#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.

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 >:

[legend]

Public Types
using	ElastixType

using	FixedImageType = typename ElastixType::FixedImageType

using	ITKBaseType = itk::MultiResolutionImageRegistrationMethod2<FixedImageType, MovingImageType>

using	MovingImageType = typename ElastixType::MovingImageType

using	RegistrationType

using	Self = RegistrationBase

using	Superclass = BaseComponentSE<TElastix>

using	UseMaskErosionArrayType = std::vector<bool>

Public Types inherited from elastix::BaseComponentSE< TElastix >
using	ElastixType = TElastix

using	RegistrationType = typename ElastixType::RegistrationBaseType

using	Self = BaseComponentSE

using	Superclass = BaseComponent

Public Member Functions
ITKBaseType *	GetAsITKBaseType ()

const ITKBaseType *	GetAsITKBaseType () const

virtual const char *	GetClassName () const

	ITK_DISALLOW_COPY_AND_MOVE (RegistrationBase)

	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 >
void	AddTargetCellToIterationInfo (const char *const name)

const Configuration *	GetConfiguration () const

ElastixType *	GetElastix () const

auto &	GetIterationInfoAt (const char *const name)

RegistrationType *	GetRegistration () const

	ITK_DISALLOW_COPY_AND_MOVE (BaseComponentSE)

void	RemoveTargetCellFromIterationInfo (const char *const name)

void	SetConfiguration (const Configuration *_arg)

void	SetElastix (ElastixType *_arg)

Public Member Functions inherited from elastix::BaseComponent
virtual void	AfterEachIteration ()

virtual void	AfterEachIterationBase ()

virtual void	AfterEachResolution ()

virtual void	AfterEachResolutionBase ()

virtual void	AfterRegistration ()

virtual void	AfterRegistrationBase ()

virtual int	BeforeAll ()

virtual int	BeforeAllBase ()

virtual void	BeforeEachResolution ()

virtual void	BeforeEachResolutionBase ()

virtual void	BeforeRegistration ()

virtual void	BeforeRegistrationBase ()

virtual const char *	elxGetClassName () const

const char *	GetComponentLabel () const

	ITK_DISALLOW_COPY_AND_MOVE (BaseComponent)

	itkTypeMacroNoParent (BaseComponent)

void	SetComponentLabel (const char *label, unsigned int idx)

Protected Types
using	FixedImagePyramidType = typename ITKBaseType::FixedImagePyramidType

using	FixedMaskErodeFilterPointer = typename FixedMaskErodeFilterType::Pointer

using	FixedMaskErodeFilterType = itk::ErodeMaskImageFilter<FixedMaskImageType>

using	FixedMaskImagePointer = typename FixedMaskImageType::Pointer

using	FixedMaskImageType = typename ElastixType::FixedMaskType

using	FixedMaskSpatialObjectPointer = typename FixedMaskSpatialObjectType::Pointer

using	FixedMaskSpatialObjectType = itk::ImageMaskSpatialObject<Self::FixedImageDimension>

using	MaskPixelType = typename ElastixType::MaskPixelType

using	MovingImagePyramidType = typename ITKBaseType::MovingImagePyramidType

using	MovingMaskErodeFilterPointer = typename MovingMaskErodeFilterType::Pointer

using	MovingMaskErodeFilterType = itk::ErodeMaskImageFilter<MovingMaskImageType>

using	MovingMaskImagePointer = typename MovingMaskImageType::Pointer

using	MovingMaskImageType = typename ElastixType::MovingMaskType

using	MovingMaskSpatialObjectPointer = typename MovingMaskSpatialObjectType::Pointer

using	MovingMaskSpatialObjectType = itk::ImageMaskSpatialObject<Self::MovingImageDimension>

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 ()=default

	~RegistrationBase () override=default

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
	elxDeclarePureVirtualGetSelfMacro (ITKBaseType)

Additional Inherited Members
Static Public Member Functions inherited from elastix::BaseComponent
template<typename TBaseComponent >
static auto	AsITKBaseType (TBaseComponent *const baseComponent) -> decltype(baseComponent->GetAsITKBaseType())

static void	InitializeElastixExecutable ()

static bool	IsElastixLibrary ()

Protected Attributes inherited from elastix::BaseComponentSE< TElastix >
Configuration::ConstPointer	m_Configuration {}

itk::WeakPointer< TElastix >	m_Elastix {}

RegistrationType *	m_Registration {}

Member Typedef Documentation

◆ ElastixType

template<class TElastix >

using elastix::BaseComponentSE< TElastix >::ElastixType

Elastix typedef.

Definition at line 57 of file elxBaseComponentSE.h.

◆ FixedImagePyramidType

template<class TElastix >

using elastix::RegistrationBase< TElastix >::FixedImagePyramidType = typename ITKBaseType::FixedImagePyramidType

protected

Definition at line 165 of file elxRegistrationBase.h.

◆ FixedImageType

template<class TElastix >

using elastix::RegistrationBase< TElastix >::FixedImageType = typename ElastixType::FixedImageType

Other typedef's.

Definition at line 92 of file elxRegistrationBase.h.

◆ FixedMaskErodeFilterPointer

template<class TElastix >

using elastix::RegistrationBase< TElastix >::FixedMaskErodeFilterPointer = typename FixedMaskErodeFilterType::Pointer

protected

Definition at line 170 of file elxRegistrationBase.h.

◆ FixedMaskErodeFilterType

template<class TElastix >

using elastix::RegistrationBase< TElastix >::FixedMaskErodeFilterType = itk::ErodeMaskImageFilter<FixedMaskImageType>

protected

Some typedef's used for eroding the masks

Definition at line 169 of file elxRegistrationBase.h.

◆ FixedMaskImagePointer

template<class TElastix >

using elastix::RegistrationBase< TElastix >::FixedMaskImagePointer = typename FixedMaskImageType::Pointer

protected

Definition at line 158 of file elxRegistrationBase.h.

◆ FixedMaskImageType

template<class TElastix >

using elastix::RegistrationBase< TElastix >::FixedMaskImageType = typename ElastixType::FixedMaskType

protected

Definition at line 156 of file elxRegistrationBase.h.

◆ FixedMaskSpatialObjectPointer

template<class TElastix >

using elastix::RegistrationBase< TElastix >::FixedMaskSpatialObjectPointer = typename FixedMaskSpatialObjectType::Pointer

protected

Definition at line 162 of file elxRegistrationBase.h.

◆ FixedMaskSpatialObjectType

template<class TElastix >

using elastix::RegistrationBase< TElastix >::FixedMaskSpatialObjectType = itk::ImageMaskSpatialObject<Self::FixedImageDimension>

protected

Definition at line 160 of file elxRegistrationBase.h.

◆ ITKBaseType

template<class TElastix >

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

Typedef for ITKBaseType.

Definition at line 101 of file elxRegistrationBase.h.

◆ MaskPixelType

template<class TElastix >

using elastix::RegistrationBase< TElastix >::MaskPixelType = typename ElastixType::MaskPixelType

protected

Typedef's for mask support.

Definition at line 155 of file elxRegistrationBase.h.

◆ MovingImagePyramidType

template<class TElastix >

using elastix::RegistrationBase< TElastix >::MovingImagePyramidType = typename ITKBaseType::MovingImagePyramidType

protected

Definition at line 166 of file elxRegistrationBase.h.

◆ MovingImageType

template<class TElastix >

using elastix::RegistrationBase< TElastix >::MovingImageType = typename ElastixType::MovingImageType

Definition at line 93 of file elxRegistrationBase.h.

◆ MovingMaskErodeFilterPointer

template<class TElastix >

using elastix::RegistrationBase< TElastix >::MovingMaskErodeFilterPointer = typename MovingMaskErodeFilterType::Pointer

protected

Definition at line 172 of file elxRegistrationBase.h.

◆ MovingMaskErodeFilterType

template<class TElastix >

using elastix::RegistrationBase< TElastix >::MovingMaskErodeFilterType = itk::ErodeMaskImageFilter<MovingMaskImageType>

protected

Definition at line 171 of file elxRegistrationBase.h.

◆ MovingMaskImagePointer

template<class TElastix >

using elastix::RegistrationBase< TElastix >::MovingMaskImagePointer = typename MovingMaskImageType::Pointer

protected

Definition at line 159 of file elxRegistrationBase.h.

◆ MovingMaskImageType

template<class TElastix >

using elastix::RegistrationBase< TElastix >::MovingMaskImageType = typename ElastixType::MovingMaskType

protected

Definition at line 157 of file elxRegistrationBase.h.

◆ MovingMaskSpatialObjectPointer

template<class TElastix >

using elastix::RegistrationBase< TElastix >::MovingMaskSpatialObjectPointer = typename MovingMaskSpatialObjectType::Pointer

protected

Definition at line 163 of file elxRegistrationBase.h.

◆ MovingMaskSpatialObjectType

template<class TElastix >

using elastix::RegistrationBase< TElastix >::MovingMaskSpatialObjectType = itk::ImageMaskSpatialObject<Self::MovingImageDimension>

protected

Definition at line 161 of file elxRegistrationBase.h.

◆ RegistrationType

template<class TElastix >

using elastix::BaseComponentSE< TElastix >::RegistrationType

RegistrationType; NB: this is the elx::RegistrationBase not an itk::Object or something like that.

Definition at line 62 of file elxBaseComponentSE.h.

◆ Self

template<class TElastix >

using elastix::RegistrationBase< TElastix >::Self = RegistrationBase

Standard ITK stuff.

Definition at line 81 of file elxRegistrationBase.h.

◆ Superclass

template<class TElastix >

using elastix::RegistrationBase< TElastix >::Superclass = BaseComponentSE<TElastix>

Definition at line 82 of file elxRegistrationBase.h.

◆ UseMaskErosionArrayType

template<class TElastix >

using elastix::RegistrationBase< TElastix >::UseMaskErosionArrayType = std::vector<bool>

Typedef for mask erosion options

Definition at line 104 of file elxRegistrationBase.h.

Constructor & Destructor Documentation

◆ RegistrationBase()

template<class TElastix >

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

protecteddefault

The constructor.

◆ ~RegistrationBase()

template<class TElastix >

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

overrideprotecteddefault

The destructor.

Member Function Documentation

◆ elxDeclarePureVirtualGetSelfMacro()

template<class TElastix >

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

private

◆ 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 >

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

inline

Retrieves this object as ITKBaseType.

Definition at line 108 of file elxRegistrationBase.h.

◆ GetAsITKBaseType() [2/2]

template<class TElastix >

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

inline

Retrieves this object as ITKBaseType, to use in const functions.

Definition at line 116 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 >.

◆ ITK_DISALLOW_COPY_AND_MOVE()

template<class TElastix >

elastix::RegistrationBase< TElastix >::ITK_DISALLOW_COPY_AND_MOVE ( RegistrationBase< 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.

◆ 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.

Detailed Description

Public Types

Public Member Functions

Protected Types

Protected Member Functions

Private Member Functions

Additional Inherited Members

Member Typedef Documentation

◆ ElastixType

◆ FixedImagePyramidType

◆ FixedImageType

◆ FixedMaskErodeFilterPointer

◆ FixedMaskErodeFilterType

◆ FixedMaskImagePointer

◆ FixedMaskImageType

◆ FixedMaskSpatialObjectPointer

◆ FixedMaskSpatialObjectType

◆ ITKBaseType

◆ MaskPixelType

◆ MovingImagePyramidType

◆ MovingImageType

◆ MovingMaskErodeFilterPointer

◆ MovingMaskErodeFilterType

◆ MovingMaskImagePointer

◆ MovingMaskImageType

◆ MovingMaskSpatialObjectPointer

◆ MovingMaskSpatialObjectType

◆ RegistrationType

◆ Self

◆ Superclass

◆ UseMaskErosionArrayType

Constructor & Destructor Documentation

◆ RegistrationBase()

◆ ~RegistrationBase()

Member Function Documentation

◆ elxDeclarePureVirtualGetSelfMacro()

◆ GenerateFixedMaskSpatialObject()

◆ GenerateMovingMaskSpatialObject()

◆ GetAsITKBaseType() [1/2]

◆ GetAsITKBaseType() [2/2]

◆ GetClassName()

◆ ITK_DISALLOW_COPY_AND_MOVE()

◆ itkStaticConstMacro() [1/2]

◆ itkStaticConstMacro() [2/2]

◆ ReadMaskParameters()