MONAI Label segmentation tool operating on 3D volumes. More...

#include <mitkMonaiLabel3DTool.h>

Inheritance diagram for mitk::MonaiLabel3DTool:

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Collaboration diagram for mitk::MonaiLabel3DTool:

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Public Member Functions
	mitkClassMacro (MonaiLabel3DTool, MonaiLabelTool)

Pointer	Clone () const

const char *	GetName () const override
	Return the human-readable name of this tool ("MONAI Label 3D"). More...

us::ModuleResource	GetIconResource () const override
	Return the toolbar icon resource for this tool. More...

void	Activated () override
	Activate the tool and configure label transfer scope to all labels. More...

void	WriteImage (const Image *inputAtTimeStep, const std::string &inputImagePath) const override
	Write the input 3D image to disk. More...

void	WriteBackResults (MultiLabelSegmentation previewImage, MultiLabelSegmentation segResults, TimeStepType timeStep) const override
	Write segmentation results back into the preview image for the given time step. More...

Public Member Functions inherited from mitk::MonaiLabelTool
	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

mitk::Label::AlgorithmType	GetAlgorithmType () const override
	AUTOMATIC for auto-segmentation models (no per-image human input, like nnUNet), SEMIAUTOMATIC for interactive deepgrow/deepedit models or when no model is selected. More...

void	FetchOverallInfo (const std::string &hostName, const int &port)
	Fetches MonaiLabel server metadata via GET REST call. More...

const std::vector< MonaiModelInfo >	GetAutoSegmentationModels (const int dim=-1) const
	Returns the auto-segmentation model information for the given dimension. More...

const std::vector< MonaiModelInfo >	GetInteractiveSegmentationModels (const int dim=-1) const
	Returns the interactive segmentation model information for the given dimension. More...

const std::vector< MonaiModelInfo >	GetScribbleSegmentationModels (const int dim=-1) const
	Returns the scribble segmentation model information for the given dimension. More...

MonaiModelInfo	GetModelInfoFromName (const std::string) const
	Returns full model info for the given 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

virtual void	SetTimeout (unsigned int _arg)

virtual unsigned int	GetTimeout () const

const MonaiAppMetadata *	GetInfoParameters () const

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

bool	HasPicks () const
	Checks if any seed point exists in either the positive or negative point set. 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...

mitk::Label::AlgorithmType	GetAlgorithmType () const override
	Preview tools are SEMIAUTOMATIC by default (the user supplies seeds/parameters). Fully automatic preview tools (e.g. TotalSegmentator) override this again to AUTOMATIC. More...

void	ConfirmSegmentation ()
	Confirms the current preview segmentation and transfers it to the working image. More...

virtual void	SetCreateAllTimeSteps (bool _arg)
	If true, the preview is computed for all time steps at once. More...

virtual bool	GetCreateAllTimeSteps ()

virtual void	CreateAllTimeStepsOn ()

virtual void	CreateAllTimeStepsOff ()

virtual void	SetKeepActiveAfterAccept (bool _arg)
	If true, the tool stays active after the segmentation is accepted. More...

virtual bool	GetKeepActiveAfterAccept ()

virtual void	KeepActiveAfterAcceptOn ()

virtual void	KeepActiveAfterAcceptOff ()

virtual void	SetIsTimePointChangeAware (bool _arg)
	If true, the tool reacts to time point changes and updates the preview. More...

virtual bool	GetIsTimePointChangeAware ()

virtual void	IsTimePointChangeAwareOn ()

virtual void	IsTimePointChangeAwareOff ()

virtual void	SetResetsToEmptyPreview (bool _arg)
	If true, the preview is reset to empty on activation. More...

virtual bool	GetResetsToEmptyPreview ()

virtual void	ResetsToEmptyPreviewOn ()

virtual void	ResetsToEmptyPreviewOff ()

virtual void	SetUseSpecialPreviewColor (bool _arg)
	If true, a special color is used for the preview rendering. More...

virtual bool	GetUseSpecialPreviewColor ()

virtual void	UseSpecialPreviewColorOn ()

virtual void	UseSpecialPreviewColorOff ()

virtual void	SetRequestDeactivationConfirmation (bool _arg)
	If true, a confirmation dialog is shown before deactivating the tool. More...

virtual bool	GetRequestDeactivationConfirmation ()

virtual void	RequestDeactivationConfirmationOn ()

virtual void	RequestDeactivationConfirmationOff ()

Color	GetSpecialPreviewColor () const
	Returns the special preview color. More...

void	SetMergeStyle (MultiLabelSegmentation::MergeStyle mergeStyle)
	Sets how the preview content is merged into the working image upon confirmation. More...

virtual MultiLabelSegmentation::MergeStyle	GetMergeStyle ()

void	SetOverwriteStyle (MultiLabelSegmentation::OverwriteStyle overwriteStyle)
	Sets whether locked labels should be overwritten during transfer. More...

virtual MultiLabelSegmentation::OverwriteStyle	GetOverwriteStyle ()

void	SetLabelTransferScope (LabelTransferScope labelTransferScope)
	Sets which labels from the preview are transferred on confirmation. More...

virtual LabelTransferScope	GetLabelTransferScope ()

void	SetSelectedLabels (const SelectedLabelVectorType &labelsToTransfer)
	Sets the labels to transfer from preview to working image on confirmation. More...

virtual SelectedLabelVectorType	GetSelectedLabels ()

void	SetLabelTransferMode (LabelTransferMode labelTransferMode)
	Sets how labels are transferred from preview to the working image. More...

virtual LabelTransferMode	GetLabelTransferMode ()

bool	CanHandle (const BaseData referenceData, const BaseData workingData) const override
	Checks if a tool can handle the given reference data and optional working data. More...

void	UpdatePreview (bool ignoreLazyPreviewSetting=false)
	Triggers the update of the preview segmentation. More...

bool	IsUpdating () const

std::string	GetCurrentSegmentationName ()
	Returns the name of the currently selected segmentation node. More...

virtual DataNode *	GetTargetSegmentationNode () const
	Returns the currently selected segmentation node. More...

MultiLabelSegmentation *	GetTargetSegmentation () const

MultiLabelSegmentation *	GetPreviewSegmentation ()

const MultiLabelSegmentation *	GetPreviewSegmentation () const

DataNode *	GetPreviewSegmentationNode ()

void	SetPreviewOpacity (float opacity)

virtual float	GetPreviewOpacity () const

void	SetPreviewVisibility (bool visible)

virtual bool	GetPreviewVisibility () const

Public Member Functions inherited from mitk::Tool
	mitkClassMacro (Tool, EventStateMachine)

virtual us::ModuleResource	GetCursorIconResource () const
	Returns the cursor icon of the tool wrapped by a usModuleResource. More...

virtual bool	IsEligibleForAutoInit () const
	Returns whether this tool is eligible for auto-initialization by ToolManager. More...

virtual void	InitializeStateMachine ()
	Initializes the state machine for this tool based on the interaction type. More...

virtual itk::Object::Pointer	GetGUI (const std::string &toolkitPrefix, const std::string &toolkitPostfix)
	Interface for GUI creation. More...

virtual NodePredicateBase::ConstPointer	GetReferenceDataPreference () const
	Returns a predicate describing valid reference data for this tool. More...

virtual NodePredicateBase::ConstPointer	GetWorkingDataPreference () const
	Returns a predicate describing valid working data for this tool. More...

Public Member Functions inherited from mitk::EventStateMachine
	mitkClassMacro (EventStateMachine, InteractionEventHandler)

bool	LoadStateMachine (const std::string &filename, const us::Module *module=nullptr)
	Load a state machine pattern from an XML resource file. More...

bool	HandleEvent (InteractionEvent event, DataNode dataNode)
	Process an incoming interaction event. More...

void	EnableUndo (bool enable)
	Enable or disable the undo mechanism for this state machine. More...

void	EnableInteraction (bool enable)
	Enable or disable the state machine. More...

Public Member Functions inherited from mitk::InteractionEventHandler
	mitkClassMacroItkParent (InteractionEventHandler, itk::Object)

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 ()
	Disable this observer so it no longer receives notifications. More...

void	Enable ()
	Enable this observer so it receives notifications. More...

bool	IsEnabled () const
	Check whether this observer is currently enabled. More...

Static Public Member Functions
static Pointer	New ()

Protected Member Functions
	MonaiLabel3DTool ()=default

	~MonaiLabel3DTool ()=default

Protected Member Functions inherited from mitk::MonaiLabelTool
	MonaiLabelTool ()

	~MonaiLabelTool ()

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

void	ConnectActionsAndFunctions () override

virtual void	OnAddPositivePoint (StateMachineAction , InteractionEvent interactionEvent)
	Add positive seed point action of StateMachine pattern. More...

virtual void	OnAddNegativePoint (StateMachineAction , InteractionEvent interactionEvent)
	Add negative seed point action of StateMachine pattern. More...

virtual void	OnDelete (StateMachineAction , InteractionEvent )
	Delete action of StateMachine pattern. More...

void	OnMove (StateMachineAction , InteractionEvent )

void	OnRelease (StateMachineAction , InteractionEvent )

void	OnPrimaryButtonPressed (StateMachineAction , InteractionEvent )

void	ClearSeeds ()
	Clears all seed points and updates the preview to reset the segmentation. More...

virtual std::string	ConvertPointsAsListString (const mitk::BaseGeometry *baseGeometry, const PointSet::Pointer pointSet) const
	Converts point coordinates from a given point set to a CSV string. 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)
	Called before the preview content is transferred to the segmentation on confirmation. More...

const Image *	GetSegmentationInput () const

const Image *	GetReferenceData () const

void	ResetPreviewNode ()

void	ResetPreviewContent ()

void	ResetPreviewContentAtTimeStep (unsigned int timeStep)

TimePointType	GetLastTimePointOfUpdate () const

MultiLabelSegmentation::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. More...

virtual void	OnTimePointChanged ()

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
	Called by the Dispatcher to notify this observer about an InteractionEvent. More...

bool	FilterEvents (InteractionEvent , DataNode ) override

Protected Member Functions inherited from mitk::EventStateMachine
	EventStateMachine ()

	~EventStateMachine () override

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 class	LabelTransferScope { ActiveLabel , SelectedLabels , AllLabels }
	Defines which labels from the preview are transferred on confirmation. More...

enum class	LabelTransferMode { MapLabel , AddLabel }
	Defines how labels are transferred from preview to the working image. More...

using	SelectedLabelVectorType = std::vector< Label::PixelType >
	Type for the vector of selected label values. More...

Public Types inherited from mitk::Tool
typedef mitk::Label::PixelType	DefaultSegmentationDataType

Public Types inherited from mitk::EventStateMachine
typedef itk::SmartPointer< StateMachineState >	StateMachineStateType

Public Attributes inherited from mitk::MonaiLabelTool
std::unique_ptr< MonaiLabelRequest >	m_RequestParameters
	Holds the selected model and server data for the POST inference 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 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::MultiLabelSegmentation source, mitk::MultiLabelSegmentation target)
	Copies label information (not pixel content) from one segmentation to another. More...

Protected Attributes inherited from mitk::MonaiLabelTool
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

Detailed Description

MONAI Label segmentation tool operating on 3D volumes.

See also: mitk::MonaiLabelTool

This tool sends the full 3D volume to a MONAI Label server for AI-based segmentation and writes the result back into the preview segmentation volume.

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

Definition at line 39 of file mitkMonaiLabel3DTool.h.

Constructor & Destructor Documentation

◆ MonaiLabel3DTool()

mitk::MonaiLabel3DTool::MonaiLabel3DTool ( )

protecteddefault

◆ ~MonaiLabel3DTool()

mitk::MonaiLabel3DTool::~MonaiLabel3DTool ( )

protecteddefault

Member Function Documentation

◆ Activated()

void mitk::MonaiLabel3DTool::Activated ( )

overridevirtual

Activate the tool and configure label transfer scope to all labels.

Reimplemented from mitk::Tool.

◆ Clone()

Pointer mitk::MonaiLabel3DTool::Clone ( ) const

◆ GetIconResource()

us::ModuleResource mitk::MonaiLabel3DTool::GetIconResource ( ) const

overridevirtual

Return the toolbar icon resource for this tool.

Reimplemented from mitk::Tool.

◆ GetName()

const char* mitk::MonaiLabel3DTool::GetName ( ) const

overridevirtual

Return the human-readable name of this tool ("MONAI Label 3D").

Implements mitk::Tool.

◆ mitkClassMacro()

mitk::MonaiLabel3DTool::mitkClassMacro	(	MonaiLabel3DTool	,
		MonaiLabelTool
	)

◆ New()

static Pointer mitk::MonaiLabel3DTool::New ( )

static

◆ WriteBackResults()

void mitk::MonaiLabel3DTool::WriteBackResults	(	MultiLabelSegmentation *	previewImage,
		MultiLabelSegmentation *	segResults,
		TimeStepType	timeStep
	)		const

overridevirtual

Write segmentation results back into the preview image for the given time step.

Parameters

previewImage	The preview segmentation to write into.
segResults	The segmentation results returned by the MONAI Label server.
timeStep	The time step to write into.

Implements mitk::MonaiLabelTool.

◆ WriteImage()

void mitk::MonaiLabel3DTool::WriteImage	(	const Image *	inputAtTimeStep,
		const std::string &	inputImagePath
	)		const

overridevirtual

Write the input 3D image to disk.

Parameters

inputAtTimeStep	The 3D image at the current time step.
inputImagePath	The file path where the image is saved.

Implements mitk::MonaiLabelTool.

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

mitkMonaiLabel3DTool.h

Public Member Functions

Static Public Member Functions

Protected Member Functions

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ MonaiLabel3DTool()

◆ ~MonaiLabel3DTool()

Member Function Documentation

◆ Activated()

◆ Clone()

◆ GetIconResource()

◆ GetName()

◆ mitkClassMacro()

◆ New()

◆ WriteBackResults()

◆ WriteImage()