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k-means Cluster Anlysis Algorithm.
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Description : The package aims at providing an implementation of
k-means Clustering Algorithm in Java. The package does not
provide for any UI and it is up to the user to display the
output in the required format.
---------------JCA.java-------------
package org.c4s.algorithm.cluster;
import java.util.Vector;
/**
This class is the entry point for constructing Cluster Analysis
objects.
Each instance of JCA object is associated with one or more
clusters,
and a Vector of DataPoint objects. The JCA and DataPoint classes
are
the only classes available from other packages.
@see DataPoint
**/
public class JCA {
private Cluster[] clusters;
private int miter;
private Vector mDataPoints = new Vector();
private double mSWCSS;
public JCA(int k, int iter, Vector dataPoints) {
clusters = new Cluster[k];
for (int i = 0; i < k; i++) {
clusters[i] = new Cluster("Cluster" + i);
}
this.miter = iter;
this.mDataPoints = dataPoints;
}
private void calcSWCSS() {
double temp = 0;
for (int i = 0; i < clusters.length; i++) {
temp = temp + clusters[i].getSumSqr();
}
mSWCSS = temp;
}
public void startAnalysis() {
//set Starting centroid positions - Start of Step 1
setInitialCentroids();
int n = 0;
//assign DataPoint to clusters
loop1: while (true) {
for (int l = 0; l < clusters.length; l++)
{
clusters[l].addDataPoint((DataPoint)mDataPoints.elementAt(n));
n++;
if (n >= mDataPoints.size())
break loop1;
}
}
//calculate E for all the clusters
calcSWCSS();
//recalculate Cluster centroids - Start of Step 2
for (int i = 0; i < clusters.length; i++) {
clusters[i].getCentroid().calcCentroid();
}
//recalculate E for all the clusters
calcSWCSS();
for (int i = 0; i < miter; i++) {
//enter the loop for cluster 1
for (int j = 0; j < clusters.length; j++) {
for (int k = 0; k < clusters[j].getNumDataPoints(); k++) {
//pick the first element of the first cluster
//get the current Euclidean distance
double tempEuDt = clusters[j].getDataPoint(k).getCurrentEuDt();
Cluster tempCluster = null;
boolean matchFoundFlag = false;
//call testEuclidean distance for all clusters
for (int l = 0; l < clusters.length; l++) {
//if testEuclidean < currentEuclidean then
if (tempEuDt >
clusters[j].getDataPoint(k).testEuclideanDistance(clusters[l].getCentroid()))
{
tempEuDt =
clusters[j].getDataPoint(k).testEuclideanDistance(clusters[l].getCentroid());
tempCluster = clusters[l];
matchFoundFlag = true;
}
//if statement - Check whether the Last EuDt is > Present EuDt
}
//for variable 'l' - Looping between different Clusters for
matching a Data Point.
//add DataPoint to the cluster and calcSWCSS
if (matchFoundFlag) {
tempCluster.addDataPoint(clusters[j].getDataPoint(k));
clusters[j].removeDataPoint(clusters[j].getDataPoint(k));
for (int m = 0; m < clusters.length; m++) {
clusters[m].getCentroid().calcCentroid();
}
//for variable 'm' - Recalculating centroids for all Clusters
calcSWCSS();
}
//if statement - A Data Point is eligible for transfer between
Clusters.
}
//for variable 'k' - Looping through all Data Points of the
current Cluster.
}//for variable 'j' - Looping through all the Clusters.
}//for variable 'i' - Number of iterations.
}
public Vector[] getClusterOutput() {
Vector v[] = new Vector[clusters.length];
for (int i = 0; i < clusters.length; i++) {
v[i] = clusters[i].getDataPoints();
}
return v;
}
private void setInitialCentroids() {
//kn = (round((max-min)/k)*n)+min where n is from 0 to (k-1).
double cx = 0, cy = 0;
for (int n = 1; n <= clusters.length; n++) {
cx = (((getMaxXValue() - getMinXValue()) / (clusters.length +
1)) * n) + getMinXValue();
cy = (((getMaxYValue() - getMinYValue()) / (clusters.length +
1)) * n) + getMinYValue();
Centroid c1 = new Centroid(cx, cy);
clusters[n - 1].setCentroid(c1);
c1.setCluster(clusters[n - 1]);
}
}
private double getMaxXValue() {
double temp;
temp = ((DataPoint) mDataPoints.elementAt(0)).getX();
for (int i = 0; i < mDataPoints.size(); i++) {
DataPoint dp = (DataPoint) mDataPoints.elementAt(i);
temp = (dp.getX() > temp) ? dp.getX() : temp;
}
return temp;
}
private double getMinXValue() {
double temp = 0;
temp = ((DataPoint) mDataPoints.elementAt(0)).getX();
for (int i = 0; i < mDataPoints.size(); i++) {
DataPoint dp = (DataPoint) mDataPoints.elementAt(i);
temp = (dp.getX() < temp) ? dp.getX() : temp;
}
return temp;
}
private double getMaxYValue() {
double temp = 0;
temp = ((DataPoint) mDataPoints.elementAt(0)).getY();
for (int i = 0; i < mDataPoints.size(); i++) {
DataPoint dp = (DataPoint) mDataPoints.elementAt(i);
temp = (dp.getY() > temp) ? dp.getY() : temp;
}
return temp;
}
private double getMinYValue() {
double temp = 0;
temp = ((DataPoint) mDataPoints.elementAt(0)).getY();
for (int i = 0; i < mDataPoints.size(); i++) {
DataPoint dp = (DataPoint) mDataPoints.elementAt(i);
temp = (dp.getY() < temp) ? dp.getY() : temp;
}
return temp;
}
public int getKValue() {
return clusters.length;
}
public int getIterations() {
return miter;
}
public int getTotalDataPoints() {
return mDataPoints.size();
}
public double getSWCSS() {
return mSWCSS;
}
public Cluster getCluster(int pos) {
return clusters[pos];
}
}
/*-----------------Cluster.java----------------*/
package org.c4s.algorithm.cluster;
import java.util.Vector;
/**
* This class represents a Cluster in a Cluster Analysis
Instance. A Cluster is associated
* with one and only one JCA Instance. A Cluster is related to
more than one DataPoints and
* one centroid.
* @author Shyam Sivaraman
* @version 1.1
* @see DataPoint
* @see Centroid
*/
class Cluster {
private String mName;
private Centroid mCentroid;
private double mSumSqr;
private Vector mDataPoints;
public Cluster(String name) {
this.mName = name;
this.mCentroid = null; //will be set by calling setCentroid()
mDataPoints = new Vector();
}
public void setCentroid(Centroid c) {
mCentroid = c;
}
public Centroid getCentroid() {
return mCentroid;
}
public void addDataPoint(DataPoint dp) { //called from
CAInstance
dp.setCluster(this); //initiates a inner call to
calcEuclideanDistance() in DP.
this.mDataPoints.addElement(dp);
calcSumOfSquares();
}
public void removeDataPoint(DataPoint dp) {
this.mDataPoints.removeElement(dp);
calcSumOfSquares();
}
public int getNumDataPoints() {
return this.mDataPoints.size();
}
public DataPoint getDataPoint(int pos) {
return (DataPoint) this.mDataPoints.elementAt(pos);
}
public void calcSumOfSquares() { //called from Centroid
int size = this.mDataPoints.size();
double temp = 0;
for (int i = 0; i < size; i++) {
temp = temp + ((DataPoint)
this.mDataPoints.elementAt(i)).getCurrentEuDt();
}
this.mSumSqr = temp;
}
public double getSumSqr() {
return this.mSumSqr;
}
public String getName() {
return this.mName;
}
public Vector getDataPoints() {
return this.mDataPoints;
}
}
/*---------------Centroid.java-----------------*/
package org.c4s.algorithm.cluster;
/**
* This class represents the Centroid for a Cluster. The initial
centroid is calculated
* using a equation which divides the sample space for each
dimension into equal parts
* depending upon the value of k.
* @author Shyam Sivaraman
* @version 1.0
* @see Cluster
*/
class Centroid {
private double mCx, mCy;
private Cluster mCluster;
public Centroid(double cx, double cy) {
this.mCx = cx;
this.mCy = cy;
}
public void calcCentroid() { //only called by CAInstance
int numDP = mCluster.getNumDataPoints();
double tempX = 0, tempY = 0;
int i;
//caluclating the new Centroid
for (i = 0; i < numDP; i++) {
tempX = tempX + mCluster.getDataPoint(i).getX();
//total for x
tempY = tempY + mCluster.getDataPoint(i).getY();
//total for y
}
this.mCx = tempX / numDP;
this.mCy = tempY / numDP;
//calculating the new Euclidean Distance for each Data Point
tempX = 0;
tempY = 0;
for (i = 0; i < numDP; i++) {
mCluster.getDataPoint(i).calcEuclideanDistance();
}
//calculate the new Sum of Squares for the Cluster
mCluster.calcSumOfSquares();
}
public void setCluster(Cluster c) {
this.mCluster = c;
}
public double getCx() {
return mCx;
}
public double getCy() {
return mCy;
}
public Cluster getCluster() {
return mCluster;
}
}
/*----------------DataPoint.java----------------*/
package org.c4s.algorithm.cluster;
/**
This class represents a candidate for Cluster analysis. A
candidate must have
a name and two independent variables on the basis of which it is
to be clustered.
A Data Point must have two variables and a name. A Vector of
Data Point object
is fed into the constructor of the JCA class. JCA and DataPoint
are the only
classes which may be available from other packages.
@author Shyam Sivaraman
@version 1.0
@see JCA
@see Cluster
*/
public class DataPoint {
private double mX,mY;
private String mObjName;
private Cluster mCluster;
private double mEuDt;
public DataPoint(double x, double y, String name) {
this.mX = x;
this.mY = y;
this.mObjName = name;
this.mCluster = null;
}
public void setCluster(Cluster cluster) {
this.mCluster = cluster;
calcEuclideanDistance();
}
public void calcEuclideanDistance() {
//called when DP is added to a cluster or when a Centroid is
recalculated.
mEuDt = Math.sqrt(Math.pow((mX -
mCluster.getCentroid().getCx()),
2) + Math.pow((mY - mCluster.getCentroid().getCy()), 2));
}
public double testEuclideanDistance(Centroid c) {
return Math.sqrt(Math.pow((mX - c.getCx()), 2) + Math.pow((mY -
c.getCy()), 2));
}
public double getX() {
return mX;
}
public double getY() {
return mY;
}
public Cluster getCluster() {
return mCluster;
}
public double getCurrentEuDt() {
return mEuDt;
}
public String getObjName() {
return mObjName;
}
}
/*-----------------PrgMain.java---------------*/
import org.c4s.algorithm.cluster.DataPoint;
import org.c4s.algorithm.cluster.JCA;
import java.util.Vector;
import java.util.Iterator;
/**
* Created by IntelliJ IDEA.
* User: shyam.s
* Date: Apr 18, 2004
* Time: 4:26:06 PM
*/
public class PrgMain {
public static void main (String args[]){
Vector dataPoints = new Vector();
dataPoints.add(new DataPoint(22,21,"p53"));
dataPoints.add(new DataPoint(19,20,"bcl2"));
dataPoints.add(new DataPoint(18,22,"fas"));
dataPoints.add(new DataPoint(1,3,"amylase"));
dataPoints.add(new DataPoint(3,2,"maltase"));
JCA jca = new JCA(2,1000,dataPoints);
jca.startAnalysis();
Vector[] v = jca.getClusterOutput();
for (int i=0; i<v.length; i++){
Vector tempV = v[i];
System.out.println("-----------Cluster"+i+"---------");
Iterator iter = tempV.iterator();
while(iter.hasNext()){
DataPoint dpTemp = (DataPoint)iter.next();
System.out.println(dpTemp.getObjName()+"
["+dpTemp.getX()+","+dpTemp.getY()+"]");
}
}
}
}
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