elastix::RegistrationBase< TElastix > Class Template Reference

#include <elxRegistrationBase.h>

Detailed Description

template<class TElastix>
class elastix::RegistrationBase< TElastix >

This class is the elastix base class for all Registration schemes.

This class contains all the common functionality for Registrations.

Parameters:

ErodeMask: a flag to determine if the masks should be eroded from one resolution level to another. Choose from {"true", "false"}
example: (ErodeMask "false")
The default is "true". The parameter may be specified for each resolution differently, but that's not obliged. The actual amount of erosion depends on the image pyramid.
Erosion of the mask prevents the border / edge of the mask taken into account. This can be useful for example for ultrasound images, where you don't want to take into account values outside the US-beam, but where you also don't want to match the edge / border of this beam. For example for MRI's of the head, the borders of the head may be wanted to match, and there erosion should be avoided.

ErodeFixedMask: a flag to determine if the fixed mask(s) should be eroded from one resolution level to another. Choose from {"true", "false"}
example: (ErodeFixedMask "true" "false") This setting overrules ErodeMask.

ErodeMovingMask: a flag to determine if the moving mask(s) should be eroded from one resolution level to another. Choose from {"true", "false"}
example: (ErodeMovingMask "true" "false") This setting overrules ErodeMask.

ErodeFixedMask<i>: a flag to determine if the i-th fixed mask should be eroded from one resolution level to another. Choose from {"true", "false"}
example: (ErodeFixedMask2 "true" "false") This setting overrules ErodeMask and ErodeFixedMask.

ErodeMovingMask<i>: a flag to determine if the i-th moving mask should be eroded from one resolution level to another. Choose from {"true", "false"}
example: (ErodeMovingMask2 "true" "false") This setting overrules ErodeMask and ErodeMovingMask.

Definition at line 75 of file elxRegistrationBase.h.

Inheritance diagram for elastix::RegistrationBase< TElastix >:

Public Types
typedef Superclass::ConfigurationPointer	ConfigurationPointer
typedef Superclass::ConfigurationType	ConfigurationType
typedef Superclass::ElastixPointer	ElastixPointer
typedef Superclass::ElastixType	ElastixType
typedef ElastixType::FixedImageType	FixedImageType
typedef itk::MultiResolutionImageRegistrationMethod2< FixedImageType, MovingImageType >	ITKBaseType
typedef ElastixType::MovingImageType	MovingImageType
typedef Superclass::RegistrationPointer	RegistrationPointer
typedef Superclass::RegistrationType	RegistrationType
typedef RegistrationBase	Self
typedef BaseComponentSE< TElastix >	Superclass
typedef std::vector< bool >	UseMaskErosionArrayType
Public Types inherited from elastix::BaseComponentSE< TElastix >
typedef Configuration::Pointer	ConfigurationPointer
typedef Configuration	ConfigurationType
typedef itk::WeakPointer< ElastixType >	ElastixPointer
typedef TElastix	ElastixType
typedef RegistrationType *	RegistrationPointer
typedef ElastixType::RegistrationBaseType	RegistrationType
typedef BaseComponentSE	Self
typedef BaseComponent	Superclass

Public Member Functions
virtual ITKBaseType *	GetAsITKBaseType (void)
virtual const ITKBaseType *	GetAsITKBaseType (void) const
virtual const char *	GetClassName () const
	itkStaticConstMacro (FixedImageDimension, unsigned int, FixedImageType::ImageDimension)
	itkStaticConstMacro (MovingImageDimension, unsigned int, MovingImageType::ImageDimension)
virtual bool	ReadMaskParameters (UseMaskErosionArrayType &useMaskErosionArray, const unsigned int nrOfMasks, const std::string &whichMask, const unsigned int level) const
Public Member Functions inherited from elastix::BaseComponentSE< TElastix >
ConfigurationType *	GetConfiguration (void) const
ElastixType *	GetElastix (void) const
RegistrationPointer	GetRegistration (void) const
	ITK_DISALLOW_COPY_AND_ASSIGN (BaseComponentSE)
void	SetConfiguration (ConfigurationType *_arg)
void	SetElastix (ElastixType *_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 Types
typedef ITKBaseType::FixedImagePyramidType	FixedImagePyramidType
typedef FixedMaskErodeFilterType::Pointer	FixedMaskErodeFilterPointer
typedef itk::ErodeMaskImageFilter< FixedMaskImageType >	FixedMaskErodeFilterType
typedef FixedMaskImageType::Pointer	FixedMaskImagePointer
typedef ElastixType::FixedMaskType	FixedMaskImageType
typedef FixedMaskSpatialObjectType::Pointer	FixedMaskSpatialObjectPointer
typedef itk::ImageMaskSpatialObject< itkGetStaticConstMacro(FixedImageDimension) >	FixedMaskSpatialObjectType
typedef ElastixType::MaskPixelType	MaskPixelType
typedef ITKBaseType::MovingImagePyramidType	MovingImagePyramidType
typedef MovingMaskErodeFilterType::Pointer	MovingMaskErodeFilterPointer
typedef itk::ErodeMaskImageFilter< MovingMaskImageType >	MovingMaskErodeFilterType
typedef MovingMaskImageType::Pointer	MovingMaskImagePointer
typedef ElastixType::MovingMaskType	MovingMaskImageType
typedef MovingMaskSpatialObjectType::Pointer	MovingMaskSpatialObjectPointer
typedef itk::ImageMaskSpatialObject< itkGetStaticConstMacro(MovingImageDimension) >	MovingMaskSpatialObjectType

Protected Member Functions
FixedMaskSpatialObjectPointer	GenerateFixedMaskSpatialObject (const FixedMaskImageType *maskImage, bool useMaskErosion, const FixedImagePyramidType *pyramid, unsigned int level) const
MovingMaskSpatialObjectPointer	GenerateMovingMaskSpatialObject (const MovingMaskImageType *maskImage, bool useMaskErosion, const MovingImagePyramidType *pyramid, unsigned int level) const
	RegistrationBase ()
	~RegistrationBase () override
Protected Member Functions inherited from elastix::BaseComponentSE< TElastix >
	BaseComponentSE ()=default
	~BaseComponentSE () override=default
Protected Member Functions inherited from elastix::BaseComponent
	BaseComponent ()=default
virtual	~BaseComponent ()=default

Private Member Functions
void	operator= (const Self &)
	RegistrationBase (const Self &)

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 ()
Protected Attributes inherited from elastix::BaseComponentSE< TElastix >
ConfigurationPointer	m_Configuration {}
ElastixPointer	m_Elastix {}
RegistrationPointer	m_Registration {}

Member Typedef Documentation

ConfigurationPointer

template<class TElastix >

typedef Superclass::ConfigurationPointer elastix::RegistrationBase< TElastix >::ConfigurationPointer

Definition at line 90 of file elxRegistrationBase.h.

ConfigurationType

template<class TElastix >

typedef Superclass::ConfigurationType elastix::RegistrationBase< TElastix >::ConfigurationType

Definition at line 89 of file elxRegistrationBase.h.

ElastixPointer

template<class TElastix >

typedef Superclass::ElastixPointer elastix::RegistrationBase< TElastix >::ElastixPointer

Definition at line 88 of file elxRegistrationBase.h.

ElastixType

template<class TElastix >

typedef Superclass::ElastixType elastix::RegistrationBase< TElastix >::ElastixType

Typedef's from Elastix.

Definition at line 87 of file elxRegistrationBase.h.

FixedImagePyramidType

template<class TElastix >

typedef ITKBaseType::FixedImagePyramidType elastix::RegistrationBase< TElastix >::FixedImagePyramidType

protected

Definition at line 172 of file elxRegistrationBase.h.

FixedImageType

template<class TElastix >

typedef ElastixType::FixedImageType elastix::RegistrationBase< TElastix >::FixedImageType

Other typedef's.

Definition at line 95 of file elxRegistrationBase.h.

FixedMaskErodeFilterPointer

template<class TElastix >

typedef FixedMaskErodeFilterType::Pointer elastix::RegistrationBase< TElastix >::FixedMaskErodeFilterPointer

protected

Definition at line 177 of file elxRegistrationBase.h.

FixedMaskErodeFilterType

template<class TElastix >

typedef itk::ErodeMaskImageFilter< FixedMaskImageType > elastix::RegistrationBase< TElastix >::FixedMaskErodeFilterType

protected

Some typedef's used for eroding the masks

Definition at line 176 of file elxRegistrationBase.h.

FixedMaskImagePointer

template<class TElastix >

typedef FixedMaskImageType::Pointer elastix::RegistrationBase< TElastix >::FixedMaskImagePointer

protected

Definition at line 161 of file elxRegistrationBase.h.

FixedMaskImageType

template<class TElastix >

typedef ElastixType::FixedMaskType elastix::RegistrationBase< TElastix >::FixedMaskImageType

protected

Definition at line 159 of file elxRegistrationBase.h.

FixedMaskSpatialObjectPointer

template<class TElastix >

typedef FixedMaskSpatialObjectType::Pointer elastix::RegistrationBase< TElastix >::FixedMaskSpatialObjectPointer

protected

Definition at line 168 of file elxRegistrationBase.h.

FixedMaskSpatialObjectType

template<class TElastix >

typedef itk::ImageMaskSpatialObject< itkGetStaticConstMacro( FixedImageDimension ) > elastix::RegistrationBase< TElastix >::FixedMaskSpatialObjectType

protected

Definition at line 164 of file elxRegistrationBase.h.

ITKBaseType

template<class TElastix >

typedef itk::MultiResolutionImageRegistrationMethod2< FixedImageType, MovingImageType > elastix::RegistrationBase< TElastix >::ITKBaseType

Typedef for ITKBaseType.

Definition at line 105 of file elxRegistrationBase.h.

MaskPixelType

template<class TElastix >

typedef ElastixType::MaskPixelType elastix::RegistrationBase< TElastix >::MaskPixelType

protected

Typedef's for mask support.

Definition at line 158 of file elxRegistrationBase.h.

MovingImagePyramidType

template<class TElastix >

typedef ITKBaseType::MovingImagePyramidType elastix::RegistrationBase< TElastix >::MovingImagePyramidType

protected

Definition at line 173 of file elxRegistrationBase.h.

MovingImageType

template<class TElastix >

typedef ElastixType::MovingImageType elastix::RegistrationBase< TElastix >::MovingImageType

Definition at line 96 of file elxRegistrationBase.h.

MovingMaskErodeFilterPointer

template<class TElastix >

typedef MovingMaskErodeFilterType::Pointer elastix::RegistrationBase< TElastix >::MovingMaskErodeFilterPointer

protected

Definition at line 179 of file elxRegistrationBase.h.

MovingMaskErodeFilterType

template<class TElastix >

typedef itk::ErodeMaskImageFilter< MovingMaskImageType > elastix::RegistrationBase< TElastix >::MovingMaskErodeFilterType

protected

Definition at line 178 of file elxRegistrationBase.h.

MovingMaskImagePointer

template<class TElastix >

typedef MovingMaskImageType::Pointer elastix::RegistrationBase< TElastix >::MovingMaskImagePointer

protected

Definition at line 162 of file elxRegistrationBase.h.

MovingMaskImageType

template<class TElastix >

typedef ElastixType::MovingMaskType elastix::RegistrationBase< TElastix >::MovingMaskImageType

protected

Definition at line 160 of file elxRegistrationBase.h.

MovingMaskSpatialObjectPointer

template<class TElastix >

typedef MovingMaskSpatialObjectType::Pointer elastix::RegistrationBase< TElastix >::MovingMaskSpatialObjectPointer

protected

Definition at line 170 of file elxRegistrationBase.h.

MovingMaskSpatialObjectType

template<class TElastix >

typedef itk::ImageMaskSpatialObject< itkGetStaticConstMacro( MovingImageDimension ) > elastix::RegistrationBase< TElastix >::MovingMaskSpatialObjectType

protected

Definition at line 166 of file elxRegistrationBase.h.

RegistrationPointer

template<class TElastix >

typedef Superclass::RegistrationPointer elastix::RegistrationBase< TElastix >::RegistrationPointer

Definition at line 92 of file elxRegistrationBase.h.

RegistrationType

template<class TElastix >

typedef Superclass::RegistrationType elastix::RegistrationBase< TElastix >::RegistrationType

Definition at line 91 of file elxRegistrationBase.h.

Self

template<class TElastix >

typedef RegistrationBase elastix::RegistrationBase< TElastix >::Self

Standard ITK stuff.

Definition at line 80 of file elxRegistrationBase.h.

Superclass

template<class TElastix >

typedef BaseComponentSE< TElastix > elastix::RegistrationBase< TElastix >::Superclass

Definition at line 81 of file elxRegistrationBase.h.

UseMaskErosionArrayType

template<class TElastix >

typedef std::vector< bool > elastix::RegistrationBase< TElastix >::UseMaskErosionArrayType

Typedef for mask erosion options

Definition at line 108 of file elxRegistrationBase.h.

Constructor & Destructor Documentation

RegistrationBase() [1/2]

template<class TElastix >

elastix::RegistrationBase< TElastix >::RegistrationBase ( )

inlineprotected

The constructor.

Definition at line 153 of file elxRegistrationBase.h.

~RegistrationBase()

template<class TElastix >

elastix::RegistrationBase< TElastix >::~RegistrationBase ( )

inlineoverrideprotected

The destructor.

Definition at line 155 of file elxRegistrationBase.h.

RegistrationBase() [2/2]

template<class TElastix >

elastix::RegistrationBase< TElastix >::RegistrationBase ( const Self &  )

private

The private constructor.

Member Function Documentation

GenerateFixedMaskSpatialObject()

template<class TElastix >

FixedMaskSpatialObjectPointer elastix::RegistrationBase< TElastix >::GenerateFixedMaskSpatialObject ( const FixedMaskImageType *  maskImage, bool  useMaskErosion, const FixedImagePyramidType *  pyramid, unsigned int  level  ) const

protected

Generate a spatial object from a mask image, possibly after eroding the image Input:

• the mask as an image, consisting of 1's and 0's;
• a boolean that determines whether mask erosion is needed
• the image pyramid, which is needed to determines the amount of erosion (can be set to 0 if useMaskErosion == false
• the resolution level Output:
• the mask as a spatial object, which can be set in a metric for example

This function is used by the registration components

GenerateMovingMaskSpatialObject()

template<class TElastix >

MovingMaskSpatialObjectPointer elastix::RegistrationBase< TElastix >::GenerateMovingMaskSpatialObject ( const MovingMaskImageType *  maskImage, bool  useMaskErosion, const MovingImagePyramidType *  pyramid, unsigned int  level  ) const

protected

Generate a spatial object from a mask image, possibly after eroding the image Input:

• the mask as an image, consisting of 1's and 0's;
• a boolean that determines whether mask erosion is needed
• the image pyramid, which is needed to determines the amount of erosion (can be set to 0 if useMaskErosion == false
• the resolution level Output:
• the mask as a spatial object, which can be set in a metric for example

This function is used by the registration components

GetAsITKBaseType() [1/2]

template<class TElastix >

virtual ITKBaseType * elastix::RegistrationBase< TElastix >::GetAsITKBaseType ( void  )

inlinevirtual

Cast to ITKBaseType.

Definition at line 111 of file elxRegistrationBase.h.

GetAsITKBaseType() [2/2]

template<class TElastix >

virtual const ITKBaseType * elastix::RegistrationBase< TElastix >::GetAsITKBaseType ( void  ) const

inlinevirtual

Cast to ITKBaseType, to use in const functions.

Definition at line 118 of file elxRegistrationBase.h.

GetClassName()

template<class TElastix >

virtual const char * elastix::RegistrationBase< TElastix >::GetClassName ( ) const

virtual

Run-time type information (and related methods).

Reimplemented in elastix::MultiMetricMultiResolutionRegistration< TElastix >, elastix::MultiResolutionRegistration< TElastix >, and elastix::MultiResolutionRegistrationWithFeatures< TElastix >.

itkStaticConstMacro() [1/2]

template<class TElastix >

elastix::RegistrationBase< TElastix >::itkStaticConstMacro	(	FixedImageDimension	,
		unsigned int	,
		FixedImageType::ImageDimension
	)

Get the dimension of the fixed image.

itkStaticConstMacro() [2/2]

template<class TElastix >

elastix::RegistrationBase< TElastix >::itkStaticConstMacro	(	MovingImageDimension	,
		unsigned int	,
		MovingImageType::ImageDimension
	)

Get the dimension of the moving image.

operator=()

template<class TElastix >

void elastix::RegistrationBase< TElastix >::operator= ( const Self &  )

private

The private copy constructor.

ReadMaskParameters()

template<class TElastix >

virtual bool elastix::RegistrationBase< TElastix >::ReadMaskParameters ( UseMaskErosionArrayType &  useMaskErosionArray, const unsigned int  nrOfMasks, const std::string &  whichMask, const unsigned int  level  ) const

virtual

Function to read the mask parameters from the configuration object.

Todo:

: move to RegistrationBase Input:

• an array that will contain a bool for each mask, saying if it needs erosion or not
• the number of masks
• whichMask: "Fixed" or "Moving"
• the current resolution level Output:
• The function returns a bool that says if any mask needs erosion. If the number of masks is zero, this bool will be false.
• The useMaskErosionArray, which indicates for each mask whether it should be eroded. If the number of masks is zero, this array will be empty.

The function first checks Erode<Fixed,Moving>Mask<i>, with i the mask number, then Erode<Fixed,Moving>Mask, and finally ErodeMask. So, if you do not specify Erode<Fixed,Moving>Mask<i>, Erode<Fixed,Moving>Mask is tried, and then ErodeMask. If you specify ErodeMask, that option will be used for all masks, fixed and moving! All options can be specified for each resolution specifically, or at once for all resolutions.