nnUNet segmentation tool. More...

#include <mitknnUnetTool.h>

Inheritance diagram for mitk::nnUNetTool:

[legend]

Collaboration diagram for mitk::nnUNetTool:

[legend]

Public Member Functions
	mitkClassMacro (nnUNetTool, 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...

virtual void	SetnnUNetDirectory (std::string _arg)

virtual std::string	GetnnUNetDirectory () const

virtual void	SetModelDirectory (std::string _arg)

virtual std::string	GetModelDirectory () const

virtual void	SetPythonPath (std::string _arg)

virtual std::string	GetPythonPath () const

virtual void	SetMitkTempDir (std::string _arg)

virtual std::string	GetMitkTempDir () const

virtual void	SetPostProcessingJsonDirectory (std::string _arg)

virtual std::string	GetPostProcessingJsonDirectory () const

virtual void	SetMixedPrecision (bool _arg)

virtual bool	GetMixedPrecision () const

virtual void	MixedPrecisionOn ()

virtual void	MixedPrecisionOff ()

virtual void	SetMirror (bool _arg)

virtual bool	GetMirror () const

virtual void	MirrorOn ()

virtual void	MirrorOff ()

virtual void	SetMultiModal (bool _arg)

virtual bool	GetMultiModal () const

virtual void	MultiModalOn ()

virtual void	MultiModalOff ()

virtual void	SetNoPip (bool _arg)

virtual bool	GetNoPip () const

virtual void	NoPipOn ()

virtual void	NoPipOff ()

virtual void	SetEnsemble (bool _arg)

virtual bool	GetEnsemble () const

virtual void	EnsembleOn ()

virtual void	EnsembleOff ()

virtual void	SetPredict (bool _arg)

virtual bool	GetPredict () const

virtual void	PredictOn ()

virtual void	PredictOff ()

virtual void	SetGpuId (unsigned int _arg)

virtual unsigned int	GetGpuId () const

void	RenderOutputBuffer ()
	Renders the output LabelSetImage. To called in the main thread. More...

LabelSetImage::Pointer	GetOutputBuffer ()
	Get the Output Buffer object. More...

void	ClearOutputBuffer ()
	Sets the outputBuffer to nullptr. More...

mitk::DataStorage *	GetDataStorage ()
	Returns the DataStorage from the ToolManager. More...

mitk::DataNode *	GetRefNode ()

void	SetOutputBuffer (LabelSetImage::Pointer)

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 ()

void	SetMergeStyle (MultiLabelSegmentation::MergeStyle mergeStyle)

virtual MultiLabelSegmentation::MergeStyle	GetMergeStyle ()

void	SetOverwriteStyle (MultiLabelSegmentation::OverwriteStyle overwriteStyle)

virtual MultiLabelSegmentation::OverwriteStyle	GetOverwriteStyle ()

void	SetLabelTransferMode (LabelTransferMode LabelTransferMode)

virtual LabelTransferMode	GetLabelTransferMode ()

void	SetSelectedLabels (const SelectedLabelVectorType &labelsToTransfer)

virtual SelectedLabelVectorType	GetSelectedLabels ()

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 *	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::EventStateMachine
static const char *	GetStaticNameOfClass ()

Static Public Member Functions inherited from mitk::InteractionEventHandler
static const char *	GetStaticNameOfClass ()

Public Attributes
std::vector< ModelParams >	m_ParamQ
	vector of ModelParams. Size > 1 only for ensemble prediction. More...

std::vector< mitk::Image::ConstPointer >	m_OtherModalPaths
	Holds paths to other input image modalities. More...

mitk::Image::ConstPointer	m_InputBuffer

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
	nnUNetTool ()
	Construct a new nnUNet Tool object and temp directory. More...

	~nnUNetTool ()
	Destroy the nnUNet Tool object and deletes the temp directory. More...

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...

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	TransferPrepare ()

const Image *	GetSegmentationInput () const

const Image *	GetReferenceData () const

void	ResetPreviewNode ()

void	ResetPreviewContent ()

void	ResetPreviewContentAtTimeStep (unsigned int timeStep)

TimePointType	GetLastTimePointOfUpdate () const

virtual Label::PixelType	GetUserDefinedActiveLabel () const

virtual void	SetWorkingPlaneGeometry (PlaneGeometry *_arg)

virtual const PlaneGeometry *	GetWorkingPlaneGeometry ()

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	LabelTransferMode { LabelTransferMode::ActiveLabel, LabelTransferMode::SelectedLabels, LabelTransferMode::AllLabels }

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

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 (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

nnUNet segmentation tool.

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

Definition at line 68 of file mitknnUnetTool.h.

Constructor & Destructor Documentation

◆ nnUNetTool()

mitk::nnUNetTool::nnUNetTool ( )

protected

Construct a new nnUNet Tool object and temp directory.

◆ ~nnUNetTool()

mitk::nnUNetTool::~nnUNetTool ( )

protected

Destroy the nnUNet Tool object and deletes the temp directory.

Member Function Documentation

◆ Activated()

void mitk::nnUNetTool::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.

◆ ClearOutputBuffer()

void mitk::nnUNetTool::ClearOutputBuffer ( )

Sets the outputBuffer to nullptr.

◆ Clone()

Pointer mitk::nnUNetTool::Clone ( ) const

◆ DoUpdatePreview()

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

overrideprotectedvirtual

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

Saves the inputAtTimeStep in a temporary directory.
Copies other modalities, renames and saves in the temporary directory, if required.
Sets RESULTS_FOLDER and CUDA_VISIBLE_DEVICES variables in the environment.

Iterates through the parameter queue (m_ParamQ) and executes "nnUNet_predict" command with the parameters
Expects an output image to be saved in the temporary directory by the python proces. Loads it as LabelSetImage and sets to previewImage.

Parameters

inputAtTimeStep
oldSegAtTimeStep
previewImage
timeStep

Implements mitk::SegWithPreviewTool.

◆ EnsembleOff()

virtual void mitk::nnUNetTool::EnsembleOff ( )

virtual

◆ EnsembleOn()

virtual void mitk::nnUNetTool::EnsembleOn ( )

virtual

◆ GetDataStorage()

mitk::DataStorage* mitk::nnUNetTool::GetDataStorage ( )

Returns the DataStorage from the ToolManager.

◆ GetEnsemble()

virtual bool mitk::nnUNetTool::GetEnsemble ( ) const

virtual

◆ GetGpuId()

virtual unsigned int mitk::nnUNetTool::GetGpuId ( ) const

virtual

◆ GetIconResource()

us::ModuleResource mitk::nnUNetTool::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.

◆ GetMirror()

virtual bool mitk::nnUNetTool::GetMirror ( ) const

virtual

◆ GetMitkTempDir()

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

virtual

◆ GetMixedPrecision()

virtual bool mitk::nnUNetTool::GetMixedPrecision ( ) const

virtual

◆ GetModelDirectory()

virtual std::string mitk::nnUNetTool::GetModelDirectory ( ) const

virtual

◆ GetMultiModal()

virtual bool mitk::nnUNetTool::GetMultiModal ( ) const

virtual

◆ GetName()

const char* mitk::nnUNetTool::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.

◆ GetnnUNetDirectory()

virtual std::string mitk::nnUNetTool::GetnnUNetDirectory ( ) const

virtual

◆ GetNoPip()

virtual bool mitk::nnUNetTool::GetNoPip ( ) const

virtual

◆ GetOutputBuffer()

LabelSetImage::Pointer mitk::nnUNetTool::GetOutputBuffer ( )

Get the Output Buffer object.

Returns: LabelSetImage::Pointer

◆ GetPostProcessingJsonDirectory()

virtual std::string mitk::nnUNetTool::GetPostProcessingJsonDirectory ( ) const

virtual

◆ GetPredict()

virtual bool mitk::nnUNetTool::GetPredict ( ) const

virtual

◆ GetPythonPath()

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

virtual

◆ GetRefNode()

mitk::DataNode* mitk::nnUNetTool::GetRefNode ( )

◆ GetXPM()

const char** mitk::nnUNetTool::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.

◆ MirrorOff()

virtual void mitk::nnUNetTool::MirrorOff ( )

virtual

◆ MirrorOn()

virtual void mitk::nnUNetTool::MirrorOn ( )

virtual

◆ mitkClassMacro()

mitk::nnUNetTool::mitkClassMacro	(	nnUNetTool	,
		SegWithPreviewTool
	)

◆ MixedPrecisionOff()

virtual void mitk::nnUNetTool::MixedPrecisionOff ( )

virtual

◆ MixedPrecisionOn()

virtual void mitk::nnUNetTool::MixedPrecisionOn ( )

virtual

◆ MultiModalOff()

virtual void mitk::nnUNetTool::MultiModalOff ( )

virtual

◆ MultiModalOn()

virtual void mitk::nnUNetTool::MultiModalOn ( )

virtual

◆ New()

static Pointer mitk::nnUNetTool::New ( )

static

◆ NoPipOff()

virtual void mitk::nnUNetTool::NoPipOff ( )

virtual

◆ NoPipOn()

virtual void mitk::nnUNetTool::NoPipOn ( )

virtual

◆ PredictOff()

virtual void mitk::nnUNetTool::PredictOff ( )

virtual

◆ PredictOn()

virtual void mitk::nnUNetTool::PredictOn ( )

virtual

◆ RenderOutputBuffer()

void mitk::nnUNetTool::RenderOutputBuffer ( )

Renders the output LabelSetImage. To called in the main thread.

◆ SetEnsemble()

virtual void mitk::nnUNetTool::SetEnsemble ( bool _arg )

virtual

◆ SetGpuId()

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

virtual

◆ SetMirror()

virtual void mitk::nnUNetTool::SetMirror ( bool _arg )

virtual

◆ SetMitkTempDir()

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

virtual

◆ SetMixedPrecision()

virtual void mitk::nnUNetTool::SetMixedPrecision ( bool _arg )

virtual

◆ SetModelDirectory()

virtual void mitk::nnUNetTool::SetModelDirectory ( std::string _arg )

virtual

◆ SetMultiModal()

virtual void mitk::nnUNetTool::SetMultiModal ( bool _arg )

virtual

◆ SetnnUNetDirectory()

virtual void mitk::nnUNetTool::SetnnUNetDirectory ( std::string _arg )

virtual

◆ SetNoPip()

virtual void mitk::nnUNetTool::SetNoPip ( bool _arg )

virtual

◆ SetOutputBuffer()

void mitk::nnUNetTool::SetOutputBuffer ( LabelSetImage::Pointer )

◆ SetPostProcessingJsonDirectory()

virtual void mitk::nnUNetTool::SetPostProcessingJsonDirectory ( std::string _arg )

virtual

◆ SetPredict()

virtual void mitk::nnUNetTool::SetPredict ( bool _arg )

virtual

◆ SetPythonPath()

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

virtual

Member Data Documentation

◆ m_InputBuffer

mitk::Image::ConstPointer mitk::nnUNetTool::m_InputBuffer

Definition at line 135 of file mitknnUnetTool.h.

◆ m_OtherModalPaths

std::vector<mitk::Image::ConstPointer> mitk::nnUNetTool::m_OtherModalPaths

Holds paths to other input image modalities.

Definition at line 133 of file mitknnUnetTool.h.

◆ m_ParamQ

std::vector<ModelParams> mitk::nnUNetTool::m_ParamQ

vector of ModelParams. Size > 1 only for ensemble prediction.

Definition at line 121 of file mitknnUnetTool.h.

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

mitknnUnetTool.h

Public Member Functions

Static Public Member Functions

Public Attributes

Protected Member Functions

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ nnUNetTool()

◆ ~nnUNetTool()

Member Function Documentation

◆ Activated()

◆ ClearOutputBuffer()

◆ Clone()

◆ DoUpdatePreview()

◆ EnsembleOff()

◆ EnsembleOn()

◆ GetDataStorage()

◆ GetEnsemble()

◆ GetGpuId()

◆ GetIconResource()

◆ GetMirror()

◆ GetMitkTempDir()

◆ GetMixedPrecision()

◆ GetModelDirectory()

◆ GetMultiModal()

◆ GetName()

◆ GetnnUNetDirectory()

◆ GetNoPip()

◆ GetOutputBuffer()

◆ GetPostProcessingJsonDirectory()

◆ GetPredict()

◆ GetPythonPath()

◆ GetRefNode()

◆ GetXPM()

◆ MirrorOff()

◆ MirrorOn()

◆ mitkClassMacro()

◆ MixedPrecisionOff()

◆ MixedPrecisionOn()

◆ MultiModalOff()

◆ MultiModalOn()

◆ New()

◆ NoPipOff()

◆ NoPipOn()

◆ PredictOff()

◆ PredictOn()

◆ RenderOutputBuffer()

◆ SetEnsemble()

◆ SetGpuId()

◆ SetMirror()

◆ SetMitkTempDir()

◆ SetMixedPrecision()

◆ SetModelDirectory()

◆ SetMultiModal()

◆ SetnnUNetDirectory()

◆ SetNoPip()

◆ SetOutputBuffer()

◆ SetPostProcessingJsonDirectory()

◆ SetPredict()

◆ SetPythonPath()

Member Data Documentation

◆ m_InputBuffer

◆ m_OtherModalPaths

◆ m_ParamQ