Package gov.nih.mipav.model.algorithms

Class DBSCANClusteringSegment

java.lang.Object

java.lang.Thread

gov.nih.mipav.model.algorithms.AlgorithmBase

gov.nih.mipav.model.algorithms.DBSCANClusteringSegment

All Implemented Interfaces:

java.awt.event.ActionListener, java.awt.event.WindowListener, java.lang.Runnable, java.util.EventListener

public class DBSCANClusteringSegment
extends AlgorithmBase

% Copyright (c) 2013 Peter Kovesi % www.peterkovesi.com/matlabfns/ % % Permission is hereby granted, free of charge, to any person obtaining a copy % of this software and associated documentation files (the "Software"), to deal % in the Software without restriction, subject to the following conditions: % % The above copyright notice and this permission notice shall be included in % all copies or substantial portions of the Software. % % The Software is provided "as is", without warranty of any kind. The image must be a color image First the slic.m software performs a SLIC Simple Linear Iterative Clustering SuperPixels. SLIC is followed by SPDBSCAN.m to perform a DBSCAN clustering of superpixels. This results in a simple and fast segmentation of an image. Ported MATLAB files: slic.m Implementation of Achanta, Shaji, Smith, Lucchi, Fua and Susstrunk's SLIC Superpixels. spdbscan.m Implements DBSCAN clustering of superpixels. mcleanupregions.m Morphological version of cleanupregions.m The output is not quite as nice but the execution is much faster. finddisconnected.m Finds groupings of disconnected labeled regions. Used by mcleanupregions.m to reduce execution time. makeregionsdistinct.m Ensures labeled regions are distinct. renumberregions.m Ensures all regions in labeled image have a unique label and that the label numbering forms a contiguous sequence. regionadjacency.m Computes adjacency matrix for an image of labeled segmented regions. References: R. Achanta, A. Shaji, K. Smith, A. Lucchi, P. Fua and S. Susstrunk. "SLIC Superpixels Compared to State-of-the-Art Superpixel Methods" PAMI. Vol 34 No 11. November 2012. pp 2274-2281. Martin Ester, Hans-Peter Kriegel, Jorg Sander, Xiaowei Xu (1996). "A density-based algorithm for discovering clusters in large spatial databases with noise". Proceedings of the Second International Conference on Knowledge Discovery and Data Mining (KDD-96). AAAI Press. pp. 226-231.

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
(package private) class	DBSCANClusteringSegment.AmAl
(package private) class	DBSCANClusteringSegment.Renum
(package private) class	DBSCANClusteringSegment.SP

Nested classes/interfaces inherited from class java.lang.Thread

java.lang.Thread.State, java.lang.Thread.UncaughtExceptionHandler

Field Summary

Fields

Modifier and Type	Field	Description
private int	center
private double	Ec
private int	k
private double	m
private int	MEAN_CENTER
private int	MEDIAN_CENTER
private int	mw1
private int	mw2
private int	nItr
private double	seRadius

Fields inherited from class gov.nih.mipav.model.algorithms.AlgorithmBase

destFlag, destImage, image25D, mask, maxProgressValue, minProgressValue, multiThreadingEnabled, nthreads, progress, progressModulus, progressStep, runningInSeparateThread, separable, srcImage, threadStopped

Fields inherited from class java.lang.Thread

MAX_PRIORITY, MIN_PRIORITY, NORM_PRIORITY

Constructor Summary

Constructors

Constructor	Description
DBSCANClusteringSegment(ModelImage destImg, ModelImage srcImg, int k, double m, double seRadius, int center, int mw1, int mw2, int nItr, double Ec)

Method Summary

Modifier and Type	Method	Description
private int	bwlabel4(int[][] bl)
private double[][]	dist(double[] C, double[][][] im, int r1, int c1, double S, double m)
private java.util.Vector<java.util.Vector<java.lang.Integer>>	finddisconnected(int[][] l)
private int	makeregionsdistinct(int[][] seg, int connectivity)
private DBSCANClusteringSegment.AmAl	mcleanupregions(int[][] seg, double seRadius)
private DBSCANClusteringSegment.AmAl	regionadjacency(int[][] L, int connectivity)
private java.util.Vector<java.lang.Integer>	regionQueryM(DBSCANClusteringSegment.SP Sp, DBSCANClusteringSegment.AmAl amal, int n, double Ec)
private DBSCANClusteringSegment.Renum	renumberregions(int[][] L)
void	runAlgorithm()	Actually runs the algorithm.

Methods inherited from class gov.nih.mipav.model.algorithms.AlgorithmBase

actionPerformed, addListener, addProgressChangeListener, calculateImageSize, calculatePrincipleAxis, computeElapsedTime, computeElapsedTime, convertIntoFloat, delinkProgressToAlgorithm, delinkProgressToAlgorithmMulti, displayError, errorCleanUp, finalize, fireProgressStateChanged, fireProgressStateChanged, fireProgressStateChanged, fireProgressStateChanged, fireProgressStateChanged, generateProgressValues, getDestImage, getElapsedTime, getMask, getMaxProgressValue, getMinProgressValue, getNumberOfThreads, getProgress, getProgressChangeListener, getProgressChangeListeners, getProgressModulus, getProgressStep, getProgressValues, getSrcImage, isCompleted, isImage25D, isMultiThreadingEnabled, isRunningInSeparateThread, isThreadStopped, linkProgressToAlgorithm, linkProgressToAlgorithm, makeProgress, notifyListeners, removeListener, removeProgressChangeListener, run, setCompleted, setImage25D, setMask, setMaxProgressValue, setMinProgressValue, setMultiThreadingEnabled, setNumberOfThreads, setProgress, setProgressModulus, setProgressStep, setProgressValues, setProgressValues, setRunningInSeparateThread, setSrcImage, setStartTime, setThreadStopped, startMethod, windowActivated, windowClosed, windowClosing, windowDeactivated, windowDeiconified, windowIconified, windowOpened

Methods inherited from class java.lang.Thread

activeCount, checkAccess, clone, countStackFrames, currentThread, dumpStack, enumerate, getAllStackTraces, getContextClassLoader, getDefaultUncaughtExceptionHandler, getId, getName, getPriority, getStackTrace, getState, getThreadGroup, getUncaughtExceptionHandler, holdsLock, interrupt, interrupted, isAlive, isDaemon, isInterrupted, join, join, join, onSpinWait, resume, setContextClassLoader, setDaemon, setDefaultUncaughtExceptionHandler, setName, setPriority, setUncaughtExceptionHandler, sleep, sleep, start, stop, suspend, toString, yield

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, wait, wait, wait

Field Detail

MEAN_CENTER

private final int MEAN_CENTER

See Also:

Constant Field Values

MEDIAN_CENTER

private final int MEDIAN_CENTER

See Also:

Constant Field Values

k

private int k

m

private double m

seRadius

private double seRadius

center

private int center

mw1

private int mw1

mw2

private int mw2

nItr

private int nItr

Ec

private double Ec

Constructor Detail

DBSCANClusteringSegment

public DBSCANClusteringSegment(ModelImage destImg,
                               ModelImage srcImg,
                               int k,
                               double m,
                               double seRadius,
                               int center,
                               int mw1,
                               int mw2,
                               int nItr,
                               double Ec)

Method Detail

runAlgorithm

public void runAlgorithm()

Description copied from class: AlgorithmBase

Actually runs the algorithm. Implemented by inheriting algorithms.

Specified by:

runAlgorithm in class AlgorithmBase

regionQueryM

private java.util.Vector<java.lang.Integer> regionQueryM(DBSCANClusteringSegment.SP Sp,
                                                         DBSCANClusteringSegment.AmAl amal,
                                                         int n,
                                                         double Ec)

mcleanupregions

private DBSCANClusteringSegment.AmAl mcleanupregions(int[][] seg,
                                                     double seRadius)

renumberregions

private DBSCANClusteringSegment.Renum renumberregions(int[][] L)

finddisconnected

private java.util.Vector<java.util.Vector<java.lang.Integer>> finddisconnected(int[][] l)

regionadjacency

private DBSCANClusteringSegment.AmAl regionadjacency(int[][] L,
                                                     int connectivity)

makeregionsdistinct

private int makeregionsdistinct(int[][] seg,
                                int connectivity)

bwlabel4

private int bwlabel4(int[][] bl)

dist

private double[][] dist(double[] C,
                        double[][][] im,
                        int r1,
                        int c1,
                        double S,
                        double m)