#include <elxTransformBase.h>

Detailed Description

template<class TElastix>
class elastix::TransformBase< TElastix >

This class is the elastix base class for all Transforms.

This class contains the common functionality for all Transforms.

The parameters used in this class are:

Parameters:: HowToCombineTransforms: Indicates how to use the initial transform
(given by the command-line argument -t0, or, if using multiple parameter files, by the result of registration using the previous parameter file). Possible options are "Add" and "Compose".
"Add" combines the initial transform and the current transform (which is currently optimized) by addition: ;
"Compose" by composition: .
example: (HowToCombineTransforms "Add")
Default: "Add".

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. 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.

HowToCombineTransforms: Indicates how to use the initial transform (given by the command-line argument -t0, or, if using multiple parameter files, by the result of registration using the previous parameter file). Possible options are "Add" and "Compose".
"Add" combines the initial transform and the current transform (which is currently optimized) by addition: ;
"Compose" by composition: .
example: (HowToCombineTransforms "Add")
Default: "Compose".

Size: The size (number of voxels in each dimension) of the fixed image that was used during registration, and which is used for resampling the deformed moving image.
example: (Size 100 90 90)
Mandatory parameter.

Index: The starting index of the fixed image region that was used during registration, and which is used for resampling the deformed moving image.
example: (Index 0 0 0)
Currently always zero.

Spacing: The voxel spacing of the fixed image that was used during registration, and which is used for resampling the deformed moving image.
example: (Spacing 1.0 1.0 1.0)
Default: 1.0 for each dimension.

Origin: The origin (location of the first voxel in world coordinate) of the fixed image that was used during registration, and which is used for resampling the deformed moving image.
example: (Origin 5.0 10.0 11.0)
Default: 0.0 for each dimension.

Direction: The direction cosines matrix of the fixed image that was used during registration, and which is used for resampling the deformed moving image if the UseDirectionCosines parameter is set to "true".
example: (Direction -1.0 0.0 0.0 0.0 1.0 0.0 0.0 0.0 0.1)
Default: identity matrix. Elements are sorted as follows: [ d11 d21 d31 d12 d22 d32 d13 d23 d33] (in 3D).

TransformParameters: the transform parameter vector that defines the transformation.
example (TransformParameters 0.03 1.0 0.2 ...)
The number of entries is stored the NumberOfParameters entry.

NumberOfParameters: the length of the transform parameter vector.
example (NumberOfParameters 722)

InitialTransformParametersFileName: The location/name of an initial transform that will be loaded when loading the current transform parameter file. Note that transform parameter file can also contain an initial transform. Recursively all transforms are thus automatically loaded when loading the last transform parameter file.
example (InitialTransformParametersFileName "./res/TransformParameters.0.txt")
The location is relative to the path from where elastix/transformix is started!
Default: "NoInitialTransform", which (obviously) means that there is no initial transform to be loaded.

The command line arguments used by this class are:

Command line arguments:

-t0: optional argument for elastix for specifying an initial transform parameter file.
example: -t0 TransformParameters.txt

-def: optional argument for transformix for specifying a set of points that have to be transformed.
example: -def inputPoints.txt
The inputPoints.txt file should be structured: first line should be "index" or "point", depending if the user supplies voxel indices or real world coordinates. The second line should be the number of points that should be transformed. The third and following lines give the indices or points.
It is also possible to deform all points, thereby generating a deformation field image. This is done by:
example: -def all

Definition at line 128 of file elxTransformBase.h.

Inheritance diagram for elastix::TransformBase< TElastix >:

Public Types
typedef itk::AdvancedCombinationTransform< CoordRepType, itkGetStaticConstMacro(FixedImageDimension) >	CombinationTransformType

typedef ConfigurationType::CommandLineArgumentMapType	CommandLineArgumentMapType

typedef ConfigurationType::CommandLineEntryType	CommandLineEntryType

typedef ComponentDatabase	ComponentDatabaseType

typedef ComponentDatabaseType::ComponentDescriptionType	ComponentDescriptionType

typedef Configuration::Pointer	ConfigurationPointer

typedef Configuration	ConfigurationType

typedef ElastixType::CoordRepType	CoordRepType

typedef itk::Image< VectorPixelType, FixedImageDimension >	DeformationFieldImageType

typedef itk::WeakPointer< ElastixType >	ElastixPointer

typedef TElastix	ElastixType

typedef ElastixType::FixedImageType	FixedImageType

typedef CombinationTransformType::InitialTransformType	InitialTransformType

typedef ITKBaseType::InputPointType	InputPointType

typedef itk::AdvancedTransform< CoordRepType, itkGetStaticConstMacro(FixedImageDimension), itkGetStaticConstMacro(MovingImageDimension) >	ITKBaseType

typedef RegistrationType::ITKBaseType	ITKRegistrationType

typedef ElastixType::MovingImageType	MovingImageType

typedef itk::Object	ObjectType

typedef ITKRegistrationType::OptimizerType	OptimizerType

typedef ITKBaseType::OutputPointType	OutputPointType

typedef ElastixType::ParameterMapType	ParameterMapType

typedef ITKBaseType::ParametersType	ParametersType

typedef elx::ProgressCommand	ProgressCommandType

typedef ComponentDatabase::PtrToCreator	PtrToCreator

typedef RegistrationType *	RegistrationPointer

typedef ElastixType::RegistrationBaseType	RegistrationType

typedef OptimizerType::ScalesType	ScalesType

typedef TransformBase	Self

typedef BaseComponentSE< TElastix >	Superclass

typedef ParametersType::ValueType	ValueType

typedef itk::Vector< float, FixedImageDimension >	VectorPixelType

Public Types inherited from elastix::BaseComponentSE< TElastix >
typedef Configuration::Pointer	ConfigurationPointer

typedef Configuration	ConfigurationType

typedef itk::WeakPointer< ElastixType >	ElastixPointer

typedef TElastix	ElastixType

typedef RegistrationType *	RegistrationPointer

typedef ElastixType::RegistrationBaseType	RegistrationType

typedef BaseComponentSE	Self

typedef BaseComponent	Superclass

Public Member Functions
void	AfterRegistrationBase (void) override

int	BeforeAllBase (void) override

virtual int	BeforeAllTransformix (void)

void	BeforeRegistrationBase (void) override

virtual void	ComputeDeterminantOfSpatialJacobian (void) const

virtual void	ComputeSpatialJacobian (void) const

virtual void	CreateTransformParametersMap (const ParametersType &param, ParameterMapType *paramsMap) const

DeformationFieldImageType::Pointer	GenerateDeformationFieldImage (void) const

virtual CombinationTransformType *	GetAsCombinationTransform (void)

virtual const CombinationTransformType *	GetAsCombinationTransform (void) const

virtual ITKBaseType *	GetAsITKBaseType (void)

virtual const ITKBaseType *	GetAsITKBaseType (void) const

virtual const char *	GetClassName () const

virtual const InitialTransformType *	GetInitialTransform (void) const

virtual const char *	GetTransformParametersFileName () const

	ITK_DISALLOW_COPY_AND_ASSIGN (TransformBase)

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

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

virtual void	ReadFromFile (void)

virtual void	ReadInitialTransformFromFile (const char *transformParameterFileName)

virtual void	ReadInitialTransformFromVector (const vcl_size_t index)

virtual void	SetFinalParameters (void)

virtual void	SetInitialTransform (InitialTransformType *_arg)

virtual void	SetReadWriteTransformParameters (const bool _arg)

virtual void	SetTransformParametersFileName (const char *filename)

virtual void	TransformPoints (void) const

virtual void	TransformPointsAllPoints (void) const

virtual void	TransformPointsSomePoints (const std::string filename) const

virtual void	TransformPointsSomePointsVTK (const std::string filename) const

void	WriteDeformationFieldImage (typename DeformationFieldImageType::Pointer) const

virtual void	WriteToFile (const ParametersType &param) const

virtual void	WriteToFile (void) const

Public Member Functions inherited from elastix::BaseComponentSE< TElastix >
ConfigurationType *	GetConfiguration (void) const

ElastixType *	GetElastix (void) const

RegistrationPointer	GetRegistration (void) const

	ITK_DISALLOW_COPY_AND_ASSIGN (BaseComponentSE)

void	SetConfiguration (ConfigurationType *_arg)

void	SetElastix (ElastixType *_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)

Protected Member Functions
void	AutomaticScalesEstimation (ScalesType &scales) const

void	AutomaticScalesEstimationStackTransform (const unsigned int &numSubTransforms, ScalesType &scales) const

	TransformBase ()=default

	~TransformBase () override=default

Protected Member Functions inherited from elastix::BaseComponentSE< TElastix >
	BaseComponentSE ()=default

	~BaseComponentSE () override=default

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

virtual	~BaseComponent ()=default

Private Member Functions
std::string	GetInitialTransformParametersFileName (void) const

Private Attributes
ParametersType	m_FinalParameters

bool	m_ReadWriteTransformParameters { true }

std::string	m_TransformParametersFileName

std::unique_ptr< ParametersType >	m_TransformParametersPointer {}

bool	m_UseBinaryFormatForTransformationParameters {}

Additional Inherited Members
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 Attributes inherited from elastix::BaseComponentSE< TElastix >
ConfigurationPointer	m_Configuration {}

ElastixPointer	m_Elastix {}

RegistrationPointer	m_Registration {}

Member Typedef Documentation

◆ CombinationTransformType

template<class TElastix >

typedef itk::AdvancedCombinationTransform< CoordRepType, itkGetStaticConstMacro( FixedImageDimension ) > elastix::TransformBase< TElastix >::CombinationTransformType

Definition at line 182 of file elxTransformBase.h.

◆ CommandLineArgumentMapType

template<class TElastix >

typedef ConfigurationType::CommandLineArgumentMapType elastix::TransformBase< TElastix >::CommandLineArgumentMapType

Definition at line 150 of file elxTransformBase.h.

◆ CommandLineEntryType

template<class TElastix >

typedef ConfigurationType::CommandLineEntryType elastix::TransformBase< TElastix >::CommandLineEntryType

Definition at line 152 of file elxTransformBase.h.

◆ ComponentDatabaseType

template<class TElastix >

typedef ComponentDatabase elastix::TransformBase< TElastix >::ComponentDatabaseType

Typedef's from ComponentDatabase.

Definition at line 160 of file elxTransformBase.h.

◆ ComponentDescriptionType

template<class TElastix >

typedef ComponentDatabaseType::ComponentDescriptionType elastix::TransformBase< TElastix >::ComponentDescriptionType

Definition at line 161 of file elxTransformBase.h.

◆ ConfigurationPointer

template<class TElastix >

typedef Configuration::Pointer elastix::BaseComponentSE< TElastix >::ConfigurationPointer

Definition at line 59 of file elxBaseComponentSE.h.

◆ ConfigurationType

template<class TElastix >

typedef Configuration elastix::BaseComponentSE< TElastix >::ConfigurationType

ConfigurationType.

Definition at line 58 of file elxBaseComponentSE.h.

◆ CoordRepType

template<class TElastix >

typedef ElastixType::CoordRepType elastix::TransformBase< TElastix >::CoordRepType

Elastix typedef's.

Definition at line 155 of file elxTransformBase.h.

◆ DeformationFieldImageType

template<class TElastix >

typedef itk::Image< VectorPixelType, FixedImageDimension > elastix::TransformBase< TElastix >::DeformationFieldImageType

Definition at line 198 of file elxTransformBase.h.

◆ ElastixPointer

template<class TElastix >

typedef itk::WeakPointer< ElastixType > elastix::BaseComponentSE< TElastix >::ElastixPointer

Definition at line 55 of file elxBaseComponentSE.h.

◆ ElastixType

template<class TElastix >

typedef TElastix elastix::BaseComponentSE< TElastix >::ElastixType

Elastix typedef's.

Definition at line 54 of file elxBaseComponentSE.h.

◆ FixedImageType

template<class TElastix >

typedef ElastixType::FixedImageType elastix::TransformBase< TElastix >::FixedImageType

Definition at line 156 of file elxTransformBase.h.

◆ InitialTransformType

template<class TElastix >

typedef CombinationTransformType::InitialTransformType elastix::TransformBase< TElastix >::InitialTransformType

Definition at line 184 of file elxTransformBase.h.

◆ InputPointType

template<class TElastix >

typedef ITKBaseType::InputPointType elastix::TransformBase< TElastix >::InputPointType

Typedef's for TransformPoint.

Definition at line 191 of file elxTransformBase.h.

◆ ITKBaseType

template<class TElastix >

typedef itk::AdvancedTransform< CoordRepType, itkGetStaticConstMacro( FixedImageDimension ), itkGetStaticConstMacro( MovingImageDimension ) > elastix::TransformBase< TElastix >::ITKBaseType

Definition at line 180 of file elxTransformBase.h.

◆ ITKRegistrationType

template<class TElastix >

typedef RegistrationType::ITKBaseType elastix::TransformBase< TElastix >::ITKRegistrationType

Typedefs needed for AutomaticScalesEstimation function

Definition at line 201 of file elxTransformBase.h.

◆ MovingImageType

template<class TElastix >

typedef ElastixType::MovingImageType elastix::TransformBase< TElastix >::MovingImageType

Definition at line 157 of file elxTransformBase.h.

◆ ObjectType

template<class TElastix >

typedef itk::Object elastix::TransformBase< TElastix >::ObjectType

Other typedef's.

Definition at line 176 of file elxTransformBase.h.

◆ OptimizerType

template<class TElastix >

typedef ITKRegistrationType::OptimizerType elastix::TransformBase< TElastix >::OptimizerType

Definition at line 202 of file elxTransformBase.h.

◆ OutputPointType

template<class TElastix >

typedef ITKBaseType::OutputPointType elastix::TransformBase< TElastix >::OutputPointType

Definition at line 192 of file elxTransformBase.h.

◆ ParameterMapType

template<class TElastix >

typedef ElastixType::ParameterMapType elastix::TransformBase< TElastix >::ParameterMapType

Typedef that is used in the elastix dll version.

Definition at line 206 of file elxTransformBase.h.

◆ ParametersType

template<class TElastix >

typedef ITKBaseType::ParametersType elastix::TransformBase< TElastix >::ParametersType

Typedef's from Transform.

Definition at line 187 of file elxTransformBase.h.

◆ ProgressCommandType

template<class TElastix >

typedef elx::ProgressCommand elastix::TransformBase< TElastix >::ProgressCommandType

Typedef for the ProgressCommand.

Definition at line 165 of file elxTransformBase.h.

◆ PtrToCreator

template<class TElastix >

typedef ComponentDatabase::PtrToCreator elastix::TransformBase< TElastix >::PtrToCreator

Definition at line 162 of file elxTransformBase.h.

◆ RegistrationPointer

template<class TElastix >

typedef RegistrationType* elastix::BaseComponentSE< TElastix >::RegistrationPointer

Definition at line 65 of file elxBaseComponentSE.h.

◆ RegistrationType

template<class TElastix >

typedef ElastixType::RegistrationBaseType elastix::BaseComponentSE< TElastix >::RegistrationType

RegistrationType; NB: this is the elx::RegistrationBase not an itk::Object or something like that.

Definition at line 64 of file elxBaseComponentSE.h.

◆ ScalesType

template<class TElastix >

typedef OptimizerType::ScalesType elastix::TransformBase< TElastix >::ScalesType

Definition at line 203 of file elxTransformBase.h.

◆ Self

template<class TElastix >

typedef TransformBase elastix::TransformBase< TElastix >::Self

Standard ITK stuff.

Definition at line 135 of file elxTransformBase.h.

◆ Superclass

template<class TElastix >

typedef BaseComponentSE< TElastix > elastix::TransformBase< TElastix >::Superclass

Definition at line 136 of file elxTransformBase.h.

◆ ValueType

template<class TElastix >

typedef ParametersType::ValueType elastix::TransformBase< TElastix >::ValueType

Definition at line 188 of file elxTransformBase.h.

◆ VectorPixelType

template<class TElastix >

typedef itk::Vector< float, FixedImageDimension > elastix::TransformBase< TElastix >::VectorPixelType

Typedef's for TransformPointsAllPoints.

Definition at line 196 of file elxTransformBase.h.

Constructor & Destructor Documentation

◆ TransformBase()

template<class TElastix >

elastix::TransformBase< TElastix >::TransformBase ( )

protecteddefault

The default-constructor.

◆ ~TransformBase()

template<class TElastix >

elastix::TransformBase< TElastix >::~TransformBase ( )

overrideprotecteddefault

The destructor.

Member Function Documentation

◆ AfterRegistrationBase()

template<class TElastix >

void elastix::TransformBase< TElastix >::AfterRegistrationBase ( void )

overridevirtual

Execute stuff after the registration:

Get and set the final parameters for the resampler.

Reimplemented from elastix::BaseComponent.

◆ AutomaticScalesEstimation()

template<class TElastix >

void elastix::TransformBase< TElastix >::AutomaticScalesEstimation ( ScalesType & scales ) const

protected

Estimate a scales vector AutomaticScalesEstimation works like this:

N=10000 points are sampled on a uniform grid on the fixed image.
Jacobians dT/dmu are computed
Scales_i = 1/N sum_x || dT / dmu_i ||^2

◆ AutomaticScalesEstimationStackTransform()

template<class TElastix >

void elastix::TransformBase< TElastix >::AutomaticScalesEstimationStackTransform	(	const unsigned int &	numSubTransforms,
		ScalesType &	scales
	)		const

protected

Estimate a scales vector for a stack transform (elxTranslationStackTransform, elxAffineStackTransform, ...) Instead of sampling along the n dimensions of the fixed image, it samples along n-1 dimensions. Then

N=10000 points are sampled.
Jacobians dT/dmu are computed
Scales_i = 1/N sum_x || dT / dmu_i ||^2

◆ BeforeAllBase()

template<class TElastix >

int elastix::TransformBase< TElastix >::BeforeAllBase ( void )

overridevirtual

Execute stuff before everything else:

Check the appearance of an initial transform.

Reimplemented from elastix::BaseComponent.

◆ BeforeAllTransformix()

template<class TElastix >

virtual int elastix::TransformBase< TElastix >::BeforeAllTransformix ( void )

virtual

Execute stuff before the actual transformation:

Check the appearance of inputpoints to be transformed.

◆ BeforeRegistrationBase()

template<class TElastix >

void elastix::TransformBase< TElastix >::BeforeRegistrationBase ( void )

overridevirtual

Execute stuff before the actual registration:

Set the initial transform and how to group transforms.

Reimplemented from elastix::BaseComponent.

◆ ComputeDeterminantOfSpatialJacobian()

template<class TElastix >

virtual void elastix::TransformBase< TElastix >::ComputeDeterminantOfSpatialJacobian ( void ) const

virtual

Function to compute the determinant of the spatial Jacobian.

◆ ComputeSpatialJacobian()

template<class TElastix >

virtual void elastix::TransformBase< TElastix >::ComputeSpatialJacobian ( void ) const

virtual

Function to compute the determinant of the spatial Jacobian.

◆ CreateTransformParametersMap()

template<class TElastix >

virtual void elastix::TransformBase< TElastix >::CreateTransformParametersMap	(	const ParametersType &	param,
		ParameterMapType *	paramsMap
	)		const

virtual

Function to create transform-parameters map.

Reimplemented in elastix::AdvancedAffineTransformElastix< TElastix >, elastix::AdvancedBSplineTransform< TElastix >, elastix::BSplineStackTransform< TElastix >, elastix::EulerTransformElastix< TElastix >, and elastix::RecursiveBSplineTransform< TElastix >.

◆ GenerateDeformationFieldImage()

template<class TElastix >

DeformationFieldImageType::Pointer elastix::TransformBase< TElastix >::GenerateDeformationFieldImage ( void ) const

Deprecation note: The plan is to split all Compute* and TransformPoints* functions into Generate* and Write* functions, since that would facilitate a proper library interface. To keep everything functional during the transition period we need to keep the orignal Compute* and TransformPoints* functions and let them just call Generate* and Write*. These functions should be considered marked deprecated. Function to transform all coordinates from fixed to moving image.

◆ GetAsCombinationTransform() [1/2]

template<class TElastix >

virtual CombinationTransformType * elastix::TransformBase< TElastix >::GetAsCombinationTransform ( void )

inlinevirtual

Definition at line 228 of file elxTransformBase.h.

◆ GetAsCombinationTransform() [2/2]

template<class TElastix >

virtual const CombinationTransformType * elastix::TransformBase< TElastix >::GetAsCombinationTransform ( void ) const

inlinevirtual

Definition at line 222 of file elxTransformBase.h.

◆ GetAsITKBaseType() [1/2]

template<class TElastix >

virtual ITKBaseType * elastix::TransformBase< TElastix >::GetAsITKBaseType ( void )

inlinevirtual

Cast to ITKBaseType.

Definition at line 209 of file elxTransformBase.h.

◆ GetAsITKBaseType() [2/2]

template<class TElastix >

virtual const ITKBaseType * elastix::TransformBase< TElastix >::GetAsITKBaseType ( void ) const

inlinevirtual

Cast to ITKBaseType, to use in const functions.

Definition at line 216 of file elxTransformBase.h.

◆ GetClassName()

template<class TElastix >

virtual const char * elastix::TransformBase< TElastix >::GetClassName ( ) const

virtual

Run-time type information (and related methods).

◆ GetInitialTransform()

template<class TElastix >

virtual const InitialTransformType * elastix::TransformBase< TElastix >::GetInitialTransform ( void ) const

virtual

Get the initial transform.

◆ GetInitialTransformParametersFileName()

template<class TElastix >

std::string elastix::TransformBase< TElastix >::GetInitialTransformParametersFileName ( void ) const

inlineprivate

Definition at line 361 of file elxTransformBase.h.

◆ GetTransformParametersFileName()

template<class TElastix >

virtual const char * elastix::TransformBase< TElastix >::GetTransformParametersFileName ( ) const

virtual

Get the TransformParametersFileName.

◆ ITK_DISALLOW_COPY_AND_ASSIGN()

template<class TElastix >

elastix::TransformBase< TElastix >::ITK_DISALLOW_COPY_AND_ASSIGN ( TransformBase< TElastix > )

◆ itkStaticConstMacro() [1/2]

template<class TElastix >

elastix::TransformBase< TElastix >::itkStaticConstMacro	(	FixedImageDimension	,
		unsigned int	,
		FixedImageType::ImageDimension
	)

Get the dimension of the fixed image.

◆ itkStaticConstMacro() [2/2]

template<class TElastix >

elastix::TransformBase< TElastix >::itkStaticConstMacro	(	MovingImageDimension	,
		unsigned int	,
		MovingImageType::ImageDimension
	)

Get the dimension of the moving image.

◆ ReadFromFile()

template<class TElastix >

virtual void elastix::TransformBase< TElastix >::ReadFromFile ( void )

virtual

Function to read transform-parameters from a file.

◆ ReadInitialTransformFromFile()

template<class TElastix >

virtual void elastix::TransformBase< TElastix >::ReadInitialTransformFromFile ( const char * transformParameterFileName )

virtual

Function to read the initial transform parameters from a file.

◆ ReadInitialTransformFromVector()

template<class TElastix >

virtual void elastix::TransformBase< TElastix >::ReadInitialTransformFromVector ( const vcl_size_t index )

virtual

Function to read the initial transform parameters from the internally stored configuration object.

◆ SetFinalParameters()

template<class TElastix >

virtual void elastix::TransformBase< TElastix >::SetFinalParameters ( void )

virtual

Makes sure that the final parameters from the registration components are copied, set, and stored.

◆ SetInitialTransform()

template<class TElastix >

virtual void elastix::TransformBase< TElastix >::SetInitialTransform ( InitialTransformType * _arg )

virtual

Set the initial transform.

◆ SetReadWriteTransformParameters()

template<class TElastix >

virtual void elastix::TransformBase< TElastix >::SetReadWriteTransformParameters ( const bool _arg )

virtual

Macro for reading and writing the transform parameters in WriteToFile or not.

◆ SetTransformParametersFileName()

template<class TElastix >

virtual void elastix::TransformBase< TElastix >::SetTransformParametersFileName ( const char * filename )

virtual

Set the TransformParametersFileName.

◆ TransformPoints()

template<class TElastix >

virtual void elastix::TransformBase< TElastix >::TransformPoints ( void ) const

virtual

Function to transform coordinates from fixed to moving image.

◆ TransformPointsAllPoints()

template<class TElastix >

virtual void elastix::TransformBase< TElastix >::TransformPointsAllPoints ( void ) const

virtual

Legacy function that calls GenerateDeformationFieldImage and WriteDeformationFieldImage.

◆ TransformPointsSomePoints()

template<class TElastix >

virtual void elastix::TransformBase< TElastix >::TransformPointsSomePoints ( const std::string filename ) const

virtual

Function to transform coordinates from fixed to moving image.

◆ TransformPointsSomePointsVTK()

template<class TElastix >

virtual void elastix::TransformBase< TElastix >::TransformPointsSomePointsVTK ( const std::string filename ) const

virtual

Function to transform coordinates from fixed to moving image, given as VTK file.

◆ WriteDeformationFieldImage()

template<class TElastix >

void elastix::TransformBase< TElastix >::WriteDeformationFieldImage ( typename DeformationFieldImageType::Pointer ) const

◆ WriteToFile() [1/2]

template<class TElastix >

virtual void elastix::TransformBase< TElastix >::WriteToFile ( const ParametersType & param ) const

virtual

Function to write transform-parameters to a file.

◆ WriteToFile() [2/2]

template<class TElastix >

virtual void elastix::TransformBase< TElastix >::WriteToFile ( void ) const

virtual

Function to write transform-parameters to a file.

Field Documentation

◆ m_FinalParameters

template<class TElastix >

ParametersType elastix::TransformBase< TElastix >::m_FinalParameters

private

Definition at line 356 of file elxTransformBase.h.

◆ m_ReadWriteTransformParameters

template<class TElastix >

bool elastix::TransformBase< TElastix >::m_ReadWriteTransformParameters { true }

private

Boolean to decide whether or not the transform parameters are written.

Definition at line 359 of file elxTransformBase.h.

◆ m_TransformParametersFileName

template<class TElastix >

std::string elastix::TransformBase< TElastix >::m_TransformParametersFileName

private

Definition at line 355 of file elxTransformBase.h.

◆ m_TransformParametersPointer

template<class TElastix >

std::unique_ptr<ParametersType> elastix::TransformBase< TElastix >::m_TransformParametersPointer {}

private

Member variables.

Definition at line 354 of file elxTransformBase.h.

◆ m_UseBinaryFormatForTransformationParameters

template<class TElastix >

bool elastix::TransformBase< TElastix >::m_UseBinaryFormatForTransformationParameters {}

private

Boolean to decide whether or not the transform parameters are written in binary format.

Definition at line 373 of file elxTransformBase.h.

Detailed Description

Public Types

Public Member Functions

Protected Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Member Typedef Documentation

◆ CombinationTransformType

◆ CommandLineArgumentMapType

◆ CommandLineEntryType

◆ ComponentDatabaseType

◆ ComponentDescriptionType

◆ ConfigurationPointer

◆ ConfigurationType

◆ CoordRepType

◆ DeformationFieldImageType

◆ ElastixPointer

◆ ElastixType

◆ FixedImageType

◆ InitialTransformType

◆ InputPointType

◆ ITKBaseType

◆ ITKRegistrationType

◆ MovingImageType

◆ ObjectType

◆ OptimizerType

◆ OutputPointType

◆ ParameterMapType

◆ ParametersType

◆ ProgressCommandType

◆ PtrToCreator

◆ RegistrationPointer

◆ RegistrationType

◆ ScalesType

◆ Self

◆ Superclass

◆ ValueType

◆ VectorPixelType

Constructor & Destructor Documentation

◆ TransformBase()

◆ ~TransformBase()

Member Function Documentation

◆ AfterRegistrationBase()

◆ AutomaticScalesEstimation()

◆ AutomaticScalesEstimationStackTransform()

◆ BeforeAllBase()

◆ BeforeAllTransformix()

◆ BeforeRegistrationBase()

◆ ComputeDeterminantOfSpatialJacobian()

◆ ComputeSpatialJacobian()

◆ CreateTransformParametersMap()

◆ GenerateDeformationFieldImage()

◆ GetAsCombinationTransform() [1/2]

◆ GetAsCombinationTransform() [2/2]

◆ GetAsITKBaseType() [1/2]

◆ GetAsITKBaseType() [2/2]

◆ GetClassName()

◆ GetInitialTransform()

◆ GetInitialTransformParametersFileName()

◆ GetTransformParametersFileName()

◆ ITK_DISALLOW_COPY_AND_ASSIGN()

◆ itkStaticConstMacro() [1/2]

◆ itkStaticConstMacro() [2/2]

◆ ReadFromFile()

◆ ReadInitialTransformFromFile()

◆ ReadInitialTransformFromVector()

◆ SetFinalParameters()

◆ SetInitialTransform()

◆ SetReadWriteTransformParameters()

◆ SetTransformParametersFileName()

◆ TransformPoints()

◆ TransformPointsAllPoints()

◆ TransformPointsSomePoints()

◆ TransformPointsSomePointsVTK()

◆ WriteDeformationFieldImage()

◆ WriteToFile() [1/2]

◆ WriteToFile() [2/2]

Field Documentation

◆ m_FinalParameters