mitk::SegTool2D Class Reference

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...
void	Activated () override
	Called when the tool gets activated. More...
void	Deactivated () override
	Called when the tool gets deactivated. More...
virtual void	SetIsTimePointChangeAware (bool _arg)
virtual bool	GetIsTimePointChangeAware ()
virtual void	IsTimePointChangeAwareOn ()
virtual void	IsTimePointChangeAwareOff ()
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 (const Image *original, const std::string &organName, const mitk::Color &color) const
DataNode::Pointer	CreateSegmentationNode (Image *image, const std::string &organName, const mitk::Color &color) const
virtual bool	CanHandle (const BaseData *referenceData, const BaseData *workingData) const
virtual bool	ConfirmBeforeDeactivation ()
	Method call to invoke a dialog box just before exiting. The method can be reimplemented in the respective tool class with business logic on when there should be a confirmation dialog from the user before the tool exits. More...
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 coordinates) is meant by the plane. More...
static void	UpdateAllSurfaceInterpolations (const LabelSetImage *workingImage, TimeStepType timeStep, const PlaneGeometry *plane, bool detectIntersection)
	Updates the surface interpolations by extracting the contour form the given slice for all labels that have a surface contour information stored for the given plane at the given timestep. More...
static 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 an vector image. More...
static Image::Pointer	GetAffectedImageSliceAs2DImage (const PlaneGeometry *planeGeometry, const Image *image, TimeStepType timeStep, unsigned int component=0)
	Extract the slice of an image cut by given plane. The given component denotes the vector component of a vector image. More...
static Image::Pointer	GetAffectedImageSliceAs2DImageByTimePoint (const PlaneGeometry *planeGeometry, const Image *image, TimePointType timePoint, unsigned int component=0)
static void	WriteBackSegmentationResult (const DataNode *workingNode, const PlaneGeometry *planeGeometry, const Image *segmentationResult, TimeStepType timeStep)
static void	WriteSliceToVolume (Image *workingImage, const PlaneGeometry *planeGeometry, const Image *slice, TimeStepType timeStep, bool allowUndo)
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 *, const us::Module *interactorModule=nullptr)
	~SegTool2D () override
DataNode *	GetWorkingDataNode () const
	returns the segmentation node that should be modified by the tool. More...
Image *	GetWorkingData () const
DataNode *	GetReferenceDataNode () const
Image *	GetReferenceData () const
virtual void	OnTimePointChanged ()
bool	FilterEvents (InteractionEvent *interactionEvent, DataNode *dataNode) override
	Filters events that cannot be handled by 2D segmentation tools. More...
Image::Pointer	GetAffectedWorkingSlice (const InteractionPositionEvent *) const
	Extract the slice of the currently selected working image that the user just scribbles on. More...
Image::Pointer	GetAffectedReferenceSlice (const InteractionPositionEvent *) const
	Extract the slice of the currently selected reference image that the user just scribbles on. More...
Image::Pointer	GetAffectedReferenceSlice (const PlaneGeometry *planeGeometry, TimeStepType timeStep) const
void	WriteBackSegmentationResult (const InteractionPositionEvent *, const Image *segmentationResult)
void	WriteBackSegmentationResult (const PlaneGeometry *planeGeometry, const Image *segmentationResult, TimeStepType timeStep)
void	WriteBackSegmentationResults (const std::vector< SliceInformation > &sliceList, bool writeSliceToVolume=true)
int	AddContourmarker (const PlaneGeometry *planeGeometry, unsigned int sliceIndex)
	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 passed PlanarFigure's Geometry. More...
void	InteractiveSegmentationBugMessage (const std::string &message) const
virtual TimePointType	GetLastTimePointTriggered ()
Protected Member Functions inherited from mitk::Tool
virtual void	SetToolManager (ToolManager *)
ToolManager *	GetToolManager () const
mitk::DataStorage *	GetDataStorage () const
void	ConnectActionsAndFunctions () override
	Tool (const char *, const us::Module *interactorModule=nullptr)
	~Tool () override
void	Notify (InteractionEvent *interactionEvent, bool isHandled) override
bool	FilterEvents (InteractionEvent *, DataNode *) override
Protected Member Functions inherited from mitk::EventStateMachine
	EventStateMachine ()
	~EventStateMachine () override
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 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 ()
	~InteractionEventHandler () override
PropertyList::Pointer	GetAttributes () const
std::string	MapToEventVariant (InteractionEvent *interactionEvent)
virtual void	ConfigurationChanged ()

Static Protected Member Functions
static void	UpdateSurfaceInterpolation (const std::vector< SliceInformation > &sliceInfos, const Image *workingImage, bool detectIntersection, mitk::Label::PixelType activeLabelValue, bool silent=false)
	Updates the surface interpolation by extracting the contour form the given slice. More...
static void	WriteBackSegmentationResults (const DataNode *workingNode, const std::vector< SliceInformation > &sliceList, bool writeSliceToVolume=true)
	Writes all provided source slices into the data of the passed workingNode. The function does the following: 1) for every passed slice write it to workingNode (and generate and undo/redo step); 2) update the surface interpolation and 3) mark the node as modified. More...
static void	WriteSliceToVolume (Image *workingImage, const SliceInformation &sliceInfo, bool allowUndo)
static bool	IsPositionEventInsideImageRegion (InteractionPositionEvent *positionEvent, const BaseData *data)

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...
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 54 of file mitkSegTool2D.h.

Constructor & Destructor Documentation

SegTool2D() [1/2]

mitk::SegTool2D::SegTool2D ( )

protected

SegTool2D() [2/2]

mitk::SegTool2D::SegTool2D ( const char *  , const us::Module *  interactorModule = nullptr  )

protected

~SegTool2D()

mitk::SegTool2D::~SegTool2D ( )

overrideprotected

Member Function Documentation

Activated()

void mitk::SegTool2D::Activated ( )

overridevirtual

Called when the tool gets activated.

Derived tools should call their parents implementation at the beginning of the overriding function.

Reimplemented from mitk::Tool.

AddContourmarker()

int mitk::SegTool2D::AddContourmarker ( const PlaneGeometry *  planeGeometry, unsigned int  sliceIndex  )

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 passed PlanarFigure's Geometry.

Deactivated()

void mitk::SegTool2D::Deactivated ( )

overridevirtual

Called when the tool gets deactivated.

Derived tools should call their parents implementation at the end of the overriding function.

Reimplemented from mitk::Tool.

DetermineAffectedImageSlice()

static 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 coordinates) is meant by the plane.

Returns

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

Parameters

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

FilterEvents()

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

overrideprotectedvirtual

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

Currently 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.

GetAffectedImageSliceAs2DImage() [1/2]

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

static

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

Parameters

positionEvent	Event that specifies the plane that should be used to slice
image	Image that should be sliced
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.

GetAffectedImageSliceAs2DImage() [2/2]

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

static

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

Parameters

planeGeometry	Geometry defining the slice that should be cut out.
image	Image that should be sliced
timeStep	TimeStep of the image that should be sliced
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.

GetAffectedImageSliceAs2DImageByTimePoint()

static Image::Pointer mitk::SegTool2D::GetAffectedImageSliceAs2DImageByTimePoint ( const PlaneGeometry *  planeGeometry, const Image *  image, TimePointType  timePoint, unsigned int  component = 0  )

static

GetAffectedReferenceSlice() [1/2]

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

protected

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

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, or just no reference image is selected.

GetAffectedReferenceSlice() [2/2]

Image::Pointer mitk::SegTool2D::GetAffectedReferenceSlice ( const PlaneGeometry *  planeGeometry, TimeStepType  timeStep  ) const

protected

Overload version that gets the reference slice passed on the passed plane geometry and timestep.

GetAffectedWorkingSlice()

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

protected

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

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, or just no working image is selected.

GetIsTimePointChangeAware()

virtual bool mitk::SegTool2D::GetIsTimePointChangeAware ( )

virtual

GetLastTimePointTriggered()

virtual TimePointType mitk::SegTool2D::GetLastTimePointTriggered ( )

protectedvirtual

GetReferenceData()

Image* mitk::SegTool2D::GetReferenceData ( ) const

protected

GetReferenceDataNode()

DataNode* mitk::SegTool2D::GetReferenceDataNode ( ) const

protected

GetWorkingData()

Image* mitk::SegTool2D::GetWorkingData ( ) const

protected

GetWorkingDataNode()

DataNode* mitk::SegTool2D::GetWorkingDataNode ( ) const

protected

returns the segmentation node that should be modified by the tool.

InteractiveSegmentationBugMessage()

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

protected

IsPositionEventInsideImageRegion()

static bool mitk::SegTool2D::IsPositionEventInsideImageRegion ( InteractionPositionEvent *  positionEvent, const BaseData *  data  )

staticprotected

Helper function to check if a position events points to a point inside the boundingbox of a passed data instance.

IsTimePointChangeAwareOff()

virtual void mitk::SegTool2D::IsTimePointChangeAwareOff ( )

virtual

IsTimePointChangeAwareOn()

virtual void mitk::SegTool2D::IsTimePointChangeAwareOn ( )

virtual

mitkClassMacro()

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

OnTimePointChanged()

virtual void mitk::SegTool2D::OnTimePointChanged ( )

protectedvirtual

This function can be reimplemented by derived classes to react on changes of the current time point. Default implementation does nothing.

Reimplemented in mitk::LiveWireTool2D.

SetEnable3DInterpolation()

void mitk::SegTool2D::SetEnable3DInterpolation

(

bool

)

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

SetIsTimePointChangeAware()

virtual void mitk::SegTool2D::SetIsTimePointChangeAware ( bool  _arg )

virtual

SetShowMarkerNodes()

void mitk::SegTool2D::SetShowMarkerNodes

(

bool

)

UpdateAllSurfaceInterpolations()

static void mitk::SegTool2D::UpdateAllSurfaceInterpolations ( const LabelSetImage *  workingImage, TimeStepType  timeStep, const PlaneGeometry *  plane, bool  detectIntersection  )

static

Updates the surface interpolations by extracting the contour form the given slice for all labels that have a surface contour information stored for the given plane at the given timestep.

Parameters

workingImage	the segmentation image
timeStep	the time step for wich the surface interpolation information should be updated.
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

UpdateSurfaceInterpolation()

static void mitk::SegTool2D::UpdateSurfaceInterpolation ( const std::vector< SliceInformation > &  sliceInfos, const Image *  workingImage, bool  detectIntersection, mitk::Label::PixelType  activeLabelValue, bool  silent = false  )

staticprotected

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

Parameters

sliceInfos	vector of slice information instances from which the contours should be extracted
workingImage	the segmentation image
detectIntersection	if true the slice is eroded before contour extraction. If the slice is empty after the
activeLabelValue	The label value of the active label.
silent	Indicates if the modification event of the SurfaceInterpolationController should be triggered. erosion it is most likely an intersecting contour an will not be added to the SurfaceInterpolationController

WriteBackSegmentationResult() [1/3]

static void mitk::SegTool2D::WriteBackSegmentationResult ( const DataNode *  workingNode, const PlaneGeometry *  planeGeometry, const Image *  segmentationResult, TimeStepType  timeStep  )

static

Convenience overloaded version that can be called for a given planeGeometry, slice image and time step. Calls static WriteBackSegmentationResults

WriteBackSegmentationResult() [2/3]

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

protected

Convenience version that can be called for a given event (which is used to deduce timepoint and plane) and a slice image. Calls non static WriteBackSegmentationResults

WriteBackSegmentationResult() [3/3]

void mitk::SegTool2D::WriteBackSegmentationResult ( const PlaneGeometry *  planeGeometry, const Image *  segmentationResult, TimeStepType  timeStep  )

protected

Convenience version that can be called for a given planeGeometry, slice image and time step. Calls non static WriteBackSegmentationResults

WriteBackSegmentationResults() [1/2]

static void mitk::SegTool2D::WriteBackSegmentationResults ( const DataNode *  workingNode, const std::vector< SliceInformation > &  sliceList, bool  writeSliceToVolume = true  )

staticprotected

Writes all provided source slices into the data of the passed workingNode. The function does the following: 1) for every passed slice write it to workingNode (and generate and undo/redo step); 2) update the surface interpolation and 3) mark the node as modified.

Parameters

workingNode	Pointer to the node that contains the working image.
sliceList	Vector of all slices that should be written into the workingNode. If the list is empty, the function call does nothing.
writeSliceToVolume	If set to false the write operation (WriteSliceToVolume will be skipped) and only the surface interpolation will be updated.

Precondition

workingNode must point to a valid instance and contain an image instance as data.

WriteBackSegmentationResults() [2/2]

void mitk::SegTool2D::WriteBackSegmentationResults ( const std::vector< SliceInformation > &  sliceList, bool  writeSliceToVolume = true  )

protected

Overloaded version that calls the static version and also adds the contour markers.

Remarks

If the sliceList is empty, this function does nothing.

WriteSliceToVolume() [1/2]

static void mitk::SegTool2D::WriteSliceToVolume ( Image *  workingImage, const PlaneGeometry *  planeGeometry, const Image *  slice, TimeStepType  timeStep, bool  allowUndo  )

static

Convenience overloaded version that can be called for a given planeGeometry, slice image and time step. For more details see protected WriteSliceToVolume version.

WriteSliceToVolume() [2/2]

static void mitk::SegTool2D::WriteSliceToVolume ( Image *  workingImage, const SliceInformation &  sliceInfo, bool  allowUndo  )

staticprotected

Writes a provided slice into the passed working image. The content of working image that is covered by the slice will be completely overwritten. If asked for it also generates the needed undo/redo steps.

Parameters

workingImage	Pointer to the image that is the target of the write operation.
sliceInfo	SliceInfo instance that contains the slice image, the defining plane geometry and time step.
allowUndo	Indicates if undo/redo operations should be registered for the write operation performed by this call. true: undo/redo will be generated; false: no undo/redo will be generated, so this operation cannot be revoked by the user.

Precondition

workingImage must point to a valid instance.

Member Data Documentation

m_LastEventSender

BaseRenderer* mitk::SegTool2D::m_LastEventSender

protected

Definition at line 262 of file mitkSegTool2D.h.

m_LastEventSlice

unsigned int mitk::SegTool2D::m_LastEventSlice

protected

Definition at line 263 of file mitkSegTool2D.h.

---

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

• mitkSegTool2D.h