Abstract base class for segmentation tools. More...

#include <mitkSegTool2D.h>

Inheritance diagram for mitk::SegTool2D:

Collaboration diagram for mitk::SegTool2D:

Classes
struct	SliceInformation

Public Member Functions
	mitkClassMacro (SegTool2D, Tool)

void	SetShowMarkerNodes (bool)

void	SetEnable3DInterpolation (bool)
	Enables or disables the 3D interpolation after writing back the 2D segmentation result, and defaults to true. More...

Public Member Functions inherited from mitk::Tool
	mitkClassMacro (Tool, EventStateMachine)

virtual const char **	GetXPM () const =0
	Returns an icon in the XPM format. More...

virtual std::string	GetIconPath () const
	Returns the path of an icon. More...

virtual us::ModuleResource	GetCursorIconResource () const
	Returns the path of a cursor icon. More...

virtual us::ModuleResource	GetIconResource () const
	Returns the tool button icon of the tool wrapped by a usModuleResource. More...

virtual const char *	GetName () const =0
	Returns the name of this tool. Make it short! More...

virtual const char *	GetGroup () const
	Name of a group. More...

virtual void	InitializeStateMachine ()

virtual itk::Object::Pointer	GetGUI (const std::string &toolkitPrefix, const std::string &toolkitPostfix)
	Interface for GUI creation. More...

virtual NodePredicateBase::ConstPointer	GetReferenceDataPreference () const

virtual NodePredicateBase::ConstPointer	GetWorkingDataPreference () const

DataNode::Pointer	CreateEmptySegmentationNode (Image *original, const std::string &organName, const mitk::Color &color)

DataNode::Pointer	CreateSegmentationNode (Image *image, const std::string &organName, const mitk::Color &color)

virtual bool	CanHandle (BaseData *referenceData) const

Public Member Functions inherited from mitk::EventStateMachine
virtual std::vector< std::string >	GetClassHierarchy () const override

virtual const char *	GetClassName () const

bool	LoadStateMachine (const std::string &filename, const us::Module *module=nullptr)
	Loads XML resource. More...

bool	HandleEvent (InteractionEvent event, DataNode dataNode)

void	EnableUndo (bool enable)
	Enables or disabled Undo. More...

void	EnableInteraction (bool enable)
	Enables/disables the state machine. In un-enabled state it won't react to any events. More...

Public Member Functions inherited from mitk::InteractionEventHandler
bool	SetEventConfig (const std::string &filename, const us::Module *module=nullptr)
	Loads a configuration from an XML resource. More...

bool	SetEventConfig (const EventConfig &config)
	Loads a configuration from an EventConfig object. More...

EventConfig	GetEventConfig () const
	Returns the current configuration. More...

bool	AddEventConfig (const std::string &filename, const us::Module *module=nullptr)
	This method extends the configuration. More...

bool	AddEventConfig (const EventConfig &config)
	This method extends the configuration. The configuration from the EventConfig object is loaded and only the ones conflicting are replaced by the new one. This way several configurations can be combined. More...

Public Member Functions inherited from mitk::InteractionEventObserver
	InteractionEventObserver ()

virtual	~InteractionEventObserver ()

void	Disable ()

void	Enable ()

bool	IsEnabled () const

Static Public Member Functions
static bool	DetermineAffectedImageSlice (const Image image, const PlaneGeometry plane, int &affectedDimension, int &affectedSlice)
	Calculates for a given Image and PlaneGeometry, which slice of the image (in index corrdinates) is meant by the plane. More...

static void	UpdateSurfaceInterpolation (const Image slice, const Image workingImage, const PlaneGeometry *plane, bool detectIntersection)
	Updates the surface interpolation by extracting the contour form the given slice. More...

Static Public Member Functions inherited from mitk::EventStateMachine
static const char *	GetStaticNameOfClass ()

Static Public Member Functions inherited from mitk::InteractionEventHandler
static const char *	GetStaticNameOfClass ()

Protected Member Functions
	SegTool2D ()

	SegTool2D (const char *)

virtual	~SegTool2D ()

virtual bool	FilterEvents (InteractionEvent interactionEvent, DataNode dataNode) override
	Filters events that cannot be handle by 2D segmentation tools. More...

Image::Pointer	GetAffectedImageSliceAs2DImage (const InteractionPositionEvent positionEvent, const Image image, unsigned int component=0)
	Extract the slice of an image that the user just scribbles on. The given component denotes the vector component of a dwi-image. More...

Image::Pointer	GetAffectedImageSliceAs2DImage (const PlaneGeometry planeGeometry, const Image image, unsigned int timeStep, unsigned int component=0)
	Extract the slice of an image cut by given plane. The given component denotes the vector component of a dwi-image. More...

Image::Pointer	GetAffectedWorkingSlice (const InteractionPositionEvent *)
	Extract the slice of the currently selected working image that the user just scribbles on. More...

Image::Pointer	GetAffectedReferenceSlice (const InteractionPositionEvent *)
	Extract the slice of the currently selected reference image that the user just scribbles on. More...

void	WriteBackSegmentationResult (const InteractionPositionEvent , Image )

void	WriteBackSegmentationResult (const PlaneGeometry planeGeometry, Image , unsigned int timeStep)

void	WriteBackSegmentationResult (std::vector< SliceInformation > sliceList, bool writeSliceToVolume=true)

void	WritePreviewOnWorkingImage (Image targetSlice, Image sourceSlice, Image *workingImage, int paintingPixelValue, int timestep)

void	WriteSliceToVolume (SliceInformation sliceInfo)

int	AddContourmarker ()
	Adds a new node called Contourmarker to the datastorage which holds a mitk::PlanarFigure. By selecting this node the slicestack will be reoriented according to the PlanarFigure's Geometry. More...

void	InteractiveSegmentationBugMessage (const std::string &message)

Protected Member Functions inherited from mitk::Tool
virtual void	SetToolManager (ToolManager *)

void	ConnectActionsAndFunctions () override

virtual void	Activated ()
	Called when the tool gets activated. More...

virtual void	Deactivated ()
	Called when the tool gets deactivated. More...

	Tool ()

	Tool (const char *)

virtual	~Tool ()

virtual void	Notify (InteractionEvent *interactionEvent, bool isHandled) override

bool	FilterEvents (InteractionEvent , DataNode ) override

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

virtual	~EventStateMachine ()

void	AddActionFunction (const std::string &action, TActionFunctor *functor)

void	AddActionFunction (const std::string &action, const ActionFunctionDelegate &delegate)

void	AddConditionFunction (const std::string &condition, const ConditionFunctionDelegate &delegate)

StateMachineState *	GetCurrentState () const

void	ResetToStartState ()
	ResetToStartState Reset state machine to it initial starting state. More...

virtual bool	CheckCondition (const StateMachineCondition &condition, const InteractionEvent *interactionEvent)

virtual void	ExecuteAction (StateMachineAction action, InteractionEvent interactionEvent)

void	SetMouseCursor (const char *xpm[], int hotspotX, int hotspotY)
	Sets the specified mouse cursor. More...

void	ResetMouseCursor ()
	Resets the mouse cursor (if modified by the SlicesCoordinator) to its original state. More...

StateMachineTransition *	GetExecutableTransition (InteractionEvent *event)
	Returns the executable transition for the given event. More...

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

virtual	~InteractionEventHandler ()

PropertyList::Pointer	GetAttributes () const

std::string	MapToEventVariant (InteractionEvent *interactionEvent)

virtual void	ConfigurationChanged ()

Protected Attributes
BaseRenderer *	m_LastEventSender

unsigned int	m_LastEventSlice

Protected Attributes inherited from mitk::Tool
std::string	m_EventConfig
	Let subclasses change their event configuration. More...

ToolManager *	m_ToolManager

Protected Attributes inherited from mitk::EventStateMachine
bool	m_IsActive

UndoController *	m_UndoController

bool	m_UndoEnabled

Additional Inherited Members
Public Types inherited from mitk::Tool
typedef mitk::Label::PixelType	DefaultSegmentationDataType

Public Types inherited from mitk::EventStateMachine
typedef EventStateMachine	Self

typedef InteractionEventHandler	Superclass

typedef itk::SmartPointer< Self >	Pointer

typedef itk::SmartPointer< const Self >	ConstPointer

typedef std::map< std::string, TActionFunctor * >	ActionFunctionsMapType

typedef itk::SmartPointer< StateMachineState >	StateMachineStateType

Public Types inherited from mitk::InteractionEventHandler
typedef InteractionEventHandler	Self

typedef itk::Object	Superclass

typedef itk::SmartPointer< Self >	Pointer

typedef itk::SmartPointer< const Self >	ConstPointer

Public Attributes inherited from mitk::Tool
Message	GUIProcessEventsMessage
	To let GUI process new events (e.g. qApp->processEvents() ) More...

Message1< std::string >	ErrorMessage
	To send error messages (to be shown by some GUI) More...

Message1< bool >	CurrentlyBusy
	To send whether the tool is busy (to be shown by some GUI) More...

Message1< std::string >	GeneralMessage
	To send general messages (to be shown by some GUI) More...

Protected Types inherited from mitk::EventStateMachine
typedef MessageAbstractDelegate2< StateMachineAction , InteractionEvent , void >	ActionFunctionDelegate

typedef MessageAbstractDelegate1< const InteractionEvent *, bool >	ConditionFunctionDelegate

Detailed Description

Abstract base class for segmentation tools.

See also: Tool

Implements 2D segmentation specific helper methods, that might be of use to all kind of 2D segmentation tools. At the moment these are:

Determination of the slice where the user paints upon (DetermineAffectedImageSlice)
Projection of a 3D contour onto a 2D plane/slice

SegTool2D tries to structure the interaction a bit. If you pass "PressMoveRelease" as the interaction type of your derived tool, you might implement the methods OnMousePressed, OnMouseMoved, and OnMouseReleased. Yes, your guess about when they are called is correct.

Warning: Only to be instantiated by mitk::ToolManager.

$Author$

Definition at line 58 of file mitkSegTool2D.h.

Constructor & Destructor Documentation

mitk::SegTool2D::SegTool2D ( )

protected

mitk::SegTool2D::SegTool2D ( const char * type )

protected

Definition at line 63 of file mitkSegTool2D.cpp.

References mitk::Tool::m_EventConfig.

mitk::SegTool2D::~SegTool2D ( )

protectedvirtual

Definition at line 69 of file mitkSegTool2D.cpp.

Member Function Documentation

int mitk::SegTool2D::AddContourmarker ( )

protected

Adds a new node called Contourmarker to the datastorage which holds a mitk::PlanarFigure. By selecting this node the slicestack will be reoriented according to the PlanarFigure's Geometry.

Definition at line 445 of file mitkSegTool2D.cpp.

References mitk::BaseGeometry::GetCenter(), us::GetModuleContext(), ModuleContext::GetService(), ModuleContext::GetServiceReference(), mitk::BaseGeometry::GetSpacing(), mitk::PlaneGeometry::Map(), mitk::BoolProperty::New(), mitk::PlanarCircle::New(), mitk::NodePredicateProperty::New(), mitk::StringProperty::New(), and mitk::DataNode::New().

Referenced by mitk::LiveWireTool2D::OnFinish().

bool mitk::SegTool2D::DetermineAffectedImageSlice	(	const Image *	image,
		const PlaneGeometry *	plane,
		int &	affectedDimension,
		int &	affectedSlice
	)

static

Calculates for a given Image and PlaneGeometry, which slice of the image (in index corrdinates) is meant by the plane.

Returns: false, if no slice direction seems right (e.g. rotated planes)

Parameters

affectedDimension	The image dimension, which is constant for all points in the plane, e.g. Axial –> 2
affectedSlice	The index of the image slice

Definition at line 84 of file mitkSegTool2D.cpp.

References mitk::eps, mitk::BaseGeometry::GetAxisVector(), mitk::BaseGeometry::GetCenter(), mitk::Image::GetDimension(), mitk::BaseData::GetGeometry(), mitk::PlaneGeometry::GetNormal(), mitk::SlicedData::GetSlicedGeometry(), MITK_DEBUG, mitk::PlaneGeometry::Project(), ROUND, and mitk::BaseGeometry::WorldToIndex().

Referenced by QmitkSliceBasedInterpolatorWidget::AcceptAllInterpolations(), QmitkSlicesInterpolator::AcceptAllInterpolations(), QmitkSliceBasedInterpolatorWidget::Interpolate(), QmitkSlicesInterpolator::Interpolate(), and QmitkSliceBasedInterpolatorWidget::OnAcceptInterpolationClicked().

bool mitk::SegTool2D::FilterEvents	(	InteractionEvent *	interactionEvent,
		DataNode *	dataNode
	)

overrideprotectedvirtual

Filters events that cannot be handle by 2D segmentation tools.

Current an event is discarded if it was not sent by a 2D renderwindow and if it is not of type InteractionPositionEvent

Reimplemented from mitk::EventStateMachine.

Definition at line 73 of file mitkSegTool2D.cpp.

References mitk::BaseRenderer::GetMapperID(), mitk::InteractionEvent::GetSender(), and mitk::BaseRenderer::Standard2D.

mitk::Image::Pointer mitk::SegTool2D::GetAffectedImageSliceAs2DImage	(	const InteractionPositionEvent *	positionEvent,
		const Image *	image,
		unsigned int	component = `0`
	)

protected

Extract the slice of an image that the user just scribbles on. The given component denotes the vector component of a dwi-image.

Parameters

component The component to be extracted of a given multi-component image. -1 is the default parameter to denote an invalid component.

Returns: 'nullptr' if SegTool2D is either unable to determine which slice was affected, or if there was some problem getting the image data at that position.

Definition at line 207 of file mitkSegTool2D.cpp.

References mitk::BaseRenderer::GetCurrentWorldPlaneGeometry(), mitk::InteractionEvent::GetSender(), and mitk::BaseRenderer::GetTimeStep().

Referenced by mitk::PaintbrushTool::CheckIfCurrentSliceHasChanged(), mitk::SetRegionTool::OnMouseReleased(), mitk::ContourTool::OnMouseReleased(), and mitk::CorrectorTool2D::OnMouseReleased().

mitk::Image::Pointer mitk::SegTool2D::GetAffectedImageSliceAs2DImage	(	const PlaneGeometry *	planeGeometry,
		const Image *	image,
		unsigned int	timeStep,
		unsigned int	component = `0`
	)

protected

Extract the slice of an image cut by given plane. The given component denotes the vector component of a dwi-image.

Parameters

component The component to be extracted of a given multi-component image. -1 is the default parameter to denote an invalid component.

Returns: 'nullptr' if SegTool2D is either unable to determine which slice was affected, or if there was some problem getting the image data at that position.

Definition at line 220 of file mitkSegTool2D.cpp.

References mitk::TimeGeometry::GetGeometryForTimeStep(), mitk::BaseData::GetTimeGeometry(), mitk::New(), and mitk::ExtractSliceFilter::New().

mitk::Image::Pointer mitk::SegTool2D::GetAffectedReferenceSlice ( const InteractionPositionEvent * positionEvent )

protected

Extract the slice of the currently selected reference image that the user just scribbles on.

Returns: NULL if SegTool2D is either unable to determine which slice was affected, or if there was some problem getting the image data at that position, or just no reference image is selected.

Definition at line 269 of file mitkSegTool2D.cpp.

Referenced by mitk::RegionGrowingTool::OnMousePressed().

mitk::Image::Pointer mitk::SegTool2D::GetAffectedWorkingSlice ( const InteractionPositionEvent * positionEvent )

protected

Extract the slice of the currently selected working image that the user just scribbles on.

Returns: NULL if SegTool2D is either unable to determine which slice was affected, or if there was some problem getting the image data at that position, or just no working image is selected.

Definition at line 252 of file mitkSegTool2D.cpp.

Referenced by mitk::SetRegionTool::OnMousePressed(), and mitk::RegionGrowingTool::OnMousePressed().

void mitk::SegTool2D::InteractiveSegmentationBugMessage ( const std::string & message )

protected

Definition at line 525 of file mitkSegTool2D.cpp.

References MITK_ERROR.

mitk::SegTool2D::mitkClassMacro	(	SegTool2D	,
		Tool
	)

void mitk::SegTool2D::SetEnable3DInterpolation ( bool enabled )

Enables or disables the 3D interpolation after writing back the 2D segmentation result, and defaults to true.

Definition at line 440 of file mitkSegTool2D.cpp.

Referenced by QmitkSurfaceBasedInterpolatorWidget::OnToggleWidgetActivation().

void mitk::SegTool2D::SetShowMarkerNodes ( bool status )

Definition at line 435 of file mitkSegTool2D.cpp.

void mitk::SegTool2D::UpdateSurfaceInterpolation	(	const Image *	slice,
		const Image *	workingImage,
		const PlaneGeometry *	plane,
		bool	detectIntersection
	)

static

Updates the surface interpolation by extracting the contour form the given slice.

Parameters

slice	the slice from which the contour should be extracted
workingImage	the segmentation image
plane	the plane in which the slice lies
detectIntersection	if true the slice is eroded before contour extraction. If the slice is empty after the erosion it is most likely an intersecting contour an will not be added to the SurfaceInterpolationController

Definition at line 149 of file mitkSegTool2D.cpp.

References mitk::SurfaceInterpolationController::AddNewContour(), mitk::MorphologicalOperations::Ball, mitk::Image::Clone(), mitk::SurfaceInterpolationController::ContourPositionInformation::contourNormal, mitk::SurfaceInterpolationController::ContourPositionInformation::contourPoint, mitk::MorphologicalOperations::Erode(), mitk::SurfaceInterpolationController::GetInstance(), mitk::PlaneGeometry::GetNormal(), mitk::BaseGeometry::GetOrigin(), mitk::ImageTimeSelector::New(), mitk::ImageToContourFilter::New(), and mitk::SurfaceInterpolationController::RemoveContour().

Referenced by mitk::DiffSliceOperationApplier::ExecuteOperation().

void mitk::SegTool2D::WriteBackSegmentationResult	(	const InteractionPositionEvent *	positionEvent,
		Image *	slice
	)

protected

Definition at line 295 of file mitkSegTool2D.cpp.

References mitk::BaseRenderer::GetCurrentWorldPlaneGeometry(), mitk::InteractionEvent::GetSender(), and mitk::BaseRenderer::GetTimeStep().

Referenced by mitk::ContourTool::OnMouseReleased(), and mitk::CorrectorTool2D::OnMouseReleased().

void mitk::SegTool2D::WriteBackSegmentationResult	(	const PlaneGeometry *	planeGeometry,
		Image *	slice,
		unsigned int	timeStep
	)

protected

Definition at line 313 of file mitkSegTool2D.cpp.

References mitk::RenderingManager::GetInstance(), and mitk::RenderingManager::RequestUpdateAll().

void mitk::SegTool2D::WriteBackSegmentationResult	(	std::vector< SliceInformation >	sliceList,
		bool	writeSliceToVolume = `true`
	)

protected

Definition at line 333 of file mitkSegTool2D.cpp.

References mitk::SurfaceInterpolationController::AddNewContours(), mitk::SurfaceInterpolationController::GetInstance(), mitk::RenderingManager::GetInstance(), mitk::ImageTimeSelector::New(), mitk::ImageToContourFilter::New(), mitk::RenderingManager::RequestUpdateAll(), and mitk::SegTool2D::SliceInformation::slice.

void mitk::SegTool2D::WritePreviewOnWorkingImage	(	Image *	targetSlice,
		Image *	sourceSlice,
		mitk::Image *	workingImage,
		int	paintingPixelValue,
		int	timestep
	)

protected

Definition at line 622 of file mitkSegTool2D.cpp.

References AccessFixedDimensionByItk_3, and InternalWritePreviewOnWorkingImage().

Referenced by mitk::CorrectorTool2D::OnMouseReleased().

void mitk::SegTool2D::WriteSliceToVolume ( SliceInformation sliceInfo )

protected

Definition at line 370 of file mitkSegTool2D.cpp.

References mitk::UndoController::GetCurrentUndoModel(), mitk::UndoStackItem::IncCurrGroupEventId(), mitk::UndoStackItem::IncCurrObjectEventId(), mitk::New(), mitk::ExtractSliceFilter::New(), mitk::SegTool2D::SliceInformation::plane, mitk::UndoModel::SetOperationEvent(), mitk::SegTool2D::SliceInformation::slice, and mitk::SegTool2D::SliceInformation::timestep.

Member Data Documentation

BaseRenderer* mitk::SegTool2D::m_LastEventSender

protected

Definition at line 183 of file mitkSegTool2D.h.

unsigned int mitk::SegTool2D::m_LastEventSlice

protected

Definition at line 184 of file mitkSegTool2D.h.

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

Classes

Public Member Functions

Static Public Member Functions

Protected Member Functions

Protected Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation