def PrintInfo():
""" Function to write an info file, for use with plotting,
and for saving Multinest options, likelihood functions and
priors.
"""
# Import variable inside function, to avoid circular module
# imports.
import MNOptions as MN
import Priors
import Likelihood
infofile = MN.outputfiles_basename + '.info'
info = open(infofile, 'w')
info.write('''# SuperPy info file, with cube indicies.
# This info file can be used for plot labels.\n''')
for key, value in label.iteritems():
# Add 1 to the keys, so that labelling begins at 1, rather than 0.
# This is identical to the SuperBayeS info file convention.
key = str(int(key) + 1)
info.write('''lab%s=%s\n''' % (key, value))
# Write the prior types and arguements.
info.write('''# Priors.\n''')
for key in Priors.CMSSMModelTracker().param:
info.write('''%s %s %s\n''' %
(key, Priors.CMSSMModelTracker().param[key].type,
Priors.CMSSMModelTracker().param[key].arg))
# Write the likelihoods types and arguments.
info.write('''# Likelihoods.\n''')
for key in Likelihood.CMSSMConstraintTracker().constraint:
info.write(
'''%s %s %s\n''' %
(key, Likelihood.CMSSMConstraintTracker().constraint[key].type,
Likelihood.CMSSMConstraintTracker().constraint[key].arg))
# Write the MN parameters.
info.write('''# MultiNest options.\n''')
for vars in dir(MN):
if not vars.startswith("__"):
info.write('''%s %s\n''' % (vars, getattr(MN, vars)))
info.close()
def main():
TRUE_WIMP = MockGen.TRUE_WIMP
events = []
with open('mock.txt') as f:
events = f.read().splitlines()
events = [float(num) for num in events]
# define events
E_thr = 6 * const.keV
# pick start
theta = np.zeros((N, 2))
# initialize MCMC parameters
theta[0] = [const.M_D, 1000 * const.sigma]
# initialize values for energy
Emin = 1 * const.keV
Emax = fn.max_recoil_energy()
del_Er = 1
E_r = np.arange(Emin, Emax, del_Er)
events = lik.find_indices(E_r, events)
# Metropolis Hastings loop
acceptance = []
for i in tqdm(range(1, N)):
proposed_theta = proposal(theta[i - 1])
prev_lik = lik.events_likelihood(E_r, events, theta[i - 1], const.AXe,
E_thr, del_Er)
new_lik = lik.events_likelihood(E_r, events, proposed_theta, const.AXe,
E_thr, del_Er)
ratio = new_lik - prev_lik
if ratio >= 0:
theta[i] = proposed_theta
acceptance.append(1)
elif np.log(np.random.rand()) < ratio:
theta[i] = proposed_theta
acceptance.append(1)
else:
theta[i] = theta[i - 1]
print(len(acceptance) / (N + 1))
f = open('data.txt', 'w')
for thetas in theta:
f.write(str(thetas) + '\n')
f.close()
def chisquared(a0, alphas, invalpha, m0, m12, mb, mt, signmu, tanb):
""" Wrapper for likelihood.
Arguments:
a0, alphas, invalpha, m0, m12, mb, mt, signmu, tanb - nine elements of cube.
"""
ndim = 9 # Model parameters - 9 for CMSSM.
nparams = 100 # Approximate number of items in cube.
cube = [0] * nparams # Initialise cube as empty list.
# Copy arguments to cube.
for i, arg in enumerate([a0, alphas, invalpha, m0, m12, mb, mt, signmu, tanb]):
cube[i] = arg
# ndim and nparams are irrelavant.
chisquared = -2 * Likelihood.myloglike(cube, ndim, nparams)
return chisquared
def chisquared(a0, alphas, invalpha, m0, m12, mb, mt, signmu, tanb):
""" Wrapper for likelihood.
Arguments:
a0, alphas, invalpha, m0, m12, mb, mt, signmu, tanb - nine elements of cube.
"""
ndim = 9 # Model parameters - 9 for CMSSM.
nparams = 100 # Approximate number of items in cube.
cube = [0] * nparams # Initialise cube as empty list.
# Copy arguments to cube.
for i, arg in enumerate(
[a0, alphas, invalpha, m0, m12, mb, mt, signmu, tanb]):
cube[i] = arg
# ndim and nparams are irrelavant.
chisquared = -2 * Likelihood.myloglike(cube, ndim, nparams)
return chisquared
def _main():
# Open files and process reads dictionary
f = open(sys.argv[1], 'r')
reads_dict = init._process(f)
# Get contigs from first consensus sequence
contigs = cs.run_consensus(reads_dict)
contig_file = open(sys.argv[2] + '/contig.txt', 'w+')
ll_file = open(sys.argv[2] + '/likelihood.txt', 'w+')
# Set initial parameters
likelihood = 0
likelihood_new = 0
#likelihood_list = []
for i in range(NUM_ITERS):
'''FILE WRITES'''
# Contigs file write data
contig_file.write('%s\tstart\t' % (str(i)))
for c in contigs:
contig_file.write('%s\t' % (str(c)))
contig_file.write('\n')
contig_file.flush()
# Likelihood file write data
ll_file.write(
'%s\t%s\t%s\n' %
(str(i), str(likelihood), str(len(contigs)))), ll_file.flush()
#likelihood_list.append(float(likelihood))
# Reads file write data
reads_file = open(sys.argv[2] + '/reads_trial_' + str(i) + '.txt', 'w')
for r in reads_dict:
for l in reads_dict[r]:
reads_file.write(
str(l[3]) + ',' + str(l[0]) + ',' + str(l[1]) + str(',') +
str(l[3]) + '\n')
reads_file.close()
'''COMPUTATION OF ALGORITHM'''
# Update likelihood
likelihood = likelihood_new
# Map reads
reads_dict = rm.run(reads_dict, contigs)
# Run Consensus Sequence
contigs = cs.run_consensus(reads_dict)
# Print data to file
contig_file.write('%s\tmerge\t' % (str(i)))
for c in contigs:
contig_file.write('%s\t' % (str(c)))
contig_file.write('\n')
# Run merge
contigs, reads_dict = mc.run_merge(
contigs, reads_dict
) # how do we know if a merge has happened..do we need to know?
# Get new likelihood
likelihood_new = ll._likelihood(reads_dict, contigs)
'''FILE WRITES'''
# Reads file write data
reads_file = open(sys.argv[2] + '/reads_trial_' + str(i + 1) + '.txt', 'w')
for r in reads_dict:
for l in reads_dict[r]:
reads_file.write(
str(l[3]) + ',' + str(l[0]) + ',' + str(l[1]) + str(',') +
str(l[3]) + '\n')
reads_file.close()
# Print data to file
for c in contigs:
contig_file.write('1000\tend\t%s\n' % (str(c)))
ll_file.write(
'%s\t%s\t%s\n' %
(str(NUM_ITERS), str(likelihood), str(len(contigs)))), ll_file.flush()
# Tests an input point, run with
# python Tester.py a0, alphas, invalpha, m0, m12, mb, mt, signmu, tanb
# Superpy modules.
import Debug as DB # Debug options.
import Likelihood # Constraints and likelihood functions.
# External modules.
import sys
# Initialise the cube.
cols = 100
nparams = cols - 2 # Subract 2 for chi-squared and posterior weight.
ndim = 10 # For CNMSSM.
# Read the input parameters into the cube.
cube = [0] * nparams # Initialise cube to an empty list.
# Plust one to ignore first argument is name of file.
if len(sys.argv) != ndim + 1:
sys.exit("You should supply a0, alphas, invalpha, lambda, m0, m12, mb, mt, signmu, tanb")
for i in range(len(sys.argv)):
if i == 0:
continue # Ignore name of file.
# Minus one to ignore name of file, which is zeroth argument, and convert
# string to float.
cube[i - 1] = float(sys.argv[i])
# Call likelihood function.
loglike = Likelihood.myloglike(cube, ndim, nparams)
import Likelihood # Constraints and likelihood functions.
import PlotMod as PM # To access this, export PYTHONPATH=$PWD/SuperPlot
# External modules.
import sys
# Check that line number was supplied.
if len(sys.argv) != 2:
sys.exit('You should supply line number.')
# Open the chain with a GUI.
labels, data = PM.OpenData()
ndim = 10 # Number of model parameters - 10 for CNMSSM.
nparams = 100 # Approximate number of items in cube.
# Read line to re-calculate.
# Plust one to ignore first argument is name of file, e.g. python
# LineProcess.py arg1 etc
linenumber = int(sys.argv[1]) # We need to convert from string to integer.
# Initialise the cube to an empty list - it must be a list, not a dictionary.
cube = [0] * nparams
# Copy model parameters from the *.txt file to the cube.
for i in range(ndim):
# Plus 2 for chi-squared and posterior weight.
cube[i] = data[i + 2][linenumber]
# Re-calculate the cube etc with this likelihood function.
loglike = Likelihood.myloglike(cube, ndim, nparams)
def get_final_likelihood(sto_filename, tree_filename): sys.path.append(os.environ['GBPML']) import Likelihood return Likelihood.main(sto_filename, tree_filename)
def _main():
# Open files and process reads dictionary
f = open(sys.argv[1], 'r')
reads_dict = init._process(f)
# Get contigs from first consensus sequence
contigs = cs.run_consensus(reads_dict)
contig_file = open(sys.argv[2] + '/contig.txt', 'w+')
ll_file = open(sys.argv[2] + '/likelihood.txt', 'w+')
# Set initial parameters
likelihood = 0
likelihood_new = 0
#likelihood_list = []
for i in range(NUM_ITERS):
'''FILE WRITES'''
# Contigs file write data
contig_file.write('%s\tstart\t' %(str(i)))
for c in contigs:
contig_file.write('%s\t' %(str(c)))
contig_file.write('\n')
contig_file.flush()
# Likelihood file write data
ll_file.write('%s\t%s\t%s\n' %(str(i), str(likelihood), str(len(contigs)))), ll_file.flush()
#likelihood_list.append(float(likelihood))
# Reads file write data
reads_file = open(sys.argv[2] + '/reads_trial_' + str(i) + '.txt','w')
for r in reads_dict:
for l in reads_dict[r]:
reads_file.write(str(l[3])+','+str(l[0])+','+str(l[1])+str(',')+str(l[3])+'\n')
reads_file.close()
'''COMPUTATION OF ALGORITHM'''
# Update likelihood
likelihood = likelihood_new
# Map reads
reads_dict = rm.run(reads_dict, contigs)
# Run Consensus Sequence
contigs = cs.run_consensus(reads_dict)
# Print data to file
contig_file.write('%s\tmerge\t' %(str(i)))
for c in contigs:
contig_file.write('%s\t' %(str(c)))
contig_file.write('\n')
# Run merge
contigs, reads_dict = mc.run_merge(contigs,reads_dict) # how do we know if a merge has happened..do we need to know?
# Get new likelihood
likelihood_new = ll._likelihood(reads_dict,contigs)
'''FILE WRITES'''
# Reads file write data
reads_file = open(sys.argv[2] + '/reads_trial_' + str(i+1) + '.txt','w')
for r in reads_dict:
for l in reads_dict[r]:
reads_file.write(str(l[3])+','+str(l[0])+','+str(l[1])+str(',')+str(l[3])+'\n')
reads_file.close()
# Print data to file
for c in contigs:
contig_file.write('1000\tend\t%s\n' %(str(c)))
ll_file.write('%s\t%s\t%s\n' %(str(NUM_ITERS), str(likelihood), str(len(contigs)))), ll_file.flush()
def main():
E_thr = 6 * const.keV # threshold energy for generating total number of events
WIMP = TRUE_WIMP # WIMP params
target = const.AXe
E_min = 1 * const.keV
E_max = fn.max_recoil_energy()
del_Er = (E_max - E_min) / N_STEPS
E_r = np.arange(E_min, E_max, del_Er)
weights = 1 / (1 + np.exp(-1.35 * E_r + 8.1))
x, y = fn.integrate_rate(
E_r, WIMP,
target) # expected events per kg day, as a function of E_thr
y *= lik.BULK # 100 kilo target, 300 day runtime
idx = lik.find_nearest_idx(E_r, E_thr)
mean_events = y[idx] # expected number of events
num_events = stats.poisson.rvs(mean_events) # num events to generate
event_dist = fn.diff_rate(E_r, WIMP, target) # event energies distribution
idx2 = lik.find_nearest_idx(E_r, 60 * const.keV)
event_dist *= weights
event_dist = event_dist[:idx2]
E_r = E_r[:idx2]
norm_fact = np.sum(event_dist)
event_dist /= norm_fact
true_rates = event_dist * mean_events
custm = stats.rv_discrete(name='custm', values=(E_r, event_dist))
samples = custm.rvs(size=num_events)
samples = samples[samples < 100]
fig, ax = plt.subplots()
ax.hist(samples, bins=N_STEPS)
for WIMP in [
TRUE_WIMP, [500 * const.GeV, TRUE_WIMP[1]],
[const.M_D * 10, TRUE_WIMP[1]]
]:
E_min = 1 * const.keV
E_max = fn.max_recoil_energy()
del_Er = (E_max - E_min) / N_STEPS
E_r = np.arange(E_min, E_max, del_Er)
event_dist = fn.diff_rate(E_r, WIMP,
target) # event energies distribution
event_dist *= weights
event_dist = event_dist[:60]
E_r = E_r[:60]
norm_fact = np.sum(event_dist)
event_dist /= norm_fact
true_rates = event_dist * mean_events
ax.plot(E_r,
true_rates,
label=str(WIMP[0] / 10**6) + " GeV, " +
str(WIMP[1] / const.cm2) + "cm2")
ax.set_ylabel("Counts")
ax.set_xlabel("Recoil Energy (keV)")
plt.legend()
plt.show()
f = open('mock.txt', 'w')
for ele in samples:
f.write(str(ele) + '\n')
f.close()
# parameters, rather than a list.
def chisquared(a0, alphas, invalpha, m0, m12, mb, mt, signmu, tanb, lambda):
""" Wrapper for likelihood.
Arguments:
a0, alphas, invalpha, m0, m12, mb, mt, signmu, tanb, lambda - ten elements of cube.
"""
ndim = 10 # Model parameters - 10 for CNMSSM.
nparams = 100 # Approximate number of items in cube.
cube = [0] * nparams # Initialise cube as empty list.
# Copy arguments to cube.
for i, arg in enumerate([a0, alphas, invalpha, m0, m12, mb, mt, signmu, tanb, lambda]):
cube[i] = arg
# ndim and nparams are irrelavant.
chisquared = -2 * Likelihood.myloglike(cube, ndim, nparams)
return chisquared
# Setup initial values, errors etc.
kwdarg = dict(
a0=-3000,
error_a0=100,
alphas=1.18400000e-01,
fix_alphas=True,
invalpha=1.27944000e+02,
fix_invalpha=True,
m0=400,
error_m0=100,
m12=900,
error_m12=100,
mb=4.18000000e+00,
def treeLogLikelihood(conf, tree, stree, gene2species, params, baserate=None):
conf.setdefault("bestlogl", -util.INF)
if pyspidir == None or conf.get("python_only", False):
return Likelihood.treeLogLikelihood_python(conf, tree, stree,
gene2species, params,
baserate=baserate,
integration="fastsampling")
# debug info
if isDebug(DEBUG_MED):
util.tic("find logl")
# derive relative branch lengths
#tree.clearData("logl", "extra", "fracs", "params", "unfold")
recon = phylo.reconcile(tree, stree, gene2species)
events = phylo.label_events(tree, recon)
# determine if top branch unfolds
if recon[tree.root] == stree.root and \
events[tree.root] == "dup":
for child in tree.root.children:
if recon[child] != stree.root:
child.data["unfold"] = True
# top branch is "free"
params[stree.root.name] = [0,0]
this = util.Bundle(logl=0.0)
if conf.get("generate_int", False):
baserate = -99.0 # indicates in integration over gene rates is requested
elif baserate == None:
baserate = Likelihood.getBaserate(tree, stree, params, recon=recon)
phylo.midroot_recon(tree, stree, recon, events, params, baserate)
# calc likelihood in C
this.logl = treeLikelihood_C(conf, tree, recon, events, stree, params,
baserate, gene2species)
# calc probability of rare events
tree.data["eventlogl"] = Likelihood.rareEventsLikelihood(conf, tree, stree, recon, events)
# calc penality of error
tree.data["errorlogl"] = tree.data.get("error", 0.0) * \
conf.get("errorcost", 0.0)
this.logl += tree.data["errorlogl"]
# add logl of sequence evolution
this.logl += tree.data.get("distlogl", 0.0)
if baserate == -99.0: # indicates in integration over gene rates is requested
baserate = Likelihood.getBaserate(tree, stree, params, recon=recon)
tree.data["baserate"] = baserate
tree.data["logl"] = this.logl
if isDebug(DEBUG_MED):
util.toc()
debug("\n\n")
drawTreeLogl(tree, events=events)
return this.logl
parser.add_argument("--threads",
dest="threads",
help="Number of threads",
type=str,
default=8)
parser.add_argument("--logmslim",
dest="logMSlim",
help="Lower limit on stellar mass",
type=str,
default=None)
args = parser.parse_args()
ncore = int(args.threads)
logSMlim = float(args.logMSlim)
# Initiate my likelihood model
model = Likelihood.Model(logSMlim, generator=True)
print("Initiated the model")
sys.stdout.flush()
# How dense should the grid be
alphas = np.linspace(p.min_alpha, p.max_alpha, p.Nalphas)
scatters = np.linspace(p.min_scatter, p.max_scatter, p.Nscatters)
# Say x-dimension corresponds to alpha, y-dimension corresponds to scatter
XX, YY = np.meshgrid(alphas, scatters)
ndim1, ndim2 = XX.shape
# Calculate the stochastic covariance matrix at these values
Niter = 40
Ntot = XX.size
def get_final_likelihood(sto_filename, tree_filename): import Likelihood return Likelihood.main(sto_filename, tree_filename)
# File names - best to convert to absolute path here.
outputfiles_basename = os.path.abspath('./chains/CMSSM')
# These are the settings that are passed to MultiNest.
# Loglike callback function.
LogLikelihood = Likelihood.myloglike
# Prior callback function.
Prior = Priors.myprior
# Number of model parameters.
n_dims = len(Priors.CMSSMModelTracker().param)
# Total number of parameters in cube.
# This is model parameters + constraints + chi2 from constraints + 33
# sparticle/particle masses + mu + neutralino mixing.
n_params = n_dims + 2 * \
len(Likelihood.CMSSMConstraintTracker().constraint) + 33 + 1 + 16
# Which parameters to mode cluster, first n.
n_clustering_params = 2
# Should be a vector of 1s and 0s - 1 = wrapped, 0 = unwrapped.
wrapped_params = None
# Whether to separate modes.
multimodal = True
const_efficiency_mode = False
n_live_points = 10
evidence_tolerance = 1.0
sampling_efficiency = 2.0
n_iter_before_update = 1
null_log_evidence = -1e+90
# For memory allocation only, if memory exceeded, MultiNest halts.
max_modes = 5
# Seed the random number generator, if -1 seeded from system clock.
outputfiles_basename = os.path.abspath('./chains/CNMSSM')
# These are the settings that are passed to MultiNest.
# Loglike callback function.
LogLikelihood = Likelihood.myloglike
# Prior callback function.
Prior = Priors.myprior
# Number of model parameters.
n_dims = len(Priors.CNMSSMModelTracker().param)
# Total number of parameters in cube.
# This is model parameters + constraints + chi2 from constraints + 33
# sparticle/particle masses + mu + neutralino mixing.
# For NMSSM, neutralino mixing matrix is 5 by 5.
# For NMSSM, 2 extra masses for singlet and singlino.
n_params = n_dims + 2 * \
len(Likelihood.CNMSSMConstraintTracker().constraint) + 33 + 2 + 1 + 25
# Which parameters to mode cluster, first n.
n_clustering_params = 2
# Should be a vector of 1s and 0s - 1 = wrapped, 0 = unwrapped.
wrapped_params = None
# Whether to separate modes.
multimodal = True
const_efficiency_mode = False
n_live_points = 10
evidence_tolerance = 1.0
sampling_efficiency = 2.0
n_iter_before_update = 1
null_log_evidence = -1e+90
# For memory allocation only, if memory exceeded, MultiNest halts.
max_modes = 5
# Seed the random number generator, if -1 seeded from system clock.
type=str,
default=8)
parser.add_argument("--perccat",
dest="perccat",
help="Sets how much of the catalog to exclude",
type=str,
default=None)
args = parser.parse_args()
ncores = int(args.threads)
perccat = float(args.perccat)
cuts_def = p.load_pickle("../../Data/BMmatching/logMBcuts_def.p")
logBMlim = cuts_def[perccat]
# Initiate my likelihood model
model = Likelihood.Model(logBMlim, perccat, generator=True)
print("Initiated the model!")
sys.stdout.flush()
alphas = np.linspace(p.min_alpha, p.max_alpha, p.Nalphas)
scatters = np.linspace(p.min_scatter, p.max_scatter, p.Nscatters)
# Say x-dimension corresponds to alpha, y-dimension corresponds to scatter
XX, YY = np.meshgrid(alphas, scatters)
ndim1, ndim2 = XX.shape
# Calculate the stochastic covariance matrix at these values
Niter = 1
covmats = np.zeros(shape=(ndim1, ndim2, p.nbins, p.nbins))
Ntot = XX.size
k = 1
extime = list()
def scan(self, regfilt, threshold=5.0):
bins = numpy.arange(self.time.min(),
self.time.max() + 1e-4, self.timebin)
xbins = numpy.arange(self.xmin, self.xmax, 25)
ybins = numpy.arange(self.ymin, self.ymax, 25)
region = Likelihood.Region(self.xmin, self.xmax, self.ymin, self.ymax,
40, regfilt, self.expomap, self.eventfile)
ls = Likelihood.Likelihood(self.X, self.Y, region)
# Build the likelihood model
# Bkg model (isotropic)
iso = Likelihood.Isotropic("bkg", 1.0)
m = Likelihood.GlobalModel("likeModel") + iso
knownSources = []
for i, src in enumerate(self.sources):
thisSrc = Likelihood.PointSource("src%i" % (i + 1), src[0], src[1],
self.eventfile, self.hwu)
m += thisSrc
if i >= 10:
log.info("Fixing normalization of source %s" % (i + 1))
thisSrc["src%i_norm" % (i + 1)].fix()
knownSources.append(thisSrc)
ls.setModel(m)
# Minimize the mlogLike to get the background level
like0 = ls.minimize()
figIntegrated = ls.plot()
excessesFound = []
figs = [figIntegrated]
for t1, t2 in zip(bins[:-1], bins[1:]):
sys.stderr.write(".")
idx = (self.time >= t1) & (self.time < t2)
# db = DbScanner(self.X[idx],self.Y[idx])
# db = SAODetect(self.X[idx],self.Y[idx])
# db = cellDetect.CellDetect(self.X[idx],self.Y[idx],200,3)
ls = Likelihood.Likelihood(self.X[idx], self.Y[idx], region)
totCounts = ls.getTotalCounts()
if totCounts < 3:
# No need to perform any fit. Too few counts in this
# interval
log.debug("Skip interval %s - %s, less than 3 counts here" %
(t1, t2))
continue
# Build the likelihood model
# Bkg model (isotropic)
iso = Likelihood.Isotropic("bkg", 0.1)
m = Likelihood.GlobalModel("likeModel") + iso
for i, src in enumerate(knownSources):
m += src
ls.setModel(m)
# Minimize the mlogLike to get the background level
like0 = ls.minimize(verbose=0)
# ls.plot()
bkgLevel = iso['bkg_amp'].value / pow(region.binsize, 2.0)
error = iso['bkg_amp'].error / pow(region.binsize, 2.0)
# print("Bkg: %s +/- %s" %(bkgLevel, error))
db = cellDetect.CellDetect(self.X[idx], self.xmin, self.xmax,
self.Y[idx], self.ymin, self.ymax, 200,
3)
centroids = db.findExcesses(bkgLevel * pow(200, 2),
error * pow(200, 2))
newSources = []
if len(centroids) > 0:
# Verify if this source is truly significant
TSs = []
for (x, y) in centroids:
sys.stderr.write("-")
# Avoid computing the TS for a source too close to the ones already
# known
d = map(
lambda src: math.sqrt(
pow(src.xpos - x, 2) + pow(src.ypos - y, 2)),
knownSources)
dd = filter(lambda x: x < 5.0 / 0.05, d)
if len(dd) > 0:
# There is a source close to this centroid. No need
# to investigate further
continue
thisSrc = Likelihood.PointSource("testsrc", x, y,
self.eventfile, self.hwu,
knownSources[0].outfile)
ls.model += thisSrc
like1 = ls.minimize(verbose=0)
TSs.append(2 * (like0 - like1))
# print("(X,Y) = (%s,%s) -> TS = %s" %(x,y,TSs[-1]))
ls.model.removeSource("testsrc")
# Using the approximation TS = sqrt( significance )
if TSs[-1] >= pow(threshold, 2):
newSources.append([x, y, TSs[-1]])
if len(newSources) > 0:
db.centroids = numpy.array(newSources)
fig = db.plot(xbins, ybins)
figs.append(fig)
for (x, y, ts) in newSources:
excessesFound.append([t1, t2, x, y, math.sqrt(ts)])
sys.stderr.write("\n")
return excessesFound, figs
