Uses of Class
exception.InvalidSkeletonException

Packages that use InvalidSkeletonException

algorithm	Package containing all classes that are part of establishing correspondences between two skeletons' end nodes.
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.
io.out	Classes needed to save skeletons to the file system.
io.visualize	Classes needed to visualize/show skeletons and skeleton matching results.
retrieval	Classes needed to perform similarity searches in a database and mapping database entries to java classes.
test.algorithm	Test basic functionalities of the algorithm implementations.
test.retrieval	Test classes for retrieval scenarios.
utils	Contains simple helper classes.

Uses of InvalidSkeletonException in algorithm

Methods in algorithm that throw InvalidSkeletonException

CleanMatchingResult	Matching3D.go() Applying PSGM.go(Config) to the two skeletons loaded.
CleanMatchingResult	Matching2D.go() execute the PSGM algorithm.
CleanMatchingResult	PathSimilaritySkeletonGraphMatching.go(Config config) Deprecated. Execute the PSGM algorithm.
private void	Matching2D.loadSkeletons(java.lang.String skeletonfilename1, java.lang.String objectfilename1, java.lang.String skeletonfilename2, java.lang.String objectfilename2) load both skeletons, specified by the filename.
private void	PathSimilaritySkeletonGraphMatching.loadSkeletons(java.lang.String skeletonfilename1, java.lang.String objectfilename1, java.lang.String skeletonfilename2, java.lang.String objectfilename2) Deprecated. load both skeletons, specified by the filename.
private void	Matching3D.loadSkeletons(java.lang.String thinningfile1, java.lang.String thinninginfo1, java.lang.String volumefile1, java.lang.String volumeinfo1, java.lang.String thinningfile2, java.lang.String thinninginfo2, java.lang.String volumefile2, java.lang.String volumeinfo2) Load the skeletons.

Constructors in algorithm that throw InvalidSkeletonException

Matching2D(SkeletonObject so1, SkeletonObject so1_flipped, SkeletonObject so2, Config config)
Constructor that should only be used if you know what you are doing.

Matching2D(java.lang.String skeletonfilename1, java.lang.String objectfilename1, java.lang.String skeletonfilename2, java.lang.String objectfilename2)
Constructor.

Matching2D(java.lang.String skeletonfilename1, java.lang.String objectfilename1, java.lang.String skeletonfilename2, java.lang.String objectfilename2, Config config)
Constructor.

Matching2D(java.lang.String skeletonfilename1, java.lang.String objectfilename1, java.lang.String skeletonfilename2, java.lang.String objectfilename2, java.lang.String[] args)
Constructor.

Matching3D(java.lang.String thinningfile1, java.lang.String thinninginfo1, java.lang.String volumefile1, java.lang.String volumeinfo1, java.lang.String thinningfile2, java.lang.String thinninginfo2, java.lang.String volumefile2, java.lang.String volumeinfo2, Config config)
Constructor.

PathSimilaritySkeletonGraphMatching(SkeletonObject so1, SkeletonObject so1_flipped, SkeletonObject so2)
Deprecated. Constructor.

PathSimilaritySkeletonGraphMatching(java.lang.String skeletonfilename1, java.lang.String objectfilename1, java.lang.String skeletonfilename2, java.lang.String objectfilename2)
Deprecated. Constructor.

PathSimilaritySkeletonGraphMatching(java.lang.String skeletonfilename1, java.lang.String objectfilename1, java.lang.String skeletonfilename2, java.lang.String objectfilename2, boolean preprocess)
Deprecated. Constructor.

Uses of InvalidSkeletonException in algorithm.matching

Methods in algorithm.matching that throw InvalidSkeletonException

MatchList	MultipleOSB.computeAssignments(double[][] cost, Config config) Deprecated.
MatchList	MatchingAlgorithm.computeAssignments(double[][] costs, Config config) Compute the assignments for the given cost matrix.
MatchList	OSBfinalMatching.computeAssignments(double[][] costs, Config config)
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.
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.

Uses of InvalidSkeletonException in algorithm.psgm

Methods in algorithm.psgm that throw InvalidSkeletonException

static void	SkeletonPathGetter.getAllSkeletonPathVectors(SkeletonObject so1, SkeletonObject so2) use this function to set the skeletons' skeleton path vectors.
static void	SkeletonPathGetter.getAllSkeletonPathVectors(SkeletonObject so1, SkeletonObject so2, int numberOfSamplePoints) use this function to set the skeletons' skeleton path vectors.
double	CostGetter.getCost(SkeletonNode sn1, SkeletonNode sn2) Get the matching costs for the two specified end nodes.
private static int	SkeletonPathGetter.getNumberOfSamplePoints(SkeletonObject so1, SkeletonObject so2) Deprecated.
double[][]	CostGetter.getPathDistanceMatrix(SkeletonNode sn1, SkeletonNode sn2) Get the path distance matrix for a pair of end nodes to be matched.
static void	SkeletonPathGetter.getSkeletonPathRepresentation(SkeletonObject so, SkeletonPath path, int numberOfSamplePoints, double normalization) get the path vector representation for the specified skeleton path.
private static void	SkeletonPathGetter.getSkeletonPathVectors(SkeletonObject so, int numberOfSamplePoints) helper function to get skeleton path vectors for the specified skeleton.
MatchList	PSGM.go(Config config) Execute the algorithm.

Uses of InvalidSkeletonException in geometry.object

Methods in geometry.object that throw InvalidSkeletonException

boolean	SkeletonNode.equals(SkeletonNode node) check if the current skeleton node is equal to the one specified as parameter.
boolean	SkeletonPath.equals(SkeletonPath path) check if two skeleton paths are equal.
java.util.List<SkeletonNode>	SkeletonPath.getAllNodes() Get the list of all skeleton nodes on this path.
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.

Constructors in geometry.object that throw InvalidSkeletonException

SkeletonNode(Coordinates coordinates, boolean isEndNode)
constructor with specified isEndNode

Uses of InvalidSkeletonException in io.loader.load2D

Methods in io.loader.load2D that throw InvalidSkeletonException

private void	SkeletonParser2D.cleanJunctionNodes(java.util.List<SkeletonNode> junctionnodes) In some constellations, directly adjacent nodes are recognized as junction nodes.
SkeletonNode	NodeArea2D.cleanNodeArea()
protected void	SkeletonParser2D.getCriticalNodes()
protected java.util.Map<SkeletonNode,java.util.List<SkeletonBranch>>	SkeletonParser2D.sampleParts()
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 InvalidSkeletonException in io.loader.load3D

Methods in io.loader.load3D that throw InvalidSkeletonException

private void	SkeletonParser3D.cleanJunctionNodes(java.util.List<SkeletonNode> junctionnodes, int[][][] thinningcube) Clean the list of junction nodes.
SkeletonNode	NodeArea3D.cleanNodeArea()
protected void	SkeletonParser3D.getCriticalNodes()
protected java.util.Map<SkeletonNode,java.util.List<SkeletonBranch>>	SkeletonParser3D.sampleParts()
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 InvalidSkeletonException in io.loader.shared

Methods in io.loader.shared that throw InvalidSkeletonException

void	NodeArea.addNode(SkeletonNode node)
static SkeletonGraph	GraphBuilder.buildGraph(java.util.Map<SkeletonNode,java.util.List<SkeletonBranch>> allParts) Build a graph from the sampled parts.
abstract SkeletonNode	NodeArea.cleanNodeArea() extract the prefered junction node from this node area.
boolean	NodeArea.contains(SkeletonNode n) Test of this node area contains the specified skeleton node.
protected void	SkeletonParser.extractPaths(SkeletonGraph graph) From the skeleton graph, extract all skeleton paths.
protected abstract void	SkeletonParser.getCriticalNodes() extract all critical nodes, that is, end nodes and junction nodes
SkeletonObject	SkeletonParser.getSkeleton() parse the skeleton and return it, according to the specified parameters.
protected void	SkeletonParser.parse() Parse the skeleton.
protected abstract java.util.Map<SkeletonNode,java.util.List<SkeletonBranch>>	SkeletonParser.sampleParts() sample all SkeletonBranches emanating from each critical node.

Uses of InvalidSkeletonException in io.out

Methods in io.out that throw InvalidSkeletonException

static void

SkeletonToImageWriter.write(SkeletonObject obj, java.lang.String filename) create an image from the specified skeleton object and save the result to the specified location.

Uses of InvalidSkeletonException in io.visualize

Methods in io.visualize that throw InvalidSkeletonException

static java.awt.image.BufferedImage

SkeletonToBufferedImage.skeletonToImage(SkeletonObject o) create a nice image for the specified skeleton.

Uses of InvalidSkeletonException in retrieval

Methods in retrieval that throw InvalidSkeletonException

static java.util.PriorityQueue<SimilaritySearchResult>

SimilaritySearch.getSimilarities(java.lang.String database, SkeletonObject so, SkeletonObject so_flipped, java.lang.String skeletonfilename, java.lang.String objectfilename, int nosp, double alpha) Given a skeleton object, this function searches the database in src/database/database.db, performes PSGM to the input skeleton and all skeletons in the database and saves the results in the order of their similarity in a priority queue.

Uses of InvalidSkeletonException in test.algorithm

Methods in test.algorithm that throw InvalidSkeletonException

private void	SinglePathDistanceMatrixTest.loadSkeletons() load test scenario
private void	PSGMTest.loadSkeletons() loading test scenario

Uses of InvalidSkeletonException in test.retrieval

Methods in test.retrieval that throw InvalidSkeletonException

private void

SimilaritySearchTest.loadSkeleton() load the skeleton

Uses of InvalidSkeletonException in utils

Methods in utils that throw InvalidSkeletonException

static boolean

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