diff --git a/pyfstat/core.py b/pyfstat/core.py
index 130039dca0b9aa92996c3d0ef2782637df9152a1..0116573d05635040970d631f4ab5d5f3f6ab2757 100755
--- a/pyfstat/core.py
+++ b/pyfstat/core.py
@@ -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:
diff --git a/pyfstat/mcmc_based_searches.py b/pyfstat/mcmc_based_searches.py
index a32046a54317c5d092f35a28be91582e9a39a65e..8016cee5e4ebce4a4efdb044041b614cc6d72ac5 100644
--- a/pyfstat/mcmc_based_searches.py
+++ b/pyfstat/mcmc_based_searches.py
@@ -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)
diff --git a/tests.py b/tests.py
index 4c1f5651e4901bc5e9257ccf1222dd2926a4be02..b6e8fa09ee7fc0e3f50cf6c4b140690536f23fcb 100644
--- a/tests.py
+++ b/tests.py
@@ -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"