Medical Imaging Interaction Toolkit  2021.10.99-1c4db16f
Medical Imaging Interaction Toolkit
mitk::FastMarchingBaseTool Class Reference

FastMarching semgentation tool base class. More...

#include <mitkFastMarchingBaseTool.h>

Inheritance diagram for mitk::FastMarchingBaseTool:
Collaboration diagram for mitk::FastMarchingBaseTool:

Public Member Functions

 mitkClassMacro (FastMarchingBaseTool, AutoSegmentationWithPreviewTool)
 
bool CanHandle (const BaseData *referenceData, const BaseData *workingData) const override
 
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...
 
void Activated () override
 Called when the tool gets activated. More...
 
void Deactivated () override
 Called when the tool gets deactivated. More...
 
void SetUpperThreshold (double)
 Set parameter used in Threshold filter. More...
 
void SetLowerThreshold (double)
 Set parameter used in Threshold filter. More...
 
void SetStoppingValue (double)
 Set parameter used in Fast Marching filter. More...
 
void SetSigma (double)
 Set parameter used in Gradient Magnitude filter. More...
 
void SetAlpha (double)
 Set parameter used in Fast Marching filter. More...
 
void SetBeta (double)
 Set parameter used in Fast Marching filter. More...
 
void ClearSeeds ()
 Clear all seed points. More...
 
- Public Member Functions inherited from mitk::AutoSegmentationWithPreviewTool
 mitkClassMacro (AutoSegmentationWithPreviewTool, AutoSegmentationTool)
 
void ConfirmSegmentation ()
 
virtual void SetCreateAllTimeSteps (bool _arg)
 
virtual bool GetCreateAllTimeSteps ()
 
virtual void CreateAllTimeStepsOn ()
 
virtual void CreateAllTimeStepsOff ()
 
virtual void SetKeepActiveAfterAccept (bool _arg)
 
virtual bool GetKeepActiveAfterAccept ()
 
virtual void KeepActiveAfterAcceptOn ()
 
virtual void KeepActiveAfterAcceptOff ()
 
virtual void SetIsTimePointChangeAware (bool _arg)
 
virtual bool GetIsTimePointChangeAware ()
 
virtual void IsTimePointChangeAwareOn ()
 
virtual void IsTimePointChangeAwareOff ()
 
virtual void SetResetsToEmptyPreview (bool _arg)
 
virtual bool GetResetsToEmptyPreview ()
 
virtual void ResetsToEmptyPreviewOn ()
 
virtual void ResetsToEmptyPreviewOff ()
 
void UpdatePreview (bool ignoreLazyPreviewSetting=false)
 
bool IsUpdating () const
 
- Public Member Functions inherited from mitk::AutoSegmentationTool
 mitkClassMacro (AutoSegmentationTool, Tool)
 
void SetOverwriteExistingSegmentation (bool overwrite)
 
std::string GetCurrentSegmentationName ()
 Gets the name of the currently selected segmentation node. More...
 
virtual DataNodeGetTargetSegmentationNode () const
 Depending on the selected mode either returns the currently selected segmentation node or (if overwrite mode is false) creates a new one from the selected reference data. 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 * GetName () const =0
 Returns the name of this tool. Make it short! 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
 
- 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
 

Protected Member Functions

 FastMarchingBaseTool (unsigned int toolDim)
 
 ~FastMarchingBaseTool () override
 
void ConnectActionsAndFunctions () override
 
virtual void OnAddPoint (StateMachineAction *, InteractionEvent *interactionEvent)
 Add point action of StateMachine pattern. More...
 
virtual void OnDelete (StateMachineAction *, InteractionEvent *interactionEvent)
 Delete action of StateMachine pattern. More...
 
void DoUpdatePreview (const Image *inputAtTimeStep, const Image *oldSegAtTimeStep, Image *previewImage, TimeStepType timeStep) override
 
template<typename TPixel , unsigned int VImageDimension>
void DoITKFastMarching (const itk::Image< TPixel, VImageDimension > *inputImage, Image *segmentation, unsigned int timeStep, const BaseGeometry *inputGeometry)
 
- Protected Member Functions inherited from mitk::AutoSegmentationWithPreviewTool
virtual void InitiateToolByInput ()
 
virtual void UpdatePrepare ()
 
virtual void UpdateCleanUp ()
 
 AutoSegmentationWithPreviewTool (bool lazyDynamicPreviews=false)
 
 AutoSegmentationWithPreviewTool (bool lazyDynamicPreviews, const char *interactorType, const us::Module *interactorModule=nullptr)
 
 ~AutoSegmentationWithPreviewTool () override
 
ImageGetPreviewSegmentation ()
 
DataNodeGetPreviewSegmentationNode ()
 
const ImageGetSegmentationInput () const
 
const ImageGetReferenceData () const
 
void ResetPreviewNode ()
 
TimePointType GetLastTimePointOfUpdate () const
 
virtual void SetWorkingPlaneGeometry (PlaneGeometry *_arg)
 
virtual const PlaneGeometryGetWorkingPlaneGeometry ()
 
- Protected Member Functions inherited from mitk::AutoSegmentationTool
 AutoSegmentationTool ()
 
 AutoSegmentationTool (const char *interactorType, const us::Module *interactorModule=nullptr)
 
 ~AutoSegmentationTool () override
 
const char * GetGroup () const override
 Name of a group. More...
 
void EnsureTargetSegmentationNodeInDataStorage () const
 
- Protected Member Functions inherited from mitk::Tool
virtual void SetToolManager (ToolManager *)
 
ToolManagerGetToolManager () const
 
mitk::DataStorageGetDataStorage () 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)
 
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

float m_LowerThreshold
 
float m_UpperThreshold
 
float m_StoppingValue
 
float m_Sigma
 
float m_Alpha
 
float m_Beta
 
DataNode::Pointer m_SeedsAsPointSetNode
 
PointSet::Pointer m_SeedsAsPointSet
 
- Protected Attributes inherited from mitk::AutoSegmentationWithPreviewTool
mitk::ToolCommand::Pointer m_ProgressCommand
 
- Protected Attributes inherited from mitk::AutoSegmentationTool
bool m_OverwriteExistingSegmentation
 
- 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
 
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
 
- Static Public Member Functions inherited from mitk::EventStateMachine
static const char * GetStaticNameOfClass ()
 
- Static Public Member Functions inherited from mitk::InteractionEventHandler
static const char * GetStaticNameOfClass ()
 
- 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::AutoSegmentationTool
static Image::ConstPointer GetImageByTimeStep (const Image *image, unsigned int timestep)
 
static Image::ConstPointer GetImageByTimePoint (const Image *image, TimePointType timePoint)
 

Detailed Description

FastMarching semgentation tool base class.

The segmentation is done by setting one or more seed points on the image and adapting the time range and threshold. The pipeline is: Smoothing->GradientMagnitude->SigmoidFunction->FastMarching->Threshold The resulting binary image is seen as a segmentation of an object.

For detailed documentation see ITK Software Guide section 9.3.1 Fast Marching Segmentation.

Definition at line 43 of file mitkFastMarchingBaseTool.h.

Constructor & Destructor Documentation

◆ FastMarchingBaseTool()

mitk::FastMarchingBaseTool::FastMarchingBaseTool ( unsigned int  toolDim)
protected

◆ ~FastMarchingBaseTool()

mitk::FastMarchingBaseTool::~FastMarchingBaseTool ( )
overrideprotected

Member Function Documentation

◆ Activated()

void mitk::FastMarchingBaseTool::Activated ( )
overridevirtual

Called when the tool gets activated.

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

Reimplemented from mitk::AutoSegmentationWithPreviewTool.

◆ CanHandle()

bool mitk::FastMarchingBaseTool::CanHandle ( const BaseData referenceData,
const BaseData workingData 
) const
overridevirtual

Function used to check if a tool can handle the referenceData and (if specified) the working data.

Precondition
referenceData must be a valid pointer
Parameters
referenceDataPointer to the data that should be checked as valid reference for the tool.
workingDataPointer to the data that should be checked as valid working data for this tool. This parameter can be null if no working data is specified so far.

Reimplemented from mitk::AutoSegmentationWithPreviewTool.

◆ ClearSeeds()

void mitk::FastMarchingBaseTool::ClearSeeds ( )

Clear all seed points.

◆ ConnectActionsAndFunctions()

void mitk::FastMarchingBaseTool::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::FastMarchingBaseTool::Deactivated ( )
overridevirtual

Called when the tool gets deactivated.

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

Reimplemented from mitk::AutoSegmentationWithPreviewTool.

◆ DoITKFastMarching()

template<typename TPixel , unsigned int VImageDimension>
void mitk::FastMarchingBaseTool::DoITKFastMarching ( const itk::Image< TPixel, VImageDimension > *  inputImage,
Image segmentation,
unsigned int  timeStep,
const BaseGeometry inputGeometry 
)
protected

◆ DoUpdatePreview()

void mitk::FastMarchingBaseTool::DoUpdatePreview ( const Image inputAtTimeStep,
const Image oldSegAtTimeStep,
Image previewImage,
TimeStepType  timeStep 
)
overrideprotectedvirtual

This function does the real work. Here the preview for a given input image should be computed and stored in the also passed preview image at the passed time step. It also provides the current/old segmentation at the time point, which can be used, if the preview depends on the the segmenation so far.

Implements mitk::AutoSegmentationWithPreviewTool.

◆ GetCursorIconResource()

us::ModuleResource mitk::FastMarchingBaseTool::GetCursorIconResource ( ) const
overridevirtual

Returns the path of a cursor icon.

Reimplemented from mitk::Tool.

◆ GetIconResource()

us::ModuleResource mitk::FastMarchingBaseTool::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.

◆ GetXPM()

const char** mitk::FastMarchingBaseTool::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::FastMarchingBaseTool::mitkClassMacro ( FastMarchingBaseTool  ,
AutoSegmentationWithPreviewTool   
)

◆ OnAddPoint()

virtual void mitk::FastMarchingBaseTool::OnAddPoint ( StateMachineAction ,
InteractionEvent interactionEvent 
)
protectedvirtual

Add point action of StateMachine pattern.

◆ OnDelete()

virtual void mitk::FastMarchingBaseTool::OnDelete ( StateMachineAction ,
InteractionEvent interactionEvent 
)
protectedvirtual

Delete action of StateMachine pattern.

◆ SetAlpha()

void mitk::FastMarchingBaseTool::SetAlpha ( double  )

Set parameter used in Fast Marching filter.

◆ SetBeta()

void mitk::FastMarchingBaseTool::SetBeta ( double  )

Set parameter used in Fast Marching filter.

◆ SetLowerThreshold()

void mitk::FastMarchingBaseTool::SetLowerThreshold ( double  )

Set parameter used in Threshold filter.

◆ SetSigma()

void mitk::FastMarchingBaseTool::SetSigma ( double  )

Set parameter used in Gradient Magnitude filter.

◆ SetStoppingValue()

void mitk::FastMarchingBaseTool::SetStoppingValue ( double  )

Set parameter used in Fast Marching filter.

◆ SetUpperThreshold()

void mitk::FastMarchingBaseTool::SetUpperThreshold ( double  )

Set parameter used in Threshold filter.

Member Data Documentation

◆ m_Alpha

float mitk::FastMarchingBaseTool::m_Alpha
protected

Definition at line 102 of file mitkFastMarchingBaseTool.h.

◆ m_Beta

float mitk::FastMarchingBaseTool::m_Beta
protected

Definition at line 103 of file mitkFastMarchingBaseTool.h.

◆ m_LowerThreshold

float mitk::FastMarchingBaseTool::m_LowerThreshold
protected

Definition at line 98 of file mitkFastMarchingBaseTool.h.

◆ m_SeedsAsPointSet

PointSet::Pointer mitk::FastMarchingBaseTool::m_SeedsAsPointSet
protected

Definition at line 106 of file mitkFastMarchingBaseTool.h.

◆ m_SeedsAsPointSetNode

DataNode::Pointer mitk::FastMarchingBaseTool::m_SeedsAsPointSetNode
protected

Definition at line 105 of file mitkFastMarchingBaseTool.h.

◆ m_Sigma

float mitk::FastMarchingBaseTool::m_Sigma
protected

Definition at line 101 of file mitkFastMarchingBaseTool.h.

◆ m_StoppingValue

float mitk::FastMarchingBaseTool::m_StoppingValue
protected

Definition at line 100 of file mitkFastMarchingBaseTool.h.

◆ m_UpperThreshold

float mitk::FastMarchingBaseTool::m_UpperThreshold
protected

Definition at line 99 of file mitkFastMarchingBaseTool.h.


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