#include <elxElastixTemplate.h>

Detailed Description

template<class TFixedImage, class TMovingImage>
class elastix::ElastixTemplate< TFixedImage, TMovingImage >

The main elastix class, which connects components and invokes the BeforeRegistration(), BeforeEachResolution(), etc. methods.

The ElastixTemplate class ...

Parameters:

WriteTransformParametersEachIteration: Controls whether to save a transform parameter file to disk in every iteration.
example: (WriteTransformParametersEachIteration "true")
This parameter can not be specified for each resolution separately. Default value: "false".

WriteTransformParametersEachResolution: Controls whether to save a transform parameter file to disk in every resolution.
example: (WriteTransformParametersEachResolution "true")
This parameter can not be specified for each resolution separately. Default value: "false".

UseDirectionCosines: Controls whether to use or ignore the direction cosines (world matrix, transform matrix) set in the images. Voxel spacing and image origin are always taken into account, regardless the setting of this parameter.
example: (UseDirectionCosines "true")
Default: true. Recommended: true. This parameter was introduced in elastix 4.3, with a default value of false for backward compabitility. From elastix 4.8 the default value has been changed to true. Setting it to false means that you choose to ignore important information from the image, which relates voxel coordinates to world coordinates. Ignoring it may easily lead to left/right swaps for example, which could skrew up a (medical) analysis.

Definition at line 114 of file elxElastixTemplate.h.

Inheritance diagram for elastix::ElastixTemplate< TFixedImage, TMovingImage >:

Public Types
typedef AfterEachIterationCommandType::Pointer	AfterEachIterationCommandPointer

typedef itk::SimpleMemberCommand< Self >	AfterEachIterationCommandType

typedef AfterEachResolutionCommandType::Pointer	AfterEachResolutionCommandPointer

typedef itk::SimpleMemberCommand< Self >	AfterEachResolutionCommandType

typedef BaseComponent	BaseComponentType

typedef BeforeEachResolutionCommandType::Pointer	BeforeEachResolutionCommandPointer

typedef itk::SimpleMemberCommand< Self >	BeforeEachResolutionCommandType

typedef Superclass2::ConfigurationPointer	ConfigurationPointer

typedef Superclass2::ConfigurationType	ConfigurationType

typedef itk::SmartPointer< const Self >	ConstPointer

typedef itk::CostFunction::ParametersValueType	CoordRepType

typedef Superclass2::DataObjectContainerPointer	DataObjectContainerPointer

typedef Superclass2::DataObjectContainerType	DataObjectContainerType

typedef Superclass2::DataObjectPointer	DataObjectPointer

typedef Superclass2::DataObjectType	DataObjectType

typedef Superclass2::FileNameContainerPointer	FileNameContainerPointer

typedef Superclass2::FileNameContainerType	FileNameContainerType

typedef FixedImageType::DirectionType	FixedImageDirectionType

typedef FixedImageType::Pointer	FixedImagePointer

typedef FixedImagePyramidBase< Self >	FixedImagePyramidBaseType

typedef TFixedImage	FixedImageType

typedef FixedMaskType::Pointer	FixedMaskPointer

typedef itk::Image< MaskPixelType, FixedDimension >	FixedMaskType

typedef elx::ImageSamplerBase< Self >	ImageSamplerBaseType

typedef MovingImageType	InputImageType

typedef InterpolatorBase< Self >	InterpolatorBaseType

typedef unsigned char	MaskPixelType

typedef MetricBase< Self >	MetricBaseType

typedef MovingImageType::Pointer	MovingImagePointer

typedef MovingImagePyramidBase< Self >	MovingImagePyramidBaseType

typedef TMovingImage	MovingImageType

typedef MovingMaskType::Pointer	MovingMaskPointer

typedef itk::Image< MaskPixelType, MovingDimension >	MovingMaskType

typedef Superclass2::ObjectContainerPointer	ObjectContainerPointer

typedef Superclass2::ObjectContainerType	ObjectContainerType

typedef Superclass2::ObjectPointer	ObjectPointer

typedef Superclass2::ObjectType	ObjectType

typedef OptimizerBase< Self >	OptimizerBaseType

typedef MovingImageType	OutputImageType

typedef itk::ParameterMapInterface::ParameterMapType	ParameterMapType

typedef itk::SmartPointer< Self >	Pointer

typedef void(BaseComponentType::*	PtrToMemberFunction) (void)

typedef int(BaseComponentType::*	PtrToMemberFunction2) (void)

typedef RegistrationBase< Self >	RegistrationBaseType

typedef ResampleInterpolatorBase< Self >	ResampleInterpolatorBaseType

typedef ResamplerBase< Self >	ResamplerBaseType

typedef itk::DataObject	ResultDeformationFieldType

typedef itk::DataObject	ResultImageType

typedef ElastixTemplate	Self

typedef itk::Object	Superclass1

typedef ElastixBase	Superclass2

typedef itk::TimeProbe	TimerType

typedef elx::TransformBase< Self >	TransformBaseType

Public Types inherited from elastix::ElastixBase
typedef ComponentDatabaseType::Pointer	ComponentDatabasePointer

typedef ComponentDatabase	ComponentDatabaseType

typedef ConfigurationType::Pointer	ConfigurationPointer

typedef Configuration	ConfigurationType

typedef DataObjectContainerType::Pointer	DataObjectContainerPointer

typedef itk::VectorContainer< unsigned int, DataObjectPointer >	DataObjectContainerType

typedef DataObjectType::Pointer	DataObjectPointer

typedef itk::DataObject	DataObjectType

typedef ComponentDatabaseType::IndexType	DBIndexType

typedef FileNameContainerType::Pointer	FileNameContainerPointer

typedef itk::VectorContainer< unsigned int, std::string >	FileNameContainerType

typedef std::vector< double >	FlatDirectionCosinesType

typedef itk::Object	ITKBaseType

typedef ObjectContainerType::Pointer	ObjectContainerPointer

typedef itk::VectorContainer< unsigned int, ObjectPointer >	ObjectContainerType

typedef ObjectType::Pointer	ObjectPointer

typedef itk::Object	ObjectType

typedef itk::ParameterMapInterface::ParameterMapType	ParameterMapType

typedef ElastixBase	Self

typedef BaseComponent	Superclass

Public Member Functions
void	AfterEachIteration (void) override

void	AfterEachResolution (void) override

void	AfterRegistration (void) override

int	ApplyTransform (void) override

int	BeforeAll (void) override

virtual int	BeforeAllTransformix (void)

void	BeforeEachResolution (void) override

void	BeforeRegistration (void) override

	elxGetBaseMacro (FixedImagePyramid, FixedImagePyramidBaseType)

	elxGetBaseMacro (ImageSampler, ImageSamplerBaseType)

	elxGetBaseMacro (Interpolator, InterpolatorBaseType)

	elxGetBaseMacro (Metric, MetricBaseType)

	elxGetBaseMacro (MovingImagePyramid, MovingImagePyramidBaseType)

	elxGetBaseMacro (Optimizer, OptimizerBaseType)

	elxGetBaseMacro (Registration, RegistrationBaseType)

	elxGetBaseMacro (ResampleInterpolator, ResampleInterpolatorBaseType)

	elxGetBaseMacro (Resampler, ResamplerBaseType)

	elxGetBaseMacro (Transform, TransformBaseType)

virtual const char *	GetClassName () const

virtual ConfigurationPointer	GetConfiguration ()

virtual ConfigurationPointer	GetConfiguration (const vcl_size_t index)

virtual const char *	GetCurrentTransformParameterFileName () const

virtual FixedImageType *	GetFixedImage (unsigned int idx) const

virtual FixedImageType *	GetFixedImage (void) const

virtual FixedMaskType *	GetFixedMask (unsigned int idx) const

virtual FixedMaskType *	GetFixedMask (void) const

virtual unsigned int	GetIterationCounter () const

virtual MovingImageType *	GetMovingImage (unsigned int idx) const

virtual MovingImageType *	GetMovingImage (void) const

virtual MovingMaskType *	GetMovingMask (unsigned int idx) const

virtual MovingMaskType *	GetMovingMask (void) const

virtual bool	GetOriginalFixedImageDirection (FixedImageDirectionType &direction) const

virtual ResultDeformationFieldType *	GetResultDeformationField (unsigned int idx) const

virtual ResultDeformationFieldType *	GetResultDeformationField (void) const

virtual ResultImageType *	GetResultImage (unsigned int idx) const

virtual ResultImageType *	GetResultImage (void) const

	itkStaticConstMacro (Dimension, unsigned int, FixedImageType::ImageDimension)

	itkStaticConstMacro (FixedDimension, unsigned int, FixedImageType::ImageDimension)

	itkStaticConstMacro (MovingDimension, unsigned int, MovingImageType::ImageDimension)

int	Run (void) override

void	SetConfigurations (std::vector< ConfigurationPointer > &configurations) override

virtual int	SetResultDeformationField (DataObjectPointer result_deformationfield)

virtual int	SetResultImage (DataObjectPointer result_image)

Public Member Functions inherited from elastix::ElastixBase
void	AfterRegistrationBase (void) override

virtual int	ApplyTransform (void)=0

int	BeforeAllBase (void) override

virtual int	BeforeAllTransformixBase (void)

void	BeforeRegistrationBase (void) override

virtual void	CreateTransformParametersMap (void)=0

	elxGetNumberOfMacro (FixedImage)

	elxGetNumberOfMacro (FixedImageFileName)

	elxGetNumberOfMacro (FixedImagePyramid)

	elxGetNumberOfMacro (FixedMask)

	elxGetNumberOfMacro (FixedMaskFileName)

	elxGetNumberOfMacro (ImageSampler)

	elxGetNumberOfMacro (Interpolator)

	elxGetNumberOfMacro (Metric)

	elxGetNumberOfMacro (MovingImage)

	elxGetNumberOfMacro (MovingImageFileName)

	elxGetNumberOfMacro (MovingImagePyramid)

	elxGetNumberOfMacro (MovingMask)

	elxGetNumberOfMacro (MovingMaskFileName)

	elxGetNumberOfMacro (Optimizer)

	elxGetNumberOfMacro (Registration)

	elxGetNumberOfMacro (ResampleInterpolator)

	elxGetNumberOfMacro (Resampler)

	elxGetNumberOfMacro (ResultDeformationField)

	elxGetNumberOfMacro (ResultImage)

	elxGetNumberOfMacro (Transform)

	elxGetObjectMacro (ComponentDatabase, ComponentDatabaseType)

	elxGetObjectMacro (Configuration, ConfigurationType)

	elxGetObjectMacro (FinalTransform, ObjectType)

	elxGetObjectMacro (FixedImageContainer, DataObjectContainerType)

	elxGetObjectMacro (FixedImageFileNameContainer, FileNameContainerType)

	elxGetObjectMacro (FixedImagePyramidContainer, ObjectContainerType)

	elxGetObjectMacro (FixedMaskContainer, DataObjectContainerType)

	elxGetObjectMacro (FixedMaskFileNameContainer, FileNameContainerType)

	elxGetObjectMacro (ImageSamplerContainer, ObjectContainerType)

	elxGetObjectMacro (InitialTransform, ObjectType)

	elxGetObjectMacro (InterpolatorContainer, ObjectContainerType)

	elxGetObjectMacro (MetricContainer, ObjectContainerType)

	elxGetObjectMacro (MovingImageContainer, DataObjectContainerType)

	elxGetObjectMacro (MovingImageFileNameContainer, FileNameContainerType)

	elxGetObjectMacro (MovingImagePyramidContainer, ObjectContainerType)

	elxGetObjectMacro (MovingMaskContainer, DataObjectContainerType)

	elxGetObjectMacro (MovingMaskFileNameContainer, FileNameContainerType)

	elxGetObjectMacro (OptimizerContainer, ObjectContainerType)

	elxGetObjectMacro (RegistrationContainer, ObjectContainerType)

	elxGetObjectMacro (ResampleInterpolatorContainer, ObjectContainerType)

	elxGetObjectMacro (ResamplerContainer, ObjectContainerType)

	elxGetObjectMacro (ResultDeformationFieldContainer, DataObjectContainerType)

	elxGetObjectMacro (ResultImageContainer, DataObjectContainerType)

	elxGetObjectMacro (TransformContainer, ObjectContainerType)

	elxSetObjectMacro (ComponentDatabase, ComponentDatabaseType)

	elxSetObjectMacro (Configuration, ConfigurationType)

	elxSetObjectMacro (FinalTransform, ObjectType)

	elxSetObjectMacro (FixedImageContainer, DataObjectContainerType)

	elxSetObjectMacro (FixedImageFileNameContainer, FileNameContainerType)

	elxSetObjectMacro (FixedImagePyramidContainer, ObjectContainerType)

	elxSetObjectMacro (FixedMaskContainer, DataObjectContainerType)

	elxSetObjectMacro (FixedMaskFileNameContainer, FileNameContainerType)

	elxSetObjectMacro (ImageSamplerContainer, ObjectContainerType)

	elxSetObjectMacro (InitialTransform, ObjectType)

	elxSetObjectMacro (InterpolatorContainer, ObjectContainerType)

	elxSetObjectMacro (MetricContainer, ObjectContainerType)

	elxSetObjectMacro (MovingImageContainer, DataObjectContainerType)

	elxSetObjectMacro (MovingImageFileNameContainer, FileNameContainerType)

	elxSetObjectMacro (MovingImagePyramidContainer, ObjectContainerType)

	elxSetObjectMacro (MovingMaskContainer, DataObjectContainerType)

	elxSetObjectMacro (MovingMaskFileNameContainer, FileNameContainerType)

	elxSetObjectMacro (OptimizerContainer, ObjectContainerType)

	elxSetObjectMacro (RegistrationContainer, ObjectContainerType)

	elxSetObjectMacro (ResampleInterpolatorContainer, ObjectContainerType)

	elxSetObjectMacro (ResamplerContainer, ObjectContainerType)

	elxSetObjectMacro (ResultDeformationFieldContainer, DataObjectContainerType)

	elxSetObjectMacro (ResultImageContainer, DataObjectContainerType)

	elxSetObjectMacro (TransformContainer, ObjectContainerType)

virtual ITKBaseType *	GetAsITKBaseType (void)

virtual DBIndexType	GetDBIndex (void)

virtual int	GetDefaultOutputPrecision (void) const

virtual const FlatDirectionCosinesType &	GetOriginalFixedImageDirectionFlat (void) const

virtual ParameterMapType	GetTransformParametersMap (void) const =0

virtual bool	GetUseDirectionCosines (void) const

virtual int	Run (void)=0

virtual void	SetConfigurations (std::vector< ConfigurationPointer > &configurations)=0

virtual void	SetDBIndex (DBIndexType _arg)

virtual void	SetOriginalFixedImageDirectionFlat (const FlatDirectionCosinesType &arg)

Public Member Functions inherited from elastix::BaseComponent
virtual void	AfterEachIteration (void)

virtual void	AfterEachIterationBase (void)

virtual void	AfterEachResolution (void)

virtual void	AfterEachResolutionBase (void)

virtual void	AfterRegistration (void)

virtual void	AfterRegistrationBase (void)

virtual int	BeforeAll (void)

virtual int	BeforeAllBase (void)

virtual void	BeforeEachResolution (void)

virtual void	BeforeEachResolutionBase (void)

virtual void	BeforeRegistration (void)

virtual void	BeforeRegistrationBase (void)

virtual const char *	elxGetClassName (void) const

const char *	GetComponentLabel (void) const

	ITK_DISALLOW_COPY_AND_ASSIGN (BaseComponent)

	itkTypeMacroNoParent (BaseComponent)

void	SetComponentLabel (const char *label, unsigned int idx)

Static Public Member Functions
static Pointer	New ()

Static Public Member Functions inherited from elastix::BaseComponent
static std::string	ConvertSecondsToDHMS (const double totalSeconds, const unsigned int precision)

static void	InitializeElastixExecutable ()

static bool	IsElastixLibrary ()

Protected Types
typedef Superclass2::MultipleImageLoader< FixedImageType >	FixedImageLoaderType

typedef Superclass2::MultipleImageLoader< FixedMaskType >	FixedMaskLoaderType

typedef Superclass2::MultipleImageLoader< MovingImageType >	MovingImageLoaderType

typedef Superclass2::MultipleImageLoader< MovingMaskType >	MovingMaskLoaderType

Protected Member Functions
void	CallInEachComponent (PtrToMemberFunction func)

int	CallInEachComponentInt (PtrToMemberFunction2 func)

virtual void	ConfigureComponents (Self *This)

virtual void	CreateTransformParameterFile (const std::string FileName, const bool ToLog)

void	CreateTransformParametersMap (void) override

	ElastixTemplate ()

ParameterMapType	GetTransformParametersMap (void) const override

virtual void	OpenIterationInfoFile (void)

virtual void	SetOriginalFixedImageDirection (const FixedImageDirectionType &arg)

	~ElastixTemplate () override

Protected Member Functions inherited from elastix::ElastixBase
	ElastixBase ()

	~ElastixBase () override=default

Protected Member Functions inherited from elastix::BaseComponent
	BaseComponent ()=default

virtual	~BaseComponent ()=default

Protected Attributes
AfterEachIterationCommandPointer	m_AfterEachIterationCommand

AfterEachResolutionCommandPointer	m_AfterEachResolutionCommand

BeforeEachResolutionCommandPointer	m_BeforeEachResolutionCommand

std::vector< ConfigurationPointer >	m_Configurations

std::string	m_CurrentTransformParameterFileName

unsigned int	m_IterationCounter

std::ofstream	m_IterationInfoFile

TimerType	m_IterationTimer

TimerType	m_ResolutionTimer

TimerType	m_Timer0

ParameterMapType	m_TransformParametersMap

Protected Attributes inherited from elastix::ElastixBase
ComponentDatabasePointer	m_ComponentDatabase

ConfigurationPointer	m_Configuration

DBIndexType	m_DBIndex

FlatDirectionCosinesType	m_OriginalFixedImageDirection

Private Member Functions
	ElastixTemplate (const Self &)

void	operator= (const Self &)