		# Run sampler. In this case we're going to use the `dynesty` sampler
		result = bilby.run_sampler(
		likelihood=likelihood, priors=priors, injection_parameters=injection_parameters, label=label,outdir=outdir,sampler='dynesty',
		nlive=2000, sample='rwalk',walks =100,nact=50,check_point_delta_t=1800,check_point_plot=True)
		likelihood=likelihood,
		priors=priors,
		injection_parameters=injection_parameters,
		label=label,
		outdir=outdir,
		sampler='dynesty',
		npoints=1000,)

		# Make a corner plot.
		result.plot_corner()

2021_07/outdir_15p/JSD_calculation.ipynb

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2021_07/outdir_15p/bbh_in_bilby_and_vitamin_0629.log

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Original line number	Diff line number	Diff line
		17:12 INFO : Waveform generator initiated with
		frequency_domain_source_model: bilby.gw.source.lal_binary_black_hole
		time_domain_source_model: None
		parameter_conversion: bilby.gw.conversion.convert_to_lal_binary_black_hole_parameters
		17:12 INFO : Injected signal in H1:
		17:12 INFO : optimal SNR = 12.54
		17:12 INFO : matched filter SNR = 13.59-0.33j
		17:12 INFO : mass_1 = 81.9
		17:12 INFO : mass_2 = 70.91
		17:12 INFO : a_1 = 0.0
		17:12 INFO : a_2 = 0.0
		17:12 INFO : tilt_1 = 0.0
		17:12 INFO : tilt_2 = 0.0
		17:12 INFO : phi_12 = 0.0
		17:12 INFO : phi_jl = 0.0
		17:12 INFO : luminosity_distance = 1400
		17:12 INFO : theta_jn = 1.51
		17:12 INFO : psi = 1.54
		17:12 INFO : phase = 0.0
		17:12 INFO : geocent_time = 1126259642.72
		17:12 INFO : ra = 3.69
		17:12 INFO : dec = -0.94
		17:12 INFO : Injected signal in L1:
		17:12 INFO : optimal SNR = 9.82
		17:12 INFO : matched filter SNR = 10.47-0.29j
		17:12 INFO : mass_1 = 81.9
		17:12 INFO : mass_2 = 70.91
		17:12 INFO : a_1 = 0.0
		17:12 INFO : a_2 = 0.0
		17:12 INFO : tilt_1 = 0.0
		17:12 INFO : tilt_2 = 0.0
		17:12 INFO : phi_12 = 0.0
		17:12 INFO : phi_jl = 0.0
		17:12 INFO : luminosity_distance = 1400
		17:12 INFO : theta_jn = 1.51
		17:12 INFO : psi = 1.54
		17:12 INFO : phase = 0.0
		17:12 INFO : geocent_time = 1126259642.72
		17:12 INFO : ra = 3.69
		17:12 INFO : dec = -0.94
		17:12 INFO : Injected signal in V1:
		17:12 INFO : optimal SNR = 6.99
		17:12 INFO : matched filter SNR = 6.55+0.57j
		17:12 INFO : mass_1 = 81.9
		17:12 INFO : mass_2 = 70.91
		17:12 INFO : a_1 = 0.0
		17:12 INFO : a_2 = 0.0
		17:12 INFO : tilt_1 = 0.0
		17:12 INFO : tilt_2 = 0.0
		17:12 INFO : phi_12 = 0.0
		17:12 INFO : phi_jl = 0.0
		17:12 INFO : luminosity_distance = 1400
		17:12 INFO : theta_jn = 1.51
		17:12 INFO : psi = 1.54
		17:12 INFO : phase = 0.0
		17:12 INFO : geocent_time = 1126259642.72
		17:12 INFO : ra = 3.69
		17:12 INFO : dec = -0.94
		17:12 INFO : No prior given, using default BBH priors in /home/weichangfeng/.local/lib/python3.8/site-packages/bilby/gw/prior_files/precessing_spins_bbh.prior.
		17:12 INFO : Running for label 'bbh_in_bilby_and_vitamin_0629', output will be saved to 'outdir_15p'
		17:12 INFO : Using lal version 7.1.2
		17:12 INFO : Using lal git version Branch: None;Tag: lalsuite-v6.82;Id: cf792129c2473f42ce6c6ee21d8234254cefd337;;Builder: Unknown User <>;Repository status: UNCLEAN: Modified working tree
		17:12 INFO : Using lalsimulation version 2.5.1
		17:12 INFO : Using lalsimulation git version Branch: None;Tag: lalsuite-v6.82;Id: cf792129c2473f42ce6c6ee21d8234254cefd337;;Builder: Unknown User <>;Repository status: UNCLEAN: Modified working tree
		17:12 INFO : Search parameters:
		17:12 INFO : mass_1 = Uniform(minimum=30, maximum=160, name='mass_1', latex_label='$m_1$', unit='$M_{\\odot}$', boundary=None)
		17:12 INFO : mass_2 = Uniform(minimum=30, maximum=160, name='mass_2', latex_label='$m_2$', unit='$M_{\\odot}$', boundary=None)
		17:12 INFO : luminosity_distance = Uniform(minimum=1000, maximum=3000, name='luminosity_distance', latex_label='$d_L$', unit='$Mpc_{\\odot}$', boundary=None)
		17:12 INFO : dec = Cosine(minimum=-1.5707963267948966, maximum=1.5707963267948966, name='dec', latex_label='$\\mathrm{DEC}$', unit=None, boundary=None)
		17:12 INFO : ra = Uniform(minimum=0, maximum=6.283185307179586, name='ra', latex_label='$\\mathrm{RA}$', unit=None, boundary='periodic')
		17:12 INFO : theta_jn = Sine(minimum=0, maximum=3.141592653589793, name='theta_jn', latex_label='$\\theta_{JN}$', unit=None, boundary=None)
		17:12 INFO : psi = Uniform(minimum=0.0, maximum=3.141592653589793, name='psi', latex_label='$\\psi$', unit=None, boundary='periodic')
		17:12 INFO : phase = Uniform(minimum=0, maximum=6.283185307179586, name='phase', latex_label='$\\phi$', unit=None, boundary='periodic')
		17:12 INFO : geocent_time = Uniform(minimum=1126259642.65, maximum=1126259642.85, name='geocent_time', latex_label='$t_c$', unit='$s$', boundary=None)
		17:12 INFO : a_1 = 0.0
		17:12 INFO : a_2 = 0.0
		17:12 INFO : tilt_1 = 0.0
		17:12 INFO : tilt_2 = 0.0
		17:12 INFO : phi_12 = 0.0
		17:12 INFO : phi_jl = 0.0
		17:12 INFO : Single likelihood evaluation took 8.672e-04 s
		17:12 INFO : Using sampler Dynesty with kwargs {'bound': 'multi', 'sample': 'rwalk', 'verbose': True, 'periodic': None, 'reflective': None, 'check_point_delta_t': 1800, 'nlive': 2000, 'first_update': None, 'walks': 100, 'npdim': None, 'rstate': None, 'queue_size': 1, 'pool': None, 'use_pool': None, 'live_points': None, 'logl_args': None, 'logl_kwargs': None, 'ptform_args': None, 'ptform_kwargs': None, 'enlarge': 1.5, 'bootstrap': None, 'vol_dec': 0.5, 'vol_check': 8.0, 'facc': 0.2, 'slices': 5, 'update_interval': 1200, 'print_func': <bound method Dynesty._print_func of <bilby.core.sampler.dynesty.Dynesty object at 0x7fa3d48ad160>>, 'dlogz': 0.1, 'maxiter': None, 'maxcall': None, 'logl_max': inf, 'add_live': True, 'print_progress': True, 'save_bounds': False, 'n_effective': None, 'maxmcmc': 5000, 'nact': 50}
		17:12 INFO : Checkpoint every check_point_delta_t = 1800s
		17:12 INFO : Using dynesty version 1.0.1
		17:12 INFO : Using the bilby-implemented rwalk sample method with ACT estimated walks
		17:12 INFO : Resume file outdir_15p/bbh_in_bilby_and_vitamin_0629_resume.pickle does not exist.
		17:12 INFO : Generating initial points from the prior
		17:42 INFO : Written checkpoint file outdir_15p/bbh_in_bilby_and_vitamin_0629_resume.pickle
		18:13 INFO : Written checkpoint file outdir_15p/bbh_in_bilby_and_vitamin_0629_resume.pickle
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		16:10 INFO : Written checkpoint file outdir_15p/bbh_in_bilby_and_vitamin_0629_resume.pickle
		19:18 INFO : Written checkpoint file outdir_15p/bbh_in_bilby_and_vitamin_0629_resume.pickle
		19:49 INFO : Written checkpoint file outdir_15p/bbh_in_bilby_and_vitamin_0629_resume.pickle
		20:19 INFO : Written checkpoint file outdir_15p/bbh_in_bilby_and_vitamin_0629_resume.pickle
		20:50 INFO : Written checkpoint file outdir_15p/bbh_in_bilby_and_vitamin_0629_resume.pickle
		21:20 INFO : Written checkpoint file outdir_15p/bbh_in_bilby_and_vitamin_0629_resume.pickle
		21:51 INFO : Written checkpoint file outdir_15p/bbh_in_bilby_and_vitamin_0629_resume.pickle
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		01:12 INFO : Written checkpoint file outdir_15p/bbh_in_bilby_and_vitamin_0629_resume.pickle
		01:12 INFO : Writing 182 current samples to outdir_15p/bbh_in_bilby_and_vitamin_0629_samples.dat
		01:43 INFO : Written checkpoint file outdir_15p/bbh_in_bilby_and_vitamin_0629_resume.pickle
		01:43 INFO : Writing 306 current samples to outdir_15p/bbh_in_bilby_and_vitamin_0629_samples.dat
		02:13 INFO : Written checkpoint file outdir_15p/bbh_in_bilby_and_vitamin_0629_resume.pickle
		02:13 INFO : Writing 547 current samples to outdir_15p/bbh_in_bilby_and_vitamin_0629_samples.dat
		02:44 INFO : Written checkpoint file outdir_15p/bbh_in_bilby_and_vitamin_0629_resume.pickle
		02:44 INFO : Writing 660 current samples to outdir_15p/bbh_in_bilby_and_vitamin_0629_samples.dat
		03:14 INFO : Written checkpoint file outdir_15p/bbh_in_bilby_and_vitamin_0629_resume.pickle
		03:14 INFO : Writing 1377 current samples to outdir_15p/bbh_in_bilby_and_vitamin_0629_samples.dat
		03:44 INFO : Written checkpoint file outdir_15p/bbh_in_bilby_and_vitamin_0629_resume.pickle
		03:44 INFO : Writing 2485 current samples to outdir_15p/bbh_in_bilby_and_vitamin_0629_samples.dat
		04:30 INFO : Written checkpoint file outdir_15p/bbh_in_bilby_and_vitamin_0629_resume.pickle
		04:30 INFO : Writing 2906 current samples to outdir_15p/bbh_in_bilby_and_vitamin_0629_samples.dat
		03:58 INFO : Waveform generator initiated with
		frequency_domain_source_model: bilby.gw.source.lal_binary_black_hole
		time_domain_source_model: None
		parameter_conversion: bilby.gw.conversion.convert_to_lal_binary_black_hole_parameters
		03:58 INFO : Injected signal in H1:
		03:58 INFO : optimal SNR = 12.54
		03:58 INFO : matched filter SNR = 13.59-0.33j
		03:58 INFO : mass_1 = 81.9
		03:58 INFO : mass_2 = 70.91
		03:58 INFO : a_1 = 0.0
		03:58 INFO : a_2 = 0.0
		03:58 INFO : tilt_1 = 0.0
		03:58 INFO : tilt_2 = 0.0
		03:58 INFO : phi_12 = 0.0
		03:58 INFO : phi_jl = 0.0
		03:58 INFO : luminosity_distance = 1400
		03:58 INFO : theta_jn = 1.51
		03:58 INFO : psi = 1.54
		03:58 INFO : phase = 0.0
		03:58 INFO : geocent_time = 1126259642.72
		03:58 INFO : ra = 3.69
		03:58 INFO : dec = -0.94
		03:58 INFO : Injected signal in L1:
		03:58 INFO : optimal SNR = 9.82
		03:58 INFO : matched filter SNR = 10.47-0.29j
		03:58 INFO : mass_1 = 81.9
		03:58 INFO : mass_2 = 70.91
		03:58 INFO : a_1 = 0.0
		03:58 INFO : a_2 = 0.0
		03:58 INFO : tilt_1 = 0.0
		03:58 INFO : tilt_2 = 0.0
		03:58 INFO : phi_12 = 0.0
		03:58 INFO : phi_jl = 0.0
		03:58 INFO : luminosity_distance = 1400
		03:58 INFO : theta_jn = 1.51
		03:58 INFO : psi = 1.54
		03:58 INFO : phase = 0.0
		03:58 INFO : geocent_time = 1126259642.72
		03:58 INFO : ra = 3.69
		03:58 INFO : dec = -0.94
		03:58 INFO : Injected signal in V1:
		03:58 INFO : optimal SNR = 6.99
		03:58 INFO : matched filter SNR = 6.55+0.57j
		03:58 INFO : mass_1 = 81.9
		03:58 INFO : mass_2 = 70.91
		03:58 INFO : a_1 = 0.0
		03:58 INFO : a_2 = 0.0
		03:58 INFO : tilt_1 = 0.0
		03:58 INFO : tilt_2 = 0.0
		03:58 INFO : phi_12 = 0.0
		03:58 INFO : phi_jl = 0.0
		03:58 INFO : luminosity_distance = 1400
		03:58 INFO : theta_jn = 1.51
		03:58 INFO : psi = 1.54
		03:58 INFO : phase = 0.0
		03:58 INFO : geocent_time = 1126259642.72
		03:58 INFO : ra = 3.69
		03:58 INFO : dec = -0.94
		03:58 INFO : No prior given, using default BBH priors in /home/weichangfeng/.local/lib/python3.8/site-packages/bilby/gw/prior_files/precessing_spins_bbh.prior.
		03:58 INFO : Running for label 'bbh_in_bilby_and_vitamin_0629', output will be saved to 'outdir_15p'
		03:58 INFO : Using lal version 7.1.2
		03:58 INFO : Using lal git version Branch: None;Tag: lalsuite-v6.82;Id: cf792129c2473f42ce6c6ee21d8234254cefd337;;Builder: Unknown User <>;Repository status: UNCLEAN: Modified working tree
		03:58 INFO : Using lalsimulation version 2.5.1
		03:58 INFO : Using lalsimulation git version Branch: None;Tag: lalsuite-v6.82;Id: cf792129c2473f42ce6c6ee21d8234254cefd337;;Builder: Unknown User <>;Repository status: UNCLEAN: Modified working tree
		03:58 INFO : Search parameters:
		03:58 INFO : mass_1 = Uniform(minimum=30, maximum=160, name='mass_1', latex_label='$m_1$', unit='$M_{\\odot}$', boundary=None)
		03:58 INFO : mass_2 = Uniform(minimum=30, maximum=160, name='mass_2', latex_label='$m_2$', unit='$M_{\\odot}$', boundary=None)
		03:58 INFO : luminosity_distance = Uniform(minimum=1000, maximum=3000, name='luminosity_distance', latex_label='$d_L$', unit='$Mpc_{\\odot}$', boundary=None)
		03:58 INFO : dec = Cosine(minimum=-1.5707963267948966, maximum=1.5707963267948966, name='dec', latex_label='$\\mathrm{DEC}$', unit=None, boundary=None)
		03:58 INFO : ra = Uniform(minimum=0, maximum=6.283185307179586, name='ra', latex_label='$\\mathrm{RA}$', unit=None, boundary='periodic')
		03:58 INFO : theta_jn = Sine(minimum=0, maximum=3.141592653589793, name='theta_jn', latex_label='$\\theta_{JN}$', unit=None, boundary=None)
		03:58 INFO : psi = Uniform(minimum=0.0, maximum=3.141592653589793, name='psi', latex_label='$\\psi$', unit=None, boundary='periodic')
		03:58 INFO : phase = Uniform(minimum=0, maximum=6.283185307179586, name='phase', latex_label='$\\phi$', unit=None, boundary='periodic')
		03:58 INFO : geocent_time = Uniform(minimum=1126259642.65, maximum=1126259642.85, name='geocent_time', latex_label='$t_c$', unit='$s$', boundary=None)
		03:58 INFO : a_1 = 0.0
		03:58 INFO : a_2 = 0.0
		03:58 INFO : tilt_1 = 0.0
		03:58 INFO : tilt_2 = 0.0
		03:58 INFO : phi_12 = 0.0
		03:58 INFO : phi_jl = 0.0
		03:58 INFO : Single likelihood evaluation took 2.916e-03 s
		03:58 INFO : Using sampler Dynesty with kwargs {'bound': 'multi', 'sample': 'rwalk', 'verbose': True, 'periodic': None, 'reflective': None, 'check_point_delta_t': 1800, 'nlive': 2000, 'first_update': None, 'walks': 100, 'npdim': None, 'rstate': None, 'queue_size': 1, 'pool': None, 'use_pool': None, 'live_points': None, 'logl_args': None, 'logl_kwargs': None, 'ptform_args': None, 'ptform_kwargs': None, 'enlarge': 1.5, 'bootstrap': None, 'vol_dec': 0.5, 'vol_check': 8.0, 'facc': 0.2, 'slices': 5, 'update_interval': 1200, 'print_func': <bound method Dynesty._print_func of <bilby.core.sampler.dynesty.Dynesty object at 0x7f1016cba730>>, 'dlogz': 0.1, 'maxiter': None, 'maxcall': None, 'logl_max': inf, 'add_live': True, 'print_progress': True, 'save_bounds': False, 'n_effective': None, 'maxmcmc': 5000, 'nact': 50}
		03:58 INFO : Checkpoint every check_point_delta_t = 1800s
		03:58 INFO : Using dynesty version 1.0.1
		03:58 INFO : Using the bilby-implemented rwalk sample method with ACT estimated walks
		03:58 INFO : Reading resume file outdir_15p/bbh_in_bilby_and_vitamin_0629_resume.pickle
		03:58 INFO : Resume file successfully loaded.
		03:59 INFO : Written checkpoint file outdir_15p/bbh_in_bilby_and_vitamin_0629_resume.pickle
		03:59 INFO : Writing 2919 current samples to outdir_15p/bbh_in_bilby_and_vitamin_0629_samples.dat
		09:40 INFO : Run interrupted by signal 15: checkpoint and exit on 130

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