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

Inheritance diagram for vtkSlicerSegmentationsModuleLogic:

Collaboration diagram for vtkSlicerSegmentationsModuleLogic:

Public Types
enum	{ MODE_REPLACE = 0, MODE_MERGE_MAX, MODE_MERGE_MIN }

typedef vtkSlicerModuleLogic	Superclass

Public Types inherited from vtkSlicerModuleLogic
typedef vtkMRMLAbstractLogic	Superclass

Public Types inherited from vtkMRMLAbstractLogic
typedef vtkObject	Superclass

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

Public Member Functions
virtual const char *	GetClassName ()

vtkMRMLSegmentationNode *	GetDefaultSegmentationNode ()
	Get default segmentation node. All new segmentation nodes are initialized to the content of this node. More...

bool	GetDefaultSurfaceSmoothingEnabled ()
	Get/Set default closed surface smoothing enabled flag for new segmentation nodes. More...

bool	ImportLabelmapToSegmentationNodeWithTerminology (vtkMRMLLabelMapVolumeNode labelmapNode, vtkMRMLSegmentationNode segmentationNode, std::string terminologyContextName, std::string insertBeforeSegmentId="")

virtual int	IsA (const char *type)

vtkMRMLSegmentationNode *	LoadSegmentationFromFile (const char *filename, bool autoOpacities=true)

void	PrintSelf (ostream &os, vtkIndent indent) VTK_OVERRIDE

void	SetDefaultSurfaceSmoothingEnabled (bool enabled)

void	SetTerminologiesLogic (vtkSlicerTerminologiesModuleLogic *terminologiesLogic)
	Set Terminologies module logic. More...

bool	SetTerminologyToSegmentationFromLabelmapNode (vtkMRMLSegmentationNode segmentationNode, vtkMRMLLabelMapVolumeNode labelmapNode, std::string terminologyContextName)

Public Member Functions inherited from vtkSlicerModuleLogic
virtual vtkSlicerApplicationLogic *	GetApplicationLogic ()
	Get access to overall application state. More...

std::string	GetModuleShareDirectory () const

void	PrintSelf (ostream &os, vtkIndent indent) VTK_OVERRIDE

void	SetModuleShareDirectory (const std::string &shareDirectory)

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

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

void	PrintSelf (ostream &os, vtkIndent indent) VTK_OVERRIDE

virtual void	SetMRMLApplicationLogic (vtkMRMLApplicationLogic *logic)

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

Static Public Member Functions
static bool	ApplyParentTransformToOrientedImageData (vtkMRMLTransformableNode transformableNode, vtkOrientedImageData orientedImageData, bool linearInterpolation=false, double backgroundColor[4]=NULL)

static bool	ApplyParentTransformToPolyData (vtkMRMLTransformableNode transformableNode, vtkPolyData polyData)

static bool	CopyOrientedImageDataToVolumeNode (vtkOrientedImageData orientedImageData, vtkMRMLVolumeNode volumeNode, bool shallowCopy=true, bool shiftImageDataExtentToZeroStart=true)

static bool	CreateLabelmapVolumeFromOrientedImageData (vtkOrientedImageData orientedImageData, vtkMRMLLabelMapVolumeNode labelmapVolumeNode)

static vtkOrientedImageData *	CreateOrientedImageDataFromVolumeNode (vtkMRMLScalarVolumeNode volumeNode, vtkMRMLTransformNode outputParentTransformNode=NULL)

static vtkDataObject *	CreateRepresentationForOneSegment (vtkSegmentation *segmentation, std::string segmentID, std::string representationName)

static vtkSegment *	CreateSegmentFromLabelmapVolumeNode (vtkMRMLLabelMapVolumeNode labelmapVolumeNode, vtkMRMLSegmentationNode segmentationNode=NULL)

static vtkSegment *	CreateSegmentFromModelNode (vtkMRMLModelNode modelNode, vtkMRMLSegmentationNode segmentationNode=NULL)

static int	DoesLabelmapContainSingleLabel (vtkMRMLLabelMapVolumeNode *labelmapVolumeNode)

static bool	ExportAllSegmentsToLabelmapNode (vtkMRMLSegmentationNode segmentationNode, vtkMRMLLabelMapVolumeNode labelmapNode)

static bool	ExportAllSegmentsToModelHierarchy (vtkMRMLSegmentationNode segmentationNode, vtkMRMLModelHierarchyNode modelHierarchyNode)

static bool	ExportSegmentsClosedSurfaceRepresentationToFiles (std::string destinationFolder, vtkMRMLSegmentationNode segmentationNode, vtkStringArray segmentIds=NULL, std::string fileFormat="STL", bool lps=true, double sizeScale=1.0, bool merge=false)

static bool	ExportSegmentsToLabelmapNode (vtkMRMLSegmentationNode segmentationNode, std::vector< std::string > &segmentIDs, vtkMRMLLabelMapVolumeNode labelmapNode, vtkMRMLVolumeNode *referenceVolumeNode=NULL)

static bool	ExportSegmentsToLabelmapNode (vtkMRMLSegmentationNode segmentationNode, vtkStringArray segmentIDs, vtkMRMLLabelMapVolumeNode labelmapNode, vtkMRMLVolumeNode referenceVolumeNode=NULL)

static bool	ExportSegmentsToModelHierarchy (vtkMRMLSegmentationNode segmentationNode, std::vector< std::string > &segmentIDs, vtkMRMLModelHierarchyNode modelHierarchyNode)

static bool	ExportSegmentsToModelHierarchy (vtkMRMLSegmentationNode segmentationNode, vtkStringArray segmentIds, vtkMRMLModelHierarchyNode *modelHierarchyNode)

static bool	ExportSegmentToRepresentationNode (vtkSegment segment, vtkMRMLNode representationNode)

static bool	ExportVisibleSegmentsToLabelmapNode (vtkMRMLSegmentationNode segmentationNode, vtkMRMLLabelMapVolumeNode labelmapNode, vtkMRMLVolumeNode *referenceVolumeNode=NULL)

static bool	ExportVisibleSegmentsToModelHierarchy (vtkMRMLSegmentationNode segmentationNode, vtkMRMLModelHierarchyNode modelHierarchyNode)

static void	GetAllLabelValues (vtkIntArray labels, vtkImageData labelmap)
	Utility function that returns all non-empty label values in a labelmap. More...

static vtkMRMLSegmentationNode *	GetSegmentationNodeForSegment (vtkMRMLScene scene, vtkSegment segment, std::string &segmentId)

static vtkMRMLSegmentationNode *	GetSegmentationNodeForSegmentation (vtkMRMLScene scene, vtkSegmentation segmentation)

static vtkMRMLSegmentationNode *	GetSegmentationNodeForSegmentSubjectHierarchyItem (vtkIdType segmentShItemID, vtkMRMLScene *scene)
	Utility function for getting the segmentation node for a segment subject hierarchy item. More...

static bool	GetSegmentBinaryLabelmapRepresentation (vtkMRMLSegmentationNode segmentationNode, std::string segmentID, vtkOrientedImageData imageData, bool applyParentTransform=true)

static bool	GetSegmentClosedSurfaceRepresentation (vtkMRMLSegmentationNode segmentationNode, std::string segmentID, vtkPolyData polyData, bool applyParentTransform=true)

static vtkSegment *	GetSegmentForSegmentSubjectHierarchyItem (vtkIdType segmentShItemID, vtkMRMLScene *scene)
	Utility function for getting the segment object for a segment subject hierarchy item. More...

static bool	GetSegmentRepresentation (vtkMRMLSegmentationNode segmentationNode, std::string segmentID, std::string representationName, vtkDataObject segmentRepresentation, bool applyParentTransform=true)

static bool	GetTransformBetweenRepresentationAndSegmentation (vtkMRMLTransformableNode representationNode, vtkMRMLSegmentationNode segmentationNode, vtkGeneralTransform *representationToSegmentationTransform)

static bool	ImportLabelmapToSegmentationNode (vtkMRMLLabelMapVolumeNode labelmapNode, vtkMRMLSegmentationNode segmentationNode, std::string insertBeforeSegmentId="")

static bool	ImportLabelmapToSegmentationNode (vtkOrientedImageData labelmapImage, vtkMRMLSegmentationNode segmentationNode, std::string baseSegmentName="", std::string insertBeforeSegmentId="")

static bool	ImportLabelmapToSegmentationNode (vtkMRMLLabelMapVolumeNode labelmapNode, vtkMRMLSegmentationNode segmentationNode, vtkStringArray *updatedSegmentIDs)

static bool	ImportLabelmapToSegmentationNode (vtkOrientedImageData labelmapImage, vtkMRMLSegmentationNode segmentationNode, vtkStringArray updatedSegmentIDs, vtkGeneralTransform labelmapToSegmentationTransform=NULL)

static bool	ImportModelHierarchyToSegmentationNode (vtkMRMLModelHierarchyNode modelHierarchyNode, vtkMRMLSegmentationNode segmentationNode, std::string insertBeforeSegmentId="")
	Import model hierarchy into the segmentation as segments. More...

static bool	ImportModelToSegmentationNode (vtkMRMLModelNode modelNode, vtkMRMLSegmentationNode segmentationNode, std::string insertBeforeSegmentId="")
	Import model into the segmentation as a segment. More...

static int	IsTypeOf (const char *type)

static vtkSlicerSegmentationsModuleLogic *	New ()

static vtkSlicerSegmentationsModuleLogic *	SafeDownCast (vtkObject *o)

static bool	SetBinaryLabelmapToSegment (vtkOrientedImageData labelmap, vtkMRMLSegmentationNode segmentationNode, std::string segmentID, int mergeMode=MODE_REPLACE, const int extent[6]=0)

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

static vtkSlicerModuleLogic *	New ()
	The Usual vtk class functions. More...

static vtkSlicerModuleLogic *	SafeDownCast (vtkObject *o)

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

static vtkMRMLAbstractLogic *	New ()

static vtkMRMLAbstractLogic *	SafeDownCast (vtkObject *o)

Protected Member Functions
virtual void	OnMRMLSceneNodeAdded (vtkMRMLNode *node) VTK_OVERRIDE
	Handle MRML node added events. More...

virtual void	RegisterNodes () VTK_OVERRIDE
	Register MRML Node classes to Scene. Gets called automatically when the MRMLScene is attached to this logic class. More...

virtual void	SetMRMLSceneInternal (vtkMRMLScene *newScene) VTK_OVERRIDE

	vtkSlicerSegmentationsModuleLogic ()

virtual	~vtkSlicerSegmentationsModuleLogic ()

Protected Member Functions inherited from vtkSlicerModuleLogic
	vtkSlicerModuleLogic ()

virtual	~vtkSlicerModuleLogic ()

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. More...

int	InvokePendingModifiedEvent ()

virtual void	Modified () VTK_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	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	ProcessMRMLNodesEvents (vtkObject caller, unsigned long event, void callData)

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

void	SetAndObserveMRMLSceneEventsInternal (vtkMRMLScene newScene, vtkIntArray events, vtkFloatArray *priorities=0)

void	SetDisableModifiedEvent (bool onOff)

void	SetInMRMLLogicsCallbackFlag (int flag)

void	SetInMRMLNodesCallbackFlag (int flag)

void	SetInMRMLSceneCallbackFlag (int flag)

void	SetProcessingMRMLSceneEvent (int event)

bool	StartModify ()

virtual void	UnobserveMRMLScene ()

virtual void	UpdateFromMRMLScene ()

	vtkMRMLAbstractLogic ()

virtual	~vtkMRMLAbstractLogic ()

Static Protected Member Functions
static bool	ExportSegmentsClosedSurfaceRepresentationToObjFile (std::string destinationFolder, vtkMRMLSegmentationNode *segmentationNode, std::vector< std::string > &segmentIDs, bool lps, double sizeScale)

static bool	ExportSegmentsClosedSurfaceRepresentationToStlFiles (std::string destinationFolder, vtkMRMLSegmentationNode *segmentationNode, std::vector< std::string > &segmentIDs, bool lps, double sizeScale, bool merge)

static std::string	GetSafeFileName (std::string originalName)

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

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. More...

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

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

Protected Attributes
vtkCallbackCommand *	SubjectHierarchyUIDCallbackCommand
	Command handling subject hierarchy UID added events. More...

vtkSlicerTerminologiesModuleLogic *	TerminologiesLogic
	Terminologies module logic. More...

Detailed Description

Definition at line 51 of file vtkSlicerSegmentationsModuleLogic.h.

Member Typedef Documentation

◆ Superclass

typedef vtkSlicerModuleLogic vtkSlicerSegmentationsModuleLogic::Superclass

Definition at line 56 of file vtkSlicerSegmentationsModuleLogic.h.

Member Enumeration Documentation

◆ anonymous enum

anonymous enum

Set a labelmap image as binary labelmap representation into the segment defined by the segmentation node and segment ID. Master representation must be binary labelmap! Master representation changed event is disabled to prevent deletion of all other representation in all segments. The other representations in the given segment are re-converted. The extent of the segment binary labelmap is shrunk to the effective extent. Display update is triggered.

Parameters

mergeMode	Determines if the labelmap should replace the segment, or combined with a maximum or minimum operation.
extent	If extent is specified then only that extent of the labelmap is used.

Enumerator
MODE_REPLACE
MODE_MERGE_MAX
MODE_MERGE_MIN

Definition at line 319 of file vtkSlicerSegmentationsModuleLogic.h.

Constructor & Destructor Documentation

◆ vtkSlicerSegmentationsModuleLogic()

vtkSlicerSegmentationsModuleLogic::vtkSlicerSegmentationsModuleLogic ( )

protected

◆ ~vtkSlicerSegmentationsModuleLogic()

virtual vtkSlicerSegmentationsModuleLogic::~vtkSlicerSegmentationsModuleLogic ( )

protectedvirtual

Member Function Documentation

◆ ApplyParentTransformToOrientedImageData()

static bool vtkSlicerSegmentationsModuleLogic::ApplyParentTransformToOrientedImageData	(	vtkMRMLTransformableNode *	transformableNode,
		vtkOrientedImageData *	orientedImageData,
		bool	linearInterpolation = `false`,
		double	backgroundColor[4] = `NULL`
	)

static

Apply the parent transform of a node to an oriented image data. Useful if we want to get a labelmap representation of a segmentation in the proper geometry for processing.

Returns: Success flag

◆ ApplyParentTransformToPolyData()

static bool vtkSlicerSegmentationsModuleLogic::ApplyParentTransformToPolyData	(	vtkMRMLTransformableNode *	transformableNode,
		vtkPolyData *	polyData
	)

static

Apply the parent transform of a node to a poly data. Useful if we want to get a surface or contours representation of a segmentation in the proper geometry for processing.

Returns: Success flag

◆ CopyOrientedImageDataToVolumeNode()

static bool vtkSlicerSegmentationsModuleLogic::CopyOrientedImageDataToVolumeNode	(	vtkOrientedImageData *	orientedImageData,
		vtkMRMLVolumeNode *	volumeNode,
		bool	shallowCopy = `true`,
		bool	shiftImageDataExtentToZeroStart = `true`
	)

static

Create volume MRML node from oriented image data. Display node is not created.

Parameters

orientedImageData	Oriented image data to create volume node from
scalarVolumeNode	Volume to be populated with the oriented image data.
shallowCopy	If true then voxel array is not duplicated.
shiftImageDataExtentToZeroStart	Adjust image origin to make image extents start from zero. May be necessary for compatibility with some algorithms that assumes image extent start from 0.

Returns: Success flag

◆ CreateLabelmapVolumeFromOrientedImageData()

static bool vtkSlicerSegmentationsModuleLogic::CreateLabelmapVolumeFromOrientedImageData	(	vtkOrientedImageData *	orientedImageData,
		vtkMRMLLabelMapVolumeNode *	labelmapVolumeNode
	)

static

Create labelmap volume MRML node from oriented image data. Creates a display node if a display node does not exist. Shifts image extent to start from zero. Image is shallow-copied (voxel array is not duplicated).

Parameters

orientedImageData	Oriented image data to create labelmap from
labelmapVolumeNode	Labelmap volume to be populated with the oriented image data. The volume node must exist and be added to the MRML scene.

Returns: Success flag

◆ CreateOrientedImageDataFromVolumeNode()

static vtkOrientedImageData* vtkSlicerSegmentationsModuleLogic::CreateOrientedImageDataFromVolumeNode	(	vtkMRMLScalarVolumeNode *	volumeNode,
		vtkMRMLTransformNode *	outputParentTransformNode = `NULL`
	)

static

Create oriented image data from a volume node

Parameters

outputParentTransformNode Specifies the parent transform node where the created image data can be placed. NOTE: Need to take ownership of the created object! For example using vtkSmartPointer<vtkOrientedImageData>::Take

◆ CreateRepresentationForOneSegment()

static vtkDataObject* vtkSlicerSegmentationsModuleLogic::CreateRepresentationForOneSegment	(	vtkSegmentation *	segmentation,
		std::string	segmentID,
		std::string	representationName
	)

static

Create representation of only one segment in a segmentation. Useful if only one segment is processed, and we do not want to convert all segments to a certain segmentation to save time. NOTE: Need to take ownership of the created object! For example using vtkSmartPointer<vtkDataObject>::Take

Returns: Representation of the specified segment if found or can be created, NULL otherwise

◆ CreateSegmentFromLabelmapVolumeNode()

static vtkSegment* vtkSlicerSegmentationsModuleLogic::CreateSegmentFromLabelmapVolumeNode	(	vtkMRMLLabelMapVolumeNode *	labelmapVolumeNode,
		vtkMRMLSegmentationNode *	segmentationNode = `NULL`
	)

static

Create segment from labelmap volume MRML node. The contents are set as binary labelmap representation in the segment. Returns NULL if labelmap contains more than one label. In that case

See also: ImportLabelmapToSegmentationNode needs to be used. NOTE: Need to take ownership of the created object! For example using vtkSmartPointer<vtkSegment>::Take

Parameters

labelmapVolumeNode	Model node containing image data that will be the binary labelmap representation in the created segment
segmentationNode	Segmentation node that will be the container of the segment. It is used to get parent transform to make sure the created segment will be located the same place the image was, considering all transforms involved. NULL value means that this consideration is not needed. Default value is NULL.

Returns: Created segment that then can be added to the segmentation if needed. Need to take ownership of the created object! For example using vtkSmartPointer<vtkSegment>::Take

◆ CreateSegmentFromModelNode()

static vtkSegment* vtkSlicerSegmentationsModuleLogic::CreateSegmentFromModelNode	(	vtkMRMLModelNode *	modelNode,
		vtkMRMLSegmentationNode *	segmentationNode = `NULL`
	)

static

Create segment from model MRML node. The contents are set as closed surface model representation in the segment. NOTE: Need to take ownership of the created object! For example using vtkSmartPointer<vtkSegment>::Take

Parameters

modelNode	Model node containing poly data that will be the closed surface representation in the created segment
segmentationNode	Segmentation node that will be the container of the segment. It is used to get parent transform to make sure the created segment will be located the same place the model was, considering all transforms involved. NULL value means that this consideration is not needed. Default value is NULL.

Returns: Created segment that then can be added to the segmentation if needed. Need to take ownership of the created object! For example using vtkSmartPointer<vtkSegment>::Take

◆ DoesLabelmapContainSingleLabel()

static int vtkSlicerSegmentationsModuleLogic::DoesLabelmapContainSingleLabel ( vtkMRMLLabelMapVolumeNode * labelmapVolumeNode )

static

Utility function to determine if a labelmap contains a single label

Returns: 0 if contains no label or multiple labels, the label if it contains a single one

◆ ExportAllSegmentsToLabelmapNode()

static bool vtkSlicerSegmentationsModuleLogic::ExportAllSegmentsToLabelmapNode	(	vtkMRMLSegmentationNode *	segmentationNode,
		vtkMRMLLabelMapVolumeNode *	labelmapNode
	)

static

Export all segments into a multi-label labelmap volume node

Parameters

segmentationNode	Segmentation node from which the the segments are exported
labelmapNode	Labelmap node to export the segments to

◆ ExportAllSegmentsToModelHierarchy()

static bool vtkSlicerSegmentationsModuleLogic::ExportAllSegmentsToModelHierarchy	(	vtkMRMLSegmentationNode *	segmentationNode,
		vtkMRMLModelHierarchyNode *	modelHierarchyNode
	)

static

Export all segments into a model hierarchy, a model node from each segment

Parameters

segmentationNode	Segmentation node from which the the segments are exported
modelHierarchyNode	Model hierarchy to export the segments to

◆ ExportSegmentsClosedSurfaceRepresentationToFiles()

static bool vtkSlicerSegmentationsModuleLogic::ExportSegmentsClosedSurfaceRepresentationToFiles	(	std::string	destinationFolder,
		vtkMRMLSegmentationNode *	segmentationNode,
		vtkStringArray *	segmentIds = `NULL`,
		std::string	fileFormat = `"STL"`,
		bool	lps = `true`,
		double	sizeScale = `1.0`,
		bool	merge = `false`
	)

static

Export closed surface representation of multiple segments to files. Typically used for writing 3D printable model files.

Parameters

segmentationNode	Segmentation node from which the the segments are exported
destinationFolder	Folder name where segments will be exported to
fileFormat	Output file format (STL or OBJ).
merge	Merge all models into a single mesh. Only applicable to STL format.
lps	Save files in LPS coordinate system. If set to false then RAS coordinate system is used.
segmentIds	List of segment IDs to export

◆ ExportSegmentsClosedSurfaceRepresentationToObjFile()

static bool vtkSlicerSegmentationsModuleLogic::ExportSegmentsClosedSurfaceRepresentationToObjFile	(	std::string	destinationFolder,
		vtkMRMLSegmentationNode *	segmentationNode,
		std::vector< std::string > &	segmentIDs,
		bool	lps,
		double	sizeScale
	)

staticprotected

◆ ExportSegmentsClosedSurfaceRepresentationToStlFiles()

static bool vtkSlicerSegmentationsModuleLogic::ExportSegmentsClosedSurfaceRepresentationToStlFiles	(	std::string	destinationFolder,
		vtkMRMLSegmentationNode *	segmentationNode,
		std::vector< std::string > &	segmentIDs,
		bool	lps,
		double	sizeScale,
		bool	merge
	)

staticprotected

◆ ExportSegmentsToLabelmapNode() [1/2]

static bool vtkSlicerSegmentationsModuleLogic::ExportSegmentsToLabelmapNode	(	vtkMRMLSegmentationNode *	segmentationNode,
		std::vector< std::string > &	segmentIDs,
		vtkMRMLLabelMapVolumeNode *	labelmapNode,
		vtkMRMLVolumeNode *	referenceVolumeNode = `NULL`
	)

static

Export multiple segments into a multi-label labelmap volume node

Parameters

segmentationNode	Segmentation node from which the the segments are exported
segmentIds	List of segment IDs to export
labelmapNode	Labelmap node to export the segments to
referenceVolumeNode	If specified, then the merged labelmap node will match the geometry of referenceVolumeNode

◆ ExportSegmentsToLabelmapNode() [2/2]

static bool vtkSlicerSegmentationsModuleLogic::ExportSegmentsToLabelmapNode	(	vtkMRMLSegmentationNode *	segmentationNode,
		vtkStringArray *	segmentIDs,
		vtkMRMLLabelMapVolumeNode *	labelmapNode,
		vtkMRMLVolumeNode *	referenceVolumeNode = `NULL`
	)

static

Export multiple segments into a multi-label labelmap volume node

Parameters

segmentationNode	Segmentation node from which the the segments are exported
segmentIds	List of segment IDs to export
labelmapNode	Labelmap node to export the segments to
referenceVolumeNode	If specified, then the merged labelmap node will match the geometry of referenceVolumeNode

◆ ExportSegmentsToModelHierarchy() [1/2]

static bool vtkSlicerSegmentationsModuleLogic::ExportSegmentsToModelHierarchy	(	vtkMRMLSegmentationNode *	segmentationNode,
		std::vector< std::string > &	segmentIDs,
		vtkMRMLModelHierarchyNode *	modelHierarchyNode
	)

static

Export multiple segments into a model hierarchy, a model node from each segment

Parameters

segmentationNode	Segmentation node from which the the segments are exported
segmentIds	List of segment IDs to export
modelHierarchyNode	Model hierarchy to export the segments to

◆ ExportSegmentsToModelHierarchy() [2/2]

static bool vtkSlicerSegmentationsModuleLogic::ExportSegmentsToModelHierarchy	(	vtkMRMLSegmentationNode *	segmentationNode,
		vtkStringArray *	segmentIds,
		vtkMRMLModelHierarchyNode *	modelHierarchyNode
	)

static

Export multiple segments into a model hierarchy, a model node from each segment

Parameters

segmentationNode	Segmentation node from which the the segments are exported
segmentIds	List of segment IDs to export
modelHierarchyNode	Model hierarchy to export the segments to

◆ ExportSegmentToRepresentationNode()

static bool vtkSlicerSegmentationsModuleLogic::ExportSegmentToRepresentationNode	(	vtkSegment *	segment,
		vtkMRMLNode *	representationNode
	)

static

Export segment to representation MRML node.

If representation node is a labelmap node, then the binary labelmap representation of the segment is copied
If representation node is a model node, then the closed surface representation is copied Otherwise return with failure.

◆ ExportVisibleSegmentsToLabelmapNode()

static bool vtkSlicerSegmentationsModuleLogic::ExportVisibleSegmentsToLabelmapNode	(	vtkMRMLSegmentationNode *	segmentationNode,
		vtkMRMLLabelMapVolumeNode *	labelmapNode,
		vtkMRMLVolumeNode *	referenceVolumeNode = `NULL`
	)

static

Export visible segments into a multi-label labelmap volume node

Parameters

segmentationNode	Segmentation node from which the the visible segments are exported
labelmapNode	Labelmap node to export the segments to
referenceVolumeNode	If specified, then the merged labelmap node will match the geometry of referenceVolumeNode

◆ ExportVisibleSegmentsToModelHierarchy()

static bool vtkSlicerSegmentationsModuleLogic::ExportVisibleSegmentsToModelHierarchy	(	vtkMRMLSegmentationNode *	segmentationNode,
		vtkMRMLModelHierarchyNode *	modelHierarchyNode
	)

static

Export visible segments into a model hierarchy, a model node from each segment

Parameters

segmentationNode	Segmentation node from which the the segments are exported
modelHierarchyNode	Model hierarchy to export the visible segments to

◆ GetAllLabelValues()

static void vtkSlicerSegmentationsModuleLogic::GetAllLabelValues	(	vtkIntArray *	labels,
		vtkImageData *	labelmap
	)

static

Utility function that returns all non-empty label values in a labelmap.

◆ GetClassName()

virtual const char* vtkSlicerSegmentationsModuleLogic::GetClassName ( )

virtual

Reimplemented from vtkSlicerModuleLogic.

◆ GetDefaultSegmentationNode()

vtkMRMLSegmentationNode* vtkSlicerSegmentationsModuleLogic::GetDefaultSegmentationNode ( )

Get default segmentation node. All new segmentation nodes are initialized to the content of this node.

◆ GetDefaultSurfaceSmoothingEnabled()

bool vtkSlicerSegmentationsModuleLogic::GetDefaultSurfaceSmoothingEnabled ( )

Get/Set default closed surface smoothing enabled flag for new segmentation nodes.

◆ GetSafeFileName()

static std::string vtkSlicerSegmentationsModuleLogic::GetSafeFileName ( std::string originalName )

staticprotected

Generate a safe file name from a given string. The method is in this logic so that it does not cause confusion throughout Slicer (there is an implementation already in qSlicerSaveDataDialogPrivate::nodeFileInfo and it would be good to keep a central one)

◆ GetSegmentationNodeForSegment()

static vtkMRMLSegmentationNode* vtkSlicerSegmentationsModuleLogic::GetSegmentationNodeForSegment	(	vtkMRMLScene *	scene,
		vtkSegment *	segment,
		std::string &	segmentId
	)

static

Get segmentation node containing a given segment. As segments are out-of-MRML VTK objects, there is no direct link from it to its parent node, so must be found from the MRML scene.

Parameters

scene	MRML scene
segment	Segment to find
segmentId	Output argument for the ID of the found segment

Returns: Segmentation node containing the given segment if any, NULL otherwise

◆ GetSegmentationNodeForSegmentation()

static vtkMRMLSegmentationNode* vtkSlicerSegmentationsModuleLogic::GetSegmentationNodeForSegmentation	(	vtkMRMLScene *	scene,
		vtkSegmentation *	segmentation
	)

static

Get segmentation node containing a segmentation object. As segmentation objects are out-of-MRML VTK objects, there is no direct link from it to its parent node, so must be found from the MRML scene.

Parameters

scene	MRML scene
segmentation	Segmentation to find

Returns: Segmentation node containing the given segmentation if any, NULL otherwise

◆ GetSegmentationNodeForSegmentSubjectHierarchyItem()

static vtkMRMLSegmentationNode* vtkSlicerSegmentationsModuleLogic::GetSegmentationNodeForSegmentSubjectHierarchyItem	(	vtkIdType	segmentShItemID,
		vtkMRMLScene *	scene
	)

static

Utility function for getting the segmentation node for a segment subject hierarchy item.

◆ GetSegmentBinaryLabelmapRepresentation()

static bool vtkSlicerSegmentationsModuleLogic::GetSegmentBinaryLabelmapRepresentation	(	vtkMRMLSegmentationNode *	segmentationNode,
		std::string	segmentID,
		vtkOrientedImageData *	imageData,
		bool	applyParentTransform = `true`
	)

static

Convenience function to get binary labelmap representation of a segment in a segmentation. Uses

See also: GetSegmentRepresentation A duplicate of the oriented image data is copied into the argument image data, with the segmentation's parent transform applied if requested (on by default). The oriented image data can be used directly for processing, or to create a labelmap volume using; CreateLabelmapVolumeFromOrientedImageData.

Parameters

segmentationNode	Input segmentation node containing the segment to extract
segmentID	Segment identifier of the segment to extract
imageData	Output oriented image data into which the segment binary labelmap is copied
applyParentTransform	Flag determining whether to apply parent transform of the segmentation node. If on, then the oriented image data is in RAS, otherwise in the segmentation node's coordinate frame. On by default

Returns: Success flag

◆ GetSegmentClosedSurfaceRepresentation()

static bool vtkSlicerSegmentationsModuleLogic::GetSegmentClosedSurfaceRepresentation	(	vtkMRMLSegmentationNode *	segmentationNode,
		std::string	segmentID,
		vtkPolyData *	polyData,
		bool	applyParentTransform = `true`
	)

static

Convenience function to get closed surface representation of a segment in a segmentation. Uses

See also: GetSegmentRepresentation A duplicate of the closed surface data is copied into the argument image data, with the segmentation's parent transform applied if requested (on by default).

Parameters

segmentationNode	Input segmentation node containing the segment to extract
segmentID	Segment identifier of the segment to extract
polyData	Output polydata into which the segment polydata is copied
applyParentTransform	Flag determining whether to apply parent transform of the segmentation node. If on, then the oriented image data is in RAS, otherwise in the segmentation node's coordinate frame. On by default

Returns: Success flag

◆ GetSegmentForSegmentSubjectHierarchyItem()

static vtkSegment* vtkSlicerSegmentationsModuleLogic::GetSegmentForSegmentSubjectHierarchyItem	(	vtkIdType	segmentShItemID,
		vtkMRMLScene *	scene
	)

static

Utility function for getting the segment object for a segment subject hierarchy item.

◆ GetSegmentRepresentation()

static bool vtkSlicerSegmentationsModuleLogic::GetSegmentRepresentation	(	vtkMRMLSegmentationNode *	segmentationNode,
		std::string	segmentID,
		std::string	representationName,
		vtkDataObject *	segmentRepresentation,
		bool	applyParentTransform = `true`
	)

static

Convenience function to get a specified representation of a segment in a segmentation. A duplicate of the representation data object is copied into the argument output object, with the segmentation's parent transform applied if requested (on by default).

Parameters

segmentationNode	Input segmentation node containing the segment to extract
segmentID	Segment identifier of the segment to extract
representationName	Name of the requested representation
segmentRepresentation	Output representation data object into which the given representation in the segment is copied
applyParentTransform	Flag determining whether to apply parent transform of the segmentation node. On by default

Returns: Success flag

◆ GetTransformBetweenRepresentationAndSegmentation()

static bool vtkSlicerSegmentationsModuleLogic::GetTransformBetweenRepresentationAndSegmentation	(	vtkMRMLTransformableNode *	representationNode,
		vtkMRMLSegmentationNode *	segmentationNode,
		vtkGeneralTransform *	representationToSegmentationTransform
	)

static

Get transform between a representation node (e.g. labelmap or model) and a segmentation node. Useful if we want to add a representation to a segment, and we want to make sure that the segment will be located the same place the representation node was. The output transform is the representation node's parent transform concatenated with the inverse of the segmentation's parent transform. It needs to be applied on the representation.

Parameters

representationNode	Transformable node which contains the representation we want to add to the segment
segmentationNode	Segmentation node that will contain the segment to which the representation is added. It is the representation node's parent transform concatenated with the inverse of the segmentation's parent transform.
representationToSegmentationTransform	General transform between the representation node and the segmentation node.

Returns: Success flag

◆ ImportLabelmapToSegmentationNode() [1/4]

static bool vtkSlicerSegmentationsModuleLogic::ImportLabelmapToSegmentationNode	(	vtkMRMLLabelMapVolumeNode *	labelmapNode,
		vtkMRMLSegmentationNode *	segmentationNode,
		std::string	insertBeforeSegmentId = `""`
	)

static

Import all labels from a labelmap node to a segmentation node, each label to a separate segment. The colors of the new segments are set from the color table corresponding to the labelmap volume.

Parameters

insertBeforeSegmentId New segments will be inserted before this segment.

◆ ImportLabelmapToSegmentationNode() [2/4]

static bool vtkSlicerSegmentationsModuleLogic::ImportLabelmapToSegmentationNode	(	vtkOrientedImageData *	labelmapImage,
		vtkMRMLSegmentationNode *	segmentationNode,
		std::string	baseSegmentName = `""`,
		std::string	insertBeforeSegmentId = `""`
	)

static

Import all labels from a labelmap image to a segmentation node, each label to a separate segment The colors of the new segments are randomly generated, unless terminology context is specified, in which case the terminology entries are attempted to be mapped to the imported labels LabelmapImage is defined in the segmentation node's coordinate system (parent transform of the segmentation node is not used during import).

Parameters

baseSegmentName Prefix for the names of the new segments. Empty by default, in which case the prefix will be "Label"

◆ ImportLabelmapToSegmentationNode() [3/4]

static bool vtkSlicerSegmentationsModuleLogic::ImportLabelmapToSegmentationNode	(	vtkMRMLLabelMapVolumeNode *	labelmapNode,
		vtkMRMLSegmentationNode *	segmentationNode,
		vtkStringArray *	updatedSegmentIDs
	)

static

Update segmentation from segments in a labelmap node.

Parameters

updatedSegmentIDs Defines how label values 1..N are mapped to segment IDs (0..N-1).

◆ ImportLabelmapToSegmentationNode() [4/4]

static bool vtkSlicerSegmentationsModuleLogic::ImportLabelmapToSegmentationNode	(	vtkOrientedImageData *	labelmapImage,
		vtkMRMLSegmentationNode *	segmentationNode,
		vtkStringArray *	updatedSegmentIDs,
		vtkGeneralTransform *	labelmapToSegmentationTransform = `NULL`
	)

static

Update segmentation from segments in a labelmap node.

Parameters

updatedSegmentIDs Defines how label values 1..N are mapped to segment IDs (0..N-1).

◆ ImportLabelmapToSegmentationNodeWithTerminology()

bool vtkSlicerSegmentationsModuleLogic::ImportLabelmapToSegmentationNodeWithTerminology	(	vtkMRMLLabelMapVolumeNode *	labelmapNode,
		vtkMRMLSegmentationNode *	segmentationNode,
		std::string	terminologyContextName,
		std::string	insertBeforeSegmentId = `""`
	)

Import all labels from a labelmap node to a segmentation node, each label to a separate segment. Terminology and color is set to the segments based on the color table corresponding to the labelmap volume node.

Parameters

terminologyContextName	Terminology context the entries of which are mapped to the labels imported from the labelmap node
insertBeforeSegmentId	New segments will be inserted before this segment.

◆ ImportModelHierarchyToSegmentationNode()

static bool vtkSlicerSegmentationsModuleLogic::ImportModelHierarchyToSegmentationNode	(	vtkMRMLModelHierarchyNode *	modelHierarchyNode,
		vtkMRMLSegmentationNode *	segmentationNode,
		std::string	insertBeforeSegmentId = `""`
	)

static

Import model hierarchy into the segmentation as segments.

◆ ImportModelToSegmentationNode()

static bool vtkSlicerSegmentationsModuleLogic::ImportModelToSegmentationNode	(	vtkMRMLModelNode *	modelNode,
		vtkMRMLSegmentationNode *	segmentationNode,
		std::string	insertBeforeSegmentId = `""`
	)

static

Import model into the segmentation as a segment.

◆ IsA()

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

virtual

Reimplemented from vtkSlicerModuleLogic.

◆ IsTypeOf()

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

static

◆ LoadSegmentationFromFile()

vtkMRMLSegmentationNode* vtkSlicerSegmentationsModuleLogic::LoadSegmentationFromFile	(	const char *	filename,
		bool	autoOpacities = `true`
	)

Load segmentation from file

Parameters

filename	Path and name of file containing segmentation (nrrd, vtm, etc.)
autoOpacities	Optional flag determining whether segment opacities are calculated automatically based on containment. True by default

Returns: Loaded segmentation node

◆ New()

static vtkSlicerSegmentationsModuleLogic* vtkSlicerSegmentationsModuleLogic::New ( )

static

◆ OnMRMLSceneNodeAdded()

virtual void vtkSlicerSegmentationsModuleLogic::OnMRMLSceneNodeAdded ( vtkMRMLNode * node )

protectedvirtual

Handle MRML node added events.

Reimplemented from vtkMRMLAbstractLogic.

◆ OnSubjectHierarchyUIDAdded()

static void vtkSlicerSegmentationsModuleLogic::OnSubjectHierarchyUIDAdded	(	vtkObject *	caller,
		unsigned long	eid,
		void *	clientData,
		void *	callData
	)

staticprotected

Callback function observing UID added events for subject hierarchy nodes. In case the newly added UID is a volume node referenced from a segmentation, its geometry will be set as image geometry conversion parameter. The "other order", i.e. when the volume is loaded first and the segmentation second, should be handled at loading time of the segmentation (because then we already know about the volume)

◆ PrintSelf()

void vtkSlicerSegmentationsModuleLogic::PrintSelf	(	ostream &	os,
		vtkIndent	indent
	)

◆ RegisterNodes()

virtual void vtkSlicerSegmentationsModuleLogic::RegisterNodes ( )

protectedvirtual

Register MRML Node classes to Scene. Gets called automatically when the MRMLScene is attached to this logic class.

Reimplemented from vtkMRMLAbstractLogic.

◆ SafeDownCast()

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

static

◆ SetBinaryLabelmapToSegment()

static bool vtkSlicerSegmentationsModuleLogic::SetBinaryLabelmapToSegment	(	vtkOrientedImageData *	labelmap,
		vtkMRMLSegmentationNode *	segmentationNode,
		std::string	segmentID,
		int	mergeMode = `MODE_REPLACE`,
		const int	extent[6] = `0`
	)

static

◆ SetDefaultSurfaceSmoothingEnabled()

void vtkSlicerSegmentationsModuleLogic::SetDefaultSurfaceSmoothingEnabled ( bool enabled )

◆ SetMRMLSceneInternal()

virtual void vtkSlicerSegmentationsModuleLogic::SetMRMLSceneInternal ( vtkMRMLScene * newScene )

protectedvirtual

Called each time a new scene is set. Can be reimplemented in derivated classes. Doesn't observe the scene by default, that means that UpdateFromMRMLScene() won't be called by default when a scene is imported, closed or restored, only when a new scene is set.

See also: SetAndObserveMRMLSceneInternal() SetAndObserveMRMLSceneEventsInternal(); UpdateFromMRMLScene()

Reimplemented from vtkMRMLAbstractLogic.

◆ SetTerminologiesLogic()

void vtkSlicerSegmentationsModuleLogic::SetTerminologiesLogic ( vtkSlicerTerminologiesModuleLogic * terminologiesLogic )

Set Terminologies module logic.

◆ SetTerminologyToSegmentationFromLabelmapNode()

bool vtkSlicerSegmentationsModuleLogic::SetTerminologyToSegmentationFromLabelmapNode	(	vtkMRMLSegmentationNode *	segmentationNode,
		vtkMRMLLabelMapVolumeNode *	labelmapNode,
		std::string	terminologyContextName
	)

Assign terminology to segments in a segmentation node based on the labels of a labelmap node. Match is made based on the 3dSlicerLabel terminology type attribute. If the terminology context does not contain that attribute, match cannot be made.

Parameters

terminologyContextName Terminology context the entries of which are mapped to the labels imported from the labelmap node

Member Data Documentation

◆ SubjectHierarchyUIDCallbackCommand

vtkCallbackCommand* vtkSlicerSegmentationsModuleLogic::SubjectHierarchyUIDCallbackCommand

protected

Command handling subject hierarchy UID added events.

Definition at line 375 of file vtkSlicerSegmentationsModuleLogic.h.

◆ TerminologiesLogic

vtkSlicerTerminologiesModuleLogic* vtkSlicerSegmentationsModuleLogic::TerminologiesLogic

protected

Terminologies module logic.

Definition at line 378 of file vtkSlicerSegmentationsModuleLogic.h.

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

Modules/Loadable/Segmentations/Logic/vtkSlicerSegmentationsModuleLogic.h

Public Types

Public Member Functions

Static Public Member Functions

Protected Member Functions

Static Protected Member Functions

Protected Attributes

Detailed Description

Member Typedef Documentation

◆ Superclass

Member Enumeration Documentation

◆ anonymous enum

Constructor & Destructor Documentation

◆ vtkSlicerSegmentationsModuleLogic()

◆ ~vtkSlicerSegmentationsModuleLogic()

Member Function Documentation

◆ ApplyParentTransformToOrientedImageData()

◆ ApplyParentTransformToPolyData()

◆ CopyOrientedImageDataToVolumeNode()

◆ CreateLabelmapVolumeFromOrientedImageData()

◆ CreateOrientedImageDataFromVolumeNode()

◆ CreateRepresentationForOneSegment()

◆ CreateSegmentFromLabelmapVolumeNode()

◆ CreateSegmentFromModelNode()

◆ DoesLabelmapContainSingleLabel()

◆ ExportAllSegmentsToLabelmapNode()

◆ ExportAllSegmentsToModelHierarchy()

◆ ExportSegmentsClosedSurfaceRepresentationToFiles()

◆ ExportSegmentsClosedSurfaceRepresentationToObjFile()

◆ ExportSegmentsClosedSurfaceRepresentationToStlFiles()

◆ ExportSegmentsToLabelmapNode() [1/2]

◆ ExportSegmentsToLabelmapNode() [2/2]

◆ ExportSegmentsToModelHierarchy() [1/2]

◆ ExportSegmentsToModelHierarchy() [2/2]

◆ ExportSegmentToRepresentationNode()

◆ ExportVisibleSegmentsToLabelmapNode()

◆ ExportVisibleSegmentsToModelHierarchy()

◆ GetAllLabelValues()

◆ GetClassName()

◆ GetDefaultSegmentationNode()

◆ GetDefaultSurfaceSmoothingEnabled()

◆ GetSafeFileName()

◆ GetSegmentationNodeForSegment()

◆ GetSegmentationNodeForSegmentation()

◆ GetSegmentationNodeForSegmentSubjectHierarchyItem()

◆ GetSegmentBinaryLabelmapRepresentation()

◆ GetSegmentClosedSurfaceRepresentation()

◆ GetSegmentForSegmentSubjectHierarchyItem()

◆ GetSegmentRepresentation()

◆ GetTransformBetweenRepresentationAndSegmentation()

◆ ImportLabelmapToSegmentationNode() [1/4]

◆ ImportLabelmapToSegmentationNode() [2/4]

◆ ImportLabelmapToSegmentationNode() [3/4]

◆ ImportLabelmapToSegmentationNode() [4/4]

◆ ImportLabelmapToSegmentationNodeWithTerminology()

◆ ImportModelHierarchyToSegmentationNode()

◆ ImportModelToSegmentationNode()

◆ IsA()

◆ IsTypeOf()

◆ LoadSegmentationFromFile()

◆ New()

◆ OnMRMLSceneNodeAdded()

◆ OnSubjectHierarchyUIDAdded()

◆ PrintSelf()

◆ RegisterNodes()

◆ SafeDownCast()

◆ SetBinaryLabelmapToSegment()

◆ SetDefaultSurfaceSmoothingEnabled()

◆ SetMRMLSceneInternal()

◆ SetTerminologiesLogic()

◆ SetTerminologyToSegmentationFromLabelmapNode()

Member Data Documentation

◆ SubjectHierarchyUIDCallbackCommand

◆ TerminologiesLogic