def __init__(self, hrfDuration=25., sigmaH=0.1, fast=True, computeContrast=True, nbClasses=2, PLOT=False, nItMax=100, nItMin=1, scale=False, beta=1.0, estimateSigmaH=True, estimateHRF=True, TrueHrfFlag=False, HrfFilename='hrf.nii', estimateDrifts=True, hyper_prior_sigma_H=1000, dt=.6, estimateBeta=True, contrasts=None, simulation=False, estimateLabels=True, LabelsFilename=None, MFapprox=False, estimateMixtParam=True, constrained=False, InitVar=0.5, InitMean=2.0, MiniVemFlag=False, NbItMiniVem=5, zero_constraint=True, output_drifts=False, drifts_type="poly"): XmlInitable.__init__(self) JDEAnalyser.__init__(self, outputPrefix='jde_vem_') # Important thing : all parameters must have default values self.dt = dt #self.driftType = driftType self.hrfDuration = hrfDuration self.nbClasses = nbClasses self.nItMax = nItMax self.estimateSigmaH = estimateSigmaH self.scale = scale self.estimateDrifts = estimateDrifts self.PLOT = PLOT self.fast = fast self.simulation = simulation self.beta = beta self.sigmaH = sigmaH self.estimateHRF = estimateHRF self.TrueHrfFlag = TrueHrfFlag self.HrfFilename = HrfFilename self.nItMin = nItMin self.estimateBeta = estimateBeta self.estimateMixtParam = estimateMixtParam self.estimateLabels = estimateLabels self.LabelsFilename = LabelsFilename self.MFapprox = MFapprox self.InitVar = InitVar self.InitMean = InitMean self.MiniVemFlag = MiniVemFlag self.NbItMiniVem = NbItMiniVem if contrasts is None: contrasts = OrderedDict() self.contrasts = contrasts self.computeContrast = computeContrast self.hyper_prior_sigma_H = hyper_prior_sigma_H self.constrained = constrained self.zero_constraint = zero_constraint self.output_drifts = output_drifts self.drifts_type = drifts_type logger.info("VEM analyzer:") logger.info(" - estimate sigma H: %s", str(self.estimateSigmaH)) logger.info(" - init sigma H: %f", self.sigmaH) logger.info(" - hyper_prior_sigma_H: %f", self.hyper_prior_sigma_H) logger.info(" - estimate drift: %s", str(self.estimateDrifts))
def __init__(self, onsets=DEFAULT_ONSETS, durations=DEFAULT_STIM_DURATIONS, simulation_file=DEFAULT_SIMULATION_FILE): XmlInitable.__init__(self) assert isinstance(onsets, dict) assert durations is None or isinstance(durations, dict) self.onsets = onsets self.durations = durations self.simulation_file = simulation_file
def __init__(self, onsets=DEFAULT_ONSETS, durations=DEFAULT_STIM_DURATIONS, bold_file=DEFAULT_BOLD_SURF_FILE): XmlInitable.__init__(self) assert isinstance(onsets, dict) assert durations is None or isinstance(durations, dict) self.onsets = onsets self.durations = durations self.bold_file = bold_file
def __init__(self, onsets=DEFAULT_ONSETS, durations=DEFAULT_STIM_DURATIONS, bold_file=DEFAULT_BOLD_VOL_FILE): XmlInitable.__init__(self) assert isinstance(onsets, (dict, OrderedDict)) assert durations is None or isinstance(durations, (dict, OrderedDict)) #assert bold_file.endswith('nii') or bold_file.endswith('nii.gz') self.onsets = onsets self.durations = durations self.bold_file = bold_file
def __init__(self, sampler=BOLDGibbsSampler(), osfMax=4, dtMin=.4, dt=.6, driftParam=4, driftType='polynomial', outputPrefix='jde_mcmc_', randomSeed=None, pass_error=True, copy_sampler=True): XmlInitable.__init__(self) JDEAnalyser.__init__(self, outputPrefix, pass_error=pass_error) self.sampler = sampler self.osfMax = osfMax self.dtMin = dtMin self.dt = dt self.driftLfdParam = driftParam self.driftLfdType = driftType self.copy_sampler = copy_sampler
def __init__(self, hrfDuration=25., dt=.5, fast=True, constrained=False, nbClasses=2, PLOT=False, nItMax=1, nItMin=1, scale=False, beta=1.0, simulation=None, fmri_data=None, computeContrast=True, estimateH=True, estimateG=True, use_hyperprior=False, estimateSigmaH=True, estimateSigmaG=True, positivity=False, sigmaH=0.0001, sigmaG=0.0001, sigmaMu=0.0001, physio=True, gammaH=1000, gammaG=1000, zero_constrained=False, estimateLabels=True, estimateMixtParam=True, contrasts=None, InitVar=0.5, InitMean=2.0, estimateA=True, estimateC=True, estimateBeta=True, estimateNoise=True, estimateLA=True, phy_params=PHY_PARAMS_KHALIDOV11, prior='no', n_session=1): XmlInitable.__init__(self) JDEAnalyser.__init__(self, outputPrefix='jde_vem_asl_') # Important thing : all parameters must have default values self.hrfDuration = hrfDuration self.dt = dt self.fast = fast self.constrained = constrained self.nbClasses = nbClasses self.PLOT = PLOT self.nItMax = nItMax self.nItMin = nItMin self.scale = scale self.beta = beta self.simulation = simulation self.fmri_data = fmri_data self.estimateH = estimateH self.estimateG = estimateG self.estimateSigmaH = estimateSigmaH self.estimateSigmaG = estimateSigmaG self.sigmaH = sigmaH self.sigmaG = sigmaG self.sigmaMu = sigmaMu self.gammaH = gammaH self.gammaG = gammaG self.estimateLabels = estimateLabels self.estimateMixtParam = estimateMixtParam self.InitVar = InitVar self.InitMean = InitMean self.estimateA = estimateA self.estimateC = estimateC self.estimateBeta = estimateBeta self.estimateNoise = estimateNoise self.estimateLA = estimateLA self.use_hyperprior = use_hyperprior self.positivity = positivity self.physio = physio self.prior = prior if contrasts is None: contrasts = OrderedDict() self.contrasts = contrasts self.computeContrast = computeContrast self.phy_params = phy_params self.n_session = n_session self.zc = zero_constrained logger.info("VEM analyzer:") logger.info(" - estimate sigma H: %s", str(self.estimateSigmaH)) logger.info(" - init sigma H: %f", self.sigmaH) logger.info(" - estimate drift and perfusion baseline: %s", str(self.estimateLA))
def __init__(self, p=1, c='a'): XmlInitable.__init__(self) self.param1 = p self.param2 = c