def do_abc_rej(self, model, nbeta, nparticles, eps):
nbatch = 100
model.create_model_instance(nbeta, self.timePoints)
self.nSpecies, self.nDynPars = model.get_model_info()
#print "do_abc_rej : Species/Dynamical parameters in this model:", self.nSpecies, self.nDynPars
done = False
ntotsim = 0
naccepted = 0
acceptedDynParams = zeros([nparticles, self.nDynPars])
acceptedInits = zeros([nparticles, self.nSpecies])
acceptedIntMus = zeros([nparticles, self.nFP])
acceptedIntSgs = zeros([nparticles, self.nFP])
acceptedDists = zeros([nparticles])
while done == False:
print "\tRunning batch, nsims/nacc:", ntotsim, naccepted
#Parameters
dynParameters = self.sample_dyn_pars(nbatch)
#Initial conditions
inits = self.sample_inits(nbatch)
#Intensity parameters
intMus, intSgs = self.sample_int_pars(nbatch)
print "\tDone sampling"
sims = model.simulate(nbatch, dynParameters, inits, self.fps,
intMus, intSgs)
print "\tDone simulation"
dists = self.compare_to_data(nbatch, nbeta, sims, self.nFP,
self.fps)
print 'dists: ', dists
print "\tDone distance calculation"
accMask = self.check_distance(nbatch, dists, eps)
ntotsim += nbatch
for i in range(nbatch):
if accMask[i] == 1 and naccepted < nparticles:
acceptedDynParams[naccepted, :] = dynParameters[i, :]
acceptedInits[naccepted, :] = inits[i, :]
acceptedIntMus[naccepted, :] = intMus[i, ]
acceptedIntSgs[naccepted, :] = intSgs[i, ]
acceptedDists[naccepted] = dists[i]
naccepted += 1
if naccepted == nparticles:
done = True
print "do_abc_rej : Completed"
print " : Final acceptance rate = ", naccepted / float(
ntotsim)
return [
acceptedDynParams, acceptedInits, acceptedIntMus, acceptedIntSgs,
acceptedDists
]
def do_abc_rej(self, model, nbeta, nparticles, eps):
nbatch = 100
model.create_model_instance(nbeta, self.timePoints)
self.nSpecies, self.nDynPars = model.get_model_info()
#print "do_abc_rej : Species/Dynamical parameters in this model:", self.nSpecies, self.nDynPars
done = False
ntotsim = 0
naccepted = 0
acceptedDynParams = zeros([nparticles,self.nDynPars])
acceptedInits = zeros([nparticles,self.nSpecies])
acceptedIntMus = zeros([nparticles,self.nFP])
acceptedIntSgs = zeros([nparticles,self.nFP])
acceptedDists = zeros([nparticles])
while done == False:
print "\tRunning batch, nsims/nacc:", ntotsim, naccepted
#Parameters
dynParameters = self.sample_dyn_pars(nbatch)
#Initial conditions
inits = self.sample_inits(nbatch)
#Intensity parameters
intMus, intSgs = self.sample_int_pars(nbatch)
print "\tDone sampling"
sims = model.simulate(nbatch, dynParameters, inits, self.fps, intMus, intSgs)
print "\tDone simulation"
dists = self.compare_to_data(nbatch, nbeta, sims, self.nFP )
print 'dists: ', dists
print "\tDone distance calculation"
accMask = self.check_distance(nbatch, dists, eps)
ntotsim += nbatch
for i in range(nbatch):
if accMask[i] == 1 and naccepted < nparticles:
acceptedDynParams[naccepted, :] = dynParameters[i, :]
acceptedInits[naccepted, :] = inits[i, :]
acceptedIntMus[naccepted, :] = intMus[i, ]
acceptedIntSgs[naccepted, :] = intSgs[i, ]
acceptedDists[naccepted] = dists[i]
naccepted += 1
if naccepted == nparticles:
done = True
print "do_abc_rej : Completed"
print " : Final acceptance rate = ", naccepted/float(ntotsim)
return [acceptedDynParams, acceptedInits, acceptedIntMus, acceptedIntSgs, acceptedDists]
def do_abc_smc(self, model, nbeta, nparticles, epsilons):
npop = len(epsilons)
nbatch = 100
model.create_model_instance(nbeta, self.timePoints)
self.nSpecies, self.nDynPars = model.get_model_info()
# do the first population sampling from the prior
print "do_abc_smc : Population 0"
acceptedDynParams, acceptedInits, acceptedIntMus, acceptedIntSgs = self.do_abc_rej(
model, nbeta, nparticles, epsilons[0])
acceptedWeights = ones([nparticles]) / float(nparticles)
for pop in range(1, npop):
currDynParams = zeros([nparticles, self.nDynPars])
currInits = zeros([nparticles, self.nSpecies])
currIntMus = zeros([nparticles, self.nFP])
currIntSgs = zeros([nparticles, self.nFP])
# calculate the scales for this population
#(max-min)/2
scales_dyn = self.calculate_scales(nparticles, acceptedDynParams)
scales_inits = self.calculate_scales(nparticles, acceptedInits)
scales_Mus = self.calculate_scales(nparticles, acceptedIntMus)
scales_Sgs = self.calculate_scales(nparticles, acceptedIntSgs)
# Rejection stage
doneRej = False
ntotsim = 0
naccepted = 0
while doneRej == False:
print "\tRunning batch, nsims/nacc:", ntotsim, naccepted
#Generates a random sample from a given 1-D array
ids = numpy.random.choice(nparticles,
size=nbatch,
replace=True,
p=acceptedWeights)
print "sampled ids:", ids
dynParameters = self.sample_perturb_pars(nbatch,
self.dynPriors,
acceptedDynParams,
ids,
scales=scales_dyn)
inits = self.sample_perturb_pars(nbatch,
self.initPriors,
acceptedInits,
ids,
scales=scales_inits)
intMus = self.sample_perturb_pars(nbatch,
self.intMeanPriors,
acceptedIntMus,
ids,
scales=scales_Mus)
intSgs = self.sample_perturb_pars(nbatch,
self.intSigmaPriors,
acceptedIntSgs,
ids,
scales=scales_Sgs)
print "\tDone sampling"
sims = model.simulate(nbatch, dynParameters, inits, self.fps,
intMus, intSgs)
dists = self.compare_to_data(nbatch, nbeta, sims, self.nFP)
accMask = self.check_distance(nbatch, dists, epsilons[pop])
ntotsim += nbatch
for i in range(nbatch):
if accMask[i] == 1 and naccepted < nparticles:
currDynParams[naccepted, :] = dynParameters[i, :]
currInits[naccepted, :] = inits[i, :]
currIntMus[naccepted, :] = intMus[i, ]
currIntSgs[naccepted, :] = intSgs[i, ]
naccepted += 1
if naccepted == nparticles:
doneRej = True
print "do_abc_smc : Population", pop, "\tacceptance rate = ", naccepted / float(
ntotsim)
# update weights
#column_stack = Stack 1-D arrays as columns into a 2-D array.
currPar = column_stack(
(currDynParams, currInits, currIntMus, currIntSgs))
prevPar = column_stack((acceptedDynParams, acceptedInits,
acceptedIntMus, acceptedIntSgs))
all_scales = concatenate(
(scales_dyn, scales_inits, scales_Mus, scales_Sgs))
# print shape(currDynParams), shape(currInits), shape(currIntMus), shape(currIntSgs)
# print shape(currPar), shape(prevPar)
acceptedWeights = self.compute_weights(nparticles,
acceptedWeights,
currPar,
prevPar,
scales=all_scales)
print "acceptedWeights:"
print acceptedWeights
# update best estimates
acceptedDynParams = deepcopy(currDynParams)
acceptedInits = deepcopy(currInits)
acceptedIntMus = deepcopy(currIntMus)
acceptedIntSgs = deepcopy(currIntSgs)
print "do_abc_smc : Completed successfully"
return [
acceptedDynParams, acceptedInits, acceptedIntMus, acceptedIntSgs,
acceptedWeights
]
def do_abc_smc(self, model, nbeta, nparticles, alpha, epsilon_final,
outHan, nfp, fps, results_path):
pop = 0
finishTotal = False
nbatch = 100
model.create_model_instance(nbeta, self.timePoints)
self.nSpecies, self.nDynPars = model.get_model_info()
print "do_abc_smc : estimating starting epsilon"
tDynParams = self.sample_dyn_pars(nparticles)
tInits = self.sample_inits(nparticles)
tIntMus, tIntSgs = self.sample_int_pars(nparticles)
sims = model.simulate(nparticles, tDynParams, tInits, self.fps,
tIntMus, tIntSgs)
tDists = self.compare_to_data(nparticles, nbeta, sims, self.nFP,
self.fps)
epsilon = self.set_epsilon(tDists, alpha)
print "Epsilon pop: ", pop, epsilon
print "do_abc_smc : Population 0"
acceptedDynParams, acceptedInits, acceptedIntMus, acceptedIntSgs, currDists = self.do_abc_rej(
model, nbeta, nparticles, epsilon)
acceptedWeights = ones([nparticles]) / float(nparticles)
outfolder = results_path + "/pop" + repr(0)
os.makedirs(outfolder)
self.write_outputs(outHan, nfp, fps, outfolder, model, nbeta,
acceptedDynParams, acceptedInits, acceptedIntMus,
acceptedIntSgs, acceptedWeights)
while finishTotal == False:
#for pop in range(1, npop):
pop += 1
epsilon = self.set_epsilon(currDists, alpha)
print "Epsilon pop: ", pop, epsilon
currDynParams = zeros([nparticles, self.nDynPars])
currInits = zeros([nparticles, self.nSpecies])
currIntMus = zeros([nparticles, self.nFP])
currIntSgs = zeros([nparticles, self.nFP])
currDists = zeros(nparticles)
# calculate the scales for this population
#(max-min)/2
scales_dyn = self.calculate_scales(nparticles, acceptedDynParams)
scales_inits = self.calculate_scales(nparticles, acceptedInits)
scales_Mus = self.calculate_scales(nparticles, acceptedIntMus)
scales_Sgs = self.calculate_scales(nparticles, acceptedIntSgs)
# Rejection stage
doneRej = False
ntotsim = 0
naccepted = 0
while doneRej == False:
print "\tRunning batch, nsims/nacc:", ntotsim, naccepted
#Generates a random sample from a given 1-D array
ids = numpy.random.choice(nparticles,
size=nbatch,
replace=True,
p=acceptedWeights)
print "sampled ids:", ids
dynParameters = self.sample_perturb_pars(nbatch,
self.dynPriors,
acceptedDynParams,
ids,
scales=scales_dyn)
inits = self.sample_perturb_pars(nbatch,
self.initPriors,
acceptedInits,
ids,
scales=scales_inits)
intMus = self.sample_perturb_pars(nbatch,
self.intMeanPriors,
acceptedIntMus,
ids,
scales=scales_Mus)
intSgs = self.sample_perturb_pars(nbatch,
self.intSigmaPriors,
acceptedIntSgs,
ids,
scales=scales_Sgs)
print "\tDone sampling"
sims = model.simulate(nbatch, dynParameters, inits, self.fps,
intMus, intSgs)
dists = self.compare_to_data(nbatch, nbeta, sims, self.nFP,
self.fps)
accMask = self.check_distance(nbatch, dists, epsilon)
ntotsim += nbatch
for i in range(nbatch):
if accMask[i] == 1 and naccepted < nparticles:
currDynParams[naccepted, :] = dynParameters[i, :]
currInits[naccepted, :] = inits[i, :]
currIntMus[naccepted, :] = intMus[i, ]
currIntSgs[naccepted, :] = intSgs[i, ]
currDists[naccepted] = dists[i]
naccepted += 1
if naccepted == nparticles:
doneRej = True
print "do_abc_smc : Population", pop, "\tacceptance rate = ", naccepted / float(
ntotsim)
#pop_fold_res_path = 'Population_' + str(pop)
#os.makedirs('Population_' + str(pop))
print "Accepted parameters : ", currDynParams
# update weights
#column_stack = Stack 1-D arrays as columns into a 2-D array.
currPar = column_stack(
(currDynParams, currInits, currIntMus, currIntSgs))
prevPar = column_stack((acceptedDynParams, acceptedInits,
acceptedIntMus, acceptedIntSgs))
all_scales = concatenate(
(scales_dyn, scales_inits, scales_Mus, scales_Sgs))
# print shape(currDynParams), shape(currInits), shape(currIntMus), shape(currIntSgs)
# print shape(currPar), shape(prevPar)
acceptedWeights = self.compute_weights(nparticles,
acceptedWeights,
currPar,
prevPar,
scales=all_scales)
print "acceptedWeights:"
print acceptedWeights
# update best estimates
acceptedDynParams = deepcopy(currDynParams)
acceptedInits = deepcopy(currInits)
acceptedIntMus = deepcopy(currIntMus)
acceptedIntSgs = deepcopy(currIntSgs)
# write progress out
outfolder = results_path + "/pop" + repr(pop)
os.makedirs(outfolder)
self.write_outputs(outHan, nfp, fps, outfolder, model, nbeta,
acceptedDynParams, acceptedInits,
acceptedIntMus, acceptedIntSgs, acceptedWeights)
if epsilon <= epsilon_final:
finishTotal = True
print "do_abc_smc : Completed successfully"
return [
acceptedDynParams, acceptedInits, acceptedIntMus, acceptedIntSgs,
acceptedWeights
]
def do_abc_smc(self, model, nbeta, nparticles, alpha, epsilon_final,
outHan, nfp, fps, results_path):
pop = 0
finishTotal = False
#npop = len(epsilons)
nbatch = 100
model.create_model_instance(nbeta, self.timePoints)
self.nSpecies, self.nDynPars = model.get_model_info()
# do the first population sampling from the prior
print "do_abc_smc : Population 0"
acceptedDynParams = self.sample_dyn_pars(nbatch)
# Initial conditions
acceptedInits = self.sample_inits(nbatch)
# Intensity parameters
acceptedIntMus, acceptedIntSgs = self.sample_int_pars(nbatch)
print "\tDone sampling"
sims = model.simulate(nbatch, acceptedDynParams, acceptedInits, self.fps, acceptedIntMus, acceptedIntSgs)
print "\tDone simulation"
currDists = self.compare_to_data(nbatch, nbeta, sims, self.nFP)
#acceptedDynParams, acceptedInits, acceptedIntMus, acceptedIntSgs, acceptedDists = self.do_abc_rej(model, nbeta, nparticles, epsilons[0])
acceptedWeights = ones([nparticles])/float(nparticles)
while finishTotal == False:
#for pop in range(1, npop):
pop += 1
epsilon = self.set_epsilon(currDists, alpha)
print "Epsilon current:", epsilon
currDynParams = zeros([nparticles, self.nDynPars])
currInits = zeros([nparticles, self.nSpecies])
currIntMus = zeros([nparticles, self.nFP])
currIntSgs = zeros([nparticles, self.nFP])
currDists = zeros(nparticles)
# calculate the scales for this population
#(max-min)/2
scales_dyn = self.calculate_scales(nparticles, acceptedDynParams)
scales_inits = self.calculate_scales(nparticles, acceptedInits)
scales_Mus = self.calculate_scales(nparticles, acceptedIntMus)
scales_Sgs = self.calculate_scales(nparticles, acceptedIntSgs)
# Rejection stage
doneRej = False
ntotsim = 0
naccepted = 0
while doneRej == False:
print "\tRunning batch, nsims/nacc:", ntotsim, naccepted
#Generates a random sample from a given 1-D array
ids = numpy.random.choice(nparticles, size=nbatch, replace=True, p=acceptedWeights)
print "sampled ids:", ids
dynParameters = self.sample_perturb_pars(nbatch, self.dynPriors, acceptedDynParams, ids, scales=scales_dyn )
inits = self.sample_perturb_pars(nbatch, self.initPriors, acceptedInits, ids, scales=scales_inits)
intMus = self.sample_perturb_pars(nbatch, self.intMeanPriors, acceptedIntMus, ids, scales=scales_Mus)
intSgs = self.sample_perturb_pars(nbatch, self.intSigmaPriors, acceptedIntSgs, ids, scales=scales_Sgs)
print "\tDone sampling"
sims = model.simulate(nbatch, dynParameters, inits, self.fps, intMus, intSgs)
dists = self.compare_to_data(nbatch, nbeta, sims, self.nFP)
accMask = self.check_distance(nbatch, dists, epsilon)
ntotsim += nbatch
for i in range(nbatch):
if accMask[i] == 1 and naccepted < nparticles:
currDynParams[naccepted, :] = dynParameters[i, :]
currInits[naccepted, :] = inits[i, :]
currIntMus[naccepted, :] = intMus[i, ]
currIntSgs[naccepted, :] = intSgs[i, ]
currDists[naccepted] = dists[i]
naccepted += 1
if naccepted == nparticles:
doneRej = True
print "do_abc_smc : Population", pop, "\tacceptance rate = ", naccepted/float(ntotsim)
#pop_fold_res_path = 'Population_' + str(pop)
#os.makedirs('Population_' + str(pop))
print "Accepted parameters : ", currDynParams
# update weights
#column_stack = Stack 1-D arrays as columns into a 2-D array.
currPar = column_stack((currDynParams, currInits, currIntMus, currIntSgs))
prevPar = column_stack((acceptedDynParams, acceptedInits, acceptedIntMus, acceptedIntSgs))
all_scales = concatenate((scales_dyn, scales_inits, scales_Mus, scales_Sgs))
# print shape(currDynParams), shape(currInits), shape(currIntMus), shape(currIntSgs)
# print shape(currPar), shape(prevPar)
acceptedWeights = self.compute_weights(nparticles, acceptedWeights, currPar, prevPar, scales=all_scales)
print "acceptedWeights:"
print acceptedWeights
# update best estimates
acceptedDynParams = deepcopy(currDynParams)
acceptedInits = deepcopy(currInits)
acceptedIntMus = deepcopy(currIntMus)
acceptedIntSgs = deepcopy(currIntSgs)
# write progress out
outfolder = results_path + "/pop"+repr(pop)
os.makedirs(outfolder)
self.write_outputs(outHan, nfp, fps, outfolder, model, nbeta, acceptedDynParams, acceptedInits, acceptedIntMus, acceptedIntSgs, acceptedWeights )
if epsilon <= epsilon_final:
finishTotal = True
print "do_abc_smc : Completed successfully"
return [acceptedDynParams, acceptedInits, acceptedIntMus, acceptedIntSgs, acceptedWeights]
def do_abc_smc(self, model, nbeta, nparticles, epsilons):
npop = len(epsilons)
nbatch = 100
model.create_model_instance(nbeta, self.timePoints)
self.nSpecies, self.nDynPars = model.get_model_info()
# do the first population sampling from the prior
print "do_abc_smc : Population 0"
acceptedDynParams, acceptedInits, acceptedIntMus, acceptedIntSgs = self.do_abc_rej(model, nbeta, nparticles, epsilons[0])
acceptedWeights = ones([nparticles])/float(nparticles)
for pop in range(1, npop):
currDynParams = zeros([nparticles, self.nDynPars])
currInits = zeros([nparticles, self.nSpecies])
currIntMus = zeros([nparticles, self.nFP])
currIntSgs = zeros([nparticles, self.nFP])
# calculate the scales for this population
#(max-min)/2
scales_dyn = self.calculate_scales(nparticles, acceptedDynParams)
scales_inits = self.calculate_scales(nparticles, acceptedInits)
scales_Mus = self.calculate_scales(nparticles, acceptedIntMus)
scales_Sgs = self.calculate_scales(nparticles, acceptedIntSgs)
# Rejection stage
doneRej = False
ntotsim = 0
naccepted = 0
while doneRej == False:
print "\tRunning batch, nsims/nacc:", ntotsim, naccepted
#Generates a random sample from a given 1-D array
ids = numpy.random.choice(nparticles, size=nbatch, replace=True, p=acceptedWeights)
print "sampled ids:", ids
dynParameters = self.sample_perturb_pars(nbatch, self.dynPriors, acceptedDynParams, ids, scales=scales_dyn )
inits = self.sample_perturb_pars(nbatch, self.initPriors, acceptedInits, ids, scales=scales_inits)
intMus = self.sample_perturb_pars(nbatch, self.intMeanPriors, acceptedIntMus, ids, scales=scales_Mus)
intSgs = self.sample_perturb_pars(nbatch, self.intSigmaPriors, acceptedIntSgs, ids, scales=scales_Sgs)
print "\tDone sampling"
sims = model.simulate(nbatch, dynParameters, inits, self.fps, intMus, intSgs)
dists = self.compare_to_data(nbatch, nbeta, sims, self.nFP)
accMask = self.check_distance(nbatch, dists, epsilons[pop])
ntotsim += nbatch
for i in range(nbatch):
if accMask[i] == 1 and naccepted < nparticles:
currDynParams[naccepted, :] = dynParameters[i, :]
currInits[naccepted, :] = inits[i, :]
currIntMus[naccepted, :] = intMus[i, ]
currIntSgs[naccepted, :] = intSgs[i, ]
naccepted += 1
if naccepted == nparticles:
doneRej = True
print "do_abc_smc : Population", pop, "\tacceptance rate = ", naccepted/float(ntotsim)
# update weights
#column_stack = Stack 1-D arrays as columns into a 2-D array.
currPar = column_stack( (currDynParams, currInits, currIntMus, currIntSgs) )
prevPar = column_stack( (acceptedDynParams, acceptedInits, acceptedIntMus, acceptedIntSgs) )
all_scales = concatenate( (scales_dyn, scales_inits, scales_Mus, scales_Sgs) )
# print shape(currDynParams), shape(currInits), shape(currIntMus), shape(currIntSgs)
# print shape(currPar), shape(prevPar)
acceptedWeights = self.compute_weights(nparticles, acceptedWeights, currPar, prevPar, scales=all_scales)
print "acceptedWeights:"
print acceptedWeights
# update best estimates
acceptedDynParams = deepcopy( currDynParams )
acceptedInits = deepcopy( currInits )
acceptedIntMus = deepcopy( currIntMus )
acceptedIntSgs = deepcopy( currIntSgs )
print "do_abc_smc : Completed successfully"
return [acceptedDynParams, acceptedInits, acceptedIntMus, acceptedIntSgs, acceptedWeights]