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import numpy as np
from histogram import HistogramDD
from uncertainties import ufloat, umath
from math import sqrt
from itertools import izip, compress
from chroma.tools import profile_if_possible
class Likelihood(object):
"Class to evaluate likelihoods for detector events."
def __init__(self, sim, event=None, tbins=100, trange=(-0.5e-9, 999.5e-9),
qbins=10, qrange=(-0.5, 9.5)):
"""
Args:
- sim: chroma.sim.Simulation
The simulation object used to simulate events and build pdfs.
- event: chroma.event.Event, *optional*
The detector event being reconstructed. If None, you must call
set_event() before eval().
- tbins: int, *optional*
Number of time bins in PDF
- trange: tuple of 2 floats, *optional*
Min and max time to include in PDF
- qbins: int, *optional*
Number of charge bins in PDF
- qrange: tuple of 2 floats, *optional
Min and max charge to include in PDF
"""
self.sim = sim
self.tbins = tbins
self.trange = trange
self.qbins = qbins
self.qrange = qrange
if event is not None:
self.set_event(event)
def set_event(self, event):
"Set the detector event being reconstructed."
self.event = event
@profile_if_possible
def eval(self, vertex_generator, nevals, nreps=1):
"""
Return the negative log likelihood that the detector event set in the
constructor or by set_event() was the result of a particle generated
by `vertex_generator`. If `nreps` set to > 1, each set of photon vertices
will be propagated `nreps` times.
"""
hitcount, pdfcount = self.sim.create_pdf(nevals, vertex_generator,
self.tbins, self.trange,
self.qbins, self.qrange,
nreps=nreps)
# Normalize probabilities and put a floor to keep the log finite
hit_prob = hitcount.astype(np.float32) / (nreps * nevals)
hit_prob = np.maximum(hit_prob, 0.5 / (nreps*nevals))
# Normalize t,q PDFs
pdf = pdfcount.astype(np.float32)
norm = pdf.sum(axis=2).sum(axis=1) / (self.qrange[1] - self.qrange[0]) / (self.trange[1] - self.trange[0])
pdf /= np.maximum(norm[:,np.newaxis,np.newaxis], 1)
# NLL calculation: note that negation is at the end
# Start with the probabilties of hitting (or not) the channels
log_likelihood = ufloat((
np.log(hit_prob[self.event.channels.hit]).sum()
+np.log(1.0-hit_prob[~self.event.channels.hit]).sum(),
0.0))
# Then include the probability densities of the observed charges and times
for i, t, q in compress(izip(range(self.event.channels.hit.size),self.event.channels.t,self.event.channels.q),self.event.channels.hit):
tbin = (t - self.trange[0]) / (self.trange[1] - self.trange[0]) * self.tbins
qbin = (q - self.trange[0]) / (self.qrange[1] - self.qrange[0]) * self.qbins
if tbin < 0 or tbin >= self.tbins or qbin < 0 or qbin >= self.qbins:
probability = 0.0
nentries = 0
else:
probability = pdf[i, tbin, qbin]
# If probability is zero, avoid warning here, but catch the problem
# in the next if block
probability_err = probability / max(1, sqrt(pdfcount[i, tbin, qbin]))
nentries = norm[i]
if probability == 0.0 or np.isnan(probability):
if nentries > 0:
probability = 0.5/nentries
probability_err = probability
else:
probability = 0.5/(self.qrange[1] - self.qrange[0])/(self.trange[1] - self.trange[0])
probability_err = probability
log_likelihood += umath.log(ufloat((probability, probability_err)))
return -log_likelihood
if __name__ == '__main__':
from chroma import detectors
from chroma.sim import Simulation
from chroma.optics import water
from chroma.generator import constant_particle_gun
from chroma.tools import enable_debug_on_crash
import time
enable_debug_on_crash()
detector = detectors.find('lbne')
sim = Simulation(detector, water)
event = sim.simulate(1, constant_particle_gun('e-',(0,0,0),(1,0,0),100.0)).next()
print 'nhit = %i' % np.count_nonzero(event.hits.hit)
likelihood = Likelihood(sim, event)
for x in np.linspace(-10.0, 10.0, 10*5+1):
start = time.time()
l = likelihood.eval(constant_particle_gun('e-',(x,0,0),(1,0,0),100.0),100, nreps=10)
print 'x = %5.1f, %s (%1.1f sec)' % (x, l, time.time() - start)
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