A slice based region growing tool. More...

#include <mitkRegionGrowingTool.h>

Inheritance diagram for mitk::RegionGrowingTool:

Collaboration diagram for mitk::RegionGrowingTool:

Public Member Functions
	mitkClassMacro (RegionGrowingTool, FeedbackContourTool)

Pointer	Clone () const

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

virtual 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...

virtual 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...

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 (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 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 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 ()

virtual	~RegionGrowingTool ()

void	ConnectActionsAndFunctions () override

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

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

virtual void	OnMousePressed (StateMachineAction , InteractionEvent interactionEvent)
	OnMousePressed is called when the user clicks. Calls either OnMousePressedInside() or OnMousePressedOutside(). More...

virtual void	OnMousePressedInside ()
	OnMousePressedInside can be used to implement behaviour when the user clicks inside a segmentation. More...

virtual void	OnMousePressedOutside (StateMachineAction , InteractionEvent interactionEvent)
	OnMousePressedOutside is called when the user clicks outside of the segmented area. Grows a region. 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 (itk::Image< TPixel, imageDimension > itkImage, 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	IsInsideSegmentation (itk::Image< TPixel, imageDimension > itkImage, itk::Index< imageDimension > index, bool result)
	Template to check whether index is inside already segmented area. More...

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

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

	FeedbackContourTool (const char *)

virtual	~FeedbackContourTool ()

ContourModel *	GetFeedbackContour ()

void	SetFeedbackContour (ContourModel::Pointer)

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 (Image slice, ContourModel contourIn3D, bool correctionForIpSegmentation=false, bool constrainToInside=true)
	Projects a contour onto an image point by point. Converts from world to index coordinates. More...

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

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 *)

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

	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
Image::Pointer	m_ReferenceSlice

Image::Pointer	m_WorkingSlice

ScalarType	m_SeedValue

itk::Index< 3 >	m_SeedPoint

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::FeedbackContourTool
ContourModel::Pointer	m_FeedbackContour

DataNode::Pointer	m_FeedbackContourNode

bool	m_FeedbackContourVisible

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...

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

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.

If the first click is inside a segmentation, nothing will happen (other behaviour, for example removal of a region, can be implemented via OnMousePressedInside()).

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

$Author$

Definition at line 59 of file mitkRegionGrowingTool.h.

Constructor & Destructor Documentation

mitk::RegionGrowingTool::RegionGrowingTool ( )

protected

Definition at line 52 of file mitkRegionGrowingTool.cpp.

mitk::RegionGrowingTool::~RegionGrowingTool ( )

protectedvirtual

Definition at line 64 of file mitkRegionGrowingTool.cpp.

Member Function Documentation

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.

Definition at line 99 of file mitkRegionGrowingTool.cpp.

Pointer mitk::RegionGrowingTool::Clone ( ) const

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.

Definition at line 68 of file mitkRegionGrowingTool.cpp.

References CONNECT_FUNCTION.

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.

Definition at line 104 of file mitkRegionGrowingTool.cpp.

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

overridevirtual

Returns the path of a cursor icon.

Reimplemented from mitk::Tool.

Definition at line 87 of file mitkRegionGrowingTool.cpp.

References ModuleContext::GetModule(), us::GetModuleContext(), and us::Module::GetResource().

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.

Definition at line 80 of file mitkRegionGrowingTool.cpp.

References ModuleContext::GetModule(), us::GetModuleContext(), and us::Module::GetResource().

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.

Definition at line 94 of file mitkRegionGrowingTool.cpp.

template<typename TPixel , unsigned int imageDimension>

void mitk::RegionGrowingTool::GetNeighborhoodAverage	(	itk::Image< TPixel, imageDimension > *	itkImage,
		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.

Definition at line 111 of file mitkRegionGrowingTool.cpp.

References MITK_DEBUG.

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.

Definition at line 75 of file mitkRegionGrowingTool.cpp.

template<typename TPixel , unsigned int imageDimension>

void mitk::RegionGrowingTool::IsInsideSegmentation	(	itk::Image< TPixel, imageDimension > *	itkImage,
		itk::Index< imageDimension >	index,
		bool *	result
	)

protected

Template to check whether index is inside already segmented area.

Definition at line 173 of file mitkRegionGrowingTool.cpp.

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

static Pointer mitk::RegionGrowingTool::New ( )

static

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.

Definition at line 487 of file mitkRegionGrowingTool.cpp.

References AccessFixedDimensionByItk_3, mitk::FeedbackContourTool::BackProjectContourFrom2DSlice(), mitk::RenderingManager::ForceImmediateUpdate(), mitk::RenderingManager::GetInstance(), mitk::InteractionPositionEvent::GetPointerPositionOnScreen(), mitk::BaseRenderer::GetRenderWindow(), mitk::InteractionEvent::GetSender(), mitk::BaseRenderer::GetTimeStep(), MITK_DEBUG, mitk::ImageToContourModelFilter::New(), mitk::ContourModel::New(), mitk::Image::New(), mitk::FeedbackContourTool::ProjectContourTo2DSlice(), mitk::FeedbackContourTool::SetFeedbackContour(), and mitk::FeedbackContourTool::SetFeedbackContourVisible().

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

protectedvirtual

OnMousePressed is called when the user clicks. Calls either OnMousePressedInside() or OnMousePressedOutside().

Definition at line 276 of file mitkRegionGrowingTool.cpp.

References AccessFixedDimensionByItk_2, mitk::SegTool2D::GetAffectedReferenceSlice(), mitk::SegTool2D::GetAffectedWorkingSlice(), mitk::InteractionPositionEvent::GetPointerPositionOnScreen(), mitk::InteractionPositionEvent::GetPositionInWorld(), mitk::InteractionEvent::GetSender(), mitk::BaseRenderer::GetSlice(), and MITK_DEBUG.

void mitk::RegionGrowingTool::OnMousePressedInside ( )

protectedvirtual

OnMousePressedInside can be used to implement behaviour when the user clicks inside a segmentation.

Definition at line 333 of file mitkRegionGrowingTool.cpp.

void mitk::RegionGrowingTool::OnMousePressedOutside	(	StateMachineAction *	,
		InteractionEvent *	interactionEvent
	)

protectedvirtual

OnMousePressedOutside is called when the user clicks outside of the segmented area. Grows a region.

Definition at line 399 of file mitkRegionGrowingTool.cpp.

References AccessFixedDimensionByItk_3, mitk::FeedbackContourTool::BackProjectContourFrom2DSlice(), mitk::RenderingManager::GetInstance(), mitk::InteractionPositionEvent::GetPositionInWorld(), mitk::InteractionEvent::GetSender(), mitk::BaseRenderer::GetTimeStep(), mitk::LevelWindow::GetWindow(), MITK_DEBUG, mitk::ImageToContourModelFilter::New(), mitk::ContourModel::New(), mitk::Image::New(), mitk::FeedbackContourTool::ProjectContourTo2DSlice(), mitk::RenderingManager::RequestUpdate(), mitk::FeedbackContourTool::SetFeedbackContour(), and mitk::FeedbackContourTool::SetFeedbackContourVisible().

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

protectedvirtual

OnMouseReleased converts the feedback contour to a segmentation.

Definition at line 566 of file mitkRegionGrowingTool.cpp.

References mitk::ContourModelUtils::FillContourInSlice(), mitk::FeedbackContourTool::GetFeedbackContour(), mitk::ContourModel::GetNumberOfVertices(), mitk::InteractionEvent::GetSender(), mitk::BaseRenderer::GetTimeStep(), mitk::ContourModel::GetVertexAt(), MITK_DEBUG, mitk::ContourModel::New(), mitk::FeedbackContourTool::ProjectContourTo2DSlice(), and mitk::FeedbackContourTool::SetFeedbackContourVisible().

template<typename TPixel , unsigned int imageDimension>

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

protected

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

Definition at line 189 of file mitkRegionGrowingTool.cpp.

References mitk::GrabItkImageMemory(), MITK_DEBUG, and mitk::New().

Member Data Documentation

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

protected

Definition at line 145 of file mitkRegionGrowingTool.h.

Point2I mitk::RegionGrowingTool::m_LastScreenPosition

protected

Definition at line 146 of file mitkRegionGrowingTool.h.

Image::Pointer mitk::RegionGrowingTool::m_ReferenceSlice

protected

Definition at line 139 of file mitkRegionGrowingTool.h.

int mitk::RegionGrowingTool::m_ScreenXDifference

protected

Definition at line 148 of file mitkRegionGrowingTool.h.

int mitk::RegionGrowingTool::m_ScreenYDifference

protected

Definition at line 147 of file mitkRegionGrowingTool.h.

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

protected

Definition at line 143 of file mitkRegionGrowingTool.h.

ScalarType mitk::RegionGrowingTool::m_SeedValue

protected

Definition at line 142 of file mitkRegionGrowingTool.h.

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

protected

Definition at line 144 of file mitkRegionGrowingTool.h.

Image::Pointer mitk::RegionGrowingTool::m_WorkingSlice

protected

Definition at line 140 of file mitkRegionGrowingTool.h.

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

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