This class implements a general linear dynamic model applied between the images of a dynamic acquisition
The model is applied on a voxel-by-voxel basis between the images of the frames and/or respiratory/cardiac gates. More...

#include <iLinearModel.hh>

Inheritance diagram for iLinearModel:

Collaboration diagram for iLinearModel:

Public Member Functions
	iLinearModel ()
	Constructor of iLinearModel. Simply set all data members to default values. More...

	~iLinearModel ()
	Destructor of iLinearModel. More...

int	CheckSpecificParameters ()
	This function is used to check whether all member variables have been correctly initialized or not. More...

int	CheckSpecificParametersForAllLinearModels ()
	This function is used to check parameters for all Linear Models. . More...

virtual int	ReadAndCheckConfigurationFileSpecific ()
	This function is used to read options from a configuration file. More...

int	ReadAndCheckOptionsList (string a_listOptions)

int	ReadAndCheckConfigurationFileSpecificToAllLinearModels ()
	This function is used to read parameters that are generic for all Linear Models. . More...

int	InitializeSpecific ()
	This function is used to initialize the parametric images and basis functions for all Linear Models. More...

int	InitializeSpecificToAllLinearModels ()
	This function is used to initialize the parametric images and basis functions for all Linear Models. More...

void	ShowBasisFunctions ()
	This function is used to print the basis functions. More...

void	ShowHelpModelSpecific ()
	This function is used to print out specific help about the dynamic model and its options. It is pure virtual so must be implemented by children. More...

int	EstimateModelParameters (oImageSpace *ap_Image, int a_ite, int a_sset)

int	EstimateImageWithModel (oImageSpace *ap_Image, int a_ite, int a_sset)

int	NestedEM (oImageSpace *ap_ImageS, int a_ite)

int	EstimateParametersWithNNLS (oImageSpace *ap_ImageS, int a_ite)

int	Patlak_LS (oImageSpace *ap_ImageS, int a_ite)

	iLinearModel ()

	~iLinearModel ()

int	CheckSpecificParameters ()
	This function is used to check the parameters of the child functions before initialization if required. More...

int	CheckSpecificParametersForAllLinearModels ()

virtual int	ReadAndCheckConfigurationFileSpecific ()
	This function is used to read options from a configuration file. It is pure virtual so must be implemented by children. More...

int	ReadAndCheckOptionsList (string a_listOptions)

int	ReadAndCheckConfigurationFileSpecificToAllLinearModels ()

int	InitializeSpecific ()
	A private function used to initialize everything specific to the child model. More...

int	InitializeSpecificToAllLinearModels ()

void	ShowBasisFunctions ()

void	ShowHelpModelSpecific ()
	This function is used to print out specific help about the dynamic model and its options. It is pure virtual so must be implemented by children. More...

int	EstimateModelParameters (oImageSpace *ap_Image, int a_ite, int a_sset)

int	EstimateImageWithModel (oImageSpace *ap_Image, int a_ite, int a_sset)

int	NestedEM (oImageSpace *ap_ImageS, int a_ite)

int	EstimateParametersWithNNLS (oImageSpace *ap_ImageS, int a_ite)

int	Patlak_LS (oImageSpace *ap_ImageS, int a_ite)

Public Member Functions inherited from vDynamicModel
	vDynamicModel ()
	Constructor of vDynamicModel. Simply set all data members to default values. More...

virtual	~vDynamicModel ()
	Destructor of vDynamicModel. More...

void	SetImageDimensionsAndQuantification (oImageDimensionsAndQuantification *ap_ImageDimensionsAndQuantification)

void	SetVerbose (int a_verbose)

virtual int	CheckParameters ()
	This function is used to check parameters after the latter have been all set using Set functions. More...

int	ReadAndCheckConfigurationFile (string a_fileOptions)

int	Initialize ()
	A public function used to initialize the dynamic model. More...

void	ShowHelp ()
	This function is used to print out general help about dynamic models. More...

virtual int	EstimateModel (oImageSpace *ap_Image, int a_ite, int a_sset)

virtual int	EstimateImage (oImageSpace *ap_Image, int a_ite, int a_sset)

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

virtual int	ApplyOutputFOVMaskingOnParametricImages ()
	Mask the outside of the transaxial FOV based on the m_fovOutPercent. More...

bool	GetAICflag ()

bool	GetModelBasisFunctionsRequiredFlag ()

int	GetNbTimeBasisFunctions ()

FLTNB **	GetTimeBasisFunctions ()

virtual void	ComputeOutputParImage ()
	Compute output image using the m2p_parametricImages matrix Store the result in the m2p_outputParImages matrix. More...

void	SetUseModelInReconstruction (bool a_useModelInReconstruction)

int	NNLS (FLTNB *A, int m, int n, FLTNB B, FLTNB X, FLTNB rnorm, FLTNB wp, FLTNB zzp, int *indexp)

	vDynamicModel ()

virtual	~vDynamicModel ()

void	SetImageDimensionsAndQuantification (oImageDimensionsAndQuantification *ap_ImageDimensionsAndQuantification)

void	SetVerbose (int a_verbose)

virtual int	CheckParameters ()

int	ReadAndCheckConfigurationFile (string a_fileOptions)

int	Initialize ()

void	ShowHelp ()

virtual int	EstimateModel (oImageSpace *ap_Image, int a_ite, int a_sset)

virtual int	EstimateImage (oImageSpace *ap_Image, int a_ite, int a_sset)

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

virtual int	ApplyOutputFOVMaskingOnParametricImages ()

bool	GetAICflag ()

bool	GetModelBasisFunctionsRequiredFlag ()

int	GetNbTimeBasisFunctions ()

FLTNB **	GetTimeBasisFunctions ()

virtual void	ComputeOutputParImage ()

void	SetUseModelInReconstruction (bool a_useModelInReconstruction)

int	NNLS (FLTNB *A, int m, int n, FLTNB B, FLTNB X, FLTNB rnorm, FLTNB wp, FLTNB zzp, int *indexp)

Protected Attributes
int	m_OptimisationMethod

int	m_nbRgateBF

int	m_nbCgateBF

FLTNB **	m2p_respBasisFunctions

FLTNB **	m2p_cardBasisFunctions

FLTNB *	mp_corrBasisCoeffs

FLTNB *	mp_corrBasisFunctions

uint32_t	m_nbLinearModelCycles

int	m_basisFunctionsUpdStartIte

int	m_basisFunctionsUpdRatio

int	m_basisFunctionsUpdIdx

Protected Attributes inherited from vDynamicModel
oImageDimensionsAndQuantification *	mp_ID

int	m_verbose

int	m_nbTimeBF

int	m_nbWeightFactors

int	m_nbModelParam

int	m_nbRGModelParam

int	m_nbCGModelParam

string	m_AICfile

oArterialInputCurve *	mp_ArterialInputCurve

FLTNB **	m2p_parametricImages

FLTNB *	mp_blackListedvoxelsImage

FLTNB **	m2p_nestedModelTimeBasisFunctions

FLTNB **	m2p_outputParImages

FLTNB **	m2p_RGParametricImages

FLTNB **	m2p_CGParametricImages

string	m_fileOptions

string	m_listOptions

bool	m_checked

bool	m_initialized

bool	m_useModelInReconstruction

bool	m_saveParImageFlag

bool	m_saveBlacklistedImageMaskFlag

bool	m_AICfileProvided

bool	m_ModelSpecificBasisFunctionsRequired

bool	m_noImageUpdateFlag

bool	m_noParametersUpdateFlag

int	m_startIteUpdateFlag

FLTNB *	mp_maskModel

INTNB	m_nbVoxelsMask

FLTNB *	mp_w

FLTNB ***	m3p_nnlsA

FLTNB **	m2p_nnlsB

FLTNB **	m2p_nnlsMat

FLTNB **	m2p_nnlsX

FLTNB **	m2p_nnlsWp

int **	m2p_nnlsIdx

uint16_t	m_nnlsN =0

Detailed Description

This class implements a general linear dynamic model applied between the images of a dynamic acquisition
The model is applied on a voxel-by-voxel basis between the images of the frames and/or respiratory/cardiac gates.

Definition at line 40 of file code/include/dynamic/iLinearModel.hh.

Constructor & Destructor Documentation

◆ iLinearModel() [1/2]

iLinearModel::iLinearModel ( )

Constructor of iLinearModel. Simply set all data members to default values.

Definition at line 19 of file code/src/dynamic/iLinearModel.cc.

◆ ~iLinearModel() [1/2]

iLinearModel::~iLinearModel ( )

Destructor of iLinearModel.

Definition at line 54 of file code/src/dynamic/iLinearModel.cc.

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◆ iLinearModel() [2/2]

iLinearModel::iLinearModel ( )

◆ ~iLinearModel() [2/2]

iLinearModel::~iLinearModel ( )

Member Function Documentation

◆ CheckSpecificParameters() [1/2]

int iLinearModel::CheckSpecificParameters ( )

virtual

This function is used to check whether all member variables have been correctly initialized or not.

Returns: 0 if success, positive value otherwise.

Implements vDynamicModel.

Reimplemented in iLinearModelTemplate, iLinearModelTemplate, iLinearPatlakModel, iLinearPatlakModel, iLinearSpectralModel, and iLinearSpectralModel.

Definition at line 420 of file code/src/dynamic/iLinearModel.cc.

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◆ CheckSpecificParameters() [2/2]

int iLinearModel::CheckSpecificParameters ( )

virtual

This function is used to check the parameters of the child functions before initialization if required.

It could be overloaded by the child if needed. Default implementation is empty and return 0.

Returns: 0 if success, other value otherwise.

Implements vDynamicModel.

Reimplemented in iLinearModelTemplate, iLinearPatlakModel, and iLinearSpectralModel.

◆ CheckSpecificParametersForAllLinearModels() [1/2]

int iLinearModel::CheckSpecificParametersForAllLinearModels ( )

This function is used to check parameters for all Linear Models.
.

Returns: 0 if success, other value otherwise.

Definition at line 447 of file code/src/dynamic/iLinearModel.cc.

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◆ CheckSpecificParametersForAllLinearModels() [2/2]

int iLinearModel::CheckSpecificParametersForAllLinearModels ( )

◆ EstimateImageWithModel() [1/2]

int iLinearModel::EstimateImageWithModel	(	oImageSpace *	ap_Image,
		int	a_ite,
		int	a_sset
	)

virtual

Implements vDynamicModel.

Definition at line 1881 of file code/src/dynamic/iLinearModel.cc.

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◆ EstimateImageWithModel() [2/2]

int iLinearModel::EstimateImageWithModel	(	oImageSpace *	ap_Image,
		int	a_ite,
		int	a_sset
	)

virtual

Implements vDynamicModel.

◆ EstimateModelParameters() [1/2]

int iLinearModel::EstimateModelParameters	(	oImageSpace *	ap_Image,
		int	a_ite,
		int	a_sset
	)

virtual

Implements vDynamicModel.

Definition at line 990 of file code/src/dynamic/iLinearModel.cc.

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◆ EstimateModelParameters() [2/2]

int iLinearModel::EstimateModelParameters	(	oImageSpace *	ap_Image,
		int	a_ite,
		int	a_sset
	)

virtual

Implements vDynamicModel.

◆ EstimateParametersWithNNLS() [1/2]

int iLinearModel::EstimateParametersWithNNLS	(	oImageSpace *	ap_ImageS,
		int	a_ite
	)

◆ EstimateParametersWithNNLS() [2/2]

int iLinearModel::EstimateParametersWithNNLS	(	oImageSpace *	ap_ImageS,
		int	a_ite
	)

Definition at line 1569 of file code/src/dynamic/iLinearModel.cc.

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◆ InitializeSpecific() [1/2]

int iLinearModel::InitializeSpecific ( )

virtual

A private function used to initialize everything specific to the child model.

This function is used to initialize everything specific to the model that should be initialized. It is called by the Initialize() function. It is pure virtual so is implemented only by children.

Returns: An integer reflecting the initialization status; 0 if no problem, another value otherwise.

Implements vDynamicModel.

Reimplemented in iLinearModelTemplate, iLinearPatlakModel, and iLinearSpectralModel.

◆ InitializeSpecific() [2/2]

int iLinearModel::InitializeSpecific ( )

virtual

This function is used to initialize the parametric images and basis functions for all Linear Models.

Returns: 0 if success, other value otherwise.; 0 if success, other value otherwise.

Implements vDynamicModel.

Reimplemented in iLinearModelTemplate, iLinearModelTemplate, iLinearPatlakModel, iLinearPatlakModel, iLinearSpectralModel, and iLinearSpectralModel.

Definition at line 951 of file code/src/dynamic/iLinearModel.cc.

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◆ InitializeSpecificToAllLinearModels() [1/2]

int iLinearModel::InitializeSpecificToAllLinearModels ( )

◆ InitializeSpecificToAllLinearModels() [2/2]

int iLinearModel::InitializeSpecificToAllLinearModels ( )

This function is used to initialize the parametric images and basis functions for all Linear Models.

Returns: 0 if success, other value otherwise.; 0 if success, other value otherwise.

Definition at line 520 of file code/src/dynamic/iLinearModel.cc.

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◆ NestedEM() [1/2]

int iLinearModel::NestedEM	(	oImageSpace *	ap_ImageS,
		int	a_ite
	)

Definition at line 1072 of file code/src/dynamic/iLinearModel.cc.

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◆ NestedEM() [2/2]

int iLinearModel::NestedEM	(	oImageSpace *	ap_ImageS,
		int	a_ite
	)

◆ Patlak_LS() [1/2]

int iLinearModel::Patlak_LS	(	oImageSpace *	ap_ImageS,
		int	a_ite
	)

◆ Patlak_LS() [2/2]

int iLinearModel::Patlak_LS	(	oImageSpace *	ap_ImageS,
		int	a_ite
	)

Definition at line 1808 of file code/src/dynamic/iLinearModel.cc.

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◆ ReadAndCheckConfigurationFileSpecific() [1/2]

virtual int iLinearModel::ReadAndCheckConfigurationFileSpecific ( )

virtual

This function is used to read options from a configuration file.
It is pure virtual so must be implemented by children.

Returns: 0 if success, other value otherwise.

Implements vDynamicModel.

Reimplemented in iLinearModelTemplate, iLinearModelTemplate, iLinearPatlakModel, iLinearPatlakModel, iLinearSpectralModel, and iLinearSpectralModel.

◆ ReadAndCheckConfigurationFileSpecific() [2/2]

int iLinearModel::ReadAndCheckConfigurationFileSpecific ( )

virtual

This function is used to read options from a configuration file.

Returns: 0 if success, other value otherwise.

Implements vDynamicModel.

Reimplemented in iLinearModelTemplate, iLinearModelTemplate, iLinearPatlakModel, iLinearPatlakModel, iLinearSpectralModel, and iLinearSpectralModel.

Definition at line 212 of file code/src/dynamic/iLinearModel.cc.

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◆ ReadAndCheckConfigurationFileSpecificToAllLinearModels() [1/2]

int iLinearModel::ReadAndCheckConfigurationFileSpecificToAllLinearModels ( )

This function is used to read parameters that are generic for all Linear Models.
.

Returns: 0 if success, other value otherwise.

Definition at line 236 of file code/src/dynamic/iLinearModel.cc.

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◆ ReadAndCheckConfigurationFileSpecificToAllLinearModels() [2/2]

int iLinearModel::ReadAndCheckConfigurationFileSpecificToAllLinearModels ( )

◆ ReadAndCheckOptionsList() [1/2]

int iLinearModel::ReadAndCheckOptionsList ( string a_listOptions )

virtual

Implements vDynamicModel.

Reimplemented in iLinearModelTemplate, iLinearModelTemplate, iLinearPatlakModel, iLinearPatlakModel, iLinearSpectralModel, and iLinearSpectralModel.

Definition at line 391 of file code/src/dynamic/iLinearModel.cc.

◆ ReadAndCheckOptionsList() [2/2]

int iLinearModel::ReadAndCheckOptionsList ( string a_listOptions )

virtual

Implements vDynamicModel.

Reimplemented in iLinearModelTemplate, iLinearPatlakModel, and iLinearSpectralModel.

◆ ShowBasisFunctions() [1/2]

void iLinearModel::ShowBasisFunctions ( )

This function is used to print the basis functions.

Definition at line 919 of file code/src/dynamic/iLinearModel.cc.

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◆ ShowBasisFunctions() [2/2]

void iLinearModel::ShowBasisFunctions ( )

◆ ShowHelpModelSpecific() [1/2]

void iLinearModel::ShowHelpModelSpecific ( )

virtual

This function is used to print out specific help about the dynamic model and its options. It is pure virtual so must be implemented by children.

Implements vDynamicModel.

Reimplemented in iLinearModelTemplate, iLinearModelTemplate, iLinearPatlakModel, iLinearPatlakModel, iLinearSpectralModel, and iLinearSpectralModel.

Definition at line 117 of file code/src/dynamic/iLinearModel.cc.

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◆ ShowHelpModelSpecific() [2/2]

void iLinearModel::ShowHelpModelSpecific ( )

virtual

This function is used to print out specific help about the dynamic model and its options. It is pure virtual so must be implemented by children.

Implements vDynamicModel.

Reimplemented in iLinearModelTemplate, iLinearPatlakModel, and iLinearSpectralModel.

Member Data Documentation

◆ m2p_cardBasisFunctions

FLTNB ** iLinearModel::m2p_cardBasisFunctions

protected

Vector containing the cardiac gating model temporal basis functions
2 pointers:
1: index of the temporal function
2: coefficient of the functions for each cardiac gate

Definition at line 183 of file code/include/dynamic/iLinearModel.hh.

◆ m2p_respBasisFunctions

FLTNB ** iLinearModel::m2p_respBasisFunctions

protected

Vector containing the respiratory gating model temporal basis functions
2 pointers:
1: index of the temporal function
2: coefficient of the functions for each respiratory gate

Definition at line 179 of file code/include/dynamic/iLinearModel.hh.

◆ m_basisFunctionsUpdIdx

int iLinearModel::m_basisFunctionsUpdIdx

protected

Index to compute the ratio for the parametric images/basis functions updates cycle

Definition at line 195 of file code/include/dynamic/iLinearModel.hh.

◆ m_basisFunctionsUpdRatio

int iLinearModel::m_basisFunctionsUpdRatio

protected

Ratio for the parametric images/basis functions updates cycle.
Cycles consist in 'm_basisFunctionsUpdRate' iterations of the parametric images, following by 'm_basisFunctionsUpdRate' iterations of the basis functions

Definition at line 193 of file code/include/dynamic/iLinearModel.hh.

◆ m_basisFunctionsUpdStartIte

int iLinearModel::m_basisFunctionsUpdStartIte

protected

Starting iteration for the update of basis functions.
If negative, no update of the basis functions is performed (only parametric images are updated)

Definition at line 191 of file code/include/dynamic/iLinearModel.hh.

◆ m_nbCgateBF

int iLinearModel::m_nbCgateBF

protected

Number of time basis functions applied to cardiac gates in the model

Definition at line 175 of file code/include/dynamic/iLinearModel.hh.

◆ m_nbLinearModelCycles

uint32_t iLinearModel::m_nbLinearModelCycles

protected

Number of iteration of the model (one cycle consists in several updates of either the parametric images or the basis function)

Definition at line 190 of file code/include/dynamic/iLinearModel.hh.

◆ m_nbRgateBF

int iLinearModel::m_nbRgateBF

protected

Number of time basis functions applied to respiratory gates in the model

Definition at line 174 of file code/include/dynamic/iLinearModel.hh.

◆ m_OptimisationMethod

int iLinearModel::m_OptimisationMethod

protected

Number indicating the method to estimate parameters, from the available options.

Definition at line 173 of file code/include/dynamic/iLinearModel.hh.

◆ mp_corrBasisCoeffs

FLTNB * iLinearModel::mp_corrBasisCoeffs

protected

Image matrix containing correction factors for the parametric images updates

Definition at line 188 of file code/include/dynamic/iLinearModel.hh.

◆ mp_corrBasisFunctions

FLTNB * iLinearModel::mp_corrBasisFunctions

protected

Vector containing correction factors for the temporal basis functions updates

Definition at line 189 of file code/include/dynamic/iLinearModel.hh.

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

Public Member Functions

Protected Attributes

Detailed Description

Constructor & Destructor Documentation

◆ iLinearModel() [1/2]

◆ ~iLinearModel() [1/2]

◆ iLinearModel() [2/2]

◆ ~iLinearModel() [2/2]

Member Function Documentation

◆ CheckSpecificParameters() [1/2]

◆ CheckSpecificParameters() [2/2]

◆ CheckSpecificParametersForAllLinearModels() [1/2]

◆ CheckSpecificParametersForAllLinearModels() [2/2]

◆ EstimateImageWithModel() [1/2]

◆ EstimateImageWithModel() [2/2]

◆ EstimateModelParameters() [1/2]

◆ EstimateModelParameters() [2/2]

◆ EstimateParametersWithNNLS() [1/2]

◆ EstimateParametersWithNNLS() [2/2]

◆ InitializeSpecific() [1/2]

◆ InitializeSpecific() [2/2]

◆ InitializeSpecificToAllLinearModels() [1/2]

◆ InitializeSpecificToAllLinearModels() [2/2]

◆ NestedEM() [1/2]

◆ NestedEM() [2/2]

◆ Patlak_LS() [1/2]

◆ Patlak_LS() [2/2]

◆ ReadAndCheckConfigurationFileSpecific() [1/2]

◆ ReadAndCheckConfigurationFileSpecific() [2/2]

◆ ReadAndCheckConfigurationFileSpecificToAllLinearModels() [1/2]

◆ ReadAndCheckConfigurationFileSpecificToAllLinearModels() [2/2]

◆ ReadAndCheckOptionsList() [1/2]

◆ ReadAndCheckOptionsList() [2/2]

◆ ShowBasisFunctions() [1/2]

◆ ShowBasisFunctions() [2/2]

◆ ShowHelpModelSpecific() [1/2]

◆ ShowHelpModelSpecific() [2/2]

Member Data Documentation

◆ m2p_cardBasisFunctions

◆ m2p_respBasisFunctions

◆ m_basisFunctionsUpdIdx

◆ m_basisFunctionsUpdRatio

◆ m_basisFunctionsUpdStartIte

◆ m_nbCgateBF

◆ m_nbLinearModelCycles

◆ m_nbRgateBF

◆ m_OptimisationMethod

◆ mp_corrBasisCoeffs

◆ mp_corrBasisFunctions