diff --git a/pyfstat.py b/pyfstat.py
index 6c0199d2838fb8282488d93153e132a8f15cb89c..3bdda11241845c78109f51b94c043ebb08a963a6 100755
--- a/pyfstat.py
+++ b/pyfstat.py
@@ -198,8 +198,9 @@ class ComputeFstat(object):
@initializer
def __init__(self, tref, sftfilepath=None, minStartTime=None,
maxStartTime=None, binary=False, transient=True, BSGL=False,
- BSGL_PREFACTOR=1, detector=None, minCoverFreq=None,
- maxCoverFreq=None, earth_ephem=None, sun_ephem=None,
+ BSGL_PREFACTOR=1, BSGL_FLOOR=None, detector=None,
+ minCoverFreq=None, maxCoverFreq=None, earth_ephem=None,
+ sun_ephem=None,
):
"""
Parameters
@@ -221,6 +222,8 @@ class ComputeFstat(object):
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.
@@ -305,8 +308,11 @@ class ComputeFstat(object):
self.FstatResults = lalpulsar.FstatResults()
if self.BSGL:
- logging.info('Initialising BSGL with prefactor {:2.2f}, this will'
- ' fail if numDet < 2'.format(self.BSGL_PREFACTOR))
+ if len(names) < 2:
+ raise ValueError("Can't use BSGL with single detector data")
+ logging.info('Initialising BSGL with prefactor {:2.2f} and floor'
+ '{:2.2f}'.format(self.BSGL_PREFACTOR, self.BSGL_FLOOR)
+ )
# Tuning parameters - to be reviewed
numDetectors = 2
Fstar0sc = 15.
@@ -362,7 +368,10 @@ class ComputeFstat(object):
self.twoFX[1] = self.FstatResults.twoFPerDet(1)
BSGL = lalpulsar.ComputeBSGL(twoF, self.twoFX,
self.BSGLSetup)
- return self.BSGL_PREFACTOR * BSGL/np.log10(np.exp(1))
+ if self.BSGL_FLOOR and BSGL < self.BSGL_FLOOR:
+ return -self.BSGL_FLOOR
+ else:
+ return self.BSGL_PREFACTOR * BSGL/np.log10(np.exp(1))
self.windowRange.t0 = int(tstart) # TYPE UINT4
self.windowRange.tau = int(tend - tstart) # TYPE UINT4
@@ -387,7 +396,10 @@ class ComputeFstat(object):
BSGL = lalpulsar.ComputeBSGL(2*FS.F_mn.data[0][0], self.twoFX,
self.BSGLSetup)
- return self.BSGL_PREFACTOR * BSGL/np.log10(np.exp(1))
+ if self.BSGL_FLOOR and BSGL < self.BSGL_FLOOR:
+ return self.BSGL_FLOOR
+ else:
+ return self.BSGL_PREFACTOR * BSGL/np.log10(np.exp(1))
class SemiCoherentGlitchSearch(BaseSearchClass, ComputeFstat):
@@ -402,9 +414,9 @@ class SemiCoherentGlitchSearch(BaseSearchClass, ComputeFstat):
@initializer
def __init__(self, label, outdir, tref, tstart, tend, nglitch=0,
sftfilepath=None, theta0_idx=0, BSGL=False, BSGL_PREFACTOR=1,
- minStartTime=None, maxStartTime=None, minCoverFreq=None,
- maxCoverFreq=None, detector=None, earth_ephem=None,
- sun_ephem=None):
+ BSGL_FLOOR=None, minStartTime=None, maxStartTime=None,
+ minCoverFreq=None, maxCoverFreq=None, detector=None,
+ earth_ephem=None, sun_ephem=None):
"""
Parameters
----------
@@ -504,7 +516,7 @@ class MCMCSearch(BaseSearchClass):
binary=False, BSGL=False, minCoverFreq=None,
maxCoverFreq=None, detector=None, earth_ephem=None,
sun_ephem=None, theta0_idx=0,
- BSGL_PREFACTOR=1):
+ BSGL_PREFACTOR=1, BSGL_FLOOR=None):
"""
Parameters
label, outdir: str
@@ -595,7 +607,7 @@ 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_PREFACTOR=self.BSGL_PREFACTOR, BSGL_FLOOR=self.BSGL_FLOOR)
def logp(self, theta_vals, theta_prior, theta_keys, search):
H = [self.generic_lnprior(**theta_prior[key])(p) for p, key in
@@ -954,7 +966,7 @@ class MCMCSearch(BaseSearchClass):
raise ValueError("dist_type {} unknown".format(dist_type))
def plot_walkers(self, sampler, symbols=None, alpha=0.4, color="k", temp=0,
- burnin_idx=None):
+ lw=0.1, burnin_idx=None):
""" Plot all the chains from a sampler """
shape = sampler.chain.shape
@@ -983,9 +995,9 @@ class MCMCSearch(BaseSearchClass):
cs = chain[:, :, i].T
if burnin_idx:
axes[i].plot(idxs[:burnin_idx], cs[:burnin_idx],
- color="r", alpha=alpha)
+ color="r", alpha=alpha, lw=lw)
axes[i].plot(idxs[burnin_idx:], cs[burnin_idx:], color="k",
- alpha=alpha)
+ alpha=alpha, lw=lw)
if symbols:
axes[i].set_ylabel(symbols[i])
else:
@@ -1096,7 +1108,8 @@ class MCMCSearch(BaseSearchClass):
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_PREFACTOR=self.BSGL_PREFACTOR,
+ BSGL_FLOOR=self.BSGL_FLOOR)
return d
def save_data(self, sampler, samples, lnprobs, lnlikes):
@@ -1282,7 +1295,7 @@ class MCMCGlitchSearch(MCMCSearch):
scatter_val=1e-4, dtglitchmin=1*86400, theta0_idx=0,
detector=None, BSGL=False,
minCoverFreq=None, maxCoverFreq=None, earth_ephem=None,
- sun_ephem=None, BSGL_PREFACTOR=1):
+ sun_ephem=None, BSGL_PREFACTOR=1, BSGL_FLOOR=None):
"""
Parameters
label, outdir: str
@@ -1373,7 +1386,7 @@ _ sftfilepath: str
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_PREFACTOR=self.BSGL_PREFACTOR, BSGL_FLOOR=self.BSGL_FLOOR)
def logp(self, theta_vals, theta_prior, theta_keys, search):
if self.nglitch > 1:
@@ -1474,9 +1487,9 @@ 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, minCoverFreq=None,
- maxCoverFreq=None, earth_ephem=None, sun_ephem=None,
- detector=None):
+ BSGL=False, BSGL_PREFACTOR=1, BSGL_FLOOR=None,
+ minCoverFreq=None, maxCoverFreq=None, earth_ephem=None,
+ sun_ephem=None, detector=None):
"""
Parameters
----------
@@ -1514,7 +1527,8 @@ 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=self.BSGL, BSGL_PREFACTOR=self.BSGL_PREFACTOR,
+ BSGL_FLOOR=self.BSGL_FLOOR)
def get_array_from_tuple(self, x):
if len(x) == 1:
@@ -1696,7 +1710,7 @@ class GridGlitchSearch(GridSearch):
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_PREFACTOR=1, BSGL_FLOOR=None):
"""
Parameters
----------
@@ -1724,7 +1738,7 @@ class GridGlitchSearch(GridSearch):
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_PREFACTOR=self.BSGL_PREFACTOR, BSGL_FLOOR=self.BSGL_FLOOR)
if os.path.isdir(outdir) is False:
os.mkdir(outdir)