A slice based region growing tool. More...

#include <mitkRegionGrowingTool.h>

Inheritance diagram for mitk::RegionGrowingTool:

[legend]

Collaboration diagram for mitk::RegionGrowingTool:

[legend]

Public Member Functions
	mitkClassMacro (RegionGrowingTool, FeedbackContourTool)

Pointer	Clone () const

const char **	GetXPM () const override
	Returns an icon in the XPM format. More...

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

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

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

Public Member Functions inherited from mitk::FeedbackContourTool
	mitkClassMacro (FeedbackContourTool, SegTool2D)

Public Member Functions inherited from mitk::SegTool2D
	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 std::string	GetIconPath () const
	Returns the path of an icon. 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

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 Pointer	New ()

Static Public Member Functions inherited from mitk::SegTool2D
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 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
	RegionGrowingTool ()

	~RegionGrowingTool () override

void	ConnectActionsAndFunctions () override

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

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

virtual void	OnMousePressed (StateMachineAction , InteractionEvent interactionEvent)
	OnMousePressed is called when the user clicks. Grows a region by calling 'GetNeighborhoodAverage' and 'StartRegionGrowing'. More...

virtual void	OnMouseMoved (StateMachineAction , InteractionEvent interactionEvent)
	OnMouseMoved is called when the user moves the mouse with the left mouse button pressed. Adjusts the thresholds. Up: Increase upper threshold, decrease lower threshold. Down: Decrease upper threshold, increase lower threshold. Right: Increase both thresholds. Left: Decrease both thresholds. More...

virtual void	OnMouseReleased (StateMachineAction , InteractionEvent interactionEvent)
	OnMouseReleased converts the feedback contour to a segmentation. More...

template<typename TPixel , unsigned int imageDimension>
void	GetNeighborhoodAverage (const itk::Image< TPixel, imageDimension > itkImage, const itk::Index< imageDimension > &index, ScalarType result, unsigned int neighborhood=1)
	Template to calculate average pixel value around index using a square/cube with radius neighborhood. Example: 1 = 3x3 pixels, 2 = 5x5 pixels, etc. More...

template<typename TPixel , unsigned int imageDimension>
void	StartRegionGrowing (const itk::Image< TPixel, imageDimension > *itkImage, const itk::Index< imageDimension > &seedPoint, const std::array< ScalarType, 2 > &thresholds, mitk::Image::Pointer &outputImage)
	Template that calls an ITK filter to do the region growing. More...

template<typename TPixel , unsigned int imageDimension>
void	CalculateInitialThresholds (const itk::Image< TPixel, imageDimension > *itkImage)
	Template to calculate the initial thresholds for region growing. More...

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

	FeedbackContourTool (const char *)

	~FeedbackContourTool () override

const ContourModel *	GetFeedbackContour () const

void	InitializeFeedbackContour (bool isClosed)

void	ClearsCurrentFeedbackContour (bool isClosed)

void	UpdateCurrentFeedbackContour (const ContourModel *sourceModel, TimeStepType sourceTimeStep=0)

void	UpdateFeedbackContour (const ContourModel *sourceModel, TimeStepType feedbackTimeStep, TimeStepType sourceTimeStep=0)

void	AddVertexToCurrentFeedbackContour (const Point3D &point)

void	AddVertexToFeedbackContour (const Point3D &point, TimeStepType feedbackTimeStep)

void	SetFeedbackContourVisible (bool)

void	SetFeedbackContourColor (float r, float g, float b)
	Provide values from 0.0 (black) to 1.0 (full color) More...

void	SetFeedbackContourColorDefault ()

ContourModel::Pointer	ProjectContourTo2DSlice (const Image slice, const ContourModel contourIn3D)
	Projects a contour onto an image point by point. Converts from world to index coordinates. More...

ContourModel::Pointer	BackProjectContourFrom2DSlice (const BaseGeometry sliceGeometry, const ContourModel contourIn2D)
	Projects a slice index coordinates of a contour back into world coordinates. More...

void	WriteBackFeedbackContourAsSegmentationResult (const InteractionPositionEvent *positionEvent, int paintingPixelValue, bool setInvisibleAfterSuccess=true)

void	FillContourInSlice (ContourModel projectedContour, Image sliceImage, int paintingPixelValue=1)
	Fill a contour in a 2D slice with a specified pixel value. More...

void	FillContourInSlice (ContourModel projectedContour, unsigned int timeStep, Image sliceImage, int paintingPixelValue=1)
	Fill a contour in a 2D slice with a specified pixel value at a given time step. More...

Protected Member Functions inherited from mitk::SegTool2D
	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 ()

Protected Attributes
Image::Pointer	m_ReferenceSlice

Image::Pointer	m_WorkingSlice

ScalarType	m_SeedValue

itk::Index< 3 >	m_SeedPoint

std::array< ScalarType, 2 >	m_ThresholdExtrema

std::array< ScalarType, 2 >	m_Thresholds

std::array< ScalarType, 2 >	m_InitialThresholds

Point2I	m_LastScreenPosition

int	m_ScreenYDifference

int	m_ScreenXDifference

Protected Attributes inherited from mitk::SegTool2D
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

Static Protected Member Functions inherited from mitk::SegTool2D
static void	UpdateSurfaceInterpolation (const std::vector< SliceInformation > &sliceInfos, const Image *workingImage, bool detectIntersection, unsigned int activeLayerID, mitk::Label::PixelType activeLabelValue)
	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	WritePreviewOnWorkingImage (Image targetSlice, const Image sourceSlice, const Image *workingImage, int paintingPixelValue)

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

static bool	IsPositionEventInsideImageRegion (InteractionPositionEvent positionEvent, const BaseData data)

Detailed Description

A slice based region growing tool.

See also: FeedbackContourTool

When the user presses the mouse button, RegionGrowingTool will use the gray values at that position to initialize a region growing algorithm (in the affected 2D slice).

By moving the mouse up and down while the button is still pressed, the user can widen or narrow the threshold window, i.e. select more or less within the desired region. The current result of region growing will always be shown as a contour to the user.

After releasing the button, the current result of the region growing algorithm will be written to the working image of this tool's ToolManager.

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

$Author$

Definition at line 49 of file mitkRegionGrowingTool.h.

Constructor & Destructor Documentation

◆ RegionGrowingTool()

mitk::RegionGrowingTool::RegionGrowingTool ( )

protected

◆ ~RegionGrowingTool()

mitk::RegionGrowingTool::~RegionGrowingTool ( )

overrideprotected

Member Function Documentation

◆ Activated()

void mitk::RegionGrowingTool::Activated ( )

overrideprotectedvirtual

Called when the tool gets activated.

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

Reimplemented from mitk::FeedbackContourTool.

◆ CalculateInitialThresholds()

template<typename TPixel , unsigned int imageDimension>

void mitk::RegionGrowingTool::CalculateInitialThresholds ( const itk::Image< TPixel, imageDimension > * itkImage )

protected

Template to calculate the initial thresholds for region growing.

◆ Clone()

Pointer mitk::RegionGrowingTool::Clone ( ) const

◆ ConnectActionsAndFunctions()

void mitk::RegionGrowingTool::ConnectActionsAndFunctions ( )

overrideprotectedvirtual

Is called after loading a statemachine. Overwrite this function in specific interactor implementations. Connect actions and functions using the CONNECT_FUNCTION macro within this function.

Reimplemented from mitk::EventStateMachine.

◆ Deactivated()

void mitk::RegionGrowingTool::Deactivated ( )

overrideprotectedvirtual

Called when the tool gets deactivated.

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

Reimplemented from mitk::FeedbackContourTool.

◆ GetCursorIconResource()

us::ModuleResource mitk::RegionGrowingTool::GetCursorIconResource ( ) const

overridevirtual

Returns the path of a cursor icon.

Reimplemented from mitk::Tool.

◆ GetIconResource()

us::ModuleResource mitk::RegionGrowingTool::GetIconResource ( ) const

overridevirtual

Returns the tool button icon of the tool wrapped by a usModuleResource.

Returns: a valid ModuleResource or an invalid if this function is not reimplemented

Reimplemented from mitk::Tool.

◆ GetName()

const char* mitk::RegionGrowingTool::GetName ( ) const

overridevirtual

Returns the name of this tool. Make it short!

This name has to fit into some kind of button in most applications, so take some time to think of a good name!

Implements mitk::Tool.

◆ GetNeighborhoodAverage()

template<typename TPixel , unsigned int imageDimension>

void mitk::RegionGrowingTool::GetNeighborhoodAverage	(	const itk::Image< TPixel, imageDimension > *	itkImage,
		const itk::Index< imageDimension > &	index,
		ScalarType *	result,
		unsigned int	neighborhood = `1`
	)

protected

Template to calculate average pixel value around index using a square/cube with radius neighborhood. Example: 1 = 3x3 pixels, 2 = 5x5 pixels, etc.

◆ GetXPM()

const char** mitk::RegionGrowingTool::GetXPM ( ) const

overridevirtual

Returns an icon in the XPM format.

This icon has to fit into some kind of button in most applications, so make it smaller than 25x25 pixels.

XPM is e.g. supported by The Gimp. But if you open any XPM file in your text editor, you will see that you could also "draw" it with an editor.

Implements mitk::Tool.

◆ mitkClassMacro()

mitk::RegionGrowingTool::mitkClassMacro	(	RegionGrowingTool	,
		FeedbackContourTool
	)

◆ New()

static Pointer mitk::RegionGrowingTool::New ( )

static

◆ OnMouseMoved()

virtual void mitk::RegionGrowingTool::OnMouseMoved	(	StateMachineAction *	,
		InteractionEvent *	interactionEvent
	)

protectedvirtual

OnMouseMoved is called when the user moves the mouse with the left mouse button pressed. Adjusts the thresholds. Up: Increase upper threshold, decrease lower threshold. Down: Decrease upper threshold, increase lower threshold. Right: Increase both thresholds. Left: Decrease both thresholds.

◆ OnMousePressed()

virtual void mitk::RegionGrowingTool::OnMousePressed	(	StateMachineAction *	,
		InteractionEvent *	interactionEvent
	)

protectedvirtual

OnMousePressed is called when the user clicks. Grows a region by calling 'GetNeighborhoodAverage' and 'StartRegionGrowing'.

◆ OnMouseReleased()

virtual void mitk::RegionGrowingTool::OnMouseReleased	(	StateMachineAction *	,
		InteractionEvent *	interactionEvent
	)

protectedvirtual

OnMouseReleased converts the feedback contour to a segmentation.

◆ StartRegionGrowing()

template<typename TPixel , unsigned int imageDimension>

void mitk::RegionGrowingTool::StartRegionGrowing	(	const itk::Image< TPixel, imageDimension > *	itkImage,
		const itk::Index< imageDimension > &	seedPoint,
		const std::array< ScalarType, 2 > &	thresholds,
		mitk::Image::Pointer &	outputImage
	)

protected

Template that calls an ITK filter to do the region growing.

Member Data Documentation

◆ m_InitialThresholds

std::array<ScalarType, 2> mitk::RegionGrowingTool::m_InitialThresholds

protected

Definition at line 124 of file mitkRegionGrowingTool.h.

◆ m_LastScreenPosition

Point2I mitk::RegionGrowingTool::m_LastScreenPosition

protected

Definition at line 125 of file mitkRegionGrowingTool.h.

◆ m_ReferenceSlice

Image::Pointer mitk::RegionGrowingTool::m_ReferenceSlice

protected

Definition at line 117 of file mitkRegionGrowingTool.h.

◆ m_ScreenXDifference

int mitk::RegionGrowingTool::m_ScreenXDifference

protected

Definition at line 127 of file mitkRegionGrowingTool.h.

◆ m_ScreenYDifference

int mitk::RegionGrowingTool::m_ScreenYDifference

protected

Definition at line 126 of file mitkRegionGrowingTool.h.

◆ m_SeedPoint

itk::Index<3> mitk::RegionGrowingTool::m_SeedPoint

protected

Definition at line 121 of file mitkRegionGrowingTool.h.

◆ m_SeedValue

ScalarType mitk::RegionGrowingTool::m_SeedValue

protected

Definition at line 120 of file mitkRegionGrowingTool.h.

◆ m_ThresholdExtrema

std::array<ScalarType, 2> mitk::RegionGrowingTool::m_ThresholdExtrema

protected

Definition at line 122 of file mitkRegionGrowingTool.h.

◆ m_Thresholds

std::array<ScalarType, 2> mitk::RegionGrowingTool::m_Thresholds

protected

Definition at line 123 of file mitkRegionGrowingTool.h.

◆ m_WorkingSlice

Image::Pointer mitk::RegionGrowingTool::m_WorkingSlice

protected

Definition at line 118 of file mitkRegionGrowingTool.h.

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

mitkRegionGrowingTool.h

Public Member Functions

Static Public Member Functions

Protected Member Functions

Protected Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ RegionGrowingTool()

◆ ~RegionGrowingTool()

Member Function Documentation

◆ Activated()

◆ CalculateInitialThresholds()

◆ Clone()

◆ ConnectActionsAndFunctions()

◆ Deactivated()

◆ GetCursorIconResource()

◆ GetIconResource()

◆ GetName()

◆ GetNeighborhoodAverage()

◆ GetXPM()

◆ mitkClassMacro()

◆ New()

◆ OnMouseMoved()

◆ OnMousePressed()

◆ OnMouseReleased()

◆ StartRegionGrowing()

Member Data Documentation

◆ m_InitialThresholds

◆ m_LastScreenPosition

◆ m_ReferenceSlice

◆ m_ScreenXDifference

◆ m_ScreenYDifference

◆ m_SeedPoint

◆ m_SeedValue

◆ m_ThresholdExtrema

◆ m_Thresholds

◆ m_WorkingSlice