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core.py 46.20 KiB
""" The core tools used in pyfstat """
import os
import logging
import copy
import glob
import numpy as np
# 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
import scipy.special
import scipy.optimize
import lal
import lalpulsar
import helper_functions
helper_functions.set_up_matplotlib_defaults()
args, tqdm = helper_functions.set_up_command_line_arguments()
earth_ephem, sun_ephem = helper_functions.set_up_ephemeris_configuration()
detector_colors = {'h1': 'C0', 'l1': 'C1'}
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))
d = {}
with open(filename, 'r') as f:
d = get_dictionary_from_lines(f)
return d
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,
minStartTime, maxStartTime, IFO=None, assumeSqrtSX=None,
**kwargs):
""" Wrapper to lalapps_PredictFstat """
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))
if assumeSqrtSX:
cl_pfs.append("--assumeSqrtSX={}".format(assumeSqrtSX))
if IFO:
cl_pfs.append("--IFO={}".format(IFO))
cl_pfs.append("--minStartTime={}".format(int(minStartTime)))
cl_pfs.append("--maxStartTime={}".format(int(maxStartTime)))
cl_pfs.append("--outputFstat=/tmp/fs")
cl_pfs = " ".join(cl_pfs)
helper_functions.run_commandline(cl_pfs)
d = read_par(filename='/tmp/fs')
return float(d['twoF_expected']), float(d['twoF_sigma'])
class BaseSearchClass(object):
""" The base search class, provides general functions """
earth_ephem_default = earth_ephem
sun_ephem_default = sun_ephem
def _add_log_file(self):
""" 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)
def _shift_matrix(self, n, dT):
""" 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
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)
def _calculate_thetas(self, theta, delta_thetas, tbounds, theta0_idx=0):
""" Calculates the set of coefficients for the post-glitch signal """
thetas = [theta]
for i, dt in enumerate(delta_thetas):
if i < theta0_idx:
pre_theta_at_ith_glitch = self._shift_coefficients(
thetas[0], tbounds[i+1] - self.tref)
post_theta_at_ith_glitch = pre_theta_at_ith_glitch - dt
thetas.insert(0, self._shift_coefficients(
post_theta_at_ith_glitch, self.tref - tbounds[i+1]))
elif i >= theta0_idx:
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]))
self.thetas_at_tref = thetas
return thetas
def _get_list_of_matching_sfts(self):
# first make sure we have a list of paths, to avoid
# list comprehension trying to glob each single character
sftfilepathlist = np.atleast_1d(self.sftfilepath)
matches = [glob.glob(p) for p in sftfilepathlist]
matches = [item for sublist in matches for item in sublist]
if len(matches) > 0:
return matches
else:
raise IOError('No sfts found matching {}'.format(
self.sftfilepath))
class ComputeFstat(object):
""" Base class providing interface to `lalpulsar.ComputeFstat` """
earth_ephem_default = earth_ephem
sun_ephem_default = sun_ephem
@helper_functions.initializer
def __init__(self, tref, sftfilepath=None, minStartTime=None,
maxStartTime=None, binary=False, transient=True, BSGL=False,
detectors=None, minCoverFreq=None, maxCoverFreq=None,
earth_ephem=None, sun_ephem=None, injectSources=None,
injectSqrtSX=None, assumeSqrtSX=None, SSBprec=None):
"""
Parameters
----------
tref: int
GPS seconds of the reference time.
sftfilepath: str
File patern to match SFTs
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.
detectors: str
Two character reference to the data to use, specify None for no
contraint. If multiple-separate by comma.
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.
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
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
SSBprec: int
Flag to set the SSB calculation: 0=Newtonian, 1=relativistic,
2=relativisitic optimised, 3=DMoff, 4=NO_SPIN
"""
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
if self.sftfilepath is None:
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
logging.info('Initialising SFTCatalog')
constraints = lalpulsar.SFTConstraints()
if self.detectors:
if ',' in self.detectors:
logging.info('Using all detector data')
else:
constraints.detector = self.detectors
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(
self.sftfilepath))
SFTCatalog = lalpulsar.SFTdataFind(self.sftfilepath, constraints)
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]
self.SFT_timestamps = [float(s) for s in SFT_timestamps]
if len(SFT_timestamps) == 0:
raise ValueError('Failed to load any data')
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)
except ImportError:
pass
if len(detector_names) == 0:
raise ValueError('No data loaded.')
logging.info('Loaded {} data files from detectors {}'.format(
len(SFT_timestamps), detector_names))
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')
logging.info('Data spans from {} ({}) to {} ({})'.format(
int(SFT_timestamps[0]),
tconvert1,
int(SFT_timestamps[-1]),
tconvert2))
return SFTCatalog
def init_computefstatistic_single_point(self):
""" Initilisation step of run_computefstatistic for a single point """
SFTCatalog = self.get_SFTCatalog()
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
if self.SSBprec:
logging.info('Using SSBprec={}'.format(self.SSBprec))
FstatOAs.SSBprec = self.SSBprec
else:
FstatOAs.SSBprec = lalpulsar.FstatOptionalArgsDefaults.SSBprec
FstatOAs.Dterms = lalpulsar.FstatOptionalArgsDefaults.Dterms
FstatOAs.runningMedianWindow = lalpulsar.FstatOptionalArgsDefaults.runningMedianWindow
FstatOAs.FstatMethod = lalpulsar.FstatOptionalArgsDefaults.FstatMethod
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
FstatOAs.prevInput = lalpulsar.FstatOptionalArgsDefaults.prevInput
FstatOAs.collectTiming = lalpulsar.FstatOptionalArgsDefaults.collectTiming
if hasattr(self, 'injectSources') and type(self.injectSources) == dict:
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
elif hasattr(self, 'injectSources') and type(self.injectSources) == str:
logging.info('Injecting source from param file: {}'.format(
self.injectSources))
PPV = lalpulsar.PulsarParamsFromFile(self.injectSources, self.tref)
FstatOAs.injectSources = PPV
else:
FstatOAs.injectSources = lalpulsar.FstatOptionalArgsDefaults.injectSources
if hasattr(self, 'injectSqrtSX') and self.injectSqrtSX is not None:
raise ValueError('injectSqrtSX not implemented')
else:
FstatOAs.InjectSqrtSX = lalpulsar.FstatOptionalArgsDefaults.injectSqrtSX
if self.minCoverFreq is None or self.maxCoverFreq is None:
fAs = [d.header.f0 for d in SFTCatalog.data]
fBs = [d.header.f0 + (d.numBins-1)*d.header.deltaF
for d in SFTCatalog.data]
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))
self.FstatInput = lalpulsar.CreateFstatInput(SFTCatalog,
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:
raise ValueError("Can't use BSGL with single detectors data")
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:
twoF = 2*FS.F_mn.data[0][0]
if np.isnan(twoF):
return 0
else:
return twoF
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,
):
""" 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]
tstart = np.max([SFTminStartTime, tstart])
min_tau = np.max([SFTminStartTime - tstart, 0]) + 3600*6
max_tau = SFTmaxStartTime - tstart
taus = np.linspace(min_tau, max_tau, npoints)
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)
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']}
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,
sftfilepattern=self.sftfilepath, IFO=IFO,
**pfs_input) for t in times]
pfs, pfs_sigma = np.array(out).T
return times, pfs, pfs_sigma
def plot_twoF_cumulative(self, label, outdir, ax=None, c='k', savefig=True,
title=None, add_pfs=False, N=15,
injectSources=None, **kwargs):
if ax is None:
fig, ax = plt.subplots()
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
taus, twoFs = self.calculate_twoF_cumulative(**kwargs)
ax.plot(taus/86400., twoFs, label='All detectors', color=c)
if len(self.detector_names) > 1:
detector_names = self.detector_names
detectors = self.detectors
for d in self.detector_names:
self.detectors = d
self.init_computefstatistic_single_point()
taus, twoFs = self.calculate_twoF_cumulative(**kwargs)
ax.plot(taus/86400., twoFs, label='{}'.format(d),
color=detector_colors[d.lower()])
self.detectors = detectors
self.detector_names = detector_names
if add_pfs:
times, pfs, pfs_sigma = self.calculate_pfs(
label, outdir, N=N, pfs_input=pfs_input)
ax.fill_between(
(times-self.minStartTime)/86400., pfs-pfs_sigma, pfs+pfs_sigma,
color=c,
label=r'Predicted $\langle 2\mathcal{F} \rangle\pm $ 1-$\sigma$ band',
zorder=-10, alpha=0.2)
if len(self.detector_names) > 1:
for d in self.detector_names:
times, pfs, pfs_sigma = self.calculate_pfs(
label, outdir, IFO=d.upper(), N=N, pfs_input=pfs_input)
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)
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)
ax.legend(frameon=False, loc=2, fontsize=6)
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
def __init__(self, label, outdir, tref, nsegs=None, sftfilepath=None,
binary=False, BSGL=False, minStartTime=None,
maxStartTime=None, minCoverFreq=None, maxCoverFreq=None,
detectors=None, earth_ephem=None, sun_ephem=None,
injectSources=None, assumeSqrtSX=None, SSBprec=None):
"""
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
sftfilepath: str
File patern to match SFTs
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,
period=None, ecc=None, tp=None, argp=None,
record_segments=False):
""" Returns twoF or ln(BSGL) semi-coherently at a single point """
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]))
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))
detStat = 0
if record_segments:
self.detStat_per_segment = []
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:
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))
if np.isnan(d_detStat):
logging.debug('NaNs in semi-coherent twoF treated as zero')
d_detStat = 0
detStat += d_detStat
if record_segments:
self.detStat_per_segment.append(d_detStat)
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,
nglitch=0, sftfilepath=None, theta0_idx=0, BSGL=False,
minCoverFreq=None, maxCoverFreq=None, assumeSqrtSX=None,
detectors=None, earth_ephem=None, sun_ephem=None,
SSBprec=None, injectSources=None):
"""
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).
sftfilepath: str
File patern to match SFTs
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)
thetas = self._calculate_thetas(theta, delta_thetas, tboundaries,
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
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(
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,
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
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
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
"""
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)
self.tend = self.tstart + self.duration
if self.minStartTime is None:
self.minStartTime = self.tstart
if self.maxStartTime is None:
self.maxStartTime = self.tend
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))
self.check_inputs()
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)
self.sftfilename = lalpulsar.OfficialSFTFilename(
'H', '1', numSFTs, self.Tsft, self.minStartTime,
self.data_duration, self.label)
self.sftfilepath = '{}/{}'.format(self.outdir, self.sftfilename)
self.calculate_fmin_Band()
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))
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
"""
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()
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))
cl_mfd.append('--IFOs={}'.format(
",".join(['"{}"'.format(d) for d in self.detectors.split(",")])))
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 """
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(
self.outdir+"/*SFT_"+self.label+"*sft"))
cl_pfs.append("--assumeSqrtSX={}".format(self.sqrtSX))
cl_pfs.append("--minStartTime={}".format(int(self.minStartTime)))
cl_pfs.append("--maxStartTime={}".format(int(self.maxStartTime)))
cl_pfs = " ".join(cl_pfs)
output = helper_functions.run_commandline(cl_pfs)
twoF = float(output.split('\n')[-2])
return float(twoF)