A B C D E F G H I J L M N O P Q R S T U V W X Y Z

G

geometry - package geometry

Package containing all basic data structures.

geometry.object - package geometry.object

Package containing all skeleton data structures needed.

getAdditionalDummyNodes() - Method in class config.Config

Get how many dummy nodes are added when executing HungarianAlgorithm

getAllEndNodes() - Method in class geometry.object.Skeleton

Return the skeleton's end nodes.

getAllIncludedSkeletonPoints() - Method in class geometry.object.SkeletonPath

get a list of all skeletonnodes included in this path, but without end nodes.

getAllinnerContours() - Method in class io.loader.load2D.contours.ContourContainer

Get all inner contours.

getAllNodes() - Method in class geometry.object.SkeletonPath

Get the list of all skeleton nodes on this path.

getAllouterContours() - Method in class io.loader.load2D.contours.ContourContainer

get all outer contours.

getAllSkeletonPaths() - Method in class geometry.object.Skeleton

Get all skeleton paths.

getAllSkeletonPathVectors(SkeletonObject, SkeletonObject) - Static method in class algorithm.psgm.SkeletonPathGetter

use this function to set the skeletons' skeleton path vectors.

getAllSkeletonPathVectors(SkeletonObject, SkeletonObject, int) - Static method in class algorithm.psgm.SkeletonPathGetter

use this function to set the skeletons' skeleton path vectors.

getAllVertexNeighbors(SkeletonNode) - Method in class geometry.object.SkeletonGraph

Get all vertices in the graph directly connected to the specified vertex.

getAllVertices() - Method in class geometry.object.SkeletonGraph

Get all vertices in this graph.

getAlpha() - Method in class config.Config

Get the configuration for the weighting factor alpha.

getAngles() - Method in class algorithm.matching.Matching

getAverage(double[][]) - Static method in class utils.ArrayUtilities

get the average of all elements in a two dimensional array.

getAverageDistance() - Method in interface geometry.object.DistanceMap

Get the average distance from each pixel/voxel in the shape to the contour.

getAverageDistance() - Method in class geometry.object.DistanceMap2D

getAverageDistance() - Method in class geometry.object.DistanceMap3D

getCategory() - Method in class retrieval.DatabaseEntry

get the entry's category

getCategory() - Method in class retrieval.SimilaritySearchResult

get the category of the target skeleton object.

getCl() - Method in class retrieval.SimilaritySearchResult

get the found correspondences in the two skeleton objects, i.e.

getCleanedMatchList() - Method in class algorithm.CleanMatchingResult

Get the cleaned up, restored match list.

getCleanMatchingResult() - Method in class algorithm.psgm.PSGMResult

From the "dirty" PSGMResult, extract a cleaned up result.

getComboBox() - Method in class gui.DatabaseAccessGUI

get a JComboBox, containing all entries found in the database.

getContour() - Method in class io.loader.load2D.SkeletonParser2D

set the object's inner and outer contours.

getCoordinates() - Method in class geometry.object.SkeletonNode

get this skeleton node's coordinates.

getCost() - Method in class algorithm.matching.Matching

Get the costs for this matching.

getCost(SkeletonNode, SkeletonNode) - Method in class algorithm.psgm.CostGetter

Get the matching costs for the two specified end nodes.

getCostMatrix(double[][], List<SkeletonNode>, List<SkeletonNode>, PossibleMatchList) - Method in class algorithm.matching.OSBfinalMatching

Get the matching cost matrix as input for OSB function.

getCosts() - Method in class retrieval.SimilaritySearchResult

Get the total costs to match the two skeleton objects.

getCounter(ImagePlus) - Static method in class io.loader.load2D.contours.ContourGetter

get all inner and outer contours for the object shape in the given, binary image, using Wilhelm Burger's imageJ plugin (http://www.imagingbook.com).

getCriticalNodes() - Method in class io.loader.load2D.SkeletonParser2D

getCriticalNodes() - Method in class io.loader.load3D.SkeletonParser3D

getCriticalNodes() - Method in class io.loader.shared.SkeletonParser

extract all critical nodes, that is, end nodes and junction nodes

getDatabaseEntries() - Method in class gui.DatabaseAccessGUI

get a list of all objects stored in the database.

getDatabaseEntries() - Method in class gui.Matching3DGui

getDepth() - Method in class geometry.object.SkeletonObject

getDimensions() - Method in class geometry.object.SkeletonObject

getDistance(Coordinates) - Method in interface geometry.Coordinates

get the distance between two coordinates.

getDistance(Coordinates) - Method in class geometry.Coordinates2D

getDistance(Coordinates) - Method in class geometry.Coordinates3D

getDistance(Index) - Method in interface geometry.object.DistanceMap

Get the distance from the specified coordinates to the contour

getDistance(Index) - Method in class geometry.object.DistanceMap2D

getDistance(Index) - Method in class geometry.object.DistanceMap3D

getDistanceMap() - Method in interface geometry.object.DistanceMap

getDistanceMap() - Method in class geometry.object.DistanceMap2D

getDistanceMap() - Method in class geometry.object.DistanceMap3D

getDistanceMap() - Method in class geometry.object.SkeletonObject

returns the distance map.

getDistanceTransform(ImagePlus) - Static method in class io.loader.load2D.DistanceTransform2D

Get the specified image's distance transform.

getDistanceTransform() - Method in class io.loader.load2D.SkeletonParser2D

getDistanceTransform(int[][][]) - Static method in class io.loader.load3D.DistanceTransform3D

Deprecated.

getDistanceTransform(int[][][]) - Static method in class io.loader.load3D.SaitoToriwakiDistanceTransform

Get the distance transform for the specified 3D volume.

getDistanceTransform() - Method in class io.loader.load3D.SkeletonParser3D

getDistanceTransform() - Method in class io.loader.shared.SkeletonParser

compute and set the shape's distance transform

getEmanatingBranchLength(SkeletonObject, SkeletonNode) - Static method in class io.loader.shared.Preprocessor

Get the length of the skeleton branch emanating from the specified skeleton end node

getEndnode() - Method in class geometry.object.SkeletonBranch

getEndnode1() - Method in class geometry.object.SkeletonPath

Get the skeleton path's first end node.

getEndnode2() - Method in class geometry.object.SkeletonPath

Get the skeleton path's second end node.

getExtractSimilarityWith() - Method in class config.Config

Get the configuration which method is used to extract the similarity between two end nodes from their path distance matrix

getFinalMatchingWith() - Method in class config.Config

Get the configuration which method is used to perform the final matching.

getHandleBadMatchings() - Method in class config.Config

Get the configuration how bad matchings in the matching result are handled.

getHeight() - Method in class geometry.object.SkeletonObject

get the height of the input image, used for example for visualization.

getId() - Method in class retrieval.DatabaseEntry3D

getIndex() - Method in class geometry.object.SkeletonNode

getInnerContours() - Method in class io.loader.load2D.contours.ContourTracer

getJumpCost(double[][]) - Static method in class algorithm.psgm.OSBv5

get the cost for skipping rows.

getLength() - Method in class geometry.object.SkeletonBranch

getLength() - Method in class io.loader.load2D.contours.Contour

getMatchingByEndNodes(SkeletonNode, SkeletonNode) - Method in class algorithm.matching.PossibleMatchList

From the list of possible matchings, extract the matching between the two nodes specified by the parameters.

getMatchingcost() - Method in class algorithm.matching.PossibleMatching

getMatchingCosts(double[][]) - Static method in class algorithm.psgm.OSBv5

get the matching costs for a given distance matrix, that is, the "cheapest" path through that matrix.

getMatchlist() - Method in class algorithm.matching.MatchList

return matchlist - list containing all found matches.

getMaximalPathLength(SkeletonObject) - Method in class algorithm.psgm.CostGetter

get the length of the longest path in the specified skeleton object.

getMaximum(double[][]) - Static method in class utils.ArrayUtilities

get the maximum entry of a twodimensional array.

getMean() - Method in class algorithm.matching.MatchList

Get the average matching costs of this match list.

getMean(double[]) - Static method in class utils.ArrayUtilities

get the mean value for the specified one-dimensional array

getMedian() - Method in class algorithm.matching.MatchList

getName() - Method in class retrieval.DatabaseEntry3D

getNeighborSkeletonNodes(SkeletonNode, BufferedImage) - Static method in class io.loader.load2D.NeighborSkeletonNodes2D

return a list of all neighbor skeleton nodes.

getNeighborSkeletonNodes(SkeletonNode, int[][][], double, double, double) - Static method in class io.loader.load3D.NeighborSkeletonNodes3D

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.

getNodes() - Method in class geometry.object.SkeletonBranch

getNormalization(SkeletonObject) - Static method in class algorithm.psgm.SkeletonPathGetter

to make sure the approach is scale - invariant, get a normalization factor based on the average distance of any object pixel to the contour.

getNormalizationFactor() - Method in class algorithm.psgm.CostGetter

Get the normalization factor.

getNumberOfSamplePoints(SkeletonObject, SkeletonObject) - Static method in class algorithm.psgm.SkeletonPathGetter

Deprecated.

getNumberOfSamplePoints() - Method in class config.Config

Get the configuration how many sample points are used for the skeleton path vector creation.

getObjectfilename1() - Method in class retrieval.SearchThread

getObjectfilename2() - Method in class retrieval.SearchThread

getOuterContours() - Method in class io.loader.load2D.contours.ContourTracer

getOutgoingEdges(SkeletonNode) - Method in class geometry.object.SkeletonGraph

return the edges emanating from the specified node

getPartner1() - Method in class algorithm.matching.Matching

get the first partner index (as a row index in the cost matrix)

getPartner2() - Method in class algorithm.matching.Matching

get the second partner index (as a column index in the cost matrix)

getPathDistance() - Method in class config.Config

Get the configuration which path distance measurement is used

getPathDistanceByPath(SkeletonPath, SkeletonPath) - Method in class algorithm.psgm.CostGetter

Get the path distance between the two specified skeleton paths.

getPathDistanceByPathLength(SkeletonPath, SkeletonPath) - Method in class algorithm.psgm.CostGetter

Get the path distance between a pair of skeleton paths, based on their path length.

getPathDistanceMatrix(SkeletonNode, SkeletonNode) - Method in class algorithm.psgm.CostGetter

Get the path distance matrix for a pair of end nodes to be matched.

getPathLength() - Method in class geometry.object.SkeletonPath

get this skeleton path's length, that is, the number of skeleton nodes on this path.

getPoints() - Method in class io.loader.load2D.contours.Contour

getPossibleMatchings(double[][]) - Method in class algorithm.matching.OSBfinalMatching

Get all "imaginary" matchings that are possible.

getPost_segmentationdata() - Method in class retrieval.DatabaseEntry3D

getPost_segmentationinfo() - Method in class retrieval.DatabaseEntry3D

getPost_thinningdata() - Method in class retrieval.DatabaseEntry3D

getPost_thinninginfo() - Method in class retrieval.DatabaseEntry3D

getPre_segmentationdata() - Method in class retrieval.DatabaseEntry3D

getPre_segmentationinfo() - Method in class retrieval.DatabaseEntry3D

getPre_thinningdata() - Method in class retrieval.DatabaseEntry3D

getPre_thinninginfo() - Method in class retrieval.DatabaseEntry3D

getPreprocessing() - Method in class config.Config

Get the threshold for preprocessing the skeleton.

getPrevious() - Method in class geometry.object.SkeletonNode

get the predecessor of this skeleton node on the path.

getQueryobject() - Method in class algorithm.CleanMatchingResult

Get the query object

getSegmentationcube() - Method in class io.loader.load3D.SkeletonParser3D

Get the 3D cube containing the volume data (0 = background, 255 = foreground)

getShape() - Method in class geometry.object.SkeletonObject

getShapefilename() - Method in class retrieval.SimilaritySearchResult

get the path to the shape image of the target skeleton object

getShapepath() - Method in class retrieval.DatabaseEntry

get the path to the shape image

getShortestPath(SkeletonNode, SkeletonNode) - Method in class geometry.object.SkeletonGraph

Get the shortest path in the graph from the specified start node to the specified end node.

getSimilarities(String, SkeletonObject, SkeletonObject, String, String, int, double) - Static method in class retrieval.SimilaritySearch

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.

getSkeleton() - Method in class geometry.object.SkeletonObject

Get the skeleton belonging to this object.

getSkeleton() - Method in class io.loader.shared.SkeletonParser

parse the skeleton and return it, according to the specified parameters.

getSkeleton() - Method in class io.loader.shared.SkeletonParserThread

get the parsed skeleton

getSkeletonfilename() - Method in class retrieval.SimilaritySearchResult

get the path to the skeleton image of the target skeleton object

getSkeletonfilename1() - Method in class retrieval.SearchThread

getSkeletonfilename2() - Method in class retrieval.SearchThread

getSkeletonGraph() - Method in class geometry.object.SkeletonObject

getSkeletonpath() - Method in class retrieval.DatabaseEntry

get the path to the skeleton image

getSkeletonPathByEndnodes(SkeletonNode, SkeletonNode) - Method in class geometry.object.Skeleton

get the skeleton path between the specified end nodes.

getSkeletonPathRepresentation(SkeletonObject, SkeletonPath, int, double) - Static method in class algorithm.psgm.SkeletonPathGetter

get the path vector representation for the specified skeleton path.

getSkeletonPathsByEndnode(SkeletonNode) - Method in class geometry.object.Skeleton

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.

getSkeletonPathVectors(SkeletonObject, int) - Static method in class algorithm.psgm.SkeletonPathGetter

helper function to get skeleton path vectors for the specified skeleton.

getSn1() - Method in class algorithm.matching.PossibleMatching

getSn2() - Method in class algorithm.matching.PossibleMatching

getSo() - Method in class retrieval.SimilaritySearchResult

Get the target skeleton object.

getSo1() - Method in class algorithm.Matching2D

Get the "first skeleton", the one with lesser end nodes.

getSo1() - Method in class algorithm.psgm.PSGM

Get the first skeleton object.

getSo1_flipped() - Method in class algorithm.Matching2D

Get the first skeleton (the one with lesser end nodes), but flipped horizontally)

getSo2() - Method in class algorithm.Matching2D

Get the "second skeleton", the one with more end nodes

getSo2() - Method in class algorithm.psgm.PSGM

Get the second skeleton object.

getStandardDeviation() - Method in class algorithm.matching.MatchList

getStartnode() - Method in class geometry.object.SkeletonBranch

getStd(double[]) - Static method in class utils.ArrayUtilities

get the standard deviation of the specified array.

getTargetobject() - Method in class algorithm.CleanMatchingResult

Get the target object.

getThinningCube() - Method in class io.loader.load3D.SkeletonParser3D

Read the thinning cube.

getTotalcost() - Method in class algorithm.matching.MatchList

get this matching's total cost

getUseDenominator() - Method in class config.Config

Get the configuration if the denominators in the path distance computation are used.

getUseEndnodeOrder() - Method in class config.Config

Get the configuration how end nodes are ordered.

getVectorRepresentation() - Method in class geometry.object.SkeletonPath

Get the skeleton path vector representation.

getVisualization() - Method in class io.visualize.MatchingViewer

Get an image, displaying both skeleton objects, with corresponding nodes linked by lines.

getVisualize() - Method in class config.Config

Get the configuration for the visualization.

getWidth() - Method in class geometry.object.SkeletonObject

get the width of the input image, used for example for visualization.

getX() - Method in interface geometry.Coordinates

get x coordinate

getX() - Method in class geometry.Coordinates2D

getX() - Method in interface geometry.Index

get x index

getX() - Method in class geometry.Index2D

getXDim() - Method in interface geometry.Dimensions

get the pixel's/voxel's width

getXDim() - Method in class geometry.Dimensions2D

getXy() - Method in class algorithm.matching.MatchingAngles

getXz() - Method in class algorithm.matching.MatchingAngles

getY() - Method in interface geometry.Coordinates

get y coordinate

getY() - Method in class geometry.Coordinates2D

getY() - Method in interface geometry.Index

get y index

getY() - Method in class geometry.Index2D

getYDim() - Method in interface geometry.Dimensions

get the pixel's/voxel's height

getYDim() - Method in class geometry.Dimensions2D

getYz() - Method in class algorithm.matching.MatchingAngles

getZ() - Method in interface geometry.Coordinates

get z coordinate

getZ() - Method in class geometry.Coordinates2D

getZ() - Method in class geometry.Coordinates3D

get z-coordinate

getZ() - Method in interface geometry.Index

get z index

getZ() - Method in class geometry.Index2D

getZ() - Method in class geometry.Index3D

getZDim() - Method in interface geometry.Dimensions

get the pixel's/voxel's depth

getZDim() - Method in class geometry.Dimensions2D

getZDim() - Method in class geometry.Dimensions3D

go() - Method in class algorithm.Matching2D

execute the PSGM algorithm.

go() - Method in class algorithm.Matching3D

Applying PSGM.go(Config) to the two skeletons loaded.

go(Config) - Method in class algorithm.PathSimilaritySkeletonGraphMatching

Deprecated. Execute the PSGM algorithm.

go(Config) - Method in class algorithm.psgm.PSGM

Execute the algorithm.

go() - Method in class main.AutomaticMatching

go() - Method in class main.AutomaticRetrieval

graph - Variable in class geometry.object.SkeletonGraph

the "real" skeleton graph

GraphBuilder - Class in io.loader.shared

extract a skeleton graph (see SkeletonGraph) from the sampled parts

GraphBuilder() - Constructor for class io.loader.shared.GraphBuilder

group_denominator - Variable in class gui.Matching3DGui

group_filter - Variable in class gui.Matching3DGui

group_finalmatching - Variable in class gui.Matching3DGui

group_order - Variable in class gui.Matching3DGui

group_pathdistance - Variable in class gui.Matching3DGui

group_similarity - Variable in class gui.Matching3DGui

group_visualization - Variable in class gui.Matching3DGui

gui - package gui

Package containing all graphical user interfaces.