pyhrf.jde.asl_physio_hierarchical.
ASLPhysioSampler
(nb_iterations=3000, obs_hist_pace=-1.0, glob_obs_hist_pace=-1, smpl_hist_pace=-1.0, burnin=0.3, callback=<pyhrf.jde.samplerbase.GSDefaultCallbackHandler object>, bold_response_levels=<pyhrf.jde.asl_physio_hierarchical.BOLDResponseLevelSampler object>, perf_response_levels=<pyhrf.jde.asl_physio_hierarchical.PerfResponseLevelSampler object>, labels=<pyhrf.jde.asl_physio_hierarchical.LabelSampler object>, noise_var=<pyhrf.jde.asl_physio_hierarchical.NoiseVarianceSampler object>, truebrf=<pyhrf.jde.asl_physio_hierarchical.PhysioTrueBOLDResponseSampler object>, truebrf_var=<pyhrf.jde.asl_physio_hierarchical.PhysioTrueBOLDResponseVarianceSampler object>, brf=<pyhrf.jde.asl_physio_hierarchical.PhysioBOLDResponseSampler object>, brf_var=<pyhrf.jde.asl_physio_hierarchical.PhysioBOLDResponseVarianceSampler object>, prf=<pyhrf.jde.asl_physio_hierarchical.PhysioPerfResponseSampler object>, prf_var=<pyhrf.jde.asl_physio_hierarchical.PhysioPerfResponseVarianceSampler object>, bold_mixt_params=<pyhrf.jde.asl_physio_hierarchical.BOLDMixtureSampler object>, perf_mixt_params=<pyhrf.jde.asl_physio_hierarchical.PerfMixtureSampler object>, drift=<pyhrf.jde.asl_physio_hierarchical.DriftCoeffSampler object>, drift_var=<pyhrf.jde.asl_physio_hierarchical.DriftVarianceSampler object>, perf_baseline=<pyhrf.jde.asl_physio_hierarchical.PerfBaselineSampler object>, perf_baseline_var=<pyhrf.jde.asl_physio_hierarchical.PerfBaselineVarianceSampler object>, check_final_value=None)¶Bases: pyhrf.xmlio.Initable
, pyhrf.jde.samplerbase.GibbsSampler
computeFit
()¶default_nb_its
= 3000¶finalizeSampling
()¶getGlobalOutputs
()¶inputClass
¶alias of WN_BiG_ASLSamplerInput
parametersToShow
= ['nb_its', 'response_levels', 'hrf', 'hrf_var']¶pyhrf.jde.asl_physio_hierarchical.
BOLDMixtureSampler
(val_ini=None, do_sampling=True, use_true_value=False)¶Bases: pyhrf.jde.asl_physio_hierarchical.MixtureParamsSampler
, pyhrf.xmlio.Initable
get_true_values_from_simulation_cdefs
(cdefs)¶pyhrf.jde.asl_physio_hierarchical.
BOLDResponseLevelSampler
(val_ini=None, do_sampling=True, use_true_value=False)¶Bases: pyhrf.jde.asl_physio_hierarchical.ResponseLevelSampler
, pyhrf.xmlio.Initable
computeVarYTildeOpt
(update_perf=False)¶if update_perf is True then also update sumcXg and prl.ytilde update_perf should only be used at init of variable values.
getOutputs
()¶samplingWarmUp
(v)¶pyhrf.jde.asl_physio_hierarchical.
DriftCoeffSampler
(val_ini=None, do_sampling=True, use_true_value=False)¶Bases: pyhrf.jde.samplerbase.GibbsSamplerVariable
, pyhrf.xmlio.Initable
checkAndSetInitValue
(variables)¶compute_y_tilde
()¶getOutputs
()¶linkToData
(dataInput)¶sampleNextInternal
(variables)¶Define the behaviour of the variable at each sampling step when its sampling is not activated. Must be overriden in child classes.
samplingWarmUp
(v)¶Called before the launch of the main sampling loop by the sampler engine. Should be overriden and perform precalculations.
updateNorm
()¶pyhrf.jde.asl_physio_hierarchical.
DriftVarianceSampler
(val_ini=array([ 1.]), do_sampling=True, use_true_value=False)¶Bases: pyhrf.jde.samplerbase.GibbsSamplerVariable
, pyhrf.xmlio.Initable
checkAndSetInitValue
(variables)¶linkToData
(dataInput)¶sampleNextInternal
(variables)¶Define the behaviour of the variable at each sampling step when its sampling is not activated. Must be overriden in child classes.
pyhrf.jde.asl_physio_hierarchical.
LabelSampler
(val_ini=None, do_sampling=True, use_true_value=False)¶Bases: pyhrf.jde.samplerbase.GibbsSamplerVariable
, pyhrf.xmlio.Initable
CLASSES
= array([0, 1])¶CLASS_NAMES
= ['inactiv', 'activ']¶L_CA
= 1¶L_CI
= 0¶checkAndSetInitValue
(variables)¶compute_ext_field
()¶countLabels
()¶linkToData
(dataInput)¶sampleNextInternal
(v)¶Define the behaviour of the variable at each sampling step when its sampling is not activated. Must be overriden in child classes.
samplingWarmUp
(v)¶Called before the launch of the main sampling loop by the sampler engine. Should be overriden and perform precalculations.
pyhrf.jde.asl_physio_hierarchical.
MixtureParamsSampler
(name, response_level_name, val_ini=None, do_sampling=True, use_true_value=False)¶Bases: pyhrf.jde.samplerbase.GibbsSamplerVariable
I_MEAN_CA
= 0¶I_VAR_CA
= 1¶I_VAR_CI
= 2¶L_CA
= 1¶L_CI
= 0¶NB_PARAMS
= 3¶PARAMS_NAMES
= ['Mean_Activ', 'Var_Activ', 'Var_Inactiv']¶checkAndSetInitValue
(variables)¶computeWithJeffreyPriors
(j, cardCIj, cardCAj)¶get_current_means
()¶get_current_vars
()¶get_true_values_from_simulation_dict
()¶linkToData
(dataInput)¶sampleNextInternal
(variables)¶pyhrf.jde.asl_physio_hierarchical.
NoiseVarianceSampler
(val_ini=None, do_sampling=True, use_true_value=False)¶Bases: pyhrf.jde.samplerbase.GibbsSamplerVariable
, pyhrf.xmlio.Initable
checkAndSetInitValue
(variables)¶compute_y_tilde
()¶linkToData
(dataInput)¶sampleNextInternal
(variables)¶Define the behaviour of the variable at each sampling step when its sampling is not activated. Must be overriden in child classes.
pyhrf.jde.asl_physio_hierarchical.
PerfBaselineSampler
(val_ini=None, do_sampling=True, use_true_value=False)¶Bases: pyhrf.jde.samplerbase.GibbsSamplerVariable
, pyhrf.xmlio.Initable
checkAndSetInitValue
(variables)¶compute_residuals
()¶compute_wa
(a=None)¶linkToData
(dataInput)¶sampleNextInternal
(v)¶Define the behaviour of the variable at each sampling step when its sampling is not activated. Must be overriden in child classes.
pyhrf.jde.asl_physio_hierarchical.
PerfBaselineVarianceSampler
(val_ini=None, do_sampling=True, use_true_value=False)¶Bases: pyhrf.jde.samplerbase.GibbsSamplerVariable
, pyhrf.xmlio.Initable
checkAndSetInitValue
(variables)¶linkToData
(dataInput)¶sampleNextInternal
(v)¶Define the behaviour of the variable at each sampling step when its sampling is not activated. Must be overriden in child classes.
pyhrf.jde.asl_physio_hierarchical.
PerfMixtureSampler
(val_ini=None, do_sampling=True, use_true_value=False)¶Bases: pyhrf.jde.asl_physio_hierarchical.MixtureParamsSampler
, pyhrf.xmlio.Initable
checkAndSetInitValue
(variables)¶get_true_values_from_simulation_cdefs
(cdefs)¶pyhrf.jde.asl_physio_hierarchical.
PerfResponseLevelSampler
(val_ini=None, do_sampling=True, use_true_value=False)¶Bases: pyhrf.jde.asl_physio_hierarchical.ResponseLevelSampler
, pyhrf.xmlio.Initable
checkAndSetInitValue
(variables)¶computeVarYTildeOpt
()¶pyhrf.jde.asl_physio_hierarchical.
PhysioBOLDResponseSampler
(smooth_order=2, zero_constraint=True, duration=25.0, normalise=1.0, val_ini=None, do_sampling=True, use_true_value=False, prior_type='not_regularized')¶Bases: pyhrf.jde.asl_physio_hierarchical.ResponseSampler
, pyhrf.xmlio.Initable
computeYTilde
()¶y - sum cWXg - Pl - wa
get_mat_X
()¶get_mat_XtX
()¶get_stackX
()¶sampleNextInternal
(variables)¶Sample BRF
changes to mean: changes to var:
samplingWarmUp
(v)¶Called before the launch of the main sampling loop by the sampler engine. Should be overriden and perform precalculations.
pyhrf.jde.asl_physio_hierarchical.
PhysioBOLDResponseVarianceSampler
(val_ini=array([ 0.001]), do_sampling=True, use_true_value=False)¶Bases: pyhrf.jde.samplerbase.GibbsSamplerVariable
, pyhrf.xmlio.Initable
checkAndSetInitValue
(v)¶linkToData
(dataInput)¶sampleNextInternal
(v)¶Sample variance of BRF
pyhrf.jde.asl_physio_hierarchical.
PhysioPerfResponseSampler
(smooth_order=2, zero_constraint=True, duration=25.0, normalise=1.0, val_ini=None, do_sampling=True, use_true_value=False, diff_res=True, prior_type='not_regularized')¶Bases: pyhrf.jde.asl_physio_hierarchical.ResponseSampler
, pyhrf.xmlio.Initable
computeYTilde
()¶y - sum aXh - Pl - wa
get_mat_X
()¶get_mat_XtX
()¶get_stackX
()¶sampleNextInternal
(variables)¶Sample PRF with physio prior
changes to mean: add a factor of Omega h Sigma_g^-1 v_g^-1
samplingWarmUp
(variables)¶Called before the launch of the main sampling loop by the sampler engine. Should be overriden and perform precalculations.
pyhrf.jde.asl_physio_hierarchical.
PhysioPerfResponseVarianceSampler
(val_ini=array([ 0.001]), do_sampling=True, use_true_value=False)¶Bases: pyhrf.jde.samplerbase.GibbsSamplerVariable
, pyhrf.xmlio.Initable
checkAndSetInitValue
(v)¶linkToData
(dataInput)¶sampleNextInternal
(v)¶Sample variance of PRF
pyhrf.jde.asl_physio_hierarchical.
PhysioTrueBOLDResponseSampler
(smooth_order=2, zero_constraint=True, duration=25.0, normalise=1.0, val_ini=None, do_sampling=True, use_true_value=False, prior_type='regularized')¶Bases: pyhrf.jde.asl_physio_hierarchical.ResponseSampler
, pyhrf.xmlio.Initable
get_mat_X
()¶get_mat_XtX
()¶get_stackX
()¶sampleNextInternal
(variables)¶Sample TRUE BRF
pyhrf.jde.asl_physio_hierarchical.
PhysioTrueBOLDResponseVarianceSampler
(val_ini=array([ 0.001]), do_sampling=True, use_true_value=False)¶Bases: pyhrf.jde.samplerbase.GibbsSamplerVariable
, pyhrf.xmlio.Initable
checkAndSetInitValue
(v)¶linkToData
(dataInput)¶sampleNextInternal
(v)¶Sample variance of BRF
pyhrf.jde.asl_physio_hierarchical.
ResponseLevelSampler
(name, response_name, mixture_name, val_ini=None, do_sampling=True, use_true_value=False)¶Bases: pyhrf.jde.samplerbase.GibbsSamplerVariable
checkAndSetInitValue
(variables)¶computeRR
()¶computeVarYTildeOpt
()¶linkToData
(dataInput)¶sampleNextInternal
(variables)¶samplingWarmUp
(variables)¶pyhrf.jde.asl_physio_hierarchical.
ResponseSampler
(name, response_level_name, variance_name, prior_type, smooth_order=2, zero_constraint=True, duration=25.0, normalise=1.0, val_ini=None, do_sampling=True, use_true_value=False)¶Bases: pyhrf.jde.samplerbase.GibbsSamplerVariable
Generic parent class to perfusion response & BOLD response samplers
calcXResp
(resp, stackX=None)¶checkAndSetInitValue
(variables)¶computeYTilde
()¶getOutputs
()¶get_mat_X
()¶get_mat_XtX
()¶get_rlrl
()¶get_stackX
()¶get_ybar
()¶linkToData
(dataInput)¶sampleNextInternal
(variables)¶setFinalValue
()¶updateNorm
()¶updateXResp
()¶pyhrf.jde.asl_physio_hierarchical.
WN_BiG_ASLSamplerInput
(data, dt, typeLFD, paramLFD, hrfZc, hrfDuration)¶Bases: pyhrf.jde.models.WN_BiG_Drift_BOLDSamplerInput
cleanPrecalculations
()¶makePrecalculations
()¶pyhrf.jde.asl_physio_hierarchical.
b
()¶pyhrf.jde.asl_physio_hierarchical.
compute_StS_StY
(rls, v_b, mx, mxtx, ybar, rlrl, yaj, ajak_vb)¶yaj and ajak_vb are only used to store intermediate quantities, they’re not inputs.
pyhrf.jde.asl_physio_hierarchical.
compute_StS_StY_deterministic
(brls, prls, v_b, mx, mxtx, mwx, mxtwx, mwxtwx, ybar, rlrl_bold, rlrl_perf, brlprl, omega, yj, ajak_vb)¶yj, ajak_vb and cjck_vb are only used to store intermediate quantities, they’re not inputs.
pyhrf.jde.asl_physio_hierarchical.
compute_bRpR
(brl, prl, nbConditions, nbVoxels)¶