diff --git a/pyfstat.py b/pyfstat.py
index ab3493ddb0ed493b5420ee5adfa634d4065ec77d..8494d8b8996f228ee3bdc824599583a370aa9489 100755
--- a/pyfstat.py
+++ b/pyfstat.py
@@ -198,9 +198,8 @@ class ComputeFstat(object):
@initializer
def __init__(self, tref, sftfilepath=None, minStartTime=None,
maxStartTime=None, binary=False, transient=True, BSGL=False,
- BSGL_PREFACTOR=1, BSGL_FLOOR=None, detector=None,
- minCoverFreq=None, maxCoverFreq=None, earth_ephem=None,
- sun_ephem=None,
+ detector=None, minCoverFreq=None, maxCoverFreq=None,
+ earth_ephem=None, sun_ephem=None,
):
"""
Parameters
@@ -218,12 +217,6 @@ 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.
- BSGL_PREFACTOR: float
- If BSGL is True, one can specify a prefactor to multiply the
- computed BSGL value by, useful in MCMC searches to amplify the
- peaks.
- BSGL_FLOOR: float
- IF BSGL < BSGL_FLOOR -> BSGL_FLOOR
detector: str
Two character reference to the data to use, specify None for no
contraint.
@@ -311,15 +304,8 @@ class ComputeFstat(object):
if self.BSGL:
if len(names) < 2:
raise ValueError("Can't use BSGL with single detector data")
- if self.BSGL_FLOOR is None:
- logging.info('Initialising BSGL with prefactor {:2.2f}'
- .format(self.BSGL_PREFACTOR)
- )
else:
- logging.info('Initialising BSGL with prefactor {:0.2f} and '
- 'floor {}'.format(self.BSGL_PREFACTOR,
- self.BSGL_FLOOR)
- )
+ logging.info('Initialising BSGL')
# Tuning parameters - to be reviewed
numDetectors = 2
@@ -348,7 +334,7 @@ class ComputeFstat(object):
F2, Alpha, Delta, asini=None,
period=None, ecc=None, tp=None,
argp=None):
- """ Returns the twoF fully-coherently at a single point """
+ """ 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
@@ -374,12 +360,9 @@ class ComputeFstat(object):
twoF = np.float(self.FstatResults.twoF[0])
self.twoFX[0] = self.FstatResults.twoFPerDet(0)
self.twoFX[1] = self.FstatResults.twoFPerDet(1)
- BSGL = lalpulsar.ComputeBSGL(twoF, self.twoFX,
- self.BSGLSetup)
- if self.BSGL_FLOOR is not None and BSGL < self.BSGL_FLOOR:
- return self.BSGL_FLOOR
- else:
- return self.BSGL_PREFACTOR * BSGL/np.log10(np.exp(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
@@ -401,13 +384,10 @@ class ComputeFstat(object):
self.twoFX[0] = 2*FS0.F_mn.data[0][0]
self.twoFX[1] = 2*FS1.F_mn.data[0][0]
- BSGL = lalpulsar.ComputeBSGL(2*FS.F_mn.data[0][0], self.twoFX,
- self.BSGLSetup)
+ log10_BSGL = lalpulsar.ComputeBSGL(
+ 2*FS.F_mn.data[0][0], self.twoFX, self.BSGLSetup)
- if self.BSGL_FLOOR and BSGL < self.BSGL_FLOOR:
- return self.BSGL_FLOOR
- else:
- return self.BSGL_PREFACTOR * BSGL/np.log10(np.exp(1))
+ 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,
@@ -455,17 +435,16 @@ 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 two segments either side of the proposed glitch and the
- fully-coherent F-stat in each segment is averaged to give the semi-coherent
+ 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
"""
@initializer
def __init__(self, label, outdir, tref, tstart, tend, nglitch=0,
- sftfilepath=None, theta0_idx=0, BSGL=False, BSGL_PREFACTOR=1,
- BSGL_FLOOR=None, minStartTime=None, maxStartTime=None,
- minCoverFreq=None, maxCoverFreq=None, detector=None,
- earth_ephem=None, sun_ephem=None):
+ sftfilepath=None, theta0_idx=0, BSGL=False, minStartTime=None,
+ maxStartTime=None, minCoverFreq=None, maxCoverFreq=None,
+ detector=None, earth_ephem=None, sun_ephem=None):
"""
Parameters
----------
@@ -564,8 +543,7 @@ class MCMCSearch(BaseSearchClass):
log10temperature_min=-5, theta_initial=None, scatter_val=1e-10,
binary=False, BSGL=False, minCoverFreq=None,
maxCoverFreq=None, detector=None, earth_ephem=None,
- sun_ephem=None, theta0_idx=0,
- BSGL_PREFACTOR=1, BSGL_FLOOR=None):
+ sun_ephem=None, theta0_idx=0):
"""
Parameters
label, outdir: str
@@ -656,7 +634,6 @@ class MCMCSearch(BaseSearchClass):
earth_ephem=self.earth_ephem, sun_ephem=self.sun_ephem,
detector=self.detector, BSGL=self.BSGL, transient=False,
minStartTime=self.minStartTime, maxStartTime=self.maxStartTime,
- BSGL_PREFACTOR=self.BSGL_PREFACTOR, BSGL_FLOOR=self.BSGL_FLOOR,
binary=self.binary)
def logp(self, theta_vals, theta_prior, theta_keys, search):
@@ -1198,9 +1175,7 @@ class MCMCSearch(BaseSearchClass):
ntemps=self.ntemps, theta_keys=self.theta_keys,
theta_prior=self.theta_prior, scatter_val=self.scatter_val,
log10temperature_min=self.log10temperature_min,
- theta0_idx=self.theta0_idx, BSGL=self.BSGL,
- BSGL_PREFACTOR=self.BSGL_PREFACTOR,
- BSGL_FLOOR=self.BSGL_FLOOR)
+ theta0_idx=self.theta0_idx, BSGL=self.BSGL)
return d
def save_data(self, sampler, samples, lnprobs, lnlikes):
@@ -1397,7 +1372,7 @@ class MCMCSearch(BaseSearchClass):
return pdf.real
def p_val_twoFhat(self, twoFhat, ntrials, twoFhatmax=500, Npoints=1000):
- """ Caluculate the p-value for the given twoFhat in Gaussian noise
+ """ Caluculate the p-value for the given twoFhat in Gaussian noise
Parameters
----------
@@ -1434,7 +1409,7 @@ class MCMCGlitchSearch(MCMCSearch):
scatter_val=1e-10, dtglitchmin=1*86400, theta0_idx=0,
detector=None, BSGL=False,
minCoverFreq=None, maxCoverFreq=None, earth_ephem=None,
- sun_ephem=None, BSGL_PREFACTOR=1, BSGL_FLOOR=None):
+ sun_ephem=None):
"""
Parameters
label, outdir: str
@@ -1524,8 +1499,7 @@ _ sftfilepath: str
maxCoverFreq=self.maxCoverFreq, earth_ephem=self.earth_ephem,
sun_ephem=self.sun_ephem, detector=self.detector, BSGL=self.BSGL,
nglitch=self.nglitch, theta0_idx=self.theta0_idx,
- minStartTime=self.minStartTime, maxStartTime=self.maxStartTime,
- BSGL_PREFACTOR=self.BSGL_PREFACTOR, BSGL_FLOOR=self.BSGL_FLOOR)
+ minStartTime=self.minStartTime, maxStartTime=self.maxStartTime)
def logp(self, theta_vals, theta_prior, theta_keys, search):
if self.nglitch > 1:
@@ -1746,9 +1720,8 @@ class GridSearch(BaseSearchClass):
@initializer
def __init__(self, label, outdir, sftfilepath, F0s=[0], F1s=[0], F2s=[0],
Alphas=[0], Deltas=[0], tref=None, tstart=None, tend=None,
- BSGL=False, BSGL_PREFACTOR=1, BSGL_FLOOR=None,
- minCoverFreq=None, maxCoverFreq=None, earth_ephem=None,
- sun_ephem=None, detector=None):
+ BSGL=False, minCoverFreq=None, maxCoverFreq=None,
+ earth_ephem=None, sun_ephem=None, detector=None):
"""
Parameters
----------
@@ -1786,8 +1759,7 @@ class GridSearch(BaseSearchClass):
earth_ephem=self.earth_ephem, sun_ephem=self.sun_ephem,
detector=self.detector, transient=False,
minStartTime=self.minStartTime, maxStartTime=self.maxStartTime,
- BSGL=self.BSGL, BSGL_PREFACTOR=self.BSGL_PREFACTOR,
- BSGL_FLOOR=self.BSGL_FLOOR)
+ BSGL=self.BSGL)
def get_array_from_tuple(self, x):
if len(x) == 1:
@@ -1968,8 +1940,8 @@ class GridGlitchSearch(GridSearch):
F1s=[0], F2s=[0], delta_F0s=[0], delta_F1s=[0], tglitchs=None,
Alphas=[0], Deltas=[0], tref=None, tstart=None, tend=None,
minCoverFreq=None, maxCoverFreq=None, write_after=1000,
- earth_ephem=None, sun_ephem=None,
- BSGL_PREFACTOR=1, BSGL_FLOOR=None):
+ earth_ephem=None, sun_ephem=None):
+
"""
Parameters
----------
@@ -1996,8 +1968,7 @@ class GridGlitchSearch(GridSearch):
label=label, outdir=outdir, sftfilepath=self.sftfilepath,
tref=tref, tstart=tstart, tend=tend, minCoverFreq=minCoverFreq,
maxCoverFreq=maxCoverFreq, earth_ephem=self.earth_ephem,
- sun_ephem=self.sun_ephem, BSGL=self.BSGL,
- BSGL_PREFACTOR=self.BSGL_PREFACTOR, BSGL_FLOOR=self.BSGL_FLOOR)
+ sun_ephem=self.sun_ephem, BSGL=self.BSGL)
if os.path.isdir(outdir) is False:
os.mkdir(outdir)