elastix::ElastixBase Class Reference

#include <elxElastixBase.h>

Detailed Description

This class creates an interface for elastix.

The ElastixBase class creates an interface for elastix. This is specified in ElastixTemplate, where all functions are defined. Functionality that does not depend on the pixel type and the dimension of the images to be registered, is defined in this class.

The parameters used by this class are:

Parameters:

RandomSeed: Sets a global seed for the random generator.
example: (RandomSeed 121212)
It must be a positive integer number. Default: 121212.

DefaultOutputPrecision: Set the default precision of floating values in the output. Most importantly, it affects the output precision of the parameters in the transform parameter file.
example: (DefaultOutputPrecision 6)
Default value: 6.

The command line arguments used by this class are:

Command line arguments:

-f: mandatory argument for elastix with the file name of the fixed image.
example: -f fixedImage.mhd

-m: mandatory argument for elastix with the file name of the moving image.
example: -m movingImage.mhd

-out: mandatory argument for both elastix and transformix with the name of the directory that is going to contain everything that elastix or tranformix returns as output.
example: -out outputdirectory

-p: mandatory argument for elastix with the name of the parameter file.
example: -p parameters.txt
Multiple parameter files are allowed. It means that multiple registrations are runned in sequence, with the output of some registration as input to the next.

-fMask: Optional argument for elastix with the file name of a mask for the fixed image. The mask image should contain of zeros and ones, zeros indicating pixels that are not used for the registration.
example: -fMask fixedmask.mhd

-mMask: Optional argument for elastix with the file name of a mask for the moving image. The mask image should contain of zeros and ones, zeros indicating pixels that are not used for the registration.
example: -mMask movingmask.mhd

-tp: mandatory argument for transformix with the name of the transform parameter file.
example: -tp TransformParameters.txt
In one such a transform parameter file a reference can be used to another transform parameter file, which is then used as an initial transform.

-priority: optional argument for both elastix and transformix to specify the priority setting of this process. Choose one from {belownormal, high}.
example: -priority high
This argument is only valid for running under Windows. For Linux, run elastix with "nice".

-threads: optional argument for both elastix and transformix to specify the maximum number of threads used by this process. Default: no maximum.
example: -threads 2

-in: optional argument for transformix with the file name of an input image.
example: -in inputImage.mhd
If this option is skipped, a deformation field of the transform will be generated.

Definition at line 143 of file elxElastixBase.h.

Inheritance diagram for elastix::ElastixBase:

Data Structures
class	MultipleDataObjectFiller
class	MultipleImageLoader

Public Types
typedef ComponentDatabaseType::Pointer	ComponentDatabasePointer
typedef ComponentDatabase	ComponentDatabaseType
typedef ConfigurationType::Pointer	ConfigurationPointer
typedef Configuration	ConfigurationType
typedef DataObjectContainerType::Pointer	DataObjectContainerPointer
typedef itk::VectorContainer< unsigned int, DataObjectPointer >	DataObjectContainerType
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< double >	FlatDirectionCosinesType
typedef itk::Object	ITKBaseType
typedef ObjectContainerType::Pointer	ObjectContainerPointer
typedef itk::VectorContainer< unsigned int, ObjectPointer >	ObjectContainerType
typedef ObjectType::Pointer	ObjectPointer
typedef itk::Object	ObjectType
typedef itk::ParameterMapInterface::ParameterMapType	ParameterMapType
typedef ElastixBase	Self
typedef BaseComponent	Superclass

Public Member Functions
void	AfterRegistrationBase (void) override
virtual int	ApplyTransform (void)=0
int	BeforeAllBase (void) override
virtual int	BeforeAllTransformixBase (void)
void	BeforeRegistrationBase (void) override
virtual void	CreateTransformParametersMap (void)=0
	elxGetNumberOfMacro (FixedImage)
	elxGetNumberOfMacro (FixedImageFileName)
	elxGetNumberOfMacro (FixedImagePyramid)
	elxGetNumberOfMacro (FixedMask)
	elxGetNumberOfMacro (FixedMaskFileName)
	elxGetNumberOfMacro (ImageSampler)
	elxGetNumberOfMacro (Interpolator)
	elxGetNumberOfMacro (Metric)
	elxGetNumberOfMacro (MovingImage)
	elxGetNumberOfMacro (MovingImageFileName)
	elxGetNumberOfMacro (MovingImagePyramid)
	elxGetNumberOfMacro (MovingMask)
	elxGetNumberOfMacro (MovingMaskFileName)
	elxGetNumberOfMacro (Optimizer)
	elxGetNumberOfMacro (Registration)
	elxGetNumberOfMacro (ResampleInterpolator)
	elxGetNumberOfMacro (Resampler)
	elxGetNumberOfMacro (ResultDeformationField)
	elxGetNumberOfMacro (ResultImage)
	elxGetNumberOfMacro (Transform)
	elxGetObjectMacro (ComponentDatabase, ComponentDatabaseType)
	elxGetObjectMacro (Configuration, ConfigurationType)
	elxGetObjectMacro (FinalTransform, ObjectType)
	elxGetObjectMacro (FixedImageContainer, DataObjectContainerType)
	elxGetObjectMacro (FixedImageFileNameContainer, FileNameContainerType)
	elxGetObjectMacro (FixedImagePyramidContainer, ObjectContainerType)
	elxGetObjectMacro (FixedMaskContainer, DataObjectContainerType)
	elxGetObjectMacro (FixedMaskFileNameContainer, FileNameContainerType)
	elxGetObjectMacro (ImageSamplerContainer, ObjectContainerType)
	elxGetObjectMacro (InitialTransform, ObjectType)
	elxGetObjectMacro (InterpolatorContainer, ObjectContainerType)
	elxGetObjectMacro (MetricContainer, ObjectContainerType)
	elxGetObjectMacro (MovingImageContainer, DataObjectContainerType)
	elxGetObjectMacro (MovingImageFileNameContainer, FileNameContainerType)
	elxGetObjectMacro (MovingImagePyramidContainer, ObjectContainerType)
	elxGetObjectMacro (MovingMaskContainer, DataObjectContainerType)
	elxGetObjectMacro (MovingMaskFileNameContainer, FileNameContainerType)
	elxGetObjectMacro (OptimizerContainer, ObjectContainerType)
	elxGetObjectMacro (RegistrationContainer, ObjectContainerType)
	elxGetObjectMacro (ResampleInterpolatorContainer, ObjectContainerType)
	elxGetObjectMacro (ResamplerContainer, ObjectContainerType)
	elxGetObjectMacro (ResultDeformationFieldContainer, DataObjectContainerType)
	elxGetObjectMacro (ResultImageContainer, DataObjectContainerType)
	elxGetObjectMacro (TransformContainer, ObjectContainerType)
	elxSetObjectMacro (ComponentDatabase, ComponentDatabaseType)
	elxSetObjectMacro (Configuration, ConfigurationType)
	elxSetObjectMacro (FinalTransform, ObjectType)
	elxSetObjectMacro (FixedImageContainer, DataObjectContainerType)
	elxSetObjectMacro (FixedImageFileNameContainer, FileNameContainerType)
	elxSetObjectMacro (FixedImagePyramidContainer, ObjectContainerType)
	elxSetObjectMacro (FixedMaskContainer, DataObjectContainerType)
	elxSetObjectMacro (FixedMaskFileNameContainer, FileNameContainerType)
	elxSetObjectMacro (ImageSamplerContainer, ObjectContainerType)
	elxSetObjectMacro (InitialTransform, ObjectType)
	elxSetObjectMacro (InterpolatorContainer, ObjectContainerType)
	elxSetObjectMacro (MetricContainer, ObjectContainerType)
	elxSetObjectMacro (MovingImageContainer, DataObjectContainerType)
	elxSetObjectMacro (MovingImageFileNameContainer, FileNameContainerType)
	elxSetObjectMacro (MovingImagePyramidContainer, ObjectContainerType)
	elxSetObjectMacro (MovingMaskContainer, DataObjectContainerType)
	elxSetObjectMacro (MovingMaskFileNameContainer, FileNameContainerType)
	elxSetObjectMacro (OptimizerContainer, ObjectContainerType)
	elxSetObjectMacro (RegistrationContainer, ObjectContainerType)
	elxSetObjectMacro (ResampleInterpolatorContainer, ObjectContainerType)
	elxSetObjectMacro (ResamplerContainer, ObjectContainerType)
	elxSetObjectMacro (ResultDeformationFieldContainer, DataObjectContainerType)
	elxSetObjectMacro (ResultImageContainer, DataObjectContainerType)
	elxSetObjectMacro (TransformContainer, ObjectContainerType)
virtual ITKBaseType *	GetAsITKBaseType (void)
virtual DBIndexType	GetDBIndex (void)
virtual int	GetDefaultOutputPrecision (void) const
virtual const FlatDirectionCosinesType &	GetOriginalFixedImageDirectionFlat (void) const
virtual ParameterMapType	GetTransformParametersMap (void) const =0
virtual bool	GetUseDirectionCosines (void) const
virtual int	Run (void)=0
virtual void	SetConfigurations (std::vector< ConfigurationPointer > &configurations)=0
virtual void	SetDBIndex (DBIndexType _arg)
virtual void	SetOriginalFixedImageDirectionFlat (const FlatDirectionCosinesType &arg)
Public Member Functions inherited from elastix::BaseComponent
virtual void	AfterEachIteration (void)
virtual void	AfterEachIterationBase (void)
virtual void	AfterEachResolution (void)
virtual void	AfterEachResolutionBase (void)
virtual void	AfterRegistration (void)
virtual void	AfterRegistrationBase (void)
virtual int	BeforeAll (void)
virtual int	BeforeAllBase (void)
virtual void	BeforeEachResolution (void)
virtual void	BeforeEachResolutionBase (void)
virtual void	BeforeRegistration (void)
virtual void	BeforeRegistrationBase (void)
virtual const char *	elxGetClassName (void) const
const char *	GetComponentLabel (void) const
	ITK_DISALLOW_COPY_AND_ASSIGN (BaseComponent)
	itkTypeMacroNoParent (BaseComponent)
void	SetComponentLabel (const char *label, unsigned int idx)

Protected Member Functions
	ElastixBase ()
	~ElastixBase () override=default
Protected Member Functions inherited from elastix::BaseComponent
	BaseComponent ()=default
virtual	~BaseComponent ()=default

Protected Attributes
ComponentDatabasePointer	m_ComponentDatabase
ConfigurationPointer	m_Configuration
DBIndexType	m_DBIndex
FlatDirectionCosinesType	m_OriginalFixedImageDirection

Private Member Functions
	ElastixBase (const Self &)
FileNameContainerPointer	GenerateFileNameContainer (const std::string &optionkey, int &errorcode, bool printerrors, bool printinfo) const
void	operator= (const Self &)

Private Attributes
int	m_DefaultOutputPrecision
ObjectPointer	m_FinalTransform
DataObjectContainerPointer	m_FixedImageContainer
FileNameContainerPointer	m_FixedImageFileNameContainer
ObjectContainerPointer	m_FixedImagePyramidContainer
DataObjectContainerPointer	m_FixedMaskContainer
FileNameContainerPointer	m_FixedMaskFileNameContainer
ObjectContainerPointer	m_ImageSamplerContainer
ObjectPointer	m_InitialTransform
ObjectContainerPointer	m_InterpolatorContainer
xl::xoutrow_type	m_IterationInfo
ObjectContainerPointer	m_MetricContainer
DataObjectContainerPointer	m_MovingImageContainer
FileNameContainerPointer	m_MovingImageFileNameContainer
ObjectContainerPointer	m_MovingImagePyramidContainer
DataObjectContainerPointer	m_MovingMaskContainer
FileNameContainerPointer	m_MovingMaskFileNameContainer
ObjectContainerPointer	m_OptimizerContainer
ObjectContainerPointer	m_RegistrationContainer
ObjectContainerPointer	m_ResampleInterpolatorContainer
ObjectContainerPointer	m_ResamplerContainer
DataObjectContainerPointer	m_ResultDeformationFieldContainer
DataObjectContainerPointer	m_ResultImageContainer
ObjectContainerPointer	m_TransformContainer
bool	m_UseDirectionCosines

Additional Inherited Members
Static Public Member Functions inherited from elastix::BaseComponent
static std::string	ConvertSecondsToDHMS (const double totalSeconds, const unsigned int precision)
static void	InitializeElastixExecutable ()
static bool	IsElastixLibrary ()

Member Typedef Documentation

ComponentDatabasePointer

typedef ComponentDatabaseType::Pointer elastix::ElastixBase::ComponentDatabasePointer

Definition at line 170 of file elxElastixBase.h.

ComponentDatabaseType

typedef ComponentDatabase elastix::ElastixBase::ComponentDatabaseType

Other typedef's.

Definition at line 169 of file elxElastixBase.h.

ConfigurationPointer

typedef ConfigurationType::Pointer elastix::ElastixBase::ConfigurationPointer

Definition at line 153 of file elxElastixBase.h.

ConfigurationType

typedef Configuration elastix::ElastixBase::ConfigurationType

Typedefs used in this class.

Definition at line 152 of file elxElastixBase.h.

DataObjectContainerPointer

typedef DataObjectContainerType::Pointer elastix::ElastixBase::DataObjectContainerPointer

Definition at line 163 of file elxElastixBase.h.

DataObjectContainerType

typedef itk::VectorContainer< unsigned int, DataObjectPointer > elastix::ElastixBase::DataObjectContainerType

Definition at line 162 of file elxElastixBase.h.

DataObjectPointer

typedef DataObjectType::Pointer elastix::ElastixBase::DataObjectPointer

Definition at line 157 of file elxElastixBase.h.

DataObjectType

typedef itk::DataObject elastix::ElastixBase::DataObjectType

Definition at line 156 of file elxElastixBase.h.

DBIndexType

typedef ComponentDatabaseType::IndexType elastix::ElastixBase::DBIndexType

Definition at line 171 of file elxElastixBase.h.

FileNameContainerPointer

typedef FileNameContainerType::Pointer elastix::ElastixBase::FileNameContainerPointer

Definition at line 166 of file elxElastixBase.h.

FileNameContainerType

typedef itk::VectorContainer< unsigned int, std::string > elastix::ElastixBase::FileNameContainerType

Definition at line 165 of file elxElastixBase.h.

FlatDirectionCosinesType

typedef std::vector< double > elastix::ElastixBase::FlatDirectionCosinesType

Definition at line 172 of file elxElastixBase.h.

ITKBaseType

typedef itk::Object elastix::ElastixBase::ITKBaseType

The itk class that ElastixTemplate is expected to inherit from Of course ElastixTemplate also inherits from this class (ElastixBase).

Definition at line 180 of file elxElastixBase.h.

ObjectContainerPointer

typedef ObjectContainerType::Pointer elastix::ElastixBase::ObjectContainerPointer

Definition at line 160 of file elxElastixBase.h.

ObjectContainerType

typedef itk::VectorContainer< unsigned int, ObjectPointer > elastix::ElastixBase::ObjectContainerType

Definition at line 159 of file elxElastixBase.h.

ObjectPointer

typedef ObjectType::Pointer elastix::ElastixBase::ObjectPointer

Definition at line 155 of file elxElastixBase.h.

ObjectType

typedef itk::Object elastix::ElastixBase::ObjectType

Definition at line 154 of file elxElastixBase.h.

ParameterMapType

typedef itk::ParameterMapInterface::ParameterMapType elastix::ElastixBase::ParameterMapType

Typedef that is used in the elastix dll version.

Definition at line 175 of file elxElastixBase.h.

Self

typedef ElastixBase elastix::ElastixBase::Self

Standard typedefs etc.

Definition at line 148 of file elxElastixBase.h.

Superclass

typedef BaseComponent elastix::ElastixBase::Superclass

Definition at line 149 of file elxElastixBase.h.

Constructor & Destructor Documentation

ElastixBase() [1/2]

elastix::ElastixBase::ElastixBase ( )

protected

~ElastixBase()

elastix::ElastixBase::~ElastixBase ( )

overrideprotecteddefault

ElastixBase() [2/2]

elastix::ElastixBase::ElastixBase ( const Self &  )

private

Member Function Documentation

AfterRegistrationBase()

void elastix::ElastixBase::AfterRegistrationBase ( void  )

overridevirtual

Reimplemented from elastix::BaseComponent.

ApplyTransform()

virtual int elastix::ElastixBase::ApplyTransform ( void  )

pure virtual

Empty ApplyTransform()-function to be overridden.

Implemented in elastix::ElastixTemplate< TFixedImage, TMovingImage >.

BeforeAllBase()

int elastix::ElastixBase::BeforeAllBase ( void  )

overridevirtual

Function that is called at the very beginning of ElastixTemplate::Run(). It checks the command line input arguments.

Reimplemented from elastix::BaseComponent.

BeforeAllTransformixBase()

virtual int elastix::ElastixBase::BeforeAllTransformixBase ( void  )

virtual

Function that is called at the very beginning of ElastixTemplate::ApplyTransform(). It checks the command line input arguments.

BeforeRegistrationBase()

void elastix::ElastixBase::BeforeRegistrationBase ( void  )

overridevirtual

Functions called before and after registration. They install/uninstall the xout["iteration"] field.

Reimplemented from elastix::BaseComponent.

CreateTransformParametersMap()

virtual void elastix::ElastixBase::CreateTransformParametersMap ( void  )

pure virtual

Creates transformation parameters map.

Implemented in elastix::ElastixTemplate< TFixedImage, TMovingImage >.

elxGetNumberOfMacro() [1/20]

elastix::ElastixBase::elxGetNumberOfMacro

(

FixedImage

)

elxGetNumberOfMacro() [2/20]

elastix::ElastixBase::elxGetNumberOfMacro

(

FixedImageFileName

)

elxGetNumberOfMacro() [3/20]

elastix::ElastixBase::elxGetNumberOfMacro

(

FixedImagePyramid

)

elxGetNumberOfMacro() [4/20]

elastix::ElastixBase::elxGetNumberOfMacro

(

FixedMask

)

elxGetNumberOfMacro() [5/20]

elastix::ElastixBase::elxGetNumberOfMacro

(

FixedMaskFileName

)

elxGetNumberOfMacro() [6/20]

elastix::ElastixBase::elxGetNumberOfMacro

(

ImageSampler

)

elxGetNumberOfMacro() [7/20]

elastix::ElastixBase::elxGetNumberOfMacro

(

Interpolator

)

elxGetNumberOfMacro() [8/20]

elastix::ElastixBase::elxGetNumberOfMacro

(

Metric

)

elxGetNumberOfMacro() [9/20]

elastix::ElastixBase::elxGetNumberOfMacro

(

MovingImage

)

elxGetNumberOfMacro() [10/20]

elastix::ElastixBase::elxGetNumberOfMacro

(

MovingImageFileName

)

elxGetNumberOfMacro() [11/20]

elastix::ElastixBase::elxGetNumberOfMacro

(

MovingImagePyramid

)

elxGetNumberOfMacro() [12/20]

elastix::ElastixBase::elxGetNumberOfMacro

(

MovingMask

)

elxGetNumberOfMacro() [13/20]

elastix::ElastixBase::elxGetNumberOfMacro

(

MovingMaskFileName

)

elxGetNumberOfMacro() [14/20]

elastix::ElastixBase::elxGetNumberOfMacro

(

Optimizer

)

elxGetNumberOfMacro() [15/20]

elastix::ElastixBase::elxGetNumberOfMacro

(

Registration

)

Define some convenience functions: GetNumberOfMetrics() for example.

elxGetNumberOfMacro() [16/20]

elastix::ElastixBase::elxGetNumberOfMacro

(

ResampleInterpolator

)

elxGetNumberOfMacro() [17/20]

elastix::ElastixBase::elxGetNumberOfMacro

(

Resampler

)

elxGetNumberOfMacro() [18/20]

elastix::ElastixBase::elxGetNumberOfMacro

(

ResultDeformationField

)

elxGetNumberOfMacro() [19/20]

elastix::ElastixBase::elxGetNumberOfMacro

(

ResultImage

)

elxGetNumberOfMacro() [20/20]

elastix::ElastixBase::elxGetNumberOfMacro

(

Transform

)

elxGetObjectMacro() [1/24]

elastix::ElastixBase::elxGetObjectMacro	(	ComponentDatabase	,
		ComponentDatabaseType
	)

Functions to get/set the ComponentDatabase The component database contains pointers to functions that create components.

elxGetObjectMacro() [2/24]

elastix::ElastixBase::elxGetObjectMacro	(	Configuration	,
		ConfigurationType
	)

Set/Get the Configuration Object.

elxGetObjectMacro() [3/24]

elastix::ElastixBase::elxGetObjectMacro	(	FinalTransform	,
		ObjectType
	)

elxGetObjectMacro() [4/24]

elastix::ElastixBase::elxGetObjectMacro	(	FixedImageContainer	,
		DataObjectContainerType
	)

Set/Get the fixed/moving image containers.

elxGetObjectMacro() [5/24]

elastix::ElastixBase::elxGetObjectMacro	(	FixedImageFileNameContainer	,
		FileNameContainerType
	)

Set/Get The Image FileName containers. Normally, these are filled in the BeforeAllBase function.

elxGetObjectMacro() [6/24]

elastix::ElastixBase::elxGetObjectMacro	(	FixedImagePyramidContainer	,
		ObjectContainerType
	)

elxGetObjectMacro() [7/24]

elastix::ElastixBase::elxGetObjectMacro	(	FixedMaskContainer	,
		DataObjectContainerType
	)

Set/Get the fixed/moving mask containers.

elxGetObjectMacro() [8/24]

elastix::ElastixBase::elxGetObjectMacro	(	FixedMaskFileNameContainer	,
		FileNameContainerType
	)

Set/Get The Mask FileName containers. Normally, these are filled in the BeforeAllBase function.

elxGetObjectMacro() [9/24]

elastix::ElastixBase::elxGetObjectMacro	(	ImageSamplerContainer	,
		ObjectContainerType
	)

elxGetObjectMacro() [10/24]

elastix::ElastixBase::elxGetObjectMacro	(	InitialTransform	,
		ObjectType
	)

elxGetObjectMacro() [11/24]

elastix::ElastixBase::elxGetObjectMacro	(	InterpolatorContainer	,
		ObjectContainerType
	)

elxGetObjectMacro() [12/24]

elastix::ElastixBase::elxGetObjectMacro	(	MetricContainer	,
		ObjectContainerType
	)

elxGetObjectMacro() [13/24]

elastix::ElastixBase::elxGetObjectMacro	(	MovingImageContainer	,
		DataObjectContainerType
	)

elxGetObjectMacro() [14/24]

elastix::ElastixBase::elxGetObjectMacro	(	MovingImageFileNameContainer	,
		FileNameContainerType
	)

elxGetObjectMacro() [15/24]

elastix::ElastixBase::elxGetObjectMacro	(	MovingImagePyramidContainer	,
		ObjectContainerType
	)

elxGetObjectMacro() [16/24]

elastix::ElastixBase::elxGetObjectMacro	(	MovingMaskContainer	,
		DataObjectContainerType
	)

elxGetObjectMacro() [17/24]

elastix::ElastixBase::elxGetObjectMacro	(	MovingMaskFileNameContainer	,
		FileNameContainerType
	)

elxGetObjectMacro() [18/24]

elastix::ElastixBase::elxGetObjectMacro	(	OptimizerContainer	,
		ObjectContainerType
	)

elxGetObjectMacro() [19/24]

elastix::ElastixBase::elxGetObjectMacro	(	RegistrationContainer	,
		ObjectContainerType
	)

Get the component containers. The component containers store components, such as the metric, in the form of an itk::Object::Pointer.

elxGetObjectMacro() [20/24]

elastix::ElastixBase::elxGetObjectMacro	(	ResampleInterpolatorContainer	,
		ObjectContainerType
	)

elxGetObjectMacro() [21/24]

elastix::ElastixBase::elxGetObjectMacro	(	ResamplerContainer	,
		ObjectContainerType
	)

elxGetObjectMacro() [22/24]

elastix::ElastixBase::elxGetObjectMacro	(	ResultDeformationFieldContainer	,
		DataObjectContainerType
	)

Set/Get the result image container.

elxGetObjectMacro() [23/24]

elastix::ElastixBase::elxGetObjectMacro	(	ResultImageContainer	,
		DataObjectContainerType
	)

Set/Get the result image container.

elxGetObjectMacro() [24/24]

elastix::ElastixBase::elxGetObjectMacro	(	TransformContainer	,
		ObjectContainerType
	)

elxSetObjectMacro() [1/24]

elastix::ElastixBase::elxSetObjectMacro	(	ComponentDatabase	,
		ComponentDatabaseType
	)

elxSetObjectMacro() [2/24]

elastix::ElastixBase::elxSetObjectMacro	(	Configuration	,
		ConfigurationType
	)

elxSetObjectMacro() [3/24]

elastix::ElastixBase::elxSetObjectMacro	(	FinalTransform	,
		ObjectType
	)

Set/Get the final transform The type is ObjectType, but the pointer should actually point to an itk::Transform type (or inherited from that one). You can use this to set it as an initial transform in another ElastixBase instantiation.

elxSetObjectMacro() [4/24]

elastix::ElastixBase::elxSetObjectMacro	(	FixedImageContainer	,
		DataObjectContainerType
	)

elxSetObjectMacro() [5/24]

elastix::ElastixBase::elxSetObjectMacro	(	FixedImageFileNameContainer	,
		FileNameContainerType
	)

elxSetObjectMacro() [6/24]

elastix::ElastixBase::elxSetObjectMacro	(	FixedImagePyramidContainer	,
		ObjectContainerType
	)

elxSetObjectMacro() [7/24]

elastix::ElastixBase::elxSetObjectMacro	(	FixedMaskContainer	,
		DataObjectContainerType
	)

elxSetObjectMacro() [8/24]

elastix::ElastixBase::elxSetObjectMacro	(	FixedMaskFileNameContainer	,
		FileNameContainerType
	)

elxSetObjectMacro() [9/24]

elastix::ElastixBase::elxSetObjectMacro	(	ImageSamplerContainer	,
		ObjectContainerType
	)

elxSetObjectMacro() [10/24]

elastix::ElastixBase::elxSetObjectMacro	(	InitialTransform	,
		ObjectType
	)

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

elxSetObjectMacro() [11/24]

elastix::ElastixBase::elxSetObjectMacro	(	InterpolatorContainer	,
		ObjectContainerType
	)

elxSetObjectMacro() [12/24]

elastix::ElastixBase::elxSetObjectMacro	(	MetricContainer	,
		ObjectContainerType
	)

elxSetObjectMacro() [13/24]

elastix::ElastixBase::elxSetObjectMacro	(	MovingImageContainer	,
		DataObjectContainerType
	)

elxSetObjectMacro() [14/24]

elastix::ElastixBase::elxSetObjectMacro	(	MovingImageFileNameContainer	,
		FileNameContainerType
	)

elxSetObjectMacro() [15/24]

elastix::ElastixBase::elxSetObjectMacro	(	MovingImagePyramidContainer	,
		ObjectContainerType
	)

elxSetObjectMacro() [16/24]

elastix::ElastixBase::elxSetObjectMacro	(	MovingMaskContainer	,
		DataObjectContainerType
	)

elxSetObjectMacro() [17/24]

elastix::ElastixBase::elxSetObjectMacro	(	MovingMaskFileNameContainer	,
		FileNameContainerType
	)

elxSetObjectMacro() [18/24]

elastix::ElastixBase::elxSetObjectMacro	(	OptimizerContainer	,
		ObjectContainerType
	)

elxSetObjectMacro() [19/24]

elastix::ElastixBase::elxSetObjectMacro	(	RegistrationContainer	,
		ObjectContainerType
	)

Set the component containers. The component containers store components, such as the metric, in the form of an itk::Object::Pointer.

elxSetObjectMacro() [20/24]

elastix::ElastixBase::elxSetObjectMacro	(	ResampleInterpolatorContainer	,
		ObjectContainerType
	)

elxSetObjectMacro() [21/24]

elastix::ElastixBase::elxSetObjectMacro	(	ResamplerContainer	,
		ObjectContainerType
	)

elxSetObjectMacro() [22/24]

elastix::ElastixBase::elxSetObjectMacro	(	ResultDeformationFieldContainer	,
		DataObjectContainerType
	)

elxSetObjectMacro() [23/24]

elastix::ElastixBase::elxSetObjectMacro	(	ResultImageContainer	,
		DataObjectContainerType
	)

elxSetObjectMacro() [24/24]

elastix::ElastixBase::elxSetObjectMacro	(	TransformContainer	,
		ObjectContainerType
	)

GenerateFileNameContainer()

FileNameContainerPointer elastix::ElastixBase::GenerateFileNameContainer ( const std::string &  optionkey, int &  errorcode, bool  printerrors, bool  printinfo  ) const

private

Read a series of command line options that satisfy the following syntax: {-f,-f0} <filename0> [-f1 <filename1> [ -f2 <filename2> ... ] ]

This function is used by BeforeAllBase, and is not meant be used at other locations. The errorcode remains the input value if no errors occur. It is set to errorcode | 1 if the option was not given.

GetAsITKBaseType()

virtual ITKBaseType * elastix::ElastixBase::GetAsITKBaseType ( void  )

inlinevirtual

Cast to ITKBaseType.

Definition at line 183 of file elxElastixBase.h.

GetDBIndex()

virtual DBIndexType elastix::ElastixBase::GetDBIndex ( void  )

inlinevirtual

Definition at line 196 of file elxElastixBase.h.

GetDefaultOutputPrecision()

virtual int elastix::ElastixBase::GetDefaultOutputPrecision ( void  ) const

inlinevirtual

Get the default precision of xout. (The value assumed when no DefaultOutputPrecision is given in the parameter file.

Definition at line 340 of file elxElastixBase.h.

GetOriginalFixedImageDirectionFlat()

virtual const FlatDirectionCosinesType & elastix::ElastixBase::GetOriginalFixedImageDirectionFlat ( void  ) const

virtual

GetTransformParametersMap()

virtual ParameterMapType elastix::ElastixBase::GetTransformParametersMap ( void  ) const

pure virtual

Gets transformation parameters map.

Implemented in elastix::ElastixTemplate< TFixedImage, TMovingImage >.

GetUseDirectionCosines()

virtual bool elastix::ElastixBase::GetUseDirectionCosines ( void  ) const

virtual

Get whether direction cosines should be taken into account (true) or ignored (false). This depends on the UseDirectionCosines parameter.

operator=()

void elastix::ElastixBase::operator= ( const Self &  )

private

Run()

virtual int elastix::ElastixBase::Run ( void  )

pure virtual

Empty Run()-function to be overridden.

Implemented in elastix::ElastixTemplate< TFixedImage, TMovingImage >.

SetConfigurations()

virtual void elastix::ElastixBase::SetConfigurations ( std::vector< ConfigurationPointer > &  configurations )

pure virtual

Set configuration vector. Library only.

Implemented in elastix::ElastixTemplate< TFixedImage, TMovingImage >.

SetDBIndex()

virtual void elastix::ElastixBase::SetDBIndex ( DBIndexType  _arg )

virtual

Set the database index of the instantiated elastix object.

SetOriginalFixedImageDirectionFlat()

virtual void elastix::ElastixBase::SetOriginalFixedImageDirectionFlat ( const FlatDirectionCosinesType &  arg )

virtual

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

Field Documentation

m_ComponentDatabase

ComponentDatabasePointer elastix::ElastixBase::m_ComponentDatabase

protected

Definition at line 374 of file elxElastixBase.h.

m_Configuration

ConfigurationPointer elastix::ElastixBase::m_Configuration

protected

Definition at line 372 of file elxElastixBase.h.

m_DBIndex

DBIndexType elastix::ElastixBase::m_DBIndex

protected

Definition at line 373 of file elxElastixBase.h.

m_DefaultOutputPrecision

int elastix::ElastixBase::m_DefaultOutputPrecision

private

Definition at line 508 of file elxElastixBase.h.

m_FinalTransform

ObjectPointer elastix::ElastixBase::m_FinalTransform

private

Definition at line 544 of file elxElastixBase.h.

m_FixedImageContainer

DataObjectContainerPointer elastix::ElastixBase::m_FixedImageContainer

private

The Image and Mask containers. These are stored as pointers to itk::DataObject.

Definition at line 525 of file elxElastixBase.h.

m_FixedImageFileNameContainer

FileNameContainerPointer elastix::ElastixBase::m_FixedImageFileNameContainer

private

The image and mask FileNameContainers.

Definition at line 537 of file elxElastixBase.h.

m_FixedImagePyramidContainer

ObjectContainerPointer elastix::ElastixBase::m_FixedImagePyramidContainer

private

The component containers. These containers contain SmartPointer's to itk::Object.

Definition at line 513 of file elxElastixBase.h.

m_FixedMaskContainer

DataObjectContainerPointer elastix::ElastixBase::m_FixedMaskContainer

private

Definition at line 527 of file elxElastixBase.h.

m_FixedMaskFileNameContainer

FileNameContainerPointer elastix::ElastixBase::m_FixedMaskFileNameContainer

private

Definition at line 539 of file elxElastixBase.h.

m_ImageSamplerContainer

ObjectContainerPointer elastix::ElastixBase::m_ImageSamplerContainer

private

Definition at line 516 of file elxElastixBase.h.

m_InitialTransform

ObjectPointer elastix::ElastixBase::m_InitialTransform

private

The initial and final transform.

Definition at line 543 of file elxElastixBase.h.

m_InterpolatorContainer

ObjectContainerPointer elastix::ElastixBase::m_InterpolatorContainer

private

Definition at line 515 of file elxElastixBase.h.

m_IterationInfo

xl::xoutrow_type elastix::ElastixBase::m_IterationInfo

private

Definition at line 506 of file elxElastixBase.h.

m_MetricContainer

ObjectContainerPointer elastix::ElastixBase::m_MetricContainer

private

Definition at line 517 of file elxElastixBase.h.

m_MovingImageContainer

DataObjectContainerPointer elastix::ElastixBase::m_MovingImageContainer

private

Definition at line 526 of file elxElastixBase.h.

m_MovingImageFileNameContainer

FileNameContainerPointer elastix::ElastixBase::m_MovingImageFileNameContainer

private

Definition at line 538 of file elxElastixBase.h.

m_MovingImagePyramidContainer

ObjectContainerPointer elastix::ElastixBase::m_MovingImagePyramidContainer

private

Definition at line 514 of file elxElastixBase.h.

m_MovingMaskContainer

DataObjectContainerPointer elastix::ElastixBase::m_MovingMaskContainer

private

Definition at line 528 of file elxElastixBase.h.

m_MovingMaskFileNameContainer

FileNameContainerPointer elastix::ElastixBase::m_MovingMaskFileNameContainer

private

Definition at line 540 of file elxElastixBase.h.

m_OptimizerContainer

ObjectContainerPointer elastix::ElastixBase::m_OptimizerContainer

private

Definition at line 518 of file elxElastixBase.h.

m_OriginalFixedImageDirection

FlatDirectionCosinesType elastix::ElastixBase::m_OriginalFixedImageDirection

protected

Definition at line 376 of file elxElastixBase.h.

m_RegistrationContainer

ObjectContainerPointer elastix::ElastixBase::m_RegistrationContainer

private

Definition at line 519 of file elxElastixBase.h.

m_ResampleInterpolatorContainer

ObjectContainerPointer elastix::ElastixBase::m_ResampleInterpolatorContainer

private

Definition at line 521 of file elxElastixBase.h.

m_ResamplerContainer

ObjectContainerPointer elastix::ElastixBase::m_ResamplerContainer

private

Definition at line 520 of file elxElastixBase.h.

m_ResultDeformationFieldContainer

DataObjectContainerPointer elastix::ElastixBase::m_ResultDeformationFieldContainer

private

The result deformation field container. These are stored as pointers to itk::DataObject.

Definition at line 534 of file elxElastixBase.h.

m_ResultImageContainer

DataObjectContainerPointer elastix::ElastixBase::m_ResultImageContainer

private

The result image container. These are stored as pointers to itk::DataObject.

Definition at line 531 of file elxElastixBase.h.

m_TransformContainer

ObjectContainerPointer elastix::ElastixBase::m_TransformContainer

private

Definition at line 522 of file elxElastixBase.h.

m_UseDirectionCosines

bool elastix::ElastixBase::m_UseDirectionCosines

private

Use or ignore direction cosines.

Definition at line 547 of file elxElastixBase.h.