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elastix::TransformixMain Class Reference

#include <elxTransformixMain.h>

Detailed Description

A class with all functionality to configure transformix.

The TransformixMain class inherits from ElastixMain. We overwrite the Run() -function. In the new Run() the Run()-function from the ElastixTemplate-class is not called (as in elxElastixMain.cxx), because this time we don't want to start a registration, but just apply a transformation to an input image.

Definition at line 39 of file elxTransformixMain.h.

Inheritance diagram for elastix::TransformixMain:
Inheritance graph
[legend]

Public Types

using ArgumentMapType = Configuration::CommandLineArgumentMapType
 
using ComponentDatabasePointer = ComponentDatabase::Pointer
 
using ComponentDescriptionType = ComponentDatabase::ComponentDescriptionType
 
using ConstPointer = itk::SmartPointer< const Self >
 
using DataObjectContainerPointer = ElastixBase::DataObjectContainerPointer
 
using DataObjectContainerType = ElastixBase::DataObjectContainerType
 
using DataObjectPointer = itk::DataObject::Pointer
 
using DBIndexType = ComponentDatabase::IndexType
 
using ImageDimensionType = ComponentDatabase::ImageDimensionType
 
using ObjectContainerPointer = ElastixBase::ObjectContainerPointer
 
using ObjectContainerType = ElastixBase::ObjectContainerType
 
using ObjectPointer = itk::Object::Pointer
 
using ParameterMapType = itk::ParameterMapInterface::ParameterMapType
 
using PixelTypeDescriptionType = ComponentDatabase::PixelTypeDescriptionType
 
using Pointer = itk::SmartPointer< Self >
 
using PtrToCreator = ComponentDatabase::PtrToCreator
 
using Self = TransformixMain
 
using Superclass = ElastixMain
 
- Public Types inherited from elastix::ElastixMain
using ArgumentMapType = Configuration::CommandLineArgumentMapType
 
using ComponentDatabasePointer = ComponentDatabase::Pointer
 
using ComponentDescriptionType = ComponentDatabase::ComponentDescriptionType
 
using ConfigurationPointer = Configuration::Pointer
 
using ConstPointer = itk::SmartPointer< const Self >
 
using DataObjectContainerPointer = ElastixBase::DataObjectContainerPointer
 
using DataObjectContainerType = ElastixBase::DataObjectContainerType
 
using DataObjectPointer = itk::DataObject::Pointer
 
using DBIndexType = ComponentDatabase::IndexType
 
using FlatDirectionCosinesType = ElastixBase::FlatDirectionCosinesType
 
using ImageDimensionType = ComponentDatabase::ImageDimensionType
 
using ObjectContainerPointer = ElastixBase::ObjectContainerPointer
 
using ObjectContainerType = ElastixBase::ObjectContainerType
 
using ObjectPointer = itk::Object::Pointer
 
using ParameterMapType = itk::ParameterMapInterface::ParameterMapType
 
using PixelTypeDescriptionType = ComponentDatabase::PixelTypeDescriptionType
 
using Pointer = itk::SmartPointer< Self >
 
using PtrToCreator = ComponentDatabase::PtrToCreator
 
using Self = ElastixMain
 
using Superclass = itk::Object
 

Public Member Functions

virtual const char * GetClassName () const
 
 ITK_DISALLOW_COPY_AND_MOVE (TransformixMain)
 
int Run () override
 
int Run (const ArgumentMapType &argmap) override
 
int Run (const ArgumentMapType &argmap, const ParameterMapType &inputMap) override
 
int Run (const ArgumentMapType &argmap, const std::vector< ParameterMapType > &inputMaps, itk::TransformBase *=nullptr)
 
virtual void SetInputImageContainer (DataObjectContainerType *inputImageContainer)
 
- Public Member Functions inherited from elastix::ElastixMain
virtual void EnterCommandLineArguments (const ArgumentMapType &argmap)
 
virtual void EnterCommandLineArguments (const ArgumentMapType &argmap, const ParameterMapType &inputMap)
 
virtual void EnterCommandLineArguments (const ArgumentMapType &argmap, const std::vector< ParameterMapType > &inputMaps)
 
virtual const char * GetClassName () const
 
virtual DBIndexType GetDBIndex () const
 
ElastixBaseGetElastixBase () const
 
unsigned int GetElastixLevel ()
 
virtual ImageDimensionType GetFixedImageDimension () const
 
virtual PixelTypeDescriptionType GetFixedImagePixelType () const
 
virtual ImageDimensionType GetMovingImageDimension () const
 
virtual PixelTypeDescriptionType GetMovingImagePixelType () const
 
virtual const FlatDirectionCosinesTypeGetOriginalFixedImageDirectionFlat () const
 
unsigned int GetTotalNumberOfElastixLevels ()
 
virtual ParameterMapType GetTransformParametersMap () const
 
 ITK_DISALLOW_COPY_AND_MOVE (ElastixMain)
 
 itkGetModifiableObjectMacro (Configuration, Configuration)
 
 itkGetModifiableObjectMacro (Elastix, itk::Object)
 
 itkGetModifiableObjectMacro (FinalTransform, itk::Object)
 
 itkGetModifiableObjectMacro (FixedImageContainer, DataObjectContainerType)
 
 itkGetModifiableObjectMacro (FixedMaskContainer, DataObjectContainerType)
 
 itkGetModifiableObjectMacro (InitialTransform, itk::Object)
 
 itkGetModifiableObjectMacro (MovingImageContainer, DataObjectContainerType)
 
 itkGetModifiableObjectMacro (MovingMaskContainer, DataObjectContainerType)
 
 itkGetModifiableObjectMacro (ResultDeformationFieldContainer, DataObjectContainerType)
 
 itkGetModifiableObjectMacro (ResultImageContainer, DataObjectContainerType)
 
virtual int Run ()
 
virtual int Run (const ArgumentMapType &argmap)
 
virtual int Run (const ArgumentMapType &argmap, const ParameterMapType &inputMap)
 
virtual void SetConfiguration (Configuration *_arg)
 
void SetElastixLevel (unsigned int level)
 
virtual void SetFixedImageContainer (DataObjectContainerType *_arg)
 
virtual void SetFixedImageDimension (ImageDimensionType _arg)
 
virtual void SetFixedImagePixelType (PixelTypeDescriptionType _arg)
 
virtual void SetFixedMaskContainer (DataObjectContainerType *_arg)
 
virtual void SetInitialTransform (itk::Object *_arg)
 
virtual void SetMaximumNumberOfThreads () const
 
virtual void SetMovingImageContainer (DataObjectContainerType *_arg)
 
virtual void SetMovingImageDimension (ImageDimensionType _arg)
 
virtual void SetMovingImagePixelType (PixelTypeDescriptionType _arg)
 
virtual void SetMovingMaskContainer (DataObjectContainerType *_arg)
 
virtual void SetOriginalFixedImageDirectionFlat (const FlatDirectionCosinesType &arg)
 
virtual void SetProcessPriority () const
 
virtual void SetResultDeformationFieldContainer (DataObjectContainerType *_arg)
 
virtual void SetResultImageContainer (DataObjectContainerType *_arg)
 
void SetTotalNumberOfElastixLevels (unsigned int levels)
 

Static Public Member Functions

static Pointer New ()
 
- Static Public Member Functions inherited from elastix::ElastixMain
static const ComponentDatabaseGetComponentDatabase ()
 
static Pointer New ()
 

Protected Member Functions

int InitDBIndex () override
 
 TransformixMain ()=default
 
 ~TransformixMain () override
 
- Protected Member Functions inherited from elastix::ElastixMain
virtual ObjectPointer CreateComponent (const ComponentDescriptionType &name)
 
virtual ObjectContainerPointer CreateComponents (const ComponentDescriptionType &key, const ComponentDescriptionType &defaultComponentName, int &errorcode, bool mandatoryComponent=true)
 
 ElastixMain ()
 
void GetImageInformationFromFile (const std::string &filename, ImageDimensionType &imageDimension) const
 
virtual int InitDBIndex ()
 
 ~ElastixMain () override
 

Private Member Functions

int RunWithTransform (itk::TransformBase *)
 

Additional Inherited Members

- Protected Attributes inherited from elastix::ElastixMain
ConfigurationPointer m_Configuration { Configuration::New() }
 
std::vector< ConfigurationPointerm_Configurations {}
 
DBIndexType m_DBIndex { 0 }
 
ObjectPointer m_Elastix { nullptr }
 
ObjectPointer m_FinalTransform { nullptr }
 
DataObjectContainerPointer m_FixedImageContainer { nullptr }
 
ImageDimensionType m_FixedImageDimension { 0 }
 
PixelTypeDescriptionType m_FixedImagePixelType {}
 
DataObjectContainerPointer m_FixedMaskContainer { nullptr }
 
ObjectPointer m_InitialTransform { nullptr }
 
DataObjectContainerPointer m_MovingImageContainer { nullptr }
 
ImageDimensionType m_MovingImageDimension { 0 }
 
PixelTypeDescriptionType m_MovingImagePixelType {}
 
DataObjectContainerPointer m_MovingMaskContainer { nullptr }
 
FlatDirectionCosinesType m_OriginalFixedImageDirection {}
 
DataObjectContainerPointer m_ResultDeformationFieldContainer { nullptr }
 
DataObjectContainerPointer m_ResultImageContainer { nullptr }
 
ParameterMapType m_TransformParametersMap {}
 

Member Typedef Documentation

◆ ArgumentMapType

Elastix components.

Definition at line 150 of file elxElastixMain.h.

◆ ComponentDatabasePointer

Typedefs for the database that holds pointers to New() functions. Those functions are used to instantiate components, such as the metric etc.

Definition at line 161 of file elxElastixMain.h.

◆ ComponentDescriptionType

Definition at line 163 of file elxElastixMain.h.

◆ ConstPointer

using elastix::TransformixMain::ConstPointer = itk::SmartPointer<const Self>

Definition at line 48 of file elxTransformixMain.h.

◆ DataObjectContainerPointer

Definition at line 155 of file elxElastixMain.h.

◆ DataObjectContainerType

Definition at line 153 of file elxElastixMain.h.

◆ DataObjectPointer

using elastix::ElastixMain::DataObjectPointer = itk::DataObject::Pointer

Definition at line 147 of file elxElastixMain.h.

◆ DBIndexType

Definition at line 166 of file elxElastixMain.h.

◆ ImageDimensionType

Definition at line 165 of file elxElastixMain.h.

◆ ObjectContainerPointer

Definition at line 154 of file elxElastixMain.h.

◆ ObjectContainerType

Definition at line 152 of file elxElastixMain.h.

◆ ObjectPointer

using elastix::ElastixMain::ObjectPointer = itk::Object::Pointer

Typedef's from Superclass. typedef's from itk base Object.

Definition at line 146 of file elxElastixMain.h.

◆ ParameterMapType

Typedef that is used in the elastix dll version.

Definition at line 169 of file elxElastixMain.h.

◆ PixelTypeDescriptionType

Definition at line 164 of file elxElastixMain.h.

◆ Pointer

using elastix::TransformixMain::Pointer = itk::SmartPointer<Self>

Definition at line 47 of file elxTransformixMain.h.

◆ PtrToCreator

Definition at line 162 of file elxElastixMain.h.

◆ Self

Standard itk.

Definition at line 45 of file elxTransformixMain.h.

◆ Superclass

Definition at line 46 of file elxTransformixMain.h.

Constructor & Destructor Documentation

◆ TransformixMain()

elastix::TransformixMain::TransformixMain ( )
protecteddefault

◆ ~TransformixMain()

elastix::TransformixMain::~TransformixMain ( )
overrideprotected

Member Function Documentation

◆ GetClassName()

virtual const char * elastix::TransformixMain::GetClassName ( ) const
virtual

Run-time type information (and related methods).

Reimplemented from elastix::ElastixMain.

◆ InitDBIndex()

int elastix::TransformixMain::InitDBIndex ( )
overrideprotectedvirtual

InitDBIndex sets m_DBIndex to the value obtained from the ComponentDatabase.

Reimplemented from elastix::ElastixMain.

◆ ITK_DISALLOW_COPY_AND_MOVE()

elastix::TransformixMain::ITK_DISALLOW_COPY_AND_MOVE ( TransformixMain  )

◆ New()

static Pointer elastix::TransformixMain::New ( )
static

Method for creation through the object factory.

◆ Run() [1/4]

int elastix::TransformixMain::Run ( )
overridevirtual

Overwrite Run() from base-class.

Reimplemented from elastix::ElastixMain.

◆ Run() [2/4]

int elastix::TransformixMain::Run ( const ArgumentMapType argmap)
overridevirtual

Overwrite Run( argmap ) from superclass. Simply calls the superclass.

Reimplemented from elastix::ElastixMain.

◆ Run() [3/4]

int elastix::TransformixMain::Run ( const ArgumentMapType argmap,
const ParameterMapType inputMap 
)
overridevirtual

Reimplemented from elastix::ElastixMain.

◆ Run() [4/4]

int elastix::TransformixMain::Run ( const ArgumentMapType argmap,
const std::vector< ParameterMapType > &  inputMaps,
itk::TransformBase *  = nullptr 
)

Run version for using transformix as library.

◆ RunWithTransform()

int elastix::TransformixMain::RunWithTransform ( itk::TransformBase *  )
private

Does Run with an optionally specified Transform.

◆ SetInputImageContainer()

virtual void elastix::TransformixMain::SetInputImageContainer ( DataObjectContainerType inputImageContainer)
virtual

Get and Set input- and outputImage.



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