# 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.
"""Provides I/O support for multinest.
"""
from .base_sampler import BaseSamplerFile
[docs]class MultinestFile(BaseSamplerFile):
"""Class to handle file IO for the ``multinest`` sampler."""
name = 'multinest_file'
[docs] def write_samples(self, samples, parameters=None):
"""Writes samples to the given file.
Results are written to ``samples_group/{vararg}``, where ``{vararg}``
is the name of a model params. The samples are written as an
array of length ``niterations``.
Parameters
----------
samples : dict
The samples to write. Each array in the dictionary should have
length niterations.
parameters : list, optional
Only write the specified parameters to the file. If None, will
write all of the keys in the ``samples`` dict.
"""
niterations = len(tuple(samples.values())[0])
assert all(len(p) == niterations for p in samples.values()), (
"all samples must have the same shape")
group = self.samples_group + '/{name}'
if parameters is None:
parameters = samples.keys()
# loop over number of dimensions
for param in parameters:
dataset_name = group.format(name=param)
try:
fp_niterations = len(self[dataset_name])
if niterations != fp_niterations:
# resize the dataset
self[dataset_name].resize(niterations, axis=0)
except KeyError:
# dataset doesn't exist yet
self.create_dataset(dataset_name, (niterations,),
maxshape=(None,),
dtype=samples[param].dtype,
fletcher32=True)
self[dataset_name][:] = samples[param]
[docs] def write_logevidence(self, lnz, dlnz, importance_lnz, importance_dlnz):
"""Writes the given log evidence and its error.
Results are saved to file's 'log_evidence' and 'dlog_evidence'
attributes, as well as the importance-weighted versions of these
stats if they exist.
Parameters
----------
lnz : float
The log of the evidence.
dlnz : float
The error in the estimate of the log evidence.
importance_lnz : float, optional
The importance-weighted log of the evidence.
importance_dlnz : float, optional
The error in the importance-weighted estimate of the log evidence.
"""
self.attrs['log_evidence'] = lnz
self.attrs['dlog_evidence'] = dlnz
if all([e is not None for e in [importance_lnz, importance_dlnz]]):
self.attrs['importance_log_evidence'] = importance_lnz
self.attrs['importance_dlog_evidence'] = importance_dlnz
[docs] def read_raw_samples(self, fields, iteration=None):
if isinstance(fields, str):
fields = [fields]
# load
group = self.samples_group + '/{name}'
arrays = {}
for name in fields:
if iteration is not None:
arr = self[group.format(name=name)][int(iteration)]
else:
arr = self[group.format(name=name)][:]
arrays[name] = arr
return arrays
[docs] def write_resume_point(self):
"""Keeps a list of the number of iterations that were in a file when a
run was resumed from a checkpoint."""
try:
resume_pts = self.attrs["resume_points"].tolist()
except KeyError:
resume_pts = []
try:
niterations = self.niterations
except KeyError:
niterations = 0
resume_pts.append(niterations)
self.attrs["resume_points"] = resume_pts
@property
def niterations(self):
"""Returns the number of iterations the sampler was run for."""
return self[self.sampler_group].attrs['niterations']
[docs] def write_niterations(self, niterations):
"""Writes the given number of iterations to the sampler group."""
self[self.sampler_group].attrs['niterations'] = niterations