ensemble.py

#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""
An affine invariant Markov chain Monte Carlo (MCMC) sampler.

Goodman & Weare, Ensemble Samplers With Affine Invariance
   Comm. App. Math. Comp. Sci., Vol. 5 (2010), No. 1, 65–80

"""

from __future__ import (division, print_function, absolute_import,
                        unicode_literals)

__all__ = ["EnsembleSampler"]

import multiprocessing
import numpy as np

try:
    import acor
    acor = acor
except ImportError:
    acor = None

from emcee.sampler import Sampler


class EnsembleSampler(Sampler):
    """
    A generalized Ensemble sampler that uses 2 ensembles for parallelization.
    The ``__init__`` function will raise an ``AssertionError`` if
    ``k < 2 * dim`` (and you haven't set the ``live_dangerously`` parameter)
    or if ``k`` is odd.

    **Warning**: The :attr:`chain` member of this object has the shape:
    ``(nwalkers, nlinks, dim)`` where ``nlinks`` is the number of steps
    taken by the chain and ``k`` is the number of walkers.  Use the
    :attr:`flatchain` property to get the chain flattened to
    ``(nlinks, dim)``. For users of pre-1.0 versions, this shape is
    different so be careful!

    :param nwalkers:
        The number of Goodman & Weare "walkers".

    :param dim:
        Number of dimensions in the parameter space.

    :param lnpostfn:
        A function that takes a vector in the parameter space as input and
        returns the natural logarithm of the posterior probability for that
        position.

    :param a: (optional)
        The proposal scale parameter. (default: ``2.0``)

    :param args: (optional)
        A list of extra arguments for ``lnpostfn``. ``lnpostfn`` will be
        called with the sequence ``lnpostfn(p, *args)``.

    :param postargs: (optional)
        Alias of ``args`` for backwards compatibility.

    :param threads: (optional)
        The number of threads to use for parallelization. If ``threads == 1``,
        then the ``multiprocessing`` module is not used but if
        ``threads > 1``, then a ``Pool`` object is created and calls to
        ``lnpostfn`` are run in parallel.

    :param pool: (optional)
        An alternative method of using the parallelized algorithm. If
        provided, the value of ``threads`` is ignored and the
        object provided by ``pool`` is used for all parallelization. It
        can be any object with a ``map`` method that follows the same
        calling sequence as the built-in ``map`` function.

    """
    def __init__(self, nwalkers, dim, lnpostfn, a=2.0, args=[], postargs=None,
            threads=1, pool=None, live_dangerously=False):
        self.k = nwalkers
        self.a = a
        self.threads = threads
        self.pool = pool

        if postargs is not None:
            args = postargs
        super(EnsembleSampler, self).__init__(dim, lnpostfn, args=args)

        # Do a little bit of _magic_ to make the likelihood call with
        # ``args`` pickleable.
        self.lnprobfn = _function_wrapper(self.lnprobfn, self.args)

        assert self.k % 2 == 0, "The number of walkers must be even."
        if not live_dangerously:
            assert self.k >= 2 * self.dim, (
                    "The number of walkers needs to be more than twice the "
                    + "dimension of your parameter space... unless you're "
                    + "crazy!")

        if self.threads > 1 and self.pool is None:
            self.pool = multiprocessing.Pool(self.threads)

    def reset(self):
        """
        Clear the ``chain`` and ``lnprobability`` array. Also reset the
        bookkeeping parameters.

        """
        super(EnsembleSampler, self).reset()
        self.naccepted = np.zeros(self.k)
        self._chain = np.empty((self.k, 0, self.dim))
        self._lnprob = np.empty((self.k, 0))

        # Initialize list for storing optional metadata blobs.
        self._blobs = []

    def sample(self, p0, lnprob0=None, rstate0=None, blobs0=None,
            iterations=1, thin=1, storechain=True, mh_proposal=None):
        """
        Advance the chain ``iterations`` steps as a generator.

        :param p0:
            A list of the initial positions of the walkers in the
            parameter space. It should have the shape ``(nwalkers, dim)``.

        :param lnprob0: (optional)
            The list of log posterior probabilities for the walkers at
            positions given by ``p0``. If ``lnprob is None``, the initial
            values are calculated. It should have the shape ``(k, dim)``.

        :param rstate0: (optional)
            The state of the random number generator.
            See the :attr:`Sampler.random_state` property for details.

        :param iterations: (optional)
            The number of steps to run.

        :param thin: (optional)
            If you only want to store and yield every ``thin`` samples in the
            chain, set thin to an integer greater than 1.

        :param storechain: (optional)
            By default, the sampler stores (in memory) the positions and
            log-probabilities of the samples in the chain. If you are
            using another method to store the samples to a file or if you
            don't need to analyse the samples after the fact (for burn-in
            for example) set ``storechain`` to ``False``.

        :param mh_proposal: (optional)
            A function that returns a list of positions for ``nwalkers``
            walkers given a current list of positions of the same size. See
            :class:`utils.MH_proposal_axisaligned` for an example.

        At each iteration, this generator yields:

        * ``pos`` — A list of the current positions of the walkers in the
          parameter space. The shape of this object will be
          ``(nwalkers, dim)``.

        * ``lnprob`` — The list of log posterior probabilities for the
          walkers at positions given by ``pos`` . The shape of this object
          is ``(nwalkers, dim)``.

        * ``rstate`` — The current state of the random number generator.

        * ``blobs`` — (optional) The metadata "blobs" associated with the
          current position. The value is only returned if ``lnpostfn``
          returns blobs too.

        """
        # Try to set the initial value of the random number generator. This
        # fails silently if it doesn't work but that's what we want because
        # we'll just interpret any garbage as letting the generator stay in
        # it's current state.
        self.random_state = rstate0

        p = np.array(p0)
        halfk = int(self.k / 2)

        # If the initial log-probabilities were not provided, calculate them
        # now.
        lnprob = lnprob0
        blobs = blobs0
        if lnprob is None:
            lnprob, blobs = self._get_lnprob(p)

        # Store the initial size of the stored chain.
        i0 = self._chain.shape[1]

        # Here, we resize chain in advance for performance. This actually
        # makes a pretty big difference.
        if storechain:
            N = int(iterations / thin)
            self._chain = np.concatenate((self._chain,
                    np.zeros((self.k, N, self.dim))), axis=1)
            self._lnprob = np.concatenate((self._lnprob,
                                           np.zeros((self.k, N))), axis=1)

        for i in range(int(iterations)):
            self.iterations += 1

            # If we were passed a Metropolis-Hastings proposal
            # function, use it.
            if mh_proposal is not None:
                # Draw proposed positions & evaluate lnprob there
                q = mh_proposal(p)
                newlnp, blob = self._get_lnprob(q)

                # Accept if newlnp is better; and ...
                acc = (newlnp > lnprob)

                # ... sometimes accept for steps that got worse
                worse = np.flatnonzero(acc == False)
                acc[worse] = ((newlnp[worse] - lnprob[worse]) >
                              np.log(self._random.rand(len(worse))))
                del worse

                # Update the accepted walkers.
                lnprob[acc] = newlnp[acc]
                p[acc] = q[acc]
                self.naccepted[acc] += 1

                if blob is not None:
                    assert blobs is not None, (
                            "If you start sampling "
                        + "with a given lnprob, you also need to "
                        + "provide the current list of blobs at that "
                        + "position.")
                    ind = np.arange(self.k)[acc]
                    for j in ind:
                        blobs[j] = blob[j]

            else:
                # Loop over the two ensembles, calculating the proposed
                # positions.

                # Slices for the first and second halves
                first, second = slice(halfk), slice(halfk, self.k)
                for S0, S1 in [(first, second), (second, first)]:
                    q, newlnp, acc, blob = self._propose_stretch(p[S0], p[S1],
                                                        lnprob[S0])
                    if np.any(acc):
                        # Update the positions, log probabilities and
                        # acceptance counts.
                        lnprob[S0][acc] = newlnp[acc]
                        p[S0][acc] = q[acc]
                        self.naccepted[S0][acc] += 1

                        if blob is not None:
                            assert blobs is not None, (
                                  "If you start sampling "
                                + "with a given lnprob, you also need to "
                                + "provide the current list of blobs at that "
                                + "position.")
                            ind = np.arange(len(acc))[acc]
                            indfull = np.arange(self.k)[S0][acc]
                            for j in range(len(ind)):
                                blobs[indfull[j]] = blob[ind[j]]

            if storechain and i % thin == 0:
                ind = i0 + int(i / thin)
                self._chain[:, ind, :] = p
                self._lnprob[:, ind] = lnprob
                if blobs is not None:
                    self._blobs.append(list(blobs))

            # Yield the result as an iterator so that the user can do all
            # sorts of fun stuff with the results so far.
            if blobs is not None:
                # This is a bit of a hack to keep things backwards compatible.
                yield p, lnprob, self.random_state, blobs
            else:
                yield p, lnprob, self.random_state

    def _propose_stretch(self, p0, p1, lnprob0):
        """
        Propose a new position for one sub-ensemble given the positions of
        another.

        :param p0:
            The positions from which to jump.

        :param p1:
            The positions of the other ensemble.

        :param lnprob0:
            The log-probabilities at ``p0``.

        This method returns:

        * ``q`` — The new proposed positions for the walkers in ``ensemble``.

        * ``newlnprob`` — The vector of log-probabilities at the positions
          given by ``q``.

        * ``accept`` — A vector of type ``bool`` indicating whether or not
          the proposed position for each walker should be accepted.

        * ``blob`` — The new meta data blobs or ``None`` if nothing was
          returned by ``lnprobfn``.

        """
        s = np.atleast_2d(p0)
        Ns = len(s)
        c = np.atleast_2d(p1)
        Nc = len(c)

        # Generate the vectors of random numbers that will produce the
        # proposal.
        zz = ((self.a - 1.) * self._random.rand(Ns) + 1) ** 2. / self.a
        rint = self._random.randint(Nc, size=(Ns,))

        # Calculate the proposed positions and the log-probability there.
        q = c[rint] - zz[:, np.newaxis] * (c[rint] - s)
        newlnprob, blob = self._get_lnprob(q)

        # Decide whether or not the proposals should be accepted.
        lnpdiff = (self.dim - 1.) * np.log(zz) + newlnprob - lnprob0
        accept = (lnpdiff > np.log(self._random.rand(len(lnpdiff))))

        return q, newlnprob, accept, blob

    def _get_lnprob(self, pos=None):
        """
        Calculate the vector of log-probability for the walkers.

        :param pos: (optional)
            The position vector in parameter space where the probability
            should be calculated. This defaults to the current position
            unless a different one is provided.

        This method returns:

        * ``lnprob`` — A vector of log-probabilities with one entry for each
          walker in this sub-ensemble.

        * ``blob`` — The list of meta data returned by the ``lnpostfn`` at
          this position or ``None`` if nothing was returned.

        """
        if pos is None:
            p = self.pos
        else:
            p = pos

        # If the `pool` property of the sampler has been set (i.e. we want
        # to use `multiprocessing`), use the `pool`'s map method. Otherwise,
        # just use the built-in `map` function.
        if self.pool is not None:
            M = self.pool.map
        else:
            M = map

        # Run the log-probability calculations (optionally in parallel).
        results = list(M(self.lnprobfn, [p[i] for i in range(len(p))]))

        try:
            lnprob = np.array([float(l[0]) for l in results])
            blob = [l[1] for l in results]
        except (IndexError, TypeError):
            lnprob = np.array([float(l) for l in results])
            blob = None

        return lnprob, blob

    @property
    def blobs(self):
        """
        Get the list of "blobs" produced by sampling. The result is a list
        (of length ``iterations``) of ``list`` s (of length ``nwalkers``) of
        arbitrary objects. **Note**: this will actually be an empty list if
        your ``lnpostfn`` doesn't return any metadata.

        """
        return self._blobs

    @property
    def chain(self):
        """
        A pointer to the Markov chain itself. The shape of this array is
        ``(k, dim, iterations)``.

        """
        return super(EnsembleSampler, self).chain

    @property
    def flatchain(self):
        """
        A shortcut for accessing chain flattened along the zeroth (walker)
        axis.

        """
        s = self.chain.shape
        return self.chain.reshape(s[0] * s[1], s[2])

    @property
    def lnprobability(self):
        """
        A pointer to the matrix of the value of ``lnprobfn`` produced at each
        step for each walker. The shape is ``(k, iterations)``.

        """
        return super(EnsembleSampler, self).lnprobability

    @property
    def flatlnprobability(self):
        """
        A shortcut to return the equivalent of ``lnprobability`` but aligned
        to ``flatchain`` rather than ``chain``.

        """
        return super(EnsembleSampler, self).lnprobability.flatten()

    @property
    def acceptance_fraction(self):
        """
        An array (length: ``k``) of the fraction of steps accepted for each
        walker.

        """
        return super(EnsembleSampler, self).acceptance_fraction

    @property
    def acor(self):
        """
        The autocorrelation time of each parameter in the chain (length:
        ``dim``) as estimated by the ``acor`` module.

        """
        if acor is None:
            raise ImportError("acor")
        s = self.dim
        t = np.zeros(s)
        for i in range(s):
            t[i] = acor.acor(self.chain[:, :, i])[0]
        return t


class _function_wrapper(object):
    """
    This is a hack to make the likelihood function pickleable when ``args``
    are also included.

    """
    def __init__(self, f, args):
        self.f = f
        self.args = args

    def __call__(self, x):
        try:
            return self.f(x, *self.args)
        except:
            import traceback
            print("emcee: Exception while calling your likelihood function:")
            print("  params:", x)
            print("  args:", self.args)
            print("  exception:")
            traceback.print_exc()
            raise