Base class for all pharmacokinetic perfusion models that use an Arterial Input Function (AIF). 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
	Array type for the Arterial Input Function AIF(t). More...

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
	Type defining the time grid used by models. More...

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
	Type representing the model output signal as an array of doubles. More...

using	ParameterValueType = double
	Type of a single parameter value. More...

typedef itk::Array< ParameterValueType >	ParametersType
	Type representing a vector of parameter values. More...

typedef std::string	ParameterNameType
	Type used for parameter names. More...

typedef std::vector< ParameterNameType >	ParameterNamesType
	Type for a list of parameter names. More...

typedef ParametersType::SizeValueType	ParametersSizeType
	Type for the count of parameters. More...

typedef ParameterNamesType	DerivedParameterNamesType
	Type for a list of derived parameter names. More...

typedef ParametersSizeType	DerivedParametersSizeType
	Type for the count of derived parameters. More...

typedef std::map< ParameterNameType, double >	ParamterScaleMapType
	Map type associating parameter names to their scaling factors. More...

typedef std::map< ParameterNameType, std::string >	ParamterUnitMapType
	Map type associating parameter names to their unit strings. More...

typedef std::map< ParameterNameType, double >	DerivedParamterScaleMapType
	Map type associating derived parameter names to their scaling factors. More...

typedef std::map< ParameterNameType, std::string >	DerivedParamterUnitMapType
	Map type associating derived parameter names to their unit strings. More...

typedef std::string	FunctionStringType
	Type for the function string representation of the model. More...

typedef std::string	ModellClassIDType
	Type for the unique class identifier of the model. More...

Public Member Functions
virtual const char *	GetClassName () const

virtual const AterialInputFunctionType &	GetAterialInputFunctionValues ()
	Returns the currently set AIF concentration values. More...

virtual const TimeGridType &	GetAterialInputFunctionTimeGrid ()
	Returns the currently set AIF time grid. More...

virtual void	SetAterialInputFunctionValues (AterialInputFunctionType _arg)
	Sets the AIF concentration values. More...

virtual void	SetAterialInputFunctionTimeGrid (TimeGridType _arg)
	Sets the AIF time grid. More...

std::string	GetXAxisName () const override
	Returns the X axis name ("Time"). More...

std::string	GetXAxisUnit () const override
	Returns the X axis unit ("s"). More...

std::string	GetYAxisName () const override
	Returns the Y axis name ("Concentration"). More...

std::string	GetYAxisUnit () const override
	Returns the Y axis unit ("mM"). More...

const TimeGridType &	GetCurrentAterialInputFunctionTimeGrid () const
	Returns the time grid currently used for the AIF. More...

const AterialInputFunctionType	GetAterialInputFunction (TimeGridType currentTimeGrid) const
	Returns the AIF values interpolated to the given time grid. More...

ParameterNamesType	GetStaticParameterNames () const override
	Returns the names of all static parameters (AIF, AIF time grid). More...

ParametersSizeType	GetNumberOfStaticParameters () const override
	Returns the number of static parameters (always 2). More...

ParamterUnitMapType	GetStaticParameterUnits () const override
	Returns the unit map for all static parameters. More...

Public Member Functions inherited from mitk::ModelBase
ParamterScaleMapType	GetParameterScales () const override
	Default implementation returns a scale of 1.0 for every defined parameter. More...

ParamterUnitMapType	GetParameterUnits () const override
	Default implementation returns no unit string ("") for every defined parameter. More...

DerivedParamterScaleMapType	GetDerivedParameterScales () const override
	Default implementation returns a scale of 1.0 for every defined derived parameter. More...

DerivedParamterUnitMapType	GetDerivedParameterUnits () const override
	Default implementation returns no unit string ("") for every defined derived parameter. More...

std::string	GetModelDisplayName () const override
	Default implementation returns GetClassID as display name. More...

std::string	GetModelType () const override
	Default implementation returns "Unknown" as model type. More...

FunctionStringType	GetFunctionString () const override
	Default implementation returns an empty function string. More...

ModellClassIDType	GetClassID () const override
	Default implementation returns the class name of the concrete instance as ID. More...

std::string	GetXName () const override
	Default implementation returns an empty string. More...

DerivedParameterNamesType	GetDerivedParameterNames () const override
	Returns the names of derived parameters that can be computed by the model. More...

DerivedParametersSizeType	GetNumberOfDerivedParameters () const override
	Returns the number of derived parameters that can be computed by the model. More...

void	SetStaticParameters (const StaticParameterMapType &parameters, bool allParameters=true)
	Sets the static parameters of the model before it is used. More...

StaticParameterMapType	GetStaticParameters () const
	Retrieves the static parameters of the model (e.g. for serialization). More...

DerivedParameterMapType	GetDerivedParameters (const ParametersType &parameters) const
	Computes all derived parameters for the given model parameters. More...

virtual void	SetTimeGrid (const TimeGridType &grid)
	Sets the time grid of the model. More...

virtual const TimeGridType &	GetTimeGrid ()
	Gets the time grid of the model. More...

ModelResultType	GetSignal (const ParametersType &parameters) const
	Computes and returns the model signal for the given parameters. More...

Public Member Functions inherited from mitk::ModelTraitsInterface
virtual ParameterNamesType	GetParameterNames () const =0
	Returns the names of parameters that must be defined when using the model to compute the signal (GetSignal()). More...

virtual ParametersSizeType	GetNumberOfParameters () const =0
	Returns the number of parameters that must be defined when using the model to compute the signal (GetSignal()). More...

Static Public Attributes
static const std::string	NAME_STATIC_PARAMETER_AIF
	Name identifier for the AIF static parameter ("Arterial Input Function"). More...

static const std::string	NAME_STATIC_PARAMETER_AIFTimeGrid
	Name identifier for the AIF time grid static parameter. More...

static const std::string	UNIT_STATIC_PARAMETER_AIF
	Unit string for the AIF static parameter (mM). More...

static const std::string	UNIT_STATIC_PARAMETER_AIFTimeGrid
	Unit string for the AIF time grid static parameter (s). More...

static const unsigned int	NUMBER_OF_STATIC_PARAMETERS
	Number of static parameters (AIF values + AIF time grid = 2). More...

static const std::string	X_AXIS_NAME
	Display name for the X axis ("Time"). More...

static const std::string	X_AXIS_UNIT
	Unit for the X axis ("s"). More...

static const std::string	Y_AXIS_NAME
	Display name for the Y axis ("Concentration"). More...

static const std::string	Y_AXIS_UNIT
	Unit for the Y axis ("mM"). More...

Protected Member Functions
	AIFBasedModelBase ()

	~AIFBasedModelBase () override

	AIFBasedModelBase (const AIFBasedModelBase &source)

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
	Sets a single static parameter by name. More...

StaticParameterValuesType	GetStaticParameterValue (const ParameterNameType &name) const override
	Retrieves a single static parameter value by name. More...

Protected Member Functions inherited from mitk::ModelBase
virtual ModelResultType	ComputeModelfunction (const ParametersType &parameters) const =0
	Computes the model function for the given parameters. More...

virtual DerivedParameterMapType	ComputeDerivedParameters (const ParametersType &parameters) const
	Computes derived parameters from the given model parameters. More...

	ModelBase ()

	~ModelBase () override

	ModelBase (const ModelBase &source)

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 pharmacokinetic perfusion models that use an Arterial Input Function (AIF).

All AIF-based models require an array of AIF concentration values and the corresponding time grid AIF(t). This class provides accessors for setting the AIF values and optionally a dedicated AIF time grid. It also provides interpolation of the AIF to a specified time grid that differs from the AIF's own time grid.

The AIF must be set via an itk::Array. If no dedicated AIF time grid is specified, the model's own time grid is assumed (e.g. when the AIF is derived from the same data set being fitted). In that case, AIF values must have the same length as the model time grid; otherwise validation will fail.

See also: ModelBase, AIFBasedModelParameterizerBase, AterialInputFunctionGenerator

Definition at line 38 of file mitkAIFBasedModelBase.h.

Member Typedef Documentation

◆ AterialInputFunctionType

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

Array type for the Arterial Input Function AIF(t).

Definition at line 77 of file mitkAIFBasedModelBase.h.

◆ ConstPointer

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

Definition at line 45 of file mitkAIFBasedModelBase.h.

◆ Pointer

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

Definition at line 44 of file mitkAIFBasedModelBase.h.

◆ Self

typedef AIFBasedModelBase mitk::AIFBasedModelBase::Self

Definition at line 42 of file mitkAIFBasedModelBase.h.

◆ Superclass

typedef ModelBase mitk::AIFBasedModelBase::Superclass

Definition at line 43 of file mitkAIFBasedModelBase.h.

Constructor & Destructor Documentation

◆ AIFBasedModelBase() [1/2]

mitk::AIFBasedModelBase::AIFBasedModelBase ( )

protected

◆ ~AIFBasedModelBase()

mitk::AIFBasedModelBase::~AIFBasedModelBase ( )

overrideprotected

◆ AIFBasedModelBase() [2/2]

mitk::AIFBasedModelBase::AIFBasedModelBase ( const AIFBasedModelBase & source )

protected

Member Function Documentation

◆ GetAterialInputFunction()

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

Returns the AIF values interpolated to the given time grid.

If currentTimeGrid is empty (size 0), the original uninterpolated AIF values are returned.

Parameters

[in] currentTimeGrid The time grid to interpolate the AIF onto.

Returns: Interpolated AIF values matching the requested time grid.

◆ GetAterialInputFunctionTimeGrid()

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

virtual

Returns the currently set AIF time grid.

◆ GetAterialInputFunctionValues()

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

virtual

Returns the currently set AIF concentration values.

◆ GetClassName()

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

virtual

Run-time type information (and related methods).

Reimplemented from mitk::ModelBase.

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

◆ GetCurrentAterialInputFunctionTimeGrid()

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

Returns the time grid currently used for the AIF.

If a dedicated AIF time grid has been set, it is returned. Otherwise the model's own time grid is returned.

Returns: Reference to the active AIF time grid.

◆ GetNumberOfStaticParameters()

ParametersSizeType mitk::AIFBasedModelBase::GetNumberOfStaticParameters ( ) const

overridevirtual

Returns the number of static parameters (always 2).

Returns: Number of static parameters.

Implements mitk::ModelBase.

◆ GetStaticParameterNames()

ParameterNamesType mitk::AIFBasedModelBase::GetStaticParameterNames ( ) const

overridevirtual

Returns the names of all static parameters (AIF, AIF time grid).

Returns: Vector of static parameter name strings.

Implements mitk::ModelBase.

◆ GetStaticParameterUnits()

ParamterUnitMapType mitk::AIFBasedModelBase::GetStaticParameterUnits ( ) const

overridevirtual

Returns the unit map for all static parameters.

Returns: Map of parameter names to their unit strings.

Reimplemented from mitk::ModelBase.

◆ GetStaticParameterValue()

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

overrideprotectedvirtual

Retrieves a single static parameter value by name.

Helper function called by GetStaticParameters(). Must be implemented in derived classes.

Implements mitk::ModelBase.

◆ GetXAxisName()

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

overridevirtual

Returns the X axis name ("Time").

Returns: The X axis display name.

Reimplemented from mitk::ModelBase.

◆ GetXAxisUnit()

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

overridevirtual

Returns the X axis unit ("s").

Returns: The X axis unit string.

Reimplemented from mitk::ModelBase.

◆ GetYAxisName()

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

overridevirtual

Returns the Y axis name ("Concentration").

Returns: The Y axis display name.

Reimplemented from mitk::ModelBase.

◆ GetYAxisUnit()

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

overridevirtual

Returns the Y axis unit ("mM").

Returns: The Y axis unit string.

Reimplemented from mitk::ModelBase.

◆ PrintSelf()

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

overrideprotected

◆ SetAterialInputFunctionTimeGrid()

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

virtual

Sets the AIF time grid.

Parameters

[in] _arg Array of time points in seconds corresponding to the AIF values.

◆ SetAterialInputFunctionValues()

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

virtual

Sets the AIF concentration values.

Parameters

[in] _arg Array of AIF concentration values in mM.

◆ SetStaticParameter()

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

overrideprotectedvirtual

Sets a single static parameter by name.

Helper function called by SetStaticParameters(). Must be implemented in derived classes.

Implements mitk::ModelBase.

◆ 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.

Member Data Documentation

◆ m_AterialInputFunctionTimeGrid

TimeGridType mitk::AIFBasedModelBase::m_AterialInputFunctionTimeGrid

protected

Definition at line 153 of file mitkAIFBasedModelBase.h.

◆ m_AterialInputFunctionValues

AterialInputFunctionType mitk::AIFBasedModelBase::m_AterialInputFunctionValues

protected

Definition at line 154 of file mitkAIFBasedModelBase.h.

◆ NAME_STATIC_PARAMETER_AIF

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

static

Name identifier for the AIF static parameter ("Arterial Input Function").

Definition at line 52 of file mitkAIFBasedModelBase.h.

◆ NAME_STATIC_PARAMETER_AIFTimeGrid

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

static

Name identifier for the AIF time grid static parameter.

Definition at line 54 of file mitkAIFBasedModelBase.h.

◆ NUMBER_OF_STATIC_PARAMETERS

const unsigned int mitk::AIFBasedModelBase::NUMBER_OF_STATIC_PARAMETERS

static

Number of static parameters (AIF values + AIF time grid = 2).

Definition at line 62 of file mitkAIFBasedModelBase.h.

◆ UNIT_STATIC_PARAMETER_AIF

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

static

Unit string for the AIF static parameter (mM).

Definition at line 57 of file mitkAIFBasedModelBase.h.

◆ UNIT_STATIC_PARAMETER_AIFTimeGrid

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

static

Unit string for the AIF time grid static parameter (s).

Definition at line 59 of file mitkAIFBasedModelBase.h.

◆ X_AXIS_NAME

const std::string mitk::AIFBasedModelBase::X_AXIS_NAME

static

Display name for the X axis ("Time").

Definition at line 65 of file mitkAIFBasedModelBase.h.

◆ X_AXIS_UNIT

const std::string mitk::AIFBasedModelBase::X_AXIS_UNIT

static

Unit for the X axis ("s").

Definition at line 68 of file mitkAIFBasedModelBase.h.

◆ Y_AXIS_NAME

const std::string mitk::AIFBasedModelBase::Y_AXIS_NAME

static

Display name for the Y axis ("Concentration").

Definition at line 71 of file mitkAIFBasedModelBase.h.

◆ Y_AXIS_UNIT

const std::string mitk::AIFBasedModelBase::Y_AXIS_UNIT

static

Unit for the Y axis ("mM").

Definition at line 74 of file mitkAIFBasedModelBase.h.

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

mitkAIFBasedModelBase.h

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() [1/2]

◆ ~AIFBasedModelBase()

◆ AIFBasedModelBase() [2/2]

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

◆ NUMBER_OF_STATIC_PARAMETERS

◆ UNIT_STATIC_PARAMETER_AIF

◆ UNIT_STATIC_PARAMETER_AIFTimeGrid

◆ X_AXIS_NAME

◆ X_AXIS_UNIT

◆ Y_AXIS_NAME

◆ Y_AXIS_UNIT