Source code for pycbc.inference.sampler.emcee_pt

# Copyright (C) 2016  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
# 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.

This modules provides classes and functions for using the emcee_pt sampler
packages for parameter estimation.

import logging
import numpy
import emcee

from pycbc.pool import choose_pool

from .base import (BaseSampler, setup_output)
from .base_mcmc import (BaseMCMC, EnsembleSupport, raw_samples_to_dict,
from .base_multitemper import (MultiTemperedSupport,
                               ensemble_compute_acf, ensemble_compute_acl)
from ..burn_in import EnsembleMultiTemperedMCMCBurnInTests
from import EmceePTFile
from .. import models

# This is a hack that will allow us to continue using emcee's abandoned
# PTSampler, which relied on `numpy.float`, until the end of time.
numpy.float = float

if emcee.__version__ >= '3.0.0':
    raise ImportError

[docs]class EmceePTSampler(MultiTemperedSupport, EnsembleSupport, BaseMCMC, BaseSampler): """This class is used to construct a parallel-tempered MCMC sampler from the emcee package's PTSampler. Parameters ---------- model : model A model from ``pycbc.inference.models``. ntemps : int Number of temeratures to use in the sampler. nwalkers : int Number of walkers to use in sampler. betas : array An array of inverse temperature values to be used in emcee_pt's temperature ladder. If not provided, ``emcee_pt`` will use the number of temperatures and the number of dimensions of the parameter space to construct the ladder with geometrically spaced temperatures. loglikelihood_function : str, optional Set the function to call from the model for the ``loglikelihood``. Default is ``loglikelihood``. nprocesses : int, optional The number of parallel processes to use. Default is 1 (no paralleliztion). use_mpi : bool, optional Use MPI for parallelization. Default (False) will use python's multiprocessing. """ name = "emcee_pt" _io = EmceePTFile burn_in_class = EnsembleMultiTemperedMCMCBurnInTests def __init__(self, model, ntemps, nwalkers, betas=None, checkpoint_interval=None, checkpoint_signal=None, loglikelihood_function=None, nprocesses=1, use_mpi=False): self.model = model # create a wrapper for calling the model if loglikelihood_function is None: loglikelihood_function = 'loglikelihood' # frustratingly, emcee_pt does not support blob data, so we have to # turn it off model_call = models.CallModel(model, loglikelihood_function, return_all_stats=False) # these are used to help paralleize over multiple cores / MPI models._global_instance = model_call model_call = models._call_global_model prior_call = models._call_global_model_logprior self.pool = choose_pool(mpi=use_mpi, processes=nprocesses) # construct the sampler: PTSampler needs the likelihood and prior # functions separately ndim = len(model.variable_params) self._sampler = emcee.PTSampler(ntemps, nwalkers, ndim, model_call, prior_call, pool=self.pool, betas=betas) self.nwalkers = nwalkers self._ntemps = ntemps self._checkpoint_interval = checkpoint_interval self._checkpoint_signal = checkpoint_signal @property def io(self): return self._io @property def base_shape(self): return (self.ntemps, self.nwalkers,) @property def betas(self): return self._sampler.betas
[docs] @staticmethod def compute_acf(filename, **kwargs): r"""Computes the autocorrelation function. Calls :py:func:`base_multitemper.ensemble_compute_acf`; see that function for details. Parameters ---------- filename : str Name of a samples file to compute ACFs for. \**kwargs : All other keyword arguments are passed to :py:func:`base_multitemper.ensemble_compute_acf`. Returns ------- dict : Dictionary of arrays giving the ACFs for each parameter. If ``per-walker=True`` is passed as a keyword argument, the arrays will have shape ``ntemps x nwalkers x niterations``. Otherwise, the returned array will have shape ``ntemps x niterations``. """ return ensemble_compute_acf(filename, **kwargs)
[docs] @staticmethod def compute_acl(filename, **kwargs): r"""Computes the autocorrelation length. Calls :py:func:`base_multitemper.ensemble_compute_acl`; see that function for details. Parameters ----------- filename : str Name of a samples file to compute ACLs for. \**kwargs : All other keyword arguments are passed to :py:func:`base_multitemper.ensemble_compute_acl`. Returns ------- dict A dictionary of ntemps-long arrays of the ACLs of each parameter. """ return ensemble_compute_acl(filename, **kwargs)
[docs] @classmethod def from_config(cls, cp, model, output_file=None, nprocesses=1, use_mpi=False): """Loads the sampler from the given config file. The following options are retrieved in the ``[sampler]`` section: * ``name`` : Required. This must match the samlper's name. * ``nwalkers`` : Required. The number of walkers to use. * ``ntemps`` : The number of temperatures to use. Either this, or ``inverse-temperatures-file`` must be provided (but not both). * ``inverse-temperatures-file`` : Path to an hdf file containing the inverse temperatures ("betas") to use. The betas will be retrieved from the file's ``.attrs['betas']``. Either this or ``ntemps`` must be provided (but not both). * ``niterations`` : The number of iterations to run the sampler for. Either this or ``effective-nsamples`` must be provided (but not both). * ``effective-nsamples`` : Run the sampler until the given number of effective samples are obtained. A ``checkpoint-interval`` must also be provided in this case. Either this or ``niterations`` must be provided (but not both). * ``thin-interval`` : Thin the samples by the given value before saving to disk. May provide this, or ``max-samples-per-chain``, but not both. If neither options are provided, will save all samples. * ``max-samples-per-chain`` : Thin the samples such that the number of samples per chain per temperature that are saved to disk never exceeds the given value. May provide this, or ``thin-interval``, but not both. If neither options are provided, will save all samples. * ``checkpoint-interval`` : Sets the checkpoint interval to use. Must be provided if using ``effective-nsamples``. * ``checkpoint-signal`` : Set the checkpoint signal, e.g., "USR2". Optional. * ``logl-function`` : The attribute of the model to use for the loglikelihood. If not provided, will default to ``loglikelihood``. Settings for burn-in tests are read from ``[sampler-burn_in]``. In particular, the ``burn-in-test`` option is used to set the burn in tests to perform. See :py:func:`MultiTemperedMCMCBurnInTests.from_config` for details. If no ``burn-in-test`` is provided, no burn in tests will be carried out. Parameters ---------- cp : WorkflowConfigParser instance Config file object to parse. model : pycbc.inference.model.BaseModel instance The model to use. output_file : str, optional The name of the output file to checkpoint and write results to. nprocesses : int, optional The number of parallel processes to use. Default is 1. use_mpi : bool, optional Use MPI for parallelization. Default is False. Returns ------- EmceePTSampler : The sampler instance. """ section = "sampler" # check name assert cp.get(section, "name") ==, ( "name in section [sampler] must match mine") # get the number of walkers to use nwalkers = int(cp.get(section, "nwalkers")) # get the temps/betas ntemps, betas = cls.betas_from_config(cp, section) # get the checkpoint interval, if it's specified checkpoint_interval = cls.checkpoint_from_config(cp, section) checkpoint_signal = cls.ckpt_signal_from_config(cp, section) # get the loglikelihood function logl = get_optional_arg_from_config(cp, section, 'logl-function') obj = cls(model, ntemps, nwalkers, betas=betas, checkpoint_interval=checkpoint_interval, checkpoint_signal=checkpoint_signal, loglikelihood_function=logl, nprocesses=nprocesses, use_mpi=use_mpi) # set target obj.set_target_from_config(cp, section) # add burn-in if it's specified obj.set_burn_in_from_config(cp) # set prethin options obj.set_thin_interval_from_config(cp, section) # Set up the output file setup_output(obj, output_file) if not obj.new_checkpoint: obj.resume_from_checkpoint() else: obj.set_start_from_config(cp) return obj
@property def samples(self): """A dict mapping ``variable_params`` to arrays of samples currently in memory. The arrays have shape ``ntemps x nwalkers x niterations``. """ # emcee stores samples to it's chain attribute as a # nwalker x niterations x ndim array raw_samples = self._sampler.chain return raw_samples_to_dict(self, raw_samples) @property def model_stats(self): """Returns the log likelihood ratio and log prior as a dict of arrays. The returned array has shape ntemps x nwalkers x niterations. Unfortunately, because ``emcee_pt`` does not have blob support, this will only return the loglikelihood and logprior (with the logjacobian set to zero) regardless of what stats the model can return. .. warning:: Since the `logjacobian` is not saved by `emcee_pt`, the `logprior` returned here is the log of the prior pdf in the sampling coordinate frame rather than the variable params frame. This differs from the variable params frame by the log of the Jacobian of the transform from one frame to the other. If no sampling transforms were used, then the `logprior` is the same. """ # likelihood has shape ntemps x nwalkers x niterations logl = self._sampler.lnlikelihood # get prior from posterior logp = self._sampler.lnprobability - logl logjacobian = numpy.zeros(logp.shape) return {'loglikelihood': logl, 'logprior': logp, 'logjacobian': logjacobian}
[docs] def clear_samples(self): """Clears the chain and blobs from memory. """ # store the iteration that the clear is occuring on self._lastclear = self.niterations self._itercounter = 0 # now clear the chain self._sampler.reset()
[docs] def set_state_from_file(self, filename): """Sets the state of the sampler back to the instance saved in a file. """ with, 'r') as fp: rstate = fp.read_random_state() # set the numpy random state numpy.random.set_state(rstate)
[docs] def run_mcmc(self, niterations): """Advance the ensemble for a number of samples. Parameters ---------- niterations : int Number of samples to get from sampler. """ pos = self._pos if pos is None: pos = self._p0 res = self._sampler.run_mcmc(pos, niterations) p, _, _ = res[0], res[1], res[2] # update the positions self._pos = p
[docs] def write_results(self, filename): """Writes samples, model stats, acceptance fraction, and random state to the given file. Parameters ----------- filename : str The file to write to. The file is opened using the ``io`` class in an an append state. """ with, 'a') as fp: # write samples fp.write_samples(self.samples, parameters=self.model.variable_params, last_iteration=self.niterations) # write stats fp.write_samples(self.model_stats, last_iteration=self.niterations) # write accpetance fp.write_acceptance_fraction(self._sampler.acceptance_fraction) # write random state fp.write_random_state()
[docs] @classmethod def calculate_logevidence(cls, filename, thin_start=None, thin_end=None, thin_interval=None): """Calculates the log evidence from the given file using ``emcee_pt``'s thermodynamic integration. Parameters ---------- filename : str Name of the file to read the samples from. Should be an ``EmceePTFile``. thin_start : int Index of the sample to begin returning stats. Default is to read stats after burn in. To start from the beginning set thin_start to 0. thin_interval : int Interval to accept every i-th sample. Default is to use the `fp.acl`. If `fp.acl` is not set, then use all stats (set thin_interval to 1). thin_end : int Index of the last sample to read. If not given then `fp.niterations` is used. Returns ------- lnZ : float The estimate of log of the evidence. dlnZ : float The error on the estimate. """ with cls._io(filename, 'r') as fp: logls = fp.read_raw_samples(['loglikelihood'], thin_start=thin_start, thin_interval=thin_interval, thin_end=thin_end, temps='all', flatten=False) logls = logls['loglikelihood'] # we need the betas that were used betas = fp.betas # annoyingly, theromdynaimc integration in PTSampler is an instance # method, so we'll implement a dummy one ntemps = fp.ntemps nwalkers = fp.nwalkers ndim = len(fp.variable_params) dummy_sampler = emcee.PTSampler(ntemps, nwalkers, ndim, None, None, betas=betas) return dummy_sampler.thermodynamic_integration_log_evidence( logls=logls, fburnin=0.)
def _correctjacobian(self, samples): """Corrects the log jacobian values stored on disk. Parameters ---------- samples : dict Dictionary of the samples. """ # flatten samples for evaluating orig_shape = list(samples.values())[0].shape flattened_samples = {p: arr.ravel() for p, arr in list(samples.items())} # convert to a list of tuples so we can use map function params = list(flattened_samples.keys()) size = flattened_samples[params[0]].size logj = numpy.zeros(size) for ii in range(size): these_samples = {p: flattened_samples[p][ii] for p in params} these_samples = self.model.sampling_transforms.apply(these_samples) self.model.update(**these_samples) logj[ii] = self.model.logjacobian return logj.reshape(orig_shape)
[docs] def finalize(self): """Calculates the log evidence and writes to the checkpoint file. If sampling transforms were used, this also corrects the jacobian stored on disk. The thin start/interval/end for calculating the log evidence are retrieved from the checkpoint file's thinning attributes. """ if self.model.sampling_transforms is not None: # fix the lobjacobian values stored on disk"Correcting logjacobian values on disk") with, 'r') as fp: samples = fp.read_raw_samples(self.variable_params, thin_start=0, thin_interval=1, thin_end=None, temps='all', flatten=False) logjacobian = self._correctjacobian(samples) # write them back out for fn in [self.checkpoint_file, self.backup_file]: with, "a") as fp: fp[fp.samples_group]['logjacobian'][()] = logjacobian"Calculating log evidence") # get the thinning settings with, 'r') as fp: thin_start = fp.thin_start thin_interval = fp.thin_interval thin_end = fp.thin_end # calculate logz, dlogz = self.calculate_logevidence( self.checkpoint_file, thin_start=thin_start, thin_end=thin_end, thin_interval=thin_interval)"log Z, dlog Z: {}, {}".format(logz, dlogz)) # write to both the checkpoint and backup for fn in [self.checkpoint_file, self.backup_file]: with, "a") as fp: fp.write_logevidence(logz, dlogz)