Package pylal :: Module bayespputils :: Class PEOutputParser

Class PEOutputParser

object --+
         |
        PEOutputParser

A parser for the output of Bayesian parameter estimation codes.

TODO: Will be abstract class when LDG moves over to Python >2.6, inherited by each method .

Instance Methods

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__init__(self, inputtype)
x.__init__(...) initializes x; see help(type(x)) for signature

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parse(self, files, **kwargs)
Parse files.

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_infmcmc_to_pos(self, files, outdir=None, deltaLogP=None, fixedBurnins=None, nDownsample=None, oldMassConvention=False, **kwargs)
Parser for lalinference_mcmcmpi output.

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_infmcmc_output_posterior_samples(self, files, runfile, outfile, logPThreshold, fixedBurnins, nskips=None, oldMassConvention=False)
Concatenate all the samples from the given files into outfile.

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_swaplabel12(self, label)

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_find_max_logP(self, files)
Given a list of files, reads them, finding the maximum log(post)

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_find_ndownsample(self, files, logPthreshold, fixedBurnins, nDownsample)
Given a list of files, threshold value, and a desired number of outputs posterior samples, return the skip number to achieve the desired number of posterior samples.

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_find_infmcmc_f_ref(self, runInfo)
Searches through header to determine reference frequency of waveforms.

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_find_infmcmc_f_lower(self, runInfo)
Searches through header to determine starting frequency of waveforms.

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_clear_infmcmc_header(self, infile)
Reads lalinference_mcmcmpi file given, returning the run info and common output header information.

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_mcmc_burnin_to_pos(self, files, spin=False, deltaLogP=None)
Parser for SPINspiral output .

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_ns_to_pos(self, files, Nlive=None, Npost=None, posfilename='posterior_samples.dat')
Parser for nested sampling output.

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_followupmcmc_to_pos(self, files)
Parser for followupMCMC output.

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_multinest_to_pos(self, files)
Parser for MultiNest output.

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_xml_to_pos(self, infile)
Parser for VOTable XML Using

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_VOTTABLE2pos(self, table)
Parser for a VOT TABLE element with FIELDs and TABLEDATA elements

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_hdf5s_to_pos(self, infiles, fixedBurnins=None, deltaLogP=None, nDownsample=None, tablename=None, **kwargs)

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_hdf5_to_table(self, infile, deltaLogP=None, fixedBurnin=None, nDownsample=None, multiple_chains=False, tablename=None, **kwargs)
Parse a HDF5 file and return an array of posterior samples ad list of parameter names.

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_hdf5_to_pos(self, infile, fixedBurnins=None, deltaLogP=None, nDownsample=None, tablename=None, **kwargs)

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_common_to_pos(self, infile, info=[None,None])
Parse a file in the 'common format' and return an array of posterior samples and list of parameter names.

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Inherited from object: __delattr__, __format__, __getattribute__, __hash__, __new__, __reduce__, __reduce_ex__, __repr__, __setattr__, __sizeof__, __str__, __subclasshook__

Properties

[hide private]

Inherited from object: __class__

Method Details

[hide private]

init(self, inputtype)
(Constructor)

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x.__init__(...) initializes x; see help(type(x)) for signature

Overrides: object.__init__: (inherited documentation)

_infmcmc_output_posterior_samples(self, files, runfile, outfile, logPThreshold, fixedBurnins, nskips=None, oldMassConvention=False)

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Concatenate all the samples from the given files into outfile. For each file, only those samples past the point where the log(post) > logPThreshold are concatenated after eliminating fixedBurnin.

_find_infmcmc_f_ref(self, runInfo)

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Searches through header to determine reference frequency of waveforms. If no fRef given, calls _find_infmcmc_f_lower to get the lower frequency bound, which is the default reference frequency for LALInference.

_find_infmcmc_f_lower(self, runInfo)

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Searches through header to determine starting frequency of waveforms. Assumes same for all IFOs.

_ns_to_pos(self, files, Nlive=None, Npost=None, posfilename='posterior_samples.dat')

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Parser for nested sampling output. files : list of input NS files Nlive : Number of live points Npost : Desired number of posterior samples posfilename : Posterior output file name (default: 'posterior_samples.dat')

_hdf5_to_table(self, infile, deltaLogP=None, fixedBurnin=None, nDownsample=None, multiple_chains=False, tablename=None, **kwargs)

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Parse a HDF5 file and return an array of posterior samples ad list of parameter names. Equivalent to '_common_to_pos' and work in progress.

_common_to_pos(self, infile, info=[None,None])

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Parse a file in the 'common format' and return an array of posterior samples and list of parameter names. Will apply inverse functions to columns with names containing sin,cos,log.

Class PEOutputParser

__init__(self, inputtype) (Constructor)

_infmcmc_output_posterior_samples(self, files, runfile, outfile, logPThreshold, fixedBurnins, nskips=None, oldMassConvention=False)

_find_infmcmc_f_ref(self, runInfo)

_find_infmcmc_f_lower(self, runInfo)

_ns_to_pos(self, files, Nlive=None, Npost=None, posfilename='posterior_samples.dat')

_hdf5_to_table(self, infile, deltaLogP=None, fixedBurnin=None, nDownsample=None, multiple_chains=False, tablename=None, **kwargs)

_common_to_pos(self, infile, info=[None,None])

init(self, inputtype)
(Constructor)