Medical Imaging Interaction Toolkit  2024.06.00
Medical Imaging Interaction Toolkit
mitk::MedSAMTool Class Reference

Medical Segment Anything Model interactive 2D tool class. More...

#include <mitkMedSAMTool.h>

Inheritance diagram for mitk::MedSAMTool:
Collaboration diagram for mitk::MedSAMTool:

Public Member Functions

 mitkClassMacro (MedSAMTool, SegmentAnythingTool)
 
Pointer Clone () const
 
const char * GetName () const override
 Returns the name of this tool. Make it short! More...
 
void Activated () override
 Called when the tool gets activated. More...
 
void Deactivated () override
 Called when the tool gets deactivated. More...
 
bool HasPicks () const override
 Checks if any point exists in the either of the pointsets. More...
 
void ClearPicks () override
 Clears all picks and updates the preview. More...
 
void ConnectActionsAndFunctions () override
 
std::string GetPointsAsCSVString (const mitk::BaseGeometry *baseGeometry) const override
 Get the Points from positive and negative pointsets as csv string. More...
 
void OnRenderWindowClicked (StateMachineAction *, InteractionEvent *interactionEvent)
 Adds bounding box in the render window when clicked. More...
 
void OnDelete (StateMachineAction *, InteractionEvent *)
 Deletes bounding box from the render window. More...
 
- Public Member Functions inherited from mitk::SegmentAnythingTool
 mitkClassMacro (SegmentAnythingTool, SegWithPreviewTool)
 
Pointer Clone () const
 
const char ** GetXPM () const override
 Returns an icon in the XPM format. More...
 
const char * GetName () const override
 Returns the name of this tool. Make it short! 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...
 
virtual void SetMitkTempDir (std::string _arg)
 
virtual std::string GetMitkTempDir () const
 
virtual void SetPythonPath (std::string _arg)
 
virtual std::string GetPythonPath () const
 
virtual void SetModelType (std::string _arg)
 
virtual std::string GetModelType () const
 
virtual void SetCheckpointPath (std::string _arg)
 
virtual std::string GetCheckpointPath () const
 
virtual void SetBackend (std::string _arg)
 
virtual std::string GetBackend () const
 
virtual void SetGpuId (int _arg)
 
virtual int GetGpuId () const
 
virtual void SetTimeOutLimit (long _arg)
 
virtual long GetTimeOutLimit () const
 
virtual void SetIsReady (bool _arg)
 
virtual bool GetIsReady () const
 
virtual void IsReadyOn ()
 
virtual void IsReadyOff ()
 
void InitSAMPythonProcess ()
 Initializes python service and starts async python daemon of SegmentAnything model. More...
 
bool IsPythonReady () const
 Checks if Python daemon is ready to accept inputs. More...
 
- Public Member Functions inherited from mitk::SegWithPreviewTool
 mitkClassMacro (SegWithPreviewTool, Tool)
 
void Activated () override
 Called when the tool gets activated. More...
 
void Deactivated () override
 Called when the tool gets deactivated. More...
 
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 ()
 
virtual void SetUseSpecialPreviewColor (bool _arg)
 
virtual bool GetUseSpecialPreviewColor ()
 
virtual void UseSpecialPreviewColorOn ()
 
virtual void UseSpecialPreviewColorOff ()
 
virtual void SetRequestDeactivationConfirmation (bool _arg)
 
virtual bool GetRequestDeactivationConfirmation ()
 
virtual void RequestDeactivationConfirmationOn ()
 
virtual void RequestDeactivationConfirmationOff ()
 
void SetMergeStyle (MultiLabelSegmentation::MergeStyle mergeStyle)
 
virtual MultiLabelSegmentation::MergeStyle GetMergeStyle ()
 
void SetOverwriteStyle (MultiLabelSegmentation::OverwriteStyle overwriteStyle)
 
virtual MultiLabelSegmentation::OverwriteStyle GetOverwriteStyle ()
 
void SetLabelTransferScope (LabelTransferScope labelTransferScope)
 
virtual LabelTransferScope GetLabelTransferScope ()
 
void SetSelectedLabels (const SelectedLabelVectorType &labelsToTransfer)
 
virtual SelectedLabelVectorType GetSelectedLabels ()
 
void SetLabelTransferMode (LabelTransferMode labelTransferMode)
 
virtual LabelTransferMode GetLabelTransferMode ()
 
bool CanHandle (const BaseData *referenceData, const BaseData *workingData) const override
 
void UpdatePreview (bool ignoreLazyPreviewSetting=false)
 
bool IsUpdating () const
 
std::string GetCurrentSegmentationName ()
 Gets the name of the currently selected segmentation node. More...
 
virtual DataNodeGetTargetSegmentationNode () const
 Returns the currently selected segmentation node. More...
 
LabelSetImageGetTargetSegmentation () const
 
LabelSetImageGetPreviewSegmentation ()
 
const LabelSetImageGetPreviewSegmentation () const
 
DataNodeGetPreviewSegmentationNode ()
 
- Public Member Functions inherited from mitk::Tool
 mitkClassMacro (Tool, EventStateMachine)
 
virtual std::string GetIconPath () const
 Returns the path of an icon. More...
 
virtual us::ModuleResource GetCursorIconResource () const
 Returns the path of a cursor icon. 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
 

Static Public Member Functions

static Pointer New ()
 
- Static Public Member Functions inherited from mitk::SegmentAnythingTool
static Pointer New ()
 
- 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

 MedSAMTool ()=default
 
 ~MedSAMTool ()=default
 
- Protected Member Functions inherited from mitk::SegmentAnythingTool
 SegmentAnythingTool ()
 
 ~SegmentAnythingTool ()=default
 
void ConnectActionsAndFunctions () override
 
virtual void OnAddPositivePoint (StateMachineAction *, InteractionEvent *interactionEvent)
 
virtual void OnAddNegativePoint (StateMachineAction *, InteractionEvent *interactionEvent)
 
void ClearSeeds ()
 
void DoUpdatePreview (const Image *inputAtTimeStep, const Image *oldSegAtTimeStep, LabelSetImage *previewImage, TimeStepType timeStep) override
 Overriden method from the tool manager to execute the segmentation Implementation: More...
 
std::vector< std::pair< mitk::Point2D, std::string > > GetPointsAsVector (const mitk::BaseGeometry *baseGeometry) const
 Get the Points from positive and negative pointsets as std::vector. More...
 
std::string GetHashForCurrentPlane (const mitk::LevelWindow &levelWindow) const
 Get the Hash For Current Plane from current working plane geometry. More...
 
void EmitSAMStatusMessageEvent (const std::string &status)
 Emits message to connected Listnerers. More...
 
void ConfirmCleanUp () override
 Cleans up segmentation preview and clears all seeds. More...
 
template<typename TPixel , unsigned int VImageDimension>
void ITKWindowing (const itk::Image< TPixel, VImageDimension > *, mitk::Image *, ScalarType, ScalarType)
 Applies ITK IntensityWindowing Filter to input image;. More...
 
- Protected Member Functions inherited from mitk::SegWithPreviewTool
 SegWithPreviewTool (bool lazyDynamicPreviews=false)
 
 SegWithPreviewTool (bool lazyDynamicPreviews, const char *interactorType, const us::Module *interactorModule=nullptr)
 
 ~SegWithPreviewTool () override
 
const char * GetGroup () const override
 Name of a group. More...
 
void EnsureTargetSegmentationNodeInDataStorage () const
 
virtual void InitiateToolByInput ()
 
virtual void UpdatePrepare ()
 
virtual void UpdateCleanUp ()
 
virtual void PreparePreviewToResultTransfer (const LabelMappingType &labelMapping)
 
const ImageGetSegmentationInput () const
 
const ImageGetReferenceData () const
 
void ResetPreviewNode ()
 
void ResetPreviewContent ()
 
void ResetPreviewContentAtTimeStep (unsigned int timeStep)
 
TimePointType GetLastTimePointOfUpdate () const
 
LabelSetImage::LabelValueType GetActiveLabelValueOfPreview () const
 
virtual Label::PixelType GetUserDefinedActiveLabel () const
 
virtual void SetWorkingPlaneGeometry (PlaneGeometry *_arg)
 
virtual const PlaneGeometryGetWorkingPlaneGeometry ()
 
bool ConfirmBeforeDeactivation () override
 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...
 
- 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 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 ()
 

Additional Inherited Members

- Public Types inherited from mitk::SegWithPreviewTool
enum  LabelTransferScope { LabelTransferScope::ActiveLabel, LabelTransferScope::SelectedLabels, LabelTransferScope::AllLabels }
 
enum  LabelTransferMode { LabelTransferMode::MapLabel, LabelTransferMode::AddLabel }
 
using SelectedLabelVectorType = std::vector< Label::PixelType >
 
- 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::SegmentAnythingTool
Message1< const std::string & > SAMStatusMessageEvent
 
- 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::SegWithPreviewTool
using LabelMappingType = std::vector< std::pair< Label::PixelType, Label::PixelType > >
 
- 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::SegmentAnythingTool
static mitk::Point2D Get2DIndicesfrom3DWorld (const mitk::BaseGeometry *baseGeometry, const mitk::Point3D &point3d)
 Convert 3D world coordinates to 2D indices. More...
 
- Static Protected Member Functions inherited from mitk::SegWithPreviewTool
static Image::ConstPointer GetImageByTimeStep (const Image *image, TimeStepType timestep)
 
static Image::Pointer GetImageByTimeStep (Image *image, TimeStepType timestep)
 
static Image::ConstPointer GetImageByTimePoint (const Image *image, TimePointType timePoint)
 
static void TransferLabelInformation (const LabelMappingType &labelMapping, const mitk::LabelSetImage *source, mitk::LabelSetImage *target)
 
static void TransferLabelSetImageContent (const LabelSetImage *source, LabelSetImage *target, TimeStepType timeStep)
 
- Protected Attributes inherited from mitk::SegmentAnythingTool
std::unique_ptr< SegmentAnythingPythonServicem_PythonService
 
- Protected Attributes inherited from mitk::SegWithPreviewTool
ToolCommand::Pointer m_ProgressCommand
 
- 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
 

Detailed Description

Medical Segment Anything Model interactive 2D tool class.

See also
mitk::Tool
QmitkInteractiveSegmentation

Definition at line 36 of file mitkMedSAMTool.h.

Constructor & Destructor Documentation

◆ MedSAMTool()

mitk::MedSAMTool::MedSAMTool ( )
protecteddefault

◆ ~MedSAMTool()

mitk::MedSAMTool::~MedSAMTool ( )
protecteddefault

Member Function Documentation

◆ Activated()

void mitk::MedSAMTool::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::Tool.

◆ ClearPicks()

void mitk::MedSAMTool::ClearPicks ( )
overridevirtual

Clears all picks and updates the preview.

Reimplemented from mitk::SegmentAnythingTool.

◆ Clone()

Pointer mitk::MedSAMTool::Clone ( ) const

◆ ConnectActionsAndFunctions()

void mitk::MedSAMTool::ConnectActionsAndFunctions ( )
overridevirtual

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::MedSAMTool::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::Tool.

◆ GetName()

const char* mitk::MedSAMTool::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.

◆ GetPointsAsCSVString()

std::string mitk::MedSAMTool::GetPointsAsCSVString ( const mitk::BaseGeometry baseGeometry) const
overridevirtual

Get the Points from positive and negative pointsets as csv string.

Parameters
baseGeometry
Returns
std::string

Reimplemented from mitk::SegmentAnythingTool.

◆ HasPicks()

bool mitk::MedSAMTool::HasPicks ( ) const
overridevirtual

Checks if any point exists in the either of the pointsets.

Returns
bool

Reimplemented from mitk::SegmentAnythingTool.

◆ mitkClassMacro()

mitk::MedSAMTool::mitkClassMacro ( MedSAMTool  ,
SegmentAnythingTool   
)

◆ New()

static Pointer mitk::MedSAMTool::New ( )
static

◆ OnDelete()

void mitk::MedSAMTool::OnDelete ( StateMachineAction ,
InteractionEvent  
)
virtual

Deletes bounding box from the render window.

Reimplemented from mitk::SegmentAnythingTool.

◆ OnRenderWindowClicked()

void mitk::MedSAMTool::OnRenderWindowClicked ( StateMachineAction ,
InteractionEvent interactionEvent 
)

Adds bounding box in the render window when clicked.


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