elastix::MainBase Class Reference

#include <elxMainBase.h>

Detailed Description

Common (abstract) base class of ElastixMain and TransformixMain.

Definition at line 44 of file elxMainBase.h.

Inheritance diagram for elastix::MainBase:

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	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 = MainBase
using	Superclass = itk::Object

Public Member Functions
virtual const char *	GetClassName () const
virtual DBIndexType	GetDBIndex () const
ElastixBase &	GetElastixBase () const
virtual ImageDimensionType	GetFixedImageDimension () const
virtual PixelTypeDescriptionType	GetFixedImagePixelType () const
virtual ImageDimensionType	GetMovingImageDimension () const
virtual PixelTypeDescriptionType	GetMovingImagePixelType () const
	ITK_DISALLOW_COPY_AND_MOVE (MainBase)
	itkGetModifiableObjectMacro (Configuration, Configuration)
	itkGetModifiableObjectMacro (Elastix, itk::Object)
	itkGetModifiableObjectMacro (MovingImageContainer, DataObjectContainerType)
	itkGetModifiableObjectMacro (ResultDeformationFieldContainer, DataObjectContainerType)
	itkGetModifiableObjectMacro (ResultImageContainer, DataObjectContainerType)
virtual int	Run ()=0
virtual int	Run (const ArgumentMapType &argmap)
virtual int	Run (const ArgumentMapType &argmap, const ParameterMapType &inputMap)
virtual void	SetConfiguration (Configuration *_arg)
virtual void	SetFixedImageDimension (ImageDimensionType _arg)
virtual void	SetFixedImagePixelType (PixelTypeDescriptionType _arg)
virtual void	SetMaximumNumberOfThreads () const
virtual void	SetMovingImageContainer (DataObjectContainerType *_arg)
virtual void	SetMovingImageDimension (ImageDimensionType _arg)
virtual void	SetMovingImagePixelType (PixelTypeDescriptionType _arg)
virtual void	SetProcessPriority () const
virtual void	SetResultDeformationFieldContainer (DataObjectContainerType *_arg)
virtual void	SetResultImageContainer (DataObjectContainerType *_arg)

Static Public Member Functions
static const ComponentDatabase &	GetComponentDatabase ()

Protected Member Functions
virtual ObjectPointer	CreateComponent (const ComponentDescriptionType &name)
virtual ObjectContainerPointer	CreateComponents (const ComponentDescriptionType &key, const ComponentDescriptionType &defaultComponentName, int &errorcode, bool mandatoryComponent=true)
virtual int	InitDBIndex ()=0
	MainBase ()
	~MainBase () override=0

Protected Attributes
DBIndexType	m_DBIndex { 0 }
ObjectPointer	m_Elastix { nullptr }
ImageDimensionType	m_FixedImageDimension { 0 }
PixelTypeDescriptionType	m_FixedImagePixelType {}
DataObjectContainerPointer	m_MovingImageContainer { nullptr }
ImageDimensionType	m_MovingImageDimension { 0 }
PixelTypeDescriptionType	m_MovingImagePixelType {}
DataObjectContainerPointer	m_ResultDeformationFieldContainer { nullptr }
DataObjectContainerPointer	m_ResultImageContainer { nullptr }
std::vector< Configuration::ConstPointer >	m_TransformConfigurations {}

Private Attributes
Configuration::Pointer	m_Configuration { Configuration::New() }

Member Typedef Documentation

ArgumentMapType

using elastix::MainBase::ArgumentMapType = Configuration::CommandLineArgumentMapType

elastix components.

Definition at line 65 of file elxMainBase.h.

ComponentDatabasePointer

using elastix::MainBase::ComponentDatabasePointer = ComponentDatabase::Pointer

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 75 of file elxMainBase.h.

ComponentDescriptionType

using elastix::MainBase::ComponentDescriptionType = ComponentDatabase::ComponentDescriptionType

Definition at line 77 of file elxMainBase.h.

ConstPointer

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

Definition at line 53 of file elxMainBase.h.

DataObjectContainerPointer

using elastix::MainBase::DataObjectContainerPointer = ElastixBase::DataObjectContainerPointer

Definition at line 69 of file elxMainBase.h.

DataObjectContainerType

using elastix::MainBase::DataObjectContainerType = ElastixBase::DataObjectContainerType

Definition at line 67 of file elxMainBase.h.

DataObjectPointer

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

Definition at line 62 of file elxMainBase.h.

DBIndexType

using elastix::MainBase::DBIndexType = ComponentDatabase::IndexType

Definition at line 80 of file elxMainBase.h.

FlatDirectionCosinesType

using elastix::MainBase::FlatDirectionCosinesType = ElastixBase::FlatDirectionCosinesType

Definition at line 70 of file elxMainBase.h.

ImageDimensionType

using elastix::MainBase::ImageDimensionType = ComponentDatabase::ImageDimensionType

Definition at line 79 of file elxMainBase.h.

ObjectContainerPointer

using elastix::MainBase::ObjectContainerPointer = ElastixBase::ObjectContainerPointer

Definition at line 68 of file elxMainBase.h.

ObjectContainerType

using elastix::MainBase::ObjectContainerType = ElastixBase::ObjectContainerType

Definition at line 66 of file elxMainBase.h.

ObjectPointer

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

Typedef's. ITK base objects.

Definition at line 61 of file elxMainBase.h.

ParameterMapType

using elastix::MainBase::ParameterMapType = itk::ParameterMapInterface::ParameterMapType

Typedef that is used in the elastix dll version.

Definition at line 83 of file elxMainBase.h.

PixelTypeDescriptionType

using elastix::MainBase::PixelTypeDescriptionType = ComponentDatabase::PixelTypeDescriptionType

Definition at line 78 of file elxMainBase.h.

Pointer

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

Definition at line 52 of file elxMainBase.h.

PtrToCreator

using elastix::MainBase::PtrToCreator = ComponentDatabase::PtrToCreator

Definition at line 76 of file elxMainBase.h.

Self

using elastix::MainBase::Self = MainBase

Standard itk.

Definition at line 50 of file elxMainBase.h.

Superclass

using elastix::MainBase::Superclass = itk::Object

Definition at line 51 of file elxMainBase.h.

Constructor & Destructor Documentation

MainBase()

elastix::MainBase::MainBase ( )

protected

~MainBase()

elastix::MainBase::~MainBase ( )

overrideprotectedpure virtual

Member Function Documentation

CreateComponent()

virtual ObjectPointer elastix::MainBase::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::MainBase::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

GetClassName()

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

virtual

Run-time type information (and related methods).

Reimplemented in elastix::ElastixMain, and elastix::TransformixMain.

GetComponentDatabase()

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

static

Function to get the ComponentDatabase.

GetDBIndex()

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

virtual

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

GetElastixBase()

ElastixBase & elastix::MainBase::GetElastixBase

(

)

const

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

GetFixedImageDimension()

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

virtual

GetFixedImagePixelType()

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

virtual

GetMovingImageDimension()

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

virtual

GetMovingImagePixelType()

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

virtual

InitDBIndex()

virtual int elastix::MainBase::InitDBIndex ( )

protectedpure virtual

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

Implemented in elastix::ElastixMain, and elastix::TransformixMain.

ITK_DISALLOW_COPY_AND_MOVE()

elastix::MainBase::ITK_DISALLOW_COPY_AND_MOVE

(

MainBase

)

itkGetModifiableObjectMacro() [1/5]

elastix::MainBase::itkGetModifiableObjectMacro	(	Configuration	,
		Configuration	)

itkGetModifiableObjectMacro() [2/5]

elastix::MainBase::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() [3/5]

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

itkGetModifiableObjectMacro() [4/5]

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

itkGetModifiableObjectMacro() [5/5]

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

Run() [1/3]

virtual int elastix::MainBase::Run ( )

pure 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.

Implemented in elastix::ElastixMain, and elastix::TransformixMain.

Run() [2/3]

virtual int elastix::MainBase::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::ElastixMain, and elastix::TransformixMain.

Run() [3/3]

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

virtual

Reimplemented in elastix::ElastixMain, and elastix::TransformixMain.

SetConfiguration()

virtual void elastix::MainBase::SetConfiguration ( Configuration * _arg )

virtual

Set/Get the configuration object.

SetFixedImageDimension()

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

virtual

SetFixedImagePixelType()

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

virtual

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

SetMaximumNumberOfThreads()

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

virtual

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

SetMovingImageContainer()

virtual void elastix::MainBase::SetMovingImageContainer ( DataObjectContainerType * _arg )

virtual

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

SetMovingImageDimension()

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

virtual

SetMovingImagePixelType()

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

virtual

SetProcessPriority()

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

virtual

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

SetResultDeformationFieldContainer()

virtual void elastix::MainBase::SetResultDeformationFieldContainer ( DataObjectContainerType * _arg )

virtual

SetResultImageContainer()

virtual void elastix::MainBase::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).

Field Documentation

m_Configuration

Configuration::Pointer elastix::MainBase::m_Configuration { Configuration::New() }

private

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

Definition at line 228 of file elxMainBase.h.

m_DBIndex

DBIndexType elastix::MainBase::m_DBIndex { 0 }

protected

Definition at line 185 of file elxMainBase.h.

m_Elastix

ObjectPointer elastix::MainBase::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 174 of file elxMainBase.h.

m_FixedImageDimension

ImageDimensionType elastix::MainBase::m_FixedImageDimension { 0 }

protected

Definition at line 181 of file elxMainBase.h.

m_FixedImagePixelType

PixelTypeDescriptionType elastix::MainBase::m_FixedImagePixelType {}

protected

Description of the ImageTypes.

Definition at line 180 of file elxMainBase.h.

m_MovingImageContainer

DataObjectContainerPointer elastix::MainBase::m_MovingImageContainer { nullptr }

protected

The images and masks.

Definition at line 188 of file elxMainBase.h.

m_MovingImageDimension

ImageDimensionType elastix::MainBase::m_MovingImageDimension { 0 }

protected

Definition at line 183 of file elxMainBase.h.

m_MovingImagePixelType

PixelTypeDescriptionType elastix::MainBase::m_MovingImagePixelType {}

protected

Definition at line 182 of file elxMainBase.h.

m_ResultDeformationFieldContainer

DataObjectContainerPointer elastix::MainBase::m_ResultDeformationFieldContainer { nullptr }

protected

Definition at line 190 of file elxMainBase.h.

m_ResultImageContainer

DataObjectContainerPointer elastix::MainBase::m_ResultImageContainer { nullptr }

protected

Definition at line 189 of file elxMainBase.h.

m_TransformConfigurations

std::vector<Configuration::ConstPointer> elastix::MainBase::m_TransformConfigurations {}

protected

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

Definition at line 177 of file elxMainBase.h.