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 Graph:

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. More...

typedef boost::function< VesselNode *(const NodeMap::value_type &) >	NodeAccess
	Helper function returning the VesselNode from a key/value pair of a NodeMap. More...

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. More...

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). More...

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). More...

typedef std::map< MLint, VesselEdge * >	EdgeMap
	Internal edge storage. More...

typedef boost::function< VesselEdge *(const EdgeMap::value_type &) >	EdgeAccess
	Helper function returning the VesselEdge from a key/value pair of a EdgeMap. More...

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. More...

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). More...

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). More...

Public Member Functions
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. More...

bool	mergeEdges (VesselEdge parent, VesselEdge child)

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. More...

void	clampToImage ()

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). More...

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

void	removeOrphanNodes ()
	Remove nodes with no edges attached. More...

Initialization
	Graph ()
	Default constructor. More...

	Graph (const Graph &g, bool reorder=false)
	Default copy constructor. More...

	Graph (const Graph &g, const VesselNode *root, bool reorder=false)
	Construct graph from tree in g. More...

	Graph (const Graph &g, const std::vector< const VesselNode * > &roots, bool reorder=false)
	Construct graph from trees in g. More...

	Graph (Graph &g, int clusterId, bool reorder=false)
	Construct graph from subgraph of g, defined by clusterId in g. More...

Graph *	deepCopy () const override
	Implement generic deepCopy functionality using copy constructor. More...

	~Graph () override
	Destructor. More...

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. More...

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. More...

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. More...

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. More...

void	insertRoot (VesselNode *node)
	Insert a node to the list of root nodes. More...

Copying Elements
void	addGraph (const Graph &g)
	Add an entire graph to the current graph. More...

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. More...

void	addSubtrees (const std::vector< const VesselNode * > &roots)
	Add subtrees rooted at nodes `roots` to this graph. More...

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. More...

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. More...

Removing Elements
bool	removeEdge (VesselEdge *edge, bool removeEmptyNodes=true)
	Remove an edge from the graph. More...

bool	removeNode (VesselNode *node)
	Remove a node from the graph. More...

void	removeRoot (VesselNode *r)
	Remove a root from the graph. More...

void	clearRoots ()
	Remove all roots that have been defined. More...

void	clearGraph ()
	Remove all elements from the graph. More...

Accessing Elements
NodeIterator	beginNode ()
	Provide iterator access to the begin of the node map. More...

NodeIterator	endNode ()
	Provide iterator access to the end of the node map. More...

ConstNodeIterator	beginNode () const
	Provide const iterator access to the begin of the node map. More...

ConstNodeIterator	endNode () const
	Provide const iterator access to the end of the node map. More...

EdgeIterator	beginEdge ()
	Provide iterator access to the begin of the edge map. More...

EdgeIterator	endEdge ()
	Provide iterator access to the end of the edge map. More...

ConstEdgeIterator	beginEdge () const
	Provide const iterator access to the begin of the edge map. More...

ConstEdgeIterator	endEdge () const
	Provide const iterator access to the end of the edge map. More...

NodeIterator	beginRoot ()
	Provide iterator access to the begin of the root map. More...

NodeIterator	endRoot ()
	Provide iterator access to the end of the root map. More...

ConstNodeIterator	beginRoot () const
	Provide const iterator access to the begin of the root map. More...

ConstNodeIterator	endRoot () const
	Provide const iterator access to the end of the root map. More...

size_t	numNodes () const
	Returns the number nodes in this graph. More...

size_t	numEdges () const
	Returns the number edges in this graph. More...

size_t	numRoots () const
	Returns the number roots in this graph. More...

const VesselNode *	getIdNode (MLint id) const
	Get node with id `id`;. More...

VesselNode *	getIdNode (MLint id)
	Get node with id `id`;. More...

const VesselEdge *	getIdEdge (MLint id) const
	Get edge with id `id`. More...

VesselEdge *	getIdEdge (MLint id)
	Get edge with id `id`. More...

const VesselNode *	getNode (Vector3 pos) const
	Get the node with minimal distance to \cpos. Uses method distance() of node classes. More...

VesselNode *	getNode (Vector3 pos)
	Get the node with minimal distance to \cpos. Uses method distance() of node classes. More...

const VesselEdge *	getEdge (Vector3 pos) const
	Get the edge with minimal distance to \cpos. Uses method distance() of edge classes. More...

VesselEdge *	getEdge (Vector3 pos)
	Get the edge with minimal distance to \cpos. Uses method distance() of edge classes. More...

const VesselNode *	getRoot (Vector3 pos) const
	Get the root node with minimal distance to \cpos. More...

VesselNode *	getRoot (Vector3 pos)
	Get the root node with minimal distance to \cpos. More...

const VesselNode *	getNode (size_t index) const
	Get node via index position. More...

VesselNode *	getNode (size_t index)
	Get node via index position. More...

const VesselEdge *	getEdge (size_t index) const
	Get edge via index position. More...

VesselEdge *	getEdge (size_t index)
	Get edge via index position. More...

const VesselNode *	getRoot (size_t index) const
	Get root via index position. More...

VesselNode *	getRoot (size_t index)
	Get root via index position. More...

size_t	getIndex (const VesselNode *node) const
	Return the index of VesselNode `node` in the nodeMap or numNodes() if node was not found. More...

size_t	getIndex (const VesselEdge *edge) const
	Return the index of VesselEdge `edge` in the edgeMap or numEdges() if edge was not found. More...

Properties
Get access to the GraphPropertyManager for nodes.
PropertyManager::Pointer	getNodePropertyManager ()

PropertyManager::ConstPointer	getNodePropertyManager () const

PropertyManager::Pointer	getEdgePropertyManager ()
	Get access to the GraphPropertyManager for edges. More...

PropertyManager::ConstPointer	getEdgePropertyManager () const

PropertyManager::Pointer	getSkeletonPropertyManager ()
	Get access to the GraphPropertyManager for skeletons. More...

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. More...

void	setToWorldMatrix (const Matrix4 &m)
	Set the conversion matrix for conversions from voxel to world coordinate. More...

const Matrix4 *	getToWorldMatrix () const
	Get the conversion matrix for conversions from voxel to world coordinate. More...

void	getToWorldMatrix (float *mat) const
	Get the conversion matrix for conversions from voxel to world coordinate. More...

Matrix4	getToVoxelMatrix () const
	Get the conversion matrix for conversions from world to voxel coordinate. More...

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

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

bool	isWorld () const
	Return whether element coordinates are given in voxel or world coordinates. More...

void	worldVoxelConvert ()
	Convert all graph coordinates from the current coordinate system to the opposite. More...

void	convertToVoxel (void)
	Convert all coordinates to voxel coordinates. More...

void	convertToWorld (void)
	Convert all coordinates to world coordinates. More...

void	setImgExt (ImageVector v)

ImageVector	getImgExt () const

MLint	extX () const

MLint	extY () const

MLint	extZ () const

void	setVoxelExt (Vector3 v)

Vector3	getVoxelExt () const

Assignment
Graph &	operator= (const Graph &g)
	Clear current graph and build new one with props of g. More...

Graph *	newGraph (bool unusedDeprecated=true) const
	Allocate new graph with same properties as this (slowly). More...

Basic graph analysis
int	separateGraph ()
	Separate graph into clusters of connected edges. More...

bool	directGraph (double FloodThresh)
	Build a rooted, directed graph. More...

void	stripCycles ()
	Strip cyclic edges from the graph. More...

Geometry
SubImageBoxd	getBoundingBox () const
	Calculate graph's bounding box from edge-bounding-boxes. More...

Persistence
void	addStateToTree (TreeNode *parent) const override
	Overload base-methods: Attaches the object state as children of the given parent node. More...

	ML_SET_ADDSTATE_VERSION (3)
	Set current addStateToTree() version number: More...

void	readStateFromTree (TreeNode *parent) override
	Reads the object state from the children of the given parent node. More...

int	getVersion (void)
	Get graph's version. More...

void	setCurrentVersion (void)
	Set graph's version to persistent version number. More...

void	setVersion (int version)
	Set version. More...

bool	getUseBinaryPersistence ()

void	useBinaryPersistence (bool use)
	Set whether to use binary persistence instead of textual representation (text being the default). More...

std::string	toBinaryData () const
	Returns string containing binary representation of all data necessary to reconstruct the graph. More...

void	fromBinaryData (const std::string &data)
	Reconstructs the graph using the binary data. More...

Protected Member Functions
void	_setRootIdToChildren (int rootId, VesselNode node, VesselEdge predEdge)
	Sets the given root id to the given node and its child edges and calls itself recursively until the node is a leaf node. More...

bool	_isContainedInImageExtent (const Vector3 &pos, const Matrix4 &toVoxelMatrix)

Static Protected Member Functions
template<typename ResultType , typename ParameterType >
static ResultType	getSecond (const ParameterType &p)

Protected Attributes
bool	_isWorld
	Is the graph in world coordinates? Default is true. More...

Matrix4	_toWorldMatrix
	Matrix transform to get from voxel to world coordinates. More...

ImageVector	_imgExt
	Extension of the image the graph is compiled from. More...

Vector3	_voxelExt
	Extension of a voxel of the image the graph is compiled from. More...

std::map< MLint, VesselNode * >	_nodes
	Maps of graph items. More...

std::map< MLint, VesselEdge * >	_edges

std::map< MLint, VesselNode * >	_roots

bool	_bFlag
	Flag for diverse usage. More...

int	_numCluster
	Number of non-connected edge-clusters. More...

Friends
class	GraphAnalyser

class	SaveTreeData

class	LoadTreeData

Communication
ActionType	_action

GraphAction *	_actionCBObject

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

ActionType	getActionValue (void) const

void	setActionValue (ActionType action)

void	setActionCallBack (GraphAction *cbObj)

graph labeling (skeleton labels)
min/max values of skeleton labels
static double	MIN_SKELETON_LABEL

static double	MAX_SKELETON_LABEL

static double	getMinSkeletonLabel (void)

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 63 of file mlGraph.h.

Member Typedef Documentation

◆ ConstEdgeAccess

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

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

Definition at line 196 of file mlGraph.h.

◆ ConstEdgeIterator

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

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

Definition at line 200 of file mlGraph.h.

◆ ConstNodeAccess

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

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

Definition at line 185 of file mlGraph.h.

◆ ConstNodeIterator

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

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

Definition at line 189 of file mlGraph.h.

◆ EdgeAccess

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

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

Definition at line 194 of file mlGraph.h.

◆ EdgeIterator

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

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

Definition at line 198 of file mlGraph.h.

◆ EdgeMap

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

Internal edge storage.

Definition at line 192 of file mlGraph.h.

◆ NodeAccess

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

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

Definition at line 183 of file mlGraph.h.

◆ NodeIterator

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

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

Definition at line 187 of file mlGraph.h.

◆ NodeMap

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

Internal node storage.

Definition at line 181 of file mlGraph.h.

Member Enumeration Documentation

◆ anonymous enum

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 73 of file mlGraph.h.

◆ ActionType

enum Graph::ActionType

Graph modification modes. Ordered from minor to mayor modifications.

Enumerator
NoAction
LabelGraph
EditGraph
ModifyRoots
ModifyNodesEdges
NewGraph
NumActionTypes

Definition at line 448 of file mlGraph.h.

Constructor & Destructor Documentation

◆ Graph() [1/5]

Graph::Graph ( )

Default constructor.

◆ Graph() [2/5]

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

Default copy constructor.

◆ Graph() [3/5]

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

Construct graph from tree in g.

◆ Graph() [4/5]

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

Construct graph from trees in g.

◆ Graph() [5/5]

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

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

◆ ~Graph()

Graph::~Graph ( )

override

Destructor.

Member Function Documentation

◆ _isContainedInImageExtent()

bool Graph::_isContainedInImageExtent	(	const Vector3 &	pos,
		const Matrix4 &	toVoxelMatrix
	)

protected

◆ _setRootIdToChildren()

void Graph::_setRootIdToChildren	(	int	rootId,
		VesselNode *	node,
		VesselEdge *	predEdge
	)

protected

Sets the given root id to the given node and its child edges and calls itself recursively until the node is a leaf node.

◆ addGraph() [1/2]

void Graph::addGraph ( const Graph & g )

inline

Add an entire graph to the current graph.

Definition at line 132 of file mlGraph.h.

◆ addGraph() [2/2]

void 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.

◆ addStateToTree()

void Graph::addStateToTree ( TreeNode * parent ) const

override

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

◆ addSubtrees()

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

Add subtrees rooted at nodes roots to this graph.

◆ beginEdge() [1/2]

EdgeIterator Graph::beginEdge ( )

inline

Provide iterator access to the begin of the edge map.

Definition at line 218 of file mlGraph.h.

◆ beginEdge() [2/2]

ConstEdgeIterator Graph::beginEdge ( ) const

inline

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

Definition at line 223 of file mlGraph.h.

◆ beginNode() [1/2]

NodeIterator Graph::beginNode ( )

inline

Provide iterator access to the begin of the node map.

Definition at line 208 of file mlGraph.h.

◆ beginNode() [2/2]

ConstNodeIterator Graph::beginNode ( ) const

inline

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

Definition at line 213 of file mlGraph.h.

◆ beginRoot() [1/2]

NodeIterator Graph::beginRoot ( )

inline

Provide iterator access to the begin of the root map.

Definition at line 228 of file mlGraph.h.

◆ beginRoot() [2/2]

ConstNodeIterator Graph::beginRoot ( ) const

inline

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

Definition at line 233 of file mlGraph.h.

◆ clampToImage()

void Graph::clampToImage ( )

◆ clearGraph()

void Graph::clearGraph ( )

Remove all elements from the graph.

◆ clearRoots()

void Graph::clearRoots ( )

Remove all roots that have been defined.

◆ closeSkeletonGaps()

void Graph::closeSkeletonGaps ( )

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

Changes eventually the Graph.

◆ convertToVoxel()

void Graph::convertToVoxel ( void )

Convert all coordinates to voxel coordinates.

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

◆ convertToWorld()

void Graph::convertToWorld ( void )

Convert all coordinates to world coordinates.

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

◆ copyParts() [1/2]

void 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 149 of file mlGraph.h.

◆ copyParts() [2/2]

void 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.

◆ createEdge() [1/2]

VesselEdge* 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.

◆ createEdge() [2/2]

VesselEdge* 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.

◆ createNode() [1/2]

VesselNode* 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 118 of file mlGraph.h.

References createNode().

Referenced by createNode().

◆ createNode() [2/2]

VesselNode* 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.

◆ deepCopy()

Graph* Graph::deepCopy ( ) const

inlineoverride

Implement generic deepCopy functionality using copy constructor.

Definition at line 98 of file mlGraph.h.

◆ directGraph()

bool Graph::directGraph ( double 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*>(<em>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(); }

◆ endEdge() [1/2]

EdgeIterator Graph::endEdge ( )

inline

Provide iterator access to the end of the edge map.

Definition at line 220 of file mlGraph.h.

◆ endEdge() [2/2]

ConstEdgeIterator Graph::endEdge ( ) const

inline

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

Definition at line 225 of file mlGraph.h.

◆ endNode() [1/2]

NodeIterator Graph::endNode ( )

inline

Provide iterator access to the end of the node map.

Definition at line 210 of file mlGraph.h.

◆ endNode() [2/2]

ConstNodeIterator Graph::endNode ( ) const

inline

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

Definition at line 215 of file mlGraph.h.

◆ endRoot() [1/2]

NodeIterator Graph::endRoot ( )

inline

Provide iterator access to the end of the root map.

Definition at line 230 of file mlGraph.h.

◆ endRoot() [2/2]

ConstNodeIterator Graph::endRoot ( ) const

inline

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

Definition at line 235 of file mlGraph.h.

◆ extX()

MLint Graph::extX ( ) const

inline

Definition at line 344 of file mlGraph.h.

◆ extY()

MLint Graph::extY ( ) const

inline

Definition at line 345 of file mlGraph.h.

◆ extZ()

MLint Graph::extZ ( ) const

inline

Definition at line 346 of file mlGraph.h.

◆ fromBinaryData()

void Graph::fromBinaryData ( const std::string & data )

Reconstructs the graph using the binary data.

◆ getActionValue()

ActionType Graph::getActionValue ( void ) const

◆ getBoundingBox()

SubImageBoxd Graph::getBoundingBox ( ) const

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

◆ getEdge() [1/4]

VesselEdge* 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.

◆ getEdge() [2/4]

const VesselEdge* 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.

◆ getEdge() [3/4]

VesselEdge* Graph::getEdge ( Vector3 pos )

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

◆ getEdge() [4/4]

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

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

◆ getEdgePropertyManager() [1/2]

PropertyManager::Pointer Graph::getEdgePropertyManager ( )

inline

Get access to the GraphPropertyManager for edges.

Definition at line 301 of file mlGraph.h.

◆ getEdgePropertyManager() [2/2]

PropertyManager::ConstPointer Graph::getEdgePropertyManager ( ) const

inline

Definition at line 302 of file mlGraph.h.

◆ getFlag()

bool Graph::getFlag ( ) const

inline

Definition at line 460 of file mlGraph.h.

◆ getIdEdge() [1/2]

VesselEdge* Graph::getIdEdge ( MLint id )

Get edge with id id.

◆ getIdEdge() [2/2]

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

Get edge with id id.

◆ getIdNode() [1/2]

VesselNode* Graph::getIdNode ( MLint id )

Get node with id id;.

◆ getIdNode() [2/2]

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

Get node with id id;.

◆ getImgExt()

ImageVector Graph::getImgExt ( ) const

inline

Definition at line 343 of file mlGraph.h.

◆ getIndex() [1/2]

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

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

◆ getIndex() [2/2]

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

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

◆ getMaxSkeletonLabel()

static double Graph::getMaxSkeletonLabel ( void )

inlinestatic

Definition at line 530 of file mlGraph.h.

◆ getMinSkeletonLabel()

static double Graph::getMinSkeletonLabel ( void )

inlinestatic

Definition at line 529 of file mlGraph.h.

◆ getNode() [1/4]

VesselNode* 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.

◆ getNode() [2/4]

const VesselNode* 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.

◆ getNode() [3/4]

VesselNode* Graph::getNode ( Vector3 pos )

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

◆ getNode() [4/4]

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

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

◆ getNodePropertyManager() [1/2]

PropertyManager::Pointer Graph::getNodePropertyManager ( )

inline

Definition at line 297 of file mlGraph.h.

◆ getNodePropertyManager() [2/2]

PropertyManager::ConstPointer Graph::getNodePropertyManager ( ) const

inline

Definition at line 298 of file mlGraph.h.

◆ getNumCluster()

int Graph::getNumCluster ( ) const

inline

Definition at line 458 of file mlGraph.h.

◆ getRoot() [1/4]

VesselNode* 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.

◆ getRoot() [2/4]

const VesselNode* 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.

◆ getRoot() [3/4]

VesselNode* Graph::getRoot ( Vector3 pos )

Get the root node with minimal distance to \cpos.

◆ getRoot() [4/4]

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

Get the root node with minimal distance to \cpos.

◆ getSecond()

template<typename ResultType , typename ParameterType >

static ResultType Graph::getSecond ( const ParameterType & p )

inlinestaticprotected

Definition at line 416 of file mlGraph.h.

◆ getSkeletonPropertyManager() [1/2]

PropertyManager::Pointer Graph::getSkeletonPropertyManager ( )

inline

Get access to the GraphPropertyManager for skeletons.

Definition at line 305 of file mlGraph.h.

◆ getSkeletonPropertyManager() [2/2]

PropertyManager::ConstPointer Graph::getSkeletonPropertyManager ( ) const

inline

Definition at line 306 of file mlGraph.h.

◆ getToVoxelMatrix()

Matrix4 Graph::getToVoxelMatrix ( ) const

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

◆ getToWorldMatrix() [1/2]

const Matrix4* Graph::getToWorldMatrix ( ) const

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

◆ getToWorldMatrix() [2/2]

void Graph::getToWorldMatrix ( float * mat ) const

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

◆ getUseBinaryPersistence()

bool Graph::getUseBinaryPersistence ( )

inline

Definition at line 490 of file mlGraph.h.

◆ getVersion()

int 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 483 of file mlGraph.h.

◆ getVoxelExt()

Vector3 Graph::getVoxelExt ( ) const

inline

Definition at line 349 of file mlGraph.h.

◆ insertRoot()

void Graph::insertRoot ( VesselNode * node )

Insert a node to the list of root nodes.

◆ isWorld()

bool Graph::isWorld ( ) const

inline

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

Definition at line 331 of file mlGraph.h.

◆ mergeEdges()

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

◆ ML_SET_ADDSTATE_VERSION()

Graph::ML_SET_ADDSTATE_VERSION ( 3 )

Set current addStateToTree() version number:

◆ newGraph()

Graph* Graph::newGraph ( bool unusedDeprecated = true ) const

Allocate new graph with same properties as this (slowly).

◆ numEdges()

size_t Graph::numEdges ( ) const

inline

Returns the number edges in this graph.

Definition at line 240 of file mlGraph.h.

◆ numNodes()

size_t Graph::numNodes ( ) const

inline

Returns the number nodes in this graph.

Definition at line 238 of file mlGraph.h.

◆ numRoots()

size_t Graph::numRoots ( ) const

inline

Returns the number roots in this graph.

Definition at line 242 of file mlGraph.h.

◆ operator=()

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

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

◆ purifyGraph()

void 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

◆ readStateFromTree()

void Graph::readStateFromTree ( TreeNode * parent )

override

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

◆ removeEdge()

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

Remove an edge from the graph.

◆ removeNode()

bool Graph::removeNode ( VesselNode * node )

Remove a node from the graph.

◆ removeOrphanNodes()

void Graph::removeOrphanNodes ( )

Remove nodes with no edges attached.

◆ removeRoot()

void Graph::removeRoot ( VesselNode * r )

Remove a root from the graph.

◆ separateGraph()

int Graph::separateGraph ( )

Separate graph into clusters of connected edges.

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

◆ setAction()

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

◆ setActionCallBack()

void Graph::setActionCallBack ( GraphAction * cbObj )

◆ setActionValue()

void Graph::setActionValue ( ActionType action )

◆ setCurrentVersion()

void Graph::setCurrentVersion ( void )

inline

Set graph's version to persistent version number.

Definition at line 485 of file mlGraph.h.

◆ setFlag()

void Graph::setFlag ( bool bFlag )

inline

Definition at line 461 of file mlGraph.h.

◆ setImgExt()

void Graph::setImgExt ( ImageVector v )

inline

Definition at line 342 of file mlGraph.h.

◆ setRootIdToAllChildren()

void 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).

◆ setToVoxel()

void Graph::setToVoxel ( void )

inline

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

Definition at line 329 of file mlGraph.h.

◆ setToWorld()

void Graph::setToWorld ( void )

inline

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

Definition at line 327 of file mlGraph.h.

◆ setToWorldMatrix() [1/2]

void Graph::setToWorldMatrix ( const Matrix4 & m )

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

◆ setToWorldMatrix() [2/2]

void Graph::setToWorldMatrix ( const Matrix4 * m )

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

◆ setVersion()

void Graph::setVersion ( int version )

inline

Set version.

Definition at line 487 of file mlGraph.h.

◆ setVoxelExt()

void Graph::setVoxelExt ( Vector3 v )

inline

Definition at line 348 of file mlGraph.h.

◆ splitEdge()

MLint 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.

◆ stripCycles()

void Graph::stripCycles ( )

Strip cyclic edges from the graph.

All cyclic edges are removed to build a graph without cycles. This only works correctly if the graph has been directed with directGraph() first.

◆ toBinaryData()

std::string Graph::toBinaryData ( ) const

Returns string containing binary representation of all data necessary to reconstruct the graph.

◆ transform()

void Graph::transform ( const Matrix4 & m )

◆ useBinaryPersistence()

void Graph::useBinaryPersistence ( bool use )

inline

Set whether to use binary persistence instead of textual representation (text being the default).

Note: Binary persistence uses Boost serialization, which from time to time is updated in an incompatible way (can load files from older Boost versions, but not newer), so older MeVisLab versions may not be able to load graph files generated by newer MeVisLab versions if utilizing binary persistence.

Definition at line 496 of file mlGraph.h.

◆ worldVoxelConvert()

void Graph::worldVoxelConvert ( )

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

Friends And Related Function Documentation

◆ GraphAnalyser

friend class GraphAnalyser

friend

Definition at line 66 of file mlGraph.h.

◆ LoadTreeData

friend class LoadTreeData

friend

Definition at line 68 of file mlGraph.h.

◆ SaveTreeData

friend class SaveTreeData

friend

Definition at line 67 of file mlGraph.h.

Member Data Documentation

◆ _action

ActionType Graph::_action

protected

Definition at line 550 of file mlGraph.h.

◆ _actionCBObject

GraphAction* Graph::_actionCBObject

protected

Definition at line 551 of file mlGraph.h.

◆ _bFlag

bool Graph::_bFlag

protected

Flag for diverse usage.

Definition at line 539 of file mlGraph.h.

◆ _edges

std::map<MLint, VesselEdge*> Graph::_edges

protected

Definition at line 429 of file mlGraph.h.

◆ _imgExt

ImageVector Graph::_imgExt

protected

Extension of the image the graph is compiled from.

Definition at line 423 of file mlGraph.h.

◆ _isWorld

bool Graph::_isWorld

protected

Is the graph in world coordinates? Default is true.

Definition at line 419 of file mlGraph.h.

◆ _nodes

std::map<MLint, VesselNode*> Graph::_nodes

protected

Maps of graph items.

Definition at line 428 of file mlGraph.h.

◆ _numCluster

int Graph::_numCluster

protected

Number of non-connected edge-clusters.

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

Definition at line 543 of file mlGraph.h.

◆ _roots

std::map<MLint, VesselNode*> Graph::_roots

protected

Definition at line 430 of file mlGraph.h.

◆ _toWorldMatrix

Matrix4 Graph::_toWorldMatrix

protected

Matrix transform to get from voxel to world coordinates.

Definition at line 421 of file mlGraph.h.

◆ _voxelExt

Vector3 Graph::_voxelExt

protected

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

Definition at line 425 of file mlGraph.h.

◆ MAX_SKELETON_LABEL

double Graph::MAX_SKELETON_LABEL

staticprotected

Definition at line 563 of file mlGraph.h.

◆ MIN_SKELETON_LABEL

double Graph::MIN_SKELETON_LABEL

staticprotected

Definition at line 562 of file mlGraph.h.

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

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

Public Types

Public Member Functions

Protected Member Functions

Static Protected Member Functions

Protected Attributes

Friends

Communication

graph labeling (skeleton labels)

Detailed Description

Member Typedef Documentation

◆ ConstEdgeAccess

◆ ConstEdgeIterator

◆ ConstNodeAccess

◆ ConstNodeIterator

◆ EdgeAccess

◆ EdgeIterator

◆ EdgeMap

◆ NodeAccess

◆ NodeIterator

◆ NodeMap

Member Enumeration Documentation

◆ anonymous enum

◆ ActionType

Constructor & Destructor Documentation

◆ Graph() [1/5]

◆ Graph() [2/5]

◆ Graph() [3/5]

◆ Graph() [4/5]

◆ Graph() [5/5]

◆ ~Graph()

Member Function Documentation

◆ _isContainedInImageExtent()

◆ _setRootIdToChildren()

◆ addGraph() [1/2]

◆ addGraph() [2/2]

◆ addStateToTree()

◆ addSubtrees()

◆ beginEdge() [1/2]

◆ beginEdge() [2/2]

◆ beginNode() [1/2]

◆ beginNode() [2/2]

◆ beginRoot() [1/2]

◆ beginRoot() [2/2]

◆ clampToImage()

◆ clearGraph()

◆ clearRoots()

◆ closeSkeletonGaps()

◆ convertToVoxel()

◆ convertToWorld()

◆ copyParts() [1/2]

◆ copyParts() [2/2]

◆ createEdge() [1/2]

◆ createEdge() [2/2]

◆ createNode() [1/2]

◆ createNode() [2/2]

◆ deepCopy()

◆ directGraph()

◆ endEdge() [1/2]

◆ endEdge() [2/2]

◆ endNode() [1/2]

◆ endNode() [2/2]

◆ endRoot() [1/2]

◆ endRoot() [2/2]

◆ extX()

◆ extY()

◆ extZ()

◆ fromBinaryData()

◆ getActionValue()

◆ getBoundingBox()

◆ getEdge() [1/4]

◆ getEdge() [2/4]

◆ getEdge() [3/4]

◆ getEdge() [4/4]

◆ getEdgePropertyManager() [1/2]

◆ getEdgePropertyManager() [2/2]

◆ getFlag()

◆ getIdEdge() [1/2]

◆ getIdEdge() [2/2]

◆ getIdNode() [1/2]

◆ getIdNode() [2/2]