pyfstat.py 55 KB
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""" Classes for various types of searches using ComputeFstatistic """
import os
import sys
import itertools
import logging
import argparse
import copy
import glob
import inspect
from functools import wraps
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import subprocess
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import numpy as np
import matplotlib
matplotlib.use('Agg')
import matplotlib.pyplot as plt
import emcee
import corner
import dill as pickle
import lalpulsar

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config_file = os.path.expanduser('~')+'/.pyfstat.conf'
if os.path.isfile(config_file):
    d = {}
    with open(config_file, 'r') as f:
        for line in f:
            k, v = line.split('=')
            k = k.replace(' ', '')
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            v = v.replace(' ', '').replace("'", "").replace('"', '').replace('\n', '')
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            d[k] = v
    earth_ephem = d['earth_ephem']
    sun_ephem = d['sun_ephem']
else:
    logging.warning('No ~/.pyfstat.conf file found please provide the paths '
                    'when initialising searches')
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    earth_ephem = None
    sun_ephem = None

plt.style.use('paper')

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parser = argparse.ArgumentParser()
parser.add_argument("-q", "--quite", help="Decrease output verbosity",
                    action="store_true")
parser.add_argument("-c", "--clean", help="Don't use cached data",
                    action="store_true")
parser.add_argument('unittest_args', nargs='*')
args, unknown = parser.parse_known_args()
sys.argv[1:] = args.unittest_args

if args.quite:
    log_level = logging.WARNING
else:
    log_level = logging.DEBUG

logging.basicConfig(level=log_level,
                    format='%(asctime)s %(levelname)-8s: %(message)s',
                    datefmt='%H:%M')

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def initializer(func):
    """ Automatically assigns the parameters to self"""
    names, varargs, keywords, defaults = inspect.getargspec(func)

    @wraps(func)
    def wrapper(self, *args, **kargs):
        for name, arg in list(zip(names[1:], args)) + list(kargs.items()):
            setattr(self, name, arg)

        for name, default in zip(reversed(names), reversed(defaults)):
            if not hasattr(self, name):
                setattr(self, name, default)

        func(self, *args, **kargs)

    return wrapper


def read_par(label, outdir):
    filename = '{}/{}.par'.format(outdir, label)
    d = {}
    with open(filename, 'r') as f:
        for line in f:
            key, val = line.rstrip('\n').split(' = ')
            d[key] = np.float64(val)
    return d


class BaseSearchClass(object):

    earth_ephem_default = earth_ephem
    sun_ephem_default = sun_ephem

    def shift_matrix(self, n, dT):
        """ Generate the shift matrix """
        m = np.zeros((n, n))
        factorial = np.math.factorial
        for i in range(n):
            for j in range(n):
                if i == j:
                    m[i, j] = 1.0
                elif i > j:
                    m[i, j] = 0.0
                else:
                    if i == 0:
                        m[i, j] = 2*np.pi*float(dT)**(j-i) / factorial(j-i)
                    else:
                        m[i, j] = float(dT)**(j-i) / factorial(j-i)

        return m

    def shift_coefficients(self, theta, dT):
        """ Shift a set of coefficients by dT

        Parameters
        ----------
        theta: array-like, shape (n,)
            vector of the expansion coefficients to transform starting from the
            lowest degree e.g [phi, F0, F1,...]
        dT: float
            difference between the two reference times as tref_new - tref_old

        Returns
        -------
        theta_new: array-like shape (n,)
            vector of the coefficients as evaluate as the new reference time
        """
        n = len(theta)
        m = self.shift_matrix(n, dT)
        return np.dot(m, theta)

    # Rewrite this to generalise to N glitches, then use everywhere!
    def calculate_thetas(self, theta, delta_thetas, tbounds):
        """ Calculates the set of coefficients for the post-glitch signal """
        thetas = [theta]
        for i, dt in enumerate(delta_thetas):
            pre_theta_at_ith_glitch = self.shift_coefficients(
                thetas[i], tbounds[i+1] - self.tref)
            post_theta_at_ith_glitch = pre_theta_at_ith_glitch + dt
            thetas.append(self.shift_coefficients(
                post_theta_at_ith_glitch, self.tref - tbounds[i+1]))
        return thetas


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class ComputeFstat(object):
    """ Base class providing interface to lalpulsar.ComputeFstat """

    earth_ephem_default = earth_ephem
    sun_ephem_default = sun_ephem

    @initializer
    def __init__(self, tref, sftlabel=None, sftdir=None,
                 minCoverFreq=None, maxCoverFreq=None,
                 detector=None, earth_ephem=None, sun_ephem=None):

        if earth_ephem is None:
            self.earth_ephem = self.earth_ephem_default
        if sun_ephem is None:
            self.sun_ephem = self.sun_ephem_default

        self.init_computefstatistic_single_point()

    def init_computefstatistic_single_point(self):
        """ Initilisation step of run_computefstatistic for a single point """

        logging.info('Initialising SFTCatalog')
        constraints = lalpulsar.SFTConstraints()
        if self.detector:
            constraints.detector = self.detector
        self.sft_filepath = self.sftdir+'/*_'+self.sftlabel+"*sft"
        SFTCatalog = lalpulsar.SFTdataFind(self.sft_filepath, constraints)
        names = list(set([d.header.name for d in SFTCatalog.data]))
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        logging.info(
            'Loaded data from detectors {} matching pattern {}'.format(
                names, self.sft_filepath))
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        logging.info('Initialising ephems')
        ephems = lalpulsar.InitBarycenter(self.earth_ephem, self.sun_ephem)

        logging.info('Initialising FstatInput')
        dFreq = 0
        self.whatToCompute = lalpulsar.FSTATQ_ATOMS_PER_DET
        FstatOptionalArgs = lalpulsar.FstatOptionalArgsDefaults

        if self.minCoverFreq is None or self.maxCoverFreq is None:
            fA = SFTCatalog.data[0].header.f0
            numBins = SFTCatalog.data[0].numBins
            fB = fA + (numBins-1)*SFTCatalog.data[0].header.deltaF
            self.minCoverFreq = fA + 0.5
            self.maxCoverFreq = fB - 0.5
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            logging.info('Min/max cover freqs not provided, using '
                         '{} and {}, est. from SFTs'.format(
                             self.minCoverFreq, self.maxCoverFreq))
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        self.FstatInput = lalpulsar.CreateFstatInput(SFTCatalog,
                                                     self.minCoverFreq,
                                                     self.maxCoverFreq,
                                                     dFreq,
                                                     ephems,
                                                     FstatOptionalArgs
                                                     )

        logging.info('Initialising PulsarDoplerParams')
        PulsarDopplerParams = lalpulsar.PulsarDopplerParams()
        PulsarDopplerParams.refTime = self.tref
        PulsarDopplerParams.Alpha = 1
        PulsarDopplerParams.Delta = 1
        PulsarDopplerParams.fkdot = np.array([0, 0, 0, 0, 0, 0, 0])
        self.PulsarDopplerParams = PulsarDopplerParams

        logging.info('Initialising FstatResults')
        self.FstatResults = lalpulsar.FstatResults()

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        self.windowRange = lalpulsar.transientWindowRange_t()
        self.windowRange.type = lalpulsar.TRANSIENT_RECTANGULAR
        self.windowRange.t0Band = 0
        self.windowRange.dt0 = 1
        self.windowRange.tauBand = 0
        self.windowRange.dtau = 1

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    def run_computefstatistic_single_point(self, tstart, tend, F0, F1,
                                           F2, Alpha, Delta):
        """ Compute the F-stat fully-coherently at a single point """

        self.PulsarDopplerParams.fkdot = np.array([F0, F1, F2, 0, 0, 0, 0])
        self.PulsarDopplerParams.Alpha = Alpha
        self.PulsarDopplerParams.Delta = Delta

        lalpulsar.ComputeFstat(self.FstatResults,
                               self.FstatInput,
                               self.PulsarDopplerParams,
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                               1,
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                               self.whatToCompute
                               )

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        self.windowRange.t0 = int(tstart)  # TYPE UINT4
        self.windowRange.tau = int(tend - tstart)  # TYPE UINT4
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        FS = lalpulsar.ComputeTransientFstatMap(
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            self.FstatResults.multiFatoms[0], self.windowRange, False)
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        return 2*FS.F_mn.data[0][0]


class SemiCoherentGlitchSearch(BaseSearchClass, ComputeFstat):
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    """ A semi-coherent glitch search

    This implements a basic `semi-coherent glitch F-stat in which the data
    is divided into two segments either side of the proposed glitch and the
    fully-coherent F-stat in each segment is averaged to give the semi-coherent
    F-stat
    """

    @initializer
    def __init__(self, label, outdir, tref, tstart, tend, sftlabel=None,
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                 nglitch=0, sftdir=None, minCoverFreq=None, maxCoverFreq=None,
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                 detector=None, earth_ephem=None, sun_ephem=None):
        """
        Parameters
        ----------
        label, outdir: str
            A label and directory to read/write data from/to
        sftlabel, sftdir: str
            A label and directory in which to find the relevant sft file. If
            None use label and outdir
        tref: int
            GPS seconds of the reference time
        minCoverFreq, maxCoverFreq: float
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            The min and max cover frequency passed to CreateFstatInput, if
            either is None the range of frequencies in the SFT less 1Hz is
            used.
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        detector: str
            Two character reference to the data to use, specify None for no
            contraint
        earth_ephem, sun_ephem: str
            Paths of the two files containing positions of Earth and Sun,
            respectively at evenly spaced times, as passed to CreateFstatInput
            If None defaults defined in BaseSearchClass will be used
        """

        if self.sftlabel is None:
            self.sftlabel = self.label
        if self.sftdir is None:
            self.sftdir = self.outdir
        self.fs_file_name = "{}/{}_FS.dat".format(self.outdir, self.label)
        if self.earth_ephem is None:
            self.earth_ephem = self.earth_ephem_default
        if self.sun_ephem is None:
            self.sun_ephem = self.sun_ephem_default
        self.init_computefstatistic_single_point()

    def compute_nglitch_fstat(self, F0, F1, F2, Alpha, Delta, *args):
        """ Compute the semi-coherent glitch F-stat """

        args = list(args)
        tboundaries = [self.tstart] + args[-self.nglitch:] + [self.tend]
        delta_F0s = [0] + args[-3*self.nglitch:-2*self.nglitch]
        delta_F1s = [0] + args[-2*self.nglitch:-self.nglitch]
        theta = [F0, F1, F2]
        tref = self.tref

        twoFSum = 0
        for i in range(self.nglitch+1):
            ts, te = tboundaries[i], tboundaries[i+1]

            if i == 0:
                theta_at_tref = theta
            else:
                # Issue here - are these correct?
                delta_theta = np.array([delta_F0s[i], delta_F1s[i], 0])
                theta_at_glitch = self.shift_coefficients(theta_at_tref,
                                                          te - tref)
                theta_post_glitch_at_glitch = theta_at_glitch + delta_theta
                theta_at_tref = self.shift_coefficients(
                    theta_post_glitch_at_glitch, tref - te)

            twoFVal = self.run_computefstatistic_single_point(
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                ts, te, theta_at_tref[0], theta_at_tref[1],
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                theta_at_tref[2], Alpha, Delta)
            twoFSum += twoFVal

        return twoFSum

    def compute_glitch_fstat_single(self, F0, F1, F2, Alpha, Delta, delta_F0,
                                    delta_F1, tglitch):
        """ Compute the semi-coherent glitch F-stat """

        theta = [F0, F1, F2]
        delta_theta = [delta_F0, delta_F1, 0]
        tref = self.tref

        theta_at_glitch = self.shift_coefficients(theta, tglitch - tref)
        theta_post_glitch_at_glitch = theta_at_glitch + delta_theta
        theta_post_glitch = self.shift_coefficients(
            theta_post_glitch_at_glitch, tref - tglitch)

        twoFsegA = self.run_computefstatistic_single_point(
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            self.tstart, tglitch, theta[0], theta[1], theta[2], Alpha,
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            Delta)

        if tglitch == self.tend:
            return twoFsegA

        twoFsegB = self.run_computefstatistic_single_point(
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            tglitch, self.tend, theta_post_glitch[0],
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            theta_post_glitch[1], theta_post_glitch[2], Alpha,
            Delta)

        return twoFsegA + twoFsegB


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class MCMCSearch(BaseSearchClass):
    """ MCMC search using ComputeFstat"""
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    @initializer
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    def __init__(self, label, outdir, sftlabel, sftdir, theta_prior, tref,
                 tstart, tend, nsteps=[100, 100, 100], nwalkers=100, ntemps=1,
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                 theta_initial=None, minCoverFreq=None,
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                 maxCoverFreq=None, scatter_val=1e-4, betas=None,
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                 detector=None, earth_ephem=None, sun_ephem=None):
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        """
        Parameters
        label, outdir: str
            A label and directory to read/write data from/to
        sftlabel, sftdir: str
            A label and directory in which to find the relevant sft file
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        theta_prior: dict
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            Dictionary of priors and fixed values for the search parameters.
            For each parameters (key of the dict), if it is to be held fixed
            the value should be the constant float, if it is be searched, the
            value should be a dictionary of the prior.
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        theta_initial: dict, array, (None)
            Either a dictionary of distribution about which to distribute the
            initial walkers about, an array (from which the walkers will be
            scattered by scatter_val, or  None in which case the prior is used.
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        tref, tstart, tend: int
            GPS seconds of the reference time, start time and end time
        nsteps: list (m,)
            List specifying the number of steps to take, the last two entries
            give the nburn and nprod of the 'production' run, all entries
            before are for iterative initialisation steps (usually just one)
            e.g. [1000, 1000, 500].
        nwalkers, ntemps: int
            Number of walkers and temperatures
        minCoverFreq, maxCoverFreq: float
            Minimum and maximum instantaneous frequency which will be covered
            over the SFT time span as passed to CreateFstatInput
        earth_ephem, sun_ephem: str
            Paths of the two files containing positions of Earth and Sun,
            respectively at evenly spaced times, as passed to CreateFstatInput
            If None defaults defined in BaseSearchClass will be used

        """

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        logging.info(
            'Set-up MCMC search for model {} on data {}'.format(
                self.label, self.sftlabel))
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        if os.path.isdir(outdir) is False:
            os.mkdir(outdir)
        self.pickle_path = '{}/{}_saved_data.p'.format(self.outdir, self.label)
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        self.theta_prior['tstart'] = self.tstart
        self.theta_prior['tend'] = self.tend
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        self.unpack_input_theta()
        self.ndim = len(self.theta_keys)
        self.sft_filepath = self.sftdir+'/*_'+self.sftlabel+"*sft"
        if earth_ephem is None:
            self.earth_ephem = self.earth_ephem_default
        if sun_ephem is None:
            self.sun_ephem = self.sun_ephem_default

        if args.clean and os.path.isfile(self.pickle_path):
            os.rename(self.pickle_path, self.pickle_path+".old")

        self.old_data_is_okay_to_use = self.check_old_data_is_okay_to_use()

    def inititate_search_object(self):
        logging.info('Setting up search object')
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        self.search = ComputeFstat(
            tref=self.tref, sftlabel=self.sftlabel,
            sftdir=self.sftdir, minCoverFreq=self.minCoverFreq,
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            maxCoverFreq=self.maxCoverFreq, earth_ephem=self.earth_ephem,
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            sun_ephem=self.sun_ephem, detector=self.detector)
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    def logp(self, theta_vals, theta_prior, theta_keys, search):
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        H = [self.generic_lnprior(**theta_prior[key])(p) for p, key in
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             zip(theta_vals, theta_keys)]
        return np.sum(H)

    def logl(self, theta, search):
        for j, theta_i in enumerate(self.theta_idxs):
            self.fixed_theta[theta_i] = theta[j]
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        FS = search.run_computefstatistic_single_point(*self.fixed_theta)
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        return FS

    def unpack_input_theta(self):
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        full_theta_keys = ['tstart', 'tend', 'F0', 'F1', 'F2', 'Alpha',
                           'Delta']
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        full_theta_keys_copy = copy.copy(full_theta_keys)

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        full_theta_symbols = ['_', '_', '$f$', '$\dot{f}$', '$\ddot{f}$',
                              r'$\alpha$', r'$\delta$']
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        self.theta_keys = []
        fixed_theta_dict = {}
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        for key, val in self.theta_prior.iteritems():
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            if type(val) is dict:
                fixed_theta_dict[key] = 0
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                self.theta_keys.append(key)
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            elif type(val) in [float, int, np.float64]:
                fixed_theta_dict[key] = val
            else:
                raise ValueError(
                    'Type {} of {} in theta not recognised'.format(
                        type(val), key))
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            full_theta_keys_copy.pop(full_theta_keys_copy.index(key))
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        if len(full_theta_keys_copy) > 0:
            raise ValueError(('Input dictionary `theta` is missing the'
                              'following keys: {}').format(
                                  full_theta_keys_copy))

        self.fixed_theta = [fixed_theta_dict[key] for key in full_theta_keys]
        self.theta_idxs = [full_theta_keys.index(k) for k in self.theta_keys]
        self.theta_symbols = [full_theta_symbols[i] for i in self.theta_idxs]

        idxs = np.argsort(self.theta_idxs)
        self.theta_idxs = [self.theta_idxs[i] for i in idxs]
        self.theta_symbols = [self.theta_symbols[i] for i in idxs]
        self.theta_keys = [self.theta_keys[i] for i in idxs]

    def check_initial_points(self, p0):
        initial_priors = np.array([
            self.logp(p, self.theta_prior, self.theta_keys, self.search)
            for p in p0[0]])
        number_of_initial_out_of_bounds = sum(initial_priors == -np.inf)
        if number_of_initial_out_of_bounds > 0:
            logging.warning(
                'Of {} initial values, {} are -np.inf due to the prior'.format(
                    len(initial_priors), number_of_initial_out_of_bounds))

    def run(self):

        if self.old_data_is_okay_to_use is True:
            logging.warning('Using saved data from {}'.format(
                self.pickle_path))
            d = self.get_saved_data()
            self.sampler = d['sampler']
            self.samples = d['samples']
            self.lnprobs = d['lnprobs']
            self.lnlikes = d['lnlikes']
            return

        self.inititate_search_object()

        sampler = emcee.PTSampler(
            self.ntemps, self.nwalkers, self.ndim, self.logl, self.logp,
            logpargs=(self.theta_prior, self.theta_keys, self.search),
            loglargs=(self.search,), betas=self.betas)

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        p0 = self.generate_initial_p0()
        p0 = self.apply_corrections_to_p0(p0)
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        self.check_initial_points(p0)

        ninit_steps = len(self.nsteps) - 2
        for j, n in enumerate(self.nsteps[:-2]):
            logging.info('Running {}/{} initialisation with {} steps'.format(
                j, ninit_steps, n))
            sampler.run_mcmc(p0, n)

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            fig, axes = self.plot_walkers(sampler, symbols=self.theta_symbols)
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            fig.savefig('{}/{}_init_{}_walkers.png'.format(
                self.outdir, self.label, j))

            p0 = self.get_new_p0(sampler, scatter_val=self.scatter_val)
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            p0 = self.apply_corrections_to_p0(p0)
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            self.check_initial_points(p0)
            sampler.reset()

        nburn = self.nsteps[-2]
        nprod = self.nsteps[-1]
        logging.info('Running final burn and prod with {} steps'.format(
            nburn+nprod))
        sampler.run_mcmc(p0, nburn+nprod)

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        fig, axes = self.plot_walkers(sampler, symbols=self.theta_symbols)
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        fig.savefig('{}/{}_walkers.png'.format(self.outdir, self.label))

        samples = sampler.chain[0, :, nburn:, :].reshape((-1, self.ndim))
        lnprobs = sampler.lnprobability[0, :, nburn:].reshape((-1))
        lnlikes = sampler.lnlikelihood[0, :, nburn:].reshape((-1))
        self.sampler = sampler
        self.samples = samples
        self.lnprobs = lnprobs
        self.lnlikes = lnlikes
        self.save_data(sampler, samples, lnprobs, lnlikes)

    def plot_corner(self, corner_figsize=(7, 7),  deltat=False,
                    add_prior=False, nstds=None, label_offset=0.4, **kwargs):

        fig, axes = plt.subplots(self.ndim, self.ndim,
                                 figsize=corner_figsize)

        samples_plt = copy.copy(self.samples)
        theta_symbols_plt = copy.copy(self.theta_symbols)
        theta_symbols_plt = [s.replace('_{glitch}', r'_\textrm{glitch}') for s
                             in theta_symbols_plt]

        if deltat:
            samples_plt[:, self.theta_keys.index('tglitch')] -= self.tref
            theta_symbols_plt[self.theta_keys.index('tglitch')] = (
                r'$t_{\textrm{glitch}} - t_{\textrm{ref}}$')

        if type(nstds) is int and 'range' not in kwargs:
            _range = []
            for j, s in enumerate(samples_plt.T):
                median = np.median(s)
                std = np.std(s)
                _range.append((median - nstds*std, median + nstds*std))
        else:
            _range = None

        fig_triangle = corner.corner(samples_plt,
                                     labels=theta_symbols_plt,
                                     fig=fig,
                                     bins=50,
                                     max_n_ticks=4,
                                     plot_contours=True,
                                     plot_datapoints=True,
                                     label_kwargs={'fontsize': 8},
                                     data_kwargs={'alpha': 0.1,
                                                  'ms': 0.5},
                                     range=_range,
                                     **kwargs)

        axes_list = fig_triangle.get_axes()
        axes = np.array(axes_list).reshape(self.ndim, self.ndim)
        plt.draw()
        for ax in axes[:, 0]:
            ax.yaxis.set_label_coords(-label_offset, 0.5)
        for ax in axes[-1, :]:
            ax.xaxis.set_label_coords(0.5, -label_offset)
        for ax in axes_list:
            ax.set_rasterized(True)
            ax.set_rasterization_zorder(-10)
        plt.tight_layout(h_pad=0.0, w_pad=0.0)
        fig.subplots_adjust(hspace=0.05, wspace=0.05)

        if add_prior:
            self.add_prior_to_corner(axes, samples_plt)

        fig_triangle.savefig('{}/{}_corner.png'.format(
            self.outdir, self.label))

    def add_prior_to_corner(self, axes, samples):
        for i, key in enumerate(self.theta_keys):
            ax = axes[i][i]
            xlim = ax.get_xlim()
            s = samples[:, i]
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            prior = self.generic_lnprior(**self.theta_prior[key])
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            x = np.linspace(s.min(), s.max(), 100)
            ax2 = ax.twinx()
            ax2.get_yaxis().set_visible(False)
            ax2.plot(x, [prior(xi) for xi in x], '-r')
            ax.set_xlim(xlim)

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    def generic_lnprior(self, **kwargs):
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        """ Return a lambda function of the pdf

        Parameters
        ----------
        kwargs: dict
            A dictionary containing 'type' of pdf and shape parameters

        """

        def logunif(x, a, b):
            above = x < b
            below = x > a
            if type(above) is not np.ndarray:
                if above and below:
                    return -np.log(b-a)
                else:
                    return -np.inf
            else:
                idxs = np.array([all(tup) for tup in zip(above, below)])
                p = np.zeros(len(x)) - np.inf
                p[idxs] = -np.log(b-a)
                return p

        def halfnorm(x, loc, scale):
            if x < 0:
                return -np.inf
            else:
                return -0.5*((x-loc)**2/scale**2+np.log(0.5*np.pi*scale**2))

        def cauchy(x, x0, gamma):
            return 1.0/(np.pi*gamma*(1+((x-x0)/gamma)**2))

        def exp(x, x0, gamma):
            if x > x0:
                return np.log(gamma) - gamma*(x - x0)
            else:
                return -np.inf

        if kwargs['type'] == 'unif':
            return lambda x: logunif(x, kwargs['lower'], kwargs['upper'])
        elif kwargs['type'] == 'halfnorm':
            return lambda x: halfnorm(x, kwargs['loc'], kwargs['scale'])
        elif kwargs['type'] == 'norm':
            return lambda x: -0.5*((x - kwargs['loc'])**2/kwargs['scale']**2
                                   + np.log(2*np.pi*kwargs['scale']**2))
        else:
            logging.info("kwargs:", kwargs)
            raise ValueError("Print unrecognise distribution")

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    def generate_rv(self, **kwargs):
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        dist_type = kwargs.pop('type')
        if dist_type == "unif":
            return np.random.uniform(low=kwargs['lower'], high=kwargs['upper'])
        if dist_type == "norm":
            return np.random.normal(loc=kwargs['loc'], scale=kwargs['scale'])
        if dist_type == "halfnorm":
            return np.abs(np.random.normal(loc=kwargs['loc'],
                                           scale=kwargs['scale']))
        if dist_type == "lognorm":
            return np.random.lognormal(
                mean=kwargs['loc'], sigma=kwargs['scale'])
        else:
            raise ValueError("dist_type {} unknown".format(dist_type))

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    def plot_walkers(self, sampler, symbols=None, alpha=0.4, color="k", temp=0,
                     start=None, stop=None, draw_vline=None):
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        """ Plot all the chains from a sampler """

        shape = sampler.chain.shape
        if len(shape) == 3:
            nwalkers, nsteps, ndim = shape
            chain = sampler.chain[:, :, :]
        if len(shape) == 4:
            ntemps, nwalkers, nsteps, ndim = shape
            if temp < ntemps:
                logging.info("Plotting temperature {} chains".format(temp))
            else:
                raise ValueError(("Requested temperature {} outside of"
                                  "available range").format(temp))
            chain = sampler.chain[temp, :, :, :]

        with plt.style.context(('classic')):
            fig, axes = plt.subplots(ndim, 1, sharex=True, figsize=(8, 4*ndim))

            if ndim > 1:
                for i in range(ndim):
                    axes[i].plot(chain[:, start:stop, i].T, color="k",
                                 alpha=alpha)
                    if symbols:
                        axes[i].set_ylabel(symbols[i])
                    if draw_vline is not None:
                        axes[i].axvline(draw_vline, lw=2, ls="--")

        return fig, axes

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    def apply_corrections_to_p0(self, p0):
        """ Apply any correction to the initial p0 values """
        return p0

    def generate_scattered_p0(self, p):
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        """ Generate a set of p0s scattered about p """
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        p0 = [[p + self.scatter_val * p * np.random.randn(self.ndim)
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               for i in xrange(self.nwalkers)]
              for j in xrange(self.ntemps)]
        return p0

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    def generate_initial_p0(self):
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        """ Generate a set of init vals for the walkers """

        if type(self.theta_initial) == dict:
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            p0 = [[[self.generate_rv(**self.theta_initial[key])
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                    for key in self.theta_keys]
                   for i in range(self.nwalkers)]
                  for j in range(self.ntemps)]
        elif self.theta_initial is None:
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            p0 = [[[self.generate_rv(**self.theta_prior[key])
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                    for key in self.theta_keys]
                   for i in range(self.nwalkers)]
                  for j in range(self.ntemps)]
        elif len(self.theta_initial) == self.ndim:
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            p0 = self.generate_scattered_p0(self.theta_initial)
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        else:
            raise ValueError('theta_initial not understood')

        return p0

    def get_new_p0(self, sampler, scatter_val=1e-3):
        """ Returns new initial positions for walkers are burn0 stage

        This returns new positions for all walkers by scattering points about
        the maximum posterior with scale `scatter_val`.

        """
        if sampler.chain[:, :, -1, :].shape[0] == 1:
            ntemps_temp = 1
        else:
            ntemps_temp = self.ntemps
        pF = sampler.chain[:, :, -1, :].reshape(
            ntemps_temp, self.nwalkers, self.ndim)[0, :, :]
        lnp = sampler.lnprobability[:, :, -1].reshape(
            self.ntemps, self.nwalkers)[0, :]
        if any(np.isnan(lnp)):
            logging.warning("The sampler has produced nan's")

        p = pF[np.nanargmax(lnp)]
        p0 = self._generate_scattered_p0(p)
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        return p0

    def get_save_data_dictionary(self):
        d = dict(nsteps=self.nsteps, nwalkers=self.nwalkers,
                 ntemps=self.ntemps, theta_keys=self.theta_keys,
                 theta_prior=self.theta_prior, scatter_val=self.scatter_val)
        return d

    def save_data(self, sampler, samples, lnprobs, lnlikes):
        d = self.get_save_data_dictionary()
        d['sampler'] = sampler
        d['samples'] = samples
        d['lnprobs'] = lnprobs
        d['lnlikes'] = lnlikes

        if os.path.isfile(self.pickle_path):
            logging.info('Saving backup of {} as {}.old'.format(
                self.pickle_path, self.pickle_path))
            os.rename(self.pickle_path, self.pickle_path+".old")
        with open(self.pickle_path, "wb") as File:
            pickle.dump(d, File)

    def get_list_of_matching_sfts(self):
        matches = glob.glob(self.sft_filepath)
        if len(matches) > 0:
            return matches
        else:
            raise IOError('No sfts found matching {}'.format(
                self.sft_filepath))

    def get_saved_data(self):
        with open(self.pickle_path, "r") as File:
            d = pickle.load(File)
        return d

    def check_old_data_is_okay_to_use(self):
        if os.path.isfile(self.pickle_path) is False:
            logging.info('No pickled data found')
            return False

        oldest_sft = min([os.path.getmtime(f) for f in
                          self.get_list_of_matching_sfts()])
        if os.path.getmtime(self.pickle_path) < oldest_sft:
            logging.info('Pickled data outdates sft files')
            return False

        old_d = self.get_saved_data().copy()
        new_d = self.get_save_data_dictionary().copy()

        old_d.pop('samples')
        old_d.pop('sampler')
        old_d.pop('lnprobs')
        old_d.pop('lnlikes')

        mod_keys = []
        for key in new_d.keys():
            if key in old_d:
                if new_d[key] != old_d[key]:
                    mod_keys.append((key, old_d[key], new_d[key]))
            else:
                raise ValueError('Keys do not match')

        if len(mod_keys) == 0:
            return True
        else:
            logging.warning("Saved data differs from requested")
            logging.info("Differences found in following keys:")
            for key in mod_keys:
                if len(key) == 3:
                    if np.isscalar(key[1]) or key[0] == 'nsteps':
                        logging.info("{} : {} -> {}".format(*key))
                    else:
                        logging.info(key[0])
                else:
                    logging.info(key)
            return False

    def get_max_twoF(self, threshold=0.05):
        """ Returns the max 2F sample and the corresponding 2F value

        Note: the sample is returned as a dictionary along with an estimate of
        the standard deviation calculated from the std of all samples with a
        twoF within `threshold` (relative) to the max twoF

        """
        if any(np.isposinf(self.lnlikes)):
            logging.info('twoF values contain positive infinite values')
        if any(np.isneginf(self.lnlikes)):
            logging.info('twoF values contain negative infinite values')
        if any(np.isnan(self.lnlikes)):
            logging.info('twoF values contain nan')
        idxs = np.isfinite(self.lnlikes)
        jmax = np.nanargmax(self.lnlikes[idxs])
        maxtwoF = self.lnlikes[jmax]
        d = {}
        close_idxs = abs((maxtwoF - self.lnlikes[idxs]) / maxtwoF) < threshold
        for i, k in enumerate(self.theta_keys):
            base_key = copy.copy(k)
            ng = 1
            while k in d:
                k = base_key + '_{}'.format(ng)
            d[k] = self.samples[jmax][i]

            s = self.samples[:, i][close_idxs]
            d[k + '_std'] = np.std(s)
        return d, maxtwoF

    def get_median_stds(self):
        """ Returns a dict of the median and std of all production samples """
        d = {}
        for s, k in zip(self.samples.T, self.theta_keys):
            d[k] = np.median(s)
            d[k+'_std'] = np.std(s)
        return d

    def write_par(self, method='med'):
        """ Writes a .par of the best-fit params with an estimated std """
        logging.info('Writing {}/{}.par using the {} method'.format(
            self.outdir, self.label, method))
        if method == 'med':
            median_std_d = self.get_median_stds()
            filename = '{}/{}.par'.format(self.outdir, self.label)
            with open(filename, 'w+') as f:
                for key, val in median_std_d.iteritems():
                    f.write('{} = {:1.16e}\n'.format(key, val))
        if method == 'twoFmax':
            max_twoF_d, _ = self.get_max_twoF()
            filename = '{}/{}.par'.format(self.outdir, self.label)
            with open(filename, 'w+') as f:
                for key, val in max_twoF_d.iteritems():
                    f.write('{} = {:1.16e}\n'.format(key, val))

    def print_summary(self):
        d, max_twoF = self.get_max_twoF()
        print('Max twoF: {}'.format(max_twoF))
        for k in np.sort(d.keys()):
            if 'std' not in k:
                print('{:10s} = {:1.9e} +/- {:1.9e}'.format(
                    k, d[k], d[k+'_std']))


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class MCMCGlitchSearch(MCMCSearch):
    """ MCMC search using the SemiCoherentGlitchSearch """
    @initializer
    def __init__(self, label, outdir, sftlabel, sftdir, theta_prior, tref,
                 tstart, tend, nsteps=[100, 100, 100], nwalkers=100, ntemps=1,
                 nglitch=0, theta_initial=None, minCoverFreq=None,
                 maxCoverFreq=None, scatter_val=1e-4, betas=None,
                 detector=None, dtglitchmin=20*86400, earth_ephem=None,
                 sun_ephem=None):
        """
        Parameters
        label, outdir: str
            A label and directory to read/write data from/to
        sftlabel, sftdir: str
            A label and directory in which to find the relevant sft file
        theta_prior: dict
            Dictionary of priors and fixed values for the search parameters.
            For each parameters (key of the dict), if it is to be held fixed
            the value should be the constant float, if it is be searched, the
            value should be a dictionary of the prior.
        theta_initial: dict, array, (None)
            Either a dictionary of distribution about which to distribute the
            initial walkers about, an array (from which the walkers will be
            scattered by scatter_val, or  None in which case the prior is used.
        nglitch: int
            The number of glitches to allow
        tref, tstart, tend: int
            GPS seconds of the reference time, start time and end time
        nsteps: list (m,)
            List specifying the number of steps to take, the last two entries
            give the nburn and nprod of the 'production' run, all entries
            before are for iterative initialisation steps (usually just one)
            e.g. [1000, 1000, 500].
        dtglitchmin: int
            The minimum duration (in seconds) of a segment between two glitches
            or a glitch and the start/end of the data
        nwalkers, ntemps: int
            Number of walkers and temperatures
        minCoverFreq, maxCoverFreq: float
            Minimum and maximum instantaneous frequency which will be covered
            over the SFT time span as passed to CreateFstatInput
        earth_ephem, sun_ephem: str
            Paths of the two files containing positions of Earth and Sun,
            respectively at evenly spaced times, as passed to CreateFstatInput
            If None defaults defined in BaseSearchClass will be used

        """

        logging.info(('Set-up MCMC glitch search with {} glitches for model {}'
                      ' on data {}').format(self.nglitch, self.label,
                                            self.sftlabel))
        if os.path.isdir(outdir) is False:
            os.mkdir(outdir)
        self.pickle_path = '{}/{}_saved_data.p'.format(self.outdir, self.label)
        self.unpack_input_theta()
        self.ndim = len(self.theta_keys)
        self.sft_filepath = self.sftdir+'/*_'+self.sftlabel+"*sft"
        if earth_ephem is None:
            self.earth_ephem = self.earth_ephem_default
        if sun_ephem is None:
            self.sun_ephem = self.sun_ephem_default

        if args.clean and os.path.isfile(self.pickle_path):
            os.rename(self.pickle_path, self.pickle_path+".old")

        self.old_data_is_okay_to_use = self.check_old_data_is_okay_to_use()

    def inititate_search_object(self):
        logging.info('Setting up search object')
        self.search = SemiCoherentGlitchSearch(
            label=self.label, outdir=self.outdir, sftlabel=self.sftlabel,
            sftdir=self.sftdir, tref=self.tref, tstart=self.tstart,
            tend=self.tend, minCoverFreq=self.minCoverFreq,
            maxCoverFreq=self.maxCoverFreq, earth_ephem=self.earth_ephem,
            sun_ephem=self.sun_ephem, detector=self.detector,
            nglitch=self.nglitch)

    def logp(self, theta_vals, theta_prior, theta_keys, search):
        if self.nglitch > 1:
            ts = [self.tstart] + theta_vals[-self.nglitch:] + [self.tend]
            if np.array_equal(ts, np.sort(ts)) is False:
                return -np.inf
            if any(np.diff(ts) < self.dtglitchmin):
                return -np.inf

        H = [self.generic_lnprior(**theta_prior[key])(p) for p, key in
             zip(theta_vals, theta_keys)]
        return np.sum(H)

    def logl(self, theta, search):
        for j, theta_i in enumerate(self.theta_idxs):
            self.fixed_theta[theta_i] = theta[j]
        FS = search.compute_nglitch_fstat(*self.fixed_theta)
        return FS

    def unpack_input_theta(self):
        glitch_keys = ['delta_F0', 'delta_F1', 'tglitch']
        full_glitch_keys = list(np.array(
            [[gk]*self.nglitch for gk in glitch_keys]).flatten())
        full_theta_keys = ['F0', 'F1', 'F2', 'Alpha', 'Delta']+full_glitch_keys
        full_theta_keys_copy = copy.copy(full_theta_keys)

        glitch_symbols = ['$\delta f$', '$\delta \dot{f}$', r'$t_{glitch}$']
        full_glitch_symbols = list(np.array(
            [[gs]*self.nglitch for gs in glitch_symbols]).flatten())
        full_theta_symbols = (['$f$', '$\dot{f}$', '$\ddot{f}$', r'$\alpha$',
                               r'$\delta$'] + full_glitch_symbols)
        self.theta_keys = []
        fixed_theta_dict = {}
        for key, val in self.theta_prior.iteritems():
            if type(val) is dict:
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