MRML node for segmentation storage on disk. More...

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

Inheritance diagram for vtkMRMLSegmentationStorageNode:

Collaboration diagram for vtkMRMLSegmentationStorageNode:

[legend]

Public Types
typedef vtkMRMLStorageNode	Superclass

Public Types inherited from vtkMRMLStorageNode
enum	{ Idle, Pending, Scheduled, Transferring, TransferDone, Cancelled, SkippedNoData }

enum	{ CoordinateSystemRAS = 0, RAS = 0, CoordinateSystemLPS = 1, LPS = 1, CoordinateSystemType_Last }

typedef vtkMRMLNode	Superclass

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

typedef vtkObject	Superclass

Public Member Functions
bool	CanReadInReferenceNode (vtkMRMLNode *refNode) override
	Return true if the reference node can be read in. More...

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

vtkMRMLNode *	CreateNodeInstance () override
	Create instance of the default node. Like New only virtual. More...

virtual void	CropToMinimumExtentOff ()

virtual void	CropToMinimumExtentOn ()

virtual const char *	GetClassName ()

virtual bool	GetCropToMinimumExtent ()

const char *	GetDefaultWriteFileExtension () override

const char *	GetNodeTagName () override
	Get node XML tag name (like Storage, Model) More...

virtual int	IsA (const char *type)

void	PrintSelf (ostream &os, vtkIndent indent) override

void	ReadXMLAttributes (const char **atts) override
	Read node attributes from XML file. More...

void	ResetSupportedWriteFileTypes ()
	Reset supported write file types. Called when master representation is changed. More...

virtual void	SetCropToMinimumExtent (bool)

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

Public Member Functions inherited from vtkMRMLStorageNode
unsigned int	AddFileName (const char *fileName)
	Add in another file name to the list of file names More...

unsigned int	AddURI (const char *uri)
	Add in another URI to the list of URI's More...

virtual bool	CanWriteFromReferenceNode (vtkMRMLNode *refNode)

virtual void	ConfigureForDataExchange ()

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

int	FileNameIsInList (const char *fileName)

const char *	GetAbsoluteFilePath (const char *inputPath)

virtual std::string	GetCompressionParameter ()

virtual std::string	GetCompressionParameterFromDisplayName (const std::string &name)
	Returns a string representing the specified preset. More...

virtual std::vector< std::string >	GetCompressionPresetDisplayNames ()
	Returns a list of displayable names of the supported compression presets. More...

virtual const std::vector< CompressionPreset >	GetCompressionPresets ()
	Get a list of all supported compression presets. More...

virtual std::string	GetDisplayNameFromCompressionParameter (const std::string &preset)
	Returns the name of the specified preset. More...

virtual void	GetFileExtensionsFromFileTypes (vtkStringArray inputFileTypes, vtkStringArray outputFileExtensions)

virtual char *	GetFileName ()

std::string	GetFileNameWithoutExtension (const char *fileName=nullptr)

std::string	GetFullNameFromFileName ()

std::string	GetFullNameFromNthFileName (int n)

const char *	GetNthFileName (int n) const
	return the nth file name, null if doesn't exist More...

const char *	GetNthURI (int n)
	Get the nth URI from the list of URI's More...

virtual int	GetNumberOfCompressionPresets ()
	Get the number of compression presets. More...

int	GetNumberOfFileNames () const
	See how many file names were generated during ExecuteInformation More...

int	GetNumberOfURIs ()
	Return how many uri names this storage node holds in it's list More...

virtual int	GetReadState ()
	Get/Set the state of reading. More...

const char *	GetReadStateAsString ()

const char *	GetStateAsString (int state)

virtual vtkMRMLStorableNode *	GetStorableNode ()

vtkTimeStamp	GetStoredTime ()

virtual std::string	GetSupportedFileExtension (const char *fileName=nullptr, bool includeReadable=true, bool includeWriteable=true)

virtual vtkStringArray *	GetSupportedReadFileTypes ()

virtual vtkStringArray *	GetSupportedWriteFileTypes ()

virtual char *	GetTempFileName ()

virtual char *	GetURI ()

virtual vtkURIHandler *	GetURIHandler ()

virtual int	GetUseCompression ()

const vtkMRMLMessageCollection *	GetUserMessages () const

vtkMRMLMessageCollection *	GetUserMessages ()

virtual char *	GetWriteFileFormat ()

virtual int	GetWriteState ()
	Get/Set the state of writing More...

const char *	GetWriteStateAsString ()

void	InvalidateFile ()

int	IsFilePathRelative (const char *filepath)

void	PrintSelf (ostream &os, vtkIndent indent) override

void	ProcessMRMLEvents (vtkObject caller, unsigned long event, void callData) override
	Propagate Progress Event generated in ReadData More...

virtual int	ReadData (vtkMRMLNode *refNode, bool temporaryFile=false)

void	ReadXMLAttributes (const char **atts) override
	Read node attributes from XML file More...

void	ResetFileNameList ()
	Clear the array of file names More...

void	ResetNthFileName (int n, const char *fileName)
	Set the nth file in FileNameList, checks that it is already defined More...

void	ResetNthURI (int n, const char *uri)
	Set the nth uri in URIList, checks that it is already defined More...

void	ResetURIList ()
	Clear the array of URIs More...

virtual void	SetCompressionParameter (std::string)
	Compression parameter that is used to save the node. More...

void	SetDataDirectory (const char *dataDirName)
	Set a new data directory for all files More...

virtual void	SetDefaultWriteFileExtension (const char *ext)

virtual void	SetFileName (const char *)

virtual void	SetReadState (int)

void	SetReadStateCancelled ()

void	SetReadStateIdle ()

void	SetReadStatePending ()

void	SetReadStateScheduled ()

void	SetReadStateSkippedNoData ()

void	SetReadStateTransferDone ()

void	SetReadStateTransferring ()

virtual void	SetTempFileName (const char *)
	A temporary file name used to calculate absolute paths More...

virtual void	SetURI (const char *)
	Location of the remote copy of this file. More...

virtual void	SetURIHandler (vtkURIHandler *uriHandler)

void	SetURIPrefix (const char *uriPrefix)
	Set a new URI base for all URI's More...

virtual void	SetUseCompression (int)

virtual void	SetWriteFileFormat (const char *)
	Allow to set specific file format that this node will write output. More...

virtual void	SetWriteState (int)

void	SetWriteStateCancelled ()

void	SetWriteStateIdle ()

void	SetWriteStatePending ()

void	SetWriteStateScheduled ()

void	SetWriteStateSkippedNoData ()

void	SetWriteStateTransferDone ()

void	SetWriteStateTransferring ()

virtual int	SupportedFileType (const char *fileName)

virtual void	UseCompressionOff ()

virtual void	UseCompressionOn ()
	Use compression on write More...

virtual int	WriteData (vtkMRMLNode *refNode)

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

Public Member Functions inherited from vtkMRMLNode
vtkMRMLNode *	AddAndObserveNodeReferenceID (const char referenceRole, const char referencedNodeID, vtkIntArray *events=nullptr)
	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=nullptr, vtkIntArray *events=nullptr)
	Add a referenceRole. More...

virtual void	AddToSceneOff ()

virtual void	AddToSceneOn ()

virtual void	CopyContent (vtkMRMLNode *node, bool deepCopy=true)
	Copy node contents from another node of the same type. Does not copy node ID, Scene, Name, SingletonTag, HideFromEditors, AddToScene, UndoEnabled, and node references. If deepCopy is set to false then a shallow copy of bulk data (such as image or mesh data) could be made; copying may be faster but the node may share some data with the source node instead of creating an independent copy. More...

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

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

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 vtkIntArray *	GetContentModifiedEvents ()

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 ()
	Get the scene this node has been added to. More...

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

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

virtual char *	GetSingletonTag ()

virtual bool	GetUndoEnabled ()

virtual bool	HasCopyContent () const
	Returns true if the class supports deep and shallow copying node content. More...

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=nullptr)
	This method allows the node to compress events. More...

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

bool	IsSingleton ()

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

virtual void	OnNodeAddedToScene ()

void	PrintSelf (ostream &os, vtkIndent indent) 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=nullptr)
	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=nullptr)
	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)
	This method is for internal use only. Use AddNode method of vtkMRMLScene to add a node to the scene. More...

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

virtual void	SetSelectable (int)

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 void	SetUndoEnabled (bool)

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

virtual void	UndoEnabledOff ()

virtual void	UndoEnabledOn ()

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...

virtual void	UpdateScene (vtkMRMLScene *)

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 int	IsTypeOf (const char *type)

static vtkMRMLSegmentationStorageNode *	New ()

static vtkMRMLSegmentationStorageNode *	SafeDownCast (vtkObject *o)

Static Public Member Functions inherited from vtkMRMLStorageNode
static const char *	GetCoordinateSystemTypeAsString (int id)
	Convert between coordinate system ID and name More...

static int	GetCoordinateSystemTypeFromString (const char *name)

static std::string	GetLowercaseExtensionFromFileName (const std::string &filename)

static int	IsTypeOf (const char *type)

static vtkMRMLStorageNode *	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	AddPolyDataFileNames (std::string path, vtkSegmentation *segmentation)

void	CreateRepresentationsBySerializedNames (vtkSegmentation *segmentation, std::string representationNames)
	Create representations based on serialized representation names string. More...

vtkMRMLSegmentationNode *	GetAssociatedDataNode ()
	Get data node that is associated with this storage node. More...

void	InitializeSupportedReadFileTypes () override
	Initialize all the supported read file types. More...

void	InitializeSupportedWriteFileTypes () override
	Initialize all the supported write file types. More...

virtual int	ReadBinaryLabelmapRepresentation (vtkMRMLSegmentationNode *segmentationNode, std::string path)
	Read binary labelmap representation from nrrd file (3D spatial + list) More...

virtual int	ReadBinaryLabelmapRepresentation4DSpatial (vtkMRMLSegmentationNode *segmentationNode, std::string path)
	Read binary labelmap representation from 4D spatial nrrd file - obsolete. More...

int	ReadDataInternal (vtkMRMLNode *refNode) override
	Read data and set it in the referenced node. More...

virtual int	ReadPolyDataRepresentation (vtkMRMLSegmentationNode *segmentationNode, std::string path)
	Read a poly data representation to file. More...

std::string	SerializeContainedRepresentationNames (vtkSegmentation *segmentation)
	Serialize contained representation names in a string. More...

	vtkMRMLSegmentationStorageNode ()

virtual int	WriteBinaryLabelmapRepresentation (vtkMRMLSegmentationNode *segmentationNode, std::string path)
	Write binary labelmap representation to file. More...

int	WriteDataInternal (vtkMRMLNode *refNode) override
	Write data from a referenced node. More...

virtual int	WritePolyDataRepresentation (vtkMRMLSegmentationNode *segmentationNode, std::string path)
	Write a poly data representation to file. More...

	~vtkMRMLSegmentationStorageNode () override

Protected Member Functions inherited from vtkMRMLStorageNode
void	operator= (const vtkMRMLStorageNode &)

void	StageReadData (vtkMRMLNode *refNode)

void	StageWriteData (vtkMRMLNode *refNode)

virtual void	UpdateCompressionPresets ()

	vtkMRMLStorageNode ()

	vtkMRMLStorageNode (const vtkMRMLStorageNode &)

	~vtkMRMLStorageNode () override

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...

virtual void	OnNodeReferenceAdded (vtkMRMLNodeReference *reference)

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

virtual void	OnNodeReferenceRemoved (vtkMRMLNodeReference *reference)
	Called when a referenced node pointer is removed (set to nullptr). More...

void	operator= (const vtkMRMLNode &)

void	ParseReferencesAttribute (const char *attValue, std::set< 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=nullptr)

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

	vtkMRMLNode ()

	vtkMRMLNode (const vtkMRMLNode &)

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

Static Protected Member Functions
static std::string	GetImageExtentAsString (vtkOrientedImageData *image)

static std::string	GetImageExtentAsString (int extent[6])

static void	GetImageExtentFromString (int extent[6], std::string extentValue)

static bool	GetSegmentationMetaDataFromDicitionary (std::string &headerValue, itk::MetaDataDictionary dictionary, std::string keyName)
	Get the metadata string for the segmentation key from the dictionary. More...

static std::string	GetSegmentationMetaDataKey (const std::string &keyName)

static std::string	GetSegmentColorAsString (vtkMRMLSegmentationNode *segmentationNode, const std::string &segmentId)

static void	GetSegmentColorFromString (double color[3], std::string colorString)

static bool	GetSegmentMetaDataFromDicitionary (std::string &headerValue, itk::MetaDataDictionary dictionary, int segmentIndex, std::string keyName)
	Get the metadata string for the segment and key from the dictionary. More...

static std::string	GetSegmentMetaDataKey (int segmentIndex, const std::string &keyName)

static std::string	GetSegmentTagsAsString (vtkSegment *segment)

static void	SetSegmentTagsFromString (vtkSegment *segment, std::string tagsValue)

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

Protected Attributes
bool	CropToMinimumExtent {false}

Protected Attributes inherited from vtkMRMLStorageNode
std::string	CompressionParameter

std::vector< CompressionPreset >	CompressionPresets

std::string	DefaultWriteFileExtension
	List of supported extensions to write in. More...

char *	FileName

std::vector< std::string >	FileNameList
	An array of file names, should contain the FileName but may not More...

vtkWeakPointer< vtkMRMLStorableNode >	LastFoundStorableNode

int	ReadState

vtkTimeStamp *	StoredTime

vtkStringArray *	SupportedReadFileTypes
	List of supported extensions to read in. More...

vtkStringArray *	SupportedWriteFileTypes

char *	TempFileName

char *	URI

vtkURIHandler *	URIHandler

std::vector< std::string >	URIList
	An array of URI's, should contain the URI but may not More...

int	UseCompression

vtkMRMLMessageCollection *	UserMessages

char *	WriteFileFormat

int	WriteState

Protected Attributes inherited from vtkMRMLNode
int	AddToScene {1}

AttributesType	Attributes

vtkIntArray *	ContentModifiedEvents

char *	Description {nullptr}

int	HideFromEditors {0}

char *	ID {nullptr}

int	InMRMLCallbackFlag {0}
	Flag to avoid event loops More...

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

vtkObserverManager *	MRMLObserverManager

char *	Name {nullptr}

NodeReferenceEventsType	NodeReferenceEvents

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

NodeReferencesType	NodeReferences

int	SaveWithScene {true}

vtkWeakPointer< vtkMRMLScene >	Scene

int	Selectable {1}

int	Selected {0}

bool	UndoEnabled {false}

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

Detailed Description

MRML node for segmentation storage on disk.

Storage nodes has methods to read/write segmentations to/from disk.

Only the master representation of the segmentation is stored on disk. If master representation is labelmap then it is stored as a 4D image volume (.seg.nrrd file). If master representation is polygonal mesh, such as closed surface, then the segmentation is stored as a VTK multiblock data set (.vtm file accompanied by a number of .vtk polydata files).

Specification of .seg.nrrd file:

Segmentation is stored in a standard 4D NRRD image file (one "list" dimension and 3 spatial dimensions). Some additional metadata is stored in custom data fields (starting with Segmentation_ and SegmentN_ prefix), which provide hints on how the segments should be displayed or what they contain. Each 3D volume is a "layer" in the image can contain many non-overlapping segments. If no segments within the segmentation overlap, then the segmentation will be saved as a 3D volume. Upon saving, segments are automatically collapsed to as few layers as possible.

Common custom fields:

Segmentation_ContainedRepresentationNames: names of segmentation representations (separated by | character) that should be displayed. Common representation names includ "Binary labelmap", "Closed surface", "Planar contours", "Fractional labelmap"
Segmentation_ConversionParameters: parameters for algorithms that compute requested representations. Each parameter definition is separated by & character. A parameter definition consists of parameter name, value, and description text, separated by | character.
Segmentation_MasterRepresentation: defines what representation is stored in the file. It is most commonly "Binary labelmap", but there are other representations, too, which are stored in an image volume - such as "Fractional labelmap".
Segmentation_ReferenceImageExtentOffset: This field allows storing an image with arbitrary extent in a NRRD file. NRRD file only stores size of the volume. This field stores voxel coordinates (separated by spaces), therefore the extent can be computed as (ReferenceImageExtentOffsetI, ReferenceImageExtentOffsetI+sizeI-1, ReferenceImageExtentOffsetJ, ReferenceImageExtentOffsetJ+sizeJ-1, ReferenceImageExtentOffsetK, ReferenceImageExtentOffsetk+sizeK-1).

Custom fields for N-th segment (N is between 0 and size of the first axis - 1):

SegmentN_ID: identifier of the segment, it is unique within the segmentation. Can be used for unanmiguously refer to a segment even if the segment's dispay name is changed.
SegmentN_Name: displayable name of the segment.
SegmentN_NameAutoGenerated: if value is 0 then it means that SegmentN_Name was chosen manually by the user, if value is 1 then it means that the segment's name is generated automatically (for example, determined from terminology).
SegmentN_Color: recommended segment display color, defined with red, green, blue values (between 0.0-1.0) separated by space character
SegmentN_ColorAutoGenerated: if value is 0 then it means that SegmentN_Color was chosen manually by the user, if value is 1 then it means that the segment's color is generated automatically (for example, color defined based on terminology).
SegmentN_Extent: 6 space-separated values (minI, maxI, minJ, maxJ, minZ, maxZ) defining extent of non-empty region within the segment.
SegmentN_Tags: List of key:value pairs for storing additional information about the segmen. Key:value pair is separated by a : character, pairs are separated from each other by | character.
SegmentN_Layer: Index of the 3D volume that contains the segment. For segmentations in which the segments do not overlap, the segmentation can be represented as a single 3D volume with 1 layer. Upon saving, segments are automatically collapsed to as few layers as possible.
SegmentN_LabelValue: The scalar value used to represent the segment within its own layer. Segments on separate layers can have the same label value.

A frequently used key is "TerminologyEntry", which defines what the segment contains using DICOM compliant terminology. Value stores 7 parts: terminology context name, category, type, type modifier, anatomic context name, anatomic region, and anatomic region modifier. Parts are separated from each other by ~ character. Five of these parts - category, type, type modifier, anatomic region, and anatomic region modifier are defined by a triplet of (coding scheme designator, code value, and code meaning). Components of the triplet are separated by ^ character.

Example: a mass in the right side of the adrenal gland would be encoded with the tag:

"TerminologyEntry: Segmentation category and type - 3D Slicer General Anatomy list ~SCT^49755003^Morphologically Altered Structure ~SCT^4147007^Mass ~^^ ~Anatomic codes - DICOM master list ~SCT^23451007^Adrenal gland ~SCT^24028007^Right"

Interpretation:

terminology context name: Segmentation category and type - 3D Slicer General Anatomy list
category: codingScheme=SCT, codeValue=49755003, codeMeaning=Morphologically Altered Structure
type: codingScheme=SCT, codeValue=4147007, codeMeaning=Mass
type modifier: not specified
anatomic context name: Anatomic codes - DICOM master list
anatomic region: codingScheme=SCT, codeValue=23451007, codeMeaning=Adrenal gland
anatomic region modifier: codingScheme=SCT, codeValue=^24028007, codeMeaning=Right

Definition at line 132 of file vtkMRMLSegmentationStorageNode.h.

Member Typedef Documentation

◆ Superclass

typedef vtkMRMLStorageNode vtkMRMLSegmentationStorageNode::Superclass

Definition at line 144 of file vtkMRMLSegmentationStorageNode.h.

Constructor & Destructor Documentation

◆ vtkMRMLSegmentationStorageNode()

vtkMRMLSegmentationStorageNode::vtkMRMLSegmentationStorageNode ( )

protected

◆ ~vtkMRMLSegmentationStorageNode()

vtkMRMLSegmentationStorageNode::~vtkMRMLSegmentationStorageNode ( )

overrideprotected

Member Function Documentation

◆ AddPolyDataFileNames()

void vtkMRMLSegmentationStorageNode::AddPolyDataFileNames	(	std::string	path,
		vtkSegmentation *	segmentation
	)

protected

Add all files corresponding to poly data representation to the storage node (multiblock dataset writes segments to individual files in a separate folder)

◆ CanReadInReferenceNode()

bool vtkMRMLSegmentationStorageNode::CanReadInReferenceNode ( vtkMRMLNode * refNode )

overridevirtual

Return true if the reference node can be read in.

Implements vtkMRMLStorageNode.

◆ Copy()

void vtkMRMLSegmentationStorageNode::Copy ( vtkMRMLNode * node )

overridevirtual

Copy the node's attributes to this object.

Reimplemented from vtkMRMLNode.

◆ CreateNodeInstance()

vtkMRMLNode* vtkMRMLSegmentationStorageNode::CreateNodeInstance ( )

overridevirtual

Create instance of the default node. Like New only virtual.

Note: Subclasses should implement this method

Implements vtkMRMLStorageNode.

◆ CreateRepresentationsBySerializedNames()

void vtkMRMLSegmentationStorageNode::CreateRepresentationsBySerializedNames	(	vtkSegmentation *	segmentation,
		std::string	representationNames
	)

protected

Create representations based on serialized representation names string.

◆ CropToMinimumExtentOff()

virtual void vtkMRMLSegmentationStorageNode::CropToMinimumExtentOff ( )

virtual

◆ CropToMinimumExtentOn()

virtual void vtkMRMLSegmentationStorageNode::CropToMinimumExtentOn ( )

virtual

◆ GetAssociatedDataNode()

vtkMRMLSegmentationNode* vtkMRMLSegmentationStorageNode::GetAssociatedDataNode ( )

protected

Get data node that is associated with this storage node.

◆ GetClassName()

virtual const char* vtkMRMLSegmentationStorageNode::GetClassName ( )

virtual

Reimplemented from vtkMRMLStorageNode.

◆ GetCropToMinimumExtent()

virtual bool vtkMRMLSegmentationStorageNode::GetCropToMinimumExtent ( )

virtual

◆ GetDefaultWriteFileExtension()

const char* vtkMRMLSegmentationStorageNode::GetDefaultWriteFileExtension ( )

overridevirtual

Return a default file extension for writing File write extension is determined dynamically from master representation type.

Reimplemented from vtkMRMLStorageNode.

◆ GetImageExtentAsString() [1/2]

static std::string vtkMRMLSegmentationStorageNode::GetImageExtentAsString ( vtkOrientedImageData * image )

staticprotected

◆ GetImageExtentAsString() [2/2]

static std::string vtkMRMLSegmentationStorageNode::GetImageExtentAsString ( int extent[6] )

staticprotected

◆ GetImageExtentFromString()

static void vtkMRMLSegmentationStorageNode::GetImageExtentFromString	(	int	extent[6],
		std::string	extentValue
	)

staticprotected

◆ GetNodeTagName()

const char* vtkMRMLSegmentationStorageNode::GetNodeTagName ( )

inlineoverridevirtual

Get node XML tag name (like Storage, Model)

Implements vtkMRMLStorageNode.

Definition at line 159 of file vtkMRMLSegmentationStorageNode.h.

◆ GetSegmentationMetaDataFromDicitionary()

static bool vtkMRMLSegmentationStorageNode::GetSegmentationMetaDataFromDicitionary	(	std::string &	headerValue,
		itk::MetaDataDictionary	dictionary,
		std::string	keyName
	)

staticprotected

Get the metadata string for the segmentation key from the dictionary.

◆ GetSegmentationMetaDataKey()

static std::string vtkMRMLSegmentationStorageNode::GetSegmentationMetaDataKey ( const std::string & keyName )

staticprotected

◆ GetSegmentColorAsString()

static std::string vtkMRMLSegmentationStorageNode::GetSegmentColorAsString	(	vtkMRMLSegmentationNode *	segmentationNode,
		const std::string &	segmentId
	)

staticprotected

◆ GetSegmentColorFromString()

static void vtkMRMLSegmentationStorageNode::GetSegmentColorFromString	(	double	color[3],
		std::string	colorString
	)

staticprotected

◆ GetSegmentMetaDataFromDicitionary()

static bool vtkMRMLSegmentationStorageNode::GetSegmentMetaDataFromDicitionary	(	std::string &	headerValue,
		itk::MetaDataDictionary	dictionary,
		int	segmentIndex,
		std::string	keyName
	)

staticprotected

Get the metadata string for the segment and key from the dictionary.

◆ GetSegmentMetaDataKey()

static std::string vtkMRMLSegmentationStorageNode::GetSegmentMetaDataKey	(	int	segmentIndex,
		const std::string &	keyName
	)

staticprotected

◆ GetSegmentTagsAsString()

static std::string vtkMRMLSegmentationStorageNode::GetSegmentTagsAsString ( vtkSegment * segment )

staticprotected

◆ InitializeSupportedReadFileTypes()

void vtkMRMLSegmentationStorageNode::InitializeSupportedReadFileTypes ( )

overrideprotectedvirtual

Initialize all the supported read file types.

Reimplemented from vtkMRMLStorageNode.

◆ InitializeSupportedWriteFileTypes()

void vtkMRMLSegmentationStorageNode::InitializeSupportedWriteFileTypes ( )

overrideprotectedvirtual

Initialize all the supported write file types.

Reimplemented from vtkMRMLStorageNode.

◆ IsA()

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

virtual

Reimplemented from vtkMRMLStorageNode.

◆ IsTypeOf()

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

static

◆ New()

static vtkMRMLSegmentationStorageNode* vtkMRMLSegmentationStorageNode::New ( )

static

◆ PrintSelf()

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

override

◆ ReadBinaryLabelmapRepresentation()

virtual int vtkMRMLSegmentationStorageNode::ReadBinaryLabelmapRepresentation	(	vtkMRMLSegmentationNode *	segmentationNode,
		std::string	path
	)

protectedvirtual

Read binary labelmap representation from nrrd file (3D spatial + list)

◆ ReadBinaryLabelmapRepresentation4DSpatial()

virtual int vtkMRMLSegmentationStorageNode::ReadBinaryLabelmapRepresentation4DSpatial	(	vtkMRMLSegmentationNode *	segmentationNode,
		std::string	path
	)

protectedvirtual

Read binary labelmap representation from 4D spatial nrrd file - obsolete.

◆ ReadDataInternal()

int vtkMRMLSegmentationStorageNode::ReadDataInternal ( vtkMRMLNode * refNode )

overrideprotectedvirtual

Read data and set it in the referenced node.

Reimplemented from vtkMRMLStorageNode.

◆ ReadPolyDataRepresentation()

virtual int vtkMRMLSegmentationStorageNode::ReadPolyDataRepresentation	(	vtkMRMLSegmentationNode *	segmentationNode,
		std::string	path
	)

protectedvirtual

Read a poly data representation to file.

◆ ReadXMLAttributes()

void vtkMRMLSegmentationStorageNode::ReadXMLAttributes ( const char ** atts )

overridevirtual

Read node attributes from XML file.

Reimplemented from vtkMRMLNode.

◆ ResetSupportedWriteFileTypes()

void vtkMRMLSegmentationStorageNode::ResetSupportedWriteFileTypes ( )

Reset supported write file types. Called when master representation is changed.

◆ SafeDownCast()

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

static

◆ SerializeContainedRepresentationNames()

std::string vtkMRMLSegmentationStorageNode::SerializeContainedRepresentationNames ( vtkSegmentation * segmentation )

protected

Serialize contained representation names in a string.

◆ SetCropToMinimumExtent()

virtual void vtkMRMLSegmentationStorageNode::SetCropToMinimumExtent ( bool )

virtual

Controls if segmentation labelmap representation is written using minimum necessary extent or the extent of reference image. If false (default): the segmentation will be saved using the same extent as the reference image. If true: the segmentation will be saved using the effective extent. This saves space (especially when saving the segmentation uncompressed), but makes voxel coordinates of the segmentation different from voxel coordinates of the reference image, which may cause problems in software that assume voxel coordinate system of the reference image is the same as the segmentation's.

◆ SetSegmentTagsFromString()

static void vtkMRMLSegmentationStorageNode::SetSegmentTagsFromString	(	vtkSegment *	segment,
		std::string	tagsValue
	)

staticprotected

◆ WriteBinaryLabelmapRepresentation()

virtual int vtkMRMLSegmentationStorageNode::WriteBinaryLabelmapRepresentation	(	vtkMRMLSegmentationNode *	segmentationNode,
		std::string	path
	)

protectedvirtual

Write binary labelmap representation to file.

◆ WriteDataInternal()

int vtkMRMLSegmentationStorageNode::WriteDataInternal ( vtkMRMLNode * refNode )

overrideprotectedvirtual

Write data from a referenced node.

Reimplemented from vtkMRMLStorageNode.

◆ WritePolyDataRepresentation()

virtual int vtkMRMLSegmentationStorageNode::WritePolyDataRepresentation	(	vtkMRMLSegmentationNode *	segmentationNode,
		std::string	path
	)

protectedvirtual

Write a poly data representation to file.

◆ WriteXML()

void vtkMRMLSegmentationStorageNode::WriteXML	(	ostream &	of,
		int	indent
	)

overridevirtual

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

Reimplemented from vtkMRMLNode.

Member Data Documentation

◆ CropToMinimumExtent

bool vtkMRMLSegmentationStorageNode::CropToMinimumExtent {false}

protected

Definition at line 247 of file vtkMRMLSegmentationStorageNode.h.

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

Libs/MRML/Core/vtkMRMLSegmentationStorageNode.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

Constructor & Destructor Documentation

◆ vtkMRMLSegmentationStorageNode()

◆ ~vtkMRMLSegmentationStorageNode()

Member Function Documentation

◆ AddPolyDataFileNames()

◆ CanReadInReferenceNode()

◆ Copy()

◆ CreateNodeInstance()

◆ CreateRepresentationsBySerializedNames()

◆ CropToMinimumExtentOff()

◆ CropToMinimumExtentOn()

◆ GetAssociatedDataNode()

◆ GetClassName()

◆ GetCropToMinimumExtent()

◆ GetDefaultWriteFileExtension()

◆ GetImageExtentAsString() [1/2]

◆ GetImageExtentAsString() [2/2]

◆ GetImageExtentFromString()

◆ GetNodeTagName()

◆ GetSegmentationMetaDataFromDicitionary()

◆ GetSegmentationMetaDataKey()

◆ GetSegmentColorAsString()

◆ GetSegmentColorFromString()

◆ GetSegmentMetaDataFromDicitionary()

◆ GetSegmentMetaDataKey()

◆ GetSegmentTagsAsString()

◆ InitializeSupportedReadFileTypes()

◆ InitializeSupportedWriteFileTypes()

◆ IsA()

◆ IsTypeOf()

◆ New()

◆ PrintSelf()

◆ ReadBinaryLabelmapRepresentation()

◆ ReadBinaryLabelmapRepresentation4DSpatial()

◆ ReadDataInternal()

◆ ReadPolyDataRepresentation()

◆ ReadXMLAttributes()

◆ ResetSupportedWriteFileTypes()

◆ SafeDownCast()

◆ SerializeContainedRepresentationNames()

◆ SetCropToMinimumExtent()

◆ SetSegmentTagsFromString()

◆ WriteBinaryLabelmapRepresentation()

◆ WriteDataInternal()

◆ WritePolyDataRepresentation()

◆ WriteXML()

Member Data Documentation

◆ CropToMinimumExtent