make_sfts.py 20 KB
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""" pyfstat tools to generate sfts """
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from __future__ import division, absolute_import, print_function
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import numpy as np
import logging
import os
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import glob
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import pkgutil
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import lal
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import lalpulsar

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from pyfstat.core import BaseSearchClass, tqdm, args, predict_fstat
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import pyfstat.helper_functions as helper_functions
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class KeyboardInterruptError(Exception):
    pass


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class Writer(BaseSearchClass):
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    """ Instance object for generating SFTs """
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    @helper_functions.initializer
    def __init__(self, label='Test', tstart=700000000, duration=100*86400,
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                 tref=None, F0=30, F1=1e-10, F2=0, Alpha=5e-3,
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                 Delta=6e-2, h0=0.1, cosi=0.0, psi=0.0, phi=0, Tsft=1800,
                 outdir=".", sqrtSX=1, Band=4, detectors='H1',
                 minStartTime=None, maxStartTime=None, add_noise=True):
        """
        Parameters
        ----------
        label: string
            a human-readable label to be used in naming the output files
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        tstart, duration : int
            start and duration (in gps seconds) of the total observation span
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        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
        """

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        self.set_ephemeris_files()
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        self.basic_setup()
        self.calculate_fmin_Band()

        self.tbounds = [self.tstart, self.tend]
        logging.info('Using segment boundaries {}'.format(self.tbounds))
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    def basic_setup(self):
        self.tstart = int(self.tstart)
        self.duration = int(self.duration)
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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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        self.minStartTime = int(self.minStartTime)
        self.maxStartTime = int(self.maxStartTime)
        self.duration_days = (self.tend-self.tstart) / 86400

        self.data_duration = self.maxStartTime - self.minStartTime
        numSFTs = int(float(self.data_duration) / self.Tsft)
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        self.theta = np.array([self.phi, self.F0, self.F1, self.F2])
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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
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        self.config_file_name = "{}/{}.cff".format(self.outdir, self.label)
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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.IFOs = (
            ",".join(['"{}"'.format(d) for d in self.detectors.split(",")]))
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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):
        """
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        Generates a .cff file
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        """

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        content = self.get_single_config_line(
            0, self.Alpha, self.Delta, self.h0, self.cosi, self.psi,
            self.phi, self.F0, self.F1, self.F2, self.tref, self.tstart,
            self.duration_days)
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        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

    def check_cached_data_okay_to_use(self, cl_mfd):
        """ 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')
        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']
        if calls[0] == cl_mfd:
            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

        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))
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        cl_mfd.append('--IFOs={}'.format(self.IFOs))
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        if self.add_noise:
            cl_mfd.append('--sqrtSX="{}"'.format(self.sqrtSX))
        if self.minStartTime is None:
            cl_mfd.append('--startTime={:0.0f}'.format(float(self.tstart)))
        else:
            cl_mfd.append('--startTime={:0.0f}'.format(
                float(self.minStartTime)))
        if self.maxStartTime is None:
            cl_mfd.append('--duration={}'.format(int(self.duration)))
        else:
            data_duration = self.maxStartTime - self.minStartTime
            cl_mfd.append('--duration={}'.format(int(data_duration)))
        cl_mfd.append('--fmin={:.16g}'.format(self.fmin))
        cl_mfd.append('--Band={:.16g}'.format(self.Band))
        cl_mfd.append('--Tsft={}'.format(self.Tsft))
        if self.h0 != 0:
            cl_mfd.append('--injectionSources="{}"'.format(
                self.config_file_name))

        cl_mfd = " ".join(cl_mfd)

        if self.check_cached_data_okay_to_use(cl_mfd) is False:
            helper_functions.run_commandline(cl_mfd)

    def predict_fstat(self):
        """ Wrapper to lalapps_PredictFstat """
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        twoF_expected, twoF_sigma = predict_fstat(
            self.h0, self.cosi, self.psi, self.Alpha, self.Delta, self.F0,
            self.sftfilepath, self.minStartTime, self.maxStartTime,
            self.detectors, self.sqrtSX) # detectors OR IFO?
        return twoF_expected
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class GlitchWriter(Writer):
    """ 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,
                 outdir=".", sqrtSX=1, Band=4, detectors='H1',
                 minStartTime=None, maxStartTime=None, add_noise=True):
        """
        Parameters
        ----------
        label: string
            a human-readable label to be used in naming the output files
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        tstart, duration : float
            start and duration (in gps seconds) of the total observation span
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        dtglitch: float
            time (in gps seconds) of the glitch after tstart. To create data
            without a glitch, set dtglitch=None
        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
        """

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        self.basic_setup()
        self.calculate_fmin_Band()

        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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        for d in self.delta_phi, self.delta_F0, self.delta_F1, self.delta_F2:
            if np.size(d) == 1:
                d = np.atleast_1d(d)
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        if self.dtglitch is None:
            self.tbounds = [self.tstart, self.tend]
        else:
            self.dtglitch = np.atleast_1d(self.dtglitch)
            self.tglitch = self.tstart + self.dtglitch
            self.tbounds = np.concatenate((
                [self.tstart], self.tglitch, [self.tend]))
        logging.info('Using segment boundaries {}'.format(self.tbounds))

        tbs = np.array(self.tbounds)
        self.durations_days = (tbs[1:] - tbs[:-1]) / 86400

        self.delta_thetas = np.atleast_2d(
                np.array([delta_phi, delta_F0, delta_F1, delta_F2]).T)

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

        """

        thetas = self._calculate_thetas(self.theta, self.delta_thetas,
                                        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()
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class FrequencyModulatedArtifactWriter(Writer):
    """ Instance object for generating SFTs containing artifacts """

    @helper_functions.initializer
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    def __init__(self, label, outdir=".", tstart=700000000,
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                 duration=86400, F0=30, F1=0, tref=None, h0=10, Tsft=1800,
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                 sqrtSX=1, Band=4, Pmod=lal.DAYSID_SI, Pmod_phi=0, Pmod_amp=1,
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                 Alpha=None, Delta=None, IFO='H1', minStartTime=None,
                 maxStartTime=None, detectors='H1'):
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        """
        Parameters
        ----------
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        tstart, duration : int
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            start and duration times (in gps seconds) of the total observation
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        Pmod, F0, F1 h0: float
            Modulation period, freq, freq-drift, and h0 of the artifact
        Alpha, Delta: float
            Sky position, in radians, of a signal of which to add the orbital
            modulation to the artifact, if not `None`.
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        Tsft: float
            the sft duration
        sqrtSX: float
            Background IFO noise

        see `lalapps_Makefakedata_v4 --help` for help with the other paramaters
        """
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        self.phi = 0
        self.F2 = 0
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        self.basic_setup()
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        self.set_ephemeris_files()
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        self.tstart = int(tstart)
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        self.duration = int(duration)
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        if os.path.isdir(self.outdir) is False:
            os.makedirs(self.outdir)
        if tref is None:
            raise ValueError('Input `tref` not specified')

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        self.nsfts = int(np.ceil(self.duration / self.Tsft))
        self.duration = self.duration / 86400.
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        self.calculate_fmin_Band()

        self.cosi = 0
        self.Fmax = F0

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        if Alpha is not None and Delta is not None:
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            self.n = np.array([np.cos(Alpha)*np.cos(Delta),
                               np.sin(Alpha)*np.cos(Delta),
                               np.sin(Delta)])
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    def get_frequency(self, t):
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        DeltaFDrift = self.F1 * (t - self.tref)

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        phir = 2*np.pi*t/self.Pmod + self.Pmod_phi

        if self.Alpha is not None and self.Delta is not None:
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            spin_posvel = lalpulsar.PosVel3D_t()
            orbit_posvel = lalpulsar.PosVel3D_t()
            det = lal.CachedDetectors[4]
            ephems = lalpulsar.InitBarycenter(self.earth_ephem, self.sun_ephem)
            lalpulsar.DetectorPosVel(
                spin_posvel, orbit_posvel, lal.LIGOTimeGPS(t), det, ephems,
                lalpulsar.DETMOTION_ORBIT)
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            # Pos and vel returned in units of c
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            DeltaFOrbital = np.dot(self.n, orbit_posvel.vel) * self.Fmax
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            if self.IFO == 'H1':
                Lambda = lal.LHO_4K_DETECTOR_LATITUDE_RAD
            elif self.IFO == 'L1':
                Lambda = lal.LLO_4K_DETECTOR_LATITUDE_RAD
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            DeltaFSpin = (
                self.Pmod_amp*lal.REARTH_SI/lal.C_SI*2*np.pi/self.Pmod*(
                   np.cos(self.Delta)*np.cos(Lambda)*np.sin(self.Alpha-phir)
                   ) * self.Fmax)
        else:
            DeltaFOrbital = 0
            DeltaFSpin = 2*np.pi*self.Pmod_amp/self.Pmod*np.cos(phir)
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        f = self.F0 + DeltaFDrift + DeltaFOrbital + DeltaFSpin
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        return f

    def get_h0(self, t):
        return self.h0

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    def concatenate_sft_files(self):
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        SFTFilename = lalpulsar.OfficialSFTFilename(
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            self.IFO[0], self.IFO[1], self.nsfts, self.Tsft, int(self.tstart),
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            int(self.duration), self.label)
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        # If the file already exists, simply remove it for now (no caching
        # implemented)
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        helper_functions.run_commandline(
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            'rm {}/{}'.format(self.outdir, SFTFilename), raise_error=False,
            log_level=10)
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        cl_splitSFTS = (
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            'lalapps_splitSFTs -fs {} -fb {} -fe {} -o {}/{} -i {}/*sft'
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            .format(self.fmin, self.Band, self.fmin+self.Band, self.outdir,
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                    SFTFilename, self.tmp_outdir))
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        helper_functions.run_commandline(cl_splitSFTS)
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        helper_functions.run_commandline('rm {} -r'.format(self.tmp_outdir))
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        files = glob.glob('{}/{}*'.format(self.outdir, SFTFilename))
        if len(files) == 1:
            fn = files[0]
            fn_new = fn.split('.')[0] + '.sft'
            helper_functions.run_commandline('mv {} {}'.format(
                fn, fn_new))
        else:
            raise IOError(
                'Attempted to rename file, but multiple files found: {}'
                .format(files))

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    def pre_compute_evolution(self):
        logging.info('Precomputing evolution parameters')
        self.lineFreqs = []
        self.linePhis = []
        self.lineh0s = []
        self.mid_times = []

        linePhi = 0
        lineFreq_old = 0
        for i in tqdm(range(self.nsfts)):
            mid_time = self.tstart + (i+.5)*self.Tsft
            lineFreq = self.get_frequency(mid_time)

            self.mid_times.append(mid_time)
            self.lineFreqs.append(lineFreq)
            self.linePhis.append(linePhi + np.pi*self.Tsft*(lineFreq_old+lineFreq))
            self.lineh0s.append(self.get_h0(mid_time))

            lineFreq_old = lineFreq

    def make_ith_sft(self, i):
        try:
            self.run_makefakedata_v4(self.mid_times[i], self.lineFreqs[i],
                                     self.linePhis[i], self.lineh0s[i],
                                     self.tmp_outdir)
        except KeyboardInterrupt:
            raise KeyboardInterruptError()

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    def make_data(self):
        self.maxStartTime = None
        self.duration = self.Tsft
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        self.tmp_outdir = '{}/{}_tmp'.format(self.outdir, self.label)
        if os.path.isdir(self.tmp_outdir) is True:
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            raise ValueError(
                'Temporary directory {} already exists, please rename'.format(
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                    self.tmp_outdir))
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        else:
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            os.makedirs(self.tmp_outdir)
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        self.pre_compute_evolution()

        logging.info('Generating SFTs')

        if args.N > 1 and pkgutil.find_loader('pathos') is not None:
            import pathos.pools
            logging.info('Using {} threads'.format(args.N))
            try:
                with pathos.pools.ProcessPool(args.N) as p:
                    list(tqdm(p.imap(self.make_ith_sft, range(self.nsfts)),
                              total=self.nsfts))
            except KeyboardInterrupt:
                p.terminate()
        else:
            logging.info(
                "No multiprocessing requested or `pathos` not install, cont."
                " without multiprocessing")
            for i in tqdm(range(self.nsfts)):
                self.make_ith_sft(i)
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        self.concatenate_sft_files()
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    def run_makefakedata_v4(self, mid_time, lineFreq, linePhi, h0, tmp_outdir):
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        """ Generate the sft data using the --lineFeature option """
        cl_mfd = []
        cl_mfd.append('lalapps_Makefakedata_v4')
        cl_mfd.append('--outSingleSFT=FALSE')
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        cl_mfd.append('--outSFTbname="{}"'.format(tmp_outdir))
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        cl_mfd.append('--IFO={}'.format(self.IFO))
        cl_mfd.append('--noiseSqrtSh="{}"'.format(self.sqrtSX))
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        cl_mfd.append('--startTime={:0.0f}'.format(mid_time-self.Tsft/2.0))
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        cl_mfd.append('--refTime={:0.0f}'.format(mid_time))
        cl_mfd.append('--duration={}'.format(int(self.duration)))
        cl_mfd.append('--fmin={:.16g}'.format(self.fmin))
        cl_mfd.append('--Band={:.16g}'.format(self.Band))
        cl_mfd.append('--Tsft={}'.format(self.Tsft))
        cl_mfd.append('--Freq={}'.format(lineFreq))
        cl_mfd.append('--phi0={}'.format(linePhi))
        cl_mfd.append('--h0={}'.format(h0))
        cl_mfd.append('--cosi={}'.format(self.cosi))
        cl_mfd.append('--lineFeature=TRUE')
        cl_mfd = " ".join(cl_mfd)
        helper_functions.run_commandline(cl_mfd, log_level=10)


class FrequencyAmplitudeModulatedArtifactWriter(FrequencyModulatedArtifactWriter):
    """ Instance object for generating SFTs containing artifacts """
    def get_h0(self, t):
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            return self.h0*np.sin(2*np.pi*t/self.Pmod+self. Pmod_phi)