Helper segment editor logic for qMRMLSegmentEditorWidget and its associated effects. More...

#include <Modules/Loadable/Segmentations/Logic/vtkSlicerSegmentEditorLogic.h>

Inheritance diagram for vtkSlicerSegmentEditorLogic:

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Collaboration diagram for vtkSlicerSegmentEditorLogic:

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Public Types
enum	Events { SegmentationHistoryChangedEvent = vtkCommand::UserEvent + 1 , PauseRenderEvent , ResumeRenderEvent }

enum	ModificationMode { ModificationModeSet , ModificationModeAdd , ModificationModeRemove , ModificationModeRemoveAll }

typedef vtkMRMLAbstractLogic	Superclass

Public Types inherited from vtkMRMLAbstractLogic
typedef vtkObject	Superclass

typedef void(vtkMRMLAbstractLogic::*	TaskFunctionPointer) (void *clientdata)

Public Member Functions
std::string	AddEmptySegment (const std::string &segmentId="", int segmentStatus=0) const

bool	CanAddSegments () const

bool	CanRedo () const

bool	CanRemoveSegments () const

bool	CanTriviallyConvertSourceRepresentationToBinaryLabelMap () const

bool	CanUndo () const

void	ClearUndoState () const
	Clears the Undo/Redo history.

bool	ContainsClosedSurfaceRepresentation () const
	true if the current segmentation is valid and contains a closed surface representation

void	CreateAndSetBlankSourceVolumeFromSegmentationGeometry () const
	Creates a blank source volume matching the segmentation geometry. Usually called when no source volume is currently set.

void	CreateAndSetBlankSourceVolumeIfNeeded () const
	If no source volume is selected but a valid geometry is specified then create and store a blank source volume.

void	ExportSegmentationToColorTableNode () const
	Export the current segmentation to a new color table node.

vtkOrientedImageData *	GetAlignedSourceVolume () const
	Current aligned source volume.

virtual const char *	GetClassName ()

std::string	GetCurrentSegmentID () const

int	GetCurrentSegmentIndex () const
	Returns the current segmentation segment index. -1 if invalid.

std::string	GetDefaultTerminologyEntry () const
	Returns the terminology entry value used as default when adding empty segments.

vtkOrientedImageData *	GetMaskLabelmap () const
	Returns the current mask labelmap.

int	GetMaximumNumberOfUndoStates () const
	Get maximum number of saved undo/redo states.

vtkOrientedImageData *	GetModifierLabelmap () const
	Returns the current modifier label map.

std::string	GetNextSegmentID (int offset, bool visibleOnly) const
	Returns the segment ID at given offset.

vtkOrientedImageData *	GetReferenceGeometryImage () const
	Returns the current reference geometry image.

std::string	GetReferenceImageGeometryString () const
	Returns the current reference geometry string.

vtkSegmentation *	GetSegmentation () const
	Current segmentation associated with the segmentation node.

bool	GetSegmentationIJKToRAS (vtkMatrix4x4 *ijkToRas) const

vtkMRMLSegmentationNode *	GetSegmentationNode () const
	Get currently selected segmentation MRML node.

vtkMRMLSegmentEditorNode *	GetSegmentEditorNode () const
	Get the segment editor parameter set node.

std::vector< std::string >	GetSegmentIDs () const
	Return all the segment IDS present in the segmentation. Empty if invalid or no segment.

vtkSegment *	GetSelectedSegment () const
	Get the current segment. nullptr if invalid or no selection.

vtkOrientedImageData *	GetSelectedSegmentLabelmap () const
	Get the current segments labelmap.

double	GetSliceSpacing (vtkMRMLSliceNode *sliceNode) const
	Return the slice spacing matching the input slice node.

vtkMRMLScalarVolumeNode *	GetSourceVolumeNode () const
	Get the current volume node.

bool	GetVerbose () const
	Returns warning verbosity.

std::vector< std::string >	GetVisibleSegmentIDs () const
	Return all segment currently visible in any view.

virtual int	IsA (const char *type)

bool	IsSegmentationDisplayableInView (vtkMRMLAbstractViewNode *viewNode) const
	Return true if the current segmentation is displayed in the input view node. False if invalid segmentation or view node.

bool	IsSegmentationNodeValid () const
	Return true if the current segmentation node is valid.

bool	IsSegmentIdValid (const std::string &segmentId) const
	Return true when Segment ID is defined and present in the current segmentation.

bool	IsSegmentIdVisible (const std::string &segmentID) const
	Return true if the segment ID is visible in any view. False if not visible or invalid.

bool	IsSelectedSegmentVisible () const
	Return true if the current segment is visible in any view.

void	ModifySegmentByLabelmap (vtkMRMLSegmentationNode segmentationNode, const char segmentID, vtkOrientedImageData *modifierLabelmap, ModificationMode modificationMode, bool isPerSegment, bool bypassMasking)

void	ModifySegmentByLabelmap (vtkMRMLSegmentationNode segmentationNode, const char segmentID, vtkOrientedImageData *modifierLabelmap, ModificationMode modificationMode, const int modificationExtent[6], bool isPerSegment, bool bypassMasking)

void	PauseRender ()
	Trigger the PauseRenderEvent.

void	Redo () const
	Restores next saved state of the segmentation.

std::string	RemoveSelectedSegment () const
	Remove the current segment and return the following segment in the list if any valid.

bool	ResetModifierLabelmapToDefault () const

void	ResumeRender ()
	Trigger the ResumeRenderEvent.

bool	SaveStateForUndo () const

void	SelectFirstSegment (bool visibleOnly) const
	Selects the first segment in the current segmentation.

void	SelectNextSegment (bool visibleOnly) const
	Selects the next segment in the current segmentation.

void	SelectPreviousSegment (bool visibleOnly) const
	Selects the previous segment in the current segmentation.

void	SelectSegmentAtOffset (int offset, bool visibleOnly) const

void	SetCurrentSegmentID (const std::string &segmentID) const
	Set selected segment by its ID.

void	SetDefaultTerminologyEntry (const std::string &entry)
	Set the default terminology to use when adding new segments.

void	SetMaximumNumberOfUndoStates (int) const
	Set maximum number of saved undo/redo states.

void	SetSegmentationHistory (const vtkSmartPointer< vtkSegmentationHistory > &segmentationHistory)

void	SetSegmentationNode (vtkMRMLNode *node) const
	Set segmentation MRML node.

void	SetSegmentationNodeID (const std::string &nodeID) const
	Set segmentation MRML node by its ID.

void	SetSegmentEditorNode (vtkMRMLSegmentEditorNode *newSegmentEditorNode)
	Set the segment editor parameter set node.

bool	SetSourceRepresentationToBinaryLabelMap () const

void	SetSourceVolumeNode (vtkMRMLNode *node) const

void	SetSourceVolumeNodeID (const std::string &nodeID) const
	Set source volume MRML node by its ID.

void	SetVerbose (bool isVerbose)

void	ToggleSegmentationSurfaceRepresentation (bool isSurfaceRepresentationOn) const
	Create/remove closed surface model for the segmentation that is automatically updated when editing.

void	ToggleSourceVolumeIntensityMask () const
	Toggle the intensity mask currently set on the segmentation.

bool	TrivialSetSourceRepresentationToBinaryLabelmap () const

void	Undo () const
	Restores previous saved state of the segmentation.

bool	UpdateAlignedSourceVolume ()
	Updates a resampled source volume in a geometry aligned with default modifierLabelmap.

bool	UpdateMaskLabelmap () const

bool	UpdateReferenceGeometryImage () const
	Update the reference geometry image to the current segmentation.

bool	UpdateSelectedSegmentLabelmap () const
	Updates selected segment labelmap in a geometry aligned with default modifierLabelmap.

void	UpdateVolume (void *volumeToUpdate, bool &success)

Public Member Functions inherited from vtkMRMLAbstractLogic
virtual vtkMRMLApplicationLogic *	GetMRMLApplicationLogic () const
	Get access to overall application state.

vtkMRMLScene *	GetMRMLScene () const
	Return a reference to the current MRML scene.

void	PrintSelf (ostream &os, vtkIndent indent) override

virtual void	SetMRMLApplicationLogic (vtkMRMLApplicationLogic *logic)

void	SetMRMLScene (vtkMRMLScene *newScene)
	Set and observe the MRMLScene.

Static Public Member Functions
static void	AppendImage (vtkOrientedImageData inputImage, vtkOrientedImageData appendedImage)
	Append image onto image. Resamples appended image and saves result in input image.

static void	AppendPolyMask (vtkOrientedImageData input, vtkPolyData polyData, vtkMRMLSliceNode sliceNode, vtkMRMLSegmentationNode segmentationNode=nullptr)
	Rasterize a poly data onto the input image into the slice view.

static void	CreateMaskImageFromPolyData (vtkPolyData polyData, vtkOrientedImageData outputMask, vtkMRMLSliceNode *sliceNode)
	Create a slice view screen space (2D) mask image for the given polydata.

static std::string	GetReferenceImageGeometryStringFromSegmentation (vtkSegmentation *segmentation)
	Returns the reference geometry string matching the input segmentation.

static double	GetSliceSpacing (vtkMRMLSliceNode sliceNode, vtkMRMLSliceLogic sliceLogic)

static void	ImageToWorldMatrix (vtkMRMLVolumeNode node, vtkMatrix4x4 ijkToRas)

static void	ImageToWorldMatrix (vtkOrientedImageData image, vtkMRMLSegmentationNode node, vtkMatrix4x4 *ijkToRas)

static bool	IsSegmentIdInList (const std::string &segmentID, const std::vector< std::string > &visibleSegmentIDs)
	Return true if the segment ID is present in the input list.

static int	IsTypeOf (const char *type)

static vtkSlicerSegmentEditorLogic *	New ()

static std::array< int, 2 >	RasToXy (double ras[3], vtkMRMLSliceNode *sliceNode)
	Convert RAS position to XY in-slice position.

static vtkSlicerSegmentEditorLogic *	SafeDownCast (vtkObject *o)

static void	XyToIjk (double xy[2], int outputIjk[3], vtkMRMLSliceNode sliceNode, vtkOrientedImageData image, vtkMRMLTransformNode *parentTransform=nullptr)
	Convert XY in-slice position to image IJK position.

static void	XyToIjk (int xy[2], int outputIjk[3], vtkMRMLSliceNode sliceNode, vtkOrientedImageData image, vtkMRMLTransformNode *parentTransform=nullptr)
	Convert XY in-slice position to image IJK position.

static std::array< int, 3 >	XyToIjk (int xy[2], vtkMRMLSliceNode sliceNode, vtkOrientedImageData image, vtkMRMLTransformNode *parentTransform=nullptr)
	Convert XY in-slice position to image IJK position, python accessor method.

static void	XyToRas (double xy[2], double outputRas[3], vtkMRMLSliceNode *sliceNode)
	Convert XY in-slice position to RAS position.

static void	XyToRas (int xy[2], double outputRas[3], vtkMRMLSliceNode *sliceNode)
	Convert XY in-slice position to RAS position.

static std::array< double, 3 >	XyToRas (int xy[2], vtkMRMLSliceNode *sliceNode)
	Convert XY in-slice position to RAS position, python accessor method.

static void	XyzToIjk (double inputXyz[3], int outputIjk[3], vtkMRMLSliceNode sliceNode, vtkOrientedImageData image, vtkMRMLTransformNode *parentTransform=nullptr)
	Convert XYZ slice view position to image IJK position,.

static std::array< int, 3 >	XyzToIjk (double inputXyz[3], vtkMRMLSliceNode sliceNode, vtkOrientedImageData image, vtkMRMLTransformNode *parentTransform=nullptr)
	Convert XYZ slice view position to image IJK position, python accessor method,.

static void	XyzToRas (double inputXyz[3], double outputRas[3], vtkMRMLSliceNode *sliceNode)

static std::array< double, 3 >	XyzToRas (double inputXyz[3], vtkMRMLSliceNode *sliceNode)

Static Public Member Functions inherited from vtkMRMLAbstractLogic
static int	IsTypeOf (const char *type)

static vtkMRMLAbstractLogic *	New ()

static vtkMRMLAbstractLogic *	SafeDownCast (vtkObject *o)

Protected Member Functions
void	ProcessMRMLNodesEvents (vtkObject caller, unsigned long event, void callData) override
	Update segment editor node, segmentation node and segment history observers.

	vtkSlicerSegmentEditorLogic ()

	~vtkSlicerSegmentEditorLogic () override

Protected Member Functions inherited from vtkMRMLAbstractLogic
int	EndModify (bool wasModifying)

virtual bool	EnterMRMLLogicsCallback () const

virtual bool	EnterMRMLNodesCallback () const

virtual bool	EnterMRMLSceneCallback () const

bool	GetDisableModifiedEvent () const

int	GetInMRMLLogicsCallbackFlag () const

int	GetInMRMLNodesCallbackFlag () const

int	GetInMRMLSceneCallbackFlag () const

vtkCallbackCommand *	GetMRMLLogicsCallbackCommand ()

vtkObserverManager *	GetMRMLLogicsObserverManager () const

vtkCallbackCommand *	GetMRMLNodesCallbackCommand ()

vtkObserverManager *	GetMRMLNodesObserverManager () const

vtkCallbackCommand *	GetMRMLSceneCallbackCommand ()

vtkObserverManager *	GetMRMLSceneObserverManager () const

int	GetPendingModifiedEventCount () const

int	GetProcessingMRMLSceneEvent () const
	Return the event id currently processed or 0 if any.

int	InvokePendingModifiedEvent ()

void	Modified () override

virtual void	ObserveMRMLScene ()

virtual void	OnMRMLNodeModified (vtkMRMLNode *)

virtual void	OnMRMLSceneEndBatchProcess ()

virtual void	OnMRMLSceneEndClose ()

virtual void	OnMRMLSceneEndImport ()

virtual void	OnMRMLSceneEndRestore ()

virtual void	OnMRMLSceneNew ()

virtual void	OnMRMLSceneNodeAdded (vtkMRMLNode *)

virtual void	OnMRMLSceneNodeRemoved (vtkMRMLNode *)

virtual void	OnMRMLSceneStartBatchProcess ()

virtual void	OnMRMLSceneStartClose ()

virtual void	OnMRMLSceneStartImport ()

virtual void	OnMRMLSceneStartRestore ()

virtual void	ProcessMRMLLogicsEvents (vtkObject caller, unsigned long event, void callData)

virtual void	ProcessMRMLSceneEvents (vtkObject caller, unsigned long event, void callData)

virtual void	RegisterNodes ()

void	SetAndObserveMRMLSceneEventsInternal (vtkMRMLScene newScene, vtkIntArray events, vtkFloatArray *priorities=nullptr)

void	SetDisableModifiedEvent (bool onOff)

void	SetInMRMLLogicsCallbackFlag (int flag)

void	SetInMRMLNodesCallbackFlag (int flag)

void	SetInMRMLSceneCallbackFlag (int flag)

virtual void	SetMRMLSceneInternal (vtkMRMLScene *newScene)

void	SetProcessingMRMLSceneEvent (int event)

bool	StartModify ()

virtual void	UnobserveMRMLScene ()

virtual void	UpdateFromMRMLScene ()

	vtkMRMLAbstractLogic ()

	~vtkMRMLAbstractLogic () override

Additional Inherited Members
Static Protected Member Functions inherited from vtkMRMLAbstractLogic
static void	MRMLLogicsCallback (vtkObject caller, unsigned long eid, void clientData, void *callData)
	MRMLLogicCallback is a static function to relay modified events from the logics.

static void	MRMLNodesCallback (vtkObject caller, unsigned long eid, void clientData, void *callData)
	MRMLNodesCallback is a static function to relay modified events from the nodes.

static void	MRMLSceneCallback (vtkObject caller, unsigned long eid, void clientData, void *callData)

Detailed Description

Helper segment editor logic for qMRMLSegmentEditorWidget and its associated effects.

Provides common logic to access and modify the segmentation.

Definition at line 62 of file vtkSlicerSegmentEditorLogic.h.

Member Typedef Documentation

◆ Superclass

typedef vtkMRMLAbstractLogic vtkSlicerSegmentEditorLogic::Superclass

Definition at line 66 of file vtkSlicerSegmentEditorLogic.h.

Member Enumeration Documentation

◆ Events

enum vtkSlicerSegmentEditorLogic::Events

Enumerator
SegmentationHistoryChangedEvent
PauseRenderEvent
ResumeRenderEvent

Definition at line 76 of file vtkSlicerSegmentEditorLogic.h.

◆ ModificationMode

enum vtkSlicerSegmentEditorLogic::ModificationMode

Enumerator
ModificationModeSet
ModificationModeAdd
ModificationModeRemove
ModificationModeRemoveAll

Definition at line 68 of file vtkSlicerSegmentEditorLogic.h.

Constructor & Destructor Documentation

◆ vtkSlicerSegmentEditorLogic()

vtkSlicerSegmentEditorLogic::vtkSlicerSegmentEditorLogic ( )

protected

◆ ~vtkSlicerSegmentEditorLogic()

vtkSlicerSegmentEditorLogic::~vtkSlicerSegmentEditorLogic ( )

overrideprotected

Member Function Documentation

◆ AddEmptySegment()

std::string vtkSlicerSegmentEditorLogic::AddEmptySegment	(	const std::string &	segmentId = "",
		int	segmentStatus = 0 ) const

Add empty segment in the current segmentation node

Parameters

segmentId	ID of added segment. If empty then a default unique ID will be generated.
segmentStatus	Status of added segment from

See also: vtkSlicerSegmentationsModuleLogic::SegmentStatus. Default: NotStarted

Returns: ID of the added segment if successful. Empty string otherwise.

◆ AppendImage()

static void vtkSlicerSegmentEditorLogic::AppendImage	(	vtkOrientedImageData *	inputImage,
		vtkOrientedImageData *	appendedImage )

static

Append image onto image. Resamples appended image and saves result in input image.

◆ AppendPolyMask()

static void vtkSlicerSegmentEditorLogic::AppendPolyMask	(	vtkOrientedImageData *	input,
		vtkPolyData *	polyData,
		vtkMRMLSliceNode *	sliceNode,
		vtkMRMLSegmentationNode *	segmentationNode = nullptr )

static

Rasterize a poly data onto the input image into the slice view.

◆ CanAddSegments()

bool vtkSlicerSegmentEditorLogic::CanAddSegments ( ) const

Returns: true if volume, segmentation and reference geometry are defined

◆ CanRedo()

bool vtkSlicerSegmentEditorLogic::CanRedo ( ) const

Returns: true if segmentation history has at least one state to redo

◆ CanRemoveSegments()

bool vtkSlicerSegmentEditorLogic::CanRemoveSegments ( ) const

Returns: true if current selected segment ID is valid

See also: IsSegmentIDValid

◆ CanTriviallyConvertSourceRepresentationToBinaryLabelMap()

bool vtkSlicerSegmentEditorLogic::CanTriviallyConvertSourceRepresentationToBinaryLabelMap ( ) const

Returns: true if the current segmentation is empty or is already set to binary label map

◆ CanUndo()

bool vtkSlicerSegmentEditorLogic::CanUndo ( ) const

Returns: true if the segmentation history has at least one state

◆ ClearUndoState()

void vtkSlicerSegmentEditorLogic::ClearUndoState ( ) const

Clears the Undo/Redo history.

◆ ContainsClosedSurfaceRepresentation()

bool vtkSlicerSegmentEditorLogic::ContainsClosedSurfaceRepresentation ( ) const

true if the current segmentation is valid and contains a closed surface representation

◆ CreateAndSetBlankSourceVolumeFromSegmentationGeometry()

void vtkSlicerSegmentEditorLogic::CreateAndSetBlankSourceVolumeFromSegmentationGeometry ( ) const

Creates a blank source volume matching the segmentation geometry. Usually called when no source volume is currently set.

◆ CreateAndSetBlankSourceVolumeIfNeeded()

void vtkSlicerSegmentEditorLogic::CreateAndSetBlankSourceVolumeIfNeeded ( ) const

If no source volume is selected but a valid geometry is specified then create and store a blank source volume.

◆ CreateMaskImageFromPolyData()

static void vtkSlicerSegmentEditorLogic::CreateMaskImageFromPolyData	(	vtkPolyData *	polyData,
		vtkOrientedImageData *	outputMask,
		vtkMRMLSliceNode *	sliceNode )

static

Create a slice view screen space (2D) mask image for the given polydata.

◆ ExportSegmentationToColorTableNode()

void vtkSlicerSegmentEditorLogic::ExportSegmentationToColorTableNode ( ) const

Export the current segmentation to a new color table node.

◆ GetAlignedSourceVolume()

vtkOrientedImageData * vtkSlicerSegmentEditorLogic::GetAlignedSourceVolume ( ) const

Current aligned source volume.

◆ GetClassName()

virtual const char * vtkSlicerSegmentEditorLogic::GetClassName ( )

virtual

Reimplemented from vtkMRMLAbstractLogic.

◆ GetCurrentSegmentID()

std::string vtkSlicerSegmentEditorLogic::GetCurrentSegmentID ( ) const

Get segment ID of selected segment

See also: GetSelectedSegmentID

◆ GetCurrentSegmentIndex()

int vtkSlicerSegmentEditorLogic::GetCurrentSegmentIndex ( ) const

Returns the current segmentation segment index. -1 if invalid.

◆ GetDefaultTerminologyEntry()

std::string vtkSlicerSegmentEditorLogic::GetDefaultTerminologyEntry ( ) const

Returns the terminology entry value used as default when adding empty segments.

◆ GetMaskLabelmap()

vtkOrientedImageData * vtkSlicerSegmentEditorLogic::GetMaskLabelmap ( ) const

Returns the current mask labelmap.

◆ GetMaximumNumberOfUndoStates()

int vtkSlicerSegmentEditorLogic::GetMaximumNumberOfUndoStates ( ) const

Get maximum number of saved undo/redo states.

◆ GetModifierLabelmap()

vtkOrientedImageData * vtkSlicerSegmentEditorLogic::GetModifierLabelmap ( ) const

Returns the current modifier label map.

◆ GetNextSegmentID()

std::string vtkSlicerSegmentEditorLogic::GetNextSegmentID	(	int	offset,
		bool	visibleOnly ) const

Returns the segment ID at given offset.

Parameters

offset	Either a positive or negative offset value
visibleOnly	if true, offset will represent the number of visible segments skipped.

Returns: Segment ID or empty string if segmentation is invalid or offset out of range.

◆ GetReferenceGeometryImage()

vtkOrientedImageData * vtkSlicerSegmentEditorLogic::GetReferenceGeometryImage ( ) const

Returns the current reference geometry image.

◆ GetReferenceImageGeometryString()

std::string vtkSlicerSegmentEditorLogic::GetReferenceImageGeometryString ( ) const

Returns the current reference geometry string.

◆ GetReferenceImageGeometryStringFromSegmentation()

static std::string vtkSlicerSegmentEditorLogic::GetReferenceImageGeometryStringFromSegmentation ( vtkSegmentation * segmentation )

static

Returns the reference geometry string matching the input segmentation.

◆ GetSegmentation()

vtkSegmentation * vtkSlicerSegmentEditorLogic::GetSegmentation ( ) const

Current segmentation associated with the segmentation node.

See also: GetSegmentationNode

◆ GetSegmentationIJKToRAS()

bool vtkSlicerSegmentEditorLogic::GetSegmentationIJKToRAS ( vtkMatrix4x4 * ijkToRas ) const

Return segmentation node's internal labelmap IJK to renderer world coordinate transform. If cannot be retrieved (segmentation is not defined, non-linearly transformed, etc.) then false is returned;

◆ GetSegmentationNode()

vtkMRMLSegmentationNode * vtkSlicerSegmentEditorLogic::GetSegmentationNode ( ) const

Get currently selected segmentation MRML node.

◆ GetSegmentEditorNode()

vtkMRMLSegmentEditorNode * vtkSlicerSegmentEditorLogic::GetSegmentEditorNode ( ) const

Get the segment editor parameter set node.

◆ GetSegmentIDs()

std::vector< std::string > vtkSlicerSegmentEditorLogic::GetSegmentIDs ( ) const

Return all the segment IDS present in the segmentation. Empty if invalid or no segment.

◆ GetSelectedSegment()

vtkSegment * vtkSlicerSegmentEditorLogic::GetSelectedSegment ( ) const

Get the current segment. nullptr if invalid or no selection.

◆ GetSelectedSegmentLabelmap()

vtkOrientedImageData * vtkSlicerSegmentEditorLogic::GetSelectedSegmentLabelmap ( ) const

Get the current segments labelmap.

◆ GetSliceSpacing() [1/2]

double vtkSlicerSegmentEditorLogic::GetSliceSpacing ( vtkMRMLSliceNode * sliceNode ) const

Return the slice spacing matching the input slice node.

◆ GetSliceSpacing() [2/2]

static double vtkSlicerSegmentEditorLogic::GetSliceSpacing	(	vtkMRMLSliceNode *	sliceNode,
		vtkMRMLSliceLogic *	sliceLogic )

static

◆ GetSourceVolumeNode()

vtkMRMLScalarVolumeNode * vtkSlicerSegmentEditorLogic::GetSourceVolumeNode ( ) const

Get the current volume node.

◆ GetVerbose()

bool vtkSlicerSegmentEditorLogic::GetVerbose ( ) const

Returns warning verbosity.

◆ GetVisibleSegmentIDs()

std::vector< std::string > vtkSlicerSegmentEditorLogic::GetVisibleSegmentIDs ( ) const

Return all segment currently visible in any view.

◆ ImageToWorldMatrix() [1/2]

static void vtkSlicerSegmentEditorLogic::ImageToWorldMatrix	(	vtkMRMLVolumeNode *	node,
		vtkMatrix4x4 *	ijkToRas )

static

Return matrix for volume node that takes into account the IJKToRAS and any linear transforms that have been applied

◆ ImageToWorldMatrix() [2/2]

static void vtkSlicerSegmentEditorLogic::ImageToWorldMatrix	(	vtkOrientedImageData *	image,
		vtkMRMLSegmentationNode *	node,
		vtkMatrix4x4 *	ijkToRas )

static

Return matrix for oriented image data that takes into account the image to world and any linear transforms that have been applied on the given segmentation

◆ IsA()

virtual int vtkSlicerSegmentEditorLogic::IsA ( const char * type )

virtual

Reimplemented from vtkMRMLAbstractLogic.

◆ IsSegmentationDisplayableInView()

bool vtkSlicerSegmentEditorLogic::IsSegmentationDisplayableInView ( vtkMRMLAbstractViewNode * viewNode ) const

Return true if the current segmentation is displayed in the input view node. False if invalid segmentation or view node.

◆ IsSegmentationNodeValid()

bool vtkSlicerSegmentEditorLogic::IsSegmentationNodeValid ( ) const

Return true if the current segmentation node is valid.

◆ IsSegmentIdInList()

static bool vtkSlicerSegmentEditorLogic::IsSegmentIdInList	(	const std::string &	segmentID,
		const std::vector< std::string > &	visibleSegmentIDs )

static

Return true if the segment ID is present in the input list.

◆ IsSegmentIdValid()

bool vtkSlicerSegmentEditorLogic::IsSegmentIdValid ( const std::string & segmentId ) const

Return true when Segment ID is defined and present in the current segmentation.

◆ IsSegmentIdVisible()

bool vtkSlicerSegmentEditorLogic::IsSegmentIdVisible ( const std::string & segmentID ) const

Return true if the segment ID is visible in any view. False if not visible or invalid.

◆ IsSelectedSegmentVisible()

bool vtkSlicerSegmentEditorLogic::IsSelectedSegmentVisible ( ) const

Return true if the current segment is visible in any view.

◆ IsTypeOf()

static int vtkSlicerSegmentEditorLogic::IsTypeOf ( const char * type )

static

◆ ModifySegmentByLabelmap() [1/2]

void vtkSlicerSegmentEditorLogic::ModifySegmentByLabelmap	(	vtkMRMLSegmentationNode *	segmentationNode,
		const char *	segmentID,
		vtkOrientedImageData *	modifierLabelmap,
		ModificationMode	modificationMode,
		bool	isPerSegment,
		bool	bypassMasking )

◆ ModifySegmentByLabelmap() [2/2]

void vtkSlicerSegmentEditorLogic::ModifySegmentByLabelmap	(	vtkMRMLSegmentationNode *	segmentationNode,
		const char *	segmentID,
		vtkOrientedImageData *	modifierLabelmap,
		ModificationMode	modificationMode,
		const int	modificationExtent[6],
		bool	isPerSegment,
		bool	bypassMasking )

◆ New()

static vtkSlicerSegmentEditorLogic * vtkSlicerSegmentEditorLogic::New ( )

static

◆ PauseRender()

void vtkSlicerSegmentEditorLogic::PauseRender ( )

Trigger the PauseRenderEvent.

◆ ProcessMRMLNodesEvents()

void vtkSlicerSegmentEditorLogic::ProcessMRMLNodesEvents	(	vtkObject *	caller,
		unsigned long	event,
		void *	callData )

overrideprotectedvirtual

Update segment editor node, segmentation node and segment history observers.

Reimplemented from vtkMRMLAbstractLogic.

◆ RasToXy()

static std::array< int, 2 > vtkSlicerSegmentEditorLogic::RasToXy	(	double	ras[3],
		vtkMRMLSliceNode *	sliceNode )

static

Convert RAS position to XY in-slice position.

◆ Redo()

void vtkSlicerSegmentEditorLogic::Redo ( ) const

Restores next saved state of the segmentation.

◆ RemoveSelectedSegment()

std::string vtkSlicerSegmentEditorLogic::RemoveSelectedSegment ( ) const

Remove the current segment and return the following segment in the list if any valid.

◆ ResetModifierLabelmapToDefault()

bool vtkSlicerSegmentEditorLogic::ResetModifierLabelmapToDefault ( ) const

Updates default modifier labelmap based on reference geometry (to set origin, spacing, and directions) and existing segments (to set extents). If reference geometry conversion parameter is empty then existing segments are used for determining origin, spacing, and directions and the resulting geometry is written to reference geometry conversion parameter.

◆ ResumeRender()

void vtkSlicerSegmentEditorLogic::ResumeRender ( )

Trigger the ResumeRenderEvent.

◆ SafeDownCast()

static vtkSlicerSegmentEditorLogic * vtkSlicerSegmentEditorLogic::SafeDownCast ( vtkObject * o )

static

◆ SaveStateForUndo()

bool vtkSlicerSegmentEditorLogic::SaveStateForUndo ( ) const

Save current segmentation before performing an edit operation to allow reverting to the current state by using undo

◆ SelectFirstSegment()

void vtkSlicerSegmentEditorLogic::SelectFirstSegment ( bool visibleOnly ) const

Selects the first segment in the current segmentation.

◆ SelectNextSegment()

void vtkSlicerSegmentEditorLogic::SelectNextSegment ( bool visibleOnly ) const

Selects the next segment in the current segmentation.

◆ SelectPreviousSegment()

void vtkSlicerSegmentEditorLogic::SelectPreviousSegment ( bool visibleOnly ) const

Selects the previous segment in the current segmentation.

◆ SelectSegmentAtOffset()

void vtkSlicerSegmentEditorLogic::SelectSegmentAtOffset	(	int	offset,
		bool	visibleOnly ) const

Select the segment offset from the currently selected one Positive offset will move down the segmentation list Negative offset will move up the segmentation list

◆ SetCurrentSegmentID()

void vtkSlicerSegmentEditorLogic::SetCurrentSegmentID ( const std::string & segmentID ) const

Set selected segment by its ID.

◆ SetDefaultTerminologyEntry()

void vtkSlicerSegmentEditorLogic::SetDefaultTerminologyEntry ( const std::string & entry )

Set the default terminology to use when adding new segments.

◆ SetMaximumNumberOfUndoStates()

void vtkSlicerSegmentEditorLogic::SetMaximumNumberOfUndoStates ( int ) const

Set maximum number of saved undo/redo states.

◆ SetSegmentationHistory()

void vtkSlicerSegmentEditorLogic::SetSegmentationHistory ( const vtkSmartPointer< vtkSegmentationHistory > & segmentationHistory )

Set the segmentation history By default, the logic creates and uses an empty segmentation history at creation.

◆ SetSegmentationNode()

void vtkSlicerSegmentEditorLogic::SetSegmentationNode ( vtkMRMLNode * node ) const

Set segmentation MRML node.

◆ SetSegmentationNodeID()

void vtkSlicerSegmentEditorLogic::SetSegmentationNodeID ( const std::string & nodeID ) const

Set segmentation MRML node by its ID.

◆ SetSegmentEditorNode()

void vtkSlicerSegmentEditorLogic::SetSegmentEditorNode ( vtkMRMLSegmentEditorNode * newSegmentEditorNode )

Set the segment editor parameter set node.

◆ SetSourceRepresentationToBinaryLabelMap()

bool vtkSlicerSegmentEditorLogic::SetSourceRepresentationToBinaryLabelMap ( ) const

Sets the source representation to binary labelmap. This method will convert any representation currently stored in the segmentation. User confirmation should be requested before this operation.

See also: CanTriviallyConvertSourceRepresentationToBinaryLabelMap; TrivialSetSourceRepresentationToBinaryLabelmap

◆ SetSourceVolumeNode()

void vtkSlicerSegmentEditorLogic::SetSourceVolumeNode ( vtkMRMLNode * node ) const

Set source volume MRML node. If source volume has multiple scalar components then only the first scalar component is used.

◆ SetSourceVolumeNodeID()

void vtkSlicerSegmentEditorLogic::SetSourceVolumeNodeID ( const std::string & nodeID ) const

Set source volume MRML node by its ID.

◆ SetVerbose()

void vtkSlicerSegmentEditorLogic::SetVerbose ( bool isVerbose )

Sets the warning verbosity. If verbose = False instance methods don't emit vtkWarnings. Default: Verbose = False.

◆ ToggleSegmentationSurfaceRepresentation()

void vtkSlicerSegmentEditorLogic::ToggleSegmentationSurfaceRepresentation ( bool isSurfaceRepresentationOn ) const

Create/remove closed surface model for the segmentation that is automatically updated when editing.

◆ ToggleSourceVolumeIntensityMask()

void vtkSlicerSegmentEditorLogic::ToggleSourceVolumeIntensityMask ( ) const

Toggle the intensity mask currently set on the segmentation.

◆ TrivialSetSourceRepresentationToBinaryLabelmap()

bool vtkSlicerSegmentEditorLogic::TrivialSetSourceRepresentationToBinaryLabelmap ( ) const

Set source representation to binary label map. Should be called only when

See also: CanTriviallyConvertSourceRepresentationToBinaryLabelMap is true. This method will not update any close surface representation or display if they already exist.; SetSourceRepresentationToBinaryLabelMap

◆ Undo()

void vtkSlicerSegmentEditorLogic::Undo ( ) const

Restores previous saved state of the segmentation.

◆ UpdateAlignedSourceVolume()

bool vtkSlicerSegmentEditorLogic::UpdateAlignedSourceVolume ( )

Updates a resampled source volume in a geometry aligned with default modifierLabelmap.

◆ UpdateMaskLabelmap()

bool vtkSlicerSegmentEditorLogic::UpdateMaskLabelmap ( ) const

Updates mask labelmap. Geometry of mask will be the same as current modifierLabelmap. This mask only considers segment-based regions (and ignores masking based on source volume intensity).

◆ UpdateReferenceGeometryImage()

bool vtkSlicerSegmentEditorLogic::UpdateReferenceGeometryImage ( ) const

Update the reference geometry image to the current segmentation.

◆ UpdateSelectedSegmentLabelmap()

bool vtkSlicerSegmentEditorLogic::UpdateSelectedSegmentLabelmap ( ) const

Updates selected segment labelmap in a geometry aligned with default modifierLabelmap.

◆ UpdateVolume()

void vtkSlicerSegmentEditorLogic::UpdateVolume	(	void *	volumeToUpdate,
		bool &	success )

Update the input volume if the pointer matches one of :

See also: GetAlignedSourceVolume; GetModifierLabelmap; GetMaskLabelmap; GetSelectedSegmentLabelmap; GetReferenceGeometryImage

◆ XyToIjk() [1/3]

static void vtkSlicerSegmentEditorLogic::XyToIjk	(	double	xy[2],
		int	outputIjk[3],
		vtkMRMLSliceNode *	sliceNode,
		vtkOrientedImageData *	image,
		vtkMRMLTransformNode *	parentTransform = nullptr )

static

Convert XY in-slice position to image IJK position.

◆ XyToIjk() [2/3]

static void vtkSlicerSegmentEditorLogic::XyToIjk	(	int	xy[2],
		int	outputIjk[3],
		vtkMRMLSliceNode *	sliceNode,
		vtkOrientedImageData *	image,
		vtkMRMLTransformNode *	parentTransform = nullptr )

static

Convert XY in-slice position to image IJK position.

◆ XyToIjk() [3/3]

static std::array< int, 3 > vtkSlicerSegmentEditorLogic::XyToIjk	(	int	xy[2],
		vtkMRMLSliceNode *	sliceNode,
		vtkOrientedImageData *	image,
		vtkMRMLTransformNode *	parentTransform = nullptr )

static

Convert XY in-slice position to image IJK position, python accessor method.

◆ XyToRas() [1/3]

static void vtkSlicerSegmentEditorLogic::XyToRas	(	double	xy[2],
		double	outputRas[3],
		vtkMRMLSliceNode *	sliceNode )

static

Convert XY in-slice position to RAS position.

◆ XyToRas() [2/3]

static void vtkSlicerSegmentEditorLogic::XyToRas	(	int	xy[2],
		double	outputRas[3],
		vtkMRMLSliceNode *	sliceNode )

static

Convert XY in-slice position to RAS position.

◆ XyToRas() [3/3]

static std::array< double, 3 > vtkSlicerSegmentEditorLogic::XyToRas	(	int	xy[2],
		vtkMRMLSliceNode *	sliceNode )

static

Convert XY in-slice position to RAS position, python accessor method.

◆ XyzToIjk() [1/2]

static void vtkSlicerSegmentEditorLogic::XyzToIjk	(	double	inputXyz[3],
		int	outputIjk[3],
		vtkMRMLSliceNode *	sliceNode,
		vtkOrientedImageData *	image,
		vtkMRMLTransformNode *	parentTransform = nullptr )

static

Convert XYZ slice view position to image IJK position,.

See also: xyzToRas

◆ XyzToIjk() [2/2]

static std::array< int, 3 > vtkSlicerSegmentEditorLogic::XyzToIjk	(	double	inputXyz[3],
		vtkMRMLSliceNode *	sliceNode,
		vtkOrientedImageData *	image,
		vtkMRMLTransformNode *	parentTransform = nullptr )

static

Convert XYZ slice view position to image IJK position, python accessor method,.

See also: xyzToRas

◆ XyzToRas() [1/2]

static void vtkSlicerSegmentEditorLogic::XyzToRas	(	double	inputXyz[3],
		double	outputRas[3],
		vtkMRMLSliceNode *	sliceNode )

static

Convert XYZ slice view position to RAS position: x,y uses slice (canvas) coordinate system and actually has a 3rd z component (index into the slice you're looking at), hence xyToRAS is really performing xyzToRAS. RAS is patient world coordinate system. Note the 1 is because the transform uses homogeneous coordinates.

◆ XyzToRas() [2/2]

static std::array< double, 3 > vtkSlicerSegmentEditorLogic::XyzToRas	(	double	inputXyz[3],
		vtkMRMLSliceNode *	sliceNode )

static

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

Modules/Loadable/Segmentations/Logic/vtkSlicerSegmentEditorLogic.h

Public Types

Public Member Functions

Static Public Member Functions

Protected Member Functions

Additional Inherited Members

Detailed Description

Member Typedef Documentation

◆ Superclass

Member Enumeration Documentation

◆ Events

◆ ModificationMode

Constructor & Destructor Documentation

◆ vtkSlicerSegmentEditorLogic()

◆ ~vtkSlicerSegmentEditorLogic()

Member Function Documentation

◆ AddEmptySegment()

◆ AppendImage()

◆ AppendPolyMask()

◆ CanAddSegments()

◆ CanRedo()

◆ CanRemoveSegments()

◆ CanTriviallyConvertSourceRepresentationToBinaryLabelMap()

◆ CanUndo()

◆ ClearUndoState()

◆ ContainsClosedSurfaceRepresentation()

◆ CreateAndSetBlankSourceVolumeFromSegmentationGeometry()

◆ CreateAndSetBlankSourceVolumeIfNeeded()

◆ CreateMaskImageFromPolyData()

◆ ExportSegmentationToColorTableNode()

◆ GetAlignedSourceVolume()

◆ GetClassName()

◆ GetCurrentSegmentID()

◆ GetCurrentSegmentIndex()

◆ GetDefaultTerminologyEntry()

◆ GetMaskLabelmap()

◆ GetMaximumNumberOfUndoStates()

◆ GetModifierLabelmap()

◆ GetNextSegmentID()

◆ GetReferenceGeometryImage()

◆ GetReferenceImageGeometryString()

◆ GetReferenceImageGeometryStringFromSegmentation()

◆ GetSegmentation()

◆ GetSegmentationIJKToRAS()

◆ GetSegmentationNode()

◆ GetSegmentEditorNode()

◆ GetSegmentIDs()

◆ GetSelectedSegment()

◆ GetSelectedSegmentLabelmap()

◆ GetSliceSpacing() [1/2]

◆ GetSliceSpacing() [2/2]

◆ GetSourceVolumeNode()

◆ GetVerbose()

◆ GetVisibleSegmentIDs()

◆ ImageToWorldMatrix() [1/2]

◆ ImageToWorldMatrix() [2/2]

◆ IsA()

◆ IsSegmentationDisplayableInView()

◆ IsSegmentationNodeValid()

◆ IsSegmentIdInList()

◆ IsSegmentIdValid()

◆ IsSegmentIdVisible()

◆ IsSelectedSegmentVisible()

◆ IsTypeOf()

◆ ModifySegmentByLabelmap() [1/2]

◆ ModifySegmentByLabelmap() [2/2]

◆ New()

◆ PauseRender()

◆ ProcessMRMLNodesEvents()

◆ RasToXy()

◆ Redo()

◆ RemoveSelectedSegment()

◆ ResetModifierLabelmapToDefault()

◆ ResumeRender()

◆ SafeDownCast()

◆ SaveStateForUndo()

◆ SelectFirstSegment()

◆ SelectNextSegment()

◆ SelectPreviousSegment()

◆ SelectSegmentAtOffset()

◆ SetCurrentSegmentID()