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 DataNode *	GetTargetSegmentationNode () const
	Returns the currently selected segmentation node. More...
LabelSetImage *	GetTargetSegmentation () const
LabelSetImage *	GetPreviewSegmentation ()
const LabelSetImage *	GetPreviewSegmentation () const
DataNode *	GetPreviewSegmentationNode ()
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 Image *	GetSegmentationInput () const
const Image *	GetReferenceData () 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 PlaneGeometry *	GetWorkingPlaneGeometry ()
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 *)
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
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)
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...
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< 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::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< SegmentAnythingPythonService >	m_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
UndoController *	m_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.

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

• mitkMedSAMTool.h