CHANGELOG.md

@@ -14,6 +14,7 @@
 ## [0.4.0] 2019-02-15
 
 ### Changed
+- Changed the logic around redundancy tests in the `PriorDict` classes
 - Fixed an accidental addition of astropy as a first-class dependency and added a check for missing dependencies to the C.I.
 - Fixed a bug in the "create-your-own-time-domain-model" example
 - Added citation guide to the readme
@@ -33,7 +34,7 @@
 - Improve the load_data_from_cache_file method
 
 ### Removed
--
+- Removed deprecated `PriorSet` classes. Use `PriorDict` instead.
 
 ## [0.3.5] 2019-01-25
 

bilby/core/prior.py

@@ -245,10 +245,28 @@ class PriorDict(OrderedDict):
         """
         return [self[key].rescale(sample) for key, sample in zip(keys, theta)]
 
-    def test_redundancy(self, key):
+    def test_redundancy(self, key, disable_logging=False):
         """Empty redundancy test, should be overwritten in subclasses"""
         return False
 
+    def test_has_redundant_keys(self):
+        """
+        Test whether there are redundant keys in self.
+
+        Return
+        ------
+        bool: Whether there are redundancies or not
+        """
+        redundant = False
+        for key in self:
+            temp = self.copy()
+            del temp[key]
+            if temp.test_redundancy(key, disable_logging=True):
+                logger.warning('{} is a redundant key in this {}.'
+                               .format(key, self.__class__.__name__))
+                redundant = True
+        return redundant
+
     def copy(self):
         """
         We have to overwrite the copy method as it fails due to the presence of

bilby/core/result.py

@@ -8,6 +8,7 @@ import numpy as np
 import deepdish
 import pandas as pd
 import corner
+import json
 import scipy.stats
 import matplotlib
 import matplotlib.pyplot as plt
@@ -19,7 +20,7 @@ from .utils import (logger, infer_parameters_from_function,
 from .prior import Prior, PriorDict, DeltaFunction
 
 
-def result_file_name(outdir, label):
+def result_file_name(outdir, label, extension='json'):
     """ Returns the standard filename used for a result file
 
     Parameters
@@ -28,17 +29,27 @@ def result_file_name(outdir, label):
         Name of the output directory
     label: str
         Naming scheme of the output file
+    extension: str, optional
+        Whether to save as `hdf5` or `json`
 
     Returns
     -------
     str: File name of the output file
     """
-    return '{}/{}_result.h5'.format(outdir, label)
+    if extension == 'hdf5':
+        return '{}/{}_result.h5'.format(outdir, label)
+    else:
+        return '{}/{}_result.json'.format(outdir, label)
 
 
 def read_in_result(filename=None, outdir=None, label=None):
-    """ Wrapper to bilby.core.result.Result.from_hdf5 """
-    return Result.from_hdf5(filename=filename, outdir=outdir, label=label)
+    """ Wrapper to bilby.core.result.Result.from_hdf5
+        or bilby.core.result.Result.from_json """
+    try:
+        result = Result.from_json(filename=filename, outdir=outdir, label=label)
+    except (IOError, ValueError):
+        result = Result.from_hdf5(filename=filename, outdir=outdir, label=label)
+    return result
 
 
 class Result(object):
@@ -155,7 +166,7 @@ class Result(object):
             if (outdir is None) and (label is None):
                 raise ValueError("No information given to load file")
             else:
-                filename = result_file_name(outdir, label)
+                filename = result_file_name(outdir, label, extension='hdf5')
         if os.path.isfile(filename):
             dictionary = deepdish.io.load(filename)
             # Some versions of deepdish/pytables return the dictionanary as
@@ -169,6 +180,50 @@ class Result(object):
         else:
             raise IOError("No result '{}' found".format(filename))
 
+    @classmethod
+    def from_json(cls, filename=None, outdir=None, label=None):
+        """ Read in a saved .json data file
+
+        Parameters
+        ----------
+        filename: str
+            If given, try to load from this filename
+        outdir, label: str
+            If given, use the default naming convention for saved results file
+
+        Returns
+        -------
+        result: bilby.core.result.Result
+
+        Raises
+        -------
+        ValueError: If no filename is given and either outdir or label is None
+                    If no bilby.core.result.Result is found in the path
+
+        """
+        if filename is None:
+            if (outdir is None) and (label is None):
+                raise ValueError("No information given to load file")
+            else:
+                filename = result_file_name(outdir, label)
+        if os.path.isfile(filename):
+            dictionary = json.load(open(filename, 'r'))
+            for key in dictionary.keys():
+                # Convert some dictionaries back to DataFrames
+                if key in ['posterior', 'nested_samples']:
+                    dictionary[key] = pd.DataFrame.from_dict(dictionary[key])
+                # Convert the loaded priors to bilby prior type
+                if key == 'priors':
+                    for param in dictionary[key].keys():
+                        dictionary[key][param] = str(dictionary[key][param])
+                    dictionary[key] = PriorDict(dictionary[key])
+            try:
+                return cls(**dictionary)
+            except TypeError as e:
+                raise IOError("Unable to load dictionary, error={}".format(e))
+        else:
+            raise IOError("No result '{}' found".format(filename))
+
     def __str__(self):
         """Print a summary """
         if getattr(self, 'posterior', None) is not None:
@@ -303,9 +358,9 @@ class Result(object):
                 pass
         return dictionary
 
-    def save_to_file(self, overwrite=False, outdir=None):
+    def save_to_file(self, overwrite=False, outdir=None, extension='json'):
         """
-        Writes the Result to a deepdish h5 file
+        Writes the Result to a json or deepdish h5 file
 
         Parameters
         ----------
@@ -314,9 +369,11 @@ class Result(object):
             default=False
         outdir: str, optional
             Path to the outdir. Default is the one stored in the result object.
+        extension: str, optional
+            Whether to save as hdf5 instead of json
         """
         outdir = self._safe_outdir_creation(outdir, self.save_to_file)
-        file_name = result_file_name(outdir, self.label)
+        file_name = result_file_name(outdir, self.label, extension)
 
         if os.path.isfile(file_name):
             if overwrite:
@@ -341,8 +398,19 @@ class Result(object):
                 if hasattr(dictionary['sampler_kwargs'][key], '__call__'):
                     dictionary['sampler_kwargs'][key] = str(dictionary['sampler_kwargs'])
 
+        # Convert to json saveable format
+        if extension != 'hdf5':
+            for key in dictionary.keys():
+                if isinstance(dictionary[key], pd.core.frame.DataFrame):
+                    dictionary[key] = dictionary[key].to_dict()
+                elif isinstance(dictionary[key], np.ndarray):
+                    dictionary[key] = dictionary[key].tolist()
+
         try:
-            deepdish.io.save(file_name, dictionary)
+            if extension == 'hdf5':
+                deepdish.io.save(file_name, dictionary)
+            else:
+                json.dump(dictionary, open(file_name, 'w'), indent=2)
         except Exception as e:
             logger.error("\n\n Saving the data has failed with the "
                          "following message:\n {} \n\n".format(e))

bilby/core/sampler/__init__.py

@@ -85,6 +85,7 @@ def run_sampler(likelihood, priors=None, label='label', outdir='outdir',
         overwritten.
     save: bool
         If true, save the priors and results to disk.
+        If hdf5, save as an hdf5 file instead of json.
     result_class: bilby.core.result.Result, or child of
         The result class to use. By default, `bilby.core.result.Result` is used,
         but objects which inherit from this class can be given providing
@@ -183,7 +184,10 @@ def run_sampler(likelihood, priors=None, label='label', outdir='outdir',
 
     result.samples_to_posterior(likelihood=likelihood, priors=priors,
                                 conversion_function=conversion_function)
-    if save:
+    if save == 'hdf5':
+        result.save_to_file(extension='hdf5')
+        logger.info("Results saved to {}/".format(outdir))
+    elif save:
         result.save_to_file()
         logger.info("Results saved to {}/".format(outdir))
     if plot:

bilby/core/sampler/base_sampler.py

@@ -241,6 +241,10 @@ class Sampler(object):
             Likelihood can't be evaluated.
 
         """
+
+        if self.priors.test_has_redundant_keys():
+            raise IllegalSamplingSetError("Your sampling set contains redundant parameters.")
+
         self._check_if_priors_can_be_sampled()
         try:
             t1 = datetime.datetime.now()
@@ -502,3 +506,7 @@ class SamplerError(Error):
 
 class SamplerNotInstalledError(SamplerError):
     """ Base class for Error raised by not installed samplers """
+
+
+class IllegalSamplingSetError(Error):
+    """ Class for illegal sets of sampling parameters """

bilby/gw/conversion.py

@@ -215,7 +215,7 @@ def convert_to_lal_binary_black_hole_parameters(parameters):
             converted_parameters['phi_jl'] = 0.0
             converted_parameters['phi_12'] = 0.0
 
-    for angle in ['tilt_1', 'tilt_2', 'iota']:
+    for angle in ['tilt_1', 'tilt_2', 'theta_jn']:
         cos_angle = str('cos_' + angle)
         if cos_angle in converted_parameters.keys():
             converted_parameters[angle] =\
@@ -827,7 +827,7 @@ def generate_component_spins(sample):
     Parameters
     ----------
     sample: A dictionary with the necessary spin conversion parameters:
-    'iota', 'phi_jl', 'tilt_1', 'tilt_2', 'phi_12', 'a_1', 'a_2', 'mass_1',
+    'theta_jn', 'phi_jl', 'tilt_1', 'tilt_2', 'phi_12', 'a_1', 'a_2', 'mass_1',
     'mass_2', 'reference_frequency', 'phase'
 
     Returns
@@ -837,7 +837,7 @@ def generate_component_spins(sample):
     """
     output_sample = sample.copy()
     spin_conversion_parameters =\
-        ['iota', 'phi_jl', 'tilt_1', 'tilt_2', 'phi_12', 'a_1', 'a_2', 'mass_1',
+        ['theta_jn', 'phi_jl', 'tilt_1', 'tilt_2', 'phi_12', 'a_1', 'a_2', 'mass_1',
          'mass_2', 'reference_frequency', 'phase']
     if all(key in output_sample.keys() for key in spin_conversion_parameters):
         output_sample['iota'], output_sample['spin_1x'],\
@@ -845,7 +845,7 @@ def generate_component_spins(sample):
             output_sample['spin_2x'], output_sample['spin_2y'],\
             output_sample['spin_2z'] =\
             transform_precessing_spins(
-                output_sample['iota'], output_sample['phi_jl'],
+                output_sample['theta_jn'], output_sample['phi_jl'],
                 output_sample['tilt_1'], output_sample['tilt_2'],
                 output_sample['phi_12'], output_sample['a_1'],
                 output_sample['a_2'],

bilby/gw/detector.py

@@ -469,16 +469,20 @@ class InterferometerStrainData(object):
 
         """
 
+        data = self.time_domain_strain
+
         if analysis_segment_start_time is not None:
-            logger.info("Removing analysis segment data from the PSD data")
             analysis_segment_end_time = analysis_segment_start_time + fft_length
-            idxs = (
-                (self.time_array < analysis_segment_start_time) +
-                (self.time_array > analysis_segment_end_time))
-            data = self.time_domain_strain[idxs]
-        else:
-            data = self.time_domain_strain
-
+            inside = (analysis_segment_start_time > self.time_array[0] +
+                      analysis_segment_end_time < self.time_array[-1])
+            if inside:
+                logger.info("Removing analysis segment data from the PSD data")
+                idxs = (
+                    (self.time_array < analysis_segment_start_time) +
+                    (self.time_array > analysis_segment_end_time))
+                data = data[idxs]
+
+        # WARNING this line can cause issues if the data is non-contiguous
         strain = gwpy.timeseries.TimeSeries(data=data, sample_rate=self.sampling_frequency)
         psd_alpha = 2 * self.roll_off / fft_length
         logger.info(

bilby/gw/prior.py

@@ -207,63 +207,48 @@ class BBHPriorDict(PriorDict):
                 filename = os.path.join(os.path.dirname(__file__), 'prior_files', filename)
         PriorDict.__init__(self, dictionary=dictionary, filename=filename)
 
-    def test_redundancy(self, key):
+    def test_redundancy(self, key, disable_logging=False):
         """
         Test whether adding the key would add be redundant.
+        Already existing keys return True.
 
         Parameters
         ----------
         key: str
             The key to test.
+        disable_logging: bool, optional
+            Disable logging in this function call. Default is False.
 
         Return
         ------
         redundant: bool
             Whether the key is redundant or not
         """
-        redundant = False
         if key in self:
             logger.debug('{} already in prior'.format(key))
-            return redundant
+            return True
+
         mass_parameters = {'mass_1', 'mass_2', 'chirp_mass', 'total_mass', 'mass_ratio', 'symmetric_mass_ratio'}
-        spin_magnitude_parameters = {'a_1', 'a_2'}
         spin_tilt_1_parameters = {'tilt_1', 'cos_tilt_1'}
         spin_tilt_2_parameters = {'tilt_2', 'cos_tilt_2'}
         spin_azimuth_parameters = {'phi_1', 'phi_2', 'phi_12', 'phi_jl'}
-        inclination_parameters = {'iota', 'cos_iota'}
+        inclination_parameters = {'theta_jn', 'cos_theta_jn'}
         distance_parameters = {'luminosity_distance', 'comoving_distance', 'redshift'}
 
-        for parameter_set in [mass_parameters, spin_magnitude_parameters, spin_azimuth_parameters]:
-            if key in parameter_set:
-                if len(parameter_set.intersection(self)) > 2:
-                    redundant = True
-                    logger.warning('{} in prior. This may lead to unexpected behaviour.'.format(
-                        parameter_set.intersection(self)))
-                    break
-            elif len(parameter_set.intersection(self)) == 2:
-                redundant = True
-                break
-        for parameter_set in [inclination_parameters, distance_parameters, spin_tilt_1_parameters,
-                              spin_tilt_2_parameters]:
+        for independent_parameters, parameter_set in \
+                zip([2, 2, 1, 1, 1, 1],
+                    [mass_parameters, spin_azimuth_parameters,
+                     spin_tilt_1_parameters, spin_tilt_2_parameters,
+                     inclination_parameters, distance_parameters]):
             if key in parameter_set:
-                if len(parameter_set.intersection(self)) > 1:
-                    redundant = True
-                    logger.warning('{} in prior. This may lead to unexpected behaviour.'.format(
-                        parameter_set.intersection(self)))
-                    break
-                elif len(parameter_set.intersection(self)) == 1:
-                    redundant = True
-                    break
-
-        return redundant
-
-
-class BBHPriorSet(BBHPriorDict):
-
-    def __init__(self, dictionary=None, filename=None):
-        """ DEPRECATED: USE BBHPriorDict INSTEAD"""
-        logger.warning("The name 'BBHPriorSet' is deprecated use 'BBHPriorDict' instead")
-        super(BBHPriorSet, self).__init__(dictionary, filename)
+                if len(parameter_set.intersection(self)) >= independent_parameters:
+                    logger.disabled = disable_logging
+                    logger.warning('{} already in prior. '
+                                   'This may lead to unexpected behaviour.'
+                                   .format(parameter_set.intersection(self)))
+                    logger.disabled = False
+                    return True
+        return False
 
 
 class BNSPriorDict(PriorDict):
@@ -286,34 +271,32 @@ class BNSPriorDict(PriorDict):
                 filename = os.path.join(os.path.dirname(__file__), 'prior_files', filename)
         PriorDict.__init__(self, dictionary=dictionary, filename=filename)
 
-    def test_redundancy(self, key):
-        logger.info("Performing redundancy check using BBHPriorDict().test_redundancy")
-        bbh_redundancy = BBHPriorDict().test_redundancy(key)
+    def test_redundancy(self, key, disable_logging=False):
+        logger.disabled = disable_logging
+        logger.info("Performing redundancy check using BBHPriorDict(self).test_redundancy")
+        logger.disabled = False
+        bbh_redundancy = BBHPriorDict(self).test_redundancy(key)
+
         if bbh_redundancy:
             return True
         redundant = False
 
-        tidal_parameters =\
+        tidal_parameters = \
             {'lambda_1', 'lambda_2', 'lambda_tilde', 'delta_lambda'}
 
         if key in tidal_parameters:
             if len(tidal_parameters.intersection(self)) > 2:
                 redundant = True
-                logger.warning('{} in prior. This may lead to unexpected behaviour.'.format(
-                    tidal_parameters.intersection(self)))
+                logger.disabled = disable_logging
+                logger.warning('{} already in prior. '
+                               'This may lead to unexpected behaviour.'
+                               .format(tidal_parameters.intersection(self)))
+                logger.disabled = False
             elif len(tidal_parameters.intersection(self)) == 2:
                 redundant = True
         return redundant
 
 
-class BNSPriorSet(BNSPriorDict):
-
-    def __init__(self, dictionary=None, filename=None):
-        """ DEPRECATED: USE BNSPriorDict INSTEAD"""
-        super(BNSPriorSet, self).__init__(dictionary, filename)
-        logger.warning("The name 'BNSPriorSet' is deprecated use 'BNSPriorDict' instead")
-
-
 Prior._default_latex_labels = {
     'mass_1': '$m_1$',
     'mass_2': '$m_2$',
@@ -334,6 +317,8 @@ Prior._default_latex_labels = {
     'ra': '$\mathrm{RA}$',
     'iota': '$\iota$',
     'cos_iota': '$\cos\iota$',
+    'theta_jn': '$\\theta_{JN}$',
+    'cos_theta_jn': '$\cos\\theta_{JN}$',
     'psi': '$\psi$',
     'phase': '$\phi$',
     'geocent_time': '$t_c$',
@@ -418,13 +403,13 @@ class CalibrationPriorDict(PriorDict):
         nodes = np.logspace(np.log10(minimum_frequency),
                             np.log10(maximum_frequency), n_nodes)
 
-        amplitude_mean_nodes =\
+        amplitude_mean_nodes = \
             UnivariateSpline(frequency_array, amplitude_median)(nodes)
-        amplitude_sigma_nodes =\
+        amplitude_sigma_nodes = \
             UnivariateSpline(frequency_array, amplitude_sigma)(nodes)
-        phase_mean_nodes =\
+        phase_mean_nodes = \
             UnivariateSpline(frequency_array, phase_median)(nodes)
-        phase_sigma_nodes =\
+        phase_sigma_nodes = \
             UnivariateSpline(frequency_array, phase_sigma)(nodes)
 
         prior = CalibrationPriorDict()
@@ -506,11 +491,3 @@ class CalibrationPriorDict(PriorDict):
                                         latex_label=latex_label)
 
         return prior
-
-
-class CalibrationPriorSet(CalibrationPriorDict):
-
-    def __init__(self, dictionary=None, filename=None):
-        """ DEPRECATED: USE BNSPriorDict INSTEAD"""
-        super(CalibrationPriorSet, self).__init__(dictionary, filename)
-        logger.warning("The name 'CalibrationPriorSet' is deprecated use 'CalibrationPriorDict' instead")

bilby/gw/prior_files/GW150914.prior

@@ -10,7 +10,7 @@ phi_jl =  Uniform(name='phi_jl', minimum=0, maximum=2 * np.pi)
 luminosity_distance =  bilby.gw.prior.UniformComovingVolume(name='luminosity_distance', minimum=1e2, maximum=1e3, unit='Mpc')
 dec =  Cosine(name='dec')
 ra =  Uniform(name='ra', minimum=0, maximum=2 * np.pi)
-iota =  Sine(name='iota')
+theta_jn =  Sine(name='theta_jn')
 psi =  Uniform(name='psi', minimum=0, maximum=np.pi)
 phase =  Uniform(name='phase', minimum=0, maximum=2 * np.pi)
 geocent_time = Uniform(1126259462.322, 1126259462.522, name='geocent_time', unit='$s$')

bilby/gw/prior_files/binary_black_holes.prior

@@ -19,7 +19,7 @@ phi_jl =  Uniform(name='phi_jl', minimum=0, maximum=2 * np.pi)
 luminosity_distance =  bilby.gw.prior.UniformComovingVolume(name='luminosity_distance', minimum=1e2, maximum=5e3, unit='Mpc')
 dec =  Cosine(name='dec')
 ra =  Uniform(name='ra', minimum=0, maximum=2 * np.pi)
-iota =  Sine(name='iota')
-# cos_iota =  Uniform(name='cos_iota', minimum=-1, maximum=1)
+theta_jn =  Sine(name='theta_jn')
+# cos_theta_jn =  Uniform(name='cos_theta_jn', minimum=-1, maximum=1)
 psi =  Uniform(name='psi', minimum=0, maximum=np.pi)
 phase =  Uniform(name='phase', minimum=0, maximum=2 * np.pi)

bilby/gw/prior_files/binary_neutron_stars.prior

@@ -13,8 +13,8 @@ chi_2 =  bilby.gw.prior.AlignedSpin(a_prior=Uniform(0, 0.05), z_prior=Uniform(-1
 luminosity_distance =  bilby.gw.prior.UniformComovingVolume(name='luminosity_distance', minimum=10, maximum=500, unit='Mpc')
 dec =  Cosine(name='dec')
 ra =  Uniform(name='ra', minimum=0, maximum=2 * np.pi)
-iota =  Sine(name='iota')
-# cos_iota =  Uniform(name='cos_iota', minimum=-1, maximum=1)
+theta_jn =  Sine(name='theta_jn')
+# cos_theta_jn =  Uniform(name='cos_theta_jn', minimum=-1, maximum=1)
 psi =  Uniform(name='psi', minimum=0, maximum=np.pi)
 phase =  Uniform(name='phase', minimum=0, maximum=2 * np.pi)
 lambda_1 = Uniform(name='lambda_1', minimum=0, maximum=3000 )

bilby/gw/source.py

@@ -21,8 +21,8 @@ except ImportError:
 
 
 def lal_binary_black_hole(
-        frequency_array, mass_1, mass_2, luminosity_distance, a_1, tilt_1, phi_12, a_2, tilt_2, phi_jl,
-        iota, phase, **kwargs):
+        frequency_array, mass_1, mass_2, luminosity_distance, a_1, tilt_1,
+        phi_12, a_2, tilt_2, phi_jl, theta_jn, phase, **kwargs):
     """ A Binary Black Hole waveform model using lalsimulation
 
     Parameters
@@ -40,15 +40,16 @@ def lal_binary_black_hole(
     tilt_1: float
         Primary tilt angle
     phi_12: float
-
+        Azimuthal angle between the two component spins
     a_2: float
         Dimensionless secondary spin magnitude
     tilt_2: float
         Secondary tilt angle
     phi_jl: float
-
-    iota: float
-        Orbital inclination
+        Azimuthal angle between the total binary angular momentum and the
+        orbital angular momentum
+    theta_jn: float
+        Angle between the total binary angular momentum and the line of sight
     phase: float
         The phase at coalescence
     kwargs: dict
@@ -59,7 +60,8 @@ def lal_binary_black_hole(
     dict: A dictionary with the plus and cross polarisation strain modes
     """
 
-    waveform_kwargs = dict(waveform_approximant='IMRPhenomPv2', reference_frequency=50.0,
+    waveform_kwargs = dict(waveform_approximant='IMRPhenomPv2',
+                           reference_frequency=50.0,
                            minimum_frequency=20.0)
     waveform_kwargs.update(kwargs)
     waveform_approximant = waveform_kwargs['waveform_approximant']
@@ -80,10 +82,11 @@ def lal_binary_black_hole(
         spin_2x = 0
         spin_2y = 0
         spin_2z = a_2
+        iota = theta_jn
     else:
         iota, spin_1x, spin_1y, spin_1z, spin_2x, spin_2y, spin_2z = (
             lalsim_SimInspiralTransformPrecessingNewInitialConditions(
-                iota, phi_jl, tilt_1, tilt_2, phi_12, a_1, a_2, mass_1,
+                theta_jn, phi_jl, tilt_1, tilt_2, phi_12, a_1, a_2, mass_1,
                 mass_2, reference_frequency, phase))
 
     longitude_ascending_nodes = 0.0
@@ -114,7 +117,8 @@ def lal_binary_black_hole(
 
 
 def lal_eccentric_binary_black_hole_no_spins(
-        frequency_array, mass_1, mass_2, eccentricity, luminosity_distance, iota, phase, **kwargs):
+        frequency_array, mass_1, mass_2, eccentricity, luminosity_distance,
+        theta_jn, phase, **kwargs):
     """ Eccentric binary black hole waveform model using lalsimulation (EccentricFD)
 
     Parameters
@@ -129,7 +133,7 @@ def lal_eccentric_binary_black_hole_no_spins(
         The orbital eccentricity of the system
     luminosity_distance: float
         The luminosity distance in megaparsec
-    iota: float
+    theta_jn: float
         Orbital inclination
     phase: float
         The phase at coalescence
@@ -161,6 +165,7 @@ def lal_eccentric_binary_black_hole_no_spins(
     spin_2x = 0.0
     spin_2y = 0.0
     spin_2z = 0.0
+    iota = theta_jn
 
     longitude_ascending_nodes = 0.0
     mean_per_ano = 0.0
@@ -246,7 +251,7 @@ def supernova_pca_model(
 
 def lal_binary_neutron_star(
         frequency_array, mass_1, mass_2, luminosity_distance, chi_1, chi_2,
-        iota, phase, lambda_1, lambda_2, **kwargs):
+        theta_jn, phase, lambda_1, lambda_2, **kwargs):
     """ A Binary Neutron Star waveform model using lalsimulation
 
     Parameters
@@ -263,7 +268,7 @@ def lal_binary_neutron_star(
         Dimensionless aligned spin
     chi_2: float
         Dimensionless aligned spin
-    iota: float
+    theta_jn: float
         Orbital inclination
     phase: float
         The phase at coalescence
@@ -308,6 +313,7 @@ def lal_binary_neutron_star(
     spin_2x = 0
     spin_2y = 0
     spin_2z = chi_2
+    iota = theta_jn
 
     longitude_ascending_nodes = 0.0
     eccentricity = 0.0
@@ -339,7 +345,7 @@ def lal_binary_neutron_star(
 
 
 def roq(frequency_array, mass_1, mass_2, luminosity_distance, a_1, tilt_1,
-        phi_12, a_2, tilt_2, phi_jl, iota, phase, **waveform_arguments):
+        phi_12, a_2, tilt_2, phi_jl, theta_jn, phase, **waveform_arguments):
     """
     See https://git.ligo.org/lscsoft/lalsuite/blob/master/lalsimulation/src/LALSimInspiral.c#L1460
 
@@ -365,7 +371,7 @@ def roq(frequency_array, mass_1, mass_2, luminosity_distance, a_1, tilt_1,
         Secondary tilt angle
     phi_jl: float
 
-    iota: float
+    theta_jn: float
         Orbital inclination
     phase: float
         The phase at coalescence
@@ -410,11 +416,12 @@ def roq(frequency_array, mass_1, mass_2, luminosity_distance, a_1, tilt_1,
         spin_2x = 0
         spin_2y = 0
         spin_2z = a_2
+        iota = theta_jn
     else:
         iota, spin_1x, spin_1y, spin_1z, spin_2x, spin_2y, spin_2z = \
             lalsim_SimInspiralTransformPrecessingNewInitialConditions(
-                iota, phi_jl, tilt_1, tilt_2, phi_12, a_1, a_2, mass_1, mass_2,
-                reference_frequency, phase)
+                theta_jn, phi_jl, tilt_1, tilt_2, phi_12, a_1, a_2, mass_1,
+                mass_2, reference_frequency, phase)
 
     chi_1_l, chi_2_l, chi_p, theta_jn, alpha, phase_aligned, zeta =\
         lalsim_SimIMRPhenomPCalculateModelParametersFromSourceFrame(

bilby/gw/utils.py

@@ -130,6 +130,7 @@ def get_polarization_tensor(ra, dec, time, psi, mode):
     elif mode.lower() == 'breathing':
         return np.einsum('i,j->ij', m, m) + np.einsum('i,j->ij', n, n)
 
+    # Calculating omega here to avoid calculation when model in [plus, cross, breathing]
     omega = np.cross(m, n)
     if mode.lower() == 'longitudinal':
         return np.sqrt(2) * np.einsum('i,j->ij', omega, omega)
@@ -138,8 +139,7 @@ def get_polarization_tensor(ra, dec, time, psi, mode):
     elif mode.lower() == 'y':
         return np.einsum('i,j->ij', n, omega) + np.einsum('i,j->ij', omega, n)
     else:
-        logger.warning("{} not a polarization mode!".format(mode))
-        return None
+        raise ValueError("{} not a polarization mode!".format(mode))
 
 
 def get_vertex_position_geocentric(latitude, longitude, elevation):
@@ -380,7 +380,7 @@ def get_open_strain_data(
     return strain
 
 
-def read_frame_file(file_name, start_time, end_time, channel=None, buffer_time=1, **kwargs):
+def read_frame_file(file_name, start_time, end_time, channel=None, buffer_time=0, **kwargs):
     """ A function which accesses the open strain data
 
     This uses `gwpy` to download the open data and then saves a cached copy for
@@ -416,23 +416,22 @@ def read_frame_file(file_name, start_time, end_time, channel=None, buffer_time=1
         except RuntimeError:
             logger.warning('Channel {} not found. Trying preset channel names'.format(channel))
 
-    while not loaded:
-        ligo_channel_types = ['GDS-CALIB_STRAIN', 'DCS-CALIB_STRAIN_C01', 'DCS-CALIB_STRAIN_C02',
-                              'DCH-CLEAN_STRAIN_C02']
-        virgo_channel_types = ['Hrec_hoft_V1O2Repro2A_16384Hz', 'FAKE_h_16384Hz_4R']
-        channel_types = dict(H1=ligo_channel_types, L1=ligo_channel_types, V1=virgo_channel_types)
-        for detector in channel_types.keys():
-            for channel_type in channel_types[detector]:
-                if loaded:
-                    break
-                channel = '{}:{}'.format(detector, channel_type)
-                try:
-                    strain = TimeSeries.read(source=file_name, channel=channel, start=start_time, end=end_time,
-                                             **kwargs)
-                    loaded = True
-                    logger.info('Successfully read strain data for channel {}.'.format(channel))
-                except RuntimeError:
-                    pass
+    ligo_channel_types = ['GDS-CALIB_STRAIN', 'DCS-CALIB_STRAIN_C01', 'DCS-CALIB_STRAIN_C02',
+                          'DCH-CLEAN_STRAIN_C02']
+    virgo_channel_types = ['Hrec_hoft_V1O2Repro2A_16384Hz', 'FAKE_h_16384Hz_4R']
+    channel_types = dict(H1=ligo_channel_types, L1=ligo_channel_types, V1=virgo_channel_types)
+    for detector in channel_types.keys():
+        for channel_type in channel_types[detector]:
+            if loaded:
+                break
+            channel = '{}:{}'.format(detector, channel_type)
+            try:
+                strain = TimeSeries.read(source=file_name, channel=channel, start=start_time, end=end_time,
+                                         **kwargs)
+                loaded = True
+                logger.info('Successfully read strain data for channel {}.'.format(channel))
+            except RuntimeError:
+                pass
 
     if loaded:
         return strain

examples/injection_examples/australian_detector.py

@@ -59,7 +59,7 @@ interferometers.append(AusIFO)
 # signal at 4 Gpc
 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=4000., iota=0.4, psi=2.659,
+    phi_12=1.7, phi_jl=0.3, luminosity_distance=4000., theta_jn=0.4, psi=2.659,
     phase=1.3, geocent_time=1126259642.413, ra=1.375, dec=0.2108)
 
 

examples/injection_examples/binary_neutron_star_example.py

@@ -28,7 +28,7 @@ np.random.seed(88170235)
 # aligned spins of both black holes (chi_1, chi_2), etc.
 injection_parameters = dict(
     mass_1=1.5, mass_2=1.3, chi_1=0.02, chi_2=0.02, luminosity_distance=50.,
-    iota=0.4, psi=2.659, phase=1.3, geocent_time=1126259642.413,
+    theta_jn=0.4, psi=2.659, phase=1.3, geocent_time=1126259642.413,
     ra=1.375, dec=-1.2108, lambda_1=400, lambda_2=450)
 
 # Set the duration and sampling frequency of the data segment that we're going
@@ -66,7 +66,7 @@ interferometers.inject_signal(parameters=injection_parameters,
 # delta_lambda rather than mass_1, mass_2, lambda_1, and lambda_2.
 priors = bilby.gw.prior.BNSPriorDict()
 for key in ['psi', 'geocent_time', 'ra', 'dec', 'chi_1', 'chi_2',
-            'iota', 'luminosity_distance', 'phase']:
+            'theta_jn', 'luminosity_distance', 'phase']:
     priors[key] = injection_parameters[key]
 priors.pop('mass_1')
 priors.pop('mass_2')

examples/injection_examples/calibration_example.py

@@ -28,7 +28,7 @@ np.random.seed(88170235)
 # 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,
+    phi_12=1.7, phi_jl=0.3, luminosity_distance=2000., theta_jn=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

examples/injection_examples/change_sampled_parameters.py

@@ -22,7 +22,7 @@ np.random.seed(151226)
 
 injection_parameters = dict(
     total_mass=66., mass_ratio=0.9, 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,
+    phi_12=1.7, phi_jl=0.3, luminosity_distance=2000, theta_jn=0.4, psi=2.659,
     phase=1.3, geocent_time=1126259642.413, ra=1.375, dec=-1.2108)
 
 waveform_arguments = dict(waveform_approximant='IMRPhenomPv2',
@@ -63,8 +63,8 @@ priors['redshift'] = bilby.prior.Uniform(
 for key in ['a_1', 'a_2', 'tilt_1', 'tilt_2', 'phi_12', 'phi_jl', 'psi',
             'ra', 'dec', 'geocent_time', 'phase']:
     priors[key] = injection_parameters[key]
-priors.pop('iota')
-priors['cos_iota'] = np.cos(injection_parameters['iota'])
+priors.pop('theta_jn')
+priors['cos_theta_jn'] = np.cos(injection_parameters['theta_jn'])
 print(priors)
 
 # Initialise GravitationalWaveTransient

examples/injection_examples/eccentric_inspiral.py

@@ -27,7 +27,7 @@ np.random.seed(150914)
 
 injection_parameters = dict(
     mass_1=35., mass_2=30., eccentricity=0.1, luminosity_distance=440.,
-    iota=0.4, psi=0.1, phase=1.2, geocent_time=1180002601.0, ra=45, dec=5.73)
+    theta_jn=0.4, psi=0.1, phase=1.2, geocent_time=1180002601.0, ra=45, dec=5.73)
 
 waveform_arguments = dict(waveform_approximant='EccentricFD',
                           reference_frequency=10., minimum_frequency=10.)
@@ -70,7 +70,7 @@ priors["luminosity_distance"] = bilby.gw.prior.UniformComovingVolume(
 priors["dec"] = bilby.core.prior.Cosine(name='dec')
 priors["ra"] = bilby.core.prior.Uniform(
     name='ra', minimum=0, maximum=2 * np.pi)
-priors["iota"] = bilby.core.prior.Sine(name='iota')
+priors["theta_jn"] = bilby.core.prior.Sine(name='theta_jn')
 priors["psi"] = bilby.core.prior.Uniform(name='psi', minimum=0, maximum=np.pi)
 priors["phase"] = bilby.core.prior.Uniform(
     name='phase', minimum=0, maximum=2 * np.pi)

examples/injection_examples/fast_tutorial.py

@@ -31,7 +31,7 @@ np.random.seed(88170235)
 # 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,
+    phi_12=1.7, phi_jl=0.3, luminosity_distance=2000., theta_jn=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
@@ -61,7 +61,7 @@ ifos.inject_signal(waveform_generator=waveform_generator,
 # 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
+# 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()

examples/injection_examples/how_to_specify_the_prior.py

@@ -17,7 +17,7 @@ np.random.seed(151012)
 
 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=4000., iota=0.4, psi=2.659,
+    phi_12=1.7, phi_jl=0.3, luminosity_distance=4000., theta_jn=0.4, psi=2.659,
     phase=1.3, geocent_time=1126259642.413, ra=1.375, dec=-1.2108)
 
 waveform_arguments = dict(waveform_approximant='IMRPhenomPv2',
@@ -41,7 +41,7 @@ ifos.inject_signal(waveform_generator=waveform_generator,
 # This loads in a predefined set of priors for BBHs.
 priors = bilby.gw.prior.BBHPriorDict()
 # These parameters will not be sampled
-for key in ['tilt_1', 'tilt_2', 'phi_12', 'phi_jl', 'phase', 'iota', 'ra',
+for key in ['tilt_1', 'tilt_2', 'phi_12', 'phi_jl', 'phase', 'theta_jn', 'ra',
             'dec', 'geocent_time', 'psi']:
     priors[key] = injection_parameters[key]
 # We can make uniform distributions.