elastix::ElastixMain Class Reference

#include <elxElastixMain.h>

Detailed Description

A class with all functionality to configure elastix.

The ElastixMain initializes the MyConfiguration class with the parameters and commandline arguments. After this, the class loads and creates all components and sets them in ElastixTemplate.

Parameters

FixedImageDimension: the dimension of the fixed image.
example: (FixedImageDimension 2)

MovingImageDimension: the dimension of the fixed image.
example: (MovingImageDimension 2)

FixedInternalImagePixelType: the pixel type of the internal fixed image representation. The fixed image is automatically converted to this type.
example: (FixedInternalImagePixelType "float")
Default/recommended: "float"

MovingInternalImagePixelType: the pixel type of the internal moving image representation. The moving image is automatically converted to this type.
example: (MovingInternalImagePixelType "float")
Default/recommended: "float"

Transform Parameters

FixedImageDimension: the dimension of the fixed image.
example: (FixedImageDimension 2)

MovingImageDimension: the dimension of the fixed image.
example: (MovingImageDimension 2)

FixedInternalImagePixelType: the pixel type of the internal fixed image representation. The fixed image is automatically converted to this type.
example: (FixedInternalImagePixelType "float")
Default/recommended: "float"

MovingInternalImagePixelType: the pixel type of the internal moving image representation. The moving image is automatically converted to this type.
example: (MovingInternalImagePixelType "float")
Default/recommended: "float"

Definition at line 68 of file elxElastixMain.h.

Inheritance diagram for elastix::ElastixMain:

Public Types
using	ConstPointer = itk::SmartPointer<const Self>
using	Pointer = itk::SmartPointer<Self>
using	Self = ElastixMain
using	Superclass = MainBase
Public Types inherited from elastix::MainBase
using	ArgumentMapType = Configuration::CommandLineArgumentMapType
using	ComponentDatabasePointer = ComponentDatabase::Pointer
using	ComponentDescriptionType = ComponentDatabase::ComponentDescriptionType
using	ConstPointer = itk::SmartPointer<const Self>
using	DataObjectContainerPointer = ElastixBase::DataObjectContainerPointer
using	DataObjectContainerType = ElastixBase::DataObjectContainerType
using	DataObjectPointer = itk::DataObject::Pointer
using	DBIndexType = ComponentDatabase::IndexType
using	FlatDirectionCosinesType = ElastixBase::FlatDirectionCosinesType
using	ImageDimensionType = ComponentDatabase::ImageDimensionType
using	ObjectContainerPointer = ElastixBase::ObjectContainerPointer
using	ObjectContainerType = ElastixBase::ObjectContainerType
using	ObjectPointer = itk::Object::Pointer
using	ParameterMapType = itk::ParameterMapInterface::ParameterMapType
using	PixelTypeDescriptionType = ComponentDatabase::PixelTypeDescriptionType
using	Pointer = itk::SmartPointer<Self>
using	PtrToCreator = ComponentDatabase::PtrToCreator
using	Self = MainBase
using	Superclass = itk::Object

Public Member Functions
virtual const char *	GetClassName () const
unsigned int	GetElastixLevel () const
virtual const FlatDirectionCosinesType &	GetOriginalFixedImageDirectionFlat () const
unsigned int	GetTotalNumberOfElastixLevels () const
virtual ParameterMapType	GetTransformParameterMap () const
	ITK_DISALLOW_COPY_AND_MOVE (ElastixMain)
	itkGetModifiableObjectMacro (FinalTransform, itk::Object)
	itkGetModifiableObjectMacro (FixedImageContainer, DataObjectContainerType)
	itkGetModifiableObjectMacro (FixedMaskContainer, DataObjectContainerType)
	itkGetModifiableObjectMacro (InitialTransform, itk::Object)
	itkGetModifiableObjectMacro (MovingMaskContainer, DataObjectContainerType)
int	Run () override
virtual int	Run (const ArgumentMapType &argmap)
virtual int	Run (const ArgumentMapType &argmap, const ParameterMapType &inputMap)
int	RunWithInitialTransformParameterMaps (const ArgumentMapType &argmap, const ParameterMapType &inputMap, const std::vector< ParameterMapType > &initialTransformParameterMaps)
void	SetElastixLevel (unsigned int level)
virtual void	SetFixedImageContainer (DataObjectContainerType *_arg)
virtual void	SetFixedMaskContainer (DataObjectContainerType *_arg)
virtual void	SetInitialTransform (itk::Object *_arg)
virtual void	SetMovingMaskContainer (DataObjectContainerType *_arg)
virtual void	SetOriginalFixedImageDirectionFlat (const FlatDirectionCosinesType &arg)
void	SetTotalNumberOfElastixLevels (unsigned int levels)
Public Member Functions inherited from elastix::MainBase
virtual DBIndexType	GetDBIndex () const
ElastixBase &	GetElastixBase () const
virtual ImageDimensionType	GetFixedImageDimension () const
virtual PixelTypeDescriptionType	GetFixedImagePixelType () const
virtual ImageDimensionType	GetMovingImageDimension () const
virtual PixelTypeDescriptionType	GetMovingImagePixelType () const
	ITK_DISALLOW_COPY_AND_MOVE (MainBase)
	itkGetModifiableObjectMacro (Configuration, Configuration)
	itkGetModifiableObjectMacro (Elastix, itk::Object)
	itkGetModifiableObjectMacro (MovingImageContainer, DataObjectContainerType)
	itkGetModifiableObjectMacro (ResultDeformationFieldContainer, DataObjectContainerType)
	itkGetModifiableObjectMacro (ResultImageContainer, DataObjectContainerType)
virtual void	SetConfiguration (Configuration *_arg)
virtual void	SetFixedImageDimension (ImageDimensionType _arg)
virtual void	SetFixedImagePixelType (PixelTypeDescriptionType _arg)
virtual void	SetMaximumNumberOfThreads () const
virtual void	SetMovingImageContainer (DataObjectContainerType *_arg)
virtual void	SetMovingImageDimension (ImageDimensionType _arg)
virtual void	SetMovingImagePixelType (PixelTypeDescriptionType _arg)
virtual void	SetProcessPriority () const
virtual void	SetResultDeformationFieldContainer (DataObjectContainerType *_arg)
virtual void	SetResultImageContainer (DataObjectContainerType *_arg)

Static Public Member Functions
static Pointer	New ()
Static Public Member Functions inherited from elastix::MainBase
static const ComponentDatabase &	GetComponentDatabase ()

Protected Member Functions
	ElastixMain ()
void	GetImageInformationFromFile (const std::string &filename, ImageDimensionType &imageDimension) const
int	InitDBIndex () override
	~ElastixMain () override
Protected Member Functions inherited from elastix::MainBase
virtual ObjectPointer	CreateComponent (const ComponentDescriptionType &name)
virtual ObjectContainerPointer	CreateComponents (const ComponentDescriptionType &key, const ComponentDescriptionType &defaultComponentName, int &errorcode, bool mandatoryComponent=true)
	MainBase ()
	~MainBase () override=0

Protected Attributes
ObjectPointer	m_FinalTransform { nullptr }
DataObjectContainerPointer	m_FixedImageContainer { nullptr }
DataObjectContainerPointer	m_FixedMaskContainer { nullptr }
ObjectPointer	m_InitialTransform { nullptr }
DataObjectContainerPointer	m_MovingMaskContainer { nullptr }
FlatDirectionCosinesType	m_OriginalFixedImageDirection {}
DataObjectContainerPointer	m_ResultImageContainer { nullptr }
ParameterMapType	m_TransformParameterMap {}
Protected Attributes inherited from elastix::MainBase
DBIndexType	m_DBIndex { 0 }
ObjectPointer	m_Elastix { nullptr }
ImageDimensionType	m_FixedImageDimension { 0 }
PixelTypeDescriptionType	m_FixedImagePixelType {}
DataObjectContainerPointer	m_MovingImageContainer { nullptr }
ImageDimensionType	m_MovingImageDimension { 0 }
PixelTypeDescriptionType	m_MovingImagePixelType {}
DataObjectContainerPointer	m_ResultDeformationFieldContainer { nullptr }
DataObjectContainerPointer	m_ResultImageContainer { nullptr }
std::vector< Configuration::ConstPointer >	m_TransformConfigurations {}

Member Typedef Documentation

ConstPointer

using elastix::ElastixMain::ConstPointer = itk::SmartPointer<const Self>

Definition at line 77 of file elxElastixMain.h.

Pointer

using elastix::ElastixMain::Pointer = itk::SmartPointer<Self>

Definition at line 76 of file elxElastixMain.h.

Self

using elastix::ElastixMain::Self = ElastixMain

Standard itk.

Definition at line 74 of file elxElastixMain.h.

Superclass

using elastix::ElastixMain::Superclass = MainBase

Definition at line 75 of file elxElastixMain.h.

Constructor & Destructor Documentation

ElastixMain()

elastix::ElastixMain::ElastixMain ( )

protected

~ElastixMain()

elastix::ElastixMain::~ElastixMain ( )

overrideprotected

Member Function Documentation

GetClassName()

virtual const char * elastix::ElastixMain::GetClassName ( ) const

virtual

Run-time type information (and related methods).

Reimplemented from elastix::MainBase.

GetElastixLevel()

unsigned int elastix::ElastixMain::GetElastixLevel

(

)

const

GetImageInformationFromFile()

void elastix::ElastixMain::GetImageInformationFromFile ( const std::string & filename, ImageDimensionType & imageDimension ) const

protected

Helper function to obtain information from images on disk.

GetOriginalFixedImageDirectionFlat()

virtual const FlatDirectionCosinesType & elastix::ElastixMain::GetOriginalFixedImageDirectionFlat ( ) const

virtual

GetTotalNumberOfElastixLevels()

unsigned int elastix::ElastixMain::GetTotalNumberOfElastixLevels

(

)

const

GetTransformParameterMap()

virtual ParameterMapType elastix::ElastixMain::GetTransformParameterMap ( ) const

virtual

GetTransformParameterMap

InitDBIndex()

int elastix::ElastixMain::InitDBIndex ( )

overrideprotectedvirtual

InitDBIndex sets m_DBIndex by asking the ImageTypes from the Configuration object and obtaining the corresponding DB index from the ComponentDatabase.

Implements elastix::MainBase.

ITK_DISALLOW_COPY_AND_MOVE()

elastix::ElastixMain::ITK_DISALLOW_COPY_AND_MOVE

(

ElastixMain

)

itkGetModifiableObjectMacro() [1/5]

elastix::ElastixMain::itkGetModifiableObjectMacro	(	FinalTransform	,
		itk::Object	)

Get the final transform (the result of running elastix). You may pass this as an InitialTransform in an other instantiation of ElastixMain. Only valid after calling Run()!

itkGetModifiableObjectMacro() [2/5]

elastix::ElastixMain::itkGetModifiableObjectMacro	(	FixedImageContainer	,
		DataObjectContainerType	)

itkGetModifiableObjectMacro() [3/5]

elastix::ElastixMain::itkGetModifiableObjectMacro	(	FixedMaskContainer	,
		DataObjectContainerType	)

itkGetModifiableObjectMacro() [4/5]

elastix::ElastixMain::itkGetModifiableObjectMacro	(	InitialTransform	,
		itk::Object	)

itkGetModifiableObjectMacro() [5/5]

elastix::ElastixMain::itkGetModifiableObjectMacro	(	MovingMaskContainer	,
		DataObjectContainerType	)

New()

static Pointer elastix::ElastixMain::New ( )

static

Method for creation through the object factory.

Run() [1/3]

int elastix::ElastixMain::Run ( )

overridevirtual

Start the registration run() without command line parameters; it assumes that EnterCommandLineParameters has been invoked already, or that m_Configuration is initialized in a different way.

Implements elastix::MainBase.

Run() [2/3]

virtual int elastix::MainBase::Run ( const ArgumentMapType & argmap )

virtual

Start the registration this version of 'run' first calls this->EnterCommandLineParameters(argc,argv) and then calls run().

Reimplemented from elastix::MainBase.

Run() [3/3]

virtual int elastix::MainBase::Run ( const ArgumentMapType & argmap, const ParameterMapType & inputMap )

virtual

Reimplemented from elastix::MainBase.

RunWithInitialTransformParameterMaps()

int elastix::ElastixMain::RunWithInitialTransformParameterMaps	(	const ArgumentMapType &	argmap,
		const ParameterMapType &	inputMap,
		const std::vector< ParameterMapType > &	initialTransformParameterMaps )

SetElastixLevel()

void elastix::ElastixMain::SetElastixLevel

(

unsigned int

level

)

Get and Set the elastix level.

SetFixedImageContainer()

virtual void elastix::ElastixMain::SetFixedImageContainer ( DataObjectContainerType * _arg )

virtual

Set/Get functions for the fixed images (if these are not used, elastix tries to read them from disk, according to the command line parameters).

SetFixedMaskContainer()

virtual void elastix::ElastixMain::SetFixedMaskContainer ( DataObjectContainerType * _arg )

virtual

Set/Get functions for the fixed and moving masks (if these are not used, elastix tries to read them from disk, according to the command line parameters).

SetInitialTransform()

virtual void elastix::ElastixMain::SetInitialTransform ( itk::Object * _arg )

virtual

Set/Get the initial transform the type is itk::Object, but the pointer should actually point to an itk::Transform type (or inherited from that one).

SetMovingMaskContainer()

virtual void elastix::ElastixMain::SetMovingMaskContainer ( DataObjectContainerType * _arg )

virtual

SetOriginalFixedImageDirectionFlat()

virtual void elastix::ElastixMain::SetOriginalFixedImageDirectionFlat ( const FlatDirectionCosinesType & arg )

virtual

Set/Get the original fixed image direction as a flat array (d11 d21 d31 d21 d22 etc )

SetTotalNumberOfElastixLevels()

void elastix::ElastixMain::SetTotalNumberOfElastixLevels

(

unsigned int

levels

)

Get and Set the total number of elastix levels.

Field Documentation

m_FinalTransform

ObjectPointer elastix::ElastixMain::m_FinalTransform { nullptr }

protected

A transform that is the result of registration.

Definition at line 167 of file elxElastixMain.h.

m_FixedImageContainer

DataObjectContainerPointer elastix::ElastixMain::m_FixedImageContainer { nullptr }

protected

The fixed images and masks.

Definition at line 161 of file elxElastixMain.h.

m_FixedMaskContainer

DataObjectContainerPointer elastix::ElastixMain::m_FixedMaskContainer { nullptr }

protected

Definition at line 162 of file elxElastixMain.h.

m_InitialTransform

ObjectPointer elastix::ElastixMain::m_InitialTransform { nullptr }

protected

The initial transform.

Definition at line 170 of file elxElastixMain.h.

m_MovingMaskContainer

DataObjectContainerPointer elastix::ElastixMain::m_MovingMaskContainer { nullptr }

protected

Definition at line 163 of file elxElastixMain.h.

m_OriginalFixedImageDirection

FlatDirectionCosinesType elastix::ElastixMain::m_OriginalFixedImageDirection {}

protected

Definition at line 177 of file elxElastixMain.h.

m_ResultImageContainer

DataObjectContainerPointer elastix::ElastixMain::m_ResultImageContainer { nullptr }

protected

Definition at line 164 of file elxElastixMain.h.

m_TransformParameterMap

ParameterMapType elastix::ElastixMain::m_TransformParameterMap {}

protected

Transformation parameters map containing parameters that is the result of registration.

Definition at line 175 of file elxElastixMain.h.