MRML node containing segmentationsSegmentation node stores a set of segments (also known as contours or segmented regions). Segments may overlap and may be stored in various representations (binary labelmap image, closed surface mesh, fractional labelmap image, etc). Segments can be stored in multiple data representations to facilitate visualization and processing. More...

#include <Libs/MRML/Core/vtkMRMLSegmentationNode.h>

Inheritance diagram for vtkMRMLSegmentationNode:

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Collaboration diagram for vtkMRMLSegmentationNode:

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Public Types
enum	{ EditAllowedEverywhere = 0, EditAllowedInsideAllSegments, EditAllowedInsideVisibleSegments, EditAllowedOutsideAllSegments, EditAllowedOutsideVisibleSegments, EditAllowedInsideSingleSegment, EditAllowed_Last }

typedef vtkMRMLDisplayableNode	Superclass

Public Types inherited from vtkMRMLDisplayableNode
enum	{ DisplayModifiedEvent = 17000 }

typedef vtkMRMLTransformableNode	Superclass

Public Types inherited from vtkMRMLTransformableNode
enum	{ TransformModifiedEvent = 15000 }
	TransformModifiedEvent is send when the parent transform is modidied. More...

typedef vtkMRMLStorableNode	Superclass

Public Types inherited from vtkMRMLStorableNode
typedef vtkMRMLNode	Superclass

Public Types inherited from vtkMRMLNode
enum	{ HierarchyModifiedEvent = 16000, IDChangedEvent = 16001, ReferenceAddedEvent, ReferenceModifiedEvent, ReferenceRemovedEvent, ReferencedNodeModifiedEvent }

typedef vtkObject	Superclass

Public Member Functions
std::string	AddSegmentFromBinaryLabelmapRepresentation (vtkOrientedImageData *imageData, std::string segmentName="", double color[3]=NULL, std::string segmentId="")

virtual std::string	AddSegmentFromClosedSurfaceRepresentation (vtkPolyData *polyData, std::string segmentName="", double color[3]=NULL, std::string segmentId="")

virtual void	ApplyTransform (vtkAbstractTransform *transform) VTK_OVERRIDE

virtual void	ApplyTransformMatrix (vtkMatrix4x4 *transformMatrix) VTK_OVERRIDE

virtual bool	CanApplyNonLinearTransforms () const VTK_OVERRIDE

virtual void	Copy (vtkMRMLNode *node) VTK_OVERRIDE
	Copy the node's attributes to this object. More...

virtual bool	CreateBinaryLabelmapRepresentation ()
	Generate binary labelmap representation for all segments. More...

virtual bool	CreateClosedSurfaceRepresentation ()

virtual void	CreateDefaultDisplayNodes () VTK_OVERRIDE
	Create and observe a segmentation display node. More...

virtual vtkMRMLStorageNode *	CreateDefaultStorageNode () VTK_OVERRIDE
	Create a segmentation storage node. More...

virtual vtkMRMLNode *	CreateNodeInstance () VTK_OVERRIDE
	Create instance of a GAD node. More...

virtual void	DeepCopy (vtkMRMLNode *node)
	Copy the entire contents of the node into this node. More...

virtual bool	GenerateEditMask (vtkOrientedImageData maskImage, int editMode, vtkOrientedImageData referenceGeometry, std::string editedSegmentID="", std::string maskSegmentID="", vtkOrientedImageData masterVolume=NULL, double editableIntensityRange[2]=NULL, vtkMRMLSegmentationDisplayNode displayNode=NULL)

virtual bool	GenerateMergedLabelmap (vtkOrientedImageData mergedImageData, int extentComputationMode, vtkOrientedImageData mergedLabelmapGeometry=NULL, const std::vector< std::string > &segmentIDs=std::vector< std::string >())

virtual bool	GenerateMergedLabelmapForAllSegments (vtkOrientedImageData mergedImageData, int extentComputationMode=vtkSegmentation::EXTENT_UNION_OF_EFFECTIVE_SEGMENTS, vtkOrientedImageData mergedLabelmapGeometry=NULL, vtkStringArray *segmentIDs=NULL)

virtual vtkOrientedImageData *	GetBinaryLabelmapRepresentation (const std::string segmentId)

virtual void	GetBounds (double bounds[6]) VTK_OVERRIDE

virtual const char *	GetClassName ()

virtual vtkPolyData *	GetClosedSurfaceRepresentation (const std::string segmentId)

virtual const char *	GetNodeTagName () VTK_OVERRIDE
	Get unique node XML tag name (like Volume, Model) More...

virtual void	GetRASBounds (double bounds[6]) VTK_OVERRIDE

virtual vtkSegmentation *	GetSegmentation ()
	Get segmentation object. More...

double *	GetSegmentCenter (const std::string &segmentID)
	Get position of the segment's center (in the segmentation node's coordinate system) More...

double *	GetSegmentCenterRAS (const std::string &segmentID)

virtual vtkIdType	GetSegmentSubjectHierarchyItem (std::string segmentID, vtkMRMLSubjectHierarchyNode *shNode)

virtual int	IsA (const char *type)

virtual void	OnSubjectHierarchyUIDAdded (vtkMRMLSubjectHierarchyNode *shNode, vtkIdType itemWithNewUID)

void	PrintSelf (ostream &os, vtkIndent indent) VTK_OVERRIDE

virtual void	ReadXMLAttributes (const char **atts) VTK_OVERRIDE
	Set node attributes from name/value pairs. More...

virtual void	RemoveBinaryLabelmapRepresentation ()
	Remove binary labelmap representation for all segments. More...

virtual void	RemoveClosedSurfaceRepresentation ()
	Remove closed surface representation for all segments. More...

void	RemoveSegment (const std::string &segmentID)
	Delete segment from segmentation. More...

void	SetAndObserveSegmentation (vtkSegmentation *segmentation)
	Set and observe segmentation object. More...

virtual bool	SetMasterRepresentationToBinaryLabelmap ()

virtual bool	SetMasterRepresentationToClosedSurface ()

virtual void	SetReferenceImageGeometryParameterFromVolumeNode (vtkMRMLScalarVolumeNode *volumeNode)
	Set reference image geometry conversion parameter from the volume node, keeping reference. More...

virtual void	WriteXML (ostream &of, int indent) VTK_OVERRIDE
	Write this node's information to a MRML file in XML format. More...

Public Member Functions inherited from vtkMRMLDisplayableNode
void	AddAndObserveDisplayNodeID (const char *displayNodeID)

virtual int	GetDisplayClassVisibility (const char *nodeClass)

vtkMRMLDisplayNode *	GetDisplayNode ()

const char *	GetDisplayNodeID ()

virtual const char *	GetDisplayNodeReferenceRole ()

virtual int	GetDisplayVisibility ()

vtkMRMLDisplayNode *	GetNthDisplayNode (int n)

const char *	GetNthDisplayNodeID (int n)

int	GetNumberOfDisplayNodes ()

bool	HasDisplayNodeID (const char *displayNodeID)
	Return true if displayNodeID is in the display node ID list. More...

void	PrintSelf (ostream &os, vtkIndent indent) VTK_OVERRIDE

virtual void	ProcessMRMLEvents (vtkObject , unsigned long, void ) VTK_OVERRIDE
	alternative method to propagate events generated in Display nodes More...

void	RemoveAllDisplayNodeIDs ()
	Remove all display node IDs and associated display nodes. More...

void	RemoveNthDisplayNodeID (int n)

void	SetAndObserveDisplayNodeID (const char *displayNodeID)

void	SetAndObserveNthDisplayNodeID (int n, const char *displayNodeID)

virtual void	SetDisplayClassVisibility (const char *nodeClass, int visible)

virtual void	SetDisplayVisibility (int visible)

virtual void	SetSelectable (int) VTK_OVERRIDE

virtual void	WriteCLI (std::vector< std::string > &vtkNotUsed(commandLine), std::string vtkNotUsed(prefix), int vtkNotUsed(coordinateSystemFlag)=0, int vtkNotUsed(multipleFlag)=1)

Public Member Functions inherited from vtkMRMLTransformableNode
vtkMRMLTransformNode *	GetParentTransformNode ()
	Associated transform MRML node More...

const char *	GetTransformNodeID ()
	Get referenced transform node id. More...

bool	HardenTransform ()

void	PrintSelf (ostream &os, vtkIndent indent) VTK_OVERRIDE

bool	SetAndObserveTransformNodeID (const char *transformNodeID)

virtual void	TransformPointFromWorld (const double inWorld[3], double outLocal[3])

virtual void	TransformPointFromWorld (const vtkVector3d &inWorld, vtkVector3d &outLocal)

virtual void	TransformPointToWorld (const double inLocal[3], double outWorld[3])

virtual void	TransformPointToWorld (const vtkVector3d &inLocal, vtkVector3d &outWorld)

Public Member Functions inherited from vtkMRMLStorableNode
void	AddAndObserveStorageNodeID (const char *storageNodeID)

virtual bool	AddDefaultStorageNode (const char *filename=NULL)

virtual std::string	GetDefaultStorageNodeClassName (const char *filename=NULL)

virtual bool	GetModifiedSinceRead ()

vtkMRMLStorageNode *	GetNthStorageNode (int n)
	Get associated display MRML node More...

const char *	GetNthStorageNodeID (int n)

int	GetNumberOfStorageNodes ()

const char *	GetSlicerDataType ()

vtkMRMLStorageNode *	GetStorageNode ()

const char *	GetStorageNodeID ()

virtual vtkTagTable *	GetUserTagTable ()
	Methods for user-specified metadata. More...

bool	HasStorageNodeID (const char *storageNodeID)
	Return true if storageNodeID is in the storage node ID list. More...

void	PrintSelf (ostream &os, vtkIndent indent) VTK_OVERRIDE

void	SetAndObserveNthStorageNodeID (int n, const char *storageNodeID)

void	SetAndObserveStorageNodeID (const char *storageNodeID)
	String ID of the storage MRML node More...

void	SetSlicerDataType (const char *type)

virtual void	StorableModified ()

virtual void	UpdateScene (vtkMRMLScene *scene) VTK_OVERRIDE
	Finds the storage node and read the data More...

Public Member Functions inherited from vtkMRMLNode
vtkMRMLNode *	AddAndObserveNodeReferenceID (const char referenceRole, const char referencedNodeID, vtkIntArray *events=0)
	Add and observe a reference node from this node for a specific referenceRole. More...

vtkMRMLNode *	AddNodeReferenceID (const char referenceRole, const char referencedNodeID)
	Convenience method that adds a referencedNodeID at the end of the list. More...

void	AddNodeReferenceRole (const char referenceRole, const char mrmlAttributeName=0, vtkIntArray *events=0)
	Add a referenceRole. More...

virtual void	AddToSceneOff ()

virtual void	AddToSceneOn ()

virtual void	CopyReferences (vtkMRMLNode *node)
	Copy the references of the node into this. More...

void	CopyWithoutModifiedEvent (vtkMRMLNode *node)

void	CopyWithScene (vtkMRMLNode *node)
	Copy everything (including Scene and ID) from another node of the same type. More...

void	CopyWithSceneWithSingleModifiedEvent (vtkMRMLNode *node)
	Copy everything (including Scene and ID) from another node of the same type. More...

void	CopyWithSingleModifiedEvent (vtkMRMLNode *node)

void	DisableModifiedEventOff ()

void	DisableModifiedEventOn ()

virtual int	EndModify (int previousDisableModifiedEventState)
	End modifying the node. More...

virtual int	GetAddToScene ()
	node added to MRML scene. More...

const char *	GetAttribute (const char *name)
	Get value of a name value pair attribute. More...

std::vector< std::string >	GetAttributeNames ()
	Get all attribute names. More...

void	GetAttributeNames (vtkStringArray *attributeNames)
	Get all attribute names. Python-wrappable version. More...

virtual char *	GetDescription ()

virtual int	GetDisableModifiedEvent ()
	Turn on/off generating InvokeEvent for set macros. More...

virtual int	GetHideFromEditors ()
	Describes if the node is hidden. More...

virtual char *	GetID ()
	ID use by other nodes to reference this node in XML. More...

virtual int	GetInMRMLCallbackFlag ()
	Flags to avoid event loops. More...

virtual int	GetModifiedEventPending ()

virtual char *	GetName ()

vtkMRMLNode *	GetNodeReference (const char *referenceRole)

const char *	GetNodeReferenceID (const char *referenceRole)
	Utility function that returns the first node id for a specific referenceRole. More...

void	GetNodeReferenceIDs (const char referenceRole, std::vector< const char > &referencedNodeIDs)
	Return a list of the referenced node IDs. More...

void	GetNodeReferenceRoles (std::vector< std::string > &roles)

void	GetNodeReferences (const char referenceRole, std::vector< vtkMRMLNode > &nodes)
	Return a list of the referenced nodes. More...

vtkMRMLNode *	GetNthNodeReference (const char *referenceRole, int n)
	Get referenced MRML node for a specific referenceRole. More...

const char *	GetNthNodeReferenceID (const char *referenceRole, int n)
	Return the string of the Nth node ID for a specific reference role. More...

const char *	GetNthNodeReferenceRole (int n)

int	GetNumberOfNodeReferenceRoles ()

int	GetNumberOfNodeReferences (const char *referenceRole)
	Return the number of node IDs for a specific reference role (and nodes as they always have the same size). More...

virtual int	GetSaveWithScene ()
	Save node with MRML scene. More...

virtual vtkMRMLScene *	GetScene ()
	Only the scene can set itself to the node. More...

virtual int	GetSelectable ()
	Describes if the node is selectable. More...

virtual int	GetSelected ()
	Get/Set for Selected. More...

virtual char *	GetSingletonTag ()

bool	HasNodeReferenceID (const char referenceRole, const char referencedNodeID)
	Return true if referencedNodeID is in the node ID list for a specific referenceRole. More...

virtual void	HideFromEditorsOff ()

virtual void	HideFromEditorsOn ()

virtual void	InvokeCustomModifiedEvent (int eventId, void *callData=NULL)
	This method allows the node to compress events. More...

virtual int	InvokePendingModifiedEvent ()
	Invokes any modified events that are `pending`. More...

bool	IsSingleton ()

virtual void	Modified () VTK_OVERRIDE
	Customized version of Modified() allowing to compress vtkCommand::ModifiedEvent. More...

virtual void	OnNodeAddedToScene ()

void	PrintSelf (ostream &os, vtkIndent indent) VTK_OVERRIDE

virtual void	ProcessChildNode (vtkMRMLNode *)
	Set dependencies between this node and a child node when parsing XML file. More...

void	RemoveAttribute (const char *name)
	Remove attribute with the specified name. More...

void	RemoveNodeReferenceIDs (const char *referenceRole)
	Remove all node IDs and associated nodes for a specific referenceRole. More...

void	RemoveNthNodeReferenceID (const char *referenceRole, int n)
	Convenience method that removes the Nth node ID from the list. More...

virtual void	Reset (vtkMRMLNode *defaultNode)
	Reset node attributes to the initial state as defined in the constructor or the passed default node. More...

virtual void	SaveWithSceneOff ()

virtual void	SaveWithSceneOn ()

virtual void	SelectableOff ()

virtual void	SelectableOn ()

virtual void	SelectedOff ()

virtual void	SelectedOn ()

virtual void	SetAddToScene (int)

void	SetAddToSceneNoModify (int value)

vtkMRMLNode *	SetAndObserveNodeReferenceID (const char referenceRole, const char referencedNodeID, vtkIntArray *events=0)
	Set and observe a reference node from this node for a specific referenceRole. More...

vtkMRMLNode *	SetAndObserveNthNodeReferenceID (const char referenceRole, int n, const char referencedNodeID, vtkIntArray *events=0)
	Set and observe the Nth node ID for a specific reference role. More...

void	SetAttribute (const char name, const char value)
	Set a name value pair attribute. More...

virtual void	SetDescription (const char *)
	Text description of this node, to be set by the user. More...

void	SetDisableModifiedEvent (int onOff)

virtual void	SetHideFromEditors (int)

void	SetInMRMLCallbackFlag (int flag)

virtual void	SetName (const char *)
	Name of this node, to be set by the user. More...

vtkMRMLNode *	SetNodeReferenceID (const char referenceRole, const char referencedNodeID)
	Set a reference to a node with specified nodeID from this node for a specific referenceRole. More...

vtkMRMLNode *	SetNthNodeReferenceID (const char referenceRole, int n, const char referencedNodeID)
	Set a N-th reference from this node with specified referencedNodeID for a specific referenceRole. More...

virtual void	SetSaveWithScene (int)

virtual void	SetScene (vtkMRMLScene *scene)

virtual void	SetSceneReferences ()
	Update the references of the node to the scene. More...

virtual void	SetSelected (int)

void	SetSingletonOff ()

void	SetSingletonOn ()

virtual void	SetSingletonTag (const char *)
	Tag that make this node a singleton in the scene. More...

virtual int	StartModify ()
	Start modifying the node. Disable Modify events. More...

virtual void	UpdateReferenceID (const char oldID, const char newID)
	Update the stored reference to another node in the scene. More...

virtual void	UpdateReferences ()
	The method should remove all pointers and observations to all nodes that are not in the scene anymore. More...

const char *	URLDecodeString (const char *inString)
	Decode a URL string. More...

const char *	URLEncodeString (const char *inString)
	Encode a URL string. More...

virtual void	WriteNodeBodyXML (ostream &of, int indent)
	Write this node's body to a MRML file in XML format. More...

std::string	XMLAttributeDecodeString (const std::string &inString)
	Decode an XML attribute string. More...

std::string	XMLAttributeEncodeString (const std::string &inString)
	Encode an XML attribute string (replaces special characters by code sequences) More...

Static Public Member Functions
static std::string	GetReferenceImageGeometryReferenceRole ()
	Expose reference identifier to get the volume node defining the reference image geometry if any. More...

static const char *	GetSegmentIDAttributeName ()

static int	IsTypeOf (const char *type)

static vtkMRMLSegmentationNode *	New ()

static vtkMRMLSegmentationNode *	SafeDownCast (vtkObject *o)

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

static vtkMRMLDisplayableNode *	SafeDownCast (vtkObject *o)

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

static vtkMRMLTransformableNode *	SafeDownCast (vtkObject *o)

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

static vtkMRMLStorableNode *	SafeDownCast (vtkObject *o)

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

static vtkMRMLNode *	SafeDownCast (vtkObject *o)

Protected Member Functions
void	OnMasterRepresentationModified ()

void	OnSegmentAdded (const char *segmentId)

void	OnSegmentModified (const char *segmentId)

void	OnSegmentRemoved (const char *segmentId)

void	operator= (const vtkMRMLSegmentationNode &)

virtual void	SetSegmentation (vtkSegmentation *)
	Set segmentation object. More...

	vtkMRMLSegmentationNode ()

	vtkMRMLSegmentationNode (const vtkMRMLSegmentationNode &)

virtual	~vtkMRMLSegmentationNode ()

Protected Member Functions inherited from vtkMRMLDisplayableNode
virtual const char *	GetDisplayNodeReferenceMRMLAttributeName ()

virtual void	OnNodeReferenceAdded (vtkMRMLNodeReference *reference) VTK_OVERRIDE
	Called when a node reference ID is added (list size increased). More...

virtual void	OnNodeReferenceModified (vtkMRMLNodeReference *reference) VTK_OVERRIDE
	Called when a node reference ID is modified. More...

virtual void	OnNodeReferenceRemoved (vtkMRMLNodeReference *reference) VTK_OVERRIDE
	Called after a node reference ID is removed (list size decreased). More...

void	operator= (const vtkMRMLDisplayableNode &)

	vtkMRMLDisplayableNode ()

	vtkMRMLDisplayableNode (const vtkMRMLDisplayableNode &)

	~vtkMRMLDisplayableNode ()

Protected Member Functions inherited from vtkMRMLTransformableNode
virtual const char *	GetTransformNodeReferenceMRMLAttributeName ()

virtual const char *	GetTransformNodeReferenceRole ()

void	operator= (const vtkMRMLTransformableNode &)

	vtkMRMLTransformableNode ()

	vtkMRMLTransformableNode (const vtkMRMLTransformableNode &)

	~vtkMRMLTransformableNode ()

Protected Member Functions inherited from vtkMRMLStorableNode
virtual const char *	GetStorageNodeReferenceMRMLAttributeName ()

virtual const char *	GetStorageNodeReferenceRole ()

virtual vtkTimeStamp	GetStoredTime ()

void	operator= (const vtkMRMLStorableNode &)

	vtkMRMLStorableNode ()

	vtkMRMLStorableNode (const vtkMRMLStorableNode &)

	~vtkMRMLStorableNode ()

Protected Member Functions inherited from vtkMRMLNode
virtual const char *	GetMRMLAttributeNameFromReferenceRole (const char *refRole)
	Return the mrml attribute name (if found) associated with a reference role. Return 0 otherwise. More...

virtual const char *	GetReferenceRoleFromMRMLAttributeName (const char *attName)
	Return the reference role (if found) associated with the attribute name found in a MRML scene file. Return 0 otherwise. More...

virtual char *	GetTempURLString ()

void	GetUpdatedReferencedNodeEventList (int &oldReferencedNodeUseCount, int &newReferencedNodeUseCount, vtkIntArray oldConsolidatedEventList, vtkIntArray newConsolidatedEventList, vtkMRMLNode oldReferencedNode, vtkMRMLNode newReferencedNode, vtkMRMLNodeReference referenceToIgnore, vtkIntArray newEvents)

virtual void	InvalidateNodeReferences ()

virtual bool	IsReferenceRoleGeneric (const char *refRole)
	Return true if the reference role is generic (ends with '/') or false otherwise. More...

void	operator= (const vtkMRMLNode &)

void	ParseReferencesAttribute (const char *attValue, std::map< std::string, std::string > &references)

virtual void	SetTempURLString (const char *)
	Get/Set the string used to manage encoding/decoding of strings/URLs with special characters. More...

vtkMRMLNode *	UpdateNodeReferenceEventObserver (vtkMRMLNode oldReferencedNode, vtkMRMLNode newReferencedNode, vtkIntArray newEvents, vtkMRMLNodeReference referenceToIgnore)

virtual void	UpdateNodeReferences (const char *referenceRole=NULL)

virtual void	UpdateNthNodeReference (const char *referenceRole, int n)

	vtkMRMLNode ()

	vtkMRMLNode (const vtkMRMLNode &)

virtual	~vtkMRMLNode ()
	critical to have a virtual destructor! More...

Static Protected Member Functions
static void	SegmentationModifiedCallback (vtkObject caller, unsigned long eid, void clientData, void *callData)
	Callback function for all events from the segmentation object. More...

Static Protected Member Functions inherited from vtkMRMLNode
static void	MRMLCallback (vtkObject caller, unsigned long eid, void clientData, void *callData)

Protected Attributes
vtkSegmentation *	Segmentation
	Segmentation object to store the actual data. More...

vtkSmartPointer< vtkCallbackCommand >	SegmentationModifiedCallbackCommand
	Command handling events from segmentation object. More...

double	SegmentCenterTmp [4]

Protected Attributes inherited from vtkMRMLStorableNode
std::string	SlicerDataType

vtkTimeStamp	StorableModifiedTime

vtkTagTable *	UserTagTable

Protected Attributes inherited from vtkMRMLNode
int	AddToScene

AttributesType	Attributes

char *	Description

int	HideFromEditors

char *	ID

int	InMRMLCallbackFlag
	Flag to avoid event loops More...

vtkCallbackCommand *	MRMLCallbackCommand
	Holders for MRML callbacks. More...

vtkObserverManager *	MRMLObserverManager

char *	Name

NodeReferenceEventsType	NodeReferenceEvents

std::map< std::string, std::string >	NodeReferenceMRMLAttributeNames

NodeReferencesType	NodeReferences

int	SaveWithScene

vtkWeakPointer< vtkMRMLScene >	Scene

int	Selectable

int	Selected

Additional Inherited Members
Protected Types inherited from vtkMRMLNode
typedef std::map< std::string, std::string >	AttributesType

typedef std::map< std::string, vtkSmartPointer< vtkIntArray > >	NodeReferenceEventsType

typedef std::vector< vtkSmartPointer< vtkMRMLNodeReference > >	NodeReferenceListType

typedef std::map< std::string, NodeReferenceListType >	NodeReferencesType

Static Protected Attributes inherited from vtkMRMLDisplayableNode
static const char *	DisplayNodeReferenceMRMLAttributeName

static const char *	DisplayNodeReferenceRole

Static Protected Attributes inherited from vtkMRMLTransformableNode
static const char *	TransformNodeReferenceMRMLAttributeName

static const char *	TransformNodeReferenceRole

Static Protected Attributes inherited from vtkMRMLStorableNode
static const char *	StorageNodeReferenceMRMLAttributeName

static const char *	StorageNodeReferenceRole

Detailed Description

MRML node containing segmentations

Segmentation node stores a set of segments (also known as contours or segmented regions). Segments may overlap and may be stored in various representations (binary labelmap image, closed surface mesh, fractional labelmap image, etc). Segments can be stored in multiple data representations to facilitate visualization and processing.

Storage and automatic conversion between representations are provided by

See also: vtkSegmentation object.

Definition at line 52 of file vtkMRMLSegmentationNode.h.

Member Typedef Documentation

◆ Superclass

typedef vtkMRMLDisplayableNode vtkMRMLSegmentationNode::Superclass

Definition at line 59 of file vtkMRMLSegmentationNode.h.

Member Enumeration Documentation

◆ anonymous enum

anonymous enum

Enumerator
EditAllowedEverywhere	Modification is allowed everywhere.
EditAllowedInsideAllSegments	Modification is allowed inside all segments.
EditAllowedInsideVisibleSegments	Modification is allowed inside all visible segments.
EditAllowedOutsideAllSegments	Modification is allowed outside all segments.
EditAllowedOutsideVisibleSegments	Modification is allowed outside all visible segments.
EditAllowedInsideSingleSegment	Modification is allowed only over the area covered by segment specified in MaskSegmentID.
EditAllowed_Last	Insert valid types above this line.

Definition at line 146 of file vtkMRMLSegmentationNode.h.

Constructor & Destructor Documentation

◆ vtkMRMLSegmentationNode() [1/2]

vtkMRMLSegmentationNode::vtkMRMLSegmentationNode ( )

protected

◆ ~vtkMRMLSegmentationNode()

virtual vtkMRMLSegmentationNode::~vtkMRMLSegmentationNode ( )

protectedvirtual

◆ vtkMRMLSegmentationNode() [2/2]

vtkMRMLSegmentationNode::vtkMRMLSegmentationNode ( const vtkMRMLSegmentationNode & )

protected

Member Function Documentation

◆ AddSegmentFromBinaryLabelmapRepresentation()

std::string vtkMRMLSegmentationNode::AddSegmentFromBinaryLabelmapRepresentation	(	vtkOrientedImageData *	imageData,
		std::string	segmentName = `""`,
		double	color[3] = `NULL`,
		std::string	segmentId = `""`
	)

Add new segment from a binary labelmap.

Returns: Segment ID of the new segment. Empty string if an error occurred.

◆ AddSegmentFromClosedSurfaceRepresentation()

virtual std::string vtkMRMLSegmentationNode::AddSegmentFromClosedSurfaceRepresentation	(	vtkPolyData *	polyData,
		std::string	segmentName = `""`,
		double	color[3] = `NULL`,
		std::string	segmentId = `""`
	)

virtual

Add new segment from a closed surface.

Returns: Segment ID of the new segment. Empty string if an error occurred.

◆ ApplyTransform()

virtual void vtkMRMLSegmentationNode::ApplyTransform ( vtkAbstractTransform * transform )

virtual

Apply a transform on the segmentation

See also: SetAndObserveTransformNodeID, CanApplyNonLinearTransforms

Reimplemented from vtkMRMLTransformableNode.

◆ ApplyTransformMatrix()

virtual void vtkMRMLSegmentationNode::ApplyTransformMatrix ( vtkMatrix4x4 * transformMatrix )

virtual

Apply a transform matrix on the segmentation

See also: SetAndObserveTransformNodeID, ApplyTransform, CanApplyNonLinearTransforms

Reimplemented from vtkMRMLTransformableNode.

◆ CanApplyNonLinearTransforms()

virtual bool vtkMRMLSegmentationNode::CanApplyNonLinearTransforms ( ) const

virtual

Returns true if the transformable node can apply non linear transforms

See also: ApplyTransform

Reimplemented from vtkMRMLTransformableNode.

◆ Copy()

virtual void vtkMRMLSegmentationNode::Copy ( vtkMRMLNode * node )

virtual

Copy the node's attributes to this object.

Reimplemented from vtkMRMLDisplayableNode.

◆ CreateBinaryLabelmapRepresentation()

virtual bool vtkMRMLSegmentationNode::CreateBinaryLabelmapRepresentation ( )

virtual

Generate binary labelmap representation for all segments.

◆ CreateClosedSurfaceRepresentation()

virtual bool vtkMRMLSegmentationNode::CreateClosedSurfaceRepresentation ( )

virtual

Generate closed surface representation for all segments. Useful for 3D visualization.

◆ CreateDefaultDisplayNodes()

virtual void vtkMRMLSegmentationNode::CreateDefaultDisplayNodes ( )

virtual

Create and observe a segmentation display node.

Reimplemented from vtkMRMLDisplayableNode.

◆ CreateDefaultStorageNode()

virtual vtkMRMLStorageNode* vtkMRMLSegmentationNode::CreateDefaultStorageNode ( )

virtual

Create a segmentation storage node.

Reimplemented from vtkMRMLStorableNode.

◆ CreateNodeInstance()

virtual vtkMRMLNode* vtkMRMLSegmentationNode::CreateNodeInstance ( )

virtual

Create instance of a GAD node.

Implements vtkMRMLDisplayableNode.

◆ DeepCopy()

virtual void vtkMRMLSegmentationNode::DeepCopy ( vtkMRMLNode * node )

virtual

Copy the entire contents of the node into this node.

◆ GenerateEditMask()

virtual bool vtkMRMLSegmentationNode::GenerateEditMask	(	vtkOrientedImageData *	maskImage,
		int	editMode,
		vtkOrientedImageData *	referenceGeometry,
		std::string	editedSegmentID = `""`,
		std::string	maskSegmentID = `""`,
		vtkOrientedImageData *	masterVolume = `NULL`,
		double	editableIntensityRange[2] = `NULL`,
		vtkMRMLSegmentationDisplayNode *	displayNode = `NULL`
	)

virtual

Generates an edit mask image. If a mask voxel is non-zero it means that the image at that position is editable.

Parameters

maskImage	output image, contains non-zero voxels where editing is not allowed
editMode	defines editable regions based on existing segments
referenceGeometry	defines image geometry (extent and IJK to world matrix) of the output
editedSegmentID	this segment will be always editable (regardless of editMode), optional
masterVolume	used for intensity-based masking
editableIntensityRange	used for intensity-based masking
displayNode	used when edit mode refers to visible segments. If not specified then the first display node is used.

Returns: Returns true is mask is successfully generated.

◆ GenerateMergedLabelmap()

virtual bool vtkMRMLSegmentationNode::GenerateMergedLabelmap	(	vtkOrientedImageData *	mergedImageData,
		int	extentComputationMode,
		vtkOrientedImageData *	mergedLabelmapGeometry = `NULL`,
		const std::vector< std::string > &	segmentIDs = `std::vector< std::string >()`
	)

virtual

Build merged labelmap of the binary labelmap representations of the specified segments

Parameters

mergedImageData	Output image data for the merged labelmap image data. Voxels of background volume will be of signed short type. Label value of n-th segment in segmentIDs list will be (n + 1). Label value of background = 0.
extentComputationMode	Determines how to compute extents (EXTENT_REFERENCE_GEOMETRY, EXTENT_UNION_OF_SEGMENTS, EXTENT_UNION_OF_SEGMENTS_PADDED, EXTENT_UNION_OF_EFFECTIVE_SEGMENTS, or EXTENT_UNION_OF_EFFECTIVE_SEGMENTS_PADDED).
mergedLabelmapGeometry	Determines geometry of merged labelmap if not NULL, automatically determined otherwise
segmentIDs	List of IDs of segments to include in the merged labelmap. If empty or missing, then all segments are included

Returns: Success flag

◆ GenerateMergedLabelmapForAllSegments()

virtual bool vtkMRMLSegmentationNode::GenerateMergedLabelmapForAllSegments	(	vtkOrientedImageData *	mergedImageData,
		int	extentComputationMode = `vtkSegmentation::EXTENT_UNION_OF_EFFECTIVE_SEGMENTS`,
		vtkOrientedImageData *	mergedLabelmapGeometry = `NULL`,
		vtkStringArray *	segmentIDs = `NULL`
	)

virtual

Python-accessible version of the more generic

See also: GenerateMergedLabelmap. The last argument specifying the list of segments to be included is omitted, which means that all the segments will be merged.; GenerateMergedLabelmap

◆ GetBinaryLabelmapRepresentation()

virtual vtkOrientedImageData* vtkMRMLSegmentationNode::GetBinaryLabelmapRepresentation ( const std::string segmentId )

virtual

Get a segment as binary labelmap. If representation does not exist yet then call CreateBinaryLabelmapRepresentation() before. If binary labelmap is the master representation then the returned object can be modified, and all other representations will be automatically updated.

◆ GetBounds()

virtual void vtkMRMLSegmentationNode::GetBounds ( double bounds[6] )

virtual

Get bounding box in global RAS form (xmin,xmax, ymin,ymax, zmin,zmax). This method always returns the bounds of the untransformed object.

See also: GetRASBounds()

Reimplemented from vtkMRMLDisplayableNode.

◆ GetClassName()

virtual const char* vtkMRMLSegmentationNode::GetClassName ( )

virtual

Reimplemented from vtkMRMLDisplayableNode.

◆ GetClosedSurfaceRepresentation()

virtual vtkPolyData* vtkMRMLSegmentationNode::GetClosedSurfaceRepresentation ( const std::string segmentId )

virtual

Get a segment as binary labelmap. If representation does not exist yet then call CreateClosedSurfaceRepresentation() before. If closed surface is the master representation then the returned object can be modified, and all other representations will be automatically updated.

◆ GetNodeTagName()

virtual const char* vtkMRMLSegmentationNode::GetNodeTagName ( )

inlinevirtual

Get unique node XML tag name (like Volume, Model)

Implements vtkMRMLDisplayableNode.

Definition at line 78 of file vtkMRMLSegmentationNode.h.

◆ GetRASBounds()

virtual void vtkMRMLSegmentationNode::GetRASBounds ( double bounds[6] )

virtual

Get bounding box in global RAS form (xmin,xmax, ymin,ymax, zmin,zmax). This method returns the bounds of the object with any transforms that may be applied to it.

See also: GetBounds()

Reimplemented from vtkMRMLDisplayableNode.

◆ GetReferenceImageGeometryReferenceRole()

static std::string vtkMRMLSegmentationNode::GetReferenceImageGeometryReferenceRole ( )

inlinestatic

Expose reference identifier to get the volume node defining the reference image geometry if any.

Definition at line 182 of file vtkMRMLSegmentationNode.h.

◆ GetSegmentation()

virtual vtkSegmentation* vtkMRMLSegmentationNode::GetSegmentation ( )

virtual

Get segmentation object.

◆ GetSegmentCenter()

double* vtkMRMLSegmentationNode::GetSegmentCenter ( const std::string & segmentID )

Get position of the segment's center (in the segmentation node's coordinate system)

◆ GetSegmentCenterRAS()

double* vtkMRMLSegmentationNode::GetSegmentCenterRAS ( const std::string & segmentID )

Get position of the segment's center in world coordinate system. It is the position returned by GetSegmentCenter() transformed by the segmentation node's parent transform.

◆ GetSegmentIDAttributeName()

static const char* vtkMRMLSegmentationNode::GetSegmentIDAttributeName ( )

inlinestatic

Definition at line 56 of file vtkMRMLSegmentationNode.h.

◆ GetSegmentSubjectHierarchyItem()

virtual vtkIdType vtkMRMLSegmentationNode::GetSegmentSubjectHierarchyItem	(	std::string	segmentID,
		vtkMRMLSubjectHierarchyNode *	shNode
	)

virtual

Get subject hierarchy item belonging to a certain segment

Parameters

segmentID	ID of segment contained by this segmentation to get the subject hierarchy virtual item for
shNode	Subject hierarchy node to search in (there should be only one in the scene and it can be got using vtkMRMLSubjectHierarchyNode::GetSubjectHierarchyNode)

◆ IsA()

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

virtual

Reimplemented from vtkMRMLDisplayableNode.

◆ IsTypeOf()

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

static

◆ New()

static vtkMRMLSegmentationNode* vtkMRMLSegmentationNode::New ( )

static

◆ OnMasterRepresentationModified()

void vtkMRMLSegmentationNode::OnMasterRepresentationModified ( )

protected

Callback function observing the master representation of the segmentation (and each segment within) Invalidates all representations other than the master. These representations will be automatically converted later on demand.

◆ OnSegmentAdded()

void vtkMRMLSegmentationNode::OnSegmentAdded ( const char * segmentId )

protected

Callback function observing segment added events. Triggers update of display properties

◆ OnSegmentModified()

void vtkMRMLSegmentationNode::OnSegmentModified ( const char * segmentId )

protected

Callback function observing segment modified events. Forwards event from the node.

◆ OnSegmentRemoved()

void vtkMRMLSegmentationNode::OnSegmentRemoved ( const char * segmentId )

protected

Callback function observing segment removed events. Triggers update of display properties

◆ OnSubjectHierarchyUIDAdded()

virtual void vtkMRMLSegmentationNode::OnSubjectHierarchyUIDAdded	(	vtkMRMLSubjectHierarchyNode *	shNode,
		vtkIdType	itemWithNewUID
	)

virtual

Function called from segmentation logic when UID is added in a subject hierarchy node. In case the newly added UID is a volume node referenced from this 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)

Parameters

shNode	Subject hierarchy node that contains the item (should be the only SH node in the scene)
itemWithNewUID	ID of subject hierarchy item that just got a new UID

◆ operator=()

void vtkMRMLSegmentationNode::operator= ( const vtkMRMLSegmentationNode & )

protected

◆ PrintSelf()

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

◆ ReadXMLAttributes()

virtual void vtkMRMLSegmentationNode::ReadXMLAttributes ( const char ** atts )

virtual

Set node attributes from name/value pairs.

Reimplemented from vtkMRMLDisplayableNode.

◆ RemoveBinaryLabelmapRepresentation()

virtual void vtkMRMLSegmentationNode::RemoveBinaryLabelmapRepresentation ( )

virtual

Remove binary labelmap representation for all segments.

◆ RemoveClosedSurfaceRepresentation()

virtual void vtkMRMLSegmentationNode::RemoveClosedSurfaceRepresentation ( )

virtual

Remove closed surface representation for all segments.

◆ RemoveSegment()

void vtkMRMLSegmentationNode::RemoveSegment ( const std::string & segmentID )

Delete segment from segmentation.

◆ SafeDownCast()

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

static

◆ SegmentationModifiedCallback()

static void vtkMRMLSegmentationNode::SegmentationModifiedCallback	(	vtkObject *	caller,
		unsigned long	eid,
		void *	clientData,
		void *	callData
	)

staticprotected

Callback function for all events from the segmentation object.

◆ SetAndObserveSegmentation()

void vtkMRMLSegmentationNode::SetAndObserveSegmentation ( vtkSegmentation * segmentation )

Set and observe segmentation object.

◆ SetMasterRepresentationToBinaryLabelmap()

virtual bool vtkMRMLSegmentationNode::SetMasterRepresentationToBinaryLabelmap ( )

virtual

Change master representation. All other representations are automatically computed from the master representation.

◆ SetMasterRepresentationToClosedSurface()

virtual bool vtkMRMLSegmentationNode::SetMasterRepresentationToClosedSurface ( )

virtual

Change master representation. All other representations are automatically computed from the master representation.

◆ SetReferenceImageGeometryParameterFromVolumeNode()

virtual void vtkMRMLSegmentationNode::SetReferenceImageGeometryParameterFromVolumeNode ( vtkMRMLScalarVolumeNode * volumeNode )

virtual

Set reference image geometry conversion parameter from the volume node, keeping reference.

◆ SetSegmentation()

virtual void vtkMRMLSegmentationNode::SetSegmentation ( vtkSegmentation * )

protectedvirtual

Set segmentation object.

◆ WriteXML()

virtual void vtkMRMLSegmentationNode::WriteXML	(	ostream &	of,
		int	indent
	)

virtual

Write this node's information to a MRML file in XML format.

Reimplemented from vtkMRMLDisplayableNode.

Member Data Documentation

◆ Segmentation

vtkSegmentation* vtkMRMLSegmentationNode::Segmentation

protected

Segmentation object to store the actual data.

Definition at line 276 of file vtkMRMLSegmentationNode.h.

◆ SegmentationModifiedCallbackCommand

vtkSmartPointer<vtkCallbackCommand> vtkMRMLSegmentationNode::SegmentationModifiedCallbackCommand

protected

Command handling events from segmentation object.

Definition at line 279 of file vtkMRMLSegmentationNode.h.

◆ SegmentCenterTmp

double vtkMRMLSegmentationNode::SegmentCenterTmp[4]

protected

Temporary buffer that holds value returned by GetSegmentCenter(...) and GetSegmentCenterRAS(...) Has 4 components to allow usage in homogeneous transformations

Definition at line 283 of file vtkMRMLSegmentationNode.h.

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

Libs/MRML/Core/vtkMRMLSegmentationNode.h

Public Types

Public Member Functions

Static Public Member Functions

Protected Member Functions

Static Protected Member Functions

Protected Attributes

Additional Inherited Members

Detailed Description

Member Typedef Documentation

◆ Superclass

Member Enumeration Documentation

◆ anonymous enum

Constructor & Destructor Documentation

◆ vtkMRMLSegmentationNode() [1/2]

◆ ~vtkMRMLSegmentationNode()

◆ vtkMRMLSegmentationNode() [2/2]

Member Function Documentation

◆ AddSegmentFromBinaryLabelmapRepresentation()

◆ AddSegmentFromClosedSurfaceRepresentation()

◆ ApplyTransform()

◆ ApplyTransformMatrix()

◆ CanApplyNonLinearTransforms()

◆ Copy()

◆ CreateBinaryLabelmapRepresentation()

◆ CreateClosedSurfaceRepresentation()

◆ CreateDefaultDisplayNodes()

◆ CreateDefaultStorageNode()

◆ CreateNodeInstance()

◆ DeepCopy()

◆ GenerateEditMask()

◆ GenerateMergedLabelmap()

◆ GenerateMergedLabelmapForAllSegments()

◆ GetBinaryLabelmapRepresentation()

◆ GetBounds()

◆ GetClassName()

◆ GetClosedSurfaceRepresentation()

◆ GetNodeTagName()

◆ GetRASBounds()

◆ GetReferenceImageGeometryReferenceRole()

◆ GetSegmentation()

◆ GetSegmentCenter()

◆ GetSegmentCenterRAS()

◆ GetSegmentIDAttributeName()

◆ GetSegmentSubjectHierarchyItem()

◆ IsA()

◆ IsTypeOf()

◆ New()

◆ OnMasterRepresentationModified()

◆ OnSegmentAdded()

◆ OnSegmentModified()

◆ OnSegmentRemoved()

◆ OnSubjectHierarchyUIDAdded()

◆ operator=()

◆ PrintSelf()

◆ ReadXMLAttributes()

◆ RemoveBinaryLabelmapRepresentation()

◆ RemoveClosedSurfaceRepresentation()

◆ RemoveSegment()

◆ SafeDownCast()

◆ SegmentationModifiedCallback()

◆ SetAndObserveSegmentation()

◆ SetMasterRepresentationToBinaryLabelmap()

◆ SetMasterRepresentationToClosedSurface()

◆ SetReferenceImageGeometryParameterFromVolumeNode()

◆ SetSegmentation()

◆ WriteXML()

Member Data Documentation

◆ Segmentation

◆ SegmentationModifiedCallbackCommand

◆ SegmentCenterTmp