This class implements the Patlak model, to model kinetics of irreversible radiotracers. More...

#include <iLinearPatlakModel.hh>

Inheritance diagram for iLinearPatlakModel:

Collaboration diagram for iLinearPatlakModel:

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

	~iLinearPatlakModel ()
	Destructor of iLinearPatlakModel. More...

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

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

int	ReadAndCheckOptionsList (string a_listOptions)

int	InitializeSpecific ()
	This function is used to initialize Patlak parametric images and basis functions. More...

void	ShowHelpModelSpecific ()
	Print out specific help about the implementation of the Patlak model and its initialization. More...

	iLinearPatlakModel ()

	~iLinearPatlakModel ()

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

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

int	ReadAndCheckOptionsList (string a_listOptions)

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

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

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

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

int	ReadAndCheckConfigurationFileSpecificToAllLinearModels ()
	This function is used to read parameters that are generic 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...

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	CheckSpecificParametersForAllLinearModels ()

int	ReadAndCheckConfigurationFileSpecificToAllLinearModels ()

int	InitializeSpecificToAllLinearModels ()

void	ShowBasisFunctions ()

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)

Additional Inherited Members
Protected Attributes inherited from iLinearModel
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 the Patlak model, to model kinetics of irreversible radiotracers.

Definition at line 25 of file code/include/dynamic/iLinearPatlakModel.hh.

Constructor & Destructor Documentation

◆ iLinearPatlakModel() [1/2]

iLinearPatlakModel::iLinearPatlakModel ( )

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

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

◆ ~iLinearPatlakModel() [1/2]

iLinearPatlakModel::~iLinearPatlakModel ( )

Destructor of iLinearPatlakModel.

Definition at line 40 of file code/src/dynamic/iLinearPatlakModel.cc.

◆ iLinearPatlakModel() [2/2]

iLinearPatlakModel::iLinearPatlakModel ( )

◆ ~iLinearPatlakModel() [2/2]

iLinearPatlakModel::~iLinearPatlakModel ( )

Member Function Documentation

◆ CheckSpecificParameters() [1/2]

int iLinearPatlakModel::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.

Reimplemented from iLinearModel.

Definition at line 174 of file code/src/dynamic/iLinearPatlakModel.cc.

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◆ CheckSpecificParameters() [2/2]

int iLinearPatlakModel::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.

Reimplemented from iLinearModel.

◆ InitializeSpecific() [1/2]

int iLinearPatlakModel::InitializeSpecific ( )

virtual

This function is used to initialize Patlak parametric images and basis functions.

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

Reimplemented from iLinearModel.

Definition at line 198 of file code/src/dynamic/iLinearPatlakModel.cc.

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◆ InitializeSpecific() [2/2]

int iLinearPatlakModel::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.

Reimplemented from iLinearModel.

◆ ReadAndCheckConfigurationFileSpecific() [1/2]

int iLinearPatlakModel::ReadAndCheckConfigurationFileSpecific ( )

virtual

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

Returns: 0 if success, other value otherwise.

Reimplemented from iLinearModel.

Definition at line 126 of file code/src/dynamic/iLinearPatlakModel.cc.

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◆ ReadAndCheckConfigurationFileSpecific() [2/2]

int iLinearPatlakModel::ReadAndCheckConfigurationFileSpecific ( )

virtual

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

Returns: 0 if success, other value otherwise.

Reimplemented from iLinearModel.

◆ ReadAndCheckOptionsList() [1/2]

int iLinearPatlakModel::ReadAndCheckOptionsList ( string a_listOptions )

virtual

Reimplemented from iLinearModel.

◆ ReadAndCheckOptionsList() [2/2]

int iLinearPatlakModel::ReadAndCheckOptionsList ( string a_listOptions )

virtual

Reimplemented from iLinearModel.

Definition at line 152 of file code/src/dynamic/iLinearPatlakModel.cc.

◆ ShowHelpModelSpecific() [1/2]

void iLinearPatlakModel::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.

Reimplemented from iLinearModel.

◆ ShowHelpModelSpecific() [2/2]

void iLinearPatlakModel::ShowHelpModelSpecific ( )

virtual

Print out specific help about the implementation of the Patlak model and its initialization.

Reimplemented from iLinearModel.

Definition at line 60 of file code/src/dynamic/iLinearPatlakModel.cc.

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

Public Member Functions

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ iLinearPatlakModel() [1/2]

◆ ~iLinearPatlakModel() [1/2]

◆ iLinearPatlakModel() [2/2]

◆ ~iLinearPatlakModel() [2/2]

Member Function Documentation

◆ CheckSpecificParameters() [1/2]

◆ CheckSpecificParameters() [2/2]

◆ InitializeSpecific() [1/2]

◆ InitializeSpecific() [2/2]

◆ ReadAndCheckConfigurationFileSpecific() [1/2]

◆ ReadAndCheckConfigurationFileSpecific() [2/2]

◆ ReadAndCheckOptionsList() [1/2]

◆ ReadAndCheckOptionsList() [2/2]

◆ ShowHelpModelSpecific() [1/2]

◆ ShowHelpModelSpecific() [2/2]