Uses of Class
geometry.object.SkeletonNode

Packages that use SkeletonNode

algorithm.matching	Package containing all classes that are used to establish a final matching between two skeletons' end nodes.
algorithm.psgm	All classes used for the computation of two skeletons' endnode similarities, as described in the paper.
geometry.object	Package containing all skeleton data structures needed.
io.loader.load2D	Contains all classes used to load a 2D skeleton from the input files.
io.loader.load3D	Contains all classes needed to load a 3D-skeleton.
io.loader.shared	Package containing all classes needed to load 2D skeletons as well as 3D skeletons.
utils	Contains simple helper classes.

Uses of SkeletonNode in algorithm.matching

Fields in algorithm.matching declared as SkeletonNode

private SkeletonNode	PossibleMatching.sn1
private SkeletonNode	PossibleMatching.sn2

Methods in algorithm.matching that return SkeletonNode

SkeletonNode	PossibleMatching.getSn1()
SkeletonNode	PossibleMatching.getSn2()

Methods in algorithm.matching that return types with arguments of type SkeletonNode

private java.util.List<SkeletonNode>

OSBfinalMatching.orderEndNodes(SkeletonObject so, SkeletonNode node) Order the skeleton's end nodes according to their distance to the specified node, measured by the length of the skeleton path between the two nodes.

Methods in algorithm.matching with parameters of type SkeletonNode

PossibleMatching	PossibleMatchList.getMatchingByEndNodes(SkeletonNode sn1, SkeletonNode sn2) From the list of possible matchings, extract the matching between the two nodes specified by the parameters.
private java.util.List<SkeletonNode>	OSBfinalMatching.orderEndNodes(SkeletonObject so, SkeletonNode node) Order the skeleton's end nodes according to their distance to the specified node, measured by the length of the skeleton path between the two nodes.
void	PossibleMatching.setSn1(SkeletonNode sn1)
void	PossibleMatching.setSn2(SkeletonNode sn2)

Method parameters in algorithm.matching with type arguments of type SkeletonNode

private double[][]	OSBfinalMatching.getCostMatrix(double[][] costs, java.util.List<SkeletonNode> orderedEndnodes1, java.util.List<SkeletonNode> orderedEndnodes2, PossibleMatchList possibleMatchings) Get the matching cost matrix as input for OSB function.
private double[][]	OSBfinalMatching.getCostMatrix(double[][] costs, java.util.List<SkeletonNode> orderedEndnodes1, java.util.List<SkeletonNode> orderedEndnodes2, PossibleMatchList possibleMatchings) Get the matching cost matrix as input for OSB function.

Constructors in algorithm.matching with parameters of type SkeletonNode

PossibleMatching(SkeletonNode sn1, SkeletonNode sn2, double matchingcost)

Uses of SkeletonNode in algorithm.psgm

Methods in algorithm.psgm with parameters of type SkeletonNode

double	CostGetter.getCost(SkeletonNode sn1, SkeletonNode sn2) Get the matching costs for the two specified end nodes.
double[][]	CostGetter.getPathDistanceMatrix(SkeletonNode sn1, SkeletonNode sn2) Get the path distance matrix for a pair of end nodes to be matched.

Uses of SkeletonNode in geometry.object

Fields in geometry.object declared as SkeletonNode

private SkeletonNode	SkeletonBranch.endnode
private SkeletonNode	SkeletonPath.endnode1 the skeleton path's first end node (the start point)
private SkeletonNode	SkeletonPath.endnode2 the skeleton path's second end node (the end point)
private SkeletonNode	SkeletonNode.previous holds the information which skeleton node is the predecessor on the path
private SkeletonNode	SkeletonBranch.startnode

Fields in geometry.object with type parameters of type SkeletonNode

private java.util.List<SkeletonNode>	SkeletonPath.allNodes a list containing all nodes on this skeleton path
private java.util.List<SkeletonNode>	Skeleton.endnodes list containing all skeleton endnodes.
private org.jgrapht.graph.SimpleDirectedWeightedGraph<SkeletonNode,SkeletonBranch>	SkeletonGraph.graph the "real" skeleton graph
private java.util.List<SkeletonNode>	SkeletonBranch.nodes
private java.util.Map<SkeletonNode,java.util.List<SkeletonPath>>	Skeleton.paths list containing all skeleton paths emanating from every skeleton node.

Methods in geometry.object that return SkeletonNode

SkeletonNode	SkeletonBranch.getEndnode()
SkeletonNode	SkeletonPath.getEndnode1() Get the skeleton path's first end node.
SkeletonNode	SkeletonPath.getEndnode2() Get the skeleton path's second end node.
SkeletonNode	SkeletonNode.getPrevious() get the predecessor of this skeleton node on the path.
SkeletonNode	SkeletonBranch.getStartnode()

Methods in geometry.object that return types with arguments of type SkeletonNode

java.util.List<SkeletonNode>	Skeleton.getAllEndNodes() Return the skeleton's end nodes.
java.util.List<SkeletonNode>	SkeletonPath.getAllIncludedSkeletonPoints() get a list of all skeletonnodes included in this path, but without end nodes.
java.util.List<SkeletonNode>	SkeletonPath.getAllNodes() Get the list of all skeleton nodes on this path.
java.util.Map<SkeletonNode,java.util.List<SkeletonPath>>	Skeleton.getAllSkeletonPaths() Get all skeleton paths.
java.util.List<SkeletonNode>	SkeletonGraph.getAllVertexNeighbors(SkeletonNode node) Get all vertices in the graph directly connected to the specified vertex.
java.util.Set<SkeletonNode>	SkeletonGraph.getAllVertices() Get all vertices in this graph.
java.util.List<SkeletonNode>	SkeletonBranch.getNodes()

Methods in geometry.object with parameters of type SkeletonNode

void	SkeletonBranch.addNode(SkeletonNode node)
void	Skeleton.addPaths(java.util.List<SkeletonPath> paths, SkeletonNode endnode) add a list of paths to the skeleton's paths.
boolean	SkeletonGraph.addVertex(SkeletonNode node) Add a new vertex to the graph.
boolean	SkeletonNode.equals(SkeletonNode node) check if the current skeleton node is equal to the one specified as parameter.
java.util.List<SkeletonNode>	SkeletonGraph.getAllVertexNeighbors(SkeletonNode node) Get all vertices in the graph directly connected to the specified vertex.
java.util.Set<SkeletonBranch>	SkeletonGraph.getOutgoingEdges(SkeletonNode node) return the edges emanating from the specified node
SkeletonPath	SkeletonGraph.getShortestPath(SkeletonNode start, SkeletonNode end) Get the shortest path in the graph from the specified start node to the specified end node.
SkeletonPath	Skeleton.getSkeletonPathByEndnodes(SkeletonNode node1, SkeletonNode node2) get the skeleton path between the specified end nodes.
java.util.List<SkeletonPath>	Skeleton.getSkeletonPathsByEndnode(SkeletonNode node) Get a list of all skeleton paths emanating from the specified end node.The specified end node has to be the key to the path map to be a match.
boolean	SkeletonGraph.removeVertex(SkeletonNode node)
void	SkeletonBranch.setEndnode(SkeletonNode endnode)
void	SkeletonPath.setEndnode1(SkeletonNode endnode1) Set the skeleton path's first end node.
void	SkeletonPath.setEndnode2(SkeletonNode endnode2) Set the skeleton path's second end node.
void	SkeletonNode.setPrevious(SkeletonNode previous) get the predecessor of this skeleton node on the path.
void	SkeletonBranch.setStartnode(SkeletonNode startnode)

Method parameters in geometry.object with type arguments of type SkeletonNode

void	Skeleton.setAllEndnodes(java.util.List<SkeletonNode> endnodes) set the skeleton's endnodes.
void	SkeletonPath.setAllNodes(java.util.List<SkeletonNode> allNodes) Set all nodes on this skeleton path.
void	SkeletonBranch.setNodes(java.util.List<SkeletonNode> nodes)
void	Skeleton.setPaths(java.util.Map<SkeletonNode,java.util.List<SkeletonPath>> allPaths) set the skeleton's skeleton paths.

Constructors in geometry.object with parameters of type SkeletonNode

SkeletonPath(SkeletonNode endnode1, SkeletonNode endnode2)
Constructor.

Uses of SkeletonNode in io.loader.load2D

Methods in io.loader.load2D that return SkeletonNode

private SkeletonNode	SkeletonParser2D.checkNeighborHood(java.awt.Point cp) check if a skeleton end node is in the 3x3 neighbor hood of the specified contour point.
SkeletonNode	NodeArea2D.cleanNodeArea()

Methods in io.loader.load2D that return types with arguments of type SkeletonNode

static java.util.List<SkeletonNode>	NeighborSkeletonNodes2D.getNeighborSkeletonNodes(SkeletonNode sn, java.awt.image.BufferedImage bimg) return a list of all neighbor skeleton nodes.
protected java.util.Map<SkeletonNode,java.util.List<SkeletonBranch>>	SkeletonParser2D.sampleParts()

Methods in io.loader.load2D with parameters of type SkeletonNode

private static SkeletonBranch	SampleParts2D.createPart(SkeletonNode startnode, SkeletonNode endnode, java.util.List<SkeletonNode> nodesOnPart) If an end node or junction node has been reached, this function can be used to create the part between the startnode and the current node.
static java.util.List<SkeletonNode>	NeighborSkeletonNodes2D.getNeighborSkeletonNodes(SkeletonNode sn, java.awt.image.BufferedImage bimg) return a list of all neighbor skeleton nodes.
private boolean	SkeletonParser2D.isNeighborOf(java.awt.Point cp, SkeletonNode n) check if the specified skeleton node is in the 3x3 neighborhood of the specified contour point.
private static boolean	SampleParts2D.isVisited(boolean[][] visited, SkeletonNode node) Test if the speicifed skeleton node has been visited.
private static void	SampleParts2D.markAsVisited(boolean[][] visited, SkeletonNode node) mark the specified skeleton node as visited.
static java.util.List<SkeletonBranch>	SampleParts2D.samplePartsPerStartNode(SkeletonNode startnode, ij.ImagePlus skeletonImage, java.util.List<SkeletonNode> endnodes, java.util.List<SkeletonNode> junctionnodes) Sample all skeleton branches emanating from the specified startnode.

Method parameters in io.loader.load2D with type arguments of type SkeletonNode

private void	SkeletonParser2D.cleanJunctionNodes(java.util.List<SkeletonNode> junctionnodes) In some constellations, directly adjacent nodes are recognized as junction nodes.
private static SkeletonBranch	SampleParts2D.createPart(SkeletonNode startnode, SkeletonNode endnode, java.util.List<SkeletonNode> nodesOnPart) If an end node or junction node has been reached, this function can be used to create the part between the startnode and the current node.
static java.util.List<SkeletonBranch>	SampleParts2D.samplePartsPerStartNode(SkeletonNode startnode, ij.ImagePlus skeletonImage, java.util.List<SkeletonNode> endnodes, java.util.List<SkeletonNode> junctionnodes) Sample all skeleton branches emanating from the specified startnode.
static java.util.List<SkeletonBranch>	SampleParts2D.samplePartsPerStartNode(SkeletonNode startnode, ij.ImagePlus skeletonImage, java.util.List<SkeletonNode> endnodes, java.util.List<SkeletonNode> junctionnodes) Sample all skeleton branches emanating from the specified startnode.

Uses of SkeletonNode in io.loader.load3D

Methods in io.loader.load3D that return SkeletonNode

SkeletonNode

NodeArea3D.cleanNodeArea()

Methods in io.loader.load3D that return types with arguments of type SkeletonNode

static java.util.List<SkeletonNode>	NeighborSkeletonNodes3D.getNeighborSkeletonNodes(SkeletonNode sn, int[][][] thinningcube, double widthDim, double heightDim, double depthDim) Get a list of all skeleton neighbor nodes for the specified node by checking the 3x3x3 neighborhood of this voxel and creating a new skeleton node for each skeleton voxel found.
protected java.util.Map<SkeletonNode,java.util.List<SkeletonBranch>>	SkeletonParser3D.sampleParts()

Methods in io.loader.load3D with parameters of type SkeletonNode

private static SkeletonBranch	SampleParts3D.createPart(SkeletonNode startnode, SkeletonNode endnode, java.util.List<SkeletonNode> nodesOnPart) If an end node or junction node has been reached, this function can be used to create the part between the startnode and the current node.
static java.util.List<SkeletonNode>	NeighborSkeletonNodes3D.getNeighborSkeletonNodes(SkeletonNode sn, int[][][] thinningcube, double widthDim, double heightDim, double depthDim) Get a list of all skeleton neighbor nodes for the specified node by checking the 3x3x3 neighborhood of this voxel and creating a new skeleton node for each skeleton voxel found.
static boolean	NeighborSkeletonNodes3D.isEdgeNeighbor(SkeletonNode n1, SkeletonNode n2) Check if two skeleton nodes are edge-connected.
static boolean	NeighborSkeletonNodes3D.isSurfaceNeighbor(SkeletonNode n1, SkeletonNode n2) Check if two skeleton nodes are surface connected.
private static boolean	SampleParts3D.isVisited(boolean[][][] visited, SkeletonNode node) Check if the specified node has already been visited.
private static void	SampleParts3D.markAsVisited(boolean[][][] visited, SkeletonNode node) Mark the the specified node as visited.
static java.util.List<SkeletonBranch>	SampleParts3D.samplePartsPerStartNode(SkeletonNode startnode, int[][][] thinningcube, java.util.List<SkeletonNode> endnodes, java.util.List<SkeletonNode> junctionnodes, double widthDim, double heightDim, double depthDim) sample all skeleton parts emanating from the specified startnode which has to be a critical node, that is, either end node or junction node.

Method parameters in io.loader.load3D with type arguments of type SkeletonNode

private void	SkeletonParser3D.cleanJunctionNodes(java.util.List<SkeletonNode> junctionnodes, int[][][] thinningcube) Clean the list of junction nodes.
private static SkeletonBranch	SampleParts3D.createPart(SkeletonNode startnode, SkeletonNode endnode, java.util.List<SkeletonNode> nodesOnPart) If an end node or junction node has been reached, this function can be used to create the part between the startnode and the current node.
static java.util.List<SkeletonBranch>	SampleParts3D.samplePartsPerStartNode(SkeletonNode startnode, int[][][] thinningcube, java.util.List<SkeletonNode> endnodes, java.util.List<SkeletonNode> junctionnodes, double widthDim, double heightDim, double depthDim) sample all skeleton parts emanating from the specified startnode which has to be a critical node, that is, either end node or junction node.
static java.util.List<SkeletonBranch>	SampleParts3D.samplePartsPerStartNode(SkeletonNode startnode, int[][][] thinningcube, java.util.List<SkeletonNode> endnodes, java.util.List<SkeletonNode> junctionnodes, double widthDim, double heightDim, double depthDim) sample all skeleton parts emanating from the specified startnode which has to be a critical node, that is, either end node or junction node.

Uses of SkeletonNode in io.loader.shared

Fields in io.loader.shared with type parameters of type SkeletonNode

protected java.util.List<SkeletonNode>	SkeletonParser.allEndnodes list containing all skeleton end nodes
protected java.util.List<SkeletonNode>	SkeletonParser.allJunctionNodes list containing all skeleton junction nodes
protected java.util.List<SkeletonNode>	NodeArea.junctionNodes List of all found junction nodes, potentially containing redundant nodes.

Methods in io.loader.shared that return SkeletonNode

abstract SkeletonNode

NodeArea.cleanNodeArea() extract the prefered junction node from this node area.

Methods in io.loader.shared that return types with arguments of type SkeletonNode

protected abstract java.util.Map<SkeletonNode,java.util.List<SkeletonBranch>>

SkeletonParser.sampleParts() sample all SkeletonBranches emanating from each critical node.

Methods in io.loader.shared with parameters of type SkeletonNode

void	NodeArea.addNode(SkeletonNode node)
boolean	NodeArea.contains(SkeletonNode n) Test of this node area contains the specified skeleton node.
static double	Preprocessor.getEmanatingBranchLength(SkeletonObject so, SkeletonNode endnode) Get the length of the skeleton branch emanating from the specified skeleton end node

Method parameters in io.loader.shared with type arguments of type SkeletonNode

static SkeletonGraph

GraphBuilder.buildGraph(java.util.Map<SkeletonNode,java.util.List<SkeletonBranch>> allParts) Build a graph from the sampled parts.

Constructor parameters in io.loader.shared with type arguments of type SkeletonNode

NodeArea(java.util.List<SkeletonNode> nodes)
Constructor.

Uses of SkeletonNode in utils

Methods in utils with parameters of type SkeletonNode

static boolean

ListUtilities.contains(java.util.List<SkeletonNode> nodes, SkeletonNode node) Test if a list haystack contains a specified skeleton node needle.

Method parameters in utils with type arguments of type SkeletonNode

static boolean

ListUtilities.contains(java.util.List<SkeletonNode> nodes, SkeletonNode node) Test if a list haystack contains a specified skeleton node needle.