Defines the basic Graph class which holds sets of nodes, edges and roots to model tubular structures with graph-like topologies such as vascular systems. More...

#include <mlGraph.h>

Inheritance diagram for ml::Graph:

List of all members.

Public Types
enum	{ node, edge }
	Global graph item-type enumeration. More...
enum	ActionType { NoAction = 0, LabelGraph, EditGraph, ModifyRoots, ModifyNodesEdges, NewGraph, NumActionTypes }
	Graph modification modes. Ordered from minor to mayor modifications. More...
typedef std::map< MLint, VesselNode * >	NodeMap
	Internal node storage.
typedef boost::function < VesselNode *(const NodeMap::value_type &) >	NodeAccess
	Helper function returning the VesselNode from a key/value pair of a NodeMap.
typedef boost::function< const VesselNode *(const NodeMap::value_type &) >	ConstNodeAccess
	Helper function returning the VesselNode as const from a key/value pair of a NodeMap.
typedef boost::transform_iterator < NodeAccess, NodeMap::iterator >	NodeIterator
	Iterator used to traverse nodes in a node map (returns data elements of the map instead of tuples).
typedef boost::transform_iterator < ConstNodeAccess, NodeMap::const_iterator >	ConstNodeIterator
	Iterator used to traverse const nodes in a node map (returns data elements of the map instead of tuples).
typedef std::map< MLint, VesselEdge * >	EdgeMap
	Internal edge storage.
typedef boost::function < VesselEdge *(const EdgeMap::value_type &) >	EdgeAccess
	Helper function returning the VesselEdge from a key/value pair of a EdgeMap.
typedef boost::function< const VesselEdge *(const EdgeMap::value_type &) >	ConstEdgeAccess
	Helper function returning the VesselEdge as const from a key/value pair of a EdgeMap.
typedef boost::transform_iterator < EdgeAccess, EdgeMap::iterator >	EdgeIterator
	Iterator used to traverse edges in a edge map (returns data elements of the map instead of tuples).
typedef boost::transform_iterator < ConstEdgeAccess, EdgeMap::const_iterator >	ConstEdgeIterator
	Iterator used to traverse const edges in a edge map (returns data elements of the map instead of tuples).
Public Member Functions
int	getNumCluster () const
bool	getFlag () const
void	setFlag (bool bFlag)
void	closeSkeletonGaps ()
	Closes gaps in the skeletons between the first or last skeleton of a VesselEdge and the closest node.
MLint	splitEdge (MLint edgeID, size_t skeletonIndex)
	Splits edge with id `edgeID` at skeleton index `skeletonIndex` and returns the ID of the additionally created edge.
bool	mergeEdges (VesselEdge parent, VesselEdge child)
void	clampToImage ()
Initialization
	Graph ()
	Default constructor.
	Graph (const Graph &g, bool reorder=false)
	Default copy constructor.
	Graph (const Graph &g, const VesselNode *root, bool reorder=false)
	Construct graph from tree in g.
	Graph (const Graph &g, const std::vector< const VesselNode * > &roots, bool reorder=false)
	Construct graph from trees in g.
	Graph (Graph &g, int clusterId, bool reorder=false)
	Construct graph from subgraph of g, defined by clusterId in g.
virtual Graph *	deepCopy () const
	Implement generic deepCopy functionality using copy constructor.
virtual	~Graph ()
	Destructor.
Creating Elements
VesselEdge *	createEdge (VesselNode predNode, VesselNode succNode, MLint useId=-1)
	Create a VesselEdge with unique id, add it to the Graph and Nodes and return a pointer to it.
VesselEdge *	createEdge (MLint predNodeId, MLint succNodeId, MLint useId=-1)
	Create a VesselEdge with unique id, add it to the Graph and Nodes identified by the respective IDs and return a pointer to it.
VesselNode *	createNode (const Vector3 &pos=Vector3(0), MLint useId=-1)
	Create a VesselNode with unique id, add it to the Graph and return a pointer to it.
VesselNode *	createNode (const ImageVector &pos, MLint useId=-1)
	Create a VesselNode with unique id, add it to the Graph and return a pointer to it.
void	insertRoot (VesselNode *node)
	Insert a node to the list of root nodes.
Copying Elements
void	addGraph (const Graph &g)
	Add an entire graph to the current graph.
void	addGraph (const Graph &g, std::map< const VesselNode , VesselNode > &nodeMapping, std::map< const VesselEdge , VesselEdge > &edgeMapping, std::map< const VesselNode , VesselNode > &rootMapping)
	Add an entire graph to this graph.
void	addSubtrees (const std::vector< const VesselNode * > &roots)
	Add subtrees rooted at nodes `roots` to this graph.
void	copyParts (const std::vector< const VesselNode * > &nodes, const std::vector< const VesselEdge * > &edges, const std::vector< const VesselNode * > &roots)
	Copy a collection of nodes, edges and roots from a different graph to this graph.
void	copyParts (const std::vector< const VesselNode * > &nodes, const std::vector< const VesselEdge * > &edges, const std::vector< const VesselNode * > &roots, std::map< const VesselNode , VesselNode > &nodeMapping, std::map< const VesselEdge , VesselEdge > &edgeMapping, std::map< const VesselNode , VesselNode > &rootMapping)
	Copy a collection of nodes, edges and roots from a different graph to this graph.
Removing Elements
bool	removeEdge (VesselEdge *edge, bool removeEmptyNodes=true)
	Remove an edge from the graph.
bool	removeNode (VesselNode *node)
	Remove a node from the graph.
void	removeRoot (VesselNode *r)
	Remove a root from the graph.
void	clearRoots ()
	Remove all roots that have been defined.
void	clearGraph ()
	Remove all elements from the graph.
Accessing Elements
NodeIterator	beginNode ()
	Provide iterator access to the begin of the node map.
NodeIterator	endNode ()
	Provide iterator access to the end of the node map.
ConstNodeIterator	beginNode () const
	Provide const iterator access to the begin of the node map.
ConstNodeIterator	endNode () const
	Provide const iterator access to the end of the node map.
EdgeIterator	beginEdge ()
	Provide iterator access to the begin of the edge map.
EdgeIterator	endEdge ()
	Provide iterator access to the end of the edge map.
ConstEdgeIterator	beginEdge () const
	Provide const iterator access to the begin of the edge map.
ConstEdgeIterator	endEdge () const
	Provide const iterator access to the end of the edge map.
NodeIterator	beginRoot ()
	Provide iterator access to the begin of the root map.
NodeIterator	endRoot ()
	Provide iterator access to the end of the root map.
ConstNodeIterator	beginRoot () const
	Provide const iterator access to the begin of the root map.
ConstNodeIterator	endRoot () const
	Provide const iterator access to the end of the root map.
size_t	numNodes () const
	Returns the number nodes in this graph.
size_t	numEdges () const
	Returns the number edges in this graph.
size_t	numRoots () const
	Returns the number roots in this graph.
const VesselNode *	getIdNode (MLint id) const
	Get node with id `id`;.
VesselNode *	getIdNode (MLint id)
	Get node with id `id`;.
const VesselEdge *	getIdEdge (MLint id) const
	Get edge with id `id`.
VesselEdge *	getIdEdge (MLint id)
	Get edge with id `id`.
const VesselNode *	getNode (Vector3 pos) const
	Get the node with minimal distance to . Uses method distance() of node classes.
VesselNode *	getNode (Vector3 pos)
	Get the node with minimal distance to . Uses method distance() of node classes.
const VesselEdge *	getEdge (Vector3 pos) const
	Get the edge with minimal distance to . Uses method distance() of edge classes.
VesselEdge *	getEdge (Vector3 pos)
	Get the edge with minimal distance to . Uses method distance() of edge classes.
const VesselNode *	getRoot (Vector3 pos) const
	Get the root node with minimal distance to .
VesselNode *	getRoot (Vector3 pos)
	Get the root node with minimal distance to .
const VesselNode *	getNode (size_t index) const
	Get node via index position.
VesselNode *	getNode (size_t index)
	Get node via index position.
const VesselEdge *	getEdge (size_t index) const
	Get edge via index position.
VesselEdge *	getEdge (size_t index)
	Get edge via index position.
const VesselNode *	getRoot (size_t index) const
	Get root via index position.
VesselNode *	getRoot (size_t index)
	Get root via index position.
size_t	getIndex (const VesselNode *node) const
	Return the index of VesselNode `node` in the nodeMap or numNodes() if node was not found.
size_t	getIndex (const VesselEdge *edge) const
	Return the index of VesselEdge `edge` in the edgeMap or numEdges() if edge was not found.
Properties
PropertyManager::Pointer	getNodePropertyManager ()
	Get access to the GraphPropertyManager for nodes.
PropertyManager::ConstPointer	getNodePropertyManager () const
PropertyManager::Pointer	getEdgePropertyManager ()
	Get access to the GraphPropertyManager for edges.
PropertyManager::ConstPointer	getEdgePropertyManager () const
PropertyManager::Pointer	getSkeletonPropertyManager ()
	Get access to the GraphPropertyManager for skeletons.
PropertyManager::ConstPointer	getSkeletonPropertyManager () const
World/Voxel Coordinates
void	transform (const Matrix4 &m)
void	setToWorldMatrix (const Matrix4 *m)
	Set the conversion matrix for conversions from voxel to world coordinate.
void	setToWorldMatrix (const Matrix4 &m)
	Set the conversion matrix for conversions from voxel to world coordinate.
const Matrix4 *	getToWorldMatrix () const
	Get the conversion matrix for conversions from voxel to world coordinate.
void	getToWorldMatrix (float *mat) const
	Get the conversion matrix for conversions from voxel to world coordinate.
Matrix4	getToVoxelMatrix () const
	Get the conversion matrix for conversions from voxel to world coordinate.
void	setToWorld (void)
	Define all element coordinates to be in world coordinates (no conversion takes place).
void	setToVoxel (void)
	Define all element coordinates to be in voxels coordinates (no conversion takes place).
bool	isWorld () const
	Return whether element coordinates are given in voxel or world coordinates.
void	worldVoxelConvert ()
	Convert all graph coordinates from the current coordinate system to the opposite.
void	convertToVoxel (void)
	Convert all coordinates to voxel coordinates.
void	convertToWorld (void)
	Convert all coordinates to world coordinates.
void	setImgExt (ImageVector v)
ImageVector	getImgExt () const
int	extX () const
int	extY () const
int	extZ () const
void	setVoxelExt (Vector3 v)
Vector3	getVoxelExt () const
Persistence
virtual void	addStateToTree (TreeNode *parent) const
	Overload base-methods: Attaches the object state as children of the given parent node.
	ML_SET_ADDSTATE_VERSION (3)
	Set current addStateToTree() version number:
virtual void	readStateFromTree (TreeNode *parent)
	Reads the object state from the children of the given parent node.
int	getVersion (void)
	Get graph's version.
void	setCurrentVersion (void)
	Set graph's version to persistent version number.
void	setVersion (int version)
	Set version.
Assignment
Graph &	operator= (const Graph &g)
	Clear current graph and build new one with props of g.
Graph *	newGraph (bool bXml=true) const
Basic graph analysis
int	separateGraph ()
	Separate graph into clusters of connected edges.
bool	directGraph (float FloodThresh)
	Build a rooted, directed graph.
void	stripCycles ()
	Strip cyclic edges from the graph First the graph is directed.
void	setRootIdToAllChildren ()
	Descends recursively from all roots to the leaves in the trees and sets the rootId of the according root to all child items (edges and nodes).
void	purifyGraph ()
	Removes orphan nodes and unsets false cyclic edges (edges with a leaf node that are marked as cyclic).
Geometry
SubImageBoxd	getBoundingBox () const
	Calculate graph's bounding box from edge-bounding-boxes.
Static Public Member Functions
static Graph *	skeletonGraphFromBase (Base *a_base)
Static Public Attributes
static graph settings
static bool	hasVesselVoxels
	If true, method Graph::readStateFromTree() restores Vessel Voxels from stored base object.
Static Protected Member Functions
template<typename ResultType , typename ParameterType >
static ResultType	getSecond (const ParameterType &p)
Protected Attributes
bool	_bFlag
	Flag for diverse usage.
bool	_isWorld
	Is the graph in world coordinates? Default is true.
Matrix4	_toWorldMatrix
	Matrix transform to get from voxel to world coordinates.
ImageVector	_imgExt
	Extension of the image the graph is compiled from.
Vector3	_voxelExt
	Extension of a voxel of the image the graph is compiled from.
std::map< MLint, VesselNode * >	_nodes
	Maps of graph items.
std::map< MLint, VesselEdge * >	_edges
std::map< MLint, VesselNode * >	_roots
int	_numCluster
	Number of non-connected edge-clusters.
Friends
class	GraphAnalyser
class	SaveTreeData
class	LoadTreeData
Communication
void	setAction (ActionType action, std::string sender)
ActionType	getActionValue (void) const
void	setActionValue (ActionType action)
void	setActionCallBack (GraphAction *cbObj)
graph labeling (skeleton labels)
static double	getMinSkeletonLabel (void)
	min/max values of skeleton labels
static double	getMaxSkeletonLabel (void)

Detailed Description

Defines the basic Graph class which holds sets of nodes, edges and roots to model tubular structures with graph-like topologies such as vascular systems.

Class Graph is a container of edge and node objects. Edges and nodes may be connected to each other to build up a graph. There may exist several unconnected sub-clusters of connected nodes and edges within the same graph. Edges are not directed a priory. One or more nodes of the graph can be defined as root nodes that are stored by reference as root objects GraphRoot in a separate container of object Graph. Method directGraph( floodThreshold ) is one way to direct the graph according to the currently defined root nodes and edge weights. The directed graph may be called then a forest, i.e. within the Graph object several trees exist, each defined by a root node and directed nodes/edges attached to it.

Important: nodes that are stored in a Graph object may belong logicaly to several trees. For example one node object may be shared by two trees that are connected by this node. Hierarchically the trees are separated when traversing the graph from roots to leaves following the edge directions.

Definition at line 59 of file mlGraph.h.

Member Typedef Documentation

typedef boost::function< const VesselEdge* (const EdgeMap::value_type &) > ml::Graph::ConstEdgeAccess

Helper function returning the VesselEdge as const from a key/value pair of a EdgeMap.

Definition at line 208 of file mlGraph.h.

typedef boost::transform_iterator<ConstEdgeAccess, EdgeMap::const_iterator> ml::Graph::ConstEdgeIterator

Iterator used to traverse const edges in a edge map (returns data elements of the map instead of tuples).

Definition at line 212 of file mlGraph.h.

typedef boost::function< const VesselNode* (const NodeMap::value_type &) > ml::Graph::ConstNodeAccess

Helper function returning the VesselNode as const from a key/value pair of a NodeMap.

Definition at line 197 of file mlGraph.h.

typedef boost::transform_iterator<ConstNodeAccess, NodeMap::const_iterator> ml::Graph::ConstNodeIterator

Iterator used to traverse const nodes in a node map (returns data elements of the map instead of tuples).

Definition at line 201 of file mlGraph.h.

typedef boost::function< VesselEdge* (const EdgeMap::value_type &) > ml::Graph::EdgeAccess

Helper function returning the VesselEdge from a key/value pair of a EdgeMap.

Definition at line 206 of file mlGraph.h.

typedef boost::transform_iterator<EdgeAccess, EdgeMap::iterator> ml::Graph::EdgeIterator

Iterator used to traverse edges in a edge map (returns data elements of the map instead of tuples).

Definition at line 210 of file mlGraph.h.

typedef std::map<MLint, VesselEdge*> ml::Graph::EdgeMap

Internal edge storage.

Definition at line 204 of file mlGraph.h.

typedef boost::function< VesselNode* (const NodeMap::value_type &) > ml::Graph::NodeAccess

Helper function returning the VesselNode from a key/value pair of a NodeMap.

Definition at line 195 of file mlGraph.h.

typedef boost::transform_iterator<NodeAccess, NodeMap::iterator> ml::Graph::NodeIterator

Iterator used to traverse nodes in a node map (returns data elements of the map instead of tuples).

Definition at line 199 of file mlGraph.h.

typedef std::map<MLint, VesselNode*> ml::Graph::NodeMap

Internal node storage.

Definition at line 193 of file mlGraph.h.

Member Enumeration Documentation

anonymous enum

Global graph item-type enumeration.

Sometimes used to distinguish different object lookup modes, e.g. when picking elements based on world coordinates.

Enumerator:

node
edge

Definition at line 69 of file mlGraph.h.

enum ml::Graph::ActionType

Graph modification modes. Ordered from minor to mayor modifications.

Enumerator:

NoAction
LabelGraph
EditGraph
ModifyRoots
ModifyNodesEdges
NewGraph
NumActionTypes

Definition at line 72 of file mlGraph.h.

Constructor & Destructor Documentation

ml::Graph::Graph ( )

Default constructor.

ml::Graph::Graph	(	const Graph &	g,
		bool	reorder = `false`
	)

Default copy constructor.

ml::Graph::Graph	(	const Graph &	g,
		const VesselNode *	root,
		bool	reorder = `false`
	)

Construct graph from tree in g.

ml::Graph::Graph	(	const Graph &	g,
		const std::vector< const VesselNode * > &	roots,
		bool	reorder = `false`
	)

Construct graph from trees in g.

ml::Graph::Graph	(	Graph &	g,
		int	clusterId,
		bool	reorder = `false`
	)

Construct graph from subgraph of g, defined by clusterId in g.

virtual ml::Graph::~Graph ( ) [virtual]

Destructor.

Member Function Documentation

void ml::Graph::addGraph ( const Graph & g ) [inline]

Add an entire graph to the current graph.

Definition at line 144 of file mlGraph.h.

void ml::Graph::addGraph	(	const Graph &	g,
		std::map< const VesselNode , VesselNode > &	nodeMapping,
		std::map< const VesselEdge , VesselEdge > &	edgeMapping,
		std::map< const VesselNode , VesselNode > &	rootMapping
	)

Add an entire graph to this graph.

If an elements ID is already in use in this graph, a new one will be generated for the copy. The node/edge/rootMappings will contain mappings from old to new IDs upon return.

virtual void ml::Graph::addStateToTree ( TreeNode * parent ) const [virtual]

Overload base-methods: Attaches the object state as children of the given parent node.

Reimplemented from ml::Base.

void ml::Graph::addSubtrees ( const std::vector< const VesselNode * > & roots )

Add subtrees rooted at nodes roots to this graph.

EdgeIterator ml::Graph::beginEdge ( ) [inline]

Provide iterator access to the begin of the edge map.

Definition at line 230 of file mlGraph.h.

ConstEdgeIterator ml::Graph::beginEdge ( ) const [inline]

Provide const iterator access to the begin of the edge map.

Definition at line 235 of file mlGraph.h.

NodeIterator ml::Graph::beginNode ( ) [inline]

Provide iterator access to the begin of the node map.

Definition at line 220 of file mlGraph.h.

ConstNodeIterator ml::Graph::beginNode ( ) const [inline]

Provide const iterator access to the begin of the node map.

Definition at line 225 of file mlGraph.h.

NodeIterator ml::Graph::beginRoot ( ) [inline]

Provide iterator access to the begin of the root map.

Definition at line 240 of file mlGraph.h.

ConstNodeIterator ml::Graph::beginRoot ( ) const [inline]

Provide const iterator access to the begin of the root map.

Definition at line 245 of file mlGraph.h.

void ml::Graph::clampToImage ( )

void ml::Graph::clearGraph ( )

Remove all elements from the graph.

void ml::Graph::clearRoots ( )

Remove all roots that have been defined.

void ml::Graph::closeSkeletonGaps ( )

Closes gaps in the skeletons between the first or last skeleton of a VesselEdge and the closest node.

Changes eventually the Graph.

void ml::Graph::convertToVoxel ( void )

Convert all coordinates to voxel coordinates.

Warning: The conversion will be applied even if the coordinates are voxel coordinates already!

void ml::Graph::convertToWorld ( void )

Convert all coordinates to world coordinates.

Warning: The conversion will be applied even if the coordinates are wiorld coordinates already!

void ml::Graph::copyParts	(	const std::vector< const VesselNode * > &	nodes,
		const std::vector< const VesselEdge * > &	edges,
		const std::vector< const VesselNode * > &	roots
	)		`[inline]`

Copy a collection of nodes, edges and roots from a different graph to this graph.

If an elements ID is already in use, a new ID will be generated for the copy.

Definition at line 161 of file mlGraph.h.

void ml::Graph::copyParts	(	const std::vector< const VesselNode * > &	nodes,
		const std::vector< const VesselEdge * > &	edges,
		const std::vector< const VesselNode * > &	roots,
		std::map< const VesselNode , VesselNode > &	nodeMapping,
		std::map< const VesselEdge , VesselEdge > &	edgeMapping,
		std::map< const VesselNode , VesselNode > &	rootMapping
	)

Copy a collection of nodes, edges and roots from a different graph to this graph.

If an elements ID is already in use, a new ID will be generated for the copy. The node/edge/rootMappings will contain mappings from old to new IDs upon return.

VesselEdge* ml::Graph::createEdge	(	VesselNode *	predNode,
		VesselNode *	succNode,
		MLint	useId = `-1`
	)

Create a VesselEdge with unique id, add it to the Graph and Nodes and return a pointer to it.

VesselEdge* ml::Graph::createEdge	(	MLint	predNodeId,
		MLint	succNodeId,
		MLint	useId = `-1`
	)

Create a VesselEdge with unique id, add it to the Graph and Nodes identified by the respective IDs and return a pointer to it.

VesselNode* ml::Graph::createNode	(	const Vector3 &	pos = `Vector3(0)`,
		MLint	useId = `-1`
	)

Create a VesselNode with unique id, add it to the Graph and return a pointer to it.

VesselNode* ml::Graph::createNode	(	const ImageVector &	pos,
		MLint	useId = `-1`
	)		`[inline]`

Create a VesselNode with unique id, add it to the Graph and return a pointer to it.

Definition at line 130 of file mlGraph.h.

References createNode().

Referenced by createNode().

virtual Graph* ml::Graph::deepCopy ( ) const [inline, virtual]

Implement generic deepCopy functionality using copy constructor.

Reimplemented from ml::Base.

Definition at line 102 of file mlGraph.h.

bool ml::Graph::directGraph ( float FloodThresh )

Build a rooted, directed graph.

take root nodes from the _roots vector
attach edges to the roots in order of their weight( VesselNode::weight , VesselEdge::weight)
weight may be set to average minimal radius for an VesselEdge or minimal radius for an VesselNode, for example

WARNING: Graph::directGraph() works for edge and node weights set only. By default all node and edge weights in a graph are set equal to 1.0. To get reasonable flooding results for edge direction, weights has to be set first according to some hierarchy dependent property, e.g. the average minimal distance of an edge. Example:

GraphAnalyser analyzeGraph(this); analyzeGraph.measureAvMinDistance(); for (Graph::EdgeIterator iE = this->beginEdge(); iE != this->endEdge(); ++iE){ dynamic_cast<VesselEdge*>(*iE)->weight = dynamic_cast<VesselEdge*>(*iE)->getAverageMinDistance(); } for (Graph::NodeIterator iN = this->beginNode(); iN != this->endNode(); ++iN){ dynamic_cast<VesselNode*>(*iN)->weight = dynamic_cast<VesselNode*>(*iN)->getMinDistance(); }

EdgeIterator ml::Graph::endEdge ( ) [inline]

Provide iterator access to the end of the edge map.

Definition at line 232 of file mlGraph.h.

ConstEdgeIterator ml::Graph::endEdge ( ) const [inline]

Provide const iterator access to the end of the edge map.

Definition at line 237 of file mlGraph.h.

NodeIterator ml::Graph::endNode ( ) [inline]

Provide iterator access to the end of the node map.

Definition at line 222 of file mlGraph.h.

ConstNodeIterator ml::Graph::endNode ( ) const [inline]

Provide const iterator access to the end of the node map.

Definition at line 227 of file mlGraph.h.

NodeIterator ml::Graph::endRoot ( ) [inline]

Provide iterator access to the end of the root map.

Definition at line 242 of file mlGraph.h.

ConstNodeIterator ml::Graph::endRoot ( ) const [inline]

Provide const iterator access to the end of the root map.

Definition at line 247 of file mlGraph.h.

int ml::Graph::extX ( ) const [inline]

Definition at line 356 of file mlGraph.h.

int ml::Graph::extY ( ) const [inline]

Definition at line 357 of file mlGraph.h.

int ml::Graph::extZ ( ) const [inline]

Definition at line 358 of file mlGraph.h.

ActionType ml::Graph::getActionValue ( void ) const

SubImageBoxd ml::Graph::getBoundingBox ( ) const

Calculate graph's bounding box from edge-bounding-boxes.

VesselEdge* ml::Graph::getEdge ( size_t index )

Get edge via index position.

Deprecated:: WARNING: This method is deprecated and slow! Please adapt your code to not use it.

const VesselEdge* ml::Graph::getEdge ( Vector3 pos ) const

Get the edge with minimal distance to . Uses method distance() of edge classes.

VesselEdge* ml::Graph::getEdge ( Vector3 pos )

Get the edge with minimal distance to . Uses method distance() of edge classes.

const VesselEdge* ml::Graph::getEdge ( size_t index ) const

Get edge via index position.

Deprecated:: WARNING: This method is deprecated and slow! Please adapt your code to not use it.

PropertyManager::Pointer ml::Graph::getEdgePropertyManager ( ) [inline]

Get access to the GraphPropertyManager for edges.

Definition at line 313 of file mlGraph.h.

PropertyManager::ConstPointer ml::Graph::getEdgePropertyManager ( ) const [inline]

Definition at line 314 of file mlGraph.h.

bool ml::Graph::getFlag ( ) const [inline]

Definition at line 366 of file mlGraph.h.

const VesselEdge* ml::Graph::getIdEdge ( MLint id ) const

Get edge with id id.

VesselEdge* ml::Graph::getIdEdge ( MLint id )

Get edge with id id.

const VesselNode* ml::Graph::getIdNode ( MLint id ) const

Get node with id id;.

VesselNode* ml::Graph::getIdNode ( MLint id )

Get node with id id;.

ImageVector ml::Graph::getImgExt ( ) const [inline]

Definition at line 355 of file mlGraph.h.

size_t ml::Graph::getIndex ( const VesselNode * node ) const

Return the index of VesselNode node in the nodeMap or numNodes() if node was not found.

size_t ml::Graph::getIndex ( const VesselEdge * edge ) const

Return the index of VesselEdge edge in the edgeMap or numEdges() if edge was not found.

static double ml::Graph::getMaxSkeletonLabel ( void ) [inline, static]

Definition at line 481 of file mlGraph.h.

static double ml::Graph::getMinSkeletonLabel ( void ) [inline, static]

min/max values of skeleton labels

Definition at line 480 of file mlGraph.h.

const VesselNode* ml::Graph::getNode ( Vector3 pos ) const

Get the node with minimal distance to . Uses method distance() of node classes.

VesselNode* ml::Graph::getNode ( Vector3 pos )

Get the node with minimal distance to . Uses method distance() of node classes.

const VesselNode* ml::Graph::getNode ( size_t index ) const

Get node via index position.

Deprecated:: WARNING: This method is deprecated and slow! Please adapt your code to not use it.

VesselNode* ml::Graph::getNode ( size_t index )

Get node via index position.

Deprecated:: WARNING: This method is deprecated and slow! Please adapt your code to not use it.

PropertyManager::Pointer ml::Graph::getNodePropertyManager ( ) [inline]

Get access to the GraphPropertyManager for nodes.

Definition at line 309 of file mlGraph.h.

PropertyManager::ConstPointer ml::Graph::getNodePropertyManager ( ) const [inline]

Definition at line 310 of file mlGraph.h.

int ml::Graph::getNumCluster ( ) const [inline]

Definition at line 364 of file mlGraph.h.

const VesselNode* ml::Graph::getRoot ( Vector3 pos ) const

Get the root node with minimal distance to .

VesselNode* ml::Graph::getRoot ( Vector3 pos )

Get the root node with minimal distance to .

const VesselNode* ml::Graph::getRoot ( size_t index ) const

Get root via index position.

Deprecated:: WARNING: This method is deprecated and slow! Please adapt your code to not use it.

VesselNode* ml::Graph::getRoot ( size_t index )

Get root via index position.

Deprecated:: WARNING: This method is deprecated and slow! Please adapt your code to not use it.

template<typename ResultType , typename ParameterType >

static ResultType ml::Graph::getSecond ( const ParameterType & p ) [inline, static, protected]

Definition at line 490 of file mlGraph.h.

PropertyManager::ConstPointer ml::Graph::getSkeletonPropertyManager ( ) const [inline]

Definition at line 318 of file mlGraph.h.

PropertyManager::Pointer ml::Graph::getSkeletonPropertyManager ( ) [inline]

Get access to the GraphPropertyManager for skeletons.

Definition at line 317 of file mlGraph.h.

Matrix4 ml::Graph::getToVoxelMatrix ( ) const

Get the conversion matrix for conversions from voxel to world coordinate.

const Matrix4* ml::Graph::getToWorldMatrix ( ) const

Get the conversion matrix for conversions from voxel to world coordinate.

void ml::Graph::getToWorldMatrix ( float * mat ) const

Get the conversion matrix for conversions from voxel to world coordinate.

int ml::Graph::getVersion ( void ) [inline]

Get graph's version.

differs from value getAddStateVersion() if graph is restored from older state and not set by setVersion().

Definition at line 395 of file mlGraph.h.

Vector3 ml::Graph::getVoxelExt ( ) const [inline]

Definition at line 361 of file mlGraph.h.

void ml::Graph::insertRoot ( VesselNode * node )

Insert a node to the list of root nodes.

bool ml::Graph::isWorld ( ) const [inline]

Return whether element coordinates are given in voxel or world coordinates.

Definition at line 343 of file mlGraph.h.

bool ml::Graph::mergeEdges	(	VesselEdge *	parent,
		VesselEdge *	child
	)

ml::Graph::ML_SET_ADDSTATE_VERSION ( 3 )

Set current addStateToTree() version number:

Graph* ml::Graph::newGraph ( bool bXml = true ) const

size_t ml::Graph::numEdges ( ) const [inline]

Returns the number edges in this graph.

Definition at line 252 of file mlGraph.h.

size_t ml::Graph::numNodes ( ) const [inline]

Returns the number nodes in this graph.

Definition at line 250 of file mlGraph.h.

size_t ml::Graph::numRoots ( ) const [inline]

Returns the number roots in this graph.

Definition at line 254 of file mlGraph.h.

Graph& ml::Graph::operator= ( const Graph & g )

Clear current graph and build new one with props of g.

void ml::Graph::purifyGraph ( )

Removes orphan nodes and unsets false cyclic edges (edges with a leaf node that are marked as cyclic).

Also, all the nodes' and edges' ids are set anew. Remove roots that have no succeeding edges, i.e. all edges are attached to other root nodes

virtual void ml::Graph::readStateFromTree ( TreeNode * parent ) [virtual]

Reads the object state from the children of the given parent node.

Reimplemented from ml::Base.

bool ml::Graph::removeEdge	(	VesselEdge *	edge,
		bool	removeEmptyNodes = `true`
	)

Remove an edge from the graph.

bool ml::Graph::removeNode ( VesselNode * node )

Remove a node from the graph.

void ml::Graph::removeRoot ( VesselNode * r )

Remove a root from the graph.

int ml::Graph::separateGraph ( )

Separate graph into clusters of connected edges.

Edges belonging to the same cluster are labeled with ascending cluster-label.

void ml::Graph::setAction	(	ActionType	action,
		std::string	sender
	)

void ml::Graph::setActionCallBack ( GraphAction * cbObj )

void ml::Graph::setActionValue ( ActionType action )

void ml::Graph::setCurrentVersion ( void ) [inline]

Set graph's version to persistent version number.

Definition at line 397 of file mlGraph.h.

void ml::Graph::setFlag ( bool bFlag ) [inline]

Definition at line 367 of file mlGraph.h.

void ml::Graph::setImgExt ( ImageVector v ) [inline]

Definition at line 354 of file mlGraph.h.

void ml::Graph::setRootIdToAllChildren ( )

Descends recursively from all roots to the leaves in the trees and sets the rootId of the according root to all child items (edges and nodes).

void ml::Graph::setToVoxel ( void ) [inline]

Define all element coordinates to be in voxels coordinates (no conversion takes place).

Definition at line 341 of file mlGraph.h.

void ml::Graph::setToWorld ( void ) [inline]

Define all element coordinates to be in world coordinates (no conversion takes place).

Definition at line 339 of file mlGraph.h.

void ml::Graph::setToWorldMatrix ( const Matrix4 * m )

Set the conversion matrix for conversions from voxel to world coordinate.

void ml::Graph::setToWorldMatrix ( const Matrix4 & m )

Set the conversion matrix for conversions from voxel to world coordinate.

void ml::Graph::setVersion ( int version ) [inline]

Set version.

Definition at line 399 of file mlGraph.h.

void ml::Graph::setVoxelExt ( Vector3 v ) [inline]

Definition at line 360 of file mlGraph.h.

static Graph* ml::Graph::skeletonGraphFromBase ( Base * a_base ) [static]

MLint ml::Graph::splitEdge	(	MLint	edgeID,
		size_t	skeletonIndex
	)

Splits edge with id edgeID at skeleton index skeletonIndex and returns the ID of the additionally created edge.

If the edge could not be split (e.g. edgeID not found, no vessel edge or not enough skeletons), -1 is returned.

void ml::Graph::stripCycles ( )

Strip cyclic edges from the graph First the graph is directed.

Than, all cyclic edges are removed to build a graph without cycles.

void ml::Graph::transform ( const Matrix4 & m )

void ml::Graph::worldVoxelConvert ( )

Convert all graph coordinates from the current coordinate system to the opposite.

Friends And Related Function Documentation

friend class GraphAnalyser [friend]

Definition at line 62 of file mlGraph.h.

friend class LoadTreeData [friend]

Definition at line 64 of file mlGraph.h.

friend class SaveTreeData [friend]

Definition at line 63 of file mlGraph.h.

Member Data Documentation

bool ml::Graph::_bFlag [protected]

Flag for diverse usage.

Definition at line 493 of file mlGraph.h.

std::map<MLint, VesselEdge*> ml::Graph::_edges [protected]

Definition at line 506 of file mlGraph.h.

ImageVector ml::Graph::_imgExt [protected]

Extension of the image the graph is compiled from.

Definition at line 500 of file mlGraph.h.

bool ml::Graph::_isWorld [protected]

Is the graph in world coordinates? Default is true.

Definition at line 496 of file mlGraph.h.

std::map<MLint, VesselNode*> ml::Graph::_nodes [protected]

Maps of graph items.

Definition at line 505 of file mlGraph.h.

int ml::Graph::_numCluster [protected]

Number of non-connected edge-clusters.

Default is -1 (not analysed this feature yet). Is determined by method separateGraph() .

Definition at line 511 of file mlGraph.h.

std::map<MLint, VesselNode*> ml::Graph::_roots [protected]

Definition at line 507 of file mlGraph.h.

Matrix4 ml::Graph::_toWorldMatrix [protected]

Matrix transform to get from voxel to world coordinates.

Definition at line 498 of file mlGraph.h.

Vector3 ml::Graph::_voxelExt [protected]

Extension of a voxel of the image the graph is compiled from.

Definition at line 502 of file mlGraph.h.

bool ml::Graph::hasVesselVoxels [static]

If true, method Graph::readStateFromTree() restores Vessel Voxels from stored base object.

default is true.

Definition at line 114 of file mlGraph.h.

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

MeVisLab/Standard/Sources/ML/MLVesselGraph/mlGraph.h

Public Types

Public Member Functions

Static Public Member Functions

Static Public Attributes

Static Protected Member Functions

Protected Attributes

Friends

Communication

graph labeling (skeleton labels)

Detailed Description

Member Typedef Documentation

Member Enumeration Documentation

Constructor & Destructor Documentation

Member Function Documentation

Friends And Related Function Documentation

Member Data Documentation