DataScience/clustering/VarMin.java

import java.io.BufferedWriter;
import java.io.FileNotFoundException;
import java.io.FileWriter;
import java.io.IOException;
import java.lang.reflect.Array;
import java.util.ArrayList;

public class VarMin {
    public ArrayList<ArrayList<Double>> data;
    public ArrayList<ArrayList<Double>> centroids;
    public ArrayList<Integer> clusterMap;
    int[] count;
    int k;
    int dim;

    public VarMin(int k){
        this.k = k;
        this.dim = 0;
    }

    //euklidische distanz
    public double distance(ArrayList<Double> p1, ArrayList<Double> p2){
        int count = Math.min(p1.size(), p2.size());
        double sum = 0;
        for(int i = 0; i < count;i++){
            sum += Math.pow(p1.get(i) - p2.get(i), 2);
        }
        return Math.sqrt(sum);
    }

    //p1 += p2
    public void addPoint(ArrayList<Double> p1, ArrayList<Double> p2){
        int count = Math.min(p1.size(), p2.size());
        for(int i = 0; i < count;i++){
            p1.set(i, p1.get(i) + p2.get(i));
        }
    }

    //p1 *= v
    public void mulPoint(ArrayList<Double> p1, Double v){
        for(int i = 0; i < p1.size();i++){
            p1.set(i, p1.get(i) * v);
        }
    }

    private void setParams(int k, int dim){
        this.k = k;
        this.dim = dim;
        centroids = new ArrayList<ArrayList<Double>>();
        for(int i = 0; i < k;i++){
            centroids.add(new ArrayList<Double>());
            for(int j = 0; j < dim;j++){
                centroids.get(i).add(0.0);
            }
        }
        clusterMap = new ArrayList<Integer>();
        count = new int[k];
    }

    public void setData(ArrayList<ArrayList<Double>> data){
        dim = data.get(0).size();
        this.data = data;
        setParams(k,dim);
        for(int i = 0; i < data.size();i++){
            clusterMap.add(0);
        }
    }

    public int getClosestCluster(ArrayList<Double> p){
        double minDist = Double.MAX_VALUE;
        int minIndex = 0;
        for(int c = 0; c < k;c++){
            double dist = distance(p, centroids.get(c));
            if(dist < minDist) {
                minDist = dist;
                minIndex = c;
            }
        }
        return minIndex;
    }

    public void initCluster(){
        int pointsPerCluster = data.size() / k;
        for(int i = 0; i < data.size();i++){
            int c = i / pointsPerCluster;
            addPoint(centroids.get(c), data.get(i));
            clusterMap.set(i, c);
        }
        for(int c = 0; c < k;c++){
            mulPoint(centroids.get(c), 1.0 / pointsPerCluster);
            count[c] = pointsPerCluster;
        }
    }

    public void calcCluster(){
        for(int c = 0; c < k;c++){
            mulPoint(centroids.get(c), 0.0);
        }
        for(int c = 0; c < k;c++){
            count[c] = 0;
        }
        for(int i = 0; i < data.size();i++){
            int c = clusterMap.get(i);
            addPoint(centroids.get(c), data.get(i));
            count[c]++;
        }
        for(int c = 0; c < k;c++){
            if(count[c] == 0){
                mulPoint(centroids.get(c),0.0);
            }else{
                mulPoint(centroids.get(c), 1.0 / count[c]);
            }
        }
    }

    public void clustering(){
        initCluster();

        System.out.println(getCompactness());
        //iteration
        boolean change = true;
        while(change){
            change = false;
            for(int i = 0; i < data.size();i++) {
                int newCluster = getClosestCluster(data.get(i));
                if(clusterMap.get(i) != newCluster){
                    change = true;
                }
                clusterMap.set(i, newCluster);
            }
            calcCluster();
            System.out.println(getCompactness());
        }
    }

    public double getCompactness(){
        double sum = 0;
        for(int i = 0; i < data.size();i++){
            sum += distance(data.get(i), centroids.get(clusterMap.get(i)));
        }
        return sum;
    }

    public ArrayList<ArrayList<ArrayList<Double>>> getCluster(){
        ArrayList<ArrayList<ArrayList<Double>>> cluster = new ArrayList<>();
        for(int i = 0; i < k;i++){
            cluster.add(new ArrayList<>());
        }
        for(int i = 0; i < data.size();i++) {
            int c = clusterMap.get(i);
            cluster.get(c).add(data.get(i));
        }
        return cluster;
    }

    public static void printCluster(ArrayList<ArrayList<ArrayList<Double>>> cluster){
        int i = 0;
        for(ArrayList<ArrayList<Double>> c : cluster){
            System.out.print("Cluster" + ++i + ": ");
            for(ArrayList<Double> p : c){
                System.out.print("(");
                for (int j = 0; j < p.size();j++) {
                    System.out.print(p.get(j));
                    if(j < p.size() - 1){
                        System.out.print(",");
                    }
                }
                System.out.print("); ");
            }
            System.out.println();
        }
    }

    public static void writeToFile(ArrayList<ArrayList<ArrayList<Double>>> cluster, String file){
        try(BufferedWriter stream = new BufferedWriter(new FileWriter(file))) {

            for(ArrayList<ArrayList<Double>> c : cluster){
                for(ArrayList<Double> p : c){
                    for (int j = 0; j < p.size();j++) {
                        stream.write(p.get(j).toString() + " ");
                    }
                    stream.write("\n");
                }
                stream.write("\n");
            }

        } catch (FileNotFoundException e) {
            e.printStackTrace();
        } catch (IOException e) {
            e.printStackTrace();
        }
    }

    public static void main(String[] args) {
        int k = 3;
        if(args.length >= 1){
            k = Integer.parseInt(args[0]);
        }
        VarMin varmin = new VarMin(k);
        ArrayList<ArrayList<Double>> data = DataFileReader.readFile("input.txt");
        varmin.setData(data);

        varmin.clustering();
        ArrayList<ArrayList<ArrayList<Double>>> cluster1 = varmin.getCluster();
        System.out.println("Result:");
        printCluster(cluster1);

        writeToFile(cluster1, "cluster.txt");
    }
}