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

All Methods Instance Methods Concrete Methods
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)

Class DBSCANClusteringSegment

Nested Class Summary

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

Field Summary

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

Fields inherited from class java.lang.Thread

Constructor Summary

Method Summary

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

Methods inherited from class java.lang.Thread

Methods inherited from class java.lang.Object

Field Detail

MEAN_CENTER

MEDIAN_CENTER

k

m

seRadius

center

mw1

mw2

nItr

Ec

Constructor Detail

DBSCANClusteringSegment

Method Detail

runAlgorithm

regionQueryM

mcleanupregions

renumberregions

finddisconnected

regionadjacency

makeregionsdistinct

bwlabel4

dist