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

#include <mitkNavigationDataLandmarkTransformFilter.h>

Inheritance diagram for mitk::NavigationDataLandmarkTransformFilter:

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Collaboration diagram for mitk::NavigationDataLandmarkTransformFilter:

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

typedef itk::VersorRigid3DTransform< double >	LandmarkTransformType

Public Member Functions
	mitkClassMacro (NavigationDataLandmarkTransformFilter, NavigationDataToNavigationDataFilter)

Pointer	Clone () const

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

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

virtual bool	IsInitialized () const

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

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

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

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

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

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

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

virtual void	SetUseICPInitialization (bool _arg)

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

virtual void	UseICPInitializationOn ()
	If set to true, source and target point correspondences are established with iterative closest point optimization. More...

virtual void	UseICPInitializationOff ()

virtual const LandmarkTransformType *	GetLandmarkTransform ()
	If set to true, source and target point correspondences are established with iterative closest point optimization. More...

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

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

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

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

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

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

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 More...

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

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

virtual std::string	GetName ()

virtual void	SetName (std::string _arg)
	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. More...

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

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

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

NavigationTool::Pointer	GetToolMetaData (DataObjectPointerArraySizeType idx)

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

virtual mitk::NavigationToolStorage::Pointer	GetToolMetaDataCollection ()

virtual void	SetToolMetaDataCollection (mitk::NavigationToolStorage::Pointer _arg)

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

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

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

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(). More...

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

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

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. More...

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

virtual void	Freeze ()

virtual void	UnFreeze ()

virtual bool	GetIsFrozen ()

Static Public Member Functions
static Pointer	New ()

Protected Types
typedef itk::Image< signed short, 3 >	ImageType
	returns the current landmark transform More...

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

typedef TransformInitializerType::LandmarkPointContainer	LandmarkPointContainer

typedef itk::QuaternionRigidTransform< double >	QuaternionTransformType

Protected Member Functions
	NavigationDataLandmarkTransformFilter ()
	Constructor. More...

	~NavigationDataLandmarkTransformFilter () override

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

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 More...

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

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

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

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

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

	~NavigationDataToNavigationDataFilter () override

void	CreateOutputsForAllInputs ()
	Create an output for each input. More...

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

	~NavigationDataSource () override

Protected Attributes
mitk::ScalarType	m_ErrorMean
	Fiducial Registration Error. More...

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

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

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

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

mitk::ScalarType	m_ErrorAbsMax
	the absolute maximum registration error More...

LandmarkPointContainer	m_SourcePoints
	positions of the source points More...

LandmarkPointContainer	m_TargetPoints
	positions of the target points More...

TransformInitializerType::Pointer	m_LandmarkTransformInitializer
	landmark based transform initializer More...

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

QuaternionTransformType::Pointer	m_QuatLandmarkTransform
	transform needed to rotate orientation More...

QuaternionTransformType::Pointer	m_QuatTransform
	further transform needed to rotate orientation More...

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

bool	m_UseICPInitialization
	find source <–> target point correspondences with iterative closest point optimization More...

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
	These Constants are used in conjunction with Microservices. More...

static const std::string	US_PROPKEY_DEVICENAME

static const std::string	US_PROPKEY_ID

static const std::string	US_PROPKEY_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

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

Definition at line 47 of file mitkNavigationDataLandmarkTransformFilter.h.

◆ ImageType

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

protected

returns the current landmark transform

Definition at line 112 of file mitkNavigationDataLandmarkTransformFilter.h.

◆ LandmarkPointContainer

typedef TransformInitializerType::LandmarkPointContainer mitk::NavigationDataLandmarkTransformFilter::LandmarkPointContainer

protected

Definition at line 118 of file mitkNavigationDataLandmarkTransformFilter.h.

◆ LandmarkTransformType

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

Definition at line 50 of file mitkNavigationDataLandmarkTransformFilter.h.

◆ QuaternionTransformType

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

protected

Definition at line 119 of file mitkNavigationDataLandmarkTransformFilter.h.

◆ TransformInitializerType

typedef 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.

References m_LandmarkTransform, m_LandmarkTransformInitializer, m_QuatLandmarkTransform, and m_QuatTransform.

◆ ~NavigationDataLandmarkTransformFilter()

mitk::NavigationDataLandmarkTransformFilter::~NavigationDataLandmarkTransformFilter ( )

overrideprotected

Definition at line 40 of file mitkNavigationDataLandmarkTransformFilter.cpp.

References m_LandmarkTransform, m_LandmarkTransformInitializer, m_QuatLandmarkTransform, and m_QuatTransform.

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.

References m_ErrorAbsMax, m_ErrorMax, m_ErrorMean, m_ErrorMin, m_ErrorRMS, m_ErrorStdDev, max(), and min().

Referenced by UpdateLandmarkTransform().

◆ Clone()

Pointer mitk::NavigationDataLandmarkTransformFilter::Clone ( ) const

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

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

it

Definition at line 291 of file mitkNavigationDataLandmarkTransformFilter.cpp.

References mitk::itk2vtk(), max(), and MITK_INFO.

Referenced by InitializeLandmarkTransform().

◆ 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.

References m_ErrorAbsMax.

Referenced by PrintSelf().

◆ 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.

References m_Errors.

◆ GetFRE()

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

Returns the Fiducial Registration Error.

Definition at line 112 of file mitkNavigationDataLandmarkTransformFilter.cpp.

References m_ErrorMean.

Referenced by PrintSelf().

◆ GetFREStdDev()

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

Returns the standard deviation of the Fiducial Registration Error.

Definition at line 118 of file mitkNavigationDataLandmarkTransformFilter.cpp.

References m_ErrorStdDev.

Referenced by PrintSelf().

◆ GetLandmarkTransform()

virtual const LandmarkTransformType* mitk::NavigationDataLandmarkTransformFilter::GetLandmarkTransform ( )

virtual

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

◆ GetMaxError()

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

Returns the maximum registration error / worst fitting landmark distance.

Definition at line 136 of file mitkNavigationDataLandmarkTransformFilter.cpp.

References m_ErrorMax.

Referenced by PrintSelf().

◆ GetMinError()

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

Returns the minimum registration error / best fitting landmark distance.

Definition at line 130 of file mitkNavigationDataLandmarkTransformFilter.cpp.

References m_ErrorMin.

Referenced by PrintSelf().

◆ GetRMSError()

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

Returns the Root Mean Square of the registration error.

Definition at line 124 of file mitkNavigationDataLandmarkTransformFilter.cpp.

References m_ErrorRMS.

Referenced by PrintSelf().

◆ GetUseICPInitialization()

virtual bool mitk::NavigationDataLandmarkTransformFilter::GetUseICPInitialization ( )

virtual

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

◆ 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.

References FindCorrespondentLandmarks(), m_SourcePoints, m_TargetPoints, m_UseICPInitialization, and UpdateLandmarkTransform().

Referenced by SetSourceLandmarks(), and SetTargetLandmarks().

◆ IsInitialized()

bool mitk::NavigationDataLandmarkTransformFilter::IsInitialized ( ) const

virtual

Definition at line 235 of file mitkNavigationDataLandmarkTransformFilter.cpp.

References m_SourcePoints, and m_TargetPoints.

Referenced by GenerateData(), PrintSelf(), SetSourceLandmarks(), and SetTargetLandmarks().

◆ mitkClassMacro()

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

◆ New()

static Pointer mitk::NavigationDataLandmarkTransformFilter::New ( )

static

◆ 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.

References GetAbsMaxError(), GetFRE(), GetFREStdDev(), GetMaxError(), GetMinError(), GetRMSError(), IsInitialized(), m_LandmarkTransform, m_SourcePoints, and m_TargetPoints.

◆ 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.

References mitk::FillVector3D(), InitializeLandmarkTransform(), IsInitialized(), m_SourcePoints, and m_TargetPoints.

Referenced by mitk::NavigationDataReferenceTransformFilter::InitializeTransform().

◆ 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.

References mitk::FillVector3D(), InitializeLandmarkTransform(), IsInitialized(), m_SourcePoints, and m_TargetPoints.

Referenced by mitk::NavigationDataReferenceTransformFilter::InitializeTransform().

◆ SetUseICPInitialization()

virtual void mitk::NavigationDataLandmarkTransformFilter::SetUseICPInitialization ( bool _arg )

virtual

◆ UpdateLandmarkTransform()

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