Medical Imaging Interaction Toolkit
2024.12.99-d991a09f
Medical Imaging Interaction Toolkit
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A slice based region growing tool. More...
#include <mitkRegionGrowingTool.h>
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... | |
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mitkClassMacro (FeedbackContourTool, SegTool2D) | |
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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 () |
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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 |
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... | |
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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... | |
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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... | |
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InteractionEventObserver () | |
virtual | ~InteractionEventObserver () |
void | Disable () |
void | Enable () |
bool | IsEnabled () const |
Static Public Member Functions | |
static Pointer | New () |
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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) |
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static const char * | GetStaticNameOfClass () |
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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... | |
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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... | |
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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 () |
void | PushCursor () |
void | PushCursor (us::ModuleResource cursorResource) |
void | PopCursor (bool popFirstCursor=false) |
void | PopAllCursors () |
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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 |
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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... | |
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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 |
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BaseRenderer * | m_LastEventSender |
unsigned int | m_LastEventSlice |
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std::string | m_EventConfig |
Let subclasses change their event configuration. More... | |
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bool | m_IsActive |
UndoController * | m_UndoController |
bool | m_UndoEnabled |
Additional Inherited Members | |
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typedef mitk::Label::PixelType | DefaultSegmentationDataType |
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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 |
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typedef InteractionEventHandler | Self |
typedef itk::Object | Superclass |
typedef itk::SmartPointer< Self > | Pointer |
typedef itk::SmartPointer< const Self > | ConstPointer |
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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... | |
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typedef MessageAbstractDelegate2< StateMachineAction *, InteractionEvent *, void > | ActionFunctionDelegate |
typedef MessageAbstractDelegate1< const InteractionEvent *, bool > | ConditionFunctionDelegate |
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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) |
A slice based region growing tool.
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.
$Author$
Definition at line 49 of file mitkRegionGrowingTool.h.
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Called when the tool gets activated.
Derived tools should call their parents implementation at the beginning of the overriding function.
Reimplemented from mitk::FeedbackContourTool.
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Template to calculate the initial thresholds for region growing.
Pointer mitk::RegionGrowingTool::Clone | ( | ) | const |
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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.
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Called when the tool gets deactivated.
Derived tools should call their parents implementation at the end of the overriding function.
Reimplemented from mitk::FeedbackContourTool.
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Returns the path of a cursor icon.
Reimplemented from mitk::Tool.
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Returns the tool button icon of the tool wrapped by a usModuleResource.
Reimplemented from mitk::Tool.
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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.
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Template to calculate average pixel value around index using a square/cube with radius neighborhood. Example: 1 = 3x3 pixels, 2 = 5x5 pixels, etc.
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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.
mitk::RegionGrowingTool::mitkClassMacro | ( | RegionGrowingTool | , |
FeedbackContourTool | |||
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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.
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OnMousePressed is called when the user clicks. Grows a region by calling 'GetNeighborhoodAverage' and 'StartRegionGrowing'.
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OnMouseReleased converts the feedback contour to a segmentation.
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Template that calls an ITK filter to do the region growing.
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Definition at line 124 of file mitkRegionGrowingTool.h.
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Definition at line 125 of file mitkRegionGrowingTool.h.
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Definition at line 117 of file mitkRegionGrowingTool.h.
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Definition at line 127 of file mitkRegionGrowingTool.h.
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Definition at line 126 of file mitkRegionGrowingTool.h.
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Definition at line 121 of file mitkRegionGrowingTool.h.
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Definition at line 120 of file mitkRegionGrowingTool.h.
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Definition at line 122 of file mitkRegionGrowingTool.h.
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Definition at line 123 of file mitkRegionGrowingTool.h.
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Definition at line 118 of file mitkRegionGrowingTool.h.