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

S

SaitoToriwakiDistanceTransform - Class in io.loader.load3D

An implementation of the 3D distance transform algorithm proposed in: T.

SaitoToriwakiDistanceTransform() - Constructor for class io.loader.load3D.SaitoToriwakiDistanceTransform

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

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

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

sample all SkeletonBranches emanating from each critical node.

SampleParts2D - Class in io.loader.load2D

Sample the skeleton branches emanating from one critical node (end or junction node).

SampleParts2D() - Constructor for class io.loader.load2D.SampleParts2D

SampleParts3D - Class in io.loader.load3D

Sample single skeleton branches in 3D data.

SampleParts3D() - Constructor for class io.loader.load3D.SampleParts3D

samplePartsPerStartNode(SkeletonNode, ImagePlus, List<SkeletonNode>, List<SkeletonNode>) - Static method in class io.loader.load2D.SampleParts2D

Sample all skeleton branches emanating from the specified startnode.

samplePartsPerStartNode(SkeletonNode, int[][][], List<SkeletonNode>, List<SkeletonNode>, double, double, double) - Static method in class io.loader.load3D.SampleParts3D

sample all skeleton parts emanating from the specified startnode which has to be a critical node, that is, either end node or junction node.

saveTo - Variable in class main.AutomaticMatching

saveTo - Variable in class main.AutomaticRetrieval

search - Variable in class gui.SearchGUI

button to start similarity search

SearchGUI - Class in gui

Simple GUI to start similarity searches in the database.

SearchGUI(String) - Constructor for class gui.SearchGUI

initialize the GUI, adding all components.

SearchThread - Class in retrieval

A thread to handle the parsing of one skeleton and comparing it with PSGM to the query object (passed as "ready-to-use" skeleton object).

SearchThread(SkeletonObject, SkeletonObject, String, String, String, String, String, int, double, PriorityQueue<SimilaritySearchResult>) - Constructor for class retrieval.SearchThread

create a new search thread.

segmentationcube - Variable in class io.loader.load3D.SkeletonParser3D

the cube containing the volume information

Sep(int, int, double, double) - Static method in class io.loader.load3D.DistanceTransform3D

Deprecated.

seperator - Static variable in class config.Constants

serialVersionUID - Static variable in exception exception.InvalidConfigParameterException

serialVersionUID - Static variable in exception exception.InvalidSkeletonException

serialVersionUID - Static variable in exception exception.InvalidWeightFunctionGivenException

serialVersionUID - Static variable in exception exception.WrongUsageOfAlgorithmException

serialVersionUID - Static variable in class geometry.object.SkeletonBranch

serialVersionUID - Static variable in class gui.DatabaseAccessGUI

serialization id

serialVersionUID - Static variable in class gui.Matching3DGui

serialVersionUID - Static variable in class gui.PSGMGui

serialization id

serialVersionUID - Static variable in class gui.SearchGUI

serizalization id

serialVersionUID - Static variable in class io.visualize.ImageViewer

serialVersionUID - Static variable in class io.visualize.MatchingViewer

setAdditionalDummyNodes(String) - Method in class config.Config

Configure how many dummy nodes will be added when executing HungarianAlgorithm

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

extract all contour points from the object's contour and save them to a list.

setAllEndnodes(List<SkeletonNode>) - Method in class geometry.object.Skeleton

set the skeleton's endnodes.

setAllinnerContours(List<Contour>) - Method in class io.loader.load2D.contours.ContourContainer

Set all inner contours

setAllNodes(List<SkeletonNode>) - Method in class geometry.object.SkeletonPath

Set all nodes on this skeleton path.

setAllouterContours(List<Contour>) - Method in class io.loader.load2D.contours.ContourContainer

set all outer contours.

setAlpha(String) - Method in class config.Config

Set the alpha value for path distance computation.

setAngles(MatchingAngles) - Method in class algorithm.matching.Matching

setCategory(String) - Method in class retrieval.DatabaseEntry

set the entry's category

setCategory(String) - Method in class retrieval.SimilaritySearchResult

set the category of the target skeleton object.

setCl(MatchList) - Method in class retrieval.SimilaritySearchResult

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

setCleanedMatchList(MatchList) - Method in class algorithm.CleanMatchingResult

Set the cleaned match list.

setContourPixel(SkeletonObject, int, int) - Method in class io.visualize.MatchingViewer

set the contour pixel in the buffered image.

setContourPixel(BufferedImage, SkeletonObject) - Static method in class io.visualize.SkeletonToBufferedImage

set the contour pixel.

setCoordinates(Coordinates) - Method in class geometry.object.SkeletonNode

set this skeleton node's coordinates.

setCorrespondenceLines(int, int) - Method in class io.visualize.MatchingViewer

display line for each correspondence.

setCost(double) - Method in class algorithm.matching.Matching

setCosts(double) - Method in class retrieval.SimilaritySearchResult

set the total costs to match the two skeleton objects

setDepth(int) - Method in class geometry.object.SkeletonObject

setDimensions(Dimensions) - Method in class geometry.object.SkeletonObject

setDistanceMap(Object) - Method in interface geometry.object.DistanceMap

set the distance map.

setDistanceMap(Object) - Method in class geometry.object.DistanceMap2D

setDistanceMap(Object) - Method in class geometry.object.DistanceMap3D

setDistanceMap(DistanceMap) - Method in class geometry.object.SkeletonObject

set the distance map.

setEndnode(SkeletonNode) - Method in class geometry.object.SkeletonBranch

setEndNode(boolean) - Method in class geometry.object.SkeletonNode

set the information if this node is an end node

setEndnode1(SkeletonNode) - Method in class geometry.object.SkeletonPath

Set the skeleton path's first end node.

setEndnode2(SkeletonNode) - Method in class geometry.object.SkeletonPath

Set the skeleton path's second end node.

setExtractSimilarityWith(String) - Method in class config.Config

conigure which algorithm to use to extract end node similarities from path distance matrices.

setFinalMatching(String) - Method in class config.Config

Configure which function to use to perform the final matching.

setFlipped(boolean) - Method in class algorithm.psgm.PSGMResult

Set if the smaller skeleton (with less end nodes) was flipped in order to get better maching results.

setHandleMatchings(String) - Method in class config.Config

Configure how bad matchings will be handled

setHeight(int) - Method in class geometry.object.SkeletonObject

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

setId(int) - Method in class retrieval.DatabaseEntry3D

setIndex(Index) - Method in class geometry.object.SkeletonNode

setMatchingcost(double) - Method in class algorithm.matching.PossibleMatching

setMl(MatchList) - Method in class algorithm.psgm.PSGMResult

Set the "dirty" matchlist

setName(String) - Method in class retrieval.DatabaseEntry3D

setNodes(List<SkeletonNode>) - Method in class geometry.object.SkeletonBranch

setNumberOfSamplePoints(String) - Method in class config.Config

Set the number of sample points for the skeleton path vector.

setOrderingEndnodes(String) - Method in class config.Config

Configure how end nodes will be ordered

setPartner1(int) - Method in class algorithm.matching.Matching

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

setPartner2(int) - Method in class algorithm.matching.Matching

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

setPathDistance(String) - Method in class config.Config

Configure which path distance measurement will be used.

setPaths(Map<SkeletonNode, List<SkeletonPath>>) - Method in class geometry.object.Skeleton

set the skeleton's skeleton paths.

setPoints(List<Point>) - Method in class io.loader.load2D.contours.Contour

setPost_segmentationdata(String) - Method in class retrieval.DatabaseEntry3D

setPost_segmentationinfo(String) - Method in class retrieval.DatabaseEntry3D

setPost_thinningdata(String) - Method in class retrieval.DatabaseEntry3D

setPost_thinninginfo(String) - Method in class retrieval.DatabaseEntry3D

setPre_segmentationdata(String) - Method in class retrieval.DatabaseEntry3D

setPre_segmentationinfo(String) - Method in class retrieval.DatabaseEntry3D

setPre_thinningdata(String) - Method in class retrieval.DatabaseEntry3D

setPre_thinninginfo(String) - Method in class retrieval.DatabaseEntry3D

setPreprocessing(String) - Method in class config.Config

Set the threshold for the preprocessor

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

get the predecessor of this skeleton node on the path.

setQueryobject(SkeletonObject) - Method in class algorithm.CleanMatchingResult

Set the query object.

setReordered(boolean) - Method in class algorithm.psgm.PSGMResult

Set if the two skeleton were reordered for the execution of the algorithm.

setSegmentationcube(int[][][]) - Method in class io.loader.load3D.SkeletonParser3D

Set the volume data.

setShape(Object) - Method in class geometry.object.SkeletonObject

setShapefilename(String) - Method in class retrieval.SimilaritySearchResult

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

setShapepath(String) - Method in class retrieval.DatabaseEntry

set the path to the shape image

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

set skeleton object's width and height, based on the input image's size.

setSkeleton(Skeleton) - Method in class geometry.object.SkeletonObject

set the skeleton belonging to this object.

setSkeletonfilename(String) - Method in class retrieval.SimilaritySearchResult

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

setSkeletonGraph(SkeletonGraph) - Method in class geometry.object.SkeletonObject

setSkeletonNode(boolean) - Method in class geometry.object.SkeletonNode

set the information if this skeleton node is a true skeleton node, that is, it not an end node.

setSkeletonpath(String) - Method in class retrieval.DatabaseEntry

set the path to the skeleton image

setSkeletonPixel(SkeletonObject, int, int) - Method in class io.visualize.MatchingViewer

set the object's skeleton pixel.

setSkeletonPixel(BufferedImage, SkeletonObject) - Static method in class io.visualize.SkeletonToBufferedImage

set the skeleton pixel.

setSkeletons(SkeletonObject, SkeletonObject) - Method in class algorithm.psgm.PSGM

set the skeletons to be matched.

setSn1(SkeletonNode) - Method in class algorithm.matching.PossibleMatching

setSn2(SkeletonNode) - Method in class algorithm.matching.PossibleMatching

setSo(SkeletonObject) - Method in class retrieval.SimilaritySearchResult

Set the target skeleton object

setSo1(SkeletonObject) - Method in class algorithm.Matching2D

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

setSo1(SkeletonObject) - Method in class algorithm.psgm.PSGMResult

Set the first skeleton, that is, the one with lesser end nodes.

setSo1_flipped(SkeletonObject) - Method in class algorithm.Matching2D

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

setSo1_flipped(SkeletonObject) - Method in class algorithm.psgm.PSGMResult

Set the flipped version of the "smaller" skeleton.

setSo2(SkeletonObject) - Method in class algorithm.Matching2D

Set the "second skeleton", the one with lesser end nodes.

setSo2(SkeletonObject) - Method in class algorithm.psgm.PSGMResult

Set the second skeleton, that is, the one with more end nodes.

setStartnode(SkeletonNode) - Method in class geometry.object.SkeletonBranch

setTargetobject(SkeletonObject) - Method in class algorithm.CleanMatchingResult

Set the Target object

setTotalcost(double) - Method in class algorithm.matching.MatchList

set this matching's total cost.

setUseDenominator(String) - Method in class config.Config

Configure if to use denominator in path distance computation

setVectorRepresentation(double[]) - Method in class geometry.object.SkeletonPath

Set the skeleton path vector representation.

setVisualization(BufferedImage) - Method in class io.visualize.MatchingViewer

Set the image viualizing the two skeleton objects and their correspondences.

setVisualize(String) - Method in class config.Config

set the visualization mode

setWidth(int) - Method in class geometry.object.SkeletonObject

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

setX(double) - Method in interface geometry.Coordinates

set x coordinate

setX(double) - Method in class geometry.Coordinates2D

setX(int) - Method in interface geometry.Index

set x index

setX(int) - Method in class geometry.Index2D

setXy(double) - Method in class algorithm.matching.MatchingAngles

setXz(double) - Method in class algorithm.matching.MatchingAngles

setY(double) - Method in interface geometry.Coordinates

set y coordinate

setY(double) - Method in class geometry.Coordinates2D

setY(int) - Method in interface geometry.Index

set y index

setY(int) - Method in class geometry.Index2D

setYz(double) - Method in class algorithm.matching.MatchingAngles

setZ(double) - Method in interface geometry.Coordinates

set z coordinate

setZ(double) - Method in class geometry.Coordinates2D

setZ(double) - Method in class geometry.Coordinates3D

set z-coordinate

setZ(int) - Method in interface geometry.Index

set z index

setZ(int) - Method in class geometry.Index2D

setZ(int) - Method in class geometry.Index3D

sgraph - Variable in class geometry.object.SkeletonObject

the skeleton's skeleton graph

shape - Variable in class geometry.object.SkeletonObject

holding information about the object's shape

shapefilename - Variable in class retrieval.SimilaritySearchResult

the path to the shape image of the target skeleton object

shapeinfoPath - Variable in class io.loader.load3D.SkeletonParser3D

the path to the volume meta information file

shapePath - Variable in class io.loader.load3D.SkeletonParser3D

the path to the volume data

shapepath - Variable in class retrieval.DatabaseEntry

the path to the shape image

show() - Method in class io.visualize.MatchingViewer3D

Show the matching result.

showAllMatchings - Static variable in class config.Constants

showAllMatchings - Variable in class gui.Matching3DGui

showBoth - Static variable in class config.Constants

showBoth - Variable in class gui.Matching3DGui

showSkeleton - Static variable in class config.Constants

showSkeleton - Variable in class gui.Matching3DGui

showVolume - Static variable in class config.Constants

showVolume - Variable in class gui.Matching3DGui

SimilaritySearch - Class in retrieval

Execute a similarity search in the database.

SimilaritySearch() - Constructor for class retrieval.SimilaritySearch

SimilaritySearchResult - Class in retrieval

Data structure to hold meta data about the matching result between a query skeleton object and a target object.

SimilaritySearchResult() - Constructor for class retrieval.SimilaritySearchResult

SimilaritySearchTest - Class in test.retrieval

Test an example usage of SimilaritySearch.

SimilaritySearchTest() - Constructor for class test.retrieval.SimilaritySearchTest

SinglePathDistanceMatrixTest - Class in test.algorithm

test the creation of a path distance matrix between two endnodes and the extracting of the total costs for this path distance matrix (testing of CostGetter).

SinglePathDistanceMatrixTest() - Constructor for class test.algorithm.SinglePathDistanceMatrixTest

Skeleton - Class in geometry.object

A data structure to hold information about the skeleton data.

Skeleton() - Constructor for class geometry.object.Skeleton

skeleton - Variable in class geometry.object.SkeletonObject

the skeleton itself

SkeletonBranch - Class in geometry.object

A skeleton branch is defined as the set of skeleton nodes between two junction nodes or between an end node and a junction node in that way, that no other junction or end nodes are crossed.

SkeletonBranch() - Constructor for class geometry.object.SkeletonBranch

skeletonColor - Static variable in class io.loader.Colors

color of skeletons in binary images

skeletonColor - Static variable in class io.visualize.MatchingViewer

skeletonColor - Static variable in class io.visualize.SkeletonToBufferedImage

define skeleton color

skeletonColor - Static variable in class test.io.DisplaySkeletonPaths

SkeletonDistanceTransformTest - Class in test.io

test the creation of 2D distance maps.

SkeletonDistanceTransformTest() - Constructor for class test.io.SkeletonDistanceTransformTest

skeletonfilename - Variable in class io.loader.load2D.SkeletonParser2D

the path to the image containing the skeleton

skeletonfilename - Variable in class retrieval.SimilaritySearchResult

the path to the skeleton image of the target skeleton object

skeletonfilename - Variable in class test.io.SkeletonToImageTest

skeletonfilename1 - Variable in class retrieval.SearchThread

the path to the skeleton image of the first skeleton object

skeletonfilename2 - Variable in class retrieval.SearchThread

the path to the skeleton image of the second skeleton object

SkeletonGraph - Class in geometry.object

A skeleton graph is a reduction of the skeleton to only end nodes and junction nodes.

SkeletonGraph() - Constructor for class geometry.object.SkeletonGraph

constructor.

skeletonImage - Variable in class io.loader.load2D.SkeletonParser2D

image containing the skeleton

SkeletonNode - Class in geometry.object

data structure to hold information about single skeleton nodes (that is, points on a skeleton) like coordinates, previous node on path etc.

SkeletonNode(Coordinates, Index) - Constructor for class geometry.object.SkeletonNode

constructor.

SkeletonNode(Coordinates, boolean) - Constructor for class geometry.object.SkeletonNode

constructor with specified isEndNode

SkeletonObject - Class in geometry.object

data structure to hold some meta information about skeletons, like distance map, width, height,...

SkeletonObject() - Constructor for class geometry.object.SkeletonObject

skeletonObject - Variable in class io.loader.shared.SkeletonParser

meta skeleton object

SkeletonParser - Class in io.loader.shared

Abstract class to handle the parsing of 2D and 3D skeletons, respectively.

SkeletonParser(Config) - Constructor for class io.loader.shared.SkeletonParser

Constructor.

SkeletonParser2D - Class in io.loader.load2D

Given the path to a binary image containing the skeleton, and the path to a binary image containing the object's shape, SkeletonParser2D creates a SkeletonObject from this given input data.

SkeletonParser2D(String, String) - Constructor for class io.loader.load2D.SkeletonParser2D

Constructor.

SkeletonParser2D(String, String, boolean) - Constructor for class io.loader.load2D.SkeletonParser2D

SkeletonParser2D(String, String, Config) - Constructor for class io.loader.load2D.SkeletonParser2D

SkeletonParser2D(String, String, Config, boolean) - Constructor for class io.loader.load2D.SkeletonParser2D

Constructor.

SkeletonParser3D - Class in io.loader.load3D

Load a skeleton from the input data.

SkeletonParser3D(String, String, String, String, Config) - Constructor for class io.loader.load3D.SkeletonParser3D

Constructor.

SkeletonParser3DTest - Class in test.io

Test the loading of 3D skeletons.

SkeletonParser3DTest() - Constructor for class test.io.SkeletonParser3DTest

SkeletonParserTest - Class in test.io

test the 2D skeleton parser class.

SkeletonParserTest() - Constructor for class test.io.SkeletonParserTest

SkeletonParserThread - Class in io.loader.shared

A thread to load a skeleton, specified by the SkeletonParser passed by argument.

SkeletonParserThread(SkeletonParser) - Constructor for class io.loader.shared.SkeletonParserThread

Constructor.

SkeletonPath - Class in geometry.object

A skeleton path between a pair of end nodes is defined as the shortest path between those endnodes with the limitation, that all points in between have to be skeleton points.

SkeletonPath(SkeletonNode, SkeletonNode) - Constructor for class geometry.object.SkeletonPath

Constructor.

skeletonpath - Variable in class retrieval.DatabaseEntry

the path to the skeleton image

SkeletonPathGetter - Class in algorithm.psgm

we use a special representation for skeleton paths in our algorithm: the idea is to sample each skeleton path in M equidistant points in both skeletons.

SkeletonPathGetter() - Constructor for class algorithm.psgm.SkeletonPathGetter

SkeletonTo3DArray(SkeletonObject) - Method in class io.visualize.MatchingViewer3D

Create a 3D cube from the specified skeleton.

SkeletonTo3DArray(SkeletonObject) - Method in class io.visualize.MatchingViewer3DPanel

Create a 3D cube from the specified skeleton.

SkeletonToBufferedImage - Class in io.visualize

create a buffered image for a specified skeleton object

SkeletonToBufferedImage() - Constructor for class io.visualize.SkeletonToBufferedImage

SkeletonToBufferedImageTest - Class in test.io

test the creation of buffered images out of skeleton objects.

SkeletonToBufferedImageTest() - Constructor for class test.io.SkeletonToBufferedImageTest

skeletonToImage(SkeletonObject) - Static method in class io.visualize.SkeletonToBufferedImage

create a nice image for the specified skeleton.

SkeletonToImageTest - Class in test.io

test the saving of skeletons to file.

SkeletonToImageTest() - Constructor for class test.io.SkeletonToImageTest

SkeletonToImageWriter - Class in io.out

This class provides functionalities to save BufferedImages or SkeletonObjects to file, using java's built-in image/io.

SkeletonToImageWriter() - Constructor for class io.out.SkeletonToImageWriter

sn1 - Variable in class algorithm.matching.PossibleMatching

sn2 - Variable in class algorithm.matching.PossibleMatching

so - Variable in class io.loader.shared.SkeletonParserThread

the parsed skeleton object

so - Variable in class retrieval.SearchThread

the query skeleton object to be compared

so - Variable in class retrieval.SimilaritySearchResult

the target object

so1 - Variable in class algorithm.matching.MultipleOSB

Deprecated. first skeleton to be matched

so1 - Variable in class algorithm.matching.OSBfinalMatching

the first skeleton to be matched

so1 - Variable in class algorithm.Matching2D

the first skeleton object (the one with lesser end nodes

so1 - Variable in class algorithm.Matching3D

first, "smaller" skeleton object (the one with less end nodes

so1 - Variable in class algorithm.PathSimilaritySkeletonGraphMatching

Deprecated. the first skeleton object (the one with lesser end nodes

so1 - Variable in class algorithm.psgm.CostGetter

first skeleton object to be matched

so1 - Variable in class algorithm.psgm.PSGM

first skeleton object

so1 - Variable in class algorithm.psgm.PSGMResult

the "smaller" skeleton object (with less end nodes)

so1 - Variable in class io.visualize.MatchingViewer

the first skeleton object that has been matched

so1 - Variable in class test.algorithm.PSGMTest

so1 - Variable in class test.algorithm.SinglePathDistanceMatrixTest

first skeleton object

so1 - Variable in class test.retrieval.SimilaritySearchTest

query skeleton

so1_flipped - Variable in class algorithm.Matching2D

the first skeleton object, read from an image flipped horizontally

so1_flipped - Variable in class algorithm.PathSimilaritySkeletonGraphMatching

Deprecated. the first skeleton object, read from an image flipped horizontally

so1_flipped - Variable in class algorithm.psgm.PSGMResult

the "smaller" skeleton object (with less end nodes) parsed from flipped image

so2 - Variable in class algorithm.matching.MultipleOSB

Deprecated. second skeleton to be matched

so2 - Variable in class algorithm.matching.OSBfinalMatching

the second skeleton to be matched

so2 - Variable in class algorithm.Matching2D

the second skeleton object (the one with more end nodes

so2 - Variable in class algorithm.Matching3D

second, " bigger" skeleton object (the one with more end nodes)

so2 - Variable in class algorithm.PathSimilaritySkeletonGraphMatching

Deprecated. the second skeleton object (the one with more end nodes

so2 - Variable in class algorithm.psgm.CostGetter

second skeleton object to be matched

so2 - Variable in class algorithm.psgm.PSGM

second skeleton object

so2 - Variable in class algorithm.psgm.PSGMResult

the "bigger" skeleton object (with more end nodes)

so2 - Variable in class io.visualize.MatchingViewer

the second skeleton object that has been matched

so2 - Variable in class test.algorithm.PSGMTest

so2 - Variable in class test.algorithm.SinglePathDistanceMatrixTest

second skeleton object

so_flipped - Variable in class retrieval.SearchThread

the query skeleton object, parsed from flipped image

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

sort a list of end nodes by traversing an object's contour in clockwise direction and checking for each contour point if there is a skeleton node in the 3x3 neighborhood.

startnode - Variable in class geometry.object.SkeletonBranch

sum(double, double) - Static method in class io.loader.load3D.DistanceTransform3D

Deprecated.