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elastix::ElastixMain Class Reference

#include <elxElastixMain.h>

Detailed Description

A class with all functionality to configure elastix.

The ElastixMain initializes the MyConfiguration class with the parameters and commandline arguments. After this, the class loads and creates all components and sets them in ElastixTemplate.

Parameters:

FixedImageDimension: the dimension of the fixed image.
example: (FixedImageDimension 2)

MovingImageDimension: the dimension of the fixed image.
example: (MovingImageDimension 2)

FixedInternalImagePixelType: the pixel type of the internal fixed image representation. The fixed image is automatically converted to this type.
example: (FixedInternalImagePixelType "float")
Default/recommended: "float"

MovingInternalImagePixelType: the pixel type of the internal moving image representation. The moving image is automatically converted to this type.
example: (MovingInternalImagePixelType "float")
Default/recommended: "float"

Transform Parameters:

FixedImageDimension: the dimension of the fixed image.
example: (FixedImageDimension 2)

MovingImageDimension: the dimension of the fixed image.
example: (MovingImageDimension 2)

FixedInternalImagePixelType: the pixel type of the internal fixed image representation. The fixed image is automatically converted to this type.
example: (FixedInternalImagePixelType "float")
Default/recommended: "float"

MovingInternalImagePixelType: the pixel type of the internal moving image representation. The moving image is automatically converted to this type.
example: (MovingInternalImagePixelType "float")
Default/recommended: "float"

Definition at line 126 of file elxElastixMain.h.

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

Public Types

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 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 const ComponentDatabaseGetComponentDatabase ()
 
static Pointer New ()
 

Protected Member Functions

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
 

Protected Attributes

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.

◆ ConfigurationPointer

Definition at line 151 of file elxElastixMain.h.

◆ ConstPointer

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

Definition at line 135 of file elxElastixMain.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.

◆ FlatDirectionCosinesType

Definition at line 156 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. ITK base objects.

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::ElastixMain::Pointer = itk::SmartPointer<Self>

Definition at line 134 of file elxElastixMain.h.

◆ PtrToCreator

Definition at line 162 of file elxElastixMain.h.

◆ Self

Standard itk.

Definition at line 132 of file elxElastixMain.h.

◆ Superclass

using elastix::ElastixMain::Superclass = itk::Object

Definition at line 133 of file elxElastixMain.h.

Constructor & Destructor Documentation

◆ ElastixMain()

elastix::ElastixMain::ElastixMain ( )
protected

◆ ~ElastixMain()

elastix::ElastixMain::~ElastixMain ( )
overrideprotected

Member Function Documentation

◆ CreateComponent()

virtual ObjectPointer elastix::ElastixMain::CreateComponent ( const ComponentDescriptionType name)
protectedvirtual

Create a component. Make sure InitDBIndex has been called before. The input is a string, e.g. "MattesMutualInformation".

◆ CreateComponents()

virtual ObjectContainerPointer elastix::ElastixMain::CreateComponents ( const ComponentDescriptionType key,
const ComponentDescriptionType defaultComponentName,
int errorcode,
bool  mandatoryComponent = true 
)
protectedvirtual

Create components. Reads from the configuration object (using the provided key) the names of the components to create and store their instantiations in the provided ObjectContainer. The errorcode remains what it was if no error occurred. Otherwise it's set to 1. The 'key' is the entry inspected in the parameter file A component named 'defaultComponentName' is used when the key is not found in the parameter file. If "" is used, no default is assumed, and an error is given when the component was not specified. If the flag mandatoryComponent is set to false, no error is given, because the component may not be needed anyway.

NB: this function should never be called with: ( !mandatoryComponent && defaultComponentName != "" ) == true

◆ EnterCommandLineArguments() [1/3]

virtual void elastix::ElastixMain::EnterCommandLineArguments ( const ArgumentMapType argmap)
virtual

Enter the command line parameters, which were given by the user, if elastix.exe is used to do a registration. The Configuration object will be initialized in this way.

◆ EnterCommandLineArguments() [2/3]

virtual void elastix::ElastixMain::EnterCommandLineArguments ( const ArgumentMapType argmap,
const ParameterMapType inputMap 
)
virtual

◆ EnterCommandLineArguments() [3/3]

virtual void elastix::ElastixMain::EnterCommandLineArguments ( const ArgumentMapType argmap,
const std::vector< ParameterMapType > &  inputMaps 
)
virtual

◆ GetClassName()

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

Run-time type information (and related methods).

Reimplemented in elastix::TransformixMain.

◆ GetComponentDatabase()

static const ComponentDatabase & elastix::ElastixMain::GetComponentDatabase ( )
static

Function to get the ComponentDatabase.

◆ GetDBIndex()

virtual DBIndexType elastix::ElastixMain::GetDBIndex ( ) const
virtual

Returns the Index that is used in elx::ComponentDatabase.

◆ GetElastixBase()

ElastixBase & elastix::ElastixMain::GetElastixBase ( ) const

Convenience function that returns the elastix component as a pointer to an ElastixBase. Use only after having called run()!

◆ GetElastixLevel()

unsigned int elastix::ElastixMain::GetElastixLevel ( )

◆ GetFixedImageDimension()

virtual ImageDimensionType elastix::ElastixMain::GetFixedImageDimension ( ) const
virtual

◆ GetFixedImagePixelType()

virtual PixelTypeDescriptionType elastix::ElastixMain::GetFixedImagePixelType ( ) const
virtual

◆ GetImageInformationFromFile()

void elastix::ElastixMain::GetImageInformationFromFile ( const std::string &  filename,
ImageDimensionType imageDimension 
) const
protected

Helper function to obtain information from images on disk.

◆ GetMovingImageDimension()

virtual ImageDimensionType elastix::ElastixMain::GetMovingImageDimension ( ) const
virtual

◆ GetMovingImagePixelType()

virtual PixelTypeDescriptionType elastix::ElastixMain::GetMovingImagePixelType ( ) const
virtual

◆ GetOriginalFixedImageDirectionFlat()

virtual const FlatDirectionCosinesType & elastix::ElastixMain::GetOriginalFixedImageDirectionFlat ( ) const
virtual

◆ GetTotalNumberOfElastixLevels()

unsigned int elastix::ElastixMain::GetTotalNumberOfElastixLevels ( )

◆ GetTransformParametersMap()

virtual ParameterMapType elastix::ElastixMain::GetTransformParametersMap ( ) const
virtual

GetTransformParametersMap

◆ InitDBIndex()

virtual int elastix::ElastixMain::InitDBIndex ( )
protectedvirtual

InitDBIndex sets m_DBIndex by asking the ImageTypes from the Configuration object and obtaining the corresponding DB index from the ComponentDatabase.

Reimplemented in elastix::TransformixMain.

◆ ITK_DISALLOW_COPY_AND_MOVE()

elastix::ElastixMain::ITK_DISALLOW_COPY_AND_MOVE ( ElastixMain  )

◆ itkGetModifiableObjectMacro() [1/10]

elastix::ElastixMain::itkGetModifiableObjectMacro ( Configuration  ,
Configuration   
)

◆ itkGetModifiableObjectMacro() [2/10]

elastix::ElastixMain::itkGetModifiableObjectMacro ( Elastix  ,
itk::Object   
)

Functions to get pointers to the elastix components. The components are returned as Object::Pointer. Before calling this functions, call run().

◆ itkGetModifiableObjectMacro() [3/10]

elastix::ElastixMain::itkGetModifiableObjectMacro ( FinalTransform  ,
itk::Object   
)

Get the final transform (the result of running elastix). You may pass this as an InitialTransform in an other instantiation of ElastixMain. Only valid after calling Run()!

◆ itkGetModifiableObjectMacro() [4/10]

elastix::ElastixMain::itkGetModifiableObjectMacro ( FixedImageContainer  ,
DataObjectContainerType   
)

◆ itkGetModifiableObjectMacro() [5/10]

elastix::ElastixMain::itkGetModifiableObjectMacro ( FixedMaskContainer  ,
DataObjectContainerType   
)

◆ itkGetModifiableObjectMacro() [6/10]

elastix::ElastixMain::itkGetModifiableObjectMacro ( InitialTransform  ,
itk::Object   
)

◆ itkGetModifiableObjectMacro() [7/10]

elastix::ElastixMain::itkGetModifiableObjectMacro ( MovingImageContainer  ,
DataObjectContainerType   
)

◆ itkGetModifiableObjectMacro() [8/10]

elastix::ElastixMain::itkGetModifiableObjectMacro ( MovingMaskContainer  ,
DataObjectContainerType   
)

◆ itkGetModifiableObjectMacro() [9/10]

elastix::ElastixMain::itkGetModifiableObjectMacro ( ResultDeformationFieldContainer  ,
DataObjectContainerType   
)

◆ itkGetModifiableObjectMacro() [10/10]

elastix::ElastixMain::itkGetModifiableObjectMacro ( ResultImageContainer  ,
DataObjectContainerType   
)

◆ New()

static Pointer elastix::ElastixMain::New ( )
static

Method for creation through the object factory.

◆ Run() [1/3]

virtual int elastix::ElastixMain::Run ( )
virtual

Start the registration run() without command line parameters; it assumes that EnterCommandLineParameters has been invoked already, or that m_Configuration is initialized in a different way.

Reimplemented in elastix::TransformixMain.

◆ Run() [2/3]

virtual int elastix::ElastixMain::Run ( const ArgumentMapType argmap)
virtual

Start the registration this version of 'run' first calls this->EnterCommandLineParameters(argc,argv) and then calls run().

Reimplemented in elastix::TransformixMain.

◆ Run() [3/3]

virtual int elastix::ElastixMain::Run ( const ArgumentMapType argmap,
const ParameterMapType inputMap 
)
virtual

Reimplemented in elastix::TransformixMain.

◆ SetConfiguration()

virtual void elastix::ElastixMain::SetConfiguration ( Configuration _arg)
virtual

Set/Get the configuration object.

◆ SetElastixLevel()

void elastix::ElastixMain::SetElastixLevel ( unsigned int  level)

Get and Set the elastix level.

◆ SetFixedImageContainer()

virtual void elastix::ElastixMain::SetFixedImageContainer ( DataObjectContainerType _arg)
virtual

Set/Get functions for the fixed and moving images (if these are not used, elastix tries to read them from disk, according to the command line parameters).

◆ SetFixedImageDimension()

virtual void elastix::ElastixMain::SetFixedImageDimension ( ImageDimensionType  _arg)
virtual

◆ SetFixedImagePixelType()

virtual void elastix::ElastixMain::SetFixedImagePixelType ( PixelTypeDescriptionType  _arg)
virtual

Set/Get functions for the description of the image type.

◆ SetFixedMaskContainer()

virtual void elastix::ElastixMain::SetFixedMaskContainer ( DataObjectContainerType _arg)
virtual

Set/Get functions for the fixed and moving masks (if these are not used, elastix tries to read them from disk, according to the command line parameters).

◆ SetInitialTransform()

virtual void elastix::ElastixMain::SetInitialTransform ( itk::Object *  _arg)
virtual

Set/Get the initial transform the type is itk::Object, but the pointer should actually point to an itk::Transform type (or inherited from that one).

◆ SetMaximumNumberOfThreads()

virtual void elastix::ElastixMain::SetMaximumNumberOfThreads ( ) const
virtual

Set maximum number of threads, which is read from the command line arguments. Syntax: -threads <int>

◆ SetMovingImageContainer()

virtual void elastix::ElastixMain::SetMovingImageContainer ( DataObjectContainerType _arg)
virtual

◆ SetMovingImageDimension()

virtual void elastix::ElastixMain::SetMovingImageDimension ( ImageDimensionType  _arg)
virtual

◆ SetMovingImagePixelType()

virtual void elastix::ElastixMain::SetMovingImagePixelType ( PixelTypeDescriptionType  _arg)
virtual

◆ SetMovingMaskContainer()

virtual void elastix::ElastixMain::SetMovingMaskContainer ( DataObjectContainerType _arg)
virtual

◆ SetOriginalFixedImageDirectionFlat()

virtual void elastix::ElastixMain::SetOriginalFixedImageDirectionFlat ( const FlatDirectionCosinesType arg)
virtual

Set/Get the original fixed image direction as a flat array (d11 d21 d31 d21 d22 etc )

◆ SetProcessPriority()

virtual void elastix::ElastixMain::SetProcessPriority ( ) const
virtual

Set process priority, which is read from the command line arguments. Syntax: -priority <high, belownormal>

◆ SetResultDeformationFieldContainer()

virtual void elastix::ElastixMain::SetResultDeformationFieldContainer ( DataObjectContainerType _arg)
virtual

◆ SetResultImageContainer()

virtual void elastix::ElastixMain::SetResultImageContainer ( DataObjectContainerType _arg)
virtual

Set/Get functions for the result images (if these are not used, elastix tries to read them from disk, according to the command line parameters).

◆ SetTotalNumberOfElastixLevels()

void elastix::ElastixMain::SetTotalNumberOfElastixLevels ( unsigned int  levels)

Get and Set the total number of elastix levels.

Field Documentation

◆ m_Configuration

ConfigurationPointer elastix::ElastixMain::m_Configuration { Configuration::New() }
protected

The configuration object, containing the parameters and command-line arguments.

Definition at line 328 of file elxElastixMain.h.

◆ m_Configurations

std::vector<ConfigurationPointer> elastix::ElastixMain::m_Configurations {}
protected

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

Definition at line 331 of file elxElastixMain.h.

◆ m_DBIndex

DBIndexType elastix::ElastixMain::m_DBIndex { 0 }
protected

Definition at line 339 of file elxElastixMain.h.

◆ m_Elastix

ObjectPointer elastix::ElastixMain::m_Elastix { nullptr }
protected

A pointer to elastix as an itk::object. In run() this pointer will be assigned to an ElastixTemplate<>.

Definition at line 325 of file elxElastixMain.h.

◆ m_FinalTransform

ObjectPointer elastix::ElastixMain::m_FinalTransform { nullptr }
protected

A transform that is the result of registration.

Definition at line 350 of file elxElastixMain.h.

◆ m_FixedImageContainer

DataObjectContainerPointer elastix::ElastixMain::m_FixedImageContainer { nullptr }
protected

The images and masks.

Definition at line 342 of file elxElastixMain.h.

◆ m_FixedImageDimension

ImageDimensionType elastix::ElastixMain::m_FixedImageDimension { 0 }
protected

Definition at line 335 of file elxElastixMain.h.

◆ m_FixedImagePixelType

PixelTypeDescriptionType elastix::ElastixMain::m_FixedImagePixelType {}
protected

Description of the ImageTypes.

Definition at line 334 of file elxElastixMain.h.

◆ m_FixedMaskContainer

DataObjectContainerPointer elastix::ElastixMain::m_FixedMaskContainer { nullptr }
protected

Definition at line 344 of file elxElastixMain.h.

◆ m_InitialTransform

ObjectPointer elastix::ElastixMain::m_InitialTransform { nullptr }
protected

The initial transform.

Definition at line 353 of file elxElastixMain.h.

◆ m_MovingImageContainer

DataObjectContainerPointer elastix::ElastixMain::m_MovingImageContainer { nullptr }
protected

Definition at line 343 of file elxElastixMain.h.

◆ m_MovingImageDimension

ImageDimensionType elastix::ElastixMain::m_MovingImageDimension { 0 }
protected

Definition at line 337 of file elxElastixMain.h.

◆ m_MovingImagePixelType

PixelTypeDescriptionType elastix::ElastixMain::m_MovingImagePixelType {}
protected

Definition at line 336 of file elxElastixMain.h.

◆ m_MovingMaskContainer

DataObjectContainerPointer elastix::ElastixMain::m_MovingMaskContainer { nullptr }
protected

Definition at line 345 of file elxElastixMain.h.

◆ m_OriginalFixedImageDirection

FlatDirectionCosinesType elastix::ElastixMain::m_OriginalFixedImageDirection {}
protected

Definition at line 360 of file elxElastixMain.h.

◆ m_ResultDeformationFieldContainer

DataObjectContainerPointer elastix::ElastixMain::m_ResultDeformationFieldContainer { nullptr }
protected

Definition at line 347 of file elxElastixMain.h.

◆ m_ResultImageContainer

DataObjectContainerPointer elastix::ElastixMain::m_ResultImageContainer { nullptr }
protected

Definition at line 346 of file elxElastixMain.h.

◆ m_TransformParametersMap

ParameterMapType elastix::ElastixMain::m_TransformParametersMap {}
protected

Transformation parameters map containing parameters that is the result of registration.

Definition at line 358 of file elxElastixMain.h.



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