MonaiLabel segmentation tool base class. More...

#include <mitkMonaiLabelTool.h>

Inheritance diagram for mitk::MonaiLabelTool:

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Collaboration diagram for mitk::MonaiLabelTool:

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Public Member Functions
	mitkClassMacro (MonaiLabelTool, SegWithPreviewTool)

Pointer	Clone () const

void	Activated () override
	Called when the tool gets activated. More...

void	Deactivated () override
	Called when the tool gets deactivated. More...

void	UpdatePrepare () override

void	FetchOverallInfo (const std::string &hostName, const int &port)
	Method does the GET Rest call to fetch MonaiLabel server metadata including all models' info. More...

const std::vector< MonaiModelInfo >	GetAutoSegmentationModels (const int dim=-1) const
	Get the Auto Segmentation Models info for the given dimension. More...

const std::vector< MonaiModelInfo >	GetInteractiveSegmentationModels (const int dim=-1) const
	Get the Interactive Segmentation Models info for the given dimension. More...

const std::vector< MonaiModelInfo >	GetScribbleSegmentationModels (const int dim=-1) const
	Get the Scribble Segmentation Models info for the given dimension. More...

MonaiModelInfo	GetModelInfoFromName (const std::string) const
	Helper function to get full model info object from model name. More...

virtual void	SetModelName (std::string _arg)

virtual std::string	GetModelName () const

virtual void	SetURL (std::string _arg)

virtual std::string	GetURL () const

virtual void	SetTempDir (std::string _arg)

virtual std::string	GetTempDir () const

const MonaiAppMetadata *	GetInfoParameters () const

void	ClearPicks ()
	Clears all picks and updates the preview. More...

bool	HasPicks () const
	Checks if any point exists in the either of the PointSetPositive or PointSetNegative. 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 const char **	GetXPM () const =0
	Returns an icon in the XPM format. More...

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 us::ModuleResource	GetIconResource () const
	Returns the tool button icon of the tool wrapped by a usModuleResource. 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

Public Attributes
std::unique_ptr< MonaiLabelRequest >	m_RequestParameters
	Variable to set selected model's and other data needed for the POST call. More...

Message1< const bool >	MonaiStatusEvent

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 Member Functions
	MonaiLabelTool ()

	~MonaiLabelTool ()

void	DoUpdatePreview (const Image inputAtTimeStep, const Image oldSegAtTimeStep, LabelSetImage *previewImage, TimeStepType timeStep) override

void	ConnectActionsAndFunctions () override

virtual void	WriteImage (const Image *, const std::string &) const =0
	Writes image to disk as the tool desires. Default implementation does nothing. More...

virtual void	OnAddPositivePoint (StateMachineAction , InteractionEvent interactionEvent)

virtual void	OnAddNegativePoint (StateMachineAction , InteractionEvent interactionEvent)

virtual void	OnDelete (StateMachineAction , InteractionEvent )

void	ClearSeeds ()

virtual std::string	ConvertPointsAsListString (const mitk::BaseGeometry *baseGeometry, const PointSet::Pointer pointSet) const
	Get the Points from given pointset as csv string. More...

virtual void	WriteBackResults (LabelSetImage , LabelSetImage , TimeStepType) const =0
	Writes back segmentation results in 3D or 2D shape to preview LabelSetImage. 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	UpdateCleanUp ()

virtual void	ConfirmCleanUp ()

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 ()

Protected Attributes
PointSet::Pointer	m_PointSetPositive

PointSet::Pointer	m_PointSetNegative

DataNode::Pointer	m_PointSetNodePositive

DataNode::Pointer	m_PointSetNodeNegative

int	m_PointSetCount

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

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

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 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::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)

Detailed Description

MonaiLabel segmentation tool base class.

Warning: Only to be instantiated by mitk::ToolManager.

Definition at line 104 of file mitkMonaiLabelTool.h.

Constructor & Destructor Documentation

◆ MonaiLabelTool()

mitk::MonaiLabelTool::MonaiLabelTool ( )

protected

◆ ~MonaiLabelTool()

mitk::MonaiLabelTool::~MonaiLabelTool ( )

protected

Member Function Documentation

◆ Activated()

void mitk::MonaiLabelTool::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::MonaiLabelTool::ClearPicks ( )

Clears all picks and updates the preview.

◆ ClearSeeds()

void mitk::MonaiLabelTool::ClearSeeds ( )

protected

◆ Clone()

Pointer mitk::MonaiLabelTool::Clone ( ) const

◆ ConnectActionsAndFunctions()

void mitk::MonaiLabelTool::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.

◆ ConvertPointsAsListString()

virtual std::string mitk::MonaiLabelTool::ConvertPointsAsListString	(	const mitk::BaseGeometry *	baseGeometry,
		const PointSet::Pointer	pointSet
	)		const

protectedvirtual

Get the Points from given pointset as csv string.

◆ Deactivated()

void mitk::MonaiLabelTool::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.

◆ DoUpdatePreview()

void mitk::MonaiLabelTool::DoUpdatePreview	(	const Image *	inputAtTimeStep,
		const Image *	oldSegAtTimeStep,
		LabelSetImage *	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 segmentation so far.

Implements mitk::SegWithPreviewTool.

◆ FetchOverallInfo()

void mitk::MonaiLabelTool::FetchOverallInfo	(	const std::string &	hostName,
		const int &	port
	)

Method does the GET Rest call to fetch MonaiLabel server metadata including all models' info.

◆ GetAutoSegmentationModels()

const std::vector<MonaiModelInfo> mitk::MonaiLabelTool::GetAutoSegmentationModels ( const int dim = -1 ) const

Get the Auto Segmentation Models info for the given dimension.

◆ GetInfoParameters()

const MonaiAppMetadata* mitk::MonaiLabelTool::GetInfoParameters ( ) const

◆ GetInteractiveSegmentationModels()

const std::vector<MonaiModelInfo> mitk::MonaiLabelTool::GetInteractiveSegmentationModels ( const int dim = -1 ) const

Get the Interactive Segmentation Models info for the given dimension.

◆ GetModelInfoFromName()

MonaiModelInfo mitk::MonaiLabelTool::GetModelInfoFromName ( const std::string ) const

Helper function to get full model info object from model name.

◆ GetModelName()

virtual std::string mitk::MonaiLabelTool::GetModelName ( ) const

virtual

◆ GetScribbleSegmentationModels()

const std::vector<MonaiModelInfo> mitk::MonaiLabelTool::GetScribbleSegmentationModels ( const int dim = -1 ) const

Get the Scribble Segmentation Models info for the given dimension.

◆ GetTempDir()

virtual std::string mitk::MonaiLabelTool::GetTempDir ( ) const

virtual

◆ GetURL()

virtual std::string mitk::MonaiLabelTool::GetURL ( ) const

virtual

◆ HasPicks()

bool mitk::MonaiLabelTool::HasPicks ( ) const

Checks if any point exists in the either of the PointSetPositive or PointSetNegative.

◆ mitkClassMacro()

mitk::MonaiLabelTool::mitkClassMacro	(	MonaiLabelTool	,
		SegWithPreviewTool
	)

◆ OnAddNegativePoint()

virtual void mitk::MonaiLabelTool::OnAddNegativePoint	(	StateMachineAction *	,
		InteractionEvent *	interactionEvent
	)

protectedvirtual

◆ OnAddPositivePoint()

virtual void mitk::MonaiLabelTool::OnAddPositivePoint	(	StateMachineAction *	,
		InteractionEvent *	interactionEvent
	)

protectedvirtual

◆ OnDelete()

virtual void mitk::MonaiLabelTool::OnDelete	(	StateMachineAction *	,
		InteractionEvent *
	)

protectedvirtual

◆ SetModelName()

virtual void mitk::MonaiLabelTool::SetModelName ( std::string _arg )

virtual

◆ SetTempDir()

virtual void mitk::MonaiLabelTool::SetTempDir ( std::string _arg )

virtual

◆ SetURL()

virtual void mitk::MonaiLabelTool::SetURL ( std::string _arg )

virtual

◆ UpdatePrepare()

void mitk::MonaiLabelTool::UpdatePrepare ( )

overridevirtual

This member function offers derived classes the possibility to alter what should happen directly before the update of the preview is performed. It is called by UpdatePreview. Default implementation does nothing.

Reimplemented from mitk::SegWithPreviewTool.

◆ WriteBackResults()

virtual void mitk::MonaiLabelTool::WriteBackResults	(	LabelSetImage *	,
		LabelSetImage *	,
		TimeStepType
	)		const

protectedpure virtual

Writes back segmentation results in 3D or 2D shape to preview LabelSetImage.

Implemented in mitk::MonaiLabel2DTool, and mitk::MonaiLabel3DTool.

◆ WriteImage()

virtual void mitk::MonaiLabelTool::WriteImage	(	const Image *	,
		const std::string &
	)		const

protectedpure virtual

Writes image to disk as the tool desires. Default implementation does nothing.

Implemented in mitk::MonaiLabel2DTool, and mitk::MonaiLabel3DTool.

Member Data Documentation

◆ m_PointSetCount

int mitk::MonaiLabelTool::m_PointSetCount

protected

Definition at line 218 of file mitkMonaiLabelTool.h.

◆ m_PointSetNegative

PointSet::Pointer mitk::MonaiLabelTool::m_PointSetNegative

protected

Definition at line 215 of file mitkMonaiLabelTool.h.

◆ m_PointSetNodeNegative

DataNode::Pointer mitk::MonaiLabelTool::m_PointSetNodeNegative

protected

Definition at line 217 of file mitkMonaiLabelTool.h.

◆ m_PointSetNodePositive

DataNode::Pointer mitk::MonaiLabelTool::m_PointSetNodePositive

protected

Definition at line 216 of file mitkMonaiLabelTool.h.

◆ m_PointSetPositive

PointSet::Pointer mitk::MonaiLabelTool::m_PointSetPositive

protected

Definition at line 214 of file mitkMonaiLabelTool.h.

◆ m_RequestParameters

std::unique_ptr<MonaiLabelRequest> mitk::MonaiLabelTool::m_RequestParameters

Variable to set selected model's and other data needed for the POST call.

Definition at line 123 of file mitkMonaiLabelTool.h.

◆ MonaiStatusEvent

Message1<const bool> mitk::MonaiLabelTool::MonaiStatusEvent

Definition at line 168 of file mitkMonaiLabelTool.h.

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

mitkMonaiLabelTool.h

Public Member Functions

Public Attributes

Protected Member Functions

Protected Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ MonaiLabelTool()

◆ ~MonaiLabelTool()

Member Function Documentation

◆ Activated()

◆ ClearPicks()

◆ ClearSeeds()

◆ Clone()

◆ ConnectActionsAndFunctions()

◆ ConvertPointsAsListString()

◆ Deactivated()

◆ DoUpdatePreview()

◆ FetchOverallInfo()

◆ GetAutoSegmentationModels()

◆ GetInfoParameters()

◆ GetInteractiveSegmentationModels()

◆ GetModelInfoFromName()

◆ GetModelName()

◆ GetScribbleSegmentationModels()

◆ GetTempDir()

◆ GetURL()

◆ HasPicks()

◆ mitkClassMacro()

◆ OnAddNegativePoint()

◆ OnAddPositivePoint()

◆ OnDelete()

◆ SetModelName()

◆ SetTempDir()

◆ SetURL()

◆ UpdatePrepare()

◆ WriteBackResults()

◆ WriteImage()

Member Data Documentation

◆ m_PointSetCount

◆ m_PointSetNegative

◆ m_PointSetNodeNegative

◆ m_PointSetNodePositive

◆ m_PointSetPositive

◆ m_RequestParameters

◆ MonaiStatusEvent