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Commit 8ffae7e2 authored by Gregory Ashton's avatar Gregory Ashton
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Adds in-memory injection capabilities

parent 5d115632
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pyfstat/core.py
View file @ 8ffae7e2
......@@ -151,9 +151,9 @@ class ComputeFstat(object):
@helper_functions.initializer
def __init__(self, tref, sftfilepath=None, minStartTime=None,
maxStartTime=None, binary=False, transient=True, BSGL=False,
detector=None, minCoverFreq=None, maxCoverFreq=None,
detectors=None, minCoverFreq=None, maxCoverFreq=None,
earth_ephem=None, sun_ephem=None, injectSources=None,
assumeSqrtSX=None):
injectSqrtSX=None, assumeSqrtSX=None):
"""
Parameters
----------
......@@ -170,9 +170,9 @@ class ComputeFstat(object):
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.
detector: str
detectors: str
Two character reference to the data to use, specify None for no
contraint.
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
......@@ -181,6 +181,11 @@ class ComputeFstat(object):
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,
......@@ -198,10 +203,32 @@ class ComputeFstat(object):
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.detector:
constraints.detector = self.detector
if self.detectors:
constraints.detectors = self.detectors
if self.minStartTime:
constraints.minStartTime = lal.LIGOTimeGPS(self.minStartTime)
if self.maxStartTime:
......@@ -231,12 +258,12 @@ class ComputeFstat(object):
int(SFT_timestamps[-1]),
subprocess.check_output('lalapps_tconvert {}'.format(
int(SFT_timestamps[-1])), shell=True).rstrip('\n')))
self.SFTCatalog = SFTCatalog
return SFTCatalog
def init_computefstatistic_single_point(self):
""" Initilisation step of run_computefstatistic for a single point """
self.get_SFTCatalog()
SFTCatalog = self.get_SFTCatalog()
logging.info('Initialising ephems')
ephems = lalpulsar.InitBarycenter(self.earth_ephem, self.sun_ephem)
......@@ -254,7 +281,6 @@ class ComputeFstat(object):
FstatOAs.Dterms = lalpulsar.FstatOptionalArgsDefaults.Dterms
FstatOAs.runningMedianWindow = lalpulsar.FstatOptionalArgsDefaults.runningMedianWindow
FstatOAs.FstatMethod = lalpulsar.FstatOptionalArgsDefaults.FstatMethod
FstatOAs.InjectSqrtSX = lalpulsar.FstatOptionalArgsDefaults.injectSqrtSX
if self.assumeSqrtSX is None:
FstatOAs.assumeSqrtSX = lalpulsar.FstatOptionalArgsDefaults.assumeSqrtSX
else:
......@@ -282,20 +308,28 @@ class ComputeFstat(object):
if 't0' not in self.injectSources:
PP.Transient.type = lalpulsar.TRANSIENT_NONE
FstatOAs.injectSources = PPV
if 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 self.SFTCatalog.data]
fAs = [d.header.f0 for d in SFTCatalog.data]
fBs = [d.header.f0 + (d.numBins-1)*d.header.deltaF
for d in self.SFTCatalog.data]
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(self.SFTCatalog,
self.FstatInput = lalpulsar.CreateFstatInput(SFTCatalog,
self.minCoverFreq,
self.maxCoverFreq,
dFreq,
......@@ -316,7 +350,7 @@ class ComputeFstat(object):
if self.BSGL:
if len(self.detector_names) < 2:
raise ValueError("Can't use BSGL with single detector data")
raise ValueError("Can't use BSGL with single detectors data")
else:
logging.info('Initialising BSGL')
......@@ -471,7 +505,7 @@ class SemiCoherentSearch(BaseSearchClass, ComputeFstat):
def __init__(self, label, outdir, tref, nsegs=None, sftfilepath=None,
binary=False, BSGL=False, minStartTime=None,
maxStartTime=None, minCoverFreq=None, maxCoverFreq=None,
detector=None, earth_ephem=None, sun_ephem=None,
detectors=None, earth_ephem=None, sun_ephem=None,
injectSources=None, assumeSqrtSX=None):
"""
Parameters
......@@ -583,7 +617,7 @@ class SemiCoherentGlitchSearch(BaseSearchClass, ComputeFstat):
def __init__(self, label, outdir, tref, minStartTime, maxStartTime,
nglitch=0, sftfilepath=None, theta0_idx=0, BSGL=False,
minCoverFreq=None, maxCoverFreq=None, assumeSqrtSX=None,
detector=None, earth_ephem=None, sun_ephem=None):
detectors=None, earth_ephem=None, sun_ephem=None):
"""
Parameters
----------
......@@ -682,7 +716,7 @@ class Writer(BaseSearchClass):
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, detector='H1',
outdir=".", sqrtSX=1, Band=4, detectors='H1',
minStartTime=None, maxStartTime=None, add_noise=True):
"""
Parameters
......@@ -888,7 +922,7 @@ transientTauDays={:1.3f}\n""")
cl.append('--outSingleSFT=TRUE')
cl.append('--outSFTdir="{}"'.format(self.outdir))
cl.append('--outLabel="{}"'.format(self.label))
cl.append('--IFOs="{}"'.format(self.detector))
cl.append('--IFOs="{}"'.format(self.detectors))
if self.add_noise:
cl.append('--sqrtSX="{}"'.format(self.sqrtSX))
if self.minStartTime is None:
......
pyfstat/mcmc_based_searches.py
View file @ 8ffae7e2
......@@ -28,7 +28,7 @@ class MCMCSearch(BaseSearchClass):
nwalkers=100, ntemps=1, log10temperature_min=-5,
theta_initial=None, scatter_val=1e-10,
binary=False, BSGL=False, minCoverFreq=None,
maxCoverFreq=None, detector=None, earth_ephem=None,
maxCoverFreq=None, detectors=None, earth_ephem=None,
sun_ephem=None, injectSources=None, assumeSqrtSX=None):
"""
Parameters
......@@ -60,7 +60,7 @@ class MCMCSearch(BaseSearchClass):
generated from np.logspace(0, log10temperature_min, ntemps).
binary: Bool
If true, search over binary parameters
detector: str
detectors: str
Two character reference to the data to use, specify None for no
contraint.
minCoverFreq, maxCoverFreq: float
......@@ -112,7 +112,7 @@ class MCMCSearch(BaseSearchClass):
tref=self.tref, sftfilepath=self.sftfilepath,
minCoverFreq=self.minCoverFreq, maxCoverFreq=self.maxCoverFreq,
earth_ephem=self.earth_ephem, sun_ephem=self.sun_ephem,
detector=self.detector, BSGL=self.BSGL, transient=False,
detectors=self.detectors, BSGL=self.BSGL, transient=False,
minStartTime=self.minStartTime, maxStartTime=self.maxStartTime,
binary=self.binary, injectSources=self.injectSources,
assumeSqrtSX=self.assumeSqrtSX)
......@@ -1016,7 +1016,7 @@ class MCMCGlitchSearch(MCMCSearch):
minStartTime, maxStartTime, nglitch=1, nsteps=[100, 100],
nwalkers=100, ntemps=1, log10temperature_min=-5,
theta_initial=None, scatter_val=1e-10, dtglitchmin=1*86400,
theta0_idx=0, detector=None, BSGL=False, minCoverFreq=None,
theta0_idx=0, detectors=None, BSGL=False, minCoverFreq=None,
maxCoverFreq=None, earth_ephem=None, sun_ephem=None):
"""
Parameters
......@@ -1060,7 +1060,7 @@ class MCMCGlitchSearch(MCMCSearch):
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)
detector: str
detectors: str
Two character reference to the data to use, specify None for no
contraint.
minCoverFreq, maxCoverFreq: float
......@@ -1104,7 +1104,7 @@ class MCMCGlitchSearch(MCMCSearch):
tref=self.tref, minStartTime=self.minStartTime,
maxStartTime=self.maxStartTime, minCoverFreq=self.minCoverFreq,
maxCoverFreq=self.maxCoverFreq, earth_ephem=self.earth_ephem,
sun_ephem=self.sun_ephem, detector=self.detector, BSGL=self.BSGL,
sun_ephem=self.sun_ephem, detectors=self.detectors, BSGL=self.BSGL,
nglitch=self.nglitch, theta0_idx=self.theta0_idx)
def logp(self, theta_vals, theta_prior, theta_keys, search):
......@@ -1263,10 +1263,10 @@ class MCMCGlitchSearch(MCMCSearch):
class MCMCSemiCoherentSearch(MCMCSearch):
""" MCMC search for a signal using the semi-coherent ComputeFstat """
@helper_functions.initializer
def __init__(self, label, outdir, sftfilepath, theta_prior, tref,
def __init__(self, label, outdir, theta_prior, tref, sftfilepath=None,
nsegs=None, nsteps=[100, 100, 100], nwalkers=100, binary=False,
ntemps=1, log10temperature_min=-5, theta_initial=None,
scatter_val=1e-10, detector=None, BSGL=False,
scatter_val=1e-10, detectors=None, BSGL=False,
minStartTime=None, maxStartTime=None, minCoverFreq=None,
maxCoverFreq=None, earth_ephem=None, sun_ephem=None,
injectSources=None, assumeSqrtSX=None):
......@@ -1304,7 +1304,7 @@ class MCMCSemiCoherentSearch(MCMCSearch):
nsegs=self.nsegs, sftfilepath=self.sftfilepath, binary=self.binary,
BSGL=self.BSGL, minStartTime=self.minStartTime,
maxStartTime=self.maxStartTime, minCoverFreq=self.minCoverFreq,
maxCoverFreq=self.maxCoverFreq, detector=self.detector,
maxCoverFreq=self.maxCoverFreq, detectors=self.detectors,
earth_ephem=self.earth_ephem, sun_ephem=self.sun_ephem,
injectSources=self.injectSources, assumeSqrtSX=self.assumeSqrtSX)
......@@ -1641,7 +1641,7 @@ class MCMCTransientSearch(MCMCSearch):
tref=self.tref, sftfilepath=self.sftfilepath,
minCoverFreq=self.minCoverFreq, maxCoverFreq=self.maxCoverFreq,
earth_ephem=self.earth_ephem, sun_ephem=self.sun_ephem,
detector=self.detector, transient=True,
detectors=self.detectors, transient=True,
minStartTime=self.minStartTime, maxStartTime=self.maxStartTime,
BSGL=self.BSGL, binary=self.binary)
......
tests.py
View file @ 8ffae7e2
......@@ -123,6 +123,29 @@ class TestComputeFstat(Test):
print predicted_FS, FS
self.assertTrue(np.abs(predicted_FS-FS)/FS < 0.2)
def test_injectSources_from_file(self):
Writer = pyfstat.Writer(self.label, outdir=outdir, add_noise=False)
Writer.make_cff()
injectSources = Writer.config_file_name
search = pyfstat.ComputeFstat(
tref=Writer.tref, assumeSqrtSX=1, injectSources=injectSources,
minCoverFreq=28, maxCoverFreq=32, minStartTime=Writer.tstart,
maxStartTime=Writer.tstart+Writer.duration,
detectors=Writer.detectors)
FS = search.run_computefstatistic_single_point(Writer.tstart,
Writer.tend,
Writer.F0,
Writer.F1,
Writer.F2,
Writer.Alpha,
Writer.Delta)
Writer.make_data()
predicted_FS = Writer.predict_fstat()
print predicted_FS, FS
self.assertTrue(np.abs(predicted_FS-FS)/FS < 0.2)
class TestSemiCoherentGlitchSearch(Test):
label = "Test"
......
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