net.sf.ij_plugins.clustering

Class KMeans3D

java.lang.Object

net.sf.ij_plugins.clustering.KMeans3D

public final class KMeans3D
extends java.lang.Object

3D version of the k-means algorithm.

Author:

Jarek Sacha

Constructor Summary

Constructors

Constructor and Description
KMeans3D()
KMeans3D(KMeansConfig config)

Method Summary

Methods

Modifier and Type	Method and Description
int	closestCluster(float[] x) Find index of the cluster closest to the sample x.
protected ij.ImageStack	encodeCentroidValueImage()
ij.ImageStack	getCentroidValueImage() Returns stack where discovered clusters can be represented by replacing pixel values in a cluster by the value of the centroid of that cluster.
float[][]	getClusterCenters() Return location of cluster centers.
long	getNumberOfStepsToConvergence()
protected float[][]	initializeClusterCenters() Initialize clusters using k-means++ approach, see http://en.wikipedia.org/wiki/K-means++
protected net.sf.ij_plugins.clustering.StackPixelIterator	newPixelIterator()
protected int	numberOfValues() Number of values in a pixel
ij.ImageStack	run(ij.ImageStack stack) Perform k-means clustering of the input stack.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

KMeans3D

public KMeans3D()

KMeans3D

public KMeans3D(KMeansConfig config)

Method Detail

run

public ij.ImageStack run(ij.ImageStack stack)

Perform k-means clustering of the input stack.

Parameters:

stack - stack representing a 3D image.

Returns:

segmented image.

numberOfValues

protected int numberOfValues()

Number of values in a pixel

encodeCentroidValueImage

protected ij.ImageStack encodeCentroidValueImage()

newPixelIterator

protected net.sf.ij_plugins.clustering.StackPixelIterator newPixelIterator()

initializeClusterCenters

protected float[][] initializeClusterCenters()

Initialize clusters using k-means++ approach, see http://en.wikipedia.org/wiki/K-means++

Returns:

initial cluster centers.

getCentroidValueImage

public final ij.ImageStack getCentroidValueImage()

Returns stack where discovered clusters can be represented by replacing pixel values in a cluster by the value of the centroid of that cluster.

Returns:

centroid value image

getNumberOfStepsToConvergence

public final long getNumberOfStepsToConvergence()

getClusterCenters

public final float[][] getClusterCenters()

Return location of cluster centers.

Returns:

array of cluster centers. First index refers to cluster number.

closestCluster

public final int closestCluster(float[] x)

Find index of the cluster closest to the sample x. run(ij.ImageStack) must be run before calling this method.

Parameters:

x - test point, number of values must be the same is input stack size.

Returns:

index of the closest cluster.

See Also:

run(ij.ImageStack)