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

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param_additionalDummyNodes - Static variable in class config.Constants

param_alpha - Static variable in class config.Constants

param_alpha - Static variable in class main.AutomaticMatching

param_alpha - Static variable in class main.AutomaticRetrieval

param_category - Static variable in class main.AutomaticMatching

param_database - Static variable in class main.AutomaticMatching

param_database - Static variable in class main.AutomaticRetrieval

param_extractSimilarityWith - Static variable in class config.Constants

param_finalMatching - Static variable in class config.Constants

param_handleBadMatchings - Static variable in class config.Constants

param_nosp - Static variable in class main.AutomaticMatching

param_nosp - Static variable in class main.AutomaticRetrieval

param_numberOfSamplePoints - Static variable in class config.Constants

param_pathdistance - Static variable in class config.Constants

param_preprocessing - Static variable in class config.Constants

param_saveTo - Static variable in class main.AutomaticMatching

param_saveTo - Static variable in class main.AutomaticRetrieval

param_useDenominator - Static variable in class config.Constants

param_useEndnodeOrder - Static variable in class config.Constants

param_visualize - Static variable in class config.Constants

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

Parse the skeleton.

parseArguments(String[]) - Method in class config.Config

Parse the arguments specified in the constructor.

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

the skeleton parser

partner1 - Variable in class algorithm.matching.Matching

index of the first matching partner in the cost matrix rows

partner2 - Variable in class algorithm.matching.Matching

index of the second matching partner in the cost matrix column

pathdistance - Variable in class config.Config

configure which path distance definition will be used.

pathLenght - Variable in class geometry.object.SkeletonPath

the skeleton path'S length (that is, the number of nodes on this path

paths - Variable in class geometry.object.Skeleton

list containing all skeleton paths emanating from every skeleton node.

PathSimilaritySkeletonGraphMatching - Class in algorithm

Deprecated. use Matching2D instead

PathSimilaritySkeletonGraphMatching(String, String, String, String) - Constructor for class algorithm.PathSimilaritySkeletonGraphMatching

Deprecated. Constructor.

PathSimilaritySkeletonGraphMatching(String, String, String, String, boolean) - Constructor for class algorithm.PathSimilaritySkeletonGraphMatching

Deprecated. Constructor.

PathSimilaritySkeletonGraphMatching(SkeletonObject, SkeletonObject, SkeletonObject) - Constructor for class algorithm.PathSimilaritySkeletonGraphMatching

Deprecated. Constructor.

PathVectorSampleTest3D - Class in test.algorithm

Test the sampling of skeleton paths in 3D skeletons.

PathVectorSampleTest3D() - Constructor for class test.algorithm.PathVectorSampleTest3D

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

Deprecated.

phaseSaitoY(double[][][], int, int, int) - Static method in class io.loader.load3D.DistanceTransform3D

Deprecated.

phaseSaitoZ(double[][][]) - Static method in class io.loader.load3D.DistanceTransform3D

Deprecated.

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

phaseY(double[][][]) - Static method in class io.loader.load3D.SaitoToriwakiDistanceTransform

phaseZ(double[][][]) - Static method in class io.loader.load3D.SaitoToriwakiDistanceTransform

pixelArray - Variable in class io.loader.load2D.contours.ContourTracer

points - Variable in class io.loader.load2D.contours.Contour

PossibleMatching - Class in algorithm.matching

Store information about possible matchings.

PossibleMatching(SkeletonNode, SkeletonNode, double) - Constructor for class algorithm.matching.PossibleMatching

possibleMatchings - Variable in class algorithm.matching.PossibleMatchList

container for all possible matchings

PossibleMatchList - Class in algorithm.matching

Container including matchings that would generally be possible, that is, each node in the first skeleton is hypothetically matched to each node in the second skeleton.

PossibleMatchList() - Constructor for class algorithm.matching.PossibleMatchList

Constructor.

post_segmentationdata - Variable in class retrieval.DatabaseEntry3D

path to the second volume data file

post_segmentationinfo - Variable in class retrieval.DatabaseEntry3D

path to the second volume info file

post_thinningdata - Variable in class retrieval.DatabaseEntry3D

path to the second skeleton data file

post_thinninginfo - Variable in class retrieval.DatabaseEntry3D

path to the second skeleton info file

pre_segmentationdata - Variable in class retrieval.DatabaseEntry3D

path to the first volume data file

pre_segmentationinfo - Variable in class retrieval.DatabaseEntry3D

path to the first volume info file

pre_thinningdata - Variable in class retrieval.DatabaseEntry3D

path to the first skeleton data file

pre_thinninginfo - Variable in class retrieval.DatabaseEntry3D

path to the first skeleton info file

prepareImage(ImagePlus) - Method in class io.loader.load2D.SkeletonParser2D

Prepare the image to make sure some conditions are fullfilled: all pixel values are 0 or 255 tell imagej that this is a binary image invert the image in case the foreground seems to be black, the background seems to be white (by now, this is estimated on the pixel in the upper left corner)

prepareMatrix(double[][], Config) - Static method in class algorithm.matching.HungarianAlgorithm

prepare the stored weight function so that it can be used by hungarian algorithm.

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

Before applying OSB, the matrix should be prepared: To allow skipping the first and last elements in the matrix, additional rows and columns are added.

preprocess - Variable in class gui.Matching3DGui

preprocessGraph(SkeletonGraph) - Method in class io.loader.shared.SkeletonParser

In case that the skeleton is not continous, throw out skeleton parts that are not connected to the "main skeleton"

preprocessing - Variable in class config.Config

Configure the threshold for the skeleton preprocessor.

preprocessL - Variable in class gui.Matching3DGui

preprocessl - Variable in class gui.PSGMGui

label for preprocessing field

Preprocessor - Class in io.loader.shared

This is a trial to eliminate spurious branches from a skeleton.

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

preprocesst - Variable in class gui.PSGMGui

text input for preprocessing threshold

PreprocessTest - Class in test.io

Test the preprocessing of skeletons (Preprocessor).

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

previous - Variable in class geometry.object.SkeletonNode

holds the information which skeleton node is the predecessor on the path

primeSomeUncoveredZero(float[][], int[], int[], int[]) - Method in class algorithm.matching.HungarianAlgorithm

finds some uncovered zero and primes it

print(String) - Method in class io.visualize.Visualize3DCube

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

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

Deprecated.

PSGM - Class in algorithm.psgm

An implementation of the skeleton based matching algorithm proposed in Path Similarity Graph Matching.

PSGM(SkeletonObject, SkeletonObject) - Constructor for class algorithm.psgm.PSGM

Constructor.

PSGMGui - Class in gui

Simple GUI for choosing two database entries and then execute the matching algorithm.

PSGMGui(String) - Constructor for class gui.PSGMGui

Creating a new PSGMGui.

PSGMResult - Class in algorithm.psgm

"dirty" matching result of the matching algorithm PSGM.

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

PSGMTest - Class in test.algorithm

test usage of path similarity graph matching.

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

PSGMTest3D - Class in test.algorithm

Test the execution of Matching3D.

PSGMTest3D() - Constructor for class test.algorithm.PSGMTest3D