Clustering

Example of how to cluster a set of points. The points are randomly drawn from three different distributions. The clustering algorithm will attempt to dermine which points belong to the same set.

Clusters

Output from example. Each cluster has its own color and each point is colorized to show the cluster it belongs to.

https://github.com/lessthanoptimal/ddogleg/tree/v0.24.0/examples/src/org/ddogleg/example/ExampleClustering.java

  1// if true it will create the clusters from a gaussian distribution.
  2// Otherwise an uniform distribution is used.
  3public static boolean gaussian = true;
  4public static Random rand = new Random(324);
  5public static boolean clicked = false;
  6
  7public static void main( String[] args ) {
  8    int dof = 2; // degree of freedom of the 2D point
  9    var points = new ArrayList<double[]>();
 10
 11    // Accessor is used instead of a list directly because it becomes more efficient in very large datasets
 12    var accessor = new ListAccessor<>(points,
 13            ( src, dst ) -> System.arraycopy(src, 0, dst, 0, dof), double[].class);
 14
 15    // create 3 clusters drawn from a uniform square distribution
 16    points.addAll(createCluster(5, 7, 2, 100));
 17    points.addAll(createCluster(1, 2, 1, 120));
 18    points.addAll(createCluster(4, 5, 1.5, 300));
 19
 20    // remove any structure from the point's ordering
 21    Collections.shuffle(points);
 22
 23    ComputeClusters<double[]> cluster = FactoryClustering.kMeans(null, dof, double[].class);
 24    ComputeClusters<double[]> cluster = FactoryClustering.gaussianMixtureModelEM_F64(1000, 500, 1e-8, dof);
 25
 26    cluster.initialize(rand.nextLong());
 27
 28    // visualization stuff
 29    var gui = new Gui(points);
 30
 31    var frame = new JFrame();
 32    frame.add(gui, BorderLayout.CENTER);
 33    frame.pack();
 34    frame.setVisible(true);
 35    frame.setDefaultCloseOperation(WindowConstants.EXIT_ON_CLOSE);
 36
 37    // Run the cluster algorithm again each time the user clicks the window
 38    // This allows you to see how stable the clusters are
 39    while (true) {
 40        int numClusters = 3;
 41        cluster.process(accessor, numClusters);
 42
 43        AssignCluster<double[]> assignment = cluster.getAssignment();
 44        gui.update(assignment);
 45
 46        while (!clicked) {
 47            Thread.yield();
 48        }
 49        clicked = false;
 50    }
 51}
 52
 53public static List<double[]> createCluster( double x, double y, double width, int N ) {
 54
 55    List<double[]> points = new ArrayList<>();
 56
 57    for (int i = 0; i < N; i++) {
 58        double[] p = new double[2];
 59
 60        if (gaussian) {
 61            p[0] = rand.nextGaussian()*width/3 + x;
 62            p[1] = rand.nextGaussian()*width/3 + y;
 63        } else {
 64            p[0] = rand.nextDouble()*width - width/2 + x;
 65            p[1] = rand.nextDouble()*width - width/2 + y;
 66        }
 67
 68        points.add(p);
 69    }
 70
 71    return points;
 72}
 73
 74/**
 75 * Basic visualization which draws the points in a window.  Each color is assigned a different random color
 76 */
 77public static class Gui extends JPanel implements MouseListener {
 78    AssignCluster<double[]> assignment;
 79    List<double[]> points;
 80    Color[] colors;
 81
 82    public Gui( List<double[]> points ) {
 83
 84        this.points = points;
 85
 86        setPreferredSize(new Dimension(300, 300));
 87        setBackground(Color.WHITE);
 88
 89        addMouseListener(this);
 90    }
 91
 92    public synchronized void update( AssignCluster<double[]> assignment ) {
 93        this.assignment = assignment;
 94        colors = new Color[assignment.getNumberOfClusters()];
 95        for (int i = 0; i < colors.length; i++) {
 96            colors[i] = new Color(rand.nextInt() | 0x080808);
 97        }
 98        repaint();
 99    }
100
101    @Override
102    public synchronized void paintComponent( Graphics g ) {
103        if (assignment == null)
104            return;
105
106        super.paintComponent(g);
107
108        Graphics2D g2 = (Graphics2D)g;
109
110        double scaleX = getWidth()/10.0;
111        double scaleY = getHeight()/10.0;
112
113        for (int i = 0; i < points.size(); i++) {
114            double[] p = points.get(i);
115            int x = (int)(p[0]*scaleX + 0.5);
116            int y = (int)(p[1]*scaleY + 0.5);
117
118            g2.setColor(colors[assignment.assign(p)]);
119            g2.fillOval(x - 2, y - 2, 5, 5);
120        }
121    }
122
123    @Override
124    public void mouseClicked( MouseEvent e ) {
125        clicked = true;
126    }
127
128    @Override
129    public void mousePressed( MouseEvent e ) {
130    }
131
132    @Override
133    public void mouseReleased( MouseEvent e ) {
134    }
135
136    @Override
137    public void mouseEntered( MouseEvent e ) {
138    }
139
140    @Override
141    public void mouseExited( MouseEvent e ) {
142    }
143}