TotalSegmentator segmentation tool. More...

#include <mitkTotalSegmentatorTool.h>

Inheritance diagram for mitk::TotalSegmentatorTool:

[legend]

Collaboration diagram for mitk::TotalSegmentatorTool:

[legend]

Public Types
enum class	Speed { Normal , Fast , Fastest }
	Model resolution: full (1.5 mm), –fast (3 mm) or –fastest (6 mm). More...

using	CommandRunner = std::function< bool(const std::string &executable, const std::vector< std::string > &args)>
	Runs `executable` with `args`, returning `true` on success (exit 0) and `false` on cancellation or failure. More...

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 Member Functions
	mitkClassMacro (TotalSegmentatorTool, SegWithPreviewTool)

Pointer	Clone () const

const char *	GetName () const override
	Returns the name of this tool. Make it short! More...

mitk::Label::AlgorithmType	GetAlgorithmType () const override
	TotalSegmentator runs with no per-image human input, so AUTOMATIC. 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...

virtual void	SetTask (std::string _arg)

virtual std::string	GetTask () const

virtual void	SetSpeed (Speed _arg)

virtual Speed	GetSpeed () const

virtual void	SetDevice (std::string _arg)

virtual std::string	GetDevice () const

virtual void	SetExecutablePath (std::string _arg)

virtual std::string	GetExecutablePath () const

void	SetLabelNameLookup (const std::map< mitk::Label::PixelType, std::string > &lookup)
	Sets the label-id-to-name lookup for the selected task. More...

void	SetCommandRunner (CommandRunner runner)

const std::string &	GetLastErrorMessage () const
	Human-readable reason the last run produced no result, or empty if it succeeded or was cancelled by the user. 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
	TotalSegmentatorTool ()

	~TotalSegmentatorTool () override

void	DoUpdatePreview (const Image inputAtTimeStep, const Image oldSegAtTimeStep, MultiLabelSegmentation *previewImage, TimeStepType timeStep) override
	Runs TotalSegmentator on the input and loads its multi-label output. More...

void	UpdatePrepare () override

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 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::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

TotalSegmentator segmentation tool.

Wraps the TotalSegmentator command-line tool. The heavy work runs in a subprocess (never in this process), which keeps MITK's own interpreter free of the virtual environment and lets the GUI keep the application responsive. To stay free of any Qt dependency, this class does not spawn the process itself: the GUI injects the resolved executable path (SetExecutablePath), a label-id-to-name lookup for the selected task (SetLabelNameLookup) and a CommandRunner that actually runs the process while showing progress and offering cancellation.

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

Definition at line 47 of file mitkTotalSegmentatorTool.h.

Member Typedef Documentation

◆ CommandRunner

using mitk::TotalSegmentatorTool::CommandRunner = std::function<bool(const std::string& executable, const std::vector<std::string>& args)>

Runs executable with args, returning true on success (exit 0) and false on cancellation or failure.

Injected by the GUI so the long-running CLI call can keep the application responsive and cancellable while this core module stays free of Qt.

Definition at line 68 of file mitkTotalSegmentatorTool.h.

Member Enumeration Documentation

◆ Speed

enum mitk::TotalSegmentatorTool::Speed

strong

Model resolution: full (1.5 mm), –fast (3 mm) or –fastest (6 mm).

Enumerator
Normal
Fast
Fastest

Definition at line 55 of file mitkTotalSegmentatorTool.h.

Constructor & Destructor Documentation

◆ TotalSegmentatorTool()

mitk::TotalSegmentatorTool::TotalSegmentatorTool ( )

protected

◆ ~TotalSegmentatorTool()

mitk::TotalSegmentatorTool::~TotalSegmentatorTool ( )

overrideprotected

Member Function Documentation

◆ Activated()

void mitk::TotalSegmentatorTool::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.

◆ Clone()

Pointer mitk::TotalSegmentatorTool::Clone ( ) const

◆ DoUpdatePreview()

void mitk::TotalSegmentatorTool::DoUpdatePreview	(	const Image *	inputAtTimeStep,
		const Image *	oldSegAtTimeStep,
		MultiLabelSegmentation *	previewImage,
		TimeStepType	timeStep
	)

overrideprotectedvirtual

Runs TotalSegmentator on the input and loads its multi-label output.

Saves the input to a temporary NIfTI, runs the CLI via the injected CommandRunner, then loads the single –ml output and names its labels. On cancellation or failure the preview is left empty.

Implements mitk::SegWithPreviewTool.

◆ GetAlgorithmType()

mitk::Label::AlgorithmType mitk::TotalSegmentatorTool::GetAlgorithmType ( ) const

overridevirtual

TotalSegmentator runs with no per-image human input, so AUTOMATIC.

Reimplemented from mitk::Tool.

◆ GetDevice()

virtual std::string mitk::TotalSegmentatorTool::GetDevice ( ) const

virtual

◆ GetExecutablePath()

virtual std::string mitk::TotalSegmentatorTool::GetExecutablePath ( ) const

virtual

◆ GetIconResource()

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

overridevirtual

Returns the tool button icon of the tool wrapped by a usModuleResource.

Returns: A valid ModuleResource or an invalid one if this function is not reimplemented.

Reimplemented from mitk::Tool.

◆ GetLastErrorMessage()

const std::string& mitk::TotalSegmentatorTool::GetLastErrorMessage ( ) const

Human-readable reason the last run produced no result, or empty if it succeeded or was cancelled by the user.

The SegWithPreviewTool base catches itk::ExceptionObject (which mitkThrow produces) and only forwards it to ErrorMessage, so such a throw never reaches the GUI's handler. DoUpdatePreview therefore catches its failures internally and records them here, letting the GUI tell a genuine failure from a user cancellation and show a meaningful message.

◆ GetName()

const char* mitk::TotalSegmentatorTool::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!

Note: The name is also recorded as label provenance via mitk::Label::AddToolUse, which reserves the separator characters "|" and ":". Avoid them in tool names (use plain spaces); names containing them are sanitized (separators replaced with "#") and a warning is logged.

Implements mitk::Tool.

◆ GetSpeed()

virtual Speed mitk::TotalSegmentatorTool::GetSpeed ( ) const

virtual

◆ GetTask()

virtual std::string mitk::TotalSegmentatorTool::GetTask ( ) const

virtual

◆ mitkClassMacro()

mitk::TotalSegmentatorTool::mitkClassMacro	(	TotalSegmentatorTool	,
		SegWithPreviewTool
	)

◆ New()

static Pointer mitk::TotalSegmentatorTool::New ( )

static

◆ SetCommandRunner()

void mitk::TotalSegmentatorTool::SetCommandRunner ( CommandRunner runner )

◆ SetDevice()

virtual void mitk::TotalSegmentatorTool::SetDevice ( std::string _arg )

virtual

◆ SetExecutablePath()

virtual void mitk::TotalSegmentatorTool::SetExecutablePath ( std::string _arg )

virtual

◆ SetLabelNameLookup()

void mitk::TotalSegmentatorTool::SetLabelNameLookup ( const std::map< mitk::Label::PixelType, std::string > & lookup )

Sets the label-id-to-name lookup for the selected task.

Ids present in the segmentation output but absent from this lookup are auto-named, so an incomplete or missing lookup never drops a structure.

◆ SetSpeed()

virtual void mitk::TotalSegmentatorTool::SetSpeed ( Speed _arg )

virtual

◆ SetTask()

virtual void mitk::TotalSegmentatorTool::SetTask ( std::string _arg )

virtual

◆ UpdatePrepare()

void mitk::TotalSegmentatorTool::UpdatePrepare ( )

overrideprotectedvirtual

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.

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

mitkTotalSegmentatorTool.h

Public Types

Public Member Functions

Static Public Member Functions

Protected Member Functions

Additional Inherited Members

Detailed Description

Member Typedef Documentation

◆ CommandRunner

Member Enumeration Documentation

◆ Speed

Constructor & Destructor Documentation

◆ TotalSegmentatorTool()

◆ ~TotalSegmentatorTool()

Member Function Documentation

◆ Activated()

◆ Clone()

◆ DoUpdatePreview()

◆ GetAlgorithmType()

◆ GetDevice()

◆ GetExecutablePath()

◆ GetIconResource()

◆ GetLastErrorMessage()

◆ GetName()

◆ GetSpeed()

◆ GetTask()

◆ mitkClassMacro()

◆ New()

◆ SetCommandRunner()

◆ SetDevice()

◆ SetExecutablePath()

◆ SetLabelNameLookup()

◆ SetSpeed()

◆ SetTask()

◆ UpdatePrepare()