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

#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 $T_0$ 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".
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)

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.

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 137 of file elxTransformBase.h.

Inheritance diagram for elastix::TransformBase< TElastix >:
Inheritance graph
[legend]

Public Types

using CombinationTransformType = itk::AdvancedCombinationTransform<CoordRepType, Self::FixedImageDimension>
 
using CommandLineArgumentMapType = Configuration ::CommandLineArgumentMapType
 
using CommandLineEntryType = Configuration ::CommandLineEntryType
 
using ComponentDescriptionType = ComponentDatabase::ComponentDescriptionType
 
using CoordRepType = ElastixBase::CoordRepType
 
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
 
virtual const char * GetClassName () const
 
 ITK_DISALLOW_COPY_AND_MOVE (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)
 
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)
 
 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
 
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<class TElastix >
using elastix::TransformBase< TElastix >::CombinationTransformType = itk::AdvancedCombinationTransform<CoordRepType, Self::FixedImageDimension>

Other typedef's.

Definition at line 171 of file elxTransformBase.h.

◆ CommandLineArgumentMapType

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

Definition at line 152 of file elxTransformBase.h.

◆ CommandLineEntryType

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

Definition at line 153 of file elxTransformBase.h.

◆ ComponentDescriptionType

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

Typedef's from ComponentDatabase.

Definition at line 161 of file elxTransformBase.h.

◆ CoordRepType

template<class TElastix >
using elastix::TransformBase< TElastix >::CoordRepType = ElastixBase::CoordRepType

Elastix typedef's.

Definition at line 156 of file elxTransformBase.h.

◆ DeformationFieldImageType

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

Definition at line 185 of file elxTransformBase.h.

◆ FixedImageType

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

Definition at line 157 of file elxTransformBase.h.

◆ InitialTransformType

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

Definition at line 173 of file elxTransformBase.h.

◆ InputPointType

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

Typedef's for TransformPoint.

Definition at line 180 of file elxTransformBase.h.

◆ ITKBaseType

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

Definition at line 172 of file elxTransformBase.h.

◆ ITKRegistrationType

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

Typedefs needed for AutomaticScalesEstimation function

Definition at line 188 of file elxTransformBase.h.

◆ MovingImageType

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

Definition at line 158 of file elxTransformBase.h.

◆ OptimizerType

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

Definition at line 189 of file elxTransformBase.h.

◆ OutputPointType

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

Definition at line 181 of file elxTransformBase.h.

◆ ParameterMapType

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

Typedef that is used in the elastix dll version.

Definition at line 199 of file elxTransformBase.h.

◆ ParametersType

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

Definition at line 177 of file elxTransformBase.h.

◆ PtrToCreator

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

Definition at line 162 of file elxTransformBase.h.

◆ RegistrationType

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

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

Definition at line 62 of file elxBaseComponentSE.h.

◆ ScalesType

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

Definition at line 190 of file elxTransformBase.h.

◆ Self

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

Standard ITK stuff.

Definition at line 143 of file elxTransformBase.h.

◆ SpatialJacobianDeterminantImageType

template<class 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 193 of file elxTransformBase.h.

◆ SpatialJacobianMatrixImageType

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

Definition at line 194 of file elxTransformBase.h.

◆ Superclass

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

Definition at line 144 of file elxTransformBase.h.

◆ ValueType

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

Typedef's for parameters.

Definition at line 176 of file elxTransformBase.h.

◆ VectorPixelType

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

Typedef's for TransformPointsAllPoints.

Definition at line 184 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 ( )
overrideprivatevirtual

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 ( )
overrideprivatevirtual

Execute stuff before everything else:

  • Check the appearance of an initial transform.

Reimplemented from elastix::BaseComponent.

◆ BeforeAllTransformix()

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

Execute stuff before the actual transformation:

  • Check the appearance of inputpoints to be transformed.

◆ BeforeRegistrationBase()

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

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

◆ ComputeAndWriteSpatialJacobianMatrixImage()

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

Computes the spatial Jacobian and writes it to file.

◆ ComputeSpatialJacobianDeterminantImage()

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

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

◆ ComputeSpatialJacobianMatrixImage()

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

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

◆ CreateChangeInformationImageFilter()

template<class 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 354 of file elxTransformBase.h.

◆ CreateDerivedTransformParameterMap()

template<class 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<class 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 330 of file elxTransformBase.h.

◆ CreateTransformParameterMap()

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

Function to create transform-parameters map.

◆ elxDeclarePureVirtualGetSelfMacro()

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

◆ GenerateDeformationFieldImage()

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

Retrieves this object as ITKBaseType.

Definition at line 203 of file elxTransformBase.h.

◆ GetAsITKBaseType() [2/2]

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

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

Definition at line 211 of file elxTransformBase.h.

◆ GetClassName()

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

Run-time type information (and related methods).

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 >, elastix::TranslationTransformElastix< TElastix >, and elastix::WeightedCombinationTransformElastix< TElastix >.

◆ GetInitialTransform()

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

Get the initial transform.

◆ GetInitialTransformParameterFileName()

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

Definition at line 426 of file elxTransformBase.h.

◆ GetTransformParameterFileName()

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

Get the TransformParameterFileName.

◆ HasITKTransformParameters()

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

Tells whether this transform is specified by TransformParameters from ITK

Definition at line 299 of file elxTransformBase.h.

◆ ITK_DISALLOW_COPY_AND_MOVE()

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

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

◆ ReadInitialTransformFromFile()

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

Function to read the initial transform parameters from a file.

◆ SetFinalParameters()

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

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

◆ SetInitialTransform()

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

Set the initial transform.

◆ SetReadWriteTransformParameters()

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

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

◆ SetTransformParameterFileName()

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

Set the TransformParameterFileName.

◆ TransformMesh()

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

Transforms the specified mesh.

Definition at line 282 of file elxTransformBase.h.

◆ TransformPoints()

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

Function to transform coordinates from fixed to moving image.

◆ TransformPointsAllPoints()

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

Legacy function that calls GenerateDeformationFieldImage and WriteDeformationFieldImage.

◆ TransformPointsSomePoints()

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

Function to transform coordinates from fixed to moving image.

◆ TransformPointsSomePointsVTK()

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

◆ WriteDerivedTransformDataToFile()

template<class 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 444 of file elxTransformBase.h.

◆ WriteToFile()

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

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 450 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 453 of file elxTransformBase.h.

◆ m_TransformParameterFileName

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

Member variables.

Definition at line 448 of file elxTransformBase.h.

◆ m_TransformParameters

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

Definition at line 449 of file elxTransformBase.h.


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