TotalSegmentator segmentation tool. More...

#include <mitkTotalSegmentatorTool.h>

Inheritance diagram for mitk::TotalSegmentatorTool:

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Collaboration diagram for mitk::TotalSegmentatorTool:

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Public Member Functions
	mitkClassMacro (TotalSegmentatorTool, SegWithPreviewTool)

Pointer	Clone () const

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

const char **	GetXPM () const override
	Returns an icon in the XPM format. 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	SetMitkTempDir (std::string _arg)

virtual std::string	GetMitkTempDir () const

virtual void	SetSubTask (std::string _arg)

virtual std::string	GetSubTask () const

virtual void	SetPythonPath (std::string _arg)

virtual std::string	GetPythonPath () const

virtual void	SetGpuId (unsigned int _arg)

virtual unsigned int	GetGpuId () const

virtual void	SetFast (bool _arg)

virtual bool	GetFast () const

virtual void	FastOn ()

virtual void	FastOff ()

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

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 void	onPythonProcessEvent (itk::Object , const itk::EventObject &e, void )
	Static function to print out everything from itk::EventObject. Used as callback in mitk::ProcessExecutor object. More...

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
	TotalSegmentatorTool ()

	~TotalSegmentatorTool ()

void	DoUpdatePreview (const Image inputAtTimeStep, const Image oldSegAtTimeStep, LabelSetImage *previewImage, TimeStepType timeStep) override
	Overridden method from the tool manager to execute the segmentation Implementation: 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)

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::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::LabelSetImage source, mitk::LabelSetImage target)

static void	TransferLabelSetImageContent (const LabelSetImage source, LabelSetImage target, TimeStepType timeStep)

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.

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

Definition at line 36 of file mitkTotalSegmentatorTool.h.

Constructor & Destructor Documentation

◆ TotalSegmentatorTool()

mitk::TotalSegmentatorTool::TotalSegmentatorTool ( )

protected

◆ ~TotalSegmentatorTool()

mitk::TotalSegmentatorTool::~TotalSegmentatorTool ( )

protected

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::SegWithPreviewTool.

◆ Clone()

Pointer mitk::TotalSegmentatorTool::Clone ( ) const

◆ DoUpdatePreview()

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

overrideprotectedvirtual

Overridden method from the tool manager to execute the segmentation Implementation:

Creates temp directory, if not done already.
Parses Label names from map_to_binary.py for using later on.
Calls "run_totalsegmentator" method.
Expects an output image to be saved in the temporary directory by the python process. Loads it as LabelSetImage and sets to previewImage.

Parameters

inputAtTimeStep
oldSegAtTimeStep
previewImage
timeStep

Implements mitk::SegWithPreviewTool.

◆ FastOff()

virtual void mitk::TotalSegmentatorTool::FastOff ( )

virtual

◆ FastOn()

virtual void mitk::TotalSegmentatorTool::FastOn ( )

virtual

◆ GetFast()

virtual bool mitk::TotalSegmentatorTool::GetFast ( ) const

virtual

◆ GetGpuId()

virtual unsigned int mitk::TotalSegmentatorTool::GetGpuId ( ) 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 if this function is not reimplemented

Reimplemented from mitk::Tool.

◆ GetMitkTempDir()

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

virtual

◆ 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!

Implements mitk::Tool.

◆ GetPythonPath()

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

virtual

◆ GetSubTask()

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

virtual

◆ GetXPM()

const char** mitk::TotalSegmentatorTool::GetXPM ( ) const

overridevirtual

Returns an icon in the XPM format.

This icon has to fit into some kind of button in most applications, so make it smaller than 25x25 pixels.

XPM is e.g. supported by The Gimp. But if you open any XPM file in your text editor, you will see that you could also "draw" it with an editor.

Implements mitk::Tool.

◆ mitkClassMacro()

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

◆ New()

static Pointer mitk::TotalSegmentatorTool::New ( )

static

◆ onPythonProcessEvent()

static void mitk::TotalSegmentatorTool::onPythonProcessEvent	(	itk::Object *	,
		const itk::EventObject &	e,
		void *
	)

static

Static function to print out everything from itk::EventObject. Used as callback in mitk::ProcessExecutor object.

◆ SetFast()

virtual void mitk::TotalSegmentatorTool::SetFast ( bool _arg )

virtual

◆ SetGpuId()

virtual void mitk::TotalSegmentatorTool::SetGpuId ( unsigned int _arg )

virtual

◆ SetMitkTempDir()

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

virtual

◆ SetPythonPath()

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

virtual

◆ SetSubTask()

virtual void mitk::TotalSegmentatorTool::SetSubTask ( 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 Member Functions

Static Public Member Functions

Protected Member Functions

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ TotalSegmentatorTool()

◆ ~TotalSegmentatorTool()

Member Function Documentation

◆ Activated()

◆ Clone()

◆ DoUpdatePreview()

◆ FastOff()

◆ FastOn()

◆ GetFast()

◆ GetGpuId()

◆ GetIconResource()

◆ GetMitkTempDir()

◆ GetName()

◆ GetPythonPath()

◆ GetSubTask()

◆ GetXPM()

◆ mitkClassMacro()

◆ New()

◆ onPythonProcessEvent()

◆ SetFast()

◆ SetGpuId()

◆ SetMitkTempDir()

◆ SetPythonPath()

◆ SetSubTask()

◆ UpdatePrepare()