NavigationDataReferenceTransformFilter applies a itk-landmark-transformation defined by source and target NavigationDatas. More...

#include <mitkNavigationDataReferenceTransformFilter.h>

Inheritance diagram for mitk::NavigationDataReferenceTransformFilter:

Public Types
typedef itk::QuaternionRigidTransform< double >	QuaternionTransformType
	Quaternion transform for calculating.

Public Types inherited from mitk::NavigationDataLandmarkTransformFilter
typedef std::vector< mitk::ScalarType >	ErrorVector

typedef itk::VersorRigid3DTransform< double >	LandmarkTransformType

Public Member Functions
	mitkClassMacro (NavigationDataReferenceTransformFilter, NavigationDataToNavigationDataFilter)

	itkFactorylessNewMacro (Self)

	itkCloneMacro (Self)

void	SetSourceNavigationDatas (const std::vector< mitk::NavigationData::Pointer > &sourceNavigationDatas)
	Set NavigationDatas whose positions are used as source points for the transform.

void	SetTargetNavigationDatas (const std::vector< mitk::NavigationData::Pointer > &sourceNavigationDatas)
	Set NavigationDatas whose positions are used as target points for the transform.

void	ReinitFilter ()
	Sets the filter back to initial settings.

const mitk::PointSet::Pointer	GetSourceLandmarks ()
	Returns the source landmarks PointSet filled with points from given ND position(s) and orientation.

const mitk::PointSet::Pointer	GetTargetLandmarks ()
	Returns the target landmarks PointSet filled with points from given ND position(s) and orientation.

bool	InitializeTransform ()
	Initializes the transform. Transform will be perfomed only if source and target points have the same size.

Public Member Functions inherited from mitk::NavigationDataLandmarkTransformFilter
	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 Member Functions
	NavigationDataReferenceTransformFilter ()
	Constructor.

	~NavigationDataReferenceTransformFilter () override
	Destructor.

mitk::PointSet::Pointer	CreateLandmarkPointsForSingleNavigationData (mitk::PointSet::Pointer landmarkContainer, const std::vector< mitk::NavigationData::Pointer > &navigationDatas)

Protected Member Functions inherited from mitk::NavigationDataLandmarkTransformFilter
	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
QuaternionTransformType::Pointer	m_QuaternionTransform
	itk Quaternion transform

mitk::PointSet::Pointer	m_SourceLandmarksFromNavigationDatas
	source points from NavigationDatas

mitk::PointSet::Pointer	m_TargetLandmarksFromNavigationDatas
	target points from NavigationDatas

Protected Attributes inherited from mitk::NavigationDataLandmarkTransformFilter
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"

Protected Types inherited from mitk::NavigationDataLandmarkTransformFilter
typedef itk::Image< signed short, 3 >	ImageType

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

typedef TransformInitializerType::LandmarkPointContainer	LandmarkPointContainer

typedef itk::QuaternionRigidTransform< double >	QuaternionTransformType

Detailed Description

NavigationDataReferenceTransformFilter applies a itk-landmark-transformation defined by source and target NavigationDatas.

Documentation

Before executing the filter SetSourceNavigationDatas and SetTargetNavigationDatas must be called. The amount of given NavigationDatas must be the same for source and target. If source or target points are changed after calling SetXXXNavigationDatas, the corresponding SetXXXNavigationDatas 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 correspondent 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 mitkNavigationDataReferenceTransformFilter.h.

Member Typedef Documentation

◆ QuaternionTransformType

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

Quaternion transform for calculating.

Definition at line 49 of file mitkNavigationDataReferenceTransformFilter.h.

Constructor & Destructor Documentation

◆ NavigationDataReferenceTransformFilter()

mitk::NavigationDataReferenceTransformFilter::NavigationDataReferenceTransformFilter ( )

protected

Constructor.

Definition at line 17 of file mitkNavigationDataReferenceTransformFilter.cpp.

◆ ~NavigationDataReferenceTransformFilter()

mitk::NavigationDataReferenceTransformFilter::~NavigationDataReferenceTransformFilter ( )

overrideprotected

Destructor.

Definition at line 29 of file mitkNavigationDataReferenceTransformFilter.cpp.

Member Function Documentation

◆ CreateLandmarkPointsForSingleNavigationData()

mitk::PointSet::Pointer mitk::NavigationDataReferenceTransformFilter::CreateLandmarkPointsForSingleNavigationData	(	mitk::PointSet::Pointer	landmarkContainer,
		const std::vector< mitk::NavigationData::Pointer > &	navigationDatas )

protected

Definition at line 121 of file mitkNavigationDataReferenceTransformFilter.cpp.

◆ GetSourceLandmarks()

const mitk::PointSet::Pointer mitk::NavigationDataReferenceTransformFilter::GetSourceLandmarks ( )

Returns the source landmarks PointSet filled with points from given ND position(s) and orientation.

Definition at line 182 of file mitkNavigationDataReferenceTransformFilter.cpp.

◆ GetTargetLandmarks()

const mitk::PointSet::Pointer mitk::NavigationDataReferenceTransformFilter::GetTargetLandmarks ( )

Returns the target landmarks PointSet filled with points from given ND position(s) and orientation.

Definition at line 187 of file mitkNavigationDataReferenceTransformFilter.cpp.

◆ InitializeTransform()

bool mitk::NavigationDataReferenceTransformFilter::InitializeTransform ( )

Initializes the transform. Transform will be perfomed only if source and target points have the same size.

Returns "true" if transform has been initialized, else "false" is returned.

Definition at line 86 of file mitkNavigationDataReferenceTransformFilter.cpp.

◆ itkCloneMacro()

mitk::NavigationDataReferenceTransformFilter::itkCloneMacro ( Self )

◆ itkFactorylessNewMacro()

mitk::NavigationDataReferenceTransformFilter::itkFactorylessNewMacro ( Self )

◆ mitkClassMacro()

mitk::NavigationDataReferenceTransformFilter::mitkClassMacro	(	NavigationDataReferenceTransformFilter	,
		NavigationDataToNavigationDataFilter	)

◆ ReinitFilter()

void mitk::NavigationDataReferenceTransformFilter::ReinitFilter ( )

Sets the filter back to initial settings.

Definition at line 106 of file mitkNavigationDataReferenceTransformFilter.cpp.

◆ SetSourceNavigationDatas()

void mitk::NavigationDataReferenceTransformFilter::SetSourceNavigationDatas ( const std::vector< mitk::NavigationData::Pointer > & sourceNavigationDatas )

Set NavigationDatas whose positions are used as source points for the transform.

Definition at line 35 of file mitkNavigationDataReferenceTransformFilter.cpp.

◆ SetTargetNavigationDatas()

void mitk::NavigationDataReferenceTransformFilter::SetTargetNavigationDatas ( const std::vector< mitk::NavigationData::Pointer > & sourceNavigationDatas )

Set NavigationDatas whose positions are used as target points for the transform.

Definition at line 61 of file mitkNavigationDataReferenceTransformFilter.cpp.

Member Data Documentation

◆ m_QuaternionTransform

QuaternionTransformType::Pointer mitk::NavigationDataReferenceTransformFilter::m_QuaternionTransform

protected

itk Quaternion transform

Definition at line 97 of file mitkNavigationDataReferenceTransformFilter.h.

◆ m_SourceLandmarksFromNavigationDatas

mitk::PointSet::Pointer mitk::NavigationDataReferenceTransformFilter::m_SourceLandmarksFromNavigationDatas

protected

source points from NavigationDatas

Definition at line 101 of file mitkNavigationDataReferenceTransformFilter.h.

◆ m_TargetLandmarksFromNavigationDatas

mitk::PointSet::Pointer mitk::NavigationDataReferenceTransformFilter::m_TargetLandmarksFromNavigationDatas

protected

target points from NavigationDatas

Definition at line 102 of file mitkNavigationDataReferenceTransformFilter.h.

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

Modules/IGT/Algorithms/mitkNavigationDataReferenceTransformFilter.h
Modules/IGT/Algorithms/mitkNavigationDataReferenceTransformFilter.cpp

Public Types

Public Member Functions

Protected Member Functions

Protected Attributes

Additional Inherited Members

Detailed Description

Member Typedef Documentation

◆ QuaternionTransformType

Constructor & Destructor Documentation

◆ NavigationDataReferenceTransformFilter()

◆ ~NavigationDataReferenceTransformFilter()

Member Function Documentation

◆ CreateLandmarkPointsForSingleNavigationData()

◆ GetSourceLandmarks()

◆ GetTargetLandmarks()

◆ InitializeTransform()

◆ itkCloneMacro()

◆ itkFactorylessNewMacro()

◆ mitkClassMacro()

◆ ReinitFilter()

◆ SetSourceNavigationDatas()

◆ SetTargetNavigationDatas()

Member Data Documentation

◆ m_QuaternionTransform

◆ m_SourceLandmarksFromNavigationDatas

◆ m_TargetLandmarksFromNavigationDatas