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elastix::TransformBase< TElastix > Class Template Referenceabstract
Components » Transforms | Core » Component Base Classes

#include <elxTransformBase.h>

Detailed Description

template<typename 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 $T_0$ and the current transform $T_1$ (which is currently optimized) by addition: $T(x) = T_0(x) + T_1(x)$;
"Compose" by composition: $T(x) = T_1 ( T_0(x) )$.
example: (HowToCombineTransforms "Add")
Default: "Add".
Transform Parameters

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 $T_0$ and the current transform $T_1$ (which is currently optimized) by addition: $T(x) = T_0(x) + T_1(x)$;
"Compose" by composition: $T(x) = T_1 ( T_0(x) )$.
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".
The matrix elements must be sorted as follows: [ d11 d21 d31 d12 d22 d32 d13 d23 d33] (in 3D). So the elements must be specified in column-major order (Fortran-style). Please note: This is not the same as ITK's convention of using row-major order (C-style) for flattening the direction matrix of an image into a list.
example: (Direction -1.0 0.0 0.0 0.0 1.0 0.0 0.0 0.0 0.1)
Default: identity matrix.

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)

InitialTransformParameterFileName: 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 (InitialTransformParameterFileName "./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.

InitialTransformParametersFileName: legacy parameter name, replaced with "InitialTransformParameterFileName", and deprecated from June 2023.

Transform Parameters
OutputTransformParameterFileFormat: The file format of the transform parameter files written to the output directory. Possible values: "txt" (the legacy parameter file format) and "TOML". Default: "txt".

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 144 of file elxTransformBase.h.

Inheritance diagram for elastix::TransformBase< TElastix >:

Public Types

using CombinationTransformType = itk::AdvancedCombinationTransform<CoordinateType, Self::FixedImageDimension>
using CommandLineArgumentMapType = Configuration ::CommandLineArgumentMapType
using CommandLineEntryType = Configuration ::CommandLineEntryType
using ComponentDescriptionType = ComponentDatabase::ComponentDescriptionType
using CoordinateType = ElastixBase::CoordinateType
using DeformationFieldImageType = itk::Image<VectorPixelType, FixedImageDimension>
using FixedImageType = typename TElastix::FixedImageType
using InitialTransformType = typename CombinationTransformType::InitialTransformType
using InputPointType = typename ITKBaseType::InputPointType
using ITKBaseType = CombinationTransformType
using ITKRegistrationType = typename RegistrationType::ITKBaseType
using MovingImageType = typename TElastix::MovingImageType
using OptimizerType = typename ITKRegistrationType::OptimizerType
using OutputPointType = typename ITKBaseType::OutputPointType
using ParameterMapType = typename TElastix::ParameterMapType
using ParametersType = itk::OptimizerParameters<ValueType>
using PtrToCreator = ComponentDatabase::PtrToCreator
using RegistrationType
using ScalesType = itk::Optimizer::ScalesType
using Self = TransformBase
using SpatialJacobianDeterminantImageType = itk::Image<float, FixedImageDimension>
using SpatialJacobianMatrixImageType
using Superclass = BaseComponentSE<TElastix>
using ValueType = double
using VectorPixelType = itk::Vector<float, FixedImageDimension>
Public Types inherited from elastix::BaseComponentSE< TElastix >
using ElastixType = TElastix
using RegistrationType = typename ElastixType::RegistrationBaseType
using Self = BaseComponentSE
using Superclass = BaseComponent

Public Member Functions

int BeforeAllTransformix ()
void ComputeAndWriteSpatialJacobianDeterminantImage () const
void ComputeAndWriteSpatialJacobianMatrixImage () const
SpatialJacobianDeterminantImageType::Pointer ComputeSpatialJacobianDeterminantImage () const
SpatialJacobianMatrixImageType::Pointer ComputeSpatialJacobianMatrixImage () const
void CreateTransformParameterMap (const ParametersType &param, ParameterMapType &parameterMap, const bool includeDerivedTransformParameters=true) const
ITKBaseType * GetAsITKBaseType ()
const ITKBaseType * GetAsITKBaseType () const
 ITK_DISALLOW_COPY_AND_MOVE (TransformBase)
 itkOverrideGetNameOfClassMacro (TransformBase)
 itkStaticConstMacro (FixedImageDimension, unsigned int, FixedImageType::ImageDimension)
 itkStaticConstMacro (MovingImageDimension, unsigned int, MovingImageType::ImageDimension)
virtual void ReadFromFile ()
void ReadInitialTransformFromFile (const std::string &transformParameterFileName)
void SetFinalParameters ()
void SetInitialTransform (InitialTransformType *_arg)
void SetReadWriteTransformParameters (const bool _arg)
void SetTransformParameterFileName (const std::string &filename)
template<typename TMesh>
TMesh::Pointer TransformMesh (const TMesh &mesh) const
void TransformPoints () const
void WriteToFile (std::ostream &transformationParameterInfo, const ParametersType &param) const
Public Member Functions inherited from elastix::BaseComponentSE< TElastix >
void AddTargetCellToIterationInfo (const char *const name)
const Configuration * GetConfiguration () const
ElastixType * GetElastix () const
auto & GetIterationInfoAt (const char *const name)
itk::Statistics::MersenneTwisterRandomVariateGenerator & GetRandomVariateGenerator ()
RegistrationType * GetRegistration () const
 ITK_DISALLOW_COPY_AND_MOVE (BaseComponentSE)
void RemoveTargetCellFromIterationInfo (const char *const name)
void SetConfiguration (const Configuration *_arg)
void SetElastix (ElastixType *_arg)
Public Member Functions inherited from elastix::BaseComponent
virtual void AfterEachIteration ()
virtual void AfterEachIterationBase ()
virtual void AfterEachResolution ()
virtual void AfterEachResolutionBase ()
virtual void AfterRegistration ()
virtual int BeforeAll ()
virtual void BeforeEachResolution ()
virtual void BeforeEachResolutionBase ()
virtual void BeforeRegistration ()
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)

Protected Member Functions

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

void AfterRegistrationBase () override
int BeforeAllBase () override
void BeforeRegistrationBase () override
template<typename TImage>
auto CreateChangeInformationImageFilter (TImage *image) const
virtual ParameterMapType CreateDerivedTransformParameterMap () const =0
template<template< typename, typename > class TSource, typename TOutputImage>
auto CreateJacobianSource () const
 elxDeclarePureVirtualGetSelfMacro (ITKBaseType)
DeformationFieldImageType::Pointer GenerateDeformationFieldImage () const
const InitialTransformType * GetInitialTransform () const
std::string GetInitialTransformParameterFileName () const
virtual const char * GetTransformParameterFileName () const
void ReadInitialTransformFromConfiguration (const Configuration::ConstPointer)
void TransformPointsAllPoints () const
void TransformPointsSomePoints (const std::string &filename) const
void TransformPointsSomePointsVTK (const std::string &filename) const
void WriteDeformationFieldImage (typename DeformationFieldImageType::Pointer) const
virtual void WriteDerivedTransformDataToFile () const

Private Attributes

ParametersType m_FinalParameters
bool m_ReadWriteTransformParameters { true }
std::string m_TransformParameterFileName
ParametersType m_TransformParameters

Additional Inherited Members

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 ()
Protected Attributes inherited from elastix::BaseComponentSE< TElastix >
Configuration::ConstPointer m_Configuration {}
itk::WeakPointer< TElastix > m_Elastix {}
RegistrationType * m_Registration {}

Member Typedef Documentation

◆ CombinationTransformType

template<typename TElastix>
using elastix::TransformBase< TElastix >::CombinationTransformType = itk::AdvancedCombinationTransform<CoordinateType, Self::FixedImageDimension>

Other typedef's.

Definition at line 178 of file elxTransformBase.h.

◆ CommandLineArgumentMapType

template<typename TElastix>
using elastix::TransformBase< TElastix >::CommandLineArgumentMapType = Configuration ::CommandLineArgumentMapType

Definition at line 159 of file elxTransformBase.h.

◆ CommandLineEntryType

template<typename TElastix>
using elastix::TransformBase< TElastix >::CommandLineEntryType = Configuration ::CommandLineEntryType

Definition at line 160 of file elxTransformBase.h.

◆ ComponentDescriptionType

template<typename TElastix>
using elastix::TransformBase< TElastix >::ComponentDescriptionType = ComponentDatabase::ComponentDescriptionType

Typedef's from ComponentDatabase.

Definition at line 168 of file elxTransformBase.h.

◆ CoordinateType

template<typename TElastix>
using elastix::TransformBase< TElastix >::CoordinateType = ElastixBase::CoordinateType

Elastix typedef's.

Definition at line 163 of file elxTransformBase.h.

◆ DeformationFieldImageType

template<typename TElastix>
using elastix::TransformBase< TElastix >::DeformationFieldImageType = itk::Image<VectorPixelType, FixedImageDimension>

Definition at line 192 of file elxTransformBase.h.

◆ FixedImageType

template<typename TElastix>
using elastix::TransformBase< TElastix >::FixedImageType = typename TElastix::FixedImageType

Definition at line 164 of file elxTransformBase.h.

◆ InitialTransformType

template<typename TElastix>
using elastix::TransformBase< TElastix >::InitialTransformType = typename CombinationTransformType::InitialTransformType

Definition at line 180 of file elxTransformBase.h.

◆ InputPointType

template<typename TElastix>
using elastix::TransformBase< TElastix >::InputPointType = typename ITKBaseType::InputPointType

Typedef's for TransformPoint.

Definition at line 187 of file elxTransformBase.h.

◆ ITKBaseType

template<typename TElastix>
using elastix::TransformBase< TElastix >::ITKBaseType = CombinationTransformType

Definition at line 179 of file elxTransformBase.h.

◆ ITKRegistrationType

template<typename TElastix>
using elastix::TransformBase< TElastix >::ITKRegistrationType = typename RegistrationType::ITKBaseType

Typedefs needed for AutomaticScalesEstimation function

Definition at line 195 of file elxTransformBase.h.

◆ MovingImageType

template<typename TElastix>
using elastix::TransformBase< TElastix >::MovingImageType = typename TElastix::MovingImageType

Definition at line 165 of file elxTransformBase.h.

◆ OptimizerType

template<typename TElastix>
using elastix::TransformBase< TElastix >::OptimizerType = typename ITKRegistrationType::OptimizerType

Definition at line 196 of file elxTransformBase.h.

◆ OutputPointType

template<typename TElastix>
using elastix::TransformBase< TElastix >::OutputPointType = typename ITKBaseType::OutputPointType

Definition at line 188 of file elxTransformBase.h.

◆ ParameterMapType

template<typename TElastix>
using elastix::TransformBase< TElastix >::ParameterMapType = typename TElastix::ParameterMapType

Typedef that is used in the elastix dll version.

Definition at line 206 of file elxTransformBase.h.

◆ ParametersType

template<typename TElastix>
using elastix::TransformBase< TElastix >::ParametersType = itk::OptimizerParameters<ValueType>

Definition at line 184 of file elxTransformBase.h.

◆ PtrToCreator

template<typename TElastix>
using elastix::TransformBase< TElastix >::PtrToCreator = ComponentDatabase::PtrToCreator

Definition at line 169 of file elxTransformBase.h.

◆ RegistrationType

template<typename TElastix>
using elastix::BaseComponentSE< TElastix >::RegistrationType

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

Definition at line 63 of file elxBaseComponentSE.h.

◆ ScalesType

template<typename TElastix>
using elastix::TransformBase< TElastix >::ScalesType = itk::Optimizer::ScalesType

Definition at line 197 of file elxTransformBase.h.

◆ Self

template<typename TElastix>
using elastix::TransformBase< TElastix >::Self = TransformBase

Standard ITK stuff.

Definition at line 150 of file elxTransformBase.h.

◆ SpatialJacobianDeterminantImageType

template<typename TElastix>
using elastix::TransformBase< TElastix >::SpatialJacobianDeterminantImageType = itk::Image<float, FixedImageDimension>

Typedefs for images of determinants of spatial Jacobian matrices, and images of spatial Jacobian matrices

Definition at line 200 of file elxTransformBase.h.

◆ SpatialJacobianMatrixImageType

template<typename TElastix>
using elastix::TransformBase< TElastix >::SpatialJacobianMatrixImageType
Initial value:
itk::Image<itk::Matrix<float, MovingImageDimension, FixedImageDimension>, FixedImageDimension>

Definition at line 201 of file elxTransformBase.h.

◆ Superclass

template<typename TElastix>
using elastix::TransformBase< TElastix >::Superclass = BaseComponentSE<TElastix>

Definition at line 151 of file elxTransformBase.h.

◆ ValueType

template<typename TElastix>
using elastix::TransformBase< TElastix >::ValueType = double

Typedef's for parameters.

Definition at line 183 of file elxTransformBase.h.

◆ VectorPixelType

template<typename TElastix>
using elastix::TransformBase< TElastix >::VectorPixelType = itk::Vector<float, FixedImageDimension>

Typedef's for TransformPointsAllPoints.

Definition at line 191 of file elxTransformBase.h.

Constructor & Destructor Documentation

◆ TransformBase()

template<typename TElastix>
elastix::TransformBase< TElastix >::TransformBase ( )
protecteddefault

The default-constructor.

◆ ~TransformBase()

template<typename TElastix>
elastix::TransformBase< TElastix >::~TransformBase ( )
overrideprotecteddefault

The destructor.

Member Function Documentation

◆ AfterRegistrationBase()

template<typename TElastix>
void elastix::TransformBase< TElastix >::AfterRegistrationBase ( )
overrideprivatevirtual

Execute stuff after the registration:

  • Get and set the final parameters for the resampler.

Reimplemented from elastix::BaseComponent.

◆ AutomaticScalesEstimation()

template<typename 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<typename 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<typename TElastix>
int elastix::TransformBase< TElastix >::BeforeAllBase ( )
overrideprivatevirtual

Execute stuff before everything else:

  • Check the appearance of an initial transform.

Reimplemented from elastix::BaseComponent.

◆ BeforeAllTransformix()

template<typename TElastix>
int elastix::TransformBase< TElastix >::BeforeAllTransformix ( )

Execute stuff before the actual transformation:

  • Check the appearance of inputpoints to be transformed.

◆ BeforeRegistrationBase()

template<typename TElastix>
void elastix::TransformBase< TElastix >::BeforeRegistrationBase ( )
overrideprivatevirtual

Execute stuff before the actual registration:

  • Set the initial transform and how to group transforms.

Reimplemented from elastix::BaseComponent.

◆ ComputeAndWriteSpatialJacobianDeterminantImage()

template<typename TElastix>
void elastix::TransformBase< TElastix >::ComputeAndWriteSpatialJacobianDeterminantImage ( ) const

Computes the determinant of the spatial Jacobian and writes it to file.

◆ ComputeAndWriteSpatialJacobianMatrixImage()

template<typename TElastix>
void elastix::TransformBase< TElastix >::ComputeAndWriteSpatialJacobianMatrixImage ( ) const

Computes the spatial Jacobian and writes it to file.

◆ ComputeSpatialJacobianDeterminantImage()

template<typename TElastix>
SpatialJacobianDeterminantImageType::Pointer elastix::TransformBase< TElastix >::ComputeSpatialJacobianDeterminantImage ( ) const

Computes the spatial Jacobian determinant for each pixel, and returns the image.

◆ ComputeSpatialJacobianMatrixImage()

template<typename TElastix>
SpatialJacobianMatrixImageType::Pointer elastix::TransformBase< TElastix >::ComputeSpatialJacobianMatrixImage ( ) const

Computes the spatial Jacobian matrix for each pixel, and returns the image.

◆ CreateChangeInformationImageFilter()

template<typename TElastix>
template<typename TImage>
auto elastix::TransformBase< TElastix >::CreateChangeInformationImageFilter ( TImage * image) const
inlineprivate

Creates an info changer that may change the direction of the image to the original value.

Definition at line 361 of file elxTransformBase.h.

◆ CreateDerivedTransformParameterMap()

template<typename TElastix>
virtual ParameterMapType elastix::TransformBase< TElastix >::CreateDerivedTransformParameterMap ( ) const
privatepure virtual

Implemented in elastix::AdvancedAffineTransformElastix< TElastix >, elastix::AdvancedBSplineTransform< TElastix >, elastix::AffineDTITransformElastix< TElastix >, elastix::AffineLogStackTransform< TElastix >, elastix::AffineLogTransformElastix< TElastix >, elastix::BSplineStackTransform< TElastix >, elastix::BSplineTransformWithDiffusion< TElastix >, elastix::DeformationFieldTransform< TElastix >, elastix::EulerStackTransform< TElastix >, elastix::EulerTransformElastix< TElastix >, elastix::ExternalTransform< TElastix >, elastix::MultiBSplineTransformWithNormal< TElastix >, elastix::RecursiveBSplineTransform< TElastix >, elastix::SimilarityTransformElastix< TElastix >, elastix::SplineKernelTransform< TElastix >, elastix::TranslationStackTransform< TElastix >, elastix::TranslationTransformElastix< TElastix >, and elastix::WeightedCombinationTransformElastix< TElastix >.

◆ CreateJacobianSource()

template<typename TElastix>
template<template< typename, typename > class TSource, typename TOutputImage>
auto elastix::TransformBase< TElastix >::CreateJacobianSource ( ) const
inlineprivate

Supports either TransformToDeterminantOfSpatialJacobianSource or TransformToSpatialJacobianSource as TSource.

Definition at line 337 of file elxTransformBase.h.

◆ CreateTransformParameterMap()

template<typename TElastix>
void elastix::TransformBase< TElastix >::CreateTransformParameterMap ( const ParametersType & param,
ParameterMapType & parameterMap,
const bool includeDerivedTransformParameters = true ) const

Function to create transform-parameters map.

◆ elxDeclarePureVirtualGetSelfMacro()

template<typename TElastix>
elastix::TransformBase< TElastix >::elxDeclarePureVirtualGetSelfMacro ( ITKBaseType )
private

◆ GenerateDeformationFieldImage()

template<typename TElastix>
DeformationFieldImageType::Pointer elastix::TransformBase< TElastix >::GenerateDeformationFieldImage ( ) const
private

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.

◆ GetAsITKBaseType() [1/2]

template<typename TElastix>
ITKBaseType * elastix::TransformBase< TElastix >::GetAsITKBaseType ( )
inline

Retrieves this object as ITKBaseType.

Definition at line 210 of file elxTransformBase.h.

◆ GetAsITKBaseType() [2/2]

template<typename TElastix>
const ITKBaseType * elastix::TransformBase< TElastix >::GetAsITKBaseType ( ) const
inline

Retrieves this object as ITKBaseType, to use in const functions.

Definition at line 218 of file elxTransformBase.h.

◆ GetInitialTransform()

template<typename TElastix>
const InitialTransformType * elastix::TransformBase< TElastix >::GetInitialTransform ( ) const
private

Get the initial transform.

◆ GetInitialTransformParameterFileName()

template<typename TElastix>
std::string elastix::TransformBase< TElastix >::GetInitialTransformParameterFileName ( ) const
inlineprivate

Definition at line 433 of file elxTransformBase.h.

◆ GetTransformParameterFileName()

template<typename TElastix>
virtual const char * elastix::TransformBase< TElastix >::GetTransformParameterFileName ( ) const
privatevirtual

Get the TransformParameterFileName.

◆ HasITKTransformParameters()

template<typename TElastix>
bool elastix::TransformBase< TElastix >::HasITKTransformParameters ( ) const
inlineprotected

Tells whether this transform is specified by TransformParameters from ITK

Definition at line 306 of file elxTransformBase.h.

◆ ITK_DISALLOW_COPY_AND_MOVE()

template<typename TElastix>
elastix::TransformBase< TElastix >::ITK_DISALLOW_COPY_AND_MOVE ( TransformBase< TElastix > )

◆ itkOverrideGetNameOfClassMacro()

template<typename TElastix>
elastix::TransformBase< TElastix >::itkOverrideGetNameOfClassMacro ( TransformBase< TElastix > )

Run-time type information (and related methods).

◆ itkStaticConstMacro() [1/2]

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

Get the dimension of the fixed image.

◆ itkStaticConstMacro() [2/2]

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

Get the dimension of the moving image.

◆ ReadFromFile()

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

Function to read transform-parameters from a file.

Reimplemented in elastix::AdvancedAffineTransformElastix< TElastix >, elastix::AdvancedBSplineTransform< TElastix >, elastix::AffineDTITransformElastix< TElastix >, elastix::AffineLogStackTransform< TElastix >, elastix::AffineLogTransformElastix< TElastix >, elastix::BSplineStackTransform< TElastix >, elastix::BSplineTransformWithDiffusion< TElastix >, elastix::DeformationFieldTransform< TElastix >, elastix::EulerStackTransform< TElastix >, elastix::EulerTransformElastix< TElastix >, elastix::ExternalTransform< TElastix >, elastix::MultiBSplineTransformWithNormal< TElastix >, elastix::RecursiveBSplineTransform< TElastix >, elastix::SimilarityTransformElastix< TElastix >, elastix::SplineKernelTransform< TElastix >, elastix::TranslationStackTransform< TElastix >, and elastix::WeightedCombinationTransformElastix< TElastix >.

◆ ReadInitialTransformFromConfiguration()

template<typename TElastix>
void elastix::TransformBase< TElastix >::ReadInitialTransformFromConfiguration ( const Configuration::ConstPointer )
private

Function to read the initial transform parameters from the specified configuration object.

◆ ReadInitialTransformFromFile()

template<typename TElastix>
void elastix::TransformBase< TElastix >::ReadInitialTransformFromFile ( const std::string & transformParameterFileName)

Function to read the initial transform parameters from a file.

◆ SetFinalParameters()

template<typename TElastix>
void elastix::TransformBase< TElastix >::SetFinalParameters ( )

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

◆ SetInitialTransform()

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

Set the initial transform.

◆ SetReadWriteTransformParameters()

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

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

◆ SetTransformParameterFileName()

template<typename TElastix>
void elastix::TransformBase< TElastix >::SetTransformParameterFileName ( const std::string & filename)

Set the TransformParameterFileName.

◆ TransformMesh()

template<typename TElastix>
template<typename TMesh>
TMesh::Pointer elastix::TransformBase< TElastix >::TransformMesh ( const TMesh & mesh) const
inline

Transforms the specified mesh.

Definition at line 289 of file elxTransformBase.h.

◆ TransformPoints()

template<typename TElastix>
void elastix::TransformBase< TElastix >::TransformPoints ( ) const

Function to transform coordinates from fixed to moving image.

◆ TransformPointsAllPoints()

template<typename TElastix>
void elastix::TransformBase< TElastix >::TransformPointsAllPoints ( ) const
private

Legacy function that calls GenerateDeformationFieldImage and WriteDeformationFieldImage.

◆ TransformPointsSomePoints()

template<typename TElastix>
void elastix::TransformBase< TElastix >::TransformPointsSomePoints ( const std::string & filename) const
private

Function to transform coordinates from fixed to moving image.

◆ TransformPointsSomePointsVTK()

template<typename TElastix>
void elastix::TransformBase< TElastix >::TransformPointsSomePointsVTK ( const std::string & filename) const
private

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

◆ WriteDeformationFieldImage()

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

◆ WriteDerivedTransformDataToFile()

template<typename TElastix>
virtual void elastix::TransformBase< TElastix >::WriteDerivedTransformDataToFile ( ) const
inlineprivatevirtual

Allows a derived transform class to write its data to file, by overriding this member function.

Reimplemented in elastix::BSplineTransformWithDiffusion< TElastix >, and elastix::DeformationFieldTransform< TElastix >.

Definition at line 451 of file elxTransformBase.h.

◆ WriteToFile()

template<typename TElastix>
void elastix::TransformBase< TElastix >::WriteToFile ( std::ostream & transformationParameterInfo,
const ParametersType & param ) const

Function to write transform-parameters to a file.

Member Data Documentation

◆ m_FinalParameters

template<typename TElastix>
ParametersType elastix::TransformBase< TElastix >::m_FinalParameters
private

Definition at line 457 of file elxTransformBase.h.

◆ m_ReadWriteTransformParameters

template<typename TElastix>
bool elastix::TransformBase< TElastix >::m_ReadWriteTransformParameters { true }
private

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

Definition at line 460 of file elxTransformBase.h.

◆ m_TransformParameterFileName

template<typename TElastix>
std::string elastix::TransformBase< TElastix >::m_TransformParameterFileName
private

Member variables.

Definition at line 455 of file elxTransformBase.h.

◆ m_TransformParameters

template<typename TElastix>
ParametersType elastix::TransformBase< TElastix >::m_TransformParameters
private

Definition at line 456 of file elxTransformBase.h.


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