# Source code for pycbc.inference.io.emcee

```
# Copyright (C) 2018 Collin Capano
# This program is free software; you can redistribute it and/or modify it
# under the terms of the GNU General Public License as published by the
# Free Software Foundation; either version 3 of the License, or (at your
# self.option) any later version.
#
# This program is distributed in the hope that it will be useful, but
# WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General
# Public License for more details.
#
# You should have received a copy of the GNU General Public License along
# with this program; if not, write to the Free Software Foundation, Inc.,
# 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
#
# =============================================================================
#
# Preamble
#
# =============================================================================
#
"""Provides IO for the emcee sampler.
"""
import numpy
from .base_sampler import BaseSamplerFile
from .base_mcmc import (EnsembleMCMCMetadataIO, CommonMCMCMetadataIO,
write_samples, ensemble_read_raw_samples)
[docs]
class EmceeFile(EnsembleMCMCMetadataIO, CommonMCMCMetadataIO, BaseSamplerFile):
"""Class to handle file IO for the ``emcee`` sampler."""
name = 'emcee_file'
[docs]
def write_samples(self, samples, **kwargs):
r"""Writes samples to the given file.
Calls :py:func:`base_mcmc.write_samples`. See that function for
details.
Parameters
----------
samples : dict
The samples to write. Each array in the dictionary should have
shape nwalkers x niterations.
\**kwargs :
All other keyword arguments are passed to
:py:func:`base_mcmc.write_samples`.
"""
write_samples(self, samples, **kwargs)
[docs]
def read_raw_samples(self, fields, **kwargs):
r"""Base function for reading samples.
Calls :py:func:`base_mcmc.ensemble_read_raw_samples`. See that function
for details.
Parameters
-----------
fields : list
The list of field names to retrieve.
\**kwargs :
All other keyword arguments are passed to
:py:func:`base_mcmc.ensemble_read_raw_samples`.
Returns
-------
dict
A dictionary of field name -> numpy array pairs.
"""
return ensemble_read_raw_samples(self, fields, **kwargs)
[docs]
def read_acceptance_fraction(self, walkers=None):
"""Reads the acceptance fraction.
Parameters
-----------
walkers : (list of) int, optional
The walker index (or a list of indices) to retrieve. If None,
samples from all walkers will be obtained.
Returns
-------
array
Array of acceptance fractions with shape (requested walkers,).
"""
group = self.sampler_group + '/acceptance_fraction'
if walkers is None:
wmask = numpy.ones(self.nwalkers, dtype=bool)
else:
wmask = numpy.zeros(self.nwalkers, dtype=bool)
wmask[walkers] = True
return self[group][wmask]
[docs]
def write_acceptance_fraction(self, acceptance_fraction):
"""Write acceptance_fraction data to file. Results are written to
the ``[sampler_group]/acceptance_fraction``.
Parameters
-----------
acceptance_fraction : numpy.ndarray
Array of acceptance fractions to write.
"""
group = self.sampler_group + '/acceptance_fraction'
try:
self[group][:] = acceptance_fraction
except KeyError:
# dataset doesn't exist yet, create it
self[group] = acceptance_fraction
```