def __init__(self, parameters=None, xmlHandler=NumpyXMLHandler(),
xmlLabel=None, xmlComment=None):
BiGaussMixtureParamsSampler.__init__(self, parameters, xmlHandler,
xmlLabel, xmlComment)
self.varCDPrAlpha = self.parameters[self.P_VAR_CD_PR_ALPHA]
self.varCDPrBeta = self.parameters[self.P_VAR_CD_PR_BETA]
self.meanCDPrMean = self.parameters[self.P_MEAN_CD_PR_MEAN]
self.meanCDPrVar = self.parameters[self.P_MEAN_CD_PR_VAR]
def checkAndSetInitValue(self, variables):
if self.currentValue is None:
curValWasNone = True
else:
curValWasNone = False
BiGaussMixtureParamsSampler.checkAndSetInitValue(self, variables)
#TODO : retrieve simulated components ...
if curValWasNone:
if not self.useTrueValue:
nc = self.nbConditions
self.currentValue[self.I_MEAN_CD] = zeros(nc) -10.
self.currentValue[self.I_VAR_CD] = zeros(nc) + 1.
def linkToData(self, dataInput):
BiGaussMixtureParamsSampler.linkToData(self, dataInput)
self.nrlCD = range(self.nbConditions)
if self.dataInput.simulData is not None :
mixtures = self.dataInput.simulData.nrls.getMixture()
itemsCond = mixtures.items()
meanCD = zeros(self.nbConditions, dtype=float)
varCD = zeros(self.nbConditions, dtype=float)
for cn,mixt in mixtures.iteritems():
genDeactiv = mixt.generators['deactiv']
indCond = self.dataInput.simulData.nrls.condIds[cn]
meanCD[indCond] = genDeactiv.mean
varCD[indCond] = genDeactiv.std**2
self.trueValue[self.I_MEAN_CD] = meanCD
self.trueValue[self.I_VAR_CD] = varCD
def __init__(self, do_sampling=True, use_true_value=False,
val_ini=None, hyper_prior_type='Jeffreys', activ_thresh=4.,
var_ci_pr_alpha=2.04, var_ci_pr_beta=.5,
var_ca_pr_alpha=2.01, var_ca_pr_beta=.5,
var_cd_pr_alpha=2.01, var_cd_pr_beta=.5,
mean_ca_pr_mean=5., mean_ca_pr_var=20.,
mean_cd_pr_mean=-20., mean_cd_pr_var=20.):
BiGaussMixtureParamsSampler.__init__(self, do_sampling, use_true_value,
val_ini, hyper_prior_type,
activ_thresh, var_ci_pr_alpha,
var_ci_pr_beta, var_ca_pr_alpha,
var_ca_pr_beta, mean_ca_pr_mean,
mean_ca_pr_var)
self.varCDPrAlpha = var_cd_pr_alpha
self.varCDPrBeta = var_cd_pr_beta
self.meanCDPrMean = mean_cd_pr_mean
self.meanCDPrVar = mean_cd_pr_var
def finalizeSampling(self):
BiGaussMixtureParamsSampler.finalizeSampling(self)
del self.nrlCD
def sampleNextInternal(self, variables):
#BiGaussMixtureParamsSampler.sampleNextInternal(self, variables)
nrlsSmpl = variables[self.samplerEngine.I_NRLS]
cardCD = nrlsSmpl.cardClass[self.L_CD,:]
if self.hyperPriorFlag:
for j in xrange(self.nbConditions):
vICD = nrlsSmpl.voxIdx[nrlsSmpl.L_CD][j]
self.nrlCD[j] = nrlsSmpl.currentValue[j, vICD]
if cardCD[j] > 0:
etaj = mean(self.nrlCD[j])
nrlCDCentered = self.nrlCD[j] - etaj
nuj = .5 * dot(nrlCDCentered, nrlCDCentered)
#r = random.gamma(0.5*(cardCA[j]-1),2/nu1j)
varCDj = 1.0/random.gamma(0.5*cardCD[j] + self.varCDPrAlpha,
1/(nuj + self.varCDPrBeta))
#meanCAj = random.normal(eta1j, (varCAj/cardCA[j])**0.5)
else :
etaj = 0.0
varCDj = 1.0/random.gamma(self.varCDPrAlpha, 1/self.varCDPrBeta)
invVarLikelihood = cardCD[j]/varCDj
meanCDVarAPost = 1/(invVarLikelihood + 1/self.meanCDPrVar)
rPrMV = self.meanCDPrMean/self.meanCDPrVar
meanCDMeanAPost = meanCDVarAPost * (etaj*invVarLikelihood + rPrMV)
meanCDj = random.normal(meanCDMeanAPost, meanCDVarAPost**0.5)
self.currentValue[self.I_MEAN_CD, j] = meanCDj
self.currentValue[self.I_VAR_CD, j] = varCDj
else:
nrlsSmpl = variables[self.samplerEngine.I_NRLS]
#for j in xrange(self.nbConditions):
for j in random.permutation(self.nbConditions):
ca = nrlsSmpl.cardClass[self.L_CA,j]
ci = nrlsSmpl.cardClass[self.L_CI,j]
cd = nrlsSmpl.cardClass[self.L_CD,j]
vICI = nrlsSmpl.voxIdx[nrlsSmpl.L_CI][j]
vICA = nrlsSmpl.voxIdx[nrlsSmpl.L_CA][j]
vICD = nrlsSmpl.voxIdx[nrlsSmpl.L_CD][j]
self.nrlCI[j] = nrlsSmpl.currentValue[j, vICI]
self.nrlCA[j] = nrlsSmpl.currentValue[j, vICA]
self.nrlCD[j] = nrlsSmpl.currentValue[j, vICD]
r = BiGaussMixtureParamsSampler.computeWithJeffreyPriors(self,j,
ci,ca)
varCIj, meanCAj, varCAj = r
meanCD, varCD = self.computeWithJeffreyPriors(j,cd)
self.currentValue[self.I_VAR_CI, j] = varCIj
self.currentValue[self.I_MEAN_CA, j] = meanCAj #absolute(meanCAj)
self.currentValue[self.I_VAR_CA, j] = varCAj
self.currentValue[self.I_MEAN_CD,j] = meanCD
self.currentValue[self.I_VAR_CD,j] = varCD
pyhrf.verbose(4, 'meanCD,%d = %f' \
%(j,self.currentValue[self.I_MEAN_CD,j]))
pyhrf.verbose(4, 'varCD,%d = %f' \
%(j,self.currentValue[self.I_VAR_CD,j]))