def calc_probability_of_LP_solution(self, help_variables):
log_prob = 0
for (i, j, is_PE_link), variable in help_variables.iteritems():
print self.contamination_ratio * self.observations[
(i, j, is_PE_link)][1] * normpdf(variable.varValue,
self.contamination_mean,
self.contamination_stddev)
if is_PE_link:
try:
log_prob += math.log(
self.contamination_ratio *
self.observations[(i, j, is_PE_link)][1] *
normpdf(variable.varValue, self.contamination_mean,
self.contamination_stddev))
except ValueError:
log_prob += -float("inf")
else:
try:
log_prob += math.log(
(1 - self.contamination_ratio) *
self.observations[(i, j, is_PE_link)][1] *
normpdf(variable.varValue, self.contamination_mean,
self.contamination_stddev))
except ValueError:
log_prob += -float("inf")
return log_prob
def Part(a, b):
expr1 = (min(len1, len2) - (param.read_len - param.s_inner)) / param.readfrequency * normcdf(a, 0, 1)
expr2 = -(-param.s_inner) / param.readfrequency * normcdf(b, 0, 1)
expr3 = (b * std_dev) / param.readfrequency * (normcdf(b, 0, 1) - normcdf(a, 0, 1))
expr4 = (std_dev / param.readfrequency) * (normpdf(b, 0, 1) - normpdf(a, 0, 1))
value = expr1 + expr2 + expr3 + expr4
return value
def calc_log_likelihood(self,mean,stddev):
log_likelihood_value = 0
exp_mean_over_bp = mean + stddev**2/float(mean+1)
for (c1,c2) in self.isizes:
log_likelihood_value += math.log( normpdf(self.isizes[(c1,c2)],exp_mean_over_bp, stddev) ) * self.observations[(c1,c2)][1]
#for isize in self.isizes[(c1,c2)]:
# log_likelihood_value += math.log( normpdf(isize,mean,stddev) )
return log_likelihood_value
def calc_log_likelihood(self,mean,stddev):
log_likelihood_value = 0
exp_mean_over_bp = mean + stddev**2/float(mean+1)
for (c1,c2) in self.isizes:
log_likelihood_value += math.log( normpdf(self.isizes[(c1,c2)],exp_mean_over_bp, stddev) ) * self.observations[(c1,c2)][1]
#for isize in self.isizes[(c1,c2)]:
# log_likelihood_value += math.log( normpdf(isize,mean,stddev) )
return log_likelihood_value
def calc_probability_of_LP_solution(self, help_variables):
log_prob = 0
for (i,j,is_PE_link),variable in help_variables.iteritems():
print self.contamination_ratio * self.observations[(i,j,is_PE_link)][1] * normpdf(variable.varValue,self.contamination_mean,self.contamination_stddev)
if is_PE_link:
try:
log_prob += math.log(self.contamination_ratio * self.observations[(i,j,is_PE_link)][1] * normpdf(variable.varValue,self.contamination_mean,self.contamination_stddev))
except ValueError:
log_prob += - float("inf")
else:
try:
log_prob += math.log((1 - self.contamination_ratio) * self.observations[(i,j,is_PE_link)][1]* normpdf(variable.varValue,self.contamination_mean,self.contamination_stddev))
except ValueError:
log_prob += - float("inf")
return log_prob