Base Class for all physiological perfusion models using an Aterial Input Function All AIF based models come with an array of AIF values and the corresponding TimeGrid ( AIF(t)) This class provides functions for setting the AIF Values and optionally a specific AIF TimeGrid. It also provides a method for interpolation of the AIF source array to a specified Timegrid that differs from AIFTimeGrid. The AIF must be set with an itk::Array. If no AIFTimeGrid is specified with the Setter, it is assumed that the AIFTimeGrid is the same as the ModelTimegrid (e.g. AIF is derived from data set to be fitted). In this case, AIFvalues must have the same length as ModelTimeGrid, otherwise an exception is generated. More...

#include <mitkAIFBasedModelBase.h>

Inheritance diagram for mitk::AIFBasedModelBase:

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Collaboration diagram for mitk::AIFBasedModelBase:

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Public Types
typedef AIFBasedModelBase	Self

typedef ModelBase	Superclass

typedef itk::SmartPointer< Self >	Pointer

typedef itk::SmartPointer< const Self >	ConstPointer

typedef itk::Array< double >	AterialInputFunctionType

Public Types inherited from mitk::ModelBase
typedef ModelBase	Self

typedef itk::Object	Superclass

typedef itk::SmartPointer< Self >	Pointer

typedef itk::SmartPointer< const Self >	ConstPointer

typedef ModelTraitsInterface::ModelResultType	ModelResultType

typedef ModelTraitsInterface::ParameterValueType	ParameterValueType

typedef ModelTraitsInterface::ParametersType	ParametersType

typedef itk::Array< double >	TimeGridType

typedef ModelTraitsInterface::ParameterNameType	ParameterNameType

typedef ModelTraitsInterface::ParameterNamesType	ParameterNamesType

typedef ModelTraitsInterface::ParametersSizeType	ParametersSizeType

typedef ModelTraitsInterface::DerivedParameterNamesType	DerivedParameterNamesType

typedef ModelTraitsInterface::DerivedParametersSizeType	DerivedParametersSizeType

typedef double	StaticParameterValueType

typedef std::vector< StaticParameterValueType >	StaticParameterValuesType

typedef std::map< ParameterNameType, StaticParameterValuesType >	StaticParameterMapType

typedef double	DerivedParameterValueType

typedef std::map< ParameterNameType, DerivedParameterValueType >	DerivedParameterMapType

Public Types inherited from mitk::ModelTraitsInterface
typedef itk::Array< double >	ModelResultType

using	ParameterValueType = double

typedef itk::Array< ParameterValueType >	ParametersType

typedef std::string	ParameterNameType

typedef std::vector< ParameterNameType >	ParameterNamesType

typedef ParametersType::SizeValueType	ParametersSizeType

typedef ParameterNamesType	DerivedParameterNamesType

typedef ParametersSizeType	DerivedParametersSizeType

typedef std::map< ParameterNameType, double >	ParamterScaleMapType

typedef std::map< ParameterNameType, std::string >	ParamterUnitMapType

typedef std::map< ParameterNameType, double >	DerivedParamterScaleMapType

typedef std::map< ParameterNameType, std::string >	DerivedParamterUnitMapType

typedef std::string	FunctionStringType

typedef std::string	ModellClassIDType

Public Member Functions
virtual const char *	GetClassName () const

virtual const AterialInputFunctionType &	GetAterialInputFunctionValues ()

virtual const TimeGridType &	GetAterialInputFunctionTimeGrid ()

virtual void	SetAterialInputFunctionValues (AterialInputFunctionType _arg)

virtual void	SetAterialInputFunctionTimeGrid (TimeGridType _arg)

std::string	GetXAxisName () const override

std::string	GetXAxisUnit () const override

std::string	GetYAxisName () const override

std::string	GetYAxisUnit () const override

const TimeGridType &	GetCurrentAterialInputFunctionTimeGrid () const

const AterialInputFunctionType	GetAterialInputFunction (TimeGridType currentTimeGrid) const

ParameterNamesType	GetStaticParameterNames () const override

ParametersSizeType	GetNumberOfStaticParameters () const override

ParamterUnitMapType	GetStaticParameterUnits () const override

Public Member Functions inherited from mitk::ModelBase
ParamterScaleMapType	GetParameterScales () const override

ParamterUnitMapType	GetParameterUnits () const override

DerivedParamterScaleMapType	GetDerivedParameterScales () const override

DerivedParamterUnitMapType	GetDerivedParameterUnits () const override

std::string	GetModelDisplayName () const override

std::string	GetModelType () const override

FunctionStringType	GetFunctionString () const override

ModellClassIDType	GetClassID () const override

std::string	GetXName () const override

DerivedParameterNamesType	GetDerivedParameterNames () const override

DerivedParametersSizeType	GetNumberOfDerivedParameters () const override

void	SetStaticParameters (const StaticParameterMapType &parameters, bool allParameters=true)

StaticParameterMapType	GetStaticParameters () const

DerivedParameterMapType	GetDerivedParameters (const ParametersType &parameters) const

virtual void	SetTimeGrid (const TimeGridType &grid)

virtual const TimeGridType &	GetTimeGrid ()

ModelResultType	GetSignal (const ParametersType &parameters) const

Public Member Functions inherited from mitk::ModelTraitsInterface
virtual ParameterNamesType	GetParameterNames () const =0

virtual ParametersSizeType	GetNumberOfParameters () const =0

Static Public Attributes
static const std::string	NAME_STATIC_PARAMETER_AIF

static const std::string	NAME_STATIC_PARAMETER_AIFTimeGrid

static const std::string	UNIT_STATIC_PARAMETER_AIF

static const std::string	UNIT_STATIC_PARAMETER_AIFTimeGrid

Protected Member Functions
	AIFBasedModelBase ()

	~AIFBasedModelBase () override

bool	ValidateModel (std::string &error) const override

void	PrintSelf (std::ostream &os, ::itk::Indent indent) const override

void	SetStaticParameter (const ParameterNameType &name, const StaticParameterValuesType &values) override

StaticParameterValuesType	GetStaticParameterValue (const ParameterNameType &name) const override

Protected Member Functions inherited from mitk::ModelBase
virtual ModelResultType	ComputeModelfunction (const ParametersType &parameters) const =0

virtual DerivedParameterMapType	ComputeDerivedParameters (const ParametersType &parameters) const

	ModelBase ()

	~ModelBase () override

void	PrintSelf (std::ostream &os, ::itk::Indent indent) const override

Protected Member Functions inherited from mitk::ModelTraitsInterface
	ModelTraitsInterface ()

virtual	~ModelTraitsInterface ()

Protected Attributes
TimeGridType	m_AterialInputFunctionTimeGrid

AterialInputFunctionType	m_AterialInputFunctionValues

Protected Attributes inherited from mitk::ModelBase
TimeGridType	m_TimeGrid

Detailed Description

Base Class for all physiological perfusion models using an Aterial Input Function All AIF based models come with an array of AIF values and the corresponding TimeGrid ( AIF(t)) This class provides functions for setting the AIF Values and optionally a specific AIF TimeGrid. It also provides a method for interpolation of the AIF source array to a specified Timegrid that differs from AIFTimeGrid. The AIF must be set with an itk::Array. If no AIFTimeGrid is specified with the Setter, it is assumed that the AIFTimeGrid is the same as the ModelTimegrid (e.g. AIF is derived from data set to be fitted). In this case, AIFvalues must have the same length as ModelTimeGrid, otherwise an exception is generated.

Definition at line 31 of file mitkAIFBasedModelBase.h.

Member Typedef Documentation

◆ AterialInputFunctionType

typedef itk::Array<double> mitk::AIFBasedModelBase::AterialInputFunctionType

Typedef for Aterial InputFunction AIF(t)

Definition at line 52 of file mitkAIFBasedModelBase.h.

◆ ConstPointer

typedef itk::SmartPointer< const Self > mitk::AIFBasedModelBase::ConstPointer

Definition at line 38 of file mitkAIFBasedModelBase.h.

◆ Pointer

typedef itk::SmartPointer< Self > mitk::AIFBasedModelBase::Pointer

Definition at line 37 of file mitkAIFBasedModelBase.h.

◆ Self

typedef AIFBasedModelBase mitk::AIFBasedModelBase::Self

Definition at line 35 of file mitkAIFBasedModelBase.h.

◆ Superclass

typedef ModelBase mitk::AIFBasedModelBase::Superclass

Definition at line 36 of file mitkAIFBasedModelBase.h.

Constructor & Destructor Documentation

◆ AIFBasedModelBase()

mitk::AIFBasedModelBase::AIFBasedModelBase ( )

protected

Definition at line 49 of file mitkAIFBasedModelBase.cpp.

◆ ~AIFBasedModelBase()

mitk::AIFBasedModelBase::~AIFBasedModelBase ( )

overrideprotected

Definition at line 53 of file mitkAIFBasedModelBase.cpp.

Member Function Documentation

◆ GetAterialInputFunction()

const mitk::AIFBasedModelBase::AterialInputFunctionType mitk::AIFBasedModelBase::GetAterialInputFunction ( TimeGridType currentTimeGrid ) const

Returns the Aterial Input function matching currentTimeGrid The original values are interpolated to the passed TimeGrid if currentTimeGrid.Size() = 0 , the Original AIF will be returned

Definition at line 71 of file mitkAIFBasedModelBase.cpp.

References GetCurrentAterialInputFunctionTimeGrid(), mitk::InterpolateSignalToNewTimeGrid(), and m_AterialInputFunctionValues.

◆ GetAterialInputFunctionTimeGrid()

virtual const TimeGridType& mitk::AIFBasedModelBase::GetAterialInputFunctionTimeGrid ( )

virtual

◆ GetAterialInputFunctionValues()

virtual const AterialInputFunctionType& mitk::AIFBasedModelBase::GetAterialInputFunctionValues ( )

virtual

◆ GetClassName()

virtual const char* mitk::AIFBasedModelBase::GetClassName ( ) const

virtual

Run-time type information (and related methods).

Reimplemented from mitk::ModelBase.

Reimplemented in mitk::NumericTwoCompartmentExchangeModel, mitk::TwoCompartmentExchangeModel, mitk::ExtendedOneTissueCompartmentModel, mitk::ExtendedToftsModel, mitk::OneTissueCompartmentModel, mitk::StandardToftsModel, mitk::NumericTwoTissueCompartmentModel, mitk::TwoTissueCompartmentFDGModel, and mitk::TwoTissueCompartmentModel.

◆ GetCurrentAterialInputFunctionTimeGrid()

const mitk::AIFBasedModelBase::TimeGridType & mitk::AIFBasedModelBase::GetCurrentAterialInputFunctionTimeGrid ( ) const

Returns the TimeGrid used for the AIF. Either the externally set AIF time grid or the time grid of the model if nothing is set.

Definition at line 58 of file mitkAIFBasedModelBase.cpp.

References m_AterialInputFunctionTimeGrid, and mitk::ModelBase::m_TimeGrid.

Referenced by GetAterialInputFunction().

◆ GetNumberOfStaticParameters()

mitk::AIFBasedModelBase::ParametersSizeType mitk::AIFBasedModelBase::GetNumberOfStaticParameters ( ) const

overridevirtual

Returns the number of static parameters that will be used when using the model to compute the signal (but are not defined via GetSignal()).

Implements mitk::ModelBase.

Reimplemented in mitk::NumericTwoCompartmentExchangeModel.

Definition at line 94 of file mitkAIFBasedModelBase.cpp.

◆ GetStaticParameterNames()

mitk::AIFBasedModelBase::ParameterNamesType mitk::AIFBasedModelBase::GetStaticParameterNames ( ) const

overridevirtual

Returns the names of static parameters that will be used when using the model to compute the signal (but are not defined via GetSignal()).

Implements mitk::ModelBase.

Reimplemented in mitk::NumericTwoCompartmentExchangeModel.

Definition at line 84 of file mitkAIFBasedModelBase.cpp.

References NAME_STATIC_PARAMETER_AIF, and NAME_STATIC_PARAMETER_AIFTimeGrid.

◆ GetStaticParameterUnits()

mitk::AIFBasedModelBase::ParamterUnitMapType mitk::AIFBasedModelBase::GetStaticParameterUnits ( ) const

overridevirtual

Default implementation returns no unit string ("") for every defined parameter.

Reimplemented from mitk::ModelBase.

Definition at line 101 of file mitkAIFBasedModelBase.cpp.

References NAME_STATIC_PARAMETER_AIF, NAME_STATIC_PARAMETER_AIFTimeGrid, UNIT_STATIC_PARAMETER_AIF, and UNIT_STATIC_PARAMETER_AIFTimeGrid.

◆ GetStaticParameterValue()

mitk::AIFBasedModelBase::StaticParameterValuesType mitk::AIFBasedModelBase::GetStaticParameterValue ( const ParameterNameType & name ) const

overrideprotectedvirtual

Helper function called by GetStaticParameters(). Implement in derived classes to realize the concrete retrieval of static parameters.

Implements mitk::ModelBase.

Reimplemented in mitk::NumericTwoCompartmentExchangeModel.

Definition at line 130 of file mitkAIFBasedModelBase.cpp.

References mitk::convertArrayToParameter(), m_AterialInputFunctionTimeGrid, m_AterialInputFunctionValues, NAME_STATIC_PARAMETER_AIF, and NAME_STATIC_PARAMETER_AIFTimeGrid.

◆ GetXAxisName()

std::string mitk::AIFBasedModelBase::GetXAxisName ( ) const

overridevirtual

Default implementation returns an empty string.

Reimplemented from mitk::ModelBase.

Definition at line 29 of file mitkAIFBasedModelBase.cpp.

◆ GetXAxisUnit()

std::string mitk::AIFBasedModelBase::GetXAxisUnit ( ) const

overridevirtual

Default implementation returns an empty string.

Reimplemented from mitk::ModelBase.

Definition at line 34 of file mitkAIFBasedModelBase.cpp.

◆ GetYAxisName()

std::string mitk::AIFBasedModelBase::GetYAxisName ( ) const

overridevirtual

Default implementation returns an empty string.

Reimplemented from mitk::ModelBase.

Definition at line 39 of file mitkAIFBasedModelBase.cpp.

◆ GetYAxisUnit()

std::string mitk::AIFBasedModelBase::GetYAxisUnit ( ) const

overridevirtual

Default implementation returns an empty string.

Reimplemented from mitk::ModelBase.

Definition at line 44 of file mitkAIFBasedModelBase.cpp.

◆ PrintSelf()

void mitk::AIFBasedModelBase::PrintSelf	(	std::ostream &	os,
		::itk::Indent	indent
	)		const

overrideprotected

Definition at line 175 of file mitkAIFBasedModelBase.cpp.

References m_AterialInputFunctionTimeGrid, m_AterialInputFunctionValues, and mitk::ModelBase::PrintSelf().

Referenced by mitk::OneTissueCompartmentModel::PrintSelf(), mitk::TwoTissueCompartmentFDGModel::PrintSelf(), mitk::ExtendedOneTissueCompartmentModel::PrintSelf(), mitk::TwoTissueCompartmentModel::PrintSelf(), mitk::NumericTwoTissueCompartmentModel::PrintSelf(), mitk::ExtendedToftsModel::PrintSelf(), mitk::StandardToftsModel::PrintSelf(), mitk::TwoCompartmentExchangeModel::PrintSelf(), and mitk::NumericTwoCompartmentExchangeModel::PrintSelf().

◆ SetAterialInputFunctionTimeGrid()

virtual void mitk::AIFBasedModelBase::SetAterialInputFunctionTimeGrid ( TimeGridType _arg )

virtual

Referenced by SetStaticParameter(), and mitk::NumericTwoCompartmentExchangeModel::SetStaticParameter().

◆ SetAterialInputFunctionValues()

virtual void mitk::AIFBasedModelBase::SetAterialInputFunctionValues ( AterialInputFunctionType _arg )

virtual

Referenced by SetStaticParameter(), and mitk::NumericTwoCompartmentExchangeModel::SetStaticParameter().

◆ SetStaticParameter()

void mitk::AIFBasedModelBase::SetStaticParameter	(	const ParameterNameType &	name,
		const StaticParameterValuesType &	values
	)

overrideprotectedvirtual

Helper function called by SetStaticParameters(). Implement in derived classes to realize the concrete setting of static parameters.

Implements mitk::ModelBase.

Reimplemented in mitk::NumericTwoCompartmentExchangeModel.

Definition at line 112 of file mitkAIFBasedModelBase.cpp.

References mitk::convertParameterToArray(), NAME_STATIC_PARAMETER_AIF, NAME_STATIC_PARAMETER_AIFTimeGrid, SetAterialInputFunctionTimeGrid(), and SetAterialInputFunctionValues().

◆ ValidateModel()

bool mitk::AIFBasedModelBase::ValidateModel ( std::string & error ) const

overrideprotectedvirtual

Reimplementation that checks if AIF and timegrid settings are valid.

Parameters

[out] error Set internally to indicate the error reason if method returns false. Is used by GetSignal() for the exception comment.

Returns: Returns true if the model is valid and can compute a signal. Otherwise it returns false.

Reimplemented from mitk::ModelBase.

Definition at line 148 of file mitkAIFBasedModelBase.cpp.

References m_AterialInputFunctionTimeGrid, m_AterialInputFunctionValues, mitk::ModelBase::m_TimeGrid, and mitk::ModelBase::ValidateModel().

Member Data Documentation

◆ m_AterialInputFunctionTimeGrid

TimeGridType mitk::AIFBasedModelBase::m_AterialInputFunctionTimeGrid

protected

Definition at line 100 of file mitkAIFBasedModelBase.h.

Referenced by GetCurrentAterialInputFunctionTimeGrid(), GetStaticParameterValue(), mitk::NumericTwoCompartmentExchangeModel::GetStaticParameterValue(), PrintSelf(), and ValidateModel().

◆ m_AterialInputFunctionValues

AterialInputFunctionType mitk::AIFBasedModelBase::m_AterialInputFunctionValues

protected

Definition at line 101 of file mitkAIFBasedModelBase.h.

Referenced by GetAterialInputFunction(), GetStaticParameterValue(), mitk::NumericTwoCompartmentExchangeModel::GetStaticParameterValue(), PrintSelf(), and ValidateModel().

◆ NAME_STATIC_PARAMETER_AIF

const std::string mitk::AIFBasedModelBase::NAME_STATIC_PARAMETER_AIF

static

Definition at line 42 of file mitkAIFBasedModelBase.h.

Referenced by GetStaticParameterNames(), mitk::NumericTwoCompartmentExchangeModel::GetStaticParameterNames(), GetStaticParameterUnits(), GetStaticParameterValue(), mitk::NumericTwoCompartmentExchangeModel::GetStaticParameterValue(), SetStaticParameter(), and mitk::NumericTwoCompartmentExchangeModel::SetStaticParameter().

◆ NAME_STATIC_PARAMETER_AIFTimeGrid

const std::string mitk::AIFBasedModelBase::NAME_STATIC_PARAMETER_AIFTimeGrid

static

Definition at line 46 of file mitkAIFBasedModelBase.h.

Referenced by GetStaticParameterNames(), mitk::NumericTwoCompartmentExchangeModel::GetStaticParameterNames(), GetStaticParameterUnits(), GetStaticParameterValue(), mitk::NumericTwoCompartmentExchangeModel::GetStaticParameterValue(), SetStaticParameter(), and mitk::NumericTwoCompartmentExchangeModel::SetStaticParameter().

◆ UNIT_STATIC_PARAMETER_AIF

const std::string mitk::AIFBasedModelBase::UNIT_STATIC_PARAMETER_AIF

static

Definition at line 48 of file mitkAIFBasedModelBase.h.

Referenced by GetStaticParameterUnits().

◆ UNIT_STATIC_PARAMETER_AIFTimeGrid

const std::string mitk::AIFBasedModelBase::UNIT_STATIC_PARAMETER_AIFTimeGrid

static

Definition at line 49 of file mitkAIFBasedModelBase.h.

Referenced by GetStaticParameterUnits().

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

Public Types

Public Member Functions

Static Public Attributes

Protected Member Functions

Protected Attributes

Detailed Description

Member Typedef Documentation

◆ AterialInputFunctionType

◆ ConstPointer

◆ Pointer

◆ Self

◆ Superclass

Constructor & Destructor Documentation

◆ AIFBasedModelBase()

◆ ~AIFBasedModelBase()

Member Function Documentation

◆ GetAterialInputFunction()

◆ GetAterialInputFunctionTimeGrid()

◆ GetAterialInputFunctionValues()

◆ GetClassName()

◆ GetCurrentAterialInputFunctionTimeGrid()

◆ GetNumberOfStaticParameters()

◆ GetStaticParameterNames()

◆ GetStaticParameterUnits()

◆ GetStaticParameterValue()

◆ GetXAxisName()

◆ GetXAxisUnit()

◆ GetYAxisName()

◆ GetYAxisUnit()

◆ PrintSelf()

◆ SetAterialInputFunctionTimeGrid()

◆ SetAterialInputFunctionValues()

◆ SetStaticParameter()

◆ ValidateModel()

Member Data Documentation

◆ m_AterialInputFunctionTimeGrid

◆ m_AterialInputFunctionValues

◆ NAME_STATIC_PARAMETER_AIF

◆ NAME_STATIC_PARAMETER_AIFTimeGrid

◆ UNIT_STATIC_PARAMETER_AIF

◆ UNIT_STATIC_PARAMETER_AIFTimeGrid