Add calibration

This MR adds calibration uncertainty to Interferometer objects.

Currently, just the cubic spline model used elsewhere is implemented.

An example of usage has been added.

• Specifying the prior will be super boring so I should add a prior file for this.

examples/injection_examples/calibration_example.py

 #!/bin/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 WMAP7.
+Tutorial to demonstrate running parameter estimation with calibration
+uncertainties included.
 """
 from __future__ import division, print_function
 
 import numpy as np
-
 import tupak
 
-# Set the duration and sampling frequency of the data segment that we're going to inject the signal into
+# Set the duration and sampling frequency of the data segment
+# that we're going to create and inject the signal into.
 
 duration = 4.
 sampling_frequency = 2048.
@@ -24,68 +22,64 @@ tupak.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),
+# 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 = dict(mass_1=36., mass_2=29., a_1=0.4, a_2=0.3, tilt_1=0.5, tilt_2=1.0, phi_12=1.7, phi_jl=0.3,
-                            luminosity_distance=2000., iota=0.4, psi=2.659, phase=1.3, geocent_time=1126259642.413,
-                            ra=1.375, dec=-1.2108)
+injection_parameters = dict(
+    mass_1=36., mass_2=29., a_1=0.4, a_2=0.3, tilt_1=0.5, tilt_2=1.0,
+    phi_12=1.7, phi_jl=0.3, luminosity_distance=2000., iota=0.4, psi=2.659,
+    phase=1.3, geocent_time=1126259642.413, ra=1.375, dec=-1.2108)
 
 # Fixed arguments passed into the source model
 waveform_arguments = dict(waveform_approximant='IMRPhenomPv2',
                           reference_frequency=50.)
 
 # Create the waveform_generator using a LAL BinaryBlackHole source function
-waveform_generator = tupak.WaveformGenerator(duration=duration,
-                                             sampling_frequency=sampling_frequency,
-                                             frequency_domain_source_model=tupak.gw.source.lal_binary_black_hole,
-                                             parameters=injection_parameters,
-                                             waveform_arguments=waveform_arguments)
-hf_signal = waveform_generator.frequency_domain_strain()
-
-# Set up interferometers.  In this case we'll use three interferometers (LIGO-Hanford (H1), LIGO-Livingston (L1),
-# and Virgo (V1)).  These default to their design sensitivity
-ifos = tupak.gw.detector.InterferometerSet(['H1', 'L1', 'V1'])
+waveform_generator = tupak.gw.WaveformGenerator(
+    duration=duration, sampling_frequency=sampling_frequency,
+    frequency_domain_source_model=tupak.gw.source.lal_binary_black_hole,
+    parameters=injection_parameters,waveform_arguments=waveform_arguments)
+
+# Set up interferometers. In this case we'll use three interferometers
+# (LIGO-Hanford (H1), LIGO-Livingston (L1), and Virgo (V1)).
+# These default to their design sensitivity
+ifos = tupak.gw.detector.InterferometerList(['H1', 'L1', 'V1'])
 for ifo in ifos:
-    injection_parameters.update({'recalib_{}_amplitude_{}'.format(ifo.name, ii): 0.1 for ii in range(5)})
-    injection_parameters.update({'recalib_{}_phase_{}'.format(ifo.name, ii): 0.01 for ii in range(5)})
+    injection_parameters.update({
+        'recalib_{}_amplitude_{}'.format(ifo.name, ii): 0.1 for ii in range(5)})
+    injection_parameters.update({
+        'recalib_{}_phase_{}'.format(ifo.name, ii): 0.01 for ii in range(5)})
     ifo.calibration_model = tupak.gw.calibration.CubicSpline(
-        prefix='recalib_{}_'.format(ifo.name), minimum_frequency=ifo.minimum_frequency,
+        prefix='recalib_{}_'.format(ifo.name),
+        minimum_frequency=ifo.minimum_frequency,
         maximum_frequency=ifo.maximum_frequency, n_points=5)
-ifos.set_strain_data_from_power_spectral_densities(sampling_frequency=sampling_frequency, duration=duration)
-ifos.inject_signal(parameters=injection_parameters, waveform_generator=waveform_generator)
-# IFOs = [tupak.gw.detector.get_interferometer_with_fake_noise_and_injection(
-#     name, injection_polarizations=hf_signal, injection_parameters=injection_parameters, duration=duration,
-#     sampling_frequency=sampling_frequency, outdir=outdir) for name in ['H1', 'L1']]
+ifos.set_strain_data_from_power_spectral_densities(
+    sampling_frequency=sampling_frequency, duration=duration)
+ifos.inject_signal(parameters=injection_parameters,
+                   waveform_generator=waveform_generator)
 
 # Set up prior, which is a dictionary
-# 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, iota 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 = tupak.gw.prior.BBHPriorSet()
-priors['geocent_time'] = tupak.core.prior.Uniform(
-    minimum=injection_parameters['geocent_time'] - 1, maximum=injection_parameters['geocent_time'] + 1,
-    name='geocent_time', latex_label='$t_c$')
-for key in ['a_1', 'a_2', 'tilt_1', 'tilt_2', 'phi_12', 'phi_jl', 'psi', 'ra', 'dec', 'geocent_time', 'phase',
-            'iota', 'luminosity_distance', 'mass_1', 'mass_2']:
-    priors[key] = injection_parameters[key]
+# Here we fix the injected cbc parameters and most of the calibration parameters
+# to the injected values.
+# We allow a subset of the calibration parameters to vary.
+priors = injection_parameters.copy()
 for key in injection_parameters:
     if 'recalib' in key:
         priors[key] = injection_parameters[key]
-for name in ['recalib_H1_amplitude_0', 'recalib_H1_amplitude_1', 'recalib_H1_amplitude_2']:
-    priors[name] = tupak.prior.Gaussian(mu=0, sigma=0.2, name=name, latex_label='H1 $A_{}$'.format(name[-1]))
+for name in ['recalib_H1_amplitude_0', 'recalib_H1_amplitude_1']:
+    priors[name] = tupak.prior.Gaussian(
+        mu=0, sigma=0.2, name=name, latex_label='H1 $A_{}$'.format(name[-1]))
 
-# Initialise the likelihood by passing in the interferometer data (IFOs) and the waveoform generator
-likelihood = tupak.GravitationalWaveTransient(interferometers=ifos, waveform_generator=waveform_generator,
-                                              time_marginalization=False, phase_marginalization=False,
-                                              distance_marginalization=False, prior=priors)
+# Initialise the likelihood by passing in the interferometer data (IFOs) and
+# the waveform generator
+likelihood = tupak.gw.GravitationalWaveTransient(
+    interferometers=ifos, waveform_generator=waveform_generator)
 
 # Run sampler.  In this case we're going to use the `dynesty` sampler
-result = tupak.run_sampler(likelihood=likelihood, priors=priors, sampler='dynesty', npoints=1000,
-                           injection_parameters=injection_parameters, outdir=outdir, label=label)
+result = tupak.run_sampler(
+    likelihood=likelihood, priors=priors, sampler='dynesty', npoints=1000,
+    injection_parameters=injection_parameters, outdir=outdir, label=label)
 
 # make some plots of the outputs
 result.plot_corner()