Medical Imaging Interaction Toolkit  2018.4.99-0d336d68
Medical Imaging Interaction Toolkit

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
 
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...
 
- 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)
 
DataNode::Pointer CreateSegmentationNode (Image *image, const std::string &organName, const mitk::Color &color)
 
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 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. 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 (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 IsInsideSegmentation (const itk::Image< TPixel, imageDimension > *itkImage, const 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 (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
 
ContourModelGetFeedbackContour ()
 
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 *, const us::Module *interactorModule=nullptr)
 
 ~SegTool2D () override
 
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 (const std::vector< SliceInformation > &sliceList, bool writeSliceToVolume=true)
 
void WritePreviewOnWorkingImage (Image *targetSlice, Image *sourceSlice, Image *workingImage, int paintingPixelValue, int timestep)
 
void WriteSliceToVolume (const 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 *, 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)
 
StateMachineStateGetCurrentState () 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...
 
StateMachineTransitionGetExecutableTransition (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::FeedbackContourTool
ContourModel::Pointer m_FeedbackContour
 
DataNode::Pointer m_FeedbackContourNode
 
bool m_FeedbackContourVisible
 
- Protected Attributes inherited from mitk::SegTool2D
BaseRendererm_LastEventSender
 
unsigned int m_LastEventSlice
 
- Protected Attributes inherited from mitk::Tool
std::string m_EventConfig
 Let subclasses change their event configuration. More...
 
ToolManagerm_ToolManager
 
- Protected Attributes inherited from mitk::EventStateMachine
bool m_IsActive
 
UndoControllerm_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< SelfPointer
 
typedef itk::SmartPointer< const SelfConstPointer
 
typedef std::map< std::string, TActionFunctor * > ActionFunctionsMapType
 
typedef itk::SmartPointer< StateMachineStateStateMachineStateType
 
- Public Types inherited from mitk::InteractionEventHandler
typedef InteractionEventHandler Self
 
typedef itk::Object Superclass
 
typedef itk::SmartPointer< SelfPointer
 
typedef itk::SmartPointer< const SelfConstPointer
 
- 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 52 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.

◆ IsInsideSegmentation()

template<typename TPixel , unsigned int imageDimension>
void mitk::RegionGrowingTool::IsInsideSegmentation ( const itk::Image< TPixel, imageDimension > *  itkImage,
const itk::Index< imageDimension > &  index,
bool *  result 
)
protected

Template to check whether index is inside already segmented area.

◆ 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. Calls either OnMousePressedInside() or OnMousePressedOutside().

◆ OnMousePressedInside()

virtual void mitk::RegionGrowingTool::OnMousePressedInside ( )
protectedvirtual

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

◆ OnMousePressedOutside()

virtual void mitk::RegionGrowingTool::OnMousePressedOutside ( StateMachineAction ,
InteractionEvent interactionEvent 
)
protectedvirtual

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

◆ 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 146 of file mitkRegionGrowingTool.h.

◆ m_LastScreenPosition

Point2I mitk::RegionGrowingTool::m_LastScreenPosition
protected

Definition at line 147 of file mitkRegionGrowingTool.h.

◆ m_ReferenceSlice

Image::Pointer mitk::RegionGrowingTool::m_ReferenceSlice
protected

Definition at line 139 of file mitkRegionGrowingTool.h.

◆ m_ScreenXDifference

int mitk::RegionGrowingTool::m_ScreenXDifference
protected

Definition at line 149 of file mitkRegionGrowingTool.h.

◆ m_ScreenYDifference

int mitk::RegionGrowingTool::m_ScreenYDifference
protected

Definition at line 148 of file mitkRegionGrowingTool.h.

◆ m_SeedPoint

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

Definition at line 143 of file mitkRegionGrowingTool.h.

◆ m_SeedValue

ScalarType mitk::RegionGrowingTool::m_SeedValue
protected

Definition at line 142 of file mitkRegionGrowingTool.h.

◆ m_ThresholdExtrema

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

Definition at line 144 of file mitkRegionGrowingTool.h.

◆ m_Thresholds

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

Definition at line 145 of file mitkRegionGrowingTool.h.

◆ m_WorkingSlice

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 file: