#include <elxElastixTemplate.h>

Detailed Description

template<typename TFixedImage, typename 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	CoordinateType = 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 *	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)
	itkOverrideGetNameOfClassMacro (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 (FixedPoints, const itk::Object)
	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 (MovingPoints, const itk::Object)
	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 (FixedPoints, const itk::Object)
	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 (MovingPoints, const itk::Object)
	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
itk::Statistics::MersenneTwisterRandomVariateGenerator &	GetRandomVariateGenerator ()
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)
	itkVirtualGetNameOfClassMacro (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_OriginalFixedImageDirectionFlat
itk::TimeProbe	m_ResolutionTimer {}
itk::TimeProbe	m_Timer0 {}
ParameterMapType	m_TransformParameterMap