core.py 46.6 KB
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""" The core tools used in pyfstat """
import os
import logging
import copy
import glob

import numpy as np
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# workaround for matplotlib on X-less remote logins
if os.environ.has_key('DISPLAY'):
    import matplotlib.pyplot as plt
else:
    logging.info('No $DISPLAY environment variable found, \
                  so importing matplotlib.pyplot with non-interactive "Agg" backend.')
    import matplotlib
    matplotlib.use('Agg')
    import matplotlib.pyplot as plt

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import scipy.special
import scipy.optimize
import lal
import lalpulsar

import helper_functions
helper_functions.set_up_matplotlib_defaults()
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args, tqdm = helper_functions.set_up_command_line_arguments()
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earth_ephem, sun_ephem = helper_functions.set_up_ephemeris_configuration()
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detector_colors = {'h1': 'C0', 'l1': 'C1'}
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def read_par(label=None, outdir=None, filename=None, suffix='par'):
    """ Read in a .par file, returns a dictionary of the values

    Note, can also read in .loudest files
    """
    if filename is None:
        filename = '{}/{}.{}'.format(outdir, label, suffix)
    if os.path.isfile(filename) is False:
        raise ValueError("No file ({}) found".format(filename))
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    d = {}
    with open(filename, 'r') as f:
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        d = get_dictionary_from_lines(f)
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    return d


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def get_dictionary_from_lines(lines):
    d = {}
    for line in lines:
        if line[0] not in ['%', '#'] and len(line.split('=')) == 2:
            try:
                key, val = line.rstrip('\n').split('=')
                key = key.strip()
                d[key] = np.float64(eval(val.rstrip('; ')))
            except SyntaxError:
                pass
    return d


def predict_fstat(h0, cosi, psi, Alpha, Delta, Freq, sftfilepattern,
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                  minStartTime, maxStartTime, IFO=None, assumeSqrtSX=None,
                  **kwargs):
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    """ Wrapper to lalapps_PredictFstat """
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    cl_pfs = []
    cl_pfs.append("lalapps_PredictFstat")
    cl_pfs.append("--h0={}".format(h0))
    cl_pfs.append("--cosi={}".format(cosi))
    cl_pfs.append("--psi={}".format(psi))
    cl_pfs.append("--Alpha={}".format(Alpha))
    cl_pfs.append("--Delta={}".format(Delta))
    cl_pfs.append("--Freq={}".format(Freq))

    cl_pfs.append("--DataFiles='{}'".format(sftfilepattern))
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    if assumeSqrtSX:
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        cl_pfs.append("--assumeSqrtSX={}".format(assumeSqrtSX))
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    if IFO:
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        cl_pfs.append("--IFO={}".format(IFO))
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    cl_pfs.append("--minStartTime={}".format(int(minStartTime)))
    cl_pfs.append("--maxStartTime={}".format(int(maxStartTime)))
    cl_pfs.append("--outputFstat=/tmp/fs")
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    cl_pfs = " ".join(cl_pfs)
    helper_functions.run_commandline(cl_pfs)
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    d = read_par(filename='/tmp/fs')
    return float(d['twoF_expected']), float(d['twoF_sigma'])


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class BaseSearchClass(object):
    """ The base search class, provides general functions """

    earth_ephem_default = earth_ephem
    sun_ephem_default = sun_ephem

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    def _add_log_file(self):
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        """ Log output to a file, requires class to have outdir and label """
        logfilename = '{}/{}.log'.format(self.outdir, self.label)
        fh = logging.FileHandler(logfilename)
        fh.setLevel(logging.INFO)
        fh.setFormatter(logging.Formatter(
            '%(asctime)s %(levelname)-8s: %(message)s',
            datefmt='%y-%m-%d %H:%M'))
        logging.getLogger().addHandler(fh)

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    def _shift_matrix(self, n, dT):
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        """ Generate the shift matrix

        Parameters
        ----------
        n: int
            The dimension of the shift-matrix to generate
        dT: float
            The time delta of the shift matrix

        Returns
        -------
        m: array (n, n)
            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

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    def _shift_coefficients(self, theta, dT):
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        """ 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)
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        m = self._shift_matrix(n, dT)
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        return np.dot(m, theta)

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    def _calculate_thetas(self, theta, delta_thetas, tbounds, theta0_idx=0):
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        """ Calculates the set of coefficients for the post-glitch signal """
        thetas = [theta]
        for i, dt in enumerate(delta_thetas):
            if i < theta0_idx:
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                pre_theta_at_ith_glitch = self._shift_coefficients(
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                    thetas[0], tbounds[i+1] - self.tref)
                post_theta_at_ith_glitch = pre_theta_at_ith_glitch - dt
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                thetas.insert(0, self._shift_coefficients(
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                    post_theta_at_ith_glitch, self.tref - tbounds[i+1]))

            elif i >= theta0_idx:
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                pre_theta_at_ith_glitch = self._shift_coefficients(
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                    thetas[i], tbounds[i+1] - self.tref)
                post_theta_at_ith_glitch = pre_theta_at_ith_glitch + dt
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                thetas.append(self._shift_coefficients(
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                    post_theta_at_ith_glitch, self.tref - tbounds[i+1]))
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        self.thetas_at_tref = thetas
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        return thetas

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    def _get_list_of_matching_sfts(self):
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        """ Returns a list of sfts matching the sftfilepattern """
        sftfilepatternlist = np.atleast_1d(self.sftfilepattern.split(';'))
        matches = [glob.glob(p) for p in sftfilepatternlist]
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        matches = [item for sublist in matches for item in sublist]
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        if len(matches) > 0:
            return matches
        else:
            raise IOError('No sfts found matching {}'.format(
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                self.sftfilepattern))
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class ComputeFstat(object):
    """ Base class providing interface to `lalpulsar.ComputeFstat` """

    earth_ephem_default = earth_ephem
    sun_ephem_default = sun_ephem

    @helper_functions.initializer
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    def __init__(self, tref, sftfilepattern=None, minStartTime=None,
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                 maxStartTime=None, binary=False, transient=True, BSGL=False,
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                 detectors=None, minCoverFreq=None, maxCoverFreq=None,
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                 earth_ephem=None, sun_ephem=None, injectSources=None,
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                 injectSqrtSX=None, assumeSqrtSX=None, SSBprec=None):
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        """
        Parameters
        ----------
        tref: int
            GPS seconds of the reference time.
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        sftfilepattern: str
            Pattern to match SFTs using wildcards (*?) and ranges [0-9];
            mutiple patterns can be given separated by colons.
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        minStartTime, maxStartTime: float GPStime
            Only use SFTs with timestemps starting from (including, excluding)
            this epoch
        binary: bool
            If true, search of binary parameters.
        transient: bool
            If true, allow for the Fstat to be computed over a transient range.
        BSGL: bool
            If true, compute the BSGL rather than the twoF value.
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        detectors: str
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            Two character reference to the data to use, specify None for no
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            contraint. If multiple-separate by comma.
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        minCoverFreq, maxCoverFreq: float
            The min and max cover frequency passed to CreateFstatInput, if
            either is None the range of frequencies in the SFT less 1Hz is
            used.
        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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        injectSources: dict or str
            Either a dictionary of the values to inject, or a string pointing
            to the .cff file to inject
        injectSqrtSX:
            Not yet implemented
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        assumeSqrtSX: float
            Don't estimate noise-floors but assume (stationary) per-IFO
            sqrt{SX} (if single value: use for all IFOs). If signal only,
            set sqrtSX=1
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        SSBprec: int
            Flag to set the SSB calculation: 0=Newtonian, 1=relativistic,
            2=relativisitic optimised, 3=DMoff, 4=NO_SPIN
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        """

        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 get_SFTCatalog(self):
        if hasattr(self, 'SFTCatalog'):
            return
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        if self.sftfilepattern is None:
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            for k in ['minStartTime', 'maxStartTime', 'detectors']:
                if getattr(self, k) is None:
                    raise ValueError('You must provide "{}" to injectSources'
                                     .format(k))
            C1 = getattr(self, 'injectSources', None) is None
            C2 = getattr(self, 'injectSqrtSX', None) is None
            if C1 and C2:
                raise ValueError('You must specify either one of injectSources'
                                 ' or injectSqrtSX')
            SFTCatalog = lalpulsar.SFTCatalog()
            Tsft = 1800
            Toverlap = 0
            Tspan = self.maxStartTime - self.minStartTime
            detNames = lal.CreateStringVector(
                *[d for d in self.detectors.split(',')])
            multiTimestamps = lalpulsar.MakeMultiTimestamps(
                self.minStartTime, Tspan, Tsft, Toverlap, detNames.length)
            SFTCatalog = lalpulsar.MultiAddToFakeSFTCatalog(
                SFTCatalog, detNames, multiTimestamps)
            return SFTCatalog

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        logging.info('Initialising SFTCatalog')
        constraints = lalpulsar.SFTConstraints()
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        if self.detectors:
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            if ',' in self.detectors:
                logging.info('Using all detector data')
            else:
                constraints.detector = self.detectors
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        if self.minStartTime:
            constraints.minStartTime = lal.LIGOTimeGPS(self.minStartTime)
        if self.maxStartTime:
            constraints.maxStartTime = lal.LIGOTimeGPS(self.maxStartTime)

        logging.info('Loading data matching pattern {}'.format(
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                     self.sftfilepattern))
        SFTCatalog = lalpulsar.SFTdataFind(self.sftfilepattern, constraints)
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        detector_names = list(set([d.header.name for d in SFTCatalog.data]))
        self.detector_names = detector_names
        SFT_timestamps = [d.header.epoch for d in SFTCatalog.data]
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        self.SFT_timestamps = [float(s) for s in SFT_timestamps]
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        if len(SFT_timestamps) == 0:
            raise ValueError('Failed to load any data')
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        if args.quite is False and args.no_interactive is False:
            try:
                from bashplotlib.histogram import plot_hist
                print('Data timestamps histogram:')
                plot_hist(SFT_timestamps, height=5, bincount=50)
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            except ImportError:
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                pass
        if len(detector_names) == 0:
            raise ValueError('No data loaded.')
        logging.info('Loaded {} data files from detectors {}'.format(
            len(SFT_timestamps), detector_names))
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        cl_tconv1 = 'lalapps_tconvert {}'.format(int(SFT_timestamps[0]))
        output    = helper_functions.run_commandline(cl_tconv1)
        tconvert1 = output.rstrip('\n')
        cl_tconv2 = 'lalapps_tconvert {}'.format(int(SFT_timestamps[-1]))
        output    = helper_functions.run_commandline(cl_tconv2)
        tconvert2 = output.rstrip('\n')
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        logging.info('Data spans from {} ({}) to {} ({})'.format(
            int(SFT_timestamps[0]),
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            tconvert1,
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            int(SFT_timestamps[-1]),
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            tconvert2))
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        return SFTCatalog
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    def init_computefstatistic_single_point(self):
        """ Initilisation step of run_computefstatistic for a single point """

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        SFTCatalog = self.get_SFTCatalog()
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        logging.info('Initialising ephems')
        ephems = lalpulsar.InitBarycenter(self.earth_ephem, self.sun_ephem)

        logging.info('Initialising FstatInput')
        dFreq = 0
        if self.transient:
            self.whatToCompute = lalpulsar.FSTATQ_ATOMS_PER_DET
        else:
            self.whatToCompute = lalpulsar.FSTATQ_2F

        FstatOAs = lalpulsar.FstatOptionalArgs()
        FstatOAs.randSeed = lalpulsar.FstatOptionalArgsDefaults.randSeed
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        if self.SSBprec:
            logging.info('Using SSBprec={}'.format(self.SSBprec))
            FstatOAs.SSBprec = self.SSBprec
        else:
            FstatOAs.SSBprec = lalpulsar.FstatOptionalArgsDefaults.SSBprec
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        FstatOAs.Dterms = lalpulsar.FstatOptionalArgsDefaults.Dterms
        FstatOAs.runningMedianWindow = lalpulsar.FstatOptionalArgsDefaults.runningMedianWindow
        FstatOAs.FstatMethod = lalpulsar.FstatOptionalArgsDefaults.FstatMethod
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        if self.assumeSqrtSX is None:
            FstatOAs.assumeSqrtSX = lalpulsar.FstatOptionalArgsDefaults.assumeSqrtSX
        else:
            mnf = lalpulsar.MultiNoiseFloor()
            assumeSqrtSX = np.atleast_1d(self.assumeSqrtSX)
            mnf.sqrtSn[:len(assumeSqrtSX)] = assumeSqrtSX
            mnf.length = len(assumeSqrtSX)
            FstatOAs.assumeSqrtSX = mnf
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        FstatOAs.prevInput = lalpulsar.FstatOptionalArgsDefaults.prevInput
        FstatOAs.collectTiming = lalpulsar.FstatOptionalArgsDefaults.collectTiming

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        if hasattr(self, 'injectSources') and type(self.injectSources) == dict:
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            logging.info('Injecting source with params: {}'.format(
                self.injectSources))
            PPV = lalpulsar.CreatePulsarParamsVector(1)
            PP = PPV.data[0]
            PP.Amp.h0 = self.injectSources['h0']
            PP.Amp.cosi = self.injectSources['cosi']
            PP.Amp.phi0 = self.injectSources['phi0']
            PP.Amp.psi = self.injectSources['psi']
            PP.Doppler.Alpha = self.injectSources['Alpha']
            PP.Doppler.Delta = self.injectSources['Delta']
            PP.Doppler.fkdot = np.array(self.injectSources['fkdot'])
            PP.Doppler.refTime = self.tref
            if 't0' not in self.injectSources:
                PP.Transient.type = lalpulsar.TRANSIENT_NONE
            FstatOAs.injectSources = PPV
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        elif hasattr(self, 'injectSources') and type(self.injectSources) == str:
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            logging.info('Injecting source from param file: {}'.format(
                self.injectSources))
            PPV = lalpulsar.PulsarParamsFromFile(self.injectSources, self.tref)
            FstatOAs.injectSources = PPV
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        else:
            FstatOAs.injectSources = lalpulsar.FstatOptionalArgsDefaults.injectSources
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        if hasattr(self, 'injectSqrtSX') and self.injectSqrtSX is not None:
            raise ValueError('injectSqrtSX not implemented')
        else:
            FstatOAs.InjectSqrtSX = lalpulsar.FstatOptionalArgsDefaults.injectSqrtSX
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        if self.minCoverFreq is None or self.maxCoverFreq is None:
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            fAs = [d.header.f0 for d in SFTCatalog.data]
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            fBs = [d.header.f0 + (d.numBins-1)*d.header.deltaF
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                   for d in SFTCatalog.data]
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            self.minCoverFreq = np.min(fAs) + 0.5
            self.maxCoverFreq = np.max(fBs) - 0.5
            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,
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                                                     self.minCoverFreq,
                                                     self.maxCoverFreq,
                                                     dFreq,
                                                     ephems,
                                                     FstatOAs
                                                     )

        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()

        if self.BSGL:
            if len(self.detector_names) < 2:
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                raise ValueError("Can't use BSGL with single detectors data")
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            else:
                logging.info('Initialising BSGL')

            # Tuning parameters - to be reviewed
            numDetectors = 2
            if hasattr(self, 'nsegs'):
                p_val_threshold = 1e-6
                Fstar0s = np.linspace(0, 1000, 10000)
                p_vals = scipy.special.gammaincc(2*self.nsegs, Fstar0s)
                Fstar0 = Fstar0s[np.argmin(np.abs(p_vals - p_val_threshold))]
                if Fstar0 == Fstar0s[-1]:
                    raise ValueError('Max Fstar0 exceeded')
            else:
                Fstar0 = 15.
            logging.info('Using Fstar0 of {:1.2f}'.format(Fstar0))
            oLGX = np.zeros(10)
            oLGX[:numDetectors] = 1./numDetectors
            self.BSGLSetup = lalpulsar.CreateBSGLSetup(numDetectors,
                                                       Fstar0,
                                                       oLGX,
                                                       True,
                                                       1)
            self.twoFX = np.zeros(10)
            self.whatToCompute = (self.whatToCompute +
                                  lalpulsar.FSTATQ_2F_PER_DET)

        if self.transient:
            logging.info('Initialising transient parameters')
            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

    def compute_fullycoherent_det_stat_single_point(
            self, F0, F1, F2, Alpha, Delta, asini=None, period=None, ecc=None,
            tp=None, argp=None):
        """ Compute the fully-coherent det. statistic at a single point """

        return self.run_computefstatistic_single_point(
            self.minStartTime, self.maxStartTime, F0, F1, F2, Alpha, Delta,
            asini, period, ecc, tp, argp)

    def run_computefstatistic_single_point(self, tstart, tend, F0, F1,
                                           F2, Alpha, Delta, asini=None,
                                           period=None, ecc=None, tp=None,
                                           argp=None):
        """ Returns twoF or ln(BSGL) 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
        if self.binary:
            self.PulsarDopplerParams.asini = asini
            self.PulsarDopplerParams.period = period
            self.PulsarDopplerParams.ecc = ecc
            self.PulsarDopplerParams.tp = tp
            self.PulsarDopplerParams.argp = argp

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

        if self.transient is False:
            if self.BSGL is False:
                return self.FstatResults.twoF[0]

            twoF = np.float(self.FstatResults.twoF[0])
            self.twoFX[0] = self.FstatResults.twoFPerDet(0)
            self.twoFX[1] = self.FstatResults.twoFPerDet(1)
            log10_BSGL = lalpulsar.ComputeBSGL(twoF, self.twoFX,
                                               self.BSGLSetup)
            return log10_BSGL/np.log10(np.exp(1))

        self.windowRange.t0 = int(tstart)  # TYPE UINT4
        self.windowRange.tau = int(tend - tstart)  # TYPE UINT4

        FS = lalpulsar.ComputeTransientFstatMap(
            self.FstatResults.multiFatoms[0], self.windowRange, False)

        if self.BSGL is False:
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            twoF = 2*FS.F_mn.data[0][0]
            if np.isnan(twoF):
                return 0
            else:
                return twoF
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        FstatResults_single = copy.copy(self.FstatResults)
        FstatResults_single.lenth = 1
        FstatResults_single.data = self.FstatResults.multiFatoms[0].data[0]
        FS0 = lalpulsar.ComputeTransientFstatMap(
            FstatResults_single.multiFatoms[0], self.windowRange, False)
        FstatResults_single.data = self.FstatResults.multiFatoms[0].data[1]
        FS1 = lalpulsar.ComputeTransientFstatMap(
            FstatResults_single.multiFatoms[0], self.windowRange, False)

        self.twoFX[0] = 2*FS0.F_mn.data[0][0]
        self.twoFX[1] = 2*FS1.F_mn.data[0][0]
        log10_BSGL = lalpulsar.ComputeBSGL(
                2*FS.F_mn.data[0][0], self.twoFX, self.BSGLSetup)

        return log10_BSGL/np.log10(np.exp(1))

    def calculate_twoF_cumulative(self, F0, F1, F2, Alpha, Delta, asini=None,
                                  period=None, ecc=None, tp=None, argp=None,
                                  tstart=None, tend=None, npoints=1000,
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                                  ):
        """ Calculate the cumulative twoF along the obseration span
        Params
        ------
        F0, F1, F2, Alpha, Delta: float
            Parameters at which to compute the cumulative twoF
        asini, period, ecc, tp, argp: float
            Binary parameters at which to compute the cumulative twoF (default
            to None)
        tstart, tend: int
            GPS times to restrict the range of data used - automatically
            truncated to the span of data available
        npoints: int
            Number of points to compute twoF along the span

        Note: the minimum cumulatibe twoF is hard-coded to be computed over
        the first 6 hours from either the first timestampe in the data (if
        tstart is smaller than it) or tstart.

        """
        SFTminStartTime = self.SFT_timestamps[0]
        SFTmaxStartTime = self.SFT_timestamps[-1]
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        tstart = np.max([SFTminStartTime, tstart])
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        min_tau = np.max([SFTminStartTime - tstart, 0]) + 3600*6
        max_tau = SFTmaxStartTime - tstart
        taus = np.linspace(min_tau, max_tau, npoints)
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        twoFs = []
        if self.transient is False:
            self.transient = True
            self.init_computefstatistic_single_point()
        for tau in taus:
            twoFs.append(self.run_computefstatistic_single_point(
                tstart=tstart, tend=tstart+tau, F0=F0, F1=F1, F2=F2,
                Alpha=Alpha, Delta=Delta, asini=asini, period=period, ecc=ecc,
                tp=tp, argp=argp))

        return taus, np.array(twoFs)

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    def calculate_pfs(self, label, outdir, N=15, IFO=None, pfs_input=None):

        if pfs_input is None:
            if os.path.isfile('{}/{}.loudest'.format(outdir, label)) is False:
                raise ValueError(
                    'Need a loudest file to add the predicted Fstat')
            loudest = read_par(label, outdir, suffix='loudest')
            pfs_input = {key: loudest[key] for key in
                         ['h0', 'cosi', 'psi', 'Alpha', 'Delta', 'Freq']}
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        times = np.linspace(self.minStartTime, self.maxStartTime, N+1)[1:]
        times = np.insert(times, 0, self.minStartTime + 86400/2.)
        out = [predict_fstat(minStartTime=self.minStartTime, maxStartTime=t,
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                             sftfilepattern=self.sftfilepattern, IFO=IFO,
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                             **pfs_input) for t in times]
        pfs, pfs_sigma = np.array(out).T
        return times, pfs, pfs_sigma

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    def plot_twoF_cumulative(self, label, outdir, ax=None, c='k', savefig=True,
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                             title=None, add_pfs=False, N=15,
                             injectSources=None, **kwargs):
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        if ax is None:
            fig, ax = plt.subplots()
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        if injectSources:
            pfs_input = dict(
                h0=injectSources['h0'], cosi=injectSources['cosi'],
                psi=injectSources['psi'], Alpha=injectSources['Alpha'],
                Delta=injectSources['Delta'], Freq=injectSources['fkdot'][0])
        else:
            pfs_input = None
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        taus, twoFs = self.calculate_twoF_cumulative(**kwargs)
        ax.plot(taus/86400., twoFs, label='All detectors', color=c)
        if len(self.detector_names) > 1:
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            detector_names = self.detector_names
            detectors = self.detectors
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            for d in self.detector_names:
                self.detectors = d
                self.init_computefstatistic_single_point()
                taus, twoFs = self.calculate_twoF_cumulative(**kwargs)
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                ax.plot(taus/86400., twoFs, label='{}'.format(d),
                        color=detector_colors[d.lower()])
            self.detectors = detectors
            self.detector_names = detector_names

        if add_pfs:
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            times, pfs, pfs_sigma = self.calculate_pfs(
                label, outdir, N=N, pfs_input=pfs_input)
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            ax.fill_between(
                (times-self.minStartTime)/86400., pfs-pfs_sigma, pfs+pfs_sigma,
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                color=c,
                label=r'Predicted $\langle 2\mathcal{F} \rangle\pm $ 1-$\sigma$ band',
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                zorder=-10, alpha=0.2)
            if len(self.detector_names) > 1:
                for d in self.detector_names:
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                    times, pfs, pfs_sigma = self.calculate_pfs(
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                        label, outdir, IFO=d.upper(), N=N, pfs_input=pfs_input)
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                    ax.fill_between(
                        (times-self.minStartTime)/86400., pfs-pfs_sigma,
                        pfs+pfs_sigma, color=detector_colors[d.lower()],
                        alpha=0.5,
                        label=(
                            'Predicted $2\mathcal{{F}}$ 1-$\sigma$ band ({})'
                            .format(d.upper())),
                        zorder=-10)
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        ax.set_xlabel(r'Days from $t_{{\rm start}}={:.0f}$'.format(
            kwargs['tstart']))
        if self.BSGL:
            ax.set_ylabel(r'$\log_{10}(\mathrm{BSGL})_{\rm cumulative}$')
        else:
            ax.set_ylabel(r'$\widetilde{2\mathcal{F}}_{\rm cumulative}$')
        ax.set_xlim(0, taus[-1]/86400)
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        ax.legend(frameon=False, loc=2, fontsize=6)
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        if title:
            ax.set_title(title)
        if savefig:
            plt.tight_layout()
            plt.savefig('{}/{}_twoFcumulative.png'.format(outdir, label))
            return taus, twoFs
        else:
            return ax


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

    @helper_functions.initializer
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    def __init__(self, label, outdir, tref, nsegs=None, sftfilepattern=None,
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                 binary=False, BSGL=False, minStartTime=None,
                 maxStartTime=None, minCoverFreq=None, maxCoverFreq=None,
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                 detectors=None, earth_ephem=None, sun_ephem=None,
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                 injectSources=None, assumeSqrtSX=None, SSBprec=None):
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        """
        Parameters
        ----------
        label, outdir: str
            A label and directory to read/write data from/to.
        tref, minStartTime, maxStartTime: int
            GPS seconds of the reference time, and start and end of the data.
        nsegs: int
            The (fixed) number of segments
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        sftfilepattern: str
            Pattern to match SFTs using wildcards (*?) and ranges [0-9];
            mutiple patterns can be given separated by colons.
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        For all other parameters, see pyfstat.ComputeFStat.
        """

        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.transient = True
        self.init_computefstatistic_single_point()
        self.init_semicoherent_parameters()

    def init_semicoherent_parameters(self):
        logging.info(('Initialising semicoherent parameters from {} to {} in'
                      ' {} segments').format(
            self.minStartTime, self.maxStartTime, self.nsegs))
        self.transient = True
        self.whatToCompute = lalpulsar.FSTATQ_2F+lalpulsar.FSTATQ_ATOMS_PER_DET
        self.tboundaries = np.linspace(self.minStartTime, self.maxStartTime,
                                       self.nsegs+1)

    def run_semi_coherent_computefstatistic_single_point(
            self, F0, F1, F2, Alpha, Delta, asini=None,
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            period=None, ecc=None, tp=None, argp=None,
            record_segments=False):
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        """ Returns twoF or ln(BSGL) semi-coherently at a single point """

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        if hasattr(self, 'SFT_timestamps'):
            if self.tboundaries[0] < self.SFT_timestamps[0]:
                logging.debug(
                    'Semi-coherent start time {} before first SFT timestamp {}'
                    .format(self.tboundaries[0], self.SFT_timestamps[0]))
            if self.tboundaries[-1] > self.SFT_timestamps[-1]:
                logging.debug(
                    'Semi-coherent end time {} after last SFT timestamp {}'
                    .format(self.tboundaries[-1], self.SFT_timestamps[-1]))
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        self.PulsarDopplerParams.fkdot = np.array([F0, F1, F2, 0, 0, 0, 0])
        self.PulsarDopplerParams.Alpha = Alpha
        self.PulsarDopplerParams.Delta = Delta
        if self.binary:
            self.PulsarDopplerParams.asini = asini
            self.PulsarDopplerParams.period = period
            self.PulsarDopplerParams.ecc = ecc
            self.PulsarDopplerParams.tp = tp
            self.PulsarDopplerParams.argp = argp

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

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        #if self.transient is False:
        #    if self.BSGL is False:
        #        return self.FstatResults.twoF[0]
        #    twoF = np.float(self.FstatResults.twoF[0])
        #    self.twoFX[0] = self.FstatResults.twoFPerDet(0)
        #    self.twoFX[1] = self.FstatResults.twoFPerDet(1)
        #    log10_BSGL = lalpulsar.ComputeBSGL(twoF, self.twoFX,
        #                                       self.BSGLSetup)
        #    return log10_BSGL/np.log10(np.exp(1))
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        detStat = 0
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        if record_segments:
            self.detStat_per_segment = []
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        for tstart, tend in zip(self.tboundaries[:-1], self.tboundaries[1:]):
            self.windowRange.t0 = int(tstart)  # TYPE UINT4
            self.windowRange.tau = int(tend - tstart)  # TYPE UINT4

            FS = lalpulsar.ComputeTransientFstatMap(
                self.FstatResults.multiFatoms[0], self.windowRange, False)

            if self.BSGL is False:
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                d_detStat = 2*FS.F_mn.data[0][0]
            else:
                FstatResults_single = copy.copy(self.FstatResults)
                FstatResults_single.lenth = 1
                FstatResults_single.data = self.FstatResults.multiFatoms[0].data[0]
                FS0 = lalpulsar.ComputeTransientFstatMap(
                    FstatResults_single.multiFatoms[0], self.windowRange, False)
                FstatResults_single.data = self.FstatResults.multiFatoms[0].data[1]
                FS1 = lalpulsar.ComputeTransientFstatMap(
                    FstatResults_single.multiFatoms[0], self.windowRange, False)

                self.twoFX[0] = 2*FS0.F_mn.data[0][0]
                self.twoFX[1] = 2*FS1.F_mn.data[0][0]
                log10_BSGL = lalpulsar.ComputeBSGL(
                        2*FS.F_mn.data[0][0], self.twoFX, self.BSGLSetup)
                d_detStat = log10_BSGL/np.log10(np.exp(1))
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            if np.isnan(d_detStat):
                logging.debug('NaNs in semi-coherent twoF treated as zero')
                d_detStat = 0
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            detStat += d_detStat
            if record_segments:
                self.detStat_per_segment.append(d_detStat)
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        return detStat


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

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

    @helper_functions.initializer
    def __init__(self, label, outdir, tref, minStartTime, maxStartTime,
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                 nglitch=0, sftfilepattern=None, theta0_idx=0, BSGL=False,
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                 minCoverFreq=None, maxCoverFreq=None, assumeSqrtSX=None,
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                 detectors=None, earth_ephem=None, sun_ephem=None,
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                 SSBprec=None, injectSources=None):
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        """
        Parameters
        ----------
        label, outdir: str
            A label and directory to read/write data from/to.
        tref, minStartTime, maxStartTime: int
            GPS seconds of the reference time, and start and end of the data.
        nglitch: int
            The (fixed) number of glitches; this can zero, but occasionally
            this causes issue (in which case just use ComputeFstat).
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        sftfilepattern: str
            Pattern to match SFTs using wildcards (*?) and ranges [0-9];
            mutiple patterns can be given separated by colons.
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        theta0_idx, int
            Index (zero-based) of which segment the theta refers to - uyseful
            if providing a tight prior on theta to allow the signal to jump
            too theta (and not just from)

        For all other parameters, see pyfstat.ComputeFStat.
        """

        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.transient = True
        self.binary = False
        self.init_computefstatistic_single_point()

    def compute_nglitch_fstat(self, F0, F1, F2, Alpha, Delta, *args):
        """ Returns the semi-coherent glitch summed twoF """

        args = list(args)
        tboundaries = ([self.minStartTime] + args[-self.nglitch:]
                       + [self.maxStartTime])
        delta_F0s = args[-3*self.nglitch:-2*self.nglitch]
        delta_F1s = args[-2*self.nglitch:-self.nglitch]
        delta_F2 = np.zeros(len(delta_F0s))
        delta_phi = np.zeros(len(delta_F0s))
        theta = [0, F0, F1, F2]
        delta_thetas = np.atleast_2d(
                np.array([delta_phi, delta_F0s, delta_F1s, delta_F2]).T)

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        thetas = self._calculate_thetas(theta, delta_thetas, tboundaries,
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                                       theta0_idx=self.theta0_idx)

        twoFSum = 0
        for i, theta_i_at_tref in enumerate(thetas):
            ts, te = tboundaries[i], tboundaries[i+1]

            twoFVal = self.run_computefstatistic_single_point(
                ts, te, theta_i_at_tref[1], theta_i_at_tref[2],
                theta_i_at_tref[3], Alpha, Delta)
            twoFSum += twoFVal

        if np.isfinite(twoFSum):
            return twoFSum
        else:
            return -np.inf

    def compute_glitch_fstat_single(self, F0, F1, F2, Alpha, Delta, delta_F0,
                                    delta_F1, tglitch):
        """ Returns the semi-coherent glitch summed twoF for nglitch=1

        Note: OBSOLETE, used only for testing
        """

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

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

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

        if tglitch == self.maxStartTime:
            return twoFsegA

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

        return twoFsegA + twoFsegB


class Writer(BaseSearchClass):
    """ Instance object for generating SFTs containing glitch signals """
    @helper_functions.initializer
    def __init__(self, label='Test', tstart=700000000, duration=100*86400,
                 dtglitch=None, delta_phi=0, delta_F0=0, delta_F1=0,
                 delta_F2=0, tref=None, F0=30, F1=1e-10, F2=0, Alpha=5e-3,
                 Delta=6e-2, h0=0.1, cosi=0.0, psi=0.0, phi=0, Tsft=1800,
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                 outdir=".", sqrtSX=1, Band=4, detectors='H1',
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                 minStartTime=None, maxStartTime=None, add_noise=True):
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        """
        Parameters
        ----------
        label: string
            a human-readable label to be used in naming the output files
        tstart, tend : float
            start and end times (in gps seconds) of the total observation span
        dtglitch: float
            time (in gps seconds) of the glitch after tstart. To create data
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            without a glitch, set dtglitch=None
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        delta_phi, delta_F0, delta_F1: float
            instanteneous glitch magnitudes in rad, Hz, and Hz/s respectively
        tref: float or None
            reference time (default is None, which sets the reference time to
            tstart)
        F0, F1, F2, Alpha, Delta, h0, cosi, psi, phi: float
            frequency, sky-position, and amplitude parameters
        Tsft: float
            the sft duration
        minStartTime, maxStartTime: float
            if not None, the total span of data, this can be used to generate
            transient signals

        see `lalapps_Makefakedata_v5 --help` for help with the other paramaters
        """

        for d in self.delta_phi, self.delta_F0, self.delta_F1, self.delta_F2:
            if np.size(d) == 1:
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                d = np.atleast_1d(d)
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        self.tend = self.tstart + self.duration
        if self.minStartTime is None:
            self.minStartTime = self.tstart
        if self.maxStartTime is None:
            self.maxStartTime = self.tend
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        if self.dtglitch is None:
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            self.tbounds = [self.tstart, self.tend]
        else:
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            self.dtglitch = np.atleast_1d(self.dtglitch)
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            self.tglitch = self.tstart + self.dtglitch
            self.tbounds = np.concatenate((
                [self.tstart], self.tglitch, [self.tend]))
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        logging.info('Using segment boundaries {}'.format(self.tbounds))
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        self.check_inputs()
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        if os.path.isdir(self.outdir) is False:
            os.makedirs(self.outdir)
        if self.tref is None:
            self.tref = self.tstart
        self.tend = self.tstart + self.duration
        tbs = np.array(self.tbounds)
        self.durations_days = (tbs[1:] - tbs[:-1]) / 86400
        self.config_file_name = "{}/{}.cff".format(outdir, label)

        self.theta = np.array([phi, F0, F1, F2])
        self.delta_thetas = np.atleast_2d(
                np.array([delta_phi, delta_F0, delta_F1, delta_F2]).T)

        self.data_duration = self.maxStartTime - self.minStartTime
        numSFTs = int(float(self.data_duration) / self.Tsft)
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        self.sftfilenames = [
            lalpulsar.OfficialSFTFilename(
                dets[0], dets[1], numSFTs, self.Tsft, self.minStartTime,
                self.data_duration, self.label)
            for dets in self.detectors.split(',')]
        self.sftfilepath = ';'.join([
            '{}/{}'.format(self.outdir, fn) for fn in self.sftfilenames])
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        self.calculate_fmin_Band()

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    def check_inputs(self):
        self.minStartTime = int(self.minStartTime)
        self.maxStartTime = int(self.maxStartTime)
        shapes = np.array([np.shape(x) for x in [self.delta_phi, self.delta_F0,
                                                 self.delta_F1, self.delta_F2]]
                          )
        if not np.all(shapes == shapes[0]):
            raise ValueError('all delta_* must be the same shape: {}'.format(
                shapes))

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    def make_data(self):
        ''' A convienience wrapper to generate a cff file then sfts '''
        self.make_cff()
        self.run_makefakedata()

    def get_single_config_line(self, i, Alpha, Delta, h0, cosi, psi, phi, F0,
                               F1, F2, tref, tstart, duration_days):
        template = (
"""[TS{}]
Alpha = {:1.18e}
Delta = {:1.18e}
h0 = {:1.18e}
cosi = {:1.18e}
psi = {:1.18e}
phi0 = {:1.18e}
Freq = {:1.18e}
f1dot = {:1.18e}
f2dot = {:1.18e}
refTime = {:10.6f}
transientWindowType=rect
transientStartTime={:10.3f}
transientTauDays={:1.3f}\n""")
        return template.format(i, Alpha, Delta, h0, cosi, psi, phi, F0, F1,
                               F2, tref, tstart, duration_days)

    def make_cff(self):
        """
        Generates an .cff file for a 'glitching' signal

        """

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        thetas = self._calculate_thetas(self.theta, self.delta_thetas,
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                                       self.tbounds)

        content = ''
        for i, (t, d, ts) in enumerate(zip(thetas, self.durations_days,
                                           self.tbounds[:-1])):
            line = self.get_single_config_line(
                i, self.Alpha, self.Delta, self.h0, self.cosi, self.psi,
                t[0], t[1], t[2], t[3], self.tref, ts, d)

            content += line

        if self.check_if_cff_file_needs_rewritting(content):
            config_file = open(self.config_file_name, "w+")
            config_file.write(content)
            config_file.close()

    def calculate_fmin_Band(self):
        self.fmin = self.F0 - .5 * self.Band

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    def check_cached_data_okay_to_use(self, cl_mfd):
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        """ Check if cached data exists and, if it does, if it can be used """

        getmtime = os.path.getmtime

        if os.path.isfile(self.sftfilepath) is False:
            logging.info('No SFT file matching {} found'.format(
                self.sftfilepath))
            return False
        else:
            logging.info('Matching SFT file found')

        if getmtime(self.sftfilepath) < getmtime(self.config_file_name):
            logging.info(
                ('The config file {} has been modified since the sft file {} '
                 + 'was created').format(
                    self.config_file_name, self.sftfilepath))
            return False

        logging.info(
            'The config file {} is older than the sft file {}'.format(
                self.config_file_name, self.sftfilepath))
        logging.info('Checking contents of cff file')
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        cl_dump = 'lalapps_SFTdumpheader {} | head -n 20'.format(self.sftfilepath)
        output  = helper_functions.run_commandline(cl_dump)
        calls   = [line for line in output.split('\n') if line[:3] == 'lal']
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        if calls[0] == cl_mfd:
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            logging.info('Contents matched, use old sft file')
            return True
        else:
            logging.info('Contents unmatched, create new sft file')
            return False

    def check_if_cff_file_needs_rewritting(self, content):
        """ Check if the .cff file has changed

        Returns True if the file should be overwritten - where possible avoid
        overwriting to allow cached data to be used
        """
        if os.path.isfile(self.config_file_name) is False:
            logging.info('No config file {} found'.format(
                self.config_file_name))
            return True
        else:
            logging.info('Config file {} already exists'.format(
                self.config_file_name))

        with open(self.config_file_name, 'r') as f:
            file_content = f.read()
            if file_content == content:
                logging.info(
                    'File contents match, no update of {} required'.format(
                        self.config_file_name))
                return False
            else:
                logging.info(
                    'File contents unmatched, updating {}'.format(
                        self.config_file_name))
                return True

    def run_makefakedata(self):
        """ Generate the sft data from the configuration file """

        # Remove old data:
        try:
            os.unlink("{}/*{}*.sft".format(self.outdir, self.label))
        except OSError:
            pass

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        cl_mfd = []
        cl_mfd.append('lalapps_Makefakedata_v5')
        cl_mfd.append('--outSingleSFT=TRUE')
        cl_mfd.append('--outSFTdir="{}"'.format(self.outdir))
        cl_mfd.append('--outLabel="{}"'.format(self.label))
        cl_mfd.append('--IFOs={}'.format(
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            ",".join(['"{}"'.format(d) for d in self.detectors.split(",")])))
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        if self.add_noise:
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            cl_mfd.append('--sqrtSX="{}"'.format(self.sqrtSX))
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        if self.minStartTime is None:
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            cl_mfd.append('--startTime={:0.0f}'.format(float(self.tstart)))
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        else:
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            cl_mfd.append('--startTime={:0.0f}'.format(float(self.minStartTime)))
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        if self.maxStartTime is None:
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            cl_mfd.append('--duration={}'.format(int(self.duration)))
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        else:
            data_duration = self.maxStartTime - self.minStartTime
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            cl_mfd.append('--duration={}'.format(int(data_duration)))
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        cl_mfd.append('--fmin={:.16g}'.format(self.fmin))
        cl_mfd.append('--Band={:.16g}'.format(self.Band))
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        cl_mfd.append('--Tsft={}'.format(self.Tsft))
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        if self.h0 != 0:
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            cl_mfd.append('--injectionSources="{}"'.format(self.config_file_name))
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        cl_mfd = " ".join(cl_mfd)
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        if self.check_cached_data_okay_to_use(cl_mfd) is False:
            helper_functions.run_commandline(cl_mfd)
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    def predict_fstat(self):
        """ Wrapper to lalapps_PredictFstat """
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        cl_pfs = []
        cl_pfs.append("lalapps_PredictFstat")
        cl_pfs.append("--h0={}".format(self.h0))
        cl_pfs.append("--cosi={}".format(self.cosi))
        cl_pfs.append("--psi={}".format(self.psi))
        cl_pfs.append("--Alpha={}".format(self.Alpha))
        cl_pfs.append("--Delta={}".format(self.Delta))
        cl_pfs.append("--Freq={}".format(self.F0))

        cl_pfs.append("--DataFiles='{}'".format(
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            self.outdir+"/*SFT_"+self.label+"*sft"))
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        cl_pfs.append("--assumeSqrtSX={}".format(self.sqrtSX))
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        cl_pfs.append("--minStartTime={}".format(int(self.minStartTime)))
        cl_pfs.append("--maxStartTime={}".format(int(self.maxStartTime)))
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        cl_pfs = " ".join(cl_pfs)
        output = helper_functions.run_commandline(cl_pfs)
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        twoF = float(output.split('\n')[-2])
        return float(twoF)