vtkSlicerSegmentationsModuleLogic Class Reference

#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, MODE_MERGE_MASK }
enum	SegmentStatus {   NotStarted, InProgress, Completed, Flagged,   LastStatus }
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, const char *nodeName=nullptr, vtkMRMLColorTableNode *colorTableNode=nullptr)
void	PrintSelf (ostream &os, vtkIndent indent) override
void	SetDefaultSurfaceSmoothingEnabled (bool enabled)
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...
virtual vtkMRMLAbstractLogic *	GetModuleLogic (const char *moduleName)
	Convenience method for getting another module's logic from the application logic. More...
std::string	GetModuleShareDirectory () const
void	PrintSelf (ostream &os, vtkIndent indent) 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) 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]=nullptr)
static bool	ApplyParentTransformToPolyData (vtkMRMLTransformableNode *transformableNode, vtkPolyData *polyData)
static bool	ClearSegment (vtkMRMLSegmentationNode *segmentationNode, std::string segmentID)
	Clear the contents of a single segment. More...
static void	CollapseBinaryLabelmaps (vtkMRMLSegmentationNode *segmentationNode, bool forceToSingleLayer)
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=nullptr)
static vtkDataObject *	CreateRepresentationForOneSegment (vtkSegmentation *segmentation, std::string segmentID, std::string representationName)
static vtkSegment *	CreateSegmentFromLabelmapVolumeNode (vtkMRMLLabelMapVolumeNode *labelmapVolumeNode, vtkMRMLSegmentationNode *segmentationNode=nullptr)
static vtkSegment *	CreateSegmentFromModelNode (vtkMRMLModelNode *modelNode, vtkMRMLSegmentationNode *segmentationNode=nullptr)
static int	DoesLabelmapContainSingleLabel (vtkMRMLLabelMapVolumeNode *labelmapVolumeNode)
static bool	ExportAllSegmentsToLabelmapNode (vtkMRMLSegmentationNode *segmentationNode, vtkMRMLLabelMapVolumeNode *labelmapNode, int extentComputationMode=vtkSegmentation::EXTENT_UNION_OF_EFFECTIVE_SEGMENTS)
static bool	ExportAllSegmentsToModels (vtkMRMLSegmentationNode *segmentationNode, vtkIdType folderItemId)
static bool	ExportSegmentsBinaryLabelmapRepresentationToFiles (std::string destinationFolder, vtkMRMLSegmentationNode *segmentationNode, vtkStringArray *segmentIds=nullptr, std::string extension="nrrd", bool useCompression=false, vtkMRMLVolumeNode *referenceVolumeNode=nullptr, int extentComputationMode=vtkSegmentation::EXTENT_REFERENCE_GEOMETRY, vtkMRMLColorTableNode *colorTableNode=nullptr)
static bool	ExportSegmentsClosedSurfaceRepresentationToFiles (std::string destinationFolder, vtkMRMLSegmentationNode *segmentationNode, vtkStringArray *segmentIds=nullptr, std::string fileFormat="STL", bool lps=true, double sizeScale=1.0, bool merge=false)
static bool	ExportSegmentsToLabelmapNode (vtkMRMLSegmentationNode *segmentationNode, const std::vector< std::string > &segmentIDs, vtkMRMLLabelMapVolumeNode *labelmapNode, vtkMRMLVolumeNode *referenceVolumeNode=nullptr, int extentComputationMode=vtkSegmentation::EXTENT_UNION_OF_EFFECTIVE_SEGMENTS, vtkMRMLColorTableNode *colorTableNode=nullptr)
static bool	ExportSegmentsToLabelmapNode (vtkMRMLSegmentationNode *segmentationNode, vtkStringArray *segmentIDs, vtkMRMLLabelMapVolumeNode *labelmapNode, vtkMRMLVolumeNode *referenceVolumeNode=nullptr, int extentComputationMode=vtkSegmentation::EXTENT_UNION_OF_EFFECTIVE_SEGMENTS, vtkMRMLColorTableNode *colorTableNode=nullptr)
static bool	ExportSegmentsToModels (vtkMRMLSegmentationNode *segmentationNode, const std::vector< std::string > &segmentIDs, vtkIdType folderItemId)
static bool	ExportSegmentsToModels (vtkMRMLSegmentationNode *segmentationNode, vtkStringArray *segmentIds, vtkIdType folderItemId)
static bool	ExportSegmentToRepresentationNode (vtkSegment *segment, vtkMRMLNode *representationNode)
static bool	ExportVisibleSegmentsToLabelmapNode (vtkMRMLSegmentationNode *segmentationNode, vtkMRMLLabelMapVolumeNode *labelmapNode, vtkMRMLVolumeNode *referenceVolumeNode=nullptr, int extentComputationMode=vtkSegmentation::EXTENT_UNION_OF_EFFECTIVE_SEGMENTS)
static bool	ExportVisibleSegmentsToModels (vtkMRMLSegmentationNode *segmentationNode, vtkIdType folderItemId)
static void	GenerateMergedLabelmapInReferenceGeometry (vtkMRMLSegmentationNode *segmentationNode, vtkMRMLVolumeNode *referenceVolumeNode, vtkStringArray *segmentIDs, int extentComputationMode, vtkOrientedImageData *mergedLabelmap_Reference, vtkIntArray *labelValues=nullptr)
static void	GetAllLabelValues (vtkIntArray *labels, vtkImageData *labelmap)
	Utility function that returns all non-empty label values in a labelmap. More...
static void	GetLabelValuesFromColorNode (vtkMRMLSegmentationNode *segmentationNode, vtkMRMLColorTableNode *colorTableNode, vtkStringArray *segmentIds, vtkIntArray *labelValues)
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 segmentation or 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 int	GetSegmentStatus (vtkSegment *segment)
static const char *	GetSegmentStatusAsHumanReadableString (int segmentStatus)
	Get the human readable segment status from the SegmentStatus enum value. More...
static const char *	GetSegmentStatusAsMachineReadableString (int segmentStatus)
	Get the machine readable segment status from the SegmentStatus enum value. More...
static int	GetSegmentStatusFromMachineReadableString (std::string statusString)
	Get the enum segment status from a machine string. More...
static bool	GetSharedSegmentIDsInMask (vtkMRMLSegmentationNode *segmentationNode, std::string sharedSegmentID, vtkOrientedImageData *mask, const int extent[6], std::vector< std::string > &segmentIDs, int maskThreshold=0.0, bool includeInputSharedSegmentID=false)
static const char *	GetStatusTagName ()
	Returns the name of the status tag. More...
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=nullptr)
static bool	ImportModelsToSegmentationNode (vtkIdType folderItemId, vtkMRMLSegmentationNode *segmentationNode, std::string insertBeforeSegmentId="")
	Import models in a folder 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 bool	IsEffectiveExentOutsideReferenceVolume (vtkMRMLVolumeNode *referenceVolumeNode, vtkMRMLSegmentationNode *segmentationNode, vtkStringArray *segmentIDs=nullptr)
static bool	IsSegmentationExentOutsideReferenceGeometry (vtkOrientedImageData *referenceGeometry, vtkOrientedImageData *segmentationGeometry)
static int	IsTypeOf (const char *type)
static vtkSlicerSegmentationsModuleLogic *	New ()
static bool	ReconvertAllRepresentations (vtkMRMLSegmentationNode *segmentationNode, const std::vector< std::string > &segmentIDs={})
static vtkSlicerSegmentationsModuleLogic *	SafeDownCast (vtkObject *o)
static bool	SetBinaryLabelmapToSegment (vtkOrientedImageData *labelmap, vtkMRMLSegmentationNode *segmentationNode, std::string segmentID, int mergeMode=MODE_REPLACE, const int extent[6]=nullptr, bool minimumOfAllSegments=false, const std::vector< std::string > &segmentIdsToOverwrite={})
static void	SetSegmentStatus (vtkSegment *segment, int status)
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
void	OnMRMLSceneNodeAdded (vtkMRMLNode *node) override
	Handle MRML node added events. More...
void	RegisterNodes () override
	Register MRML Node classes to Scene. Gets called automatically when the MRMLScene is attached to this logic class. More...
void	SetMRMLSceneInternal (vtkMRMLScene *newScene) override
	vtkSlicerSegmentationsModuleLogic ()
	~vtkSlicerSegmentationsModuleLogic () override
Protected Member Functions inherited from vtkSlicerModuleLogic
	vtkSlicerModuleLogic ()
	~vtkSlicerModuleLogic () 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. More...
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	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=nullptr)
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 ()
	~vtkMRMLAbstractLogic () override

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

Detailed Description

Definition at line 50 of file vtkSlicerSegmentationsModuleLogic.h.

Member Typedef Documentation

Superclass

typedef vtkSlicerModuleLogic vtkSlicerSegmentationsModuleLogic::Superclass

Definition at line 55 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, combined with a maximum or minimum operation, or set under the mask.
extent	If extent is specified then only that extent of the labelmap is used.

Enumerator
MODE_REPLACE
MODE_MERGE_MAX
MODE_MERGE_MIN
MODE_MERGE_MASK

Definition at line 362 of file vtkSlicerSegmentationsModuleLogic.h.

SegmentStatus

enum vtkSlicerSegmentationsModuleLogic::SegmentStatus

Enumerator
NotStarted
InProgress
Completed
Flagged
LastStatus

Definition at line 385 of file vtkSlicerSegmentationsModuleLogic.h.

Constructor & Destructor Documentation

vtkSlicerSegmentationsModuleLogic()

vtkSlicerSegmentationsModuleLogic::vtkSlicerSegmentationsModuleLogic ( )

protected

~vtkSlicerSegmentationsModuleLogic()

vtkSlicerSegmentationsModuleLogic::~vtkSlicerSegmentationsModuleLogic ( )

overrideprotected

Member Function Documentation

ApplyParentTransformToOrientedImageData()

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

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

ClearSegment()

static bool vtkSlicerSegmentationsModuleLogic::ClearSegment ( vtkMRMLSegmentationNode *  segmentationNode, std::string  segmentID  )

static

Clear the contents of a single segment.

CollapseBinaryLabelmaps()

static void vtkSlicerSegmentationsModuleLogic::CollapseBinaryLabelmaps ( vtkMRMLSegmentationNode *  segmentationNode, bool  forceToSingleLayer  )

static

Collapse all segments into fewer shared labelmap layers

Parameters

segmentationNode	Node containing the segmentation
forceToSingleLayer	If false, then the layers will not be overwritten by each other, if true then the layers can overwrite each other, but the result is guaranteed to have one layer

Returns

True if the representation was created, False otherwise

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 = nullptr  )

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, nullptr otherwise

CreateSegmentFromLabelmapVolumeNode()

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

static

Create segment from labelmap volume MRML node. The contents are set as binary labelmap representation in the segment. Returns nullptr 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. nullptr value means that this consideration is not needed. Default value is nullptr.

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 = nullptr  )

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. nullptr value means that this consideration is not needed. Default value is nullptr.

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, int  extentComputationMode = vtkSegmentation::EXTENT_UNION_OF_EFFECTIVE_SEGMENTS  )

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
extentComputationMode	Labelmap extents will be determined based on this value. By default, the minimum necessary size is used. Set value to vtkSegmentation::EXTENT_REFERENCE_GEOMETRY to use reference geometry extent.

ExportAllSegmentsToModels()

static bool vtkSlicerSegmentationsModuleLogic::ExportAllSegmentsToModels ( vtkMRMLSegmentationNode *  segmentationNode, vtkIdType  folderItemId  )

static

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

Parameters

segmentationNode	Segmentation node from which the the segments are exported
folderItemId	Subject hierarchy folder item ID to export the segments to

ExportSegmentsBinaryLabelmapRepresentationToFiles()

static bool vtkSlicerSegmentationsModuleLogic::ExportSegmentsBinaryLabelmapRepresentationToFiles ( std::string  destinationFolder, vtkMRMLSegmentationNode *  segmentationNode, vtkStringArray *  segmentIds = nullptr, std::string  extension = "nrrd", bool  useCompression = false, vtkMRMLVolumeNode *  referenceVolumeNode = nullptr, int  extentComputationMode = vtkSegmentation::EXTENT_REFERENCE_GEOMETRY, vtkMRMLColorTableNode *  colorTableNode = nullptr  )

static

Export binary surface representation of multiple segments to a single output volume.

Parameters

destinationFolder	Folder name where segments will be exported to
segmentationNode	Segmentation node that has the export color node reference.
segmentIds	List of segment ids to get values for. The order of segmentIds dictates the order of the returned label values.
extension	The file extension used for the output file. "nrrd" by default.
useCompression	If compression should be applied to the output file.
referenceVolumeNode	If specified, then the saved segmentation will match the geometry of referenceVolumeNode
extentComputationMode	If referenceVolumeNode is not specified then the saved segmentation extents will be determined based on this value.
colorTableNode	Optional color table node used to set the exported labelmap values for the segments. Segment names are matched to color names to determine the label values. If a segment name is not found in the color node, then the first unused value outside of the color table range will be used.

ExportSegmentsClosedSurfaceRepresentationToFiles()

static bool vtkSlicerSegmentationsModuleLogic::ExportSegmentsClosedSurfaceRepresentationToFiles ( std::string  destinationFolder, vtkMRMLSegmentationNode *  segmentationNode, vtkStringArray *  segmentIds = nullptr, 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, const std::vector< std::string > &  segmentIDs, bool  lps, double  sizeScale  )

staticprotected

ExportSegmentsClosedSurfaceRepresentationToStlFiles()

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

staticprotected

ExportSegmentsToLabelmapNode() [1/2]

static bool vtkSlicerSegmentationsModuleLogic::ExportSegmentsToLabelmapNode ( vtkMRMLSegmentationNode *  segmentationNode, const std::vector< std::string > &  segmentIDs, vtkMRMLLabelMapVolumeNode *  labelmapNode, vtkMRMLVolumeNode *  referenceVolumeNode = nullptr, int  extentComputationMode = vtkSegmentation::EXTENT_UNION_OF_EFFECTIVE_SEGMENTS, vtkMRMLColorTableNode *  colorTableNode = nullptr  )

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
extentComputationMode	If referenceVolumeNode is not specified then labelmap extents will be determined based on this value. By default, the minimum necessary size is used. Set value to vtkSegmentation::EXTENT_REFERENCE_GEOMETRY to use reference geometry extent.
colorTableNode	If specified then it is used for setting label values in the output labelmapNode (by matching segment name to color name). RGB values in the colorTableNode are updated with corresponding segment colors. New color table entries are added for each segment that had no corresponding entry in the table already.

ExportSegmentsToLabelmapNode() [2/2]

static bool vtkSlicerSegmentationsModuleLogic::ExportSegmentsToLabelmapNode ( vtkMRMLSegmentationNode *  segmentationNode, vtkStringArray *  segmentIDs, vtkMRMLLabelMapVolumeNode *  labelmapNode, vtkMRMLVolumeNode *  referenceVolumeNode = nullptr, int  extentComputationMode = vtkSegmentation::EXTENT_UNION_OF_EFFECTIVE_SEGMENTS, vtkMRMLColorTableNode *  colorTableNode = nullptr  )

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
extentComputationMode	If referenceVolumeNode is not specified then labelmap extents will be determined based on this value. By default, the minimum necessary size is used. Set value to vtkSegmentation::EXTENT_REFERENCE_GEOMETRY to use reference geometry extent.

ExportSegmentsToModels() [1/2]

static bool vtkSlicerSegmentationsModuleLogic::ExportSegmentsToModels ( vtkMRMLSegmentationNode *  segmentationNode, const std::vector< std::string > &  segmentIDs, vtkIdType  folderItemId  )

static

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

Parameters

segmentationNode	Segmentation node from which the the segments are exported
segmentIds	List of segment IDs to export
folderItemId	Subject hierarchy folder item ID to export the segments to

ExportSegmentsToModels() [2/2]

static bool vtkSlicerSegmentationsModuleLogic::ExportSegmentsToModels ( vtkMRMLSegmentationNode *  segmentationNode, vtkStringArray *  segmentIds, vtkIdType  folderItemId  )

static

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

Parameters

segmentationNode	Segmentation node from which the the segments are exported
segmentIds	List of segment IDs to export
folderItemId	Subject hierarchy folder item ID to export the segments to

ExportSegmentToRepresentationNode()

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

static

Export segment to representation MRML node.

1. If representation node is a labelmap node, then the binary labelmap representation of the segment is copied
2. 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 = nullptr, int  extentComputationMode = vtkSegmentation::EXTENT_UNION_OF_EFFECTIVE_SEGMENTS  )

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
extentComputationMode	If referenceVolumeNode is not specified then labelmap extents will be determined based on this value. By default, the minimum necessary size is used. Set value to vtkSegmentation::EXTENT_REFERENCE_GEOMETRY to use reference geometry extent.

ExportVisibleSegmentsToModels()

static bool vtkSlicerSegmentationsModuleLogic::ExportVisibleSegmentsToModels ( vtkMRMLSegmentationNode *  segmentationNode, vtkIdType  folderItemId  )

static

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

Parameters

segmentationNode	Segmentation node from which the the segments are exported
folderItemId	Subject hierarchy folder item ID to export the segments to

GenerateMergedLabelmapInReferenceGeometry()

static void vtkSlicerSegmentationsModuleLogic::GenerateMergedLabelmapInReferenceGeometry ( vtkMRMLSegmentationNode *  segmentationNode, vtkMRMLVolumeNode *  referenceVolumeNode, vtkStringArray *  segmentIDs, int  extentComputationMode, vtkOrientedImageData *  mergedLabelmap_Reference, vtkIntArray *  labelValues = nullptr  )

static

Generate a merged labelmap from the binary labelmap representations of the specified segments

Parameters

segmentationNode	Node containing the segmentation
referenceVolumeNode	Determines geometry of merged labelmap if not nullptr, automatically determined otherwise
segmentIDs	Segment IDs to be converted. If empty, all segments will be converted.
extentComputationMode	If referenceVolumeNode is not specified then the saved segmentation extents will be determined based on this value.
mergedLabelmap_Reference	Output merged labelmap in the reference volume coordinate system
labelValues	Output label values from the color node. Length of the array must be the same as the number of segmentIds.

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.

GetLabelValuesFromColorNode()

static void vtkSlicerSegmentationsModuleLogic::GetLabelValuesFromColorNode ( vtkMRMLSegmentationNode *  segmentationNode, vtkMRMLColorTableNode *  colorTableNode, vtkStringArray *  segmentIds, vtkIntArray *  labelValues  )

static

Gets the label values for the current segment from the color node reference. Label values found by matching color + segment name. If a segment name is not found in the table, then the label value returned for the segment is the first label value outside the table range.

Parameters

segmentationNode	Segmentation node that has the export color node reference.
colorTableNode	Color table used to get the label values for the segments.
segmentIds	List of segment ids to get values for. The order of segmentIds dictates the order of the returned label values.
labelValues	Output label values from the color node. Length of the array will be the same as the number of segmentIds.

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, nullptr 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, nullptr otherwise

GetSegmentationNodeForSegmentSubjectHierarchyItem()

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

static

Utility function for getting the segmentation node for a segmentation or 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

GetSegmentStatus()

static int vtkSlicerSegmentationsModuleLogic::GetSegmentStatus ( vtkSegment *  segment )

static

Returns the value of the status tag for the given segment. If status tag is not specified then vtkSlicerSegmentationsModuleLogic::NotStarted is returned.

GetSegmentStatusAsHumanReadableString()

static const char* vtkSlicerSegmentationsModuleLogic::GetSegmentStatusAsHumanReadableString ( int  segmentStatus )

static

Get the human readable segment status from the SegmentStatus enum value.

GetSegmentStatusAsMachineReadableString()

static const char* vtkSlicerSegmentationsModuleLogic::GetSegmentStatusAsMachineReadableString ( int  segmentStatus )

static

Get the machine readable segment status from the SegmentStatus enum value.

GetSegmentStatusFromMachineReadableString()

static int vtkSlicerSegmentationsModuleLogic::GetSegmentStatusFromMachineReadableString ( std::string  statusString )

static

Get the enum segment status from a machine string.

GetSharedSegmentIDsInMask()

static bool vtkSlicerSegmentationsModuleLogic::GetSharedSegmentIDsInMask ( vtkMRMLSegmentationNode *  segmentationNode, std::string  sharedSegmentID, vtkOrientedImageData *  mask, const int  extent[6], std::vector< std::string > &  segmentIDs, int  maskThreshold = 0.0, bool  includeInputSharedSegmentID = false  )

static

Get the list of segment IDs in the same shared labelmap that are contained within the mask

Parameters

segmentationNode	Node containing the segmentation
sharedSegmentID	Segment ID of the segment that contains the shared labelmap to be checked
mask	Mask labelmap
segmentIDs	Output list of segment IDs under the mask
includeInputSharedSegmentID	If false, sharedSegmentID will not be added to the list of output segment IDs even if it is within the mask

GetStatusTagName()

static const char* vtkSlicerSegmentationsModuleLogic::GetStatusTagName ( )

static

Returns the name of the status tag.

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 = nullptr  )

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.

ImportModelsToSegmentationNode()

static bool vtkSlicerSegmentationsModuleLogic::ImportModelsToSegmentationNode ( vtkIdType  folderItemId, vtkMRMLSegmentationNode *  segmentationNode, std::string  insertBeforeSegmentId = ""  )

static

Import models in a folder 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.

IsEffectiveExentOutsideReferenceVolume()

static bool vtkSlicerSegmentationsModuleLogic::IsEffectiveExentOutsideReferenceVolume ( vtkMRMLVolumeNode *  referenceVolumeNode, vtkMRMLSegmentationNode *  segmentationNode, vtkStringArray *  segmentIDs = nullptr  )

static

Determine if any part of the effective extent is outside of the reference volume geometry

Parameters

referenceVolumeNode	Volume node that contains the reference geometry.
segmentationNode	Segmentation node that contains the effective extent to be checked.
segmentIDs	List of segment IDs that will be used to calculate the effective extent.

Returns

True if the effective segmentation extent is outside of the reference volume, False otherwise.

IsSegmentationExentOutsideReferenceGeometry()

static bool vtkSlicerSegmentationsModuleLogic::IsSegmentationExentOutsideReferenceGeometry ( vtkOrientedImageData *  referenceGeometry, vtkOrientedImageData *  segmentationGeometry  )

static

Determine if any part of the segmentation extent is outside of the reference geometry

Parameters

referenceVolumeNode	Image that contains the reference geometry.
segmentationNode	Image that contains the segmentation geometry.

Returns

True if the segmentation extent is outside of the reference volume, False otherwise.

IsTypeOf()

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

static

LoadSegmentationFromFile()

vtkMRMLSegmentationNode* vtkSlicerSegmentationsModuleLogic::LoadSegmentationFromFile	(	const char *	filename,
		bool	autoOpacities = true,
		const char *	nodeName = nullptr,
		vtkMRMLColorTableNode *	colorTableNode = nullptr
	)

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.
nodeName	Optional string to use for the segmentation node name.
colorTableNode	Optional color node used to name the segments and set segment color.

Returns

Loaded segmentation node

New()

static vtkSlicerSegmentationsModuleLogic* vtkSlicerSegmentationsModuleLogic::New ( )

static

OnMRMLSceneNodeAdded()

void vtkSlicerSegmentationsModuleLogic::OnMRMLSceneNodeAdded ( vtkMRMLNode *  node )

overrideprotectedvirtual

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  )

override

ReconvertAllRepresentations()

static bool vtkSlicerSegmentationsModuleLogic::ReconvertAllRepresentations ( vtkMRMLSegmentationNode *  segmentationNode, const std::vector< std::string > &  segmentIDs = {}  )

static

Reconvert all representations in the segmentation from the master representation

Parameters

segmentationNode	Node containing the segmentation
sharedSegmentID	Segment IDs to be converted. If empty, all segments will be converted.

Returns

True if the representation was created, False otherwise

RegisterNodes()

void vtkSlicerSegmentationsModuleLogic::RegisterNodes ( )

overrideprotectedvirtual

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] = nullptr, bool  minimumOfAllSegments = false, const std::vector< std::string > &  segmentIdsToOverwrite = {}  )

static

SetDefaultSurfaceSmoothingEnabled()

void vtkSlicerSegmentationsModuleLogic::SetDefaultSurfaceSmoothingEnabled

(

bool

enabled

)

SetMRMLSceneInternal()

void vtkSlicerSegmentationsModuleLogic::SetMRMLSceneInternal ( vtkMRMLScene *  newScene )

overrideprotectedvirtual

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.

SetSegmentStatus()

static void vtkSlicerSegmentationsModuleLogic::SetSegmentStatus ( vtkSegment *  segment, int  status  )

static

Set the value of the status tag for the given segment. If setting of vtkSlicerSegmentationsModuleLogic::NotStarted is requested and the status tag does not exist or it is empty then the status tag is not modified.

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 490 of file vtkSlicerSegmentationsModuleLogic.h.

---

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

• Modules/Loadable/Segmentations/Logic/vtkSlicerSegmentationsModuleLogic.h