#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 103 of file elxElastixTemplate.h.

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

[legend]

Public Types
using	AfterEachIterationCommandPointer = typename AfterEachIterationCommandType::Pointer

using	AfterEachIterationCommandType = itk::SimpleMemberCommand<Self>

using	AfterEachResolutionCommandPointer = typename AfterEachResolutionCommandType::Pointer

using	AfterEachResolutionCommandType = itk::SimpleMemberCommand<Self>

using	BaseComponentType = BaseComponent

using	BeforeEachResolutionCommandPointer = typename BeforeEachResolutionCommandType::Pointer

using	BeforeEachResolutionCommandType = itk::SimpleMemberCommand<Self>

using	ConstPointer = itk::SmartPointer<const Self>

using	FixedImageDirectionType = typename FixedImageType::DirectionType

using	FixedImagePointer = typename FixedImageType::Pointer

using	FixedImagePyramidBaseType = FixedImagePyramidBase<Self>

using	FixedImageType = TFixedImage

using	FixedMaskPointer = typename FixedMaskType::Pointer

using	FixedMaskType = itk::Image<MaskPixelType, FixedDimension>

using	ImageSamplerBaseType = elx::ImageSamplerBase<Self>

using	InputImageType = MovingImageType

using	InterpolatorBaseType = InterpolatorBase<Self>

using	MaskPixelType = unsigned char

using	MetricBaseType = MetricBase<Self>

using	MovingImagePointer = typename MovingImageType::Pointer

using	MovingImagePyramidBaseType = MovingImagePyramidBase<Self>

using	MovingImageType = TMovingImage

using	MovingMaskPointer = typename MovingMaskType::Pointer

using	MovingMaskType = itk::Image<MaskPixelType, MovingDimension>

using	OptimizerBaseType = OptimizerBase<Self>

using	OutputImageType = MovingImageType

using	ParameterMapType = itk::ParameterMapInterface::ParameterMapType

using	Pointer = itk::SmartPointer<Self>

using	PtrToMemberFunction = void (BaseComponentType::*)()

using	PtrToMemberFunction2 = int (BaseComponentType::*)()

using	RegistrationBaseType = RegistrationBase<Self>

using	ResampleInterpolatorBaseType = ResampleInterpolatorBase<Self>

using	ResamplerBaseType = ResamplerBase<Self>

using	Self = ElastixTemplate

using	Superclass = ElastixBase

using	TransformBaseType = elx::TransformBase<Self>

Public Types inherited from elastix::ElastixBase
using	ComponentDatabasePointer = ComponentDatabase::Pointer

using	CoordRepType = double

using	DataObjectContainerPointer = DataObjectContainerType::Pointer

using	DataObjectContainerType = itk::VectorContainer<unsigned int, DataObjectPointer>

using	DataObjectPointer = itk::DataObject::Pointer

using	DBIndexType = ComponentDatabase::IndexType

using	FileNameContainerPointer = FileNameContainerType::Pointer

using	FileNameContainerType = itk::VectorContainer<unsigned int, std::string>

using	FlatDirectionCosinesType = std::vector<double>

using	ObjectContainerPointer = ObjectContainerType::Pointer

using	ObjectContainerType = itk::VectorContainer<unsigned int, ObjectPointer>

using	ObjectPointer = itk::Object::Pointer

using	ParameterMapType = itk::ParameterMapInterface::ParameterMapType

using	ResultDeformationFieldType = itk::DataObject

using	ResultImageType = itk::DataObject

using	Self = ElastixBase

using	Superclass = BaseComponent

Public Member Functions
void	AfterEachIteration () override

void	AfterEachResolution () override

void	AfterRegistration () override

int	ApplyTransform (bool doReadTransform) override

int	BeforeAll () override

int	BeforeAllTransformix ()

void	BeforeEachResolution () override

void	BeforeRegistration () 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 const char *	GetCurrentTransformParameterFileName () const

FixedImageType *	GetFixedImage (unsigned int idx=0) const

FixedMaskType *	GetFixedMask (unsigned int idx=0) const

virtual unsigned int	GetIterationCounter () const

MovingImageType *	GetMovingImage (unsigned int idx=0) const

MovingMaskType *	GetMovingMask (unsigned int idx=0) const

bool	GetOriginalFixedImageDirection (FixedImageDirectionType &direction) const

	ITK_DISALLOW_COPY_AND_MOVE (ElastixTemplate)

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

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

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

int	Run () override

Public Member Functions inherited from elastix::ElastixBase
void	AddTargetCellToIterationInfo (const char *const name)

int	BeforeAllBase () override

int	BeforeAllTransformixBase ()

	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 (Configuration, Configuration)

	elxGetObjectMacro (FinalTransform, itk::Object)

	elxGetObjectMacro (FixedImageContainer, DataObjectContainerType)

	elxGetObjectMacro (FixedImageFileNameContainer, FileNameContainerType)

	elxGetObjectMacro (FixedImagePyramidContainer, ObjectContainerType)

	elxGetObjectMacro (FixedMaskContainer, DataObjectContainerType)

	elxGetObjectMacro (FixedMaskFileNameContainer, FileNameContainerType)

	elxGetObjectMacro (ImageSamplerContainer, ObjectContainerType)

	elxGetObjectMacro (InitialTransform, itk::Object)

	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 (Configuration, Configuration)

	elxSetObjectMacro (FinalTransform, itk::Object)

	elxSetObjectMacro (FixedImageContainer, DataObjectContainerType)

	elxSetObjectMacro (FixedImageFileNameContainer, FileNameContainerType)

	elxSetObjectMacro (FixedImagePyramidContainer, ObjectContainerType)

	elxSetObjectMacro (FixedMaskContainer, DataObjectContainerType)

	elxSetObjectMacro (FixedMaskFileNameContainer, FileNameContainerType)

	elxSetObjectMacro (ImageSamplerContainer, ObjectContainerType)

	elxSetObjectMacro (InitialTransform, itk::Object)

	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)

DBIndexType	GetDBIndex ()

IterationInfo &	GetIterationInfo ()

std::ostream &	GetIterationInfoAt (const char *const name)

vcl_size_t	GetNumberOfTransformConfigurations () const

const FlatDirectionCosinesType &	GetOriginalFixedImageDirectionFlat () const

Configuration::ConstPointer	GetPreviousTransformConfiguration (const Configuration &configuration) const

ResultDeformationFieldType *	GetResultDeformationField (unsigned int idx=0) const

ResultImageType *	GetResultImage (const unsigned int idx=0) const

Configuration::ConstPointer	GetTransformConfiguration (const vcl_size_t index) const

ParameterMapType	GetTransformParameterMap () const

bool	GetUseDirectionCosines () const

	ITK_DISALLOW_COPY_AND_MOVE (ElastixBase)

void	SetDBIndex (DBIndexType _arg)

void	SetOriginalFixedImageDirectionFlat (const FlatDirectionCosinesType &arg)

void	SetResultDeformationField (DataObjectPointer result_deformationfield)

void	SetResultImage (DataObjectPointer result_image)

void	SetTransformConfigurations (const std::vector< Configuration::ConstPointer > &configurations)

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

virtual void	AfterEachResolutionBase ()

virtual void	AfterRegistrationBase ()

virtual void	BeforeEachResolutionBase ()

virtual void	BeforeRegistrationBase ()

virtual const char *	elxGetClassName () const

const char *	GetComponentLabel () const

	ITK_DISALLOW_COPY_AND_MOVE (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
template<typename TBaseComponent >
static auto	AsITKBaseType (TBaseComponent *const baseComponent) -> decltype(baseComponent->GetAsITKBaseType())

static void	InitializeElastixExecutable ()

static bool	IsElastixLibrary ()

Private Member Functions
void	CallInEachComponent (PtrToMemberFunction func)

int	CallInEachComponentInt (PtrToMemberFunction2 func)

void	ConfigureComponents (Self *This)

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

void	CreateTransformParameterMap () override

	ElastixTemplate ()=default

void	OpenIterationInfoFile ()

void	SetOriginalFixedImageDirection (const FixedImageDirectionType &arg)

	~ElastixTemplate () override=default

Private Attributes
AfterEachIterationCommandPointer	m_AfterEachIterationCommand {}

AfterEachResolutionCommandPointer	m_AfterEachResolutionCommand {}

BeforeEachResolutionCommandPointer	m_BeforeEachResolutionCommand {}

Additional Inherited Members
Protected Member Functions inherited from elastix::ElastixBase
	ElastixBase ()

	~ElastixBase () override=default

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

virtual	~BaseComponent ()=default

Static Protected Member Functions inherited from elastix::ElastixBase
static DataObjectContainerPointer	GenerateDataObjectContainer (DataObjectPointer dataObject)

Protected Attributes inherited from elastix::ElastixBase
std::string	m_CurrentTransformParameterFileName

DBIndexType	m_DBIndex { 0 }

unsigned int	m_IterationCounter {}

std::ofstream	m_IterationInfoFile

itk::TimeProbe	m_IterationTimer {}

FlatDirectionCosinesType	m_OriginalFixedImageDirection

itk::TimeProbe	m_ResolutionTimer {}

itk::TimeProbe	m_Timer0 {}

ParameterMapType	m_TransformParameterMap