NavigationDataLandmarkTransformFilter applies a itk-landmark-transformation defined by source and target pointsets. More...

#include <mitkNavigationDataLandmarkTransformFilter.h>

Inheritance diagram for mitk::NavigationDataLandmarkTransformFilter:

Public Types
typedef std::vector< mitk::ScalarType >	ErrorVector

typedef itk::VersorRigid3DTransform< double >	LandmarkTransformType

Public Member Functions
	mitkClassMacro (NavigationDataLandmarkTransformFilter, NavigationDataToNavigationDataFilter)

	itkFactorylessNewMacro (Self)

	itkCloneMacro (Self)

virtual void	SetSourceLandmarks (mitk::PointSet::Pointer sourcePointSet)
	Set points used as source points for landmark transform.

virtual void	SetTargetLandmarks (mitk::PointSet::Pointer targetPointSet)
	Set points used as target points for landmark transform.

virtual bool	IsInitialized () const

mitk::ScalarType	GetFRE () const
	Returns the Fiducial Registration Error.

mitk::ScalarType	GetFREStdDev () const
	Returns the standard deviation of the Fiducial Registration Error.

mitk::ScalarType	GetRMSError () const
	Returns the Root Mean Square of the registration error.

mitk::ScalarType	GetMinError () const
	Returns the minimum registration error / best fitting landmark distance.

mitk::ScalarType	GetMaxError () const
	Returns the maximum registration error / worst fitting landmark distance.

mitk::ScalarType	GetAbsMaxError () const
	Returns the absolute maximum registration error.

const ErrorVector &	GetErrorVector () const
	Returns a vector with the euclidean distance of each transformed source point to its respective target point.

	itkSetMacro (UseICPInitialization, bool)
	If set to true, source and target point correspondences are established with iterative closest point optimization.

	itkGetMacro (UseICPInitialization, bool)
	If set to true, source and target point correspondences are established with iterative closest point optimization.

	itkBooleanMacro (UseICPInitialization)
	If set to true, source and target point correspondences are established with iterative closest point optimization.

	itkGetConstObjectMacro (LandmarkTransform, LandmarkTransformType)
	returns the current landmark transform

Public Member Functions inherited from mitk::NavigationDataToNavigationDataFilter
	mitkClassMacro (NavigationDataToNavigationDataFilter, NavigationDataSource)

virtual void	SetInput (const NavigationData *nd)
	Set the input of this filter.

virtual void	SetInput (unsigned int idx, const NavigationData *nd)
	Set input with id idx of this filter.

const NavigationData *	GetInput (void) const
	Get the input of this filter.

const NavigationData *	GetInput (unsigned int idx) const
	Get the input with id idx of this filter.

const NavigationData *	GetInput (std::string navDataName) const
	Get the input with name navDataName of this filter.

DataObjectPointerArraySizeType	GetInputIndex (std::string navDataName)
	return the index of the input with name navDataName, throw std::invalid_argument exception if that name was not found

virtual void	ConnectTo (mitk::NavigationDataSource *UpstreamFilter)
	Connects the input of this filter to the outputs of the given NavigationDataSource.

Public Member Functions inherited from mitk::NavigationDataSource
	mitkClassMacroItkParent (NavigationDataSource, itk::ProcessObject)

	itkGetMacro (Name, std::string)

	itkSetMacro (Name, std::string)
	Sets the human readable name of this source. There is also a default name, but you can use this method if you need to define it on your own.

NavigationData *	GetOutput (void)
	return the output (output with id 0) of the filter

NavigationData *	GetOutput (DataObjectPointerArraySizeType idx)
	return the output with id idx of the filter

NavigationData *	GetOutput (const std::string &navDataName)
	return the output with name navDataName of the filter

NavigationTool::Pointer	GetToolMetaData (DataObjectPointerArraySizeType idx)

NavigationTool::Pointer	GetToolMetaData (const std::string &navDataName)

	itkGetMacro (ToolMetaDataCollection, mitk::NavigationToolStorage::Pointer)

	itkSetMacro (ToolMetaDataCollection, mitk::NavigationToolStorage::Pointer)

DataObjectPointerArraySizeType	GetOutputIndex (std::string navDataName)
	return the index of the output with name navDataName, -1 if no output with that name was found

virtual void	RegisterAsMicroservice ()
	Registers this object as a Microservice, making it available to every module and/or plugin. To unregister, call UnregisterMicroservice().

virtual void	UnRegisterMicroservice ()
	Registers this object as a Microservice, making it available to every module and/or plugin.

std::string	GetMicroserviceID ()
	Returns the id that this device is registered with. The id will only be valid, if the NavigationDataSource has been registered using RegisterAsMicroservice().

virtual void	GraftNthOutput (unsigned int idx, itk::DataObject *graft)
	Graft the specified DataObject onto this ProcessObject's output.

virtual void	GraftOutput (itk::DataObject *graft)
	Graft the specified DataObject onto this ProcessObject's output.

itk::DataObject::Pointer	MakeOutput (DataObjectPointerArraySizeType idx) override

itk::DataObject::Pointer	MakeOutput (const DataObjectIdentifierType &name) override

virtual void	SetParameters (const mitk::PropertyList *)
	Set all filter parameters as the PropertyList p.

virtual mitk::PropertyList::ConstPointer	GetParameters () const
	Get all filter parameters as a PropertyList.

virtual void	Freeze ()

virtual void	UnFreeze ()

	itkGetMacro (IsFrozen, bool)

Protected Types
typedef itk::Image< signed short, 3 >	ImageType

typedef itk::LandmarkBasedTransformInitializer< LandmarkTransformType, ImageType, ImageType >	TransformInitializerType

typedef TransformInitializerType::LandmarkPointContainer	LandmarkPointContainer

typedef itk::QuaternionRigidTransform< double >	QuaternionTransformType

Protected Member Functions
	NavigationDataLandmarkTransformFilter ()
	Constructor.

	~NavigationDataLandmarkTransformFilter () override

void	GenerateData () override
	transforms input NDs according to the calculated LandmarkTransform

bool	FindCorrespondentLandmarks (LandmarkPointContainer &sources, const LandmarkPointContainer &targets) const
	perform an iterative closest point matching to find corresponding landmarks that will be used for landmark transform calculation

void	InitializeLandmarkTransform (LandmarkPointContainer &sources, const LandmarkPointContainer &targets)
	initializes the transform using source and target PointSets

void	UpdateLandmarkTransform (const LandmarkPointContainer &sources, const LandmarkPointContainer &targets)
	calculates the transform using source and target PointSets

void	AccumulateStatistics (ErrorVector &vector)
	calculate error metrics for the transforms.

void	PrintSelf (std::ostream &os, itk::Indent indent) const override
	print object info to ostream

Protected Member Functions inherited from mitk::NavigationDataToNavigationDataFilter
	NavigationDataToNavigationDataFilter ()

	~NavigationDataToNavigationDataFilter () override

void	CreateOutputsForAllInputs ()
	Create an output for each input.

Protected Member Functions inherited from mitk::NavigationDataSource
	NavigationDataSource ()

	~NavigationDataSource () override

Protected Attributes
mitk::ScalarType	m_ErrorMean
	Fiducial Registration Error.

mitk::ScalarType	m_ErrorStdDev
	standard deviation of the Fiducial Registration Error

mitk::ScalarType	m_ErrorRMS
	Root Mean Square of the registration error.

mitk::ScalarType	m_ErrorMin
	minimum registration error / best fitting landmark distance

mitk::ScalarType	m_ErrorMax
	maximum registration error / worst fitting landmark distance

mitk::ScalarType	m_ErrorAbsMax
	the absolute maximum registration error

LandmarkPointContainer	m_SourcePoints
	positions of the source points

LandmarkPointContainer	m_TargetPoints
	positions of the target points

TransformInitializerType::Pointer	m_LandmarkTransformInitializer
	landmark based transform initializer

LandmarkTransformType::Pointer	m_LandmarkTransform
	transform calculated from source and target points

QuaternionTransformType::Pointer	m_QuatLandmarkTransform
	transform needed to rotate orientation

QuaternionTransformType::Pointer	m_QuatTransform
	further transform needed to rotate orientation

ErrorVector	m_Errors
	stores the euclidean distance of each transformed source landmark and its respective target landmark

bool	m_UseICPInitialization
	find source <--> target point correspondences with iterative closest point optimization

Protected Attributes inherited from mitk::NavigationDataSource
std::string	m_Name

bool	m_IsFrozen

NavigationToolStorage::Pointer	m_ToolMetaDataCollection

Additional Inherited Members
Static Public Attributes inherited from mitk::NavigationDataSource
static const std::string	US_INTERFACE_NAME = "org.mitk.services.NavigationDataSource"
	These Constants are used in conjunction with Microservices.

static const std::string	US_PROPKEY_DEVICENAME = US_INTERFACE_NAME + ".devicename"

static const std::string	US_PROPKEY_ID = US_INTERFACE_NAME + ".id"

static const std::string	US_PROPKEY_ISACTIVE = US_INTERFACE_NAME + ".isActive"

Detailed Description

NavigationDataLandmarkTransformFilter applies a itk-landmark-transformation defined by source and target pointsets.

Documentation

Before executing the filter SetSourceLandmarks and SetTargetLandmarks must be called. Before both source and target landmarks are set, the filter performs an identity transform. If source or target points are changed after calling SetXXXPoints, the corresponding SetXXXPoints method has to be called again to apply the changes. If UseICPInitialization is false (standard value, or set with SetUseICPInitialization(false) or UseICPInitializationOff()) then source landmarks and target landmarks with the same ID must correspond to each other. (--> source landmark with ID x will be mapped to target landmark with ID x). If you do not know the correspondences, call SetUseICPInitialization(true) or UseICPInitializationOn() to let the filter guess the correspondences during initialization with an iterative closest point search. This is only possible, if at least 6 source and target landmarks are available.

Definition at line 42 of file mitkNavigationDataLandmarkTransformFilter.h.

Member Typedef Documentation

◆ ErrorVector

std::vector<mitk::ScalarType> mitk::NavigationDataLandmarkTransformFilter::ErrorVector

Definition at line 49 of file mitkNavigationDataLandmarkTransformFilter.h.

◆ ImageType

itk::Image< signed short, 3> mitk::NavigationDataLandmarkTransformFilter::ImageType

protected

Definition at line 115 of file mitkNavigationDataLandmarkTransformFilter.h.

◆ LandmarkPointContainer

TransformInitializerType::LandmarkPointContainer mitk::NavigationDataLandmarkTransformFilter::LandmarkPointContainer

protected

Definition at line 118 of file mitkNavigationDataLandmarkTransformFilter.h.

◆ LandmarkTransformType

itk::VersorRigid3DTransform< double > mitk::NavigationDataLandmarkTransformFilter::LandmarkTransformType

Definition at line 50 of file mitkNavigationDataLandmarkTransformFilter.h.

◆ QuaternionTransformType

itk::QuaternionRigidTransform<double> mitk::NavigationDataLandmarkTransformFilter::QuaternionTransformType

protected

Definition at line 119 of file mitkNavigationDataLandmarkTransformFilter.h.

◆ TransformInitializerType

itk::LandmarkBasedTransformInitializer< LandmarkTransformType, ImageType, ImageType > mitk::NavigationDataLandmarkTransformFilter::TransformInitializerType

protected

Definition at line 117 of file mitkNavigationDataLandmarkTransformFilter.h.

Constructor & Destructor Documentation

◆ NavigationDataLandmarkTransformFilter()

mitk::NavigationDataLandmarkTransformFilter::NavigationDataLandmarkTransformFilter ( )

protected

Constructor.

Definition at line 24 of file mitkNavigationDataLandmarkTransformFilter.cpp.

◆ ~NavigationDataLandmarkTransformFilter()

mitk::NavigationDataLandmarkTransformFilter::~NavigationDataLandmarkTransformFilter ( )

overrideprotected

Definition at line 40 of file mitkNavigationDataLandmarkTransformFilter.cpp.

Member Function Documentation

◆ AccumulateStatistics()

void mitk::NavigationDataLandmarkTransformFilter::AccumulateStatistics ( ErrorVector & vector )

protected

calculate error metrics for the transforms.

Definition at line 148 of file mitkNavigationDataLandmarkTransformFilter.cpp.

◆ FindCorrespondentLandmarks()

bool mitk::NavigationDataLandmarkTransformFilter::FindCorrespondentLandmarks	(	LandmarkPointContainer &	sources,
		const LandmarkPointContainer &	targets ) const

protected

perform an iterative closest point matching to find corresponding landmarks that will be used for landmark transform calculation

Documentation

Perform ICP optimization to match source landmarks to target landmarks. Landmark containers must contain at least 6 landmarks for the optimization. after ICP, landmark correspondences are established and the source landmarks are sorted, so that corresponding landmarks have the same indices.

Parameters

[in,out]	sources	Source landmarks that will be mapped to the target landmarks. The sources container will be sorted, so that landmarks have the same index as their corresponding target landmarks.
[in]	targets	Target landmarks onto which the source landmarks will be mapped

Returns: true if ICP was successful and sources are sorted , false otherwise

it

Definition at line 291 of file mitkNavigationDataLandmarkTransformFilter.cpp.

◆ GenerateData()

void mitk::NavigationDataLandmarkTransformFilter::GenerateData ( )

overrideprotected

transforms input NDs according to the calculated LandmarkTransform

Definition at line 181 of file mitkNavigationDataLandmarkTransformFilter.cpp.

◆ GetAbsMaxError()

mitk::ScalarType mitk::NavigationDataLandmarkTransformFilter::GetAbsMaxError ( ) const

Returns the absolute maximum registration error.

Definition at line 142 of file mitkNavigationDataLandmarkTransformFilter.cpp.

◆ GetErrorVector()

const mitk::NavigationDataLandmarkTransformFilter::ErrorVector & mitk::NavigationDataLandmarkTransformFilter::GetErrorVector ( ) const

Returns a vector with the euclidean distance of each transformed source point to its respective target point.

Definition at line 285 of file mitkNavigationDataLandmarkTransformFilter.cpp.

◆ GetFRE()

mitk::ScalarType mitk::NavigationDataLandmarkTransformFilter::GetFRE ( ) const

Returns the Fiducial Registration Error.

Definition at line 112 of file mitkNavigationDataLandmarkTransformFilter.cpp.

◆ GetFREStdDev()

mitk::ScalarType mitk::NavigationDataLandmarkTransformFilter::GetFREStdDev ( ) const

Returns the standard deviation of the Fiducial Registration Error.

Definition at line 118 of file mitkNavigationDataLandmarkTransformFilter.cpp.

◆ GetMaxError()

mitk::ScalarType mitk::NavigationDataLandmarkTransformFilter::GetMaxError ( ) const

Returns the maximum registration error / worst fitting landmark distance.

Definition at line 136 of file mitkNavigationDataLandmarkTransformFilter.cpp.

◆ GetMinError()

mitk::ScalarType mitk::NavigationDataLandmarkTransformFilter::GetMinError ( ) const

Returns the minimum registration error / best fitting landmark distance.

Definition at line 130 of file mitkNavigationDataLandmarkTransformFilter.cpp.

◆ GetRMSError()

mitk::ScalarType mitk::NavigationDataLandmarkTransformFilter::GetRMSError ( ) const

Returns the Root Mean Square of the registration error.

Definition at line 124 of file mitkNavigationDataLandmarkTransformFilter.cpp.

◆ InitializeLandmarkTransform()

void mitk::NavigationDataLandmarkTransformFilter::InitializeLandmarkTransform	(	LandmarkPointContainer &	sources,
		const LandmarkPointContainer &	targets )

protected

initializes the transform using source and target PointSets

if UseICPInitialization is true, FindCorrespondentLandmarks() will be used to sort the source landmarks in order to establish corresponding landmark pairs before the landmark transform is build

Definition at line 49 of file mitkNavigationDataLandmarkTransformFilter.cpp.

◆ IsInitialized()

bool mitk::NavigationDataLandmarkTransformFilter::IsInitialized ( ) const

virtual

Definition at line 235 of file mitkNavigationDataLandmarkTransformFilter.cpp.

◆ itkBooleanMacro()

mitk::NavigationDataLandmarkTransformFilter::itkBooleanMacro ( UseICPInitialization )

If set to true, source and target point correspondences are established with iterative closest point optimization.

◆ itkCloneMacro()

mitk::NavigationDataLandmarkTransformFilter::itkCloneMacro ( Self )

◆ itkFactorylessNewMacro()

mitk::NavigationDataLandmarkTransformFilter::itkFactorylessNewMacro ( Self )

◆ itkGetConstObjectMacro()

mitk::NavigationDataLandmarkTransformFilter::itkGetConstObjectMacro	(	LandmarkTransform	,
		LandmarkTransformType	)

returns the current landmark transform

◆ itkGetMacro()

mitk::NavigationDataLandmarkTransformFilter::itkGetMacro	(	UseICPInitialization	,
		bool	)

If set to true, source and target point correspondences are established with iterative closest point optimization.

◆ itkSetMacro()

mitk::NavigationDataLandmarkTransformFilter::itkSetMacro	(	UseICPInitialization	,
		bool	)

If set to true, source and target point correspondences are established with iterative closest point optimization.

◆ mitkClassMacro()

mitk::NavigationDataLandmarkTransformFilter::mitkClassMacro	(	NavigationDataLandmarkTransformFilter	,
		NavigationDataToNavigationDataFilter	)

◆ PrintSelf()

void mitk::NavigationDataLandmarkTransformFilter::PrintSelf	(	std::ostream &	os,
		itk::Indent	indent ) const

overrideprotected

print object info to ostream

Definition at line 241 of file mitkNavigationDataLandmarkTransformFilter.cpp.

◆ SetSourceLandmarks()

void mitk::NavigationDataLandmarkTransformFilter::SetSourceLandmarks ( mitk::PointSet::Pointer sourcePointSet )

virtual

Set points used as source points for landmark transform.

Definition at line 68 of file mitkNavigationDataLandmarkTransformFilter.cpp.

◆ SetTargetLandmarks()

void mitk::NavigationDataLandmarkTransformFilter::SetTargetLandmarks ( mitk::PointSet::Pointer targetPointSet )

virtual

Set points used as target points for landmark transform.

Definition at line 91 of file mitkNavigationDataLandmarkTransformFilter.cpp.

◆ UpdateLandmarkTransform()

void mitk::NavigationDataLandmarkTransformFilter::UpdateLandmarkTransform	(	const LandmarkPointContainer &	sources,
		const LandmarkPointContainer &	targets )

protected

calculates the transform using source and target PointSets

Definition at line 409 of file mitkNavigationDataLandmarkTransformFilter.cpp.

Member Data Documentation

◆ m_ErrorAbsMax

mitk::ScalarType mitk::NavigationDataLandmarkTransformFilter::m_ErrorAbsMax

protected

the absolute maximum registration error

Definition at line 169 of file mitkNavigationDataLandmarkTransformFilter.h.

◆ m_ErrorMax

mitk::ScalarType mitk::NavigationDataLandmarkTransformFilter::m_ErrorMax

protected

maximum registration error / worst fitting landmark distance

Definition at line 168 of file mitkNavigationDataLandmarkTransformFilter.h.

◆ m_ErrorMean

mitk::ScalarType mitk::NavigationDataLandmarkTransformFilter::m_ErrorMean

protected

Fiducial Registration Error.

Definition at line 164 of file mitkNavigationDataLandmarkTransformFilter.h.

◆ m_ErrorMin

mitk::ScalarType mitk::NavigationDataLandmarkTransformFilter::m_ErrorMin

protected

minimum registration error / best fitting landmark distance

Definition at line 167 of file mitkNavigationDataLandmarkTransformFilter.h.

◆ m_ErrorRMS

mitk::ScalarType mitk::NavigationDataLandmarkTransformFilter::m_ErrorRMS

protected

Root Mean Square of the registration error.

Definition at line 166 of file mitkNavigationDataLandmarkTransformFilter.h.

◆ m_Errors

ErrorVector mitk::NavigationDataLandmarkTransformFilter::m_Errors

protected

stores the euclidean distance of each transformed source landmark and its respective target landmark

Definition at line 179 of file mitkNavigationDataLandmarkTransformFilter.h.

◆ m_ErrorStdDev

mitk::ScalarType mitk::NavigationDataLandmarkTransformFilter::m_ErrorStdDev

protected

standard deviation of the Fiducial Registration Error

Definition at line 165 of file mitkNavigationDataLandmarkTransformFilter.h.

◆ m_LandmarkTransform

LandmarkTransformType::Pointer mitk::NavigationDataLandmarkTransformFilter::m_LandmarkTransform

protected

transform calculated from source and target points

Definition at line 174 of file mitkNavigationDataLandmarkTransformFilter.h.

◆ m_LandmarkTransformInitializer

TransformInitializerType::Pointer mitk::NavigationDataLandmarkTransformFilter::m_LandmarkTransformInitializer

protected

landmark based transform initializer

Definition at line 173 of file mitkNavigationDataLandmarkTransformFilter.h.

◆ m_QuatLandmarkTransform

QuaternionTransformType::Pointer mitk::NavigationDataLandmarkTransformFilter::m_QuatLandmarkTransform

protected

transform needed to rotate orientation

Definition at line 176 of file mitkNavigationDataLandmarkTransformFilter.h.

◆ m_QuatTransform

QuaternionTransformType::Pointer mitk::NavigationDataLandmarkTransformFilter::m_QuatTransform

protected

further transform needed to rotate orientation

Definition at line 177 of file mitkNavigationDataLandmarkTransformFilter.h.

◆ m_SourcePoints

LandmarkPointContainer mitk::NavigationDataLandmarkTransformFilter::m_SourcePoints

protected

positions of the source points

Definition at line 171 of file mitkNavigationDataLandmarkTransformFilter.h.

◆ m_TargetPoints

LandmarkPointContainer mitk::NavigationDataLandmarkTransformFilter::m_TargetPoints

protected

positions of the target points

Definition at line 172 of file mitkNavigationDataLandmarkTransformFilter.h.

◆ m_UseICPInitialization

bool mitk::NavigationDataLandmarkTransformFilter::m_UseICPInitialization

protected

find source <--> target point correspondences with iterative closest point optimization

Definition at line 180 of file mitkNavigationDataLandmarkTransformFilter.h.

The documentation for this class was generated from the following files:

Modules/IGT/Algorithms/mitkNavigationDataLandmarkTransformFilter.h
Modules/IGT/Algorithms/mitkNavigationDataLandmarkTransformFilter.cpp

Public Types

Public Member Functions

Protected Types

Protected Member Functions

Protected Attributes

Additional Inherited Members

Detailed Description

Member Typedef Documentation

◆ ErrorVector

◆ ImageType

◆ LandmarkPointContainer

◆ LandmarkTransformType

◆ QuaternionTransformType

◆ TransformInitializerType

Constructor & Destructor Documentation

◆ NavigationDataLandmarkTransformFilter()

◆ ~NavigationDataLandmarkTransformFilter()

Member Function Documentation

◆ AccumulateStatistics()

◆ FindCorrespondentLandmarks()

◆ GenerateData()

◆ GetAbsMaxError()

◆ GetErrorVector()

◆ GetFRE()

◆ GetFREStdDev()

◆ GetMaxError()

◆ GetMinError()

◆ GetRMSError()

◆ InitializeLandmarkTransform()

◆ IsInitialized()

◆ itkBooleanMacro()

◆ itkCloneMacro()

◆ itkFactorylessNewMacro()

◆ itkGetConstObjectMacro()

◆ itkGetMacro()

◆ itkSetMacro()

◆ mitkClassMacro()

◆ PrintSelf()

◆ SetSourceLandmarks()

◆ SetTargetLandmarks()

◆ UpdateLandmarkTransform()

Member Data Documentation

◆ m_ErrorAbsMax

◆ m_ErrorMax

◆ m_ErrorMean

◆ m_ErrorMin

◆ m_ErrorRMS

◆ m_Errors

◆ m_ErrorStdDev

◆ m_LandmarkTransform

◆ m_LandmarkTransformInitializer

◆ m_QuatLandmarkTransform

◆ m_QuatTransform

◆ m_SourcePoints

◆ m_TargetPoints

◆ m_UseICPInitialization