RCP-GS : Random Clustering Prior - Gibbs Sampler. More...

#include <iRCPGSAlgorithm.hh>

Inheritance diagram for iRCPGSAlgorithm:

Collaboration diagram for iRCPGSAlgorithm:

Public Member Functions
	iRCPGSAlgorithm ()

	~iRCPGSAlgorithm ()

int	InitSpecificOptions (string a_specificOptions)

void	ShowHelpSpecific ()
	Show help for the child algorithm. More...

	iRCPGSAlgorithm ()

	~iRCPGSAlgorithm ()

int	InitSpecificOptions (string a_specificOptions)

void	ShowHelpSpecific ()
	Show help for the child algorithm. More...

Public Member Functions inherited from vAlgorithm
	vAlgorithm ()
	vAlgorithm constructor. Initialize the member variables to their default values. More...

virtual	~vAlgorithm ()
	vAlgorithm destructor. More...

int	Run ()
	Just call either the RunCPU or the RunGPU function as asked for. More...

int	RunCPU ()
	Perform the iterative loop of the algorithm. Function designed to be executed on the CPU only. More...

void	SetSaveSensitivityHistoFlag (bool a_saveSensitivityHistoFlag)

void	SetSaveSubsetImageFlag (bool a_saveImageAfterSubsets)

void	SetSaveDynamicBasisCoefficientImages (bool a_saveDynamicBasisCoefficients)

void	SetOptimizerManager (oOptimizerManager *ap_OptimizerManager)

void	SetImageDimensionsAndQuantification (oImageDimensionsAndQuantification *ap_ImageDimensionsAndQuantification)

void	SetImageSpace (oImageSpace *ap_ImageSpace)

void	SetProjectorManager (oProjectorManager *ap_ProjectorManager)

void	SetImageConvolverManager (oImageConvolverManager *ap_ImageConvolverManager)

void	SetImageProcessingManager (oImageProcessingManager *ap_ImageProcessingManager)

void	SetDynamicModelManager (oDynamicModelManager *ap_DynamicModelManager)

void	SetDeformationManager (oDeformationManager *ap_DeformationManager)

void	SetDataFile (vDataFile **a2p_DataFile)

void	SetGPUflag (bool a_flagGPU)

void	SetVerbose (int a_verboseLevel)

void	SetNbBeds (int a_nbBeds)

void	SetPathInitImage (string a_pathToInitialImage)

void	SetPathToAttenuationImage (string a_pathToAttenuationImage)

void	SetPathToSensitivityImage (string a_pathToSensitivityImage)

void	SetPathToMultiModalImage (vector< string > a_pathToMultiModalImage)

int	SetNbIterationsAndSubsets (const string &a_nbIterationsSubsets)

int	SetOutputIterations (const string &a_outputIterations)

	vAlgorithm ()

virtual	~vAlgorithm ()

int	Run ()

int	RunCPU ()

void	SetSaveSensitivityHistoFlag (bool a_saveSensitivityHistoFlag)

void	SetSaveSubsetImageFlag (bool a_saveImageAfterSubsets)

void	SetSaveDynamicBasisCoefficientImages (bool a_saveDynamicBasisCoefficients)

void	SetOptimizerManager (oOptimizerManager *ap_OptimizerManager)

void	SetImageDimensionsAndQuantification (oImageDimensionsAndQuantification *ap_ImageDimensionsAndQuantification)

void	SetImageSpace (oImageSpace *ap_ImageSpace)

void	SetProjectorManager (oProjectorManager *ap_ProjectorManager)

void	SetImageConvolverManager (oImageConvolverManager *ap_ImageConvolverManager)

void	SetImageProcessingManager (oImageProcessingManager *ap_ImageProcessingManager)

void	SetDynamicModelManager (oDynamicModelManager *ap_DynamicModelManager)

void	SetDeformationManager (oDeformationManager *ap_DeformationManager)

void	SetDataFile (vDataFile **a2p_DataFile)

void	SetGPUflag (bool a_flagGPU)

void	SetVerbose (int a_verboseLevel)

void	SetNbBeds (int a_nbBeds)

void	SetPathInitImage (string a_pathToInitialImage)

void	SetPathToAttenuationImage (string a_pathToAttenuationImage)

void	SetPathToSensitivityImage (string a_pathToSensitivityImage)

void	SetPathToMultiModalImage (vector< string > a_pathToMultiModalImage)

int	SetNbIterationsAndSubsets (const string &a_nbIterationsSubsets)

void	SetNbSkippedIterations (const string &a_skippedIterations)
	Set the number of first iterations to be skipped. More...

int	SetOutputIterations (const string &a_outputIterations)

Protected Member Functions
int	StepBeforeIterationLoop ()
	This function is called at the beginning of the RunCPU function. More...

int	StepAfterIterationLoop ()
	This function is called at the end of the RunCPU function. More...

int	StepBeforeSubsetLoop (int a_iteration)

int	StepAfterSubsetLoop (int a_iteration)

int	StepPreProcessInsideSubsetLoop (int a_iteration, int a_subset)

int	StepInnerLoopInsideSubsetLoop (int a_iteration, int a_subset, int a_bed)

int	StepPostProcessInsideSubsetLoop (int a_iteration, int a_subset)

int	StepImageOutput (int a_iteration, int a_subset=-1)

int	ReadConfigurationFile (const string &a_configurationFile)

int	StepBeforeIterationLoop ()
	This function is called at the beginning of the RunCPU function. More...

int	StepAfterIterationLoop ()
	This function is called at the end of the RunCPU function. More...

int	StepBeforeSubsetLoop (int a_iteration)

int	StepAfterSubsetLoop (int a_iteration)

int	StepPreProcessInsideSubsetLoop (int a_iteration, int a_subset)

int	StepInnerLoopInsideSubsetLoop (int a_iteration, int a_subset, int a_bed)

int	StepPostProcessInsideSubsetLoop (int a_iteration, int a_subset)

int	StepImageOutput (int a_iteration, int a_subset=-1)

int	ReadConfigurationFile (const string &a_configurationFile)

Private Member Functions
int	SampleConditionalCompleteData (int a_iteration, int a_subset, int a_bed)

int	SampleConditionalClustering (int a_iteration)

int	SampleConditionalClusterIntensity ()
	Gibbs sampler : third conditional probability (cluster intensity) More...

int	UpdateVisitedVoxels ()
	Check for voxels which do not contribute to recorded observed data. More...

int	InitializeHelperVar ()
	Allocate and initialize temporary variables, after the main variables have been initialized Assumption : the initial image and the sensitivity image have already been initialized. More...

int	ProcessMultiModalInfo ()
	Check input multimodal images. More...

int	GenerateCurrentImage ()
	Generate the current image estimation from the current sample of partition/clustering and cluster intensities. More...

int	ComputeFellowVoxelsList (vector< INTNB > &a_fellow_voxels, int a_current_voxel)

int	ComputeSumsPerClusters (int a_iteration)

int	SaveIntermediaryData (int a_iteration)

int	SampleConditionalCompleteData (int a_iteration, int a_subset, int a_bed)

int	SampleConditionalClustering (int a_iteration)

int	SampleConditionalClusterIntensity ()

int	UpdateVisitedVoxels ()

int	InitializeHelperVar ()

int	ProcessMultiModalInfo ()

int	GenerateCurrentImage ()

int	ComputeFellowVoxelsList (vector< INTNB > &a_fellow_voxels, int a_current_voxel)

int	ComputeSumsPerClusters (int a_iteration)

int	SaveIntermediaryData (int a_iteration)

Private Attributes
int	m_ddCRP

int	m_backprojection

int	m_neighbourhood

HPFLTNB	m_gammaShape

HPFLTNB	m_gammaRate

HPFLTNB	m_ddcrpAlpha

INTNB	m_multiModalLag

HPFLTNB	m_ddcrpAlphaIncrement

HPFLTNB *	mp_multiModalNoiseSigma

HPFLTNB *	mp_multiModalParam

INTNB *	mp_voxelClusterMapping

HPFLTNB *	mp_clusterValues

HPFLTNB **	mp_clusterN

HPFLTNB *	mp_clusterSensitivity

HPFLTNB **	mpp_clusterMultiModal

INTNB *	mp_clusterCount

INTNB *	mp_nextLink

vector< INTNB > *	mpv_parentLinks

vector< INTNB >	mv_newClusters

INTNB *	mp_listVoxelIndices

INTNB **	mp_listEventsIndices

INTNB ****	m4p_EventsBackprojectionTrace

bool *	mp_listRelevantVoxelIndices

HPFLTNB *	temp_count_multimodal

HPFLTNB	m_ddcrpLogAlpha

HPFLTNB	m_currentMeanClusterVolume

HPFLTNB	m_meanClusterVolumeMin

HPFLTNB	m_meanClusterVolumeMax

FLTNB *	mp_permanentBackwardImage

Additional Inherited Members
Protected Attributes inherited from vAlgorithm
int	m_nbIterations

int *	mp_nbSubsets

bool *	mp_outputIterations

int	m_verbose

bool	m_flagGPU

oImageDimensionsAndQuantification *	mp_ID

vDataFile **	m2p_DataFile

oProjectorManager *	mp_ProjectorManager

oOptimizerManager *	mp_OptimizerManager

oDeformationManager *	mp_DeformationManager

oDynamicModelManager *	mp_DynamicModelManager

oImageSpace *	mp_ImageSpace

oImageConvolverManager *	mp_ImageConvolverManager

oImageProcessingManager *	mp_ImageProcessingManager

int	m_nbBeds

string	m_pathToInitialImg

string	m_pathToAtnImg

string	m_pathToSensitivityImg

vector< string >	m_pathToMultiModalImg

bool	m_saveSensitivityHistoFlag

bool	m_saveImageAfterSubsets

bool	m_saveDynamicBasisCoefficients

int	m_nbSkippedIterations

Detailed Description

RCP-GS : Random Clustering Prior - Gibbs Sampler.

Sampling of the posterior probability distribution (Bayesian inference) Image prior : ddCRP, with intensity ~ Gamma (conjugate prior for Poisson likelihood) Multinomial distribution for the backprojection from acquired data into (latent) emissions from voxel j into projection i

Definition at line 20 of file code/include/algorithm/iRCPGSAlgorithm.hh.

Constructor & Destructor Documentation

◆ iRCPGSAlgorithm() [1/2]

iRCPGSAlgorithm::iRCPGSAlgorithm ( )

Definition at line 12 of file code/src/algorithm/iRCPGSAlgorithm.cc.

◆ ~iRCPGSAlgorithm() [1/2]

iRCPGSAlgorithm::~iRCPGSAlgorithm ( )

Definition at line 45 of file code/src/algorithm/iRCPGSAlgorithm.cc.

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◆ iRCPGSAlgorithm() [2/2]

iRCPGSAlgorithm::iRCPGSAlgorithm ( )

◆ ~iRCPGSAlgorithm() [2/2]

iRCPGSAlgorithm::~iRCPGSAlgorithm ( )

Member Function Documentation

◆ ComputeFellowVoxelsList() [1/2]

int iRCPGSAlgorithm::ComputeFellowVoxelsList	(	vector< INTNB > &	a_fellow_voxels,
		int	a_current_voxel
	)

private

Definition at line 1767 of file code/src/algorithm/iRCPGSAlgorithm.cc.

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◆ ComputeFellowVoxelsList() [2/2]

int iRCPGSAlgorithm::ComputeFellowVoxelsList	(	vector< INTNB > &	a_fellow_voxels,
		int	a_current_voxel
	)

private

◆ ComputeSumsPerClusters() [1/2]

int iRCPGSAlgorithm::ComputeSumsPerClusters ( int a_iteration )

private

Definition at line 1333 of file code/src/algorithm/iRCPGSAlgorithm.cc.

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◆ ComputeSumsPerClusters() [2/2]

int iRCPGSAlgorithm::ComputeSumsPerClusters ( int a_iteration )

private

◆ GenerateCurrentImage() [1/2]

int iRCPGSAlgorithm::GenerateCurrentImage ( )

private

◆ GenerateCurrentImage() [2/2]

int iRCPGSAlgorithm::GenerateCurrentImage ( )

private

Generate the current image estimation from the current sample of partition/clustering and cluster intensities.

Returns: 0 if success, positive value otherwise.

Definition at line 1829 of file code/src/algorithm/iRCPGSAlgorithm.cc.

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◆ InitializeHelperVar() [1/2]

int iRCPGSAlgorithm::InitializeHelperVar ( )

private

Allocate and initialize temporary variables, after the main variables have been initialized Assumption : the initial image and the sensitivity image have already been initialized.

Returns: 0 if success, positive value otherwise.

Definition at line 521 of file code/src/algorithm/iRCPGSAlgorithm.cc.

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◆ InitializeHelperVar() [2/2]

int iRCPGSAlgorithm::InitializeHelperVar ( )

private

◆ InitSpecificOptions() [1/2]

int iRCPGSAlgorithm::InitSpecificOptions ( string a_specificOptions )

virtual

Reimplemented from vAlgorithm.

Definition at line 136 of file code/src/algorithm/iRCPGSAlgorithm.cc.

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◆ InitSpecificOptions() [2/2]

int iRCPGSAlgorithm::InitSpecificOptions ( string a_specificOptions )

virtual

Reimplemented from vAlgorithm.

◆ ProcessMultiModalInfo() [1/2]

int iRCPGSAlgorithm::ProcessMultiModalInfo ( )

private

◆ ProcessMultiModalInfo() [2/2]

int iRCPGSAlgorithm::ProcessMultiModalInfo ( )

private

Check input multimodal images.

Returns: 0 if success, positive value otherwise.

Definition at line 668 of file code/src/algorithm/iRCPGSAlgorithm.cc.

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◆ ReadConfigurationFile() [1/2]

int iRCPGSAlgorithm::ReadConfigurationFile ( const string & a_configurationFile )

protected

Definition at line 441 of file code/src/algorithm/iRCPGSAlgorithm.cc.

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◆ ReadConfigurationFile() [2/2]

int iRCPGSAlgorithm::ReadConfigurationFile ( const string & a_configurationFile )

protected

◆ SampleConditionalClustering() [1/2]

int iRCPGSAlgorithm::SampleConditionalClustering ( int a_iteration )

private

◆ SampleConditionalClustering() [2/2]

int iRCPGSAlgorithm::SampleConditionalClustering ( int a_iteration )

private

Definition at line 1418 of file code/src/algorithm/iRCPGSAlgorithm.cc.

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◆ SampleConditionalClusterIntensity() [1/2]

int iRCPGSAlgorithm::SampleConditionalClusterIntensity ( )

private

◆ SampleConditionalClusterIntensity() [2/2]

int iRCPGSAlgorithm::SampleConditionalClusterIntensity ( )

private

Gibbs sampler : third conditional probability (cluster intensity)

Returns: 0 if success, positive value otherwise.

Definition at line 1715 of file code/src/algorithm/iRCPGSAlgorithm.cc.

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◆ SampleConditionalCompleteData() [1/2]

int iRCPGSAlgorithm::SampleConditionalCompleteData	(	int	a_iteration,
		int	a_subset,
		int	a_bed
	)

private

◆ SampleConditionalCompleteData() [2/2]

int iRCPGSAlgorithm::SampleConditionalCompleteData	(	int	a_iteration,
		int	a_subset,
		int	a_bed
	)

private

Definition at line 889 of file code/src/algorithm/iRCPGSAlgorithm.cc.

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◆ SaveIntermediaryData() [1/2]

int iRCPGSAlgorithm::SaveIntermediaryData ( int a_iteration )

private

◆ SaveIntermediaryData() [2/2]

int iRCPGSAlgorithm::SaveIntermediaryData ( int a_iteration )

private

◆ ShowHelpSpecific() [1/2]

void iRCPGSAlgorithm::ShowHelpSpecific ( )

virtual

Show help for the child algorithm.

Reimplemented from vAlgorithm.

Definition at line 2008 of file code/src/algorithm/iRCPGSAlgorithm.cc.

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◆ ShowHelpSpecific() [2/2]

void iRCPGSAlgorithm::ShowHelpSpecific ( )

virtual

Show help for the child algorithm.

Reimplemented from vAlgorithm.

◆ StepAfterIterationLoop() [1/2]

int iRCPGSAlgorithm::StepAfterIterationLoop ( )

protectedvirtual

This function is called at the end of the RunCPU function.

Returns: 0 if success, positive value otherwise.

Reimplemented from vAlgorithm.

Definition at line 1856 of file code/src/algorithm/iRCPGSAlgorithm.cc.

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◆ StepAfterIterationLoop() [2/2]

int iRCPGSAlgorithm::StepAfterIterationLoop ( )

protectedvirtual

This function is called at the end of the RunCPU function.

Returns: 0 if success, positive value otherwise.

Reimplemented from vAlgorithm.

◆ StepAfterSubsetLoop() [1/2]

int iRCPGSAlgorithm::StepAfterSubsetLoop ( int a_iteration )

protectedvirtual

Reimplemented from vAlgorithm.

◆ StepAfterSubsetLoop() [2/2]

int iRCPGSAlgorithm::StepAfterSubsetLoop ( int a_iteration )

protectedvirtual

Reimplemented from vAlgorithm.

Definition at line 1887 of file code/src/algorithm/iRCPGSAlgorithm.cc.

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◆ StepBeforeIterationLoop() [1/2]

int iRCPGSAlgorithm::StepBeforeIterationLoop ( )

protectedvirtual

This function is called at the beginning of the RunCPU function.

Returns: 0 if success, positive value otherwise.

Reimplemented from vAlgorithm.

Definition at line 695 of file code/src/algorithm/iRCPGSAlgorithm.cc.

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◆ StepBeforeIterationLoop() [2/2]

int iRCPGSAlgorithm::StepBeforeIterationLoop ( )

protectedvirtual

This function is called at the beginning of the RunCPU function.

Returns: 0 if success, positive value otherwise.

Reimplemented from vAlgorithm.

◆ StepBeforeSubsetLoop() [1/2]

int iRCPGSAlgorithm::StepBeforeSubsetLoop ( int a_iteration )

protectedvirtual

Reimplemented from vAlgorithm.

Definition at line 1876 of file code/src/algorithm/iRCPGSAlgorithm.cc.

◆ StepBeforeSubsetLoop() [2/2]

int iRCPGSAlgorithm::StepBeforeSubsetLoop ( int a_iteration )

protectedvirtual

Reimplemented from vAlgorithm.

◆ StepImageOutput() [1/2]

int iRCPGSAlgorithm::StepImageOutput	(	int	a_iteration,
		int	a_subset = `-1`
	)

protectedvirtual

Implements vAlgorithm.

Definition at line 1915 of file code/src/algorithm/iRCPGSAlgorithm.cc.

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◆ StepImageOutput() [2/2]

int iRCPGSAlgorithm::StepImageOutput	(	int	a_iteration,
		int	a_subset = `-1`
	)

protectedvirtual

Implements vAlgorithm.

◆ StepInnerLoopInsideSubsetLoop() [1/2]

int iRCPGSAlgorithm::StepInnerLoopInsideSubsetLoop	(	int	a_iteration,
		int	a_subset,
		int	a_bed
	)

protectedvirtual

Implements vAlgorithm.

Definition at line 756 of file code/src/algorithm/iRCPGSAlgorithm.cc.

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◆ StepInnerLoopInsideSubsetLoop() [2/2]

int iRCPGSAlgorithm::StepInnerLoopInsideSubsetLoop	(	int	a_iteration,
		int	a_subset,
		int	a_bed
	)

protectedvirtual

Implements vAlgorithm.

◆ StepPostProcessInsideSubsetLoop() [1/2]

int iRCPGSAlgorithm::StepPostProcessInsideSubsetLoop	(	int	a_iteration,
		int	a_subset
	)

protectedvirtual

Reimplemented from vAlgorithm.

Definition at line 772 of file code/src/algorithm/iRCPGSAlgorithm.cc.

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◆ StepPostProcessInsideSubsetLoop() [2/2]

int iRCPGSAlgorithm::StepPostProcessInsideSubsetLoop	(	int	a_iteration,
		int	a_subset
	)

protectedvirtual

Reimplemented from vAlgorithm.

◆ StepPreProcessInsideSubsetLoop() [1/2]

int iRCPGSAlgorithm::StepPreProcessInsideSubsetLoop	(	int	a_iteration,
		int	a_subset
	)

protectedvirtual

Reimplemented from vAlgorithm.

◆ StepPreProcessInsideSubsetLoop() [2/2]

int iRCPGSAlgorithm::StepPreProcessInsideSubsetLoop	(	int	a_iteration,
		int	a_subset
	)

protectedvirtual

Reimplemented from vAlgorithm.

Definition at line 740 of file code/src/algorithm/iRCPGSAlgorithm.cc.

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◆ UpdateVisitedVoxels() [1/2]

int iRCPGSAlgorithm::UpdateVisitedVoxels ( )

private

◆ UpdateVisitedVoxels() [2/2]

int iRCPGSAlgorithm::UpdateVisitedVoxels ( )

private

Check for voxels which do not contribute to recorded observed data.

Returns: 0 if success, positive value otherwise.

Definition at line 1397 of file code/src/algorithm/iRCPGSAlgorithm.cc.

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Member Data Documentation

◆ m4p_EventsBackprojectionTrace

INTNB **** iRCPGSAlgorithm::m4p_EventsBackprojectionTrace

private

Trace of the backprojection destination for each observed count at previous iteration, Number of beds x Number of events x Number of TOF bins x Number of counts

Definition at line 136 of file code/include/algorithm/iRCPGSAlgorithm.hh.

◆ m_backprojection

int iRCPGSAlgorithm::m_backprojection

private

flag describing the multinomial backprojection of the current iteration/subset data (sampling of conditional complete data): 0 = the previous backprojection state is cleared, as for ML-EM 1 = update of the previous backprojection state 2 = backprojection marginalized over cluster intensity, implies update of the previous backprojection state

Definition at line 111 of file code/include/algorithm/iRCPGSAlgorithm.hh.

◆ m_currentMeanClusterVolume

HPFLTNB iRCPGSAlgorithm::m_currentMeanClusterVolume

private

helper variable for the average cluster volume after each iteration/subset

Definition at line 141 of file code/include/algorithm/iRCPGSAlgorithm.hh.

◆ m_ddCRP

int iRCPGSAlgorithm::m_ddCRP

private

flag describing the ddCRP prior : 0 = no ddCRP, 1 = original ddCRP, 2 = modified ddCRP

Definition at line 110 of file code/include/algorithm/iRCPGSAlgorithm.hh.

◆ m_ddcrpAlpha

HPFLTNB iRCPGSAlgorithm::m_ddcrpAlpha

private

ddCRP : the unnormalized probability of drawing a self link

Definition at line 118 of file code/include/algorithm/iRCPGSAlgorithm.hh.

◆ m_ddcrpAlphaIncrement

HPFLTNB iRCPGSAlgorithm::m_ddcrpAlphaIncrement

private

Multiplicative increment for optimizing the ddCRP alpha parameter through iterations

Definition at line 120 of file code/include/algorithm/iRCPGSAlgorithm.hh.

◆ m_ddcrpLogAlpha

HPFLTNB iRCPGSAlgorithm::m_ddcrpLogAlpha

private

helper variable for precomputed log of ddCRP : the probability of drawing a self link (not normalized)

Definition at line 140 of file code/include/algorithm/iRCPGSAlgorithm.hh.

◆ m_gammaRate

HPFLTNB iRCPGSAlgorithm::m_gammaRate

private

Gamma prior distribution rate parameter

Definition at line 117 of file code/include/algorithm/iRCPGSAlgorithm.hh.

◆ m_gammaShape

HPFLTNB iRCPGSAlgorithm::m_gammaShape

private

Gamma prior distribution shape parameter

Definition at line 116 of file code/include/algorithm/iRCPGSAlgorithm.hh.

◆ m_meanClusterVolumeMax

HPFLTNB iRCPGSAlgorithm::m_meanClusterVolumeMax

private

Maximum threshold for average cluster volume (in mm3), used for adapting ddCRP alpha automatically through iterations

Definition at line 143 of file code/include/algorithm/iRCPGSAlgorithm.hh.

◆ m_meanClusterVolumeMin

HPFLTNB iRCPGSAlgorithm::m_meanClusterVolumeMin

private

Minimum threshold for average cluster volume (in mm3), used for adapting ddCRP alpha automatically through iterations

Definition at line 142 of file code/include/algorithm/iRCPGSAlgorithm.hh.

◆ m_multiModalLag

INTNB iRCPGSAlgorithm::m_multiModalLag

private

Number of iterations after which the multimodal images start affecting voxels clustering

Definition at line 119 of file code/include/algorithm/iRCPGSAlgorithm.hh.

◆ m_neighbourhood

int iRCPGSAlgorithm::m_neighbourhood

private

Number of voxels in the neighbourhood

Definition at line 115 of file code/include/algorithm/iRCPGSAlgorithm.hh.

◆ mp_clusterCount

INTNB * iRCPGSAlgorithm::mp_clusterCount

private

Number of voxels per cluster

Definition at line 130 of file code/include/algorithm/iRCPGSAlgorithm.hh.

◆ mp_clusterN

HPFLTNB ** iRCPGSAlgorithm::mp_clusterN

private

Ns : sum over cluster voxels and all LORs of latent backprojected variable (complete data), requires HPFLTNB precision, can be threaded

Definition at line 127 of file code/include/algorithm/iRCPGSAlgorithm.hh.

◆ mp_clusterSensitivity

HPFLTNB * iRCPGSAlgorithm::mp_clusterSensitivity

private

Sensitivity : sum over cluster voxels and all LORs of system matrix components, requires HPFLTNB precision

Definition at line 128 of file code/include/algorithm/iRCPGSAlgorithm.hh.

◆ mp_clusterValues

HPFLTNB * iRCPGSAlgorithm::mp_clusterValues

private

Values (here voxel intensities) associated with each cluster

Definition at line 126 of file code/include/algorithm/iRCPGSAlgorithm.hh.

◆ mp_listEventsIndices

INTNB ** iRCPGSAlgorithm::mp_listEventsIndices

private

List of events indices, per bed, used for random shuffling

Definition at line 135 of file code/include/algorithm/iRCPGSAlgorithm.hh.

◆ mp_listRelevantVoxelIndices

bool * iRCPGSAlgorithm::mp_listRelevantVoxelIndices

private

Indices of voxels which will be taken into account in the algorithm; all the other voxels are regarded as background and set to 0

Definition at line 138 of file code/include/algorithm/iRCPGSAlgorithm.hh.

◆ mp_listVoxelIndices

INTNB * iRCPGSAlgorithm::mp_listVoxelIndices

private

List of voxel indices, used for random shuffling

Definition at line 134 of file code/include/algorithm/iRCPGSAlgorithm.hh.

◆ mp_multiModalNoiseSigma

HPFLTNB * iRCPGSAlgorithm::mp_multiModalNoiseSigma

private

Standard deviation of Gaussian noise in multimodal images

Definition at line 122 of file code/include/algorithm/iRCPGSAlgorithm.hh.

◆ mp_multiModalParam

HPFLTNB * iRCPGSAlgorithm::mp_multiModalParam

private

Parameter for the standard deviation of the prior on multimodal images

Definition at line 123 of file code/include/algorithm/iRCPGSAlgorithm.hh.

◆ mp_nextLink

INTNB * iRCPGSAlgorithm::mp_nextLink

private

Mapping : voxel index -> next voxel index (link from this voxel to another voxel)

Definition at line 131 of file code/include/algorithm/iRCPGSAlgorithm.hh.

◆ mp_permanentBackwardImage

FLTNB * iRCPGSAlgorithm::mp_permanentBackwardImage

private

A buffer image used for holding the complete up-to-date backward image at any time. It is updated at each iteration/subset, and used in backprojection modes 1 and 2

Definition at line 144 of file code/include/algorithm/iRCPGSAlgorithm.hh.

◆ mp_voxelClusterMapping

INTNB * iRCPGSAlgorithm::mp_voxelClusterMapping

private

Mapping : voxel index -> cluster index

Definition at line 125 of file code/include/algorithm/iRCPGSAlgorithm.hh.

◆ mpp_clusterMultiModal

HPFLTNB ** iRCPGSAlgorithm::mpp_clusterMultiModal

private

Multimodal image(s) : sum over cluster voxels, requires HPFLTNB precision

Definition at line 129 of file code/include/algorithm/iRCPGSAlgorithm.hh.

◆ mpv_parentLinks

vector< INTNB > * iRCPGSAlgorithm::mpv_parentLinks

private

Mapping : voxel index -> list of previous voxels (links from other voxels to this voxel)

Definition at line 132 of file code/include/algorithm/iRCPGSAlgorithm.hh.

◆ mv_newClusters

vector< INTNB > iRCPGSAlgorithm::mv_newClusters

private

Indices of free available (empty) clusters (the number of clusters <= the number of voxels + 1)

Definition at line 133 of file code/include/algorithm/iRCPGSAlgorithm.hh.

◆ temp_count_multimodal

HPFLTNB * iRCPGSAlgorithm::temp_count_multimodal

private

helper variable for the second sampling step, just to avoid allocating repeatedly >

Definition at line 139 of file code/include/algorithm/iRCPGSAlgorithm.hh.

The documentation for this class was generated from the following files:

Public Member Functions

Protected Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ iRCPGSAlgorithm() [1/2]

◆ ~iRCPGSAlgorithm() [1/2]

◆ iRCPGSAlgorithm() [2/2]

◆ ~iRCPGSAlgorithm() [2/2]

Member Function Documentation

◆ ComputeFellowVoxelsList() [1/2]

◆ ComputeFellowVoxelsList() [2/2]

◆ ComputeSumsPerClusters() [1/2]

◆ ComputeSumsPerClusters() [2/2]

◆ GenerateCurrentImage() [1/2]

◆ GenerateCurrentImage() [2/2]

◆ InitializeHelperVar() [1/2]

◆ InitializeHelperVar() [2/2]

◆ InitSpecificOptions() [1/2]

◆ InitSpecificOptions() [2/2]

◆ ProcessMultiModalInfo() [1/2]

◆ ProcessMultiModalInfo() [2/2]

◆ ReadConfigurationFile() [1/2]

◆ ReadConfigurationFile() [2/2]

◆ SampleConditionalClustering() [1/2]

◆ SampleConditionalClustering() [2/2]

◆ SampleConditionalClusterIntensity() [1/2]

◆ SampleConditionalClusterIntensity() [2/2]

◆ SampleConditionalCompleteData() [1/2]

◆ SampleConditionalCompleteData() [2/2]

◆ SaveIntermediaryData() [1/2]

◆ SaveIntermediaryData() [2/2]

◆ ShowHelpSpecific() [1/2]

◆ ShowHelpSpecific() [2/2]

◆ StepAfterIterationLoop() [1/2]

◆ StepAfterIterationLoop() [2/2]

◆ StepAfterSubsetLoop() [1/2]

◆ StepAfterSubsetLoop() [2/2]

◆ StepBeforeIterationLoop() [1/2]

◆ StepBeforeIterationLoop() [2/2]

◆ StepBeforeSubsetLoop() [1/2]

◆ StepBeforeSubsetLoop() [2/2]

◆ StepImageOutput() [1/2]

◆ StepImageOutput() [2/2]

◆ StepInnerLoopInsideSubsetLoop() [1/2]

◆ StepInnerLoopInsideSubsetLoop() [2/2]

◆ StepPostProcessInsideSubsetLoop() [1/2]

◆ StepPostProcessInsideSubsetLoop() [2/2]

◆ StepPreProcessInsideSubsetLoop() [1/2]

◆ StepPreProcessInsideSubsetLoop() [2/2]

◆ UpdateVisitedVoxels() [1/2]

◆ UpdateVisitedVoxels() [2/2]

Member Data Documentation

◆ m4p_EventsBackprojectionTrace

◆ m_backprojection

◆ m_currentMeanClusterVolume

◆ m_ddCRP

◆ m_ddcrpAlpha

◆ m_ddcrpAlphaIncrement

◆ m_ddcrpLogAlpha

◆ m_gammaRate

◆ m_gammaShape

◆ m_meanClusterVolumeMax

◆ m_meanClusterVolumeMin

◆ m_multiModalLag

◆ m_neighbourhood

◆ mp_clusterCount

◆ mp_clusterN

◆ mp_clusterSensitivity

◆ mp_clusterValues

◆ mp_listEventsIndices

◆ mp_listRelevantVoxelIndices

◆ mp_listVoxelIndices

◆ mp_multiModalNoiseSigma

◆ mp_multiModalParam

◆ mp_nextLink

◆ mp_permanentBackwardImage

◆ mp_voxelClusterMapping