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elastix::ElastixTemplate< TFixedImage, TMovingImage > Class Template Reference

#include <elxElastixTemplate.h>

Detailed Description

template<class TFixedImage, class TMovingImage>
class elastix::ElastixTemplate< TFixedImage, TMovingImage >

The main elastix class, which connects components and invokes the BeforeRegistration(), BeforeEachResolution(), etc. methods.

The ElastixTemplate class ...

Parameters:

WriteTransformParametersEachIteration: Controls whether to save a transform parameter file to disk in every iteration.
example: (WriteTransformParametersEachIteration "true")
This parameter can not be specified for each resolution separately. Default value: "false".

WriteTransformParametersEachResolution: Controls whether to save a transform parameter file to disk in every resolution.
example: (WriteTransformParametersEachResolution "true")
This parameter can not be specified for each resolution separately. Default value: "false".

UseDirectionCosines: Controls whether to use or ignore the direction cosines (world matrix, transform matrix) set in the images. Voxel spacing and image origin are always taken into account, regardless the setting of this parameter.
example: (UseDirectionCosines "true")
Default: false. Recommended: true. The default value is false for backward compatibility reasons. This parameter was introduced in elastix 4.3. Setting it to false means that you choose to ignore important information from the image, which relates voxel coordinates to world coordinates. Ignoring it may easily lead to left/right swaps for example, which could skrew up a (medical) analysis.

Definition at line 113 of file elxElastixTemplate.h.

Inheritance diagram for elastix::ElastixTemplate< TFixedImage, TMovingImage >:
Inheritance graph
[legend]

Public Types

typedef AfterEachIterationCommandType::Pointer AfterEachIterationCommandPointer
 
typedef itk::SimpleMemberCommand< SelfAfterEachIterationCommandType
 
typedef AfterEachResolutionCommandType::Pointer AfterEachResolutionCommandPointer
 
typedef itk::SimpleMemberCommand< SelfAfterEachResolutionCommandType
 
typedef BaseComponent BaseComponentType
 
typedef BeforeEachResolutionCommandType::Pointer BeforeEachResolutionCommandPointer
 
typedef itk::SimpleMemberCommand< SelfBeforeEachResolutionCommandType
 
typedef Superclass2::ConfigurationPointer ConfigurationPointer
 
typedef Superclass2::ConfigurationType ConfigurationType
 
typedef itk::SmartPointer< const SelfConstPointer
 
typedef itk::CostFunction::ParametersValueType CoordRepType
 
typedef Superclass2::DataObjectContainerPointer DataObjectContainerPointer
 
typedef Superclass2::DataObjectContainerType DataObjectContainerType
 
typedef Superclass2::DataObjectPointer DataObjectPointer
 
typedef Superclass2::DataObjectType DataObjectType
 
typedef Superclass2::FileNameContainerPointer FileNameContainerPointer
 
typedef Superclass2::FileNameContainerType FileNameContainerType
 
typedef FixedImageType::DirectionType FixedImageDirectionType
 
typedef FixedImageType::Pointer FixedImagePointer
 
typedef FixedImagePyramidBase< SelfFixedImagePyramidBaseType
 
typedef TFixedImage FixedImageType
 
typedef FixedMaskType::Pointer FixedMaskPointer
 
typedef itk::Image< MaskPixelType, FixedDimension > FixedMaskType
 
typedef elx::ImageSamplerBase< SelfImageSamplerBaseType
 
typedef MovingImageType InputImageType
 
typedef InterpolatorBase< SelfInterpolatorBaseType
 
typedef unsigned char MaskPixelType
 
typedef MetricBase< SelfMetricBaseType
 
typedef MovingImageType::Pointer MovingImagePointer
 
typedef MovingImagePyramidBase< SelfMovingImagePyramidBaseType
 
typedef TMovingImage MovingImageType
 
typedef MovingMaskType::Pointer MovingMaskPointer
 
typedef itk::Image< MaskPixelType, MovingDimension > MovingMaskType
 
typedef Superclass2::ObjectContainerPointer ObjectContainerPointer
 
typedef Superclass2::ObjectContainerType ObjectContainerType
 
typedef Superclass2::ObjectPointer ObjectPointer
 
typedef Superclass2::ObjectType ObjectType
 
typedef OptimizerBase< SelfOptimizerBaseType
 
typedef MovingImageType OutputImageType
 
typedef itk::ParameterMapInterface::ParameterMapType ParameterMapType
 
typedef itk::SmartPointer< SelfPointer
 
typedef void(BaseComponentType::* PtrToMemberFunction) (void)
 
typedef int(BaseComponentType::* PtrToMemberFunction2) (void)
 
typedef RegistrationBase< SelfRegistrationBaseType
 
typedef ResampleInterpolatorBase< SelfResampleInterpolatorBaseType
 
typedef ResamplerBase< SelfResamplerBaseType
 
typedef itk::DataObject ResultImageType
 
typedef ElastixTemplate Self
 
typedef itk::Object Superclass1
 
typedef ElastixBase Superclass2
 
typedef itk::TimeProbe TimerType
 
typedef elx::TransformBase< SelfTransformBaseType
 
- Public Types inherited from elastix::ElastixBase
typedef ComponentDatabaseType::Pointer ComponentDatabasePointer
 
typedef ComponentDatabase ComponentDatabaseType
 
typedef ConfigurationType::Pointer ConfigurationPointer
 
typedef Configuration ConfigurationType
 
typedef DataObjectContainerType::Pointer DataObjectContainerPointer
 
typedef itk::VectorContainer< unsigned int, DataObjectPointerDataObjectContainerType
 
typedef DataObjectType::Pointer DataObjectPointer
 
typedef itk::DataObject DataObjectType
 
typedef ComponentDatabaseType::IndexType DBIndexType
 
typedef FileNameContainerType::Pointer FileNameContainerPointer
 
typedef itk::VectorContainer< unsigned int, std::string > FileNameContainerType
 
typedef std::vector< doubleFlatDirectionCosinesType
 
typedef itk::Object ITKBaseType
 
typedef ObjectContainerType::Pointer ObjectContainerPointer
 
typedef itk::VectorContainer< unsigned int, ObjectPointerObjectContainerType
 
typedef ObjectType::Pointer ObjectPointer
 
typedef itk::Object ObjectType
 
typedef itk::ParameterMapInterface::ParameterMapType ParameterMapType
 
typedef ElastixBase Self
 
typedef BaseComponent Superclass
 

Public Member Functions

virtual void AfterEachIteration (void)
 
virtual void AfterEachResolution (void)
 
virtual void AfterRegistration (void)
 
virtual int ApplyTransform (void)
 
virtual int BeforeAll (void)
 
virtual int BeforeAllTransformix (void)
 
virtual void BeforeEachResolution (void)
 
virtual void BeforeRegistration (void)
 
 elxGetBaseMacro (FixedImagePyramid, FixedImagePyramidBaseType)
 
 elxGetBaseMacro (MovingImagePyramid, MovingImagePyramidBaseType)
 
 elxGetBaseMacro (Interpolator, InterpolatorBaseType)
 
 elxGetBaseMacro (ImageSampler, ImageSamplerBaseType)
 
 elxGetBaseMacro (Metric, MetricBaseType)
 
 elxGetBaseMacro (Optimizer, OptimizerBaseType)
 
 elxGetBaseMacro (Registration, RegistrationBaseType)
 
 elxGetBaseMacro (Resampler, ResamplerBaseType)
 
 elxGetBaseMacro (ResampleInterpolator, ResampleInterpolatorBaseType)
 
 elxGetBaseMacro (Transform, TransformBaseType)
 
virtual const char * GetClassName () const
 
virtual ConfigurationPointer GetConfiguration (const vcl_size_t index)
 
virtual ConfigurationPointer GetConfiguration ()
 
virtual const char * GetCurrentTransformParameterFileName () const
 
virtual FixedImageTypeGetFixedImage (void) const
 
virtual FixedImageTypeGetFixedImage (unsigned int idx) const
 
virtual FixedMaskTypeGetFixedMask (void) const
 
virtual FixedMaskTypeGetFixedMask (unsigned int idx) const
 
virtual unsigned int GetIterationCounter () const
 
virtual MovingImageTypeGetMovingImage (void) const
 
virtual MovingImageTypeGetMovingImage (unsigned int idx) const
 
virtual MovingMaskTypeGetMovingMask (void) const
 
virtual MovingMaskTypeGetMovingMask (unsigned int idx) const
 
virtual bool GetOriginalFixedImageDirection (FixedImageDirectionType &direction) const
 
virtual ResultImageTypeGetResultImage (void) const
 
virtual ResultImageTypeGetResultImage (unsigned int idx) const
 
 itkStaticConstMacro (Dimension, unsigned int, FixedImageType::ImageDimension)
 
 itkStaticConstMacro (FixedDimension, unsigned int, FixedImageType::ImageDimension)
 
 itkStaticConstMacro (MovingDimension, unsigned int, MovingImageType::ImageDimension)
 
virtual int Run (void)
 
virtual void SetConfigurations (std::vector< ConfigurationPointer > &configurations)
 
virtual int SetResultImage (DataObjectPointer result_image)
 
- Public Member Functions inherited from elastix::ElastixBase
virtual void AfterRegistrationBase (void)
 
virtual int BeforeAllBase (void)
 
virtual int BeforeAllTransformixBase (void)
 
virtual void BeforeRegistrationBase (void)
 
 elxGetNumberOfMacro (Registration)
 
 elxGetNumberOfMacro (FixedImagePyramid)
 
 elxGetNumberOfMacro (MovingImagePyramid)
 
 elxGetNumberOfMacro (Interpolator)
 
 elxGetNumberOfMacro (ImageSampler)
 
 elxGetNumberOfMacro (Metric)
 
 elxGetNumberOfMacro (Optimizer)
 
 elxGetNumberOfMacro (Resampler)
 
 elxGetNumberOfMacro (ResampleInterpolator)
 
 elxGetNumberOfMacro (Transform)
 
 elxGetNumberOfMacro (FixedImage)
 
 elxGetNumberOfMacro (MovingImage)
 
 elxGetNumberOfMacro (FixedImageFileName)
 
 elxGetNumberOfMacro (MovingImageFileName)
 
 elxGetNumberOfMacro (FixedMask)
 
 elxGetNumberOfMacro (MovingMask)
 
 elxGetNumberOfMacro (FixedMaskFileName)
 
 elxGetNumberOfMacro (MovingMaskFileName)
 
 elxGetNumberOfMacro (ResultImage)
 
 elxGetObjectMacro (Configuration, ConfigurationType)
 
 elxGetObjectMacro (ComponentDatabase, ComponentDatabaseType)
 
 elxGetObjectMacro (RegistrationContainer, ObjectContainerType)
 
 elxGetObjectMacro (FixedImagePyramidContainer, ObjectContainerType)
 
 elxGetObjectMacro (MovingImagePyramidContainer, ObjectContainerType)
 
 elxGetObjectMacro (InterpolatorContainer, ObjectContainerType)
 
 elxGetObjectMacro (ImageSamplerContainer, ObjectContainerType)
 
 elxGetObjectMacro (MetricContainer, ObjectContainerType)
 
 elxGetObjectMacro (OptimizerContainer, ObjectContainerType)
 
 elxGetObjectMacro (ResamplerContainer, ObjectContainerType)
 
 elxGetObjectMacro (ResampleInterpolatorContainer, ObjectContainerType)
 
 elxGetObjectMacro (TransformContainer, ObjectContainerType)
 
 elxGetObjectMacro (FixedImageContainer, DataObjectContainerType)
 
 elxGetObjectMacro (MovingImageContainer, DataObjectContainerType)
 
 elxGetObjectMacro (FixedMaskContainer, DataObjectContainerType)
 
 elxGetObjectMacro (MovingMaskContainer, DataObjectContainerType)
 
 elxGetObjectMacro (ResultImageContainer, DataObjectContainerType)
 
 elxGetObjectMacro (FixedImageFileNameContainer, FileNameContainerType)
 
 elxGetObjectMacro (MovingImageFileNameContainer, FileNameContainerType)
 
 elxGetObjectMacro (FixedMaskFileNameContainer, FileNameContainerType)
 
 elxGetObjectMacro (MovingMaskFileNameContainer, FileNameContainerType)
 
 elxGetObjectMacro (InitialTransform, ObjectType)
 
 elxGetObjectMacro (FinalTransform, ObjectType)
 
 elxSetObjectMacro (Configuration, ConfigurationType)
 
 elxSetObjectMacro (ComponentDatabase, ComponentDatabaseType)
 
 elxSetObjectMacro (RegistrationContainer, ObjectContainerType)
 
 elxSetObjectMacro (FixedImagePyramidContainer, ObjectContainerType)
 
 elxSetObjectMacro (MovingImagePyramidContainer, ObjectContainerType)
 
 elxSetObjectMacro (InterpolatorContainer, ObjectContainerType)
 
 elxSetObjectMacro (ImageSamplerContainer, ObjectContainerType)
 
 elxSetObjectMacro (MetricContainer, ObjectContainerType)
 
 elxSetObjectMacro (OptimizerContainer, ObjectContainerType)
 
 elxSetObjectMacro (ResamplerContainer, ObjectContainerType)
 
 elxSetObjectMacro (ResampleInterpolatorContainer, ObjectContainerType)
 
 elxSetObjectMacro (TransformContainer, ObjectContainerType)
 
 elxSetObjectMacro (FixedImageContainer, DataObjectContainerType)
 
 elxSetObjectMacro (MovingImageContainer, DataObjectContainerType)
 
 elxSetObjectMacro (FixedMaskContainer, DataObjectContainerType)
 
 elxSetObjectMacro (MovingMaskContainer, DataObjectContainerType)
 
 elxSetObjectMacro (ResultImageContainer, DataObjectContainerType)
 
 elxSetObjectMacro (FixedImageFileNameContainer, FileNameContainerType)
 
 elxSetObjectMacro (MovingImageFileNameContainer, FileNameContainerType)
 
 elxSetObjectMacro (FixedMaskFileNameContainer, FileNameContainerType)
 
 elxSetObjectMacro (MovingMaskFileNameContainer, FileNameContainerType)
 
 elxSetObjectMacro (InitialTransform, ObjectType)
 
 elxSetObjectMacro (FinalTransform, ObjectType)
 
virtual ITKBaseTypeGetAsITKBaseType (void)
 
virtual DBIndexType GetDBIndex (void)
 
virtual int GetDefaultOutputPrecision (void) const
 
virtual const FlatDirectionCosinesTypeGetOriginalFixedImageDirectionFlat (void) const
 
virtual bool GetUseDirectionCosines (void) const
 
virtual void SetDBIndex (DBIndexType _arg)
 
virtual void SetOriginalFixedImageDirectionFlat (const FlatDirectionCosinesType &arg)
 
- Public Member Functions inherited from elastix::BaseComponent
virtual void AfterEachIterationBase (void)
 
virtual void AfterEachResolutionBase (void)
 
virtual void BeforeEachResolutionBase (void)
 
std::string ConvertSecondsToDHMS (const double totalSeconds, const unsigned int precision) const
 
virtual const char * elxGetClassName (void) const
 
virtual const char * GetComponentLabel (void) const
 
virtual void SetComponentLabel (const char *label, unsigned int idx)
 

Static Public Member Functions

static Pointer New ()
 

Protected Types

typedef Superclass2::MultipleImageLoader< FixedImageTypeFixedImageLoaderType
 
typedef Superclass2::MultipleImageLoader< FixedMaskTypeFixedMaskLoaderType
 
typedef Superclass2::MultipleImageLoader< MovingImageTypeMovingImageLoaderType
 
typedef Superclass2::MultipleImageLoader< MovingMaskTypeMovingMaskLoaderType
 

Protected Member Functions

void CallInEachComponent (PtrToMemberFunction func)
 
int CallInEachComponentInt (PtrToMemberFunction2 func)
 
virtual void ConfigureComponents (Self *This)
 
virtual void CreateTransformParameterFile (const std::string FileName, const bool ToLog)
 
virtual void CreateTransformParametersMap (void)
 
 ElastixTemplate ()
 
virtual ParameterMapType GetTransformParametersMap (void) const
 
virtual void OpenIterationInfoFile (void)
 
virtual void SetOriginalFixedImageDirection (const FixedImageDirectionType &arg)
 
virtual ~ElastixTemplate ()
 
- Protected Member Functions inherited from elastix::ElastixBase
 ElastixBase ()
 
virtual ~ElastixBase ()
 
- Protected Member Functions inherited from elastix::BaseComponent
 BaseComponent ()
 
virtual ~BaseComponent ()
 

Protected Attributes

AfterEachIterationCommandPointer m_AfterEachIterationCommand
 
AfterEachResolutionCommandPointer m_AfterEachResolutionCommand
 
BeforeEachResolutionCommandPointer m_BeforeEachResolutionCommand
 
std::vector< ConfigurationPointerm_Configurations
 
std::string m_CurrentTransformParameterFileName
 
unsigned int m_IterationCounter
 
std::ofstream m_IterationInfoFile
 
TimerType m_IterationTimer
 
TimerType m_ResolutionTimer
 
TimerType m_Timer0
 
ParameterMapType m_TransformParametersMap
 
- Protected Attributes inherited from elastix::ElastixBase
ComponentDatabasePointer m_ComponentDatabase
 
ConfigurationPointer m_Configuration
 
DBIndexType m_DBIndex
 
FlatDirectionCosinesType m_OriginalFixedImageDirection
 

Private Member Functions

 ElastixTemplate (const Self &)
 
void operator= (const Self &)
 

Member Typedef Documentation

template<class TFixedImage , class TMovingImage >
typedef AfterEachIterationCommandType::Pointer elastix::ElastixTemplate< TFixedImage, TMovingImage >::AfterEachIterationCommandPointer

Definition at line 184 of file elxElastixTemplate.h.

template<class TFixedImage , class TMovingImage >
typedef itk::SimpleMemberCommand< Self > elastix::ElastixTemplate< TFixedImage, TMovingImage >::AfterEachIterationCommandType

Definition at line 181 of file elxElastixTemplate.h.

template<class TFixedImage , class TMovingImage >
typedef AfterEachResolutionCommandType::Pointer elastix::ElastixTemplate< TFixedImage, TMovingImage >::AfterEachResolutionCommandPointer

Definition at line 183 of file elxElastixTemplate.h.

template<class TFixedImage , class TMovingImage >
typedef itk::SimpleMemberCommand< Self > elastix::ElastixTemplate< TFixedImage, TMovingImage >::AfterEachResolutionCommandType

Definition at line 180 of file elxElastixTemplate.h.

template<class TFixedImage , class TMovingImage >
typedef BaseComponent elastix::ElastixTemplate< TFixedImage, TMovingImage >::BaseComponentType

BaseComponent.

Definition at line 172 of file elxElastixTemplate.h.

template<class TFixedImage , class TMovingImage >
typedef BeforeEachResolutionCommandType::Pointer elastix::ElastixTemplate< TFixedImage, TMovingImage >::BeforeEachResolutionCommandPointer

Definition at line 182 of file elxElastixTemplate.h.

template<class TFixedImage , class TMovingImage >
typedef itk::SimpleMemberCommand< Self > elastix::ElastixTemplate< TFixedImage, TMovingImage >::BeforeEachResolutionCommandType

Commands that react on Events and call Self::Function(void).

Definition at line 179 of file elxElastixTemplate.h.

template<class TFixedImage , class TMovingImage >
typedef Superclass2::ConfigurationPointer elastix::ElastixTemplate< TFixedImage, TMovingImage >::ConfigurationPointer

Definition at line 132 of file elxElastixTemplate.h.

template<class TFixedImage , class TMovingImage >
typedef Superclass2::ConfigurationType elastix::ElastixTemplate< TFixedImage, TMovingImage >::ConfigurationType

Typedefs inherited from Superclass2.

Definition at line 128 of file elxElastixTemplate.h.

template<class TFixedImage , class TMovingImage >
typedef itk::SmartPointer< const Self > elastix::ElastixTemplate< TFixedImage, TMovingImage >::ConstPointer

Definition at line 122 of file elxElastixTemplate.h.

template<class TFixedImage , class TMovingImage >
typedef itk::CostFunction::ParametersValueType elastix::ElastixTemplate< TFixedImage, TMovingImage >::CoordRepType

Type for representation of the transform coordinates.

Definition at line 169 of file elxElastixTemplate.h.

template<class TFixedImage , class TMovingImage >
typedef Superclass2::DataObjectContainerPointer elastix::ElastixTemplate< TFixedImage, TMovingImage >::DataObjectContainerPointer

Definition at line 141 of file elxElastixTemplate.h.

template<class TFixedImage , class TMovingImage >
typedef Superclass2::DataObjectContainerType elastix::ElastixTemplate< TFixedImage, TMovingImage >::DataObjectContainerType

Definition at line 138 of file elxElastixTemplate.h.

template<class TFixedImage , class TMovingImage >
typedef Superclass2::DataObjectPointer elastix::ElastixTemplate< TFixedImage, TMovingImage >::DataObjectPointer

Definition at line 136 of file elxElastixTemplate.h.

template<class TFixedImage , class TMovingImage >
typedef Superclass2::DataObjectType elastix::ElastixTemplate< TFixedImage, TMovingImage >::DataObjectType

Definition at line 134 of file elxElastixTemplate.h.

template<class TFixedImage , class TMovingImage >
typedef Superclass2::FileNameContainerPointer elastix::ElastixTemplate< TFixedImage, TMovingImage >::FileNameContainerPointer

Definition at line 142 of file elxElastixTemplate.h.

template<class TFixedImage , class TMovingImage >
typedef Superclass2::FileNameContainerType elastix::ElastixTemplate< TFixedImage, TMovingImage >::FileNameContainerType

Definition at line 139 of file elxElastixTemplate.h.

template<class TFixedImage , class TMovingImage >
typedef FixedImageType::DirectionType elastix::ElastixTemplate< TFixedImage, TMovingImage >::FixedImageDirectionType

Typedef for the UseDirectionCosines option.

Definition at line 166 of file elxElastixTemplate.h.

template<class TFixedImage , class TMovingImage >
typedef Superclass2::MultipleImageLoader< FixedImageType > elastix::ElastixTemplate< TFixedImage, TMovingImage >::FixedImageLoaderType
protected

Classes that contain a function to load multiple images, given a filename container.

Definition at line 329 of file elxElastixTemplate.h.

template<class TFixedImage , class TMovingImage >
typedef FixedImageType::Pointer elastix::ElastixTemplate< TFixedImage, TMovingImage >::FixedImagePointer

Definition at line 147 of file elxElastixTemplate.h.

template<class TFixedImage , class TMovingImage >
typedef FixedImagePyramidBase< Self > elastix::ElastixTemplate< TFixedImage, TMovingImage >::FixedImagePyramidBaseType

The elastix basecomponent types.

Definition at line 187 of file elxElastixTemplate.h.

template<class TFixedImage , class TMovingImage >
typedef TFixedImage elastix::ElastixTemplate< TFixedImage, TMovingImage >::FixedImageType

Typedef's for this class.

Definition at line 145 of file elxElastixTemplate.h.

template<class TFixedImage , class TMovingImage >
typedef Superclass2::MultipleImageLoader< FixedMaskType > elastix::ElastixTemplate< TFixedImage, TMovingImage >::FixedMaskLoaderType
protected

Definition at line 331 of file elxElastixTemplate.h.

template<class TFixedImage , class TMovingImage >
typedef FixedMaskType::Pointer elastix::ElastixTemplate< TFixedImage, TMovingImage >::FixedMaskPointer

Definition at line 162 of file elxElastixTemplate.h.

template<class TFixedImage , class TMovingImage >
typedef itk::Image< MaskPixelType, FixedDimension > elastix::ElastixTemplate< TFixedImage, TMovingImage >::FixedMaskType

Definition at line 160 of file elxElastixTemplate.h.

template<class TFixedImage , class TMovingImage >
typedef elx::ImageSamplerBase< Self > elastix::ElastixTemplate< TFixedImage, TMovingImage >::ImageSamplerBaseType

Definition at line 190 of file elxElastixTemplate.h.

template<class TFixedImage , class TMovingImage >
typedef MovingImageType elastix::ElastixTemplate< TFixedImage, TMovingImage >::InputImageType

Typedef's for ApplyTransform.

Todo:
How useful is this? It is not consequently supported, since the the input image is stored in the MovingImageContainer anyway.

Definition at line 205 of file elxElastixTemplate.h.

template<class TFixedImage , class TMovingImage >
typedef InterpolatorBase< Self > elastix::ElastixTemplate< TFixedImage, TMovingImage >::InterpolatorBaseType

Definition at line 189 of file elxElastixTemplate.h.

template<class TFixedImage , class TMovingImage >
typedef unsigned char elastix::ElastixTemplate< TFixedImage, TMovingImage >::MaskPixelType

Types for the masks.

Definition at line 159 of file elxElastixTemplate.h.

template<class TFixedImage , class TMovingImage >
typedef MetricBase< Self > elastix::ElastixTemplate< TFixedImage, TMovingImage >::MetricBaseType

Definition at line 191 of file elxElastixTemplate.h.

template<class TFixedImage , class TMovingImage >
typedef Superclass2::MultipleImageLoader< MovingImageType > elastix::ElastixTemplate< TFixedImage, TMovingImage >::MovingImageLoaderType
protected

Definition at line 330 of file elxElastixTemplate.h.

template<class TFixedImage , class TMovingImage >
typedef MovingImageType::Pointer elastix::ElastixTemplate< TFixedImage, TMovingImage >::MovingImagePointer

Definition at line 148 of file elxElastixTemplate.h.

template<class TFixedImage , class TMovingImage >
typedef MovingImagePyramidBase< Self > elastix::ElastixTemplate< TFixedImage, TMovingImage >::MovingImagePyramidBaseType

Definition at line 188 of file elxElastixTemplate.h.

template<class TFixedImage , class TMovingImage >
typedef TMovingImage elastix::ElastixTemplate< TFixedImage, TMovingImage >::MovingImageType

Definition at line 146 of file elxElastixTemplate.h.

template<class TFixedImage , class TMovingImage >
typedef Superclass2::MultipleImageLoader< MovingMaskType > elastix::ElastixTemplate< TFixedImage, TMovingImage >::MovingMaskLoaderType
protected

Definition at line 332 of file elxElastixTemplate.h.

template<class TFixedImage , class TMovingImage >
typedef MovingMaskType::Pointer elastix::ElastixTemplate< TFixedImage, TMovingImage >::MovingMaskPointer

Definition at line 163 of file elxElastixTemplate.h.

template<class TFixedImage , class TMovingImage >
typedef itk::Image< MaskPixelType, MovingDimension > elastix::ElastixTemplate< TFixedImage, TMovingImage >::MovingMaskType

Definition at line 161 of file elxElastixTemplate.h.

template<class TFixedImage , class TMovingImage >
typedef Superclass2::ObjectContainerPointer elastix::ElastixTemplate< TFixedImage, TMovingImage >::ObjectContainerPointer

Definition at line 140 of file elxElastixTemplate.h.

template<class TFixedImage , class TMovingImage >
typedef Superclass2::ObjectContainerType elastix::ElastixTemplate< TFixedImage, TMovingImage >::ObjectContainerType

Definition at line 137 of file elxElastixTemplate.h.

template<class TFixedImage , class TMovingImage >
typedef Superclass2::ObjectPointer elastix::ElastixTemplate< TFixedImage, TMovingImage >::ObjectPointer

Definition at line 135 of file elxElastixTemplate.h.

template<class TFixedImage , class TMovingImage >
typedef Superclass2::ObjectType elastix::ElastixTemplate< TFixedImage, TMovingImage >::ObjectType

Definition at line 133 of file elxElastixTemplate.h.

template<class TFixedImage , class TMovingImage >
typedef OptimizerBase< Self > elastix::ElastixTemplate< TFixedImage, TMovingImage >::OptimizerBaseType

Definition at line 192 of file elxElastixTemplate.h.

template<class TFixedImage , class TMovingImage >
typedef MovingImageType elastix::ElastixTemplate< TFixedImage, TMovingImage >::OutputImageType

Definition at line 206 of file elxElastixTemplate.h.

template<class TFixedImage , class TMovingImage >
typedef itk::ParameterMapInterface::ParameterMapType elastix::ElastixTemplate< TFixedImage, TMovingImage >::ParameterMapType

Typedef that is used in the elastix dll version.

Definition at line 209 of file elxElastixTemplate.h.

template<class TFixedImage , class TMovingImage >
typedef itk::SmartPointer< Self > elastix::ElastixTemplate< TFixedImage, TMovingImage >::Pointer

Definition at line 121 of file elxElastixTemplate.h.

template<class TFixedImage , class TMovingImage >
typedef void(BaseComponentType::* elastix::ElastixTemplate< TFixedImage, TMovingImage >::PtrToMemberFunction) (void)

A Pointer to a member function of a BaseComponentType.

Definition at line 175 of file elxElastixTemplate.h.

template<class TFixedImage , class TMovingImage >
typedef int(BaseComponentType::* elastix::ElastixTemplate< TFixedImage, TMovingImage >::PtrToMemberFunction2) (void)

Definition at line 176 of file elxElastixTemplate.h.

template<class TFixedImage , class TMovingImage >
typedef RegistrationBase< Self > elastix::ElastixTemplate< TFixedImage, TMovingImage >::RegistrationBaseType

Definition at line 193 of file elxElastixTemplate.h.

template<class TFixedImage , class TMovingImage >
typedef ResampleInterpolatorBase< Self > elastix::ElastixTemplate< TFixedImage, TMovingImage >::ResampleInterpolatorBaseType

Definition at line 195 of file elxElastixTemplate.h.

template<class TFixedImage , class TMovingImage >
typedef ResamplerBase< Self > elastix::ElastixTemplate< TFixedImage, TMovingImage >::ResamplerBaseType

Definition at line 194 of file elxElastixTemplate.h.

template<class TFixedImage , class TMovingImage >
typedef itk::DataObject elastix::ElastixTemplate< TFixedImage, TMovingImage >::ResultImageType

Result image

Definition at line 151 of file elxElastixTemplate.h.

template<class TFixedImage , class TMovingImage >
typedef ElastixTemplate elastix::ElastixTemplate< TFixedImage, TMovingImage >::Self

Standard itk.

Definition at line 118 of file elxElastixTemplate.h.

template<class TFixedImage , class TMovingImage >
typedef itk::Object elastix::ElastixTemplate< TFixedImage, TMovingImage >::Superclass1

Definition at line 119 of file elxElastixTemplate.h.

template<class TFixedImage , class TMovingImage >
typedef ElastixBase elastix::ElastixTemplate< TFixedImage, TMovingImage >::Superclass2

Definition at line 120 of file elxElastixTemplate.h.

template<class TFixedImage , class TMovingImage >
typedef itk::TimeProbe elastix::ElastixTemplate< TFixedImage, TMovingImage >::TimerType

Typedef's for Timer class.

Definition at line 199 of file elxElastixTemplate.h.

template<class TFixedImage , class TMovingImage >
typedef elx::TransformBase< Self > elastix::ElastixTemplate< TFixedImage, TMovingImage >::TransformBaseType

Definition at line 196 of file elxElastixTemplate.h.

Constructor & Destructor Documentation

template<class TFixedImage , class TMovingImage >
elastix::ElastixTemplate< TFixedImage, TMovingImage >::ElastixTemplate ( )
protected
template<class TFixedImage , class TMovingImage >
virtual elastix::ElastixTemplate< TFixedImage, TMovingImage >::~ElastixTemplate ( )
inlineprotectedvirtual

Definition at line 326 of file elxElastixTemplate.h.

template<class TFixedImage , class TMovingImage >
elastix::ElastixTemplate< TFixedImage, TMovingImage >::ElastixTemplate ( const Self )
private

Member Function Documentation

template<class TFixedImage , class TMovingImage >
virtual void elastix::ElastixTemplate< TFixedImage, TMovingImage >::AfterEachIteration ( void  )
virtual

Reimplemented from elastix::BaseComponent.

template<class TFixedImage , class TMovingImage >
virtual void elastix::ElastixTemplate< TFixedImage, TMovingImage >::AfterEachResolution ( void  )
virtual

Reimplemented from elastix::BaseComponent.

template<class TFixedImage , class TMovingImage >
virtual void elastix::ElastixTemplate< TFixedImage, TMovingImage >::AfterRegistration ( void  )
virtual

Reimplemented from elastix::BaseComponent.

template<class TFixedImage , class TMovingImage >
virtual int elastix::ElastixTemplate< TFixedImage, TMovingImage >::ApplyTransform ( void  )
virtual

Implements elastix::ElastixBase.

template<class TFixedImage , class TMovingImage >
virtual int elastix::ElastixTemplate< TFixedImage, TMovingImage >::BeforeAll ( void  )
virtual

The Callback functions.

Reimplemented from elastix::BaseComponent.

template<class TFixedImage , class TMovingImage >
virtual int elastix::ElastixTemplate< TFixedImage, TMovingImage >::BeforeAllTransformix ( void  )
virtual
template<class TFixedImage , class TMovingImage >
virtual void elastix::ElastixTemplate< TFixedImage, TMovingImage >::BeforeEachResolution ( void  )
virtual

Reimplemented from elastix::BaseComponent.

template<class TFixedImage , class TMovingImage >
virtual void elastix::ElastixTemplate< TFixedImage, TMovingImage >::BeforeRegistration ( void  )
virtual

Reimplemented from elastix::BaseComponent.

template<class TFixedImage , class TMovingImage >
void elastix::ElastixTemplate< TFixedImage, TMovingImage >::CallInEachComponent ( PtrToMemberFunction  func)
protected

Used by the callback functions, BeforeEachResolution() etc.). This method calls a function in each component, in the following order:

  • Registration
  • Transform
  • ImageSampler
  • Metric
  • Interpolator
  • Optimizer
  • FixedImagePyramid
  • MovingImagePyramid
  • ResampleInterpolator
  • Resampler
template<class TFixedImage , class TMovingImage >
int elastix::ElastixTemplate< TFixedImage, TMovingImage >::CallInEachComponentInt ( PtrToMemberFunction2  func)
protected
template<class TFixedImage , class TMovingImage >
virtual void elastix::ElastixTemplate< TFixedImage, TMovingImage >::ConfigureComponents ( Self This)
protectedvirtual

Call in each component SetElastix(This) and set its ComponentLabel (for example "Metric1"). This makes sure that the component knows its own function in the registration process.

template<class TFixedImage , class TMovingImage >
virtual void elastix::ElastixTemplate< TFixedImage, TMovingImage >::CreateTransformParameterFile ( const std::string  FileName,
const bool  ToLog 
)
protectedvirtual

CreateTransformParameterFile.

template<class TFixedImage , class TMovingImage >
virtual void elastix::ElastixTemplate< TFixedImage, TMovingImage >::CreateTransformParametersMap ( void  )
protectedvirtual

CreateTransformParametersMap.

Implements elastix::ElastixBase.

template<class TFixedImage , class TMovingImage >
elastix::ElastixTemplate< TFixedImage, TMovingImage >::elxGetBaseMacro ( FixedImagePyramid  ,
FixedImagePyramidBaseType   
)

Functions to set/get pointers to the elastix components. Get the components as pointers to elxBaseType.

template<class TFixedImage , class TMovingImage >
elastix::ElastixTemplate< TFixedImage, TMovingImage >::elxGetBaseMacro ( MovingImagePyramid  ,
MovingImagePyramidBaseType   
)
template<class TFixedImage , class TMovingImage >
elastix::ElastixTemplate< TFixedImage, TMovingImage >::elxGetBaseMacro ( Interpolator  ,
InterpolatorBaseType   
)
template<class TFixedImage , class TMovingImage >
elastix::ElastixTemplate< TFixedImage, TMovingImage >::elxGetBaseMacro ( ImageSampler  ,
ImageSamplerBaseType   
)
template<class TFixedImage , class TMovingImage >
elastix::ElastixTemplate< TFixedImage, TMovingImage >::elxGetBaseMacro ( Metric  ,
MetricBaseType   
)
template<class TFixedImage , class TMovingImage >
elastix::ElastixTemplate< TFixedImage, TMovingImage >::elxGetBaseMacro ( Optimizer  ,
OptimizerBaseType   
)
template<class TFixedImage , class TMovingImage >
elastix::ElastixTemplate< TFixedImage, TMovingImage >::elxGetBaseMacro ( Registration  ,
RegistrationBaseType   
)
template<class TFixedImage , class TMovingImage >
elastix::ElastixTemplate< TFixedImage, TMovingImage >::elxGetBaseMacro ( Resampler  ,
ResamplerBaseType   
)
template<class TFixedImage , class TMovingImage >
elastix::ElastixTemplate< TFixedImage, TMovingImage >::elxGetBaseMacro ( ResampleInterpolator  ,
ResampleInterpolatorBaseType   
)
template<class TFixedImage , class TMovingImage >
elastix::ElastixTemplate< TFixedImage, TMovingImage >::elxGetBaseMacro ( Transform  ,
TransformBaseType   
)
template<class TFixedImage , class TMovingImage >
virtual const char* elastix::ElastixTemplate< TFixedImage, TMovingImage >::GetClassName ( ) const
virtual

Run-time type information (and related methods).

template<class TFixedImage , class TMovingImage >
virtual ConfigurationPointer elastix::ElastixTemplate< TFixedImage, TMovingImage >::GetConfiguration ( const vcl_size_t  index)
virtual

Return configuration from vector of configurations. Library only.

template<class TFixedImage , class TMovingImage >
virtual ConfigurationPointer elastix::ElastixTemplate< TFixedImage, TMovingImage >::GetConfiguration ( void  )
inlinevirtual

Definition at line 311 of file elxElastixTemplate.h.

template<class TFixedImage , class TMovingImage >
virtual const char* elastix::ElastixTemplate< TFixedImage, TMovingImage >::GetCurrentTransformParameterFileName ( ) const
virtual

Get the name of the current transform parameter file.

template<class TFixedImage , class TMovingImage >
virtual FixedImageType* elastix::ElastixTemplate< TFixedImage, TMovingImage >::GetFixedImage ( void  ) const
inlinevirtual

Get pointers to the images. They are obtained from the {Fixed,Moving}ImageContainer and casted to the appropriate type.

Definition at line 228 of file elxElastixTemplate.h.

template<class TFixedImage , class TMovingImage >
virtual FixedImageType* elastix::ElastixTemplate< TFixedImage, TMovingImage >::GetFixedImage ( unsigned int  idx) const
virtual
template<class TFixedImage , class TMovingImage >
virtual FixedMaskType* elastix::ElastixTemplate< TFixedImage, TMovingImage >::GetFixedMask ( void  ) const
inlinevirtual

Get pointers to the masks. They are obtained from the {Fixed,Moving}MaskContainer and casted to the appropriate type.

Definition at line 247 of file elxElastixTemplate.h.

template<class TFixedImage , class TMovingImage >
virtual FixedMaskType* elastix::ElastixTemplate< TFixedImage, TMovingImage >::GetFixedMask ( unsigned int  idx) const
virtual
template<class TFixedImage , class TMovingImage >
virtual unsigned int elastix::ElastixTemplate< TFixedImage, TMovingImage >::GetIterationCounter ( ) const
virtual

Get the iteration number.

template<class TFixedImage , class TMovingImage >
virtual MovingImageType* elastix::ElastixTemplate< TFixedImage, TMovingImage >::GetMovingImage ( void  ) const
inlinevirtual

Definition at line 236 of file elxElastixTemplate.h.

template<class TFixedImage , class TMovingImage >
virtual MovingImageType* elastix::ElastixTemplate< TFixedImage, TMovingImage >::GetMovingImage ( unsigned int  idx) const
virtual
template<class TFixedImage , class TMovingImage >
virtual MovingMaskType* elastix::ElastixTemplate< TFixedImage, TMovingImage >::GetMovingMask ( void  ) const
inlinevirtual

Definition at line 255 of file elxElastixTemplate.h.

template<class TFixedImage , class TMovingImage >
virtual MovingMaskType* elastix::ElastixTemplate< TFixedImage, TMovingImage >::GetMovingMask ( unsigned int  idx) const
virtual
template<class TFixedImage , class TMovingImage >
virtual bool elastix::ElastixTemplate< TFixedImage, TMovingImage >::GetOriginalFixedImageDirection ( FixedImageDirectionType direction) const
virtual

Get the original direction cosines of the fixed image. Returns false if it failed to determine the original fixed image direction. In that case the direction var is left unchanged. If no fixed image is present, it tries to read it from the parameter file.

template<class TFixedImage , class TMovingImage >
virtual ResultImageType* elastix::ElastixTemplate< TFixedImage, TMovingImage >::GetResultImage ( void  ) const
inlinevirtual

Get pointers to the result image. They are obtained from the ResultImageContainer and casted to the appropriate type.

Definition at line 266 of file elxElastixTemplate.h.

template<class TFixedImage , class TMovingImage >
virtual ResultImageType* elastix::ElastixTemplate< TFixedImage, TMovingImage >::GetResultImage ( unsigned int  idx) const
virtual
template<class TFixedImage , class TMovingImage >
virtual ParameterMapType elastix::ElastixTemplate< TFixedImage, TMovingImage >::GetTransformParametersMap ( void  ) const
protectedvirtual

GetTransformParametersMap.

Implements elastix::ElastixBase.

template<class TFixedImage , class TMovingImage >
elastix::ElastixTemplate< TFixedImage, TMovingImage >::itkStaticConstMacro ( Dimension  ,
unsigned  int,
FixedImageType::ImageDimension   
)

For using the Dimensions.

template<class TFixedImage , class TMovingImage >
elastix::ElastixTemplate< TFixedImage, TMovingImage >::itkStaticConstMacro ( FixedDimension  ,
unsigned  int,
FixedImageType::ImageDimension   
)
template<class TFixedImage , class TMovingImage >
elastix::ElastixTemplate< TFixedImage, TMovingImage >::itkStaticConstMacro ( MovingDimension  ,
unsigned  int,
MovingImageType::ImageDimension   
)
template<class TFixedImage , class TMovingImage >
static Pointer elastix::ElastixTemplate< TFixedImage, TMovingImage >::New ( )
static

Method for creation through the object factory.

template<class TFixedImage , class TMovingImage >
virtual void elastix::ElastixTemplate< TFixedImage, TMovingImage >::OpenIterationInfoFile ( void  )
protectedvirtual

Open the IterationInfoFile, where the table with iteration info is written to.

template<class TFixedImage , class TMovingImage >
void elastix::ElastixTemplate< TFixedImage, TMovingImage >::operator= ( const Self )
private
template<class TFixedImage , class TMovingImage >
virtual int elastix::ElastixTemplate< TFixedImage, TMovingImage >::Run ( void  )
virtual

Main functions: Run() for registration, and ApplyTransform() for just applying a transform to an image.

Implements elastix::ElastixBase.

template<class TFixedImage , class TMovingImage >
virtual void elastix::ElastixTemplate< TFixedImage, TMovingImage >::SetConfigurations ( std::vector< ConfigurationPointer > &  configurations)
virtual

Set configuration vector. Library only.

Implements elastix::ElastixBase.

template<class TFixedImage , class TMovingImage >
virtual void elastix::ElastixTemplate< TFixedImage, TMovingImage >::SetOriginalFixedImageDirection ( const FixedImageDirectionType arg)
protectedvirtual

Set the direction in the superclass' m_OriginalFixedImageDirection variable

template<class TFixedImage , class TMovingImage >
virtual int elastix::ElastixTemplate< TFixedImage, TMovingImage >::SetResultImage ( DataObjectPointer  result_image)
virtual

Field Documentation

template<class TFixedImage , class TMovingImage >
AfterEachIterationCommandPointer elastix::ElastixTemplate< TFixedImage, TMovingImage >::m_AfterEachIterationCommand
protected

Definition at line 336 of file elxElastixTemplate.h.

template<class TFixedImage , class TMovingImage >
AfterEachResolutionCommandPointer elastix::ElastixTemplate< TFixedImage, TMovingImage >::m_AfterEachResolutionCommand
protected

Definition at line 337 of file elxElastixTemplate.h.

template<class TFixedImage , class TMovingImage >
BeforeEachResolutionCommandPointer elastix::ElastixTemplate< TFixedImage, TMovingImage >::m_BeforeEachResolutionCommand
protected

CallBack commands.

Definition at line 335 of file elxElastixTemplate.h.

template<class TFixedImage , class TMovingImage >
std::vector< ConfigurationPointer > elastix::ElastixTemplate< TFixedImage, TMovingImage >::m_Configurations
protected

A vector of configuration objects, needed when transformix is used as library.

Definition at line 348 of file elxElastixTemplate.h.

template<class TFixedImage , class TMovingImage >
std::string elastix::ElastixTemplate< TFixedImage, TMovingImage >::m_CurrentTransformParameterFileName
protected

Store the CurrentTransformParameterFileName.

Definition at line 345 of file elxElastixTemplate.h.

template<class TFixedImage , class TMovingImage >
unsigned int elastix::ElastixTemplate< TFixedImage, TMovingImage >::m_IterationCounter
protected

Count the number of iterations.

Definition at line 351 of file elxElastixTemplate.h.

template<class TFixedImage , class TMovingImage >
std::ofstream elastix::ElastixTemplate< TFixedImage, TMovingImage >::m_IterationInfoFile
protected

Definition at line 369 of file elxElastixTemplate.h.

template<class TFixedImage , class TMovingImage >
TimerType elastix::ElastixTemplate< TFixedImage, TMovingImage >::m_IterationTimer
protected

Definition at line 341 of file elxElastixTemplate.h.

template<class TFixedImage , class TMovingImage >
TimerType elastix::ElastixTemplate< TFixedImage, TMovingImage >::m_ResolutionTimer
protected

Definition at line 342 of file elxElastixTemplate.h.

template<class TFixedImage , class TMovingImage >
TimerType elastix::ElastixTemplate< TFixedImage, TMovingImage >::m_Timer0
protected

Timers.

Definition at line 340 of file elxElastixTemplate.h.

template<class TFixedImage , class TMovingImage >
ParameterMapType elastix::ElastixTemplate< TFixedImage, TMovingImage >::m_TransformParametersMap
protected

Stores transformation parameters map.

Definition at line 364 of file elxElastixTemplate.h.



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