Source code for

# 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
# 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