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Commit 1ac37b70 authored by Gregory Ashton's avatar Gregory Ashton
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Split up the base Writer instance and add a new GlitchWriter class

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pyfstat/__init__.py
+ 1
− 1
View file @ 1ac37b70
from __future__ import division as _division
from .core import BaseSearchClass, ComputeFstat, SemiCoherentSearch, SemiCoherentGlitchSearch
from .make_sfts import Writer
from .make_sfts import Writer, GlitchWriter
from .mcmc_based_searches import MCMCSearch, MCMCGlitchSearch, MCMCSemiCoherentSearch, MCMCFollowUpSearch, MCMCTransientSearch
from .grid_based_searches import GridSearch, GridUniformPriorSearch, GridGlitchSearch, FrequencySlidingWindow, DMoff_NO_SPIN
pyfstat/make_sfts.py
+ 121
− 42
View file @ 1ac37b70
......@@ -11,11 +11,10 @@ import helper_functions
class Writer(BaseSearchClass):
""" Instance object for generating SFTs containing glitch signals """
""" Instance object for generating SFTs """
@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,
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):
......@@ -26,11 +25,6 @@ class Writer(BaseSearchClass):
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)
......@@ -45,21 +39,12 @@ class Writer(BaseSearchClass):
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()
......@@ -69,14 +54,9 @@ class Writer(BaseSearchClass):
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.duration_days = (self.tend-self.tstart) / 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.sftfilenames = [
......@@ -91,12 +71,6 @@ class Writer(BaseSearchClass):
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 '''
......@@ -125,21 +99,14 @@ transientTauDays={:1.3f}\n""")
def make_cff(self):
"""
Generates an .cff file for a 'glitching' signal
Generates a .cff file
"""
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
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)
if self.check_if_cff_file_needs_rewritting(content):
config_file = open(self.config_file_name, "w+")
......@@ -272,3 +239,115 @@ transientTauDays={:1.3f}\n""")
output = helper_functions.run_commandline(cl_pfs)
twoF = float(output.split('\n')[-2])
return float(twoF)
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
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.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])
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_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()
tests.py
+ 4
− 5
View file @ 1ac37b70
......@@ -154,8 +154,8 @@ class TestSemiCoherentGlitchSearch(Test):
duration = 100*86400
dtglitch = .5*100*86400
delta_F0 = 0
Writer = pyfstat.Writer(self.label, outdir=outdir,
duration=duration, dtglitch=dtglitch,
Writer = pyfstat.GlitchWriter(
self.label, outdir=outdir, duration=duration, dtglitch=dtglitch,
delta_F0=delta_F0)
Writer.make_data()
......@@ -204,13 +204,12 @@ class TestMCMCSearch(Test):
Alpha = 5e-3
Delta = 1.2
tref = minStartTime
delta_F0 = 0
Writer = pyfstat.Writer(F0=F0, F1=F1, F2=F2, label=self.label,
h0=h0, sqrtSX=sqrtSX,
outdir=outdir, tstart=minStartTime,
Alpha=Alpha, Delta=Delta, tref=tref,
duration=duration,
delta_F0=delta_F0, Band=4)
Band=4)
Writer.make_data()
predicted_FS = Writer.predict_fstat()
......
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