pycbc.inference.models package

Submodules

pycbc.inference.models.analytic module

This modules provides models that have analytic solutions for the log likelihood.

class pycbc.inference.models.analytic.TestEggbox(variable_params, **kwargs)

Bases: pycbc.inference.models.base.BaseModel

The test distribution is an ‘eggbox’ function:

\[\log \mathcal{L}(\Theta) = \left[ 2+\prod_{i=1}^{n}\cos\left(\frac{\theta_{i}}{2}\right)\right]^{5}\]

The number of dimensions is set by the number of variable_params that are passed.

Parameters:

• variable_params ((tuple of) string(s)) – A tuple of parameter names that will be varied.
• **kwargs – All other keyword arguments are passed to BaseModel.

name = 'test_eggbox'

class pycbc.inference.models.analytic.TestNormal(variable_params, mean=None, cov=None, **kwargs)

Bases: pycbc.inference.models.base.BaseModel

The test distribution is an multi-variate normal distribution.

The number of dimensions is set by the number of variable_params that are passed. For details on the distribution used, see scipy.stats.multivariate_normal.

Parameters:

• variable_params ((tuple of) string(s)) – A tuple of parameter names that will be varied.
• mean (array-like, optional) – The mean values of the parameters. If None provide, will use 0 for all parameters.
• cov (array-like, optional) – The covariance matrix of the parameters. If None provided, will use unit variance for all parameters, with cross-terms set to 0.
• **kwargs – All other keyword arguments are passed to BaseModel.

Examples

Create a 2D model with zero mean and unit variance:

>>> m = TestNormal(['x', 'y'])

Set the current parameters and evaluate the log posterior:

>>> m.update(x=-0.2, y=0.1)
>>> m.logposterior
-1.8628770664093453

See the current stats that were evaluated:

>>> m.current_stats
{'logjacobian': 0.0, 'loglikelihood': -1.8628770664093453, 'logprior': 0.0}

name = 'test_normal'

class pycbc.inference.models.analytic.TestPosterior(variable_params, posterior_file, nsamples, **kwargs)

Bases: pycbc.inference.models.base.BaseModel

Build a test posterior from a set of samples using a kde

Parameters:

• variable_params ((tuple of) string(s)) – A tuple of parameter names that will be varied.
• posterior_file (hdf file) – A compatible pycbc inference output file which posterior samples can be read from.
• nsamples (int) – Number of samples to draw from posterior file to build KDE.
• **kwargs – All other keyword arguments are passed to BaseModel.

name = 'test_posterior'

class pycbc.inference.models.analytic.TestPrior(variable_params, **kwargs)

Bases: pycbc.inference.models.base.BaseModel

Uses the prior as the test distribution.

Parameters:

• variable_params ((tuple of) string(s)) – A tuple of parameter names that will be varied. Must have length 2.
• **kwargs – All other keyword arguments are passed to BaseModel.

name = 'test_prior'

class pycbc.inference.models.analytic.TestRosenbrock(variable_params, **kwargs)

Bases: pycbc.inference.models.base.BaseModel

The test distribution is the Rosenbrock function:

\[\log \mathcal{L}(\Theta) = -\sum_{i=1}^{n-1}[ (1-\theta_{i})^{2}+100(\theta_{i+1} - \theta_{i}^{2})^{2}]\]

The number of dimensions is set by the number of variable_params that are passed.

Parameters:

• variable_params ((tuple of) string(s)) – A tuple of parameter names that will be varied.
• **kwargs – All other keyword arguments are passed to BaseModel.

name = 'test_rosenbrock'

class pycbc.inference.models.analytic.TestVolcano(variable_params, **kwargs)

Bases: pycbc.inference.models.base.BaseModel

The test distribution is a two-dimensional ‘volcano’ function:

\[\Theta = \sqrt{\theta_{1}^{2} + \theta_{2}^{2}} \log \mathcal{L}(\Theta) = 25\left(e^{\frac{-\Theta}{35}} + \frac{1}{2\sqrt{2\pi}} e^{-\frac{(\Theta-5)^{2}}{8}}\right)\]

Parameters:

• variable_params ((tuple of) string(s)) – A tuple of parameter names that will be varied. Must have length 2.
• **kwargs – All other keyword arguments are passed to BaseModel.

name = 'test_volcano'

pycbc.inference.models.base module

Base class for models.

class pycbc.inference.models.base.BaseModel(variable_params, static_params=None, prior=None, sampling_transforms=None, waveform_transforms=None)

Bases: object

Base class for all models.

Given some model \(h\) with parameters \(\Theta\), Bayes Theorem states that the probability of observing parameter values \(\vartheta\) is:

\[p(\vartheta|h) = \frac{p(h|\vartheta) p(\vartheta)}{p(h)}.\]

Here:

• \(p(\vartheta|h)\) is the posterior probability;
• \(p(h|\vartheta)\) is the likelihood;
• \(p(\vartheta)\) is the prior;
• \(p(h)\) is the evidence.

This class defines properties and methods for evaluating the log likelihood, log prior, and log posteror. A set of parameter values is set using the update method. Calling the class’s log(likelihood|prior|posterior) properties will then evaluate the model at those parameter values.

Classes that inherit from this class must implement a _loglikelihood function that can be called by loglikelihood.

Parameters:

• variable_params ((tuple of) string(s)) – A tuple of parameter names that will be varied.
• static_params (dict, optional) – A dictionary of parameter names -> values to keep fixed.
• prior (callable, optional) – A callable class or function that computes the log of the prior. If None provided, will use _noprior, which returns 0 for all parameter values.
• sampling_params (list, optional) – Replace one or more of the variable_params with the given parameters for sampling.
• replace_parameters (list, optional) – The variable_params to replace with sampling parameters. Must be the same length as sampling_params.
• sampling_transforms (list, optional) – List of transforms to use to go between the variable_params and the sampling parameters. Required if sampling_params is not None.
• waveform_transforms (list, optional) – A list of transforms to convert the variable_params into something understood by the likelihood model. This is useful if the prior is more easily parameterized in parameters that are different than what the likelihood is most easily defined in. Since these are used solely for converting parameters, and not for rescaling the parameter space, a Jacobian is not required for these transforms.
• Properties –
• ---------- –
• logjacobian – Returns the log of the jacobian needed to go from the parameter space of the variable_params to the sampling params.
• logprior – Returns the log of the prior.
• loglikelihood – A function that returns the log of the likelihood function.
• logposterior – A function that returns the log of the posterior.
• loglr – A function that returns the log of the likelihood ratio.
• logplr – A function that returns the log of the prior-weighted likelihood ratio.

current_params

current_stats

Return the default_stats as a dict.

This does no computation. It only returns what has already been calculated. If a stat hasn’t been calculated, it will be returned as numpy.nan.

Returns:Dictionary of stat names -> current stat values. Return type:dict

default_stats

The stats that get_current_stats returns by default.

static extra_args_from_config(cp, section, skip_args=None, dtypes=None)

Gets any additional keyword in the given config file.

Parameters:

• cp (WorkflowConfigParser) – Config file parser to read.
• section (str) – The name of the section to read.
• skip_args (list of str, optional) – Names of arguments to skip.
• dtypes (dict, optional) – A dictionary of arguments -> data types. If an argument is found in the dict, it will be cast to the given datatype. Otherwise, the argument’s value will just be read from the config file (and thus be a string).

Returns:

Dictionary of keyword arguments read from the config file.

Return type:

dict

classmethod from_config(cp, **kwargs)

Initializes an instance of this class from the given config file.

Parameters:

• cp (WorkflowConfigParser) – Config file parser to read.
• **kwargs – All additional keyword arguments are passed to the class. Any provided keyword will over ride what is in the config file.

get_current_stats(names=None)

Return one or more of the current stats as a tuple.

This function does no computation. It only returns what has already been calculated. If a stat hasn’t been calculated, it will be returned as numpy.nan.

Parameters:names (list of str, optional) – Specify the names of the stats to retrieve. If None (the default), will return default_stats. Returns:The current values of the requested stats, as a tuple. The order of the stats is the same as the names. Return type:tuple

logjacobian

The log jacobian of the sampling transforms at the current postion.

If no sampling transforms were provided, will just return 0.

Parameters:**params – The keyword arguments should specify values for all of the variable args and all of the sampling args. Returns:The value of the jacobian. Return type:float

loglikelihood

The log likelihood at the current parameters.

This will initially try to return the current_stats.loglikelihood. If that raises an AttributeError, will call _loglikelihood` to calculate it and store it to current_stats.

logposterior

Returns the log of the posterior of the current parameter values.

The logprior is calculated first. If the logprior returns -inf (possibly indicating a non-physical point), then the loglikelihood is not called.

logprior

Returns the log prior at the current parameters.

name = None

static prior_from_config(cp, variable_params, prior_section, constraint_section)

Gets arguments and keyword arguments from a config file.

Parameters:

• cp (WorkflowConfigParser) – Config file parser to read.
• variable_params (list) – List of of model parameter names.
• prior_section (str) – Section to read prior(s) from.
• constraint_section (str) – Section to read constraint(s) from.

Returns:

The prior.

Return type:

pycbc.distributions.JointDistribution

prior_rvs(size=1, prior=None)

Returns random variates drawn from the prior.

If the sampling_params are different from the variable_params, the variates are transformed to the sampling_params parameter space before being returned.

Parameters:

• size (int, optional) – Number of random values to return for each parameter. Default is 1.
• prior (JointDistribution, optional) – Use the given prior to draw values rather than the saved prior.

Returns:

A field array of the random values.

Return type:

FieldArray

sampling_params

Returns the sampling parameters.

If sampling_transforms is None, this is the same as the variable_params.

static_params

Returns the model’s static arguments.

update(**params)

Updates the current parameter positions and resets stats.

If any sampling transforms are specified, they are applied to the params before being stored.

variable_params

Returns the model parameters.

write_metadata(fp)

Writes metadata to the given file handler.

Parameters:fp (pycbc.inference.io.BaseInferenceFile instance) – The inference file to write to.

class pycbc.inference.models.base.ModelStats

Bases: object

Class to hold model’s current stat values.

getstats(names, default=nan)

Get the requested stats as a tuple.

If a requested stat is not an attribute (implying it hasn’t been stored), then the default value is returned for that stat.

Parameters:

• names (list of str) – The names of the stats to get.
• default (float, optional) – What to return if a requested stat is not an attribute of self. Default is numpy.nan.

Returns:

A tuple of the requested stats.

Return type:

tuple

getstatsdict(names, default=nan)

Get the requested stats as a dictionary.

If a requested stat is not an attribute (implying it hasn’t been stored), then the default value is returned for that stat.

Parameters:

• names (list of str) – The names of the stats to get.
• default (float, optional) – What to return if a requested stat is not an attribute of self. Default is numpy.nan.

Returns:

A dictionary of the requested stats.

Return type:

dict

statnames

Returns the names of the stats that have been stored.

class pycbc.inference.models.base.SamplingTransforms(variable_params, sampling_params, replace_parameters, sampling_transforms)

Bases: object

Provides methods for transforming between sampling parameter space and model parameter space.

apply(samples, inverse=False)

Applies the sampling transforms to the given samples.

Parameters:

• samples (dict or FieldArray) – The samples to apply the transforms to.
• inverse (bool, optional) – Whether to apply the inverse transforms (i.e., go from the sampling args to the variable_params). Default is False.

Returns:

The transformed samples, along with the original samples.

Return type:

dict or FieldArray

classmethod from_config(cp, variable_params)

Gets sampling transforms specified in a config file.

Sampling parameters and the parameters they replace are read from the sampling_params section, if it exists. Sampling transforms are read from the sampling_transforms section(s), using transforms.read_transforms_from_config.

An AssertionError is raised if no sampling_params section exists in the config file.

Parameters:

• cp (WorkflowConfigParser) – Config file parser to read.
• variable_params (list) – List of parameter names of the original variable params.

Returns:

A sampling transforms class.

Return type:

SamplingTransforms

logjacobian(**params)

Returns the log of the jacobian needed to transform pdfs in the variable_params parameter space to the sampling_params parameter space.

Let \(\mathbf{x}\) be the set of variable parameters, \(\mathbf{y} = f(\mathbf{x})\) the set of sampling parameters, and \(p_x(\mathbf{x})\) a probability density function defined over \(\mathbf{x}\). The corresponding pdf in \(\mathbf{y}\) is then:

\[p_y(\mathbf{y}) = p_x(\mathbf{x})\left|\mathrm{det}\,\mathbf{J}_{ij}\right|,\]

where \(\mathbf{J}_{ij}\) is the Jacobian of the inverse transform \(\mathbf{x} = g(\mathbf{y})\). This has elements:

\[\mathbf{J}_{ij} = \frac{\partial g_i}{\partial{y_j}}\]

This function returns \(\log \left|\mathrm{det}\,\mathbf{J}_{ij}\right|\).

Parameters:**params – The keyword arguments should specify values for all of the variable args and all of the sampling args. Returns:The value of the jacobian. Return type:float

pycbc.inference.models.base.read_sampling_params_from_config(cp, section_group=None, section='sampling_params')

Reads sampling parameters from the given config file.

Parameters are read from the [({section_group}_){section}] section. The options should list the variable args to transform; the parameters they point to should list the parameters they are to be transformed to for sampling. If a multiple parameters are transformed together, they should be comma separated. Example:

[sampling_params]
mass1, mass2 = mchirp, logitq
spin1_a = logitspin1_a

Note that only the final sampling parameters should be listed, even if multiple intermediate transforms are needed. (In the above example, a transform is needed to go from mass1, mass2 to mchirp, q, then another one needed to go from q to logitq.) These transforms should be specified in separate sections; see transforms.read_transforms_from_config for details.

Parameters:

• cp (WorkflowConfigParser) – An open config parser to read from.
• section_group (str, optional) – Append {section_group}_ to the section name. Default is None.
• section (str, optional) – The name of the section. Default is ‘sampling_params’.

Returns:

• sampling_params (list) – The list of sampling parameters to use instead.
• replaced_params (list) – The list of variable args to replace in the sampler.

pycbc.inference.models.base_data module

Base classes for models with data.

class pycbc.inference.models.base_data.BaseDataModel(variable_params, data, recalibration=None, gates=None, injection_file=None, no_save_data=False, **kwargs)

Bases: pycbc.inference.models.base.BaseModel

Base class for models that require data and a waveform generator.

This adds propeties for the log of the likelihood that the data contain noise, lognl, and the log likelihood ratio loglr.

Classes that inherit from this class must define _loglr and _lognl functions, in addition to the _loglikelihood requirement inherited from BaseModel.

Parameters:

• variable_params ((tuple of) string(s)) – A tuple of parameter names that will be varied.
• data (dict) – A dictionary of data, in which the keys are the detector names and the values are the data.
• recalibration (dict of pycbc.calibration.Recalibrate, optional) – Dictionary of detectors -> recalibration class instances for recalibrating data.
• gates (dict of tuples, optional) – Dictionary of detectors -> tuples of specifying gate times. The sort of thing returned by pycbc.gate.gates_from_cli.
• injection_file (str, optional) – If an injection was added to the data, the name of the injection file used. If provided, the injection parameters will be written to file when write_metadata is called.
• **kwargs – All other keyword arguments are passed to BaseModel.

data

The data that the class was initialized with.

Type:dict

detectors

List of detector names used.

Type:list

lognl

Returns the log likelihood of the noise.

loglr

Returns the log of the likelihood ratio.

logplr

Returns the log of the prior-weighted likelihood ratio.

See ``BaseModel`` for additional attributes and properties.

data

Dictionary mapping detector names to data.

detectors

Returns the detectors used.

loglr

The log likelihood ratio at the current parameters.

This will initially try to return the current_stats.loglr. If that raises an AttributeError, will call _loglr` to calculate it and store it to current_stats.

lognl

The log likelihood of the model assuming the data is noise.

This will initially try to return the current_stats.lognl. If that raises an AttributeError, will call _lognl` to calculate it and store it to current_stats.

logplr

Returns the log of the prior-weighted likelihood ratio at the current parameter values.

The logprior is calculated first. If the logprior returns -inf (possibly indicating a non-physical point), then loglr is not called.

write_metadata(fp)

Adds data to the metadata that’s written.

Parameters:fp (pycbc.inference.io.BaseInferenceFile instance) – The inference file to write to.

pycbc.inference.models.brute_marg module

This module provides model classes that do brute force marginalization using at the likelihood level.

class pycbc.inference.models.brute_marg.BruteParallelGaussianMarginalize(variable_params, cores=10, base_model=None, marginalize_phase=None, **kwds)

Bases: pycbc.inference.models.gaussian_noise.BaseGaussianNoise

name = 'brute_parallel_gaussian_marginalize'

class pycbc.inference.models.brute_marg.likelihood_wrapper(model)

Bases: object

pycbc.inference.models.data_utils module

Utilities for loading data for models.

exception pycbc.inference.models.data_utils.NoValidDataError

Bases: Exception

This should be raised if a continous segment of valid data could not be found.

pycbc.inference.models.data_utils.check_for_nans(strain_dict)

Checks if any data in a dictionary of strains has NaNs.

If any NaNs are found, a ValueError is raised.

Parameters:strain_dict (dict) – Dictionary of detectors -> pycbc.types.timeseries.TimeSeries.

pycbc.inference.models.data_utils.check_validtimes(detector, gps_start, gps_end, shift_to_valid=False, max_shift=None, segment_name='DATA', **kwargs)

Checks DQ server to see if the given times are in a valid segment.

If the shift_to_valid flag is provided, the times will be shifted left or right to try to find a continous valid block nearby. The shifting starts by shifting the times left by 1 second. If that does not work, it shifts the times right by one second. This continues, increasing the shift time by 1 second, until a valid block could be found, or until the shift size exceeds max_shift.

If the given times are not in a continuous valid segment, or a valid block cannot be found nearby, a NoValidDataError is raised.

Parameters:

• detector (str) – The name of the detector to query; e.g., ‘H1’.
• gps_start (int) – The GPS start time of the segment to query.
• gps_end (int) – The GPS end time of the segment to query.
• shift_to_valid (bool, optional) – If True, will try to shift the gps start and end times to the nearest continous valid segment of data. Default is False.
• max_shift (int, optional) – The maximum number of seconds to try to shift left or right to find a valid segment. Default is gps_end - gps_start.
• segment_name (str, optional) – The status flag to query; passed to pycbc.dq.query_flag(). Default is “DATA”.
• **kwargs – All other keyword arguments are passed to pycbc.dq.query_flag().

Returns:

• use_start (int) – The start time to use. If shift_to_valid is True, this may differ from the given GPS start time.
• use_end (int) – The end time to use. If shift_to_valid is True, this may differ from the given GPS end time.

pycbc.inference.models.data_utils.create_data_parser()

Creates an argument parser for loading GW data.

pycbc.inference.models.data_utils.data_from_cli(opts, check_for_valid_times=False, shift_psd_times_to_valid=False, err_on_missing_detectors=False)

Loads the data needed for a model from the given command-line options.

Gates specifed on the command line are also applied.

Parameters:

• opts (ArgumentParser parsed args) – Argument options parsed from a command line string (the sort of thing returned by parser.parse_args).
• check_for_valid_times (bool, optional) – Check that valid data exists in the requested gps times. Default is False.
• shift_psd_times_to_valid (bool, optional) – If estimating the PSD from data, shift the PSD times to a valid segment if needed. Default is False.
• err_on_missing_detectors (bool, optional) – Raise a NoValidDataError if any detector does not have valid data. Otherwise, a warning is printed, and that detector is skipped.

Returns:

• strain_dict (dict) – Dictionary of detectors -> time series strain.
• psd_strain_dict (dict or None) – If opts.psd_(start|end)_time were set, a dctionary of detectors -> time series data to use for PSD estimation. Otherwise, None.

pycbc.inference.models.data_utils.data_opts_from_config(cp, section, filter_flow)

Loads data options from a section in a config file.

Parameters:

• cp (WorkflowConfigParser) – Config file to read.
• section (str) – The section to read. All options in the section will be loaded as-if they wre command-line arguments.
• filter_flow (dict) – Dictionary of detectors -> inner product low frequency cutoffs. If a data-conditioning-low-freq cutoff wasn’t provided for any of the detectors, these values will be used. Otherwise, the data-conditioning-low-freq must be less than the inner product cutoffs. If any are not, a ValueError is raised.

Returns:

opts – An argument parser namespace that was constructed as if the options were specified on the command line.

Return type:

parsed argparse.ArgumentParser

pycbc.inference.models.data_utils.detectors_with_valid_data(detectors, gps_start_times, gps_end_times, pad_data=None, err_on_missing_detectors=False, **kwargs)

Determines which detectors have valid data.

Parameters:

• detectors (list of str) – Names of the detector names to check.
• gps_start_times (dict) – Dictionary of detector name -> start time listing the GPS start times of the segment to check for each detector.
• gps_end_times (dict) – Dictionary of detector name -> end time listing the GPS end times of the segment to check for each detector.
• pad_data (dict, optional) – Dictionary of detector name -> pad time to add to the beginning/end of the GPS start/end times before checking. A pad time for every detector in detectors must be given. Default (None) is to apply no pad to the times.
• err_on_missing_detectors (bool, optional) – If True, a NoValidDataError will be raised if any detector does not have continous valid data in its requested segment. Otherwise, the detector will not be included in the returned list of detectors with valid data. Default is False.
• **kwargs – All other keyword arguments are passed to check_validtimes.

Returns:

A dictionary of detector name -> valid times giving the detectors with valid data and their segments. If shift_to_valid was passed to check_validtimes this may not be the same as the input segments. If no valid times could be found for a detector (and err_on_missing_detectors is False), it will not be included in the returned dictionary.

Return type:

dict

pycbc.inference.models.data_utils.fd_data_from_strain_dict(opts, strain_dict, psd_strain_dict=None)

Converts a dictionary of time series to the frequency domain, and gets the PSDs.

Parameters:

• opts (ArgumentParser parsed args) – Argument options parsed from a command line string (the sort of thing returned by parser.parse_args).
• strain_dict (dict) – Dictionary of detectors -> time series data.
• psd_strain_dict (dict, optional) – Dictionary of detectors -> time series data to use for PSD estimation. If not provided, will use the strain_dict. This is ignored if opts.psd_estimation is not set. See pycbc.psd.psd_from_cli_multi_ifos() for details.

Returns:

• stilde_dict (dict) – Dictionary of detectors -> frequency series data.
• psd_dict (dict) – Dictionary of detectors -> frequency-domain PSDs.

pycbc.inference.models.data_utils.gate_overwhitened_data(stilde_dict, psd_dict, gates)

Applies gates to overwhitened data.

Parameters:

• stilde_dict (dict) – Dictionary of detectors -> frequency series data to apply the gates to.
• psd_dict (dict) – Dictionary of detectors -> PSD to use for overwhitening.
• gates (dict) – Dictionary of detectors -> gates.

Returns:

Dictionary of detectors -> frequency series data with the gates applied after overwhitening. The returned data is not overwhitened.

Return type:

dict

pycbc.inference.models.data_utils.strain_from_cli_multi_ifos(*args, **kwargs)

Wrapper around strain.from_cli_multi_ifos that tries a few times before quiting.

When running in a parallel environment, multiple concurrent queries to the segment data base can cause time out errors. If that happens, this will sleep for a few seconds, then try again a few times before giving up.

pycbc.inference.models.gaussian_noise module

This module provides model classes that assume the noise is Gaussian.

class pycbc.inference.models.gaussian_noise.BaseGaussianNoise(variable_params, data, low_frequency_cutoff, psds=None, high_frequency_cutoff=None, normalize=False, static_params=None, ignore_failed_waveforms=False, no_save_data=False, **kwargs)

Bases: pycbc.inference.models.base_data.BaseDataModel

Model for analyzing GW data with assuming a wide-sense stationary Gaussian noise model.

This model will load gravitational wave data and calculate the log noise likelihood _lognl and normalization. It also implements the _loglikelihood function as the sum of the log likelihood ratio and the lognl. It does not implement a log likelihood ratio function _loglr, however, since that can differ depending on the signal model. Models that analyze GW data assuming it is stationary Gaussian should therefore inherit from this class and implement their own _loglr function.

For more details on the inner product used, the log likelihood of the noise, and the normalization factor, see GaussianNoise.

Parameters:

• variable_params ((tuple of) string(s)) – A tuple of parameter names that will be varied.
• data (dict) – A dictionary of data, in which the keys are the detector names and the values are the data (assumed to be unwhitened). All data must have the same frequency resolution.
• low_frequency_cutoff (dict) – A dictionary of starting frequencies, in which the keys are the detector names and the values are the starting frequencies for the respective detectors to be used for computing inner products.
• psds (dict, optional) – A dictionary of FrequencySeries keyed by the detector names. The dictionary must have a psd for each detector specified in the data dictionary. If provided, the inner products in each detector will be weighted by 1/psd of that detector.
• high_frequency_cutoff (dict, optional) – A dictionary of ending frequencies, in which the keys are the detector names and the values are the ending frequencies for the respective detectors to be used for computing inner products. If not provided, the minimum of the largest frequency stored in the data and a given waveform will be used.
• normalize (bool, optional) – If True, the normalization factor \(alpha\) will be included in the log likelihood. See GaussianNoise for details. Default is to not include it.
• static_params (dict, optional) – A dictionary of parameter names -> values to keep fixed.
• ignore_failed_waveforms (bool, optional) – If the waveform generator raises an error when it tries to generate, treat the point as having zero likelihood. This allows the parameter estimation to continue. Otherwise, an error will be raised, stopping the run. Default is False.
• **kwargs – All other keyword arguments are passed to BaseDataModel.

data

Dictionary of detectors -> frequency-domain data.

Type:dict

ignore_failed_waveforms

If True, points in parameter space that cause waveform generation to fail (i.e., they raise a FailedWaveformError) will be treated as points with zero likelihood. Otherwise, such points will cause the model to raise a FailedWaveformError.

Type:bool

low_frequency_cutoff

high_frequency_cutoff

kmin

kmax

psds

psd_segments

weight

whitened_data

normalize

lognorm

det_lognl(det)

Returns the log likelihood of the noise in the given detector:

\[\log p(d_i|n_i) = \log \alpha_i - \frac{1}{2} \left<d_i | d_i\right>.\]

Parameters:det (str) – The name of the detector. Returns:The log likelihood of the noise in the requested detector. Return type:float

det_lognorm(det)

The log of the likelihood normalization in the given detector.

If self.normalize is False, will just return 0.

classmethod from_config(cp, data_section='data', data=None, psds=None, **kwargs)

Initializes an instance of this class from the given config file.

In addition to [model], a data_section (default [data]) must be in the configuration file. The data section specifies settings for loading data and estimating PSDs. See the online documentation for more details.

The following options are read from the [model] section, in addition to name (which must be set):

• {{DET}}-low-frequency-cutoff = FLOAT : The low frequency cutoff to use for each detector {{DET}}. A cutoff must be provided for every detector that may be analyzed (any additional detectors are ignored).
• {{DET}}-high-frequency-cutoff = FLOAT : (Optional) A high frequency cutoff for each detector. If not provided, the Nyquist frequency is used.
• check-for-valid-times = : (Optional) If provided, will check that there are no data quality flags on during the analysis segment and the segment used for PSD estimation in each detector. To check for flags, pycbc.dq.query_flag() is used, with settings pulled from the dq-* options in the [data] section. If a detector has bad data quality during either the analysis segment or PSD segment, it will be removed from the analysis.
• shift-psd-times-to-valid = : (Optional) If provided, the segment used for PSD estimation will automatically be shifted left or right until a continous block of data with no data quality issues can be found. If no block can be found with a maximum shift of +/- the requested psd segment length, the detector will not be analyzed.
• err-on-missing-detectors = : Raises an error if any detector is removed from the analysis because a valid time could not be found. Otherwise, a warning is printed to screen and the detector is removed from the analysis.
• normalize = : (Optional) Turn on the normalization factor.
• ignore-failed-waveforms = : Sets the ignore_failed_waveforms attribute.

Parameters:

• cp (WorkflowConfigParser) – Config file parser to read.
• data_section (str, optional) – The name of the section to load data options from.
• **kwargs – All additional keyword arguments are passed to the class. Any provided keyword will over ride what is in the config file.

high_frequency_cutoff

The high frequency cutoff of the inner product.

kmax

Dictionary of ending indices for the inner product.

This is determined from the high frequency cutoff and the delta_f of the data using pycbc.filter.matchedfilter.get_cutoff_indices(). If no high frequency cutoff was provided, this will be the indice corresponding to the Nyquist frequency.

kmin

Dictionary of starting indices for the inner product.

This is determined from the lower frequency cutoff and the delta_f of the data using pycbc.filter.matchedfilter.get_cutoff_indices().

lognorm

The log of the normalization of the log likelihood.

low_frequency_cutoff

The low frequency cutoff of the inner product.

normalize

Determines if the loglikelihood includes the normalization term.

psd_segments

Dictionary giving times used for PSD estimation for each detector.

If a detector’s PSD was not estimated from data, or the segment wasn’t provided, that detector will not be in the dictionary.

psds

Dictionary of detectors -> PSD frequency series.

If no PSD was provided for a detector, this will just be a frequency series of ones.

set_psd_segments(psds)

Sets the PSD segments from a dictionary of PSDs.

This attempts to get the PSD segment from a psd_segment attribute of each detector’s PSD frequency series. If that attribute isn’t set, then that detector is not added to the dictionary of PSD segments.

Parameters:psds (dict) – Dictionary of detector name -> PSD frequency series. The segment used for each PSD will try to be retrieved from the PSD’s .psd_segment attribute.

weight

Dictionary of detectors -> frequency series of inner-product weights.

The weights are \(\sqrt{4 \Delta f / S_n(f)}\). This is set when the PSDs are set.

whitened_data

Dictionary of detectors -> whitened data frequency series.

The whitened data is the data multiplied by the inner-product weight. Note that this includes the \(\sqrt{4 \Delta f}\) factor. This is set when the PSDs are set.

write_metadata(fp)

Adds writing the psds and lognl, since it’s a constant.

The lognl is written to the sample group’s attrs.

The analyzed detectors, their analysis segments, and the segments used for psd estimation are written to the file’s attrs, as analyzed_detectors, {{detector}}_analysis_segment, and {{detector}}_psd_segment, respectively.

Parameters:fp (pycbc.inference.io.BaseInferenceFile instance) – The inference file to write to.

class pycbc.inference.models.gaussian_noise.GaussianNoise(variable_params, data, low_frequency_cutoff, psds=None, high_frequency_cutoff=None, normalize=False, static_params=None, **kwargs)

Bases: pycbc.inference.models.gaussian_noise.BaseGaussianNoise

Model that assumes data is stationary Gaussian noise.

With Gaussian noise the log likelihood functions for signal \(\log p(d|\Theta, h)\) and for noise \(\log p(d|n)\) are given by:

\[\begin{split}\log p(d|\Theta, h) &= \log\alpha -\frac{1}{2} \sum_i \left< d_i - h_i(\Theta) | d_i - h_i(\Theta) \right> \\ \log p(d|n) &= \log\alpha -\frac{1}{2} \sum_i \left<d_i | d_i\right>\end{split}\]

where the sum is over the number of detectors, \(d_i\) is the data in each detector, and \(h_i(\Theta)\) is the model signal in each detector. The (discrete) inner product is given by:

\[\left<a_i | b_i\right> = 4\Re \Delta f \sum_{k=k_{\mathrm{min}}}^{k_{\mathrm{max}}} \frac{\tilde{a}_i^{*}[k] \tilde{b}_i[k]}{S^{(i)}_n[k]},\]

where \(\Delta f\) is the frequency resolution (given by 1 / the observation time \(T\)), \(k\) is an index over the discretely sampled frequencies \(f = k \Delta_f\), and \(S^{(i)}_n[k]\) is the PSD in the given detector. The upper cutoff on the inner product \(k_{\max}\) is by default the Nyquist frequency \(k_{\max} = N/2+1\), where \(N = \lfloor T/\Delta t \rfloor\) is the number of samples in the time domain, but this can be set manually to a smaller value.

The normalization factor \(\alpha\) is:

\[\alpha = \prod_{i} \frac{1}{\left(\pi T\right)^{N/2} \prod_{k=k_\mathrm{min}}^{k_{\mathrm{max}}} S^{(i)}_n[k]},\]

where the product is over the number of detectors. By default, the normalization constant is not included in the log likelihood, but it can be turned on using the normalize keyword argument.

Note that the log likelihood ratio has fewer terms than the log likelihood, since the normalization and \(\left<d_i|d_i\right>\) terms cancel:

\[\log \mathcal{L}(\Theta) = \sum_i \left[ \left<h_i(\Theta)|d_i\right> - \frac{1}{2} \left<h_i(\Theta)|h_i(\Theta)\right> \right]\]

Upon initialization, the data is whitened using the given PSDs. If no PSDs are given the data and waveforms returned by the waveform generator are assumed to be whitened.

For more details on initialization parameters and definition of terms, see models.BaseDataModel.

Parameters:

• variable_params ((tuple of) string(s)) – A tuple of parameter names that will be varied.
• data (dict) – A dictionary of data, in which the keys are the detector names and the values are the data (assumed to be unwhitened). The list of keys must match the waveform generator’s detectors keys, and the epoch of every data set must be the same as the waveform generator’s epoch.
• low_frequency_cutoff (dict) – A dictionary of starting frequencies, in which the keys are the detector names and the values are the starting frequencies for the respective detectors to be used for computing inner products.
• psds (dict, optional) – A dictionary of FrequencySeries keyed by the detector names. The dictionary must have a psd for each detector specified in the data dictionary. If provided, the inner products in each detector will be weighted by 1/psd of that detector.
• high_frequency_cutoff (dict, optional) – A dictionary of ending frequencies, in which the keys are the detector names and the values are the ending frequencies for the respective detectors to be used for computing inner products. If not provided, the minimum of the largest frequency stored in the data and a given waveform will be used.
• normalize (bool, optional) – If True, the normalization factor \(alpha\) will be included in the log likelihood. Default is to not include it.
• static_params (dict, optional) – A dictionary of parameter names -> values to keep fixed.
• **kwargs – All other keyword arguments are passed to BaseDataModel.

Examples

Create a signal, and set up the model using that signal:

>>> from pycbc import psd as pypsd
>>> from pycbc.inference.models import GaussianNoise
>>> from pycbc.waveform.generator import (FDomainDetFrameGenerator,
...                                       FDomainCBCGenerator)
>>> seglen = 4
>>> sample_rate = 2048
>>> N = seglen*sample_rate/2+1
>>> fmin = 30.
>>> static_params = {'approximant': 'IMRPhenomD', 'f_lower': fmin,
...                  'mass1': 38.6, 'mass2': 29.3,
...                  'spin1z': 0., 'spin2z': 0., 'ra': 1.37, 'dec': -1.26,
...                  'polarization': 2.76, 'distance': 3*500.}
>>> variable_params = ['tc']
>>> tsig = 3.1
>>> generator = FDomainDetFrameGenerator(
...     FDomainCBCGenerator, 0., detectors=['H1', 'L1'],
...     variable_args=variable_params,
...     delta_f=1./seglen, **static_params)
>>> signal = generator.generate(tc=tsig)
>>> psd = pypsd.aLIGOZeroDetHighPower(N, 1./seglen, 20.)
>>> psds = {'H1': psd, 'L1': psd}
>>> low_frequency_cutoff = {'H1': fmin, 'L1': fmin}
>>> model = GaussianNoise(variable_params, signal, low_frequency_cutoff,
                          psds=psds, static_params=static_params)

Set the current position to the coalescence time of the signal:

>>> model.update(tc=tsig)

Now compute the log likelihood ratio and prior-weighted likelihood ratio; since we have not provided a prior, these should be equal to each other:

>>> print('{:.2f}'.format(model.loglr))
282.43
>>> print('{:.2f}'.format(model.logplr))
282.43

Print all of the default_stats:

>>> print(',\n'.join(['{}: {:.2f}'.format(s, v)
...                   for (s, v) in sorted(model.current_stats.items())]))
H1_cplx_loglr: 177.76+0.00j,
H1_optimal_snrsq: 355.52,
L1_cplx_loglr: 104.67+0.00j,
L1_optimal_snrsq: 209.35,
logjacobian: 0.00,
loglikelihood: 0.00,
loglr: 282.43,
logprior: 0.00

Compute the SNR; for this system and PSD, this should be approximately 24:

>>> from pycbc.conversions import snr_from_loglr
>>> x = snr_from_loglr(model.loglr)
>>> print('{:.2f}'.format(x))
23.77

Since there is no noise, the SNR should be the same as the quadrature sum of the optimal SNRs in each detector:

>>> x = (model.det_optimal_snrsq('H1') +
...      model.det_optimal_snrsq('L1'))**0.5
>>> print('{:.2f}'.format(x))
23.77

Toggle on the normalization constant:

>>> model.normalize = True
>>> model.loglikelihood
835397.8757405131

Using the same model, evaluate the log likelihood ratio at several points in time and check that the max is at tsig:

>>> import numpy
>>> times = numpy.linspace(tsig-1, tsig+1, num=101)
>>> loglrs = numpy.zeros(len(times))
>>> for (ii, t) in enumerate(times):
...     model.update(tc=t)
...     loglrs[ii] = model.loglr
>>> print('tsig: {:.2f}, time of max loglr: {:.2f}'.format(
...     tsig, times[loglrs.argmax()]))
tsig: 3.10, time of max loglr: 3.10

Create a prior and use it (see distributions module for more details):

>>> from pycbc import distributions
>>> uniform_prior = distributions.Uniform(tc=(tsig-0.2,tsig+0.2))
>>> prior = distributions.JointDistribution(variable_params, uniform_prior)
>>> model = GaussianNoise(variable_params,
...     signal, low_frequency_cutoff, psds=psds, prior=prior,
...     static_params=static_params)
>>> model.update(tc=tsig)
>>> print('{:.2f}'.format(model.logplr))
283.35
>>> print(',\n'.join(['{}: {:.2f}'.format(s, v)
...                   for (s, v) in sorted(model.current_stats.items())]))
H1_cplx_loglr: 177.76+0.00j,
H1_optimal_snrsq: 355.52,
L1_cplx_loglr: 104.67+0.00j,
L1_optimal_snrsq: 209.35,
logjacobian: 0.00,
loglikelihood: 0.00,
loglr: 282.43,
logprior: 0.92

det_cplx_loglr(det)

Returns the complex log likelihood ratio in the given detector.

Parameters:det (str) – The name of the detector. Returns:The complex log likelihood ratio. Return type:complex float

det_optimal_snrsq(det)

Returns the opitmal SNR squared in the given detector.

Parameters:det (str) – The name of the detector. Returns:The opimtal SNR squared. Return type:float

name = 'gaussian_noise'

pycbc.inference.models.gaussian_noise.create_waveform_generator(variable_params, data, waveform_transforms=None, recalibration=None, gates=None, generator_class=<class 'pycbc.waveform.generator.FDomainDetFrameGenerator'>, **static_params)

Creates a waveform generator for use with a model.

Parameters:

• variable_params (list of str) – The names of the parameters varied.
• data (dict) – Dictionary mapping detector names to either a <pycbc.types.TimeSeries TimeSeries> or <pycbc.types.FrequencySeries FrequencySeries>.
• waveform_transforms (list, optional) – The list of transforms applied to convert variable parameters into parameters that will be understood by the waveform generator.
• recalibration (dict, optional) – Dictionary mapping detector names to <pycbc.calibration.Recalibrate> instances for recalibrating data.
• gates (dict of tuples, optional) – Dictionary of detectors -> tuples of specifying gate times. The sort of thing returned by pycbc.gate.gates_from_cli().
• generator_class (detector-frame fdomain generator, optional) – Class to use for generating waveforms. Default is waveform.generator.FDomainDetFrameGenerator.
• **static_params – All other keyword arguments are passed as static parameters to the waveform generator.

Returns:

A waveform generator for frequency domain generation.

Return type:

pycbc.waveform.FDomainDetFrameGenerator

pycbc.inference.models.gaussian_noise.get_values_from_injection(cp, injection_file, update_cp=True)

Replaces all FROM_INJECTION values in a config file with the corresponding value from the injection.

This looks for any options that start with FROM_INJECTION[:ARG] in a config file. It then replaces that value with the corresponding value from the injection file. An argument may be optionally provided, in which case the argument will be retrieved from the injection file. Functions of parameters in the injection file may be used; the syntax and functions available is the same as the --parameters argument in executables such as pycbc_inference_extract_samples. If no ARG is provided, then the option name will try to be retrieved from the injection.

For example,

mass1 = FROM_INJECTION

will cause mass1 to be retrieved from the injection file, while:

will cause the larger of mass1 and mass2 to be retrieved from the injection file. Note that if spaces are in the argument, it must be encased in single quotes.

The injection file may contain only one injection. Otherwise, a ValueError will be raised.

Parameters:

• cp (ConfigParser) – The config file within which to replace values.
• injection_file (str or None) – The injection file to get values from. A ValueError will be raised if there are any FROM_INJECTION values in the config file, and injection file is None, or if there is more than one injection.
• update_cp (bool, optional) – Update the config parser with the replaced parameters. If False, will just retrieve the parameter values to update, without updating the config file. Default is True.

Returns:

The parameters that were replaced, as a tuple of section name, option, value.

Return type:

list

pycbc.inference.models.marginalized_gaussian_noise module

This module provides model classes that assume the noise is Gaussian and allows for the likelihood to be marginalized over phase and/or time and/or distance.

class pycbc.inference.models.marginalized_gaussian_noise.MarginalizedHMPolPhase(variable_params, data, low_frequency_cutoff, psds=None, high_frequency_cutoff=None, normalize=False, polarization_samples=100, coa_phase_samples=100, static_params=None, **kwargs)

Bases: pycbc.inference.models.gaussian_noise.BaseGaussianNoise

Numerically marginalizes waveforms with higher modes over polarization and phase.

This class implements the Gaussian likelihood with an explicit numerical marginalization over polarization angle and orbital phase. This is accomplished using a fixed set of integration points distributed uniformly between 0 and 2:math:pi for both the polarization and phase. By default, 100 integration points are used for each parameter, giving \(10^4\) evaluation points in total. This can be modified using the polarization_samples and coa_phase_samples arguments.

This only works with waveforms that return separate spherical harmonic modes for each waveform. For a list of currently supported approximants, see pycbc.waveform.waveform_modes.fd_waveform_mode_approximants() and pycbc.waveform.waveform_modes.td_waveform_mode_approximants().

Parameters:

• variable_params ((tuple of) string(s)) – A tuple of parameter names that will be varied.
• data (dict) – A dictionary of data, in which the keys are the detector names and the values are the data (assumed to be unwhitened). All data must have the same frequency resolution.
• low_frequency_cutoff (dict) – A dictionary of starting frequencies, in which the keys are the detector names and the values are the starting frequencies for the respective detectors to be used for computing inner products.
• psds (dict, optional) – A dictionary of FrequencySeries keyed by the detector names. The dictionary must have a psd for each detector specified in the data dictionary. If provided, the inner products in each detector will be weighted by 1/psd of that detector.
• high_frequency_cutoff (dict, optional) – A dictionary of ending frequencies, in which the keys are the detector names and the values are the ending frequencies for the respective detectors to be used for computing inner products. If not provided, the minimum of the largest frequency stored in the data and a given waveform will be used.
• normalize (bool, optional) – If True, the normalization factor \(alpha\) will be included in the log likelihood. See GaussianNoise for details. Default is to not include it.
• polarization_samples (int, optional) – How many points to use in polarization. Default is 100.
• coa_phase_samples (int, optional) – How many points to use in phase. Defaults is 100.
• **kwargs – All other keyword arguments are passed to gaussian_noise.BaseGaussianNoisei.

name = 'marginalized_hmpolphase'

phase_fac(m)

The phase \(\exp[i m \phi]\).

class pycbc.inference.models.marginalized_gaussian_noise.MarginalizedPhaseGaussianNoise(variable_params, data, low_frequency_cutoff, psds=None, high_frequency_cutoff=None, normalize=False, static_params=None, **kwargs)

Bases: pycbc.inference.models.gaussian_noise.BaseGaussianNoise

The likelihood is analytically marginalized over phase.

This class can be used with signal models that can be written as:

\[\tilde{h}(f; \Theta, \phi) = A(f; \Theta)e^{i\Psi(f; \Theta) + i \phi},\]

where \(\phi\) is an arbitrary phase constant. This phase constant can be analytically marginalized over with a uniform prior as follows: assuming the noise is stationary and Gaussian (see GaussianNoise for details), the posterior is:

\[\begin{split}p(\Theta,\phi|d) &\propto p(\Theta)p(\phi)p(d|\Theta,\phi) \\ &\propto p(\Theta)\frac{1}{2\pi}\exp\left[ -\frac{1}{2}\sum_{i}^{N_D} \left< h_i(\Theta,\phi) - d_i, h_i(\Theta,\phi) - d_i \right>\right].\end{split}\]

Here, the sum is over the number of detectors \(N_D\), \(d_i\) and \(h_i\) are the data and signal in detector \(i\), respectively, and we have assumed a uniform prior on \(phi \in [0, 2\pi)\). With the form of the signal model given above, the inner product in the exponent can be written as:

\[\begin{split}-\frac{1}{2}\left<h_i - d_i, h_i- d_i\right> &= \left<h_i, d_i\right> - \frac{1}{2}\left<h_i, h_i\right> - \frac{1}{2}\left<d_i, d_i\right> \\ &= \Re\left\{O(h^0_i, d_i)e^{-i\phi}\right\} - \frac{1}{2}\left<h^0_i, h^0_i\right> - \frac{1}{2}\left<d_i, d_i\right>,\end{split}\]

where:

\[\begin{split}h_i^0 &\equiv \tilde{h}_i(f; \Theta, \phi=0); \\ O(h^0_i, d_i) &\equiv 4 \int_0^\infty \frac{\tilde{h}_i^*(f; \Theta,0)\tilde{d}_i(f)}{S_n(f)}\mathrm{d}f.\end{split}\]

Gathering all of the terms that are not dependent on \(\phi\) together:

\[\alpha(\Theta, d) \equiv \exp\left[-\frac{1}{2}\sum_i \left<h^0_i, h^0_i\right> + \left<d_i, d_i\right>\right],\]

we can marginalize the posterior over \(\phi\):

\[\begin{split}p(\Theta|d) &\propto p(\Theta)\alpha(\Theta,d)\frac{1}{2\pi} \int_{0}^{2\pi}\exp\left[\Re \left\{ e^{-i\phi} \sum_i O(h^0_i, d_i) \right\}\right]\mathrm{d}\phi \\ &\propto p(\Theta)\alpha(\Theta, d)\frac{1}{2\pi} \int_{0}^{2\pi}\exp\left[ x(\Theta,d)\cos(\phi) + y(\Theta, d)\sin(\phi) \right]\mathrm{d}\phi.\end{split}\]

The integral in the last line is equal to \(2\pi I_0(\sqrt{x^2+y^2})\), where \(I_0\) is the modified Bessel function of the first kind. Thus the marginalized log posterior is:

\[\log p(\Theta|d) \propto \log p(\Theta) + I_0\left(\left|\sum_i O(h^0_i, d_i)\right|\right) - \frac{1}{2}\sum_i\left[ \left<h^0_i, h^0_i\right> - \left<d_i, d_i\right> \right]\]

name = 'marginalized_phase'

class pycbc.inference.models.marginalized_gaussian_noise.MarginalizedPolarization(variable_params, data, low_frequency_cutoff, psds=None, high_frequency_cutoff=None, normalize=False, polarization_samples=1000, static_params=None, **kwargs)

Bases: pycbc.inference.models.gaussian_noise.BaseGaussianNoise

This likelihood numerically marginalizes over polarization angle

This class implements the Gaussian likelihood with an explicit numerical marginalization over polarization angle. This is accomplished using a fixed set of integration points distribution uniformation between 0 and 2pi. By default, 1000 integration points are used. The ‘polarization_samples’ argument can be passed to set an alternate number of integration points.

name = 'marginalized_polarization'

pycbc.inference.models.relbin module

This module provides model classes and functions for implementing a relative binning likelihood for parameter estimation.

class pycbc.inference.models.relbin.Relative(variable_params, data, low_frequency_cutoff, fiducial_params=None, gammas=None, epsilon=0.5, earth_rotation=False, **kwargs)

Bases: pycbc.inference.models.gaussian_noise.BaseGaussianNoise

Model that assumes the likelihood in a region around the peak is slowly varying such that a linear approximation can be made, and likelihoods can be calculated at a coarser frequency resolution. For more details on the implementation, see https://arxiv.org/abs/1806.08792.

This model requires the use of a fiducial waveform whose parameters are near the peak of the likelihood. The fiducial waveform and all template waveforms used in likelihood calculation are currently generated using the SPAtmplt approximant.

For more details on initialization parameters and definition of terms, see BaseGaussianNoise.

Parameters:

• variable_params ((tuple of) string(s)) – A tuple of parameter names that will be varied.
• data (dict) – A dictionary of data, in which the keys are the detector names and the values are the data (assumed to be unwhitened). All data must have the same frequency resolution.
• low_frequency_cutoff (dict) – A dictionary of starting frequencies, in which the keys are the detector names and the values are the starting frequencies for the respective detectors to be used for computing inner products.
• figucial_params (dict) – A dictionary of waveform parameters to be used for generating the fiducial waveform. Keys must be parameter names in the form ‘PARAM_ref’ where PARAM is a recognized extrinsic parameter or an intrinsic parameter compatible with the chosen approximant.
• gammas (array of floats, optional) – Frequency powerlaw indices to be used in computing frequency bins.
• epsilon (float, optional) – Tuning parameter used in calculating the frequency bins. Lower values will result in higher resolution and more bins.
• earth_rotation (boolean, optional) – Default is False. If True, then vary the fp/fc polarization values as a function of frequency bin, using a predetermined PN approximation for the time offsets.
• **kwargs – All other keyword arguments are passed to BaseGaussianNoise.

static extra_args_from_config(cp, section, skip_args=None, dtypes=None)

Adds reading fiducial waveform parameters from config file.

get_waveforms(params)

Get the waveform polarizations for each ifo

name = 'relative'

summary_data(ifo)

Compute summary data bin coefficients encoding linear approximation to full resolution likelihood.

Returns:Dictionary containing bin coefficients a0, b0, a1, b1, for each frequency bin. Return type:dict

write_metadata(fp)

Adds writing the fiducial parameters and epsilon to file’s attrs.

Parameters:fp (pycbc.inference.io.BaseInferenceFile instance) – The inference file to write to.

pycbc.inference.models.relbin.setup_bins(f_full, f_lo, f_hi, chi=1.0, eps=0.5, gammas=None)

Construct frequency bins for use in a relative likelihood model. For details, see [Barak, Dai & Venumadhav 2018].

Parameters:

• f_full (array) – The full resolution array of frequencies being used in the analysis.
• f_lo (float) – The starting frequency used in matched filtering. This will be the left edge of the first frequency bin.
• f_hi (float) – The ending frequency used in matched filtering. This will be the right edge of the last frequency bin.
• chi (float, optional) – Tunable parameter, see [Barak, Dai & Venumadhav 2018]
• eps (float, optional) – Tunable parameter, see [Barak, Dai & Venumadhav 2018]. Lower values result in larger number of bins.
• gammas (array, optional) – Frequency powerlaw indices to be used in computing bins.

Returns:

• nbin (int) – Number of bins.
• fbin (numpy.array of floats) – Bin edge frequencies.
• fbin_ind (numpy.array of ints) – Indices of bin edges in full frequency array.

pycbc.inference.models.relbin_cpu module

Optimized inner loop functions for the relative likelihood model

pycbc.inference.models.relbin_cpu.likelihood_parts()

pycbc.inference.models.relbin_cpu.likelihood_parts_v()

pycbc.inference.models.single_template module

This module provides model classes that assume the noise is Gaussian.

class pycbc.inference.models.single_template.SingleTemplate(variable_params, data, low_frequency_cutoff, sample_rate=32768, polarization_samples=None, **kwargs)

Bases: pycbc.inference.models.gaussian_noise.BaseGaussianNoise

Model that assumes we know all the intrinsic parameters.

This model assumes we know all the intrinsic parameters, and are only maximizing over the extrinsic ones. We also assume a dominant mode waveform approximant only and non-precessing.

Parameters:

• variable_params ((tuple of) string(s)) – A tuple of parameter names that will be varied.
• data (dict) – A dictionary of data, in which the keys are the detector names and the values are the data (assumed to be unwhitened). All data must have the same frequency resolution.
• low_frequency_cutoff (dict) – A dictionary of starting frequencies, in which the keys are the detector names and the values are the starting frequencies for the respective detectors to be used for computing inner products.
• sample_rate (int, optional) – The sample rate to use. Default is 32768.
• polarization_samples (int, optional) – Parameter to specify how finely to marginalize over polarization angle. If None, then polarization must be a parameter.
• **kwargs – All other keyword arguments are passed to BaseGaussianNoise; see that class for details.

name = 'single_template'

Module contents

This package provides classes and functions for evaluating Bayesian statistics assuming various noise models.

class pycbc.inference.models.CallModel(model, callstat, return_all_stats=True)

Bases: object

Wrapper class for calling models from a sampler.

This class can be called like a function, with the parameter values to evaluate provided as a list in the same order as the model’s variable_params. In that case, the model is updated with the provided parameters and then the callstat retrieved. If return_all_stats is set to True, then all of the stats specified by the model’s default_stats will be returned as a tuple, in addition to the stat value.

The model’s attributes are promoted to this class’s namespace, so that any attribute and method of model may be called directly from this class.

This class must be initalized prior to the creation of a Pool object.

Parameters:

• model (Model instance) – The model to call.
• callstat (str) – The statistic to call.
• return_all_stats (bool, optional) – Whether or not to return all of the other statistics along with the callstat value.

Examples

Create a wrapper around an instance of the TestNormal model, with the callstat set to logposterior:

>>> from pycbc.inference.models import TestNormal, CallModel
>>> model = TestNormal(['x', 'y'])
>>> call_model = CallModel(model, 'logposterior')

Now call on a set of parameter values:

>>> call_model([0.1, -0.2])
(-1.8628770664093453, (0.0, 0.0, -1.8628770664093453))

Note that a tuple of all of the model’s default_stats were returned in addition to the logposterior value. We can shut this off by toggling return_all_stats:

>>> call_model.return_all_stats = False
>>> call_model([0.1, -0.2])
-1.8628770664093453

Attributes of the model can be called from the call model. For example:

>>> call_model.variable_params
('x', 'y')

pycbc.inference.models.read_from_config(cp, **kwargs)

Initializes a model from the given config file.

The section must have a name argument. The name argument corresponds to the name of the class to initialize.

Parameters:

• cp (WorkflowConfigParser) – Config file parser to read.
• **kwargs – All other keyword arguments are passed to the from_config method of the class specified by the name argument.

Returns:

The initialized model.

Return type:

cls