public static double link(double r) {
if (r < 0.0) {
double s = Math.exp(r);
return s / (1.0 + s);
} else {
double s = Math.exp(-r);
return 1.0 / (1.0 + s);
}
}
public static double sumOfPowerOfDeviations(double[] data, int k, double c) {
double sum = 0;
for (int i = 0; i < data.length; i++) {
sum += Math.pow(data[i] - c, k);
}
return sum;
}
public static double skew(double[] data) {
double sum = 0;
double sumPD = 0;
double sumSq = 0;
for (int i = 0; i < data.length; i++) {
sum += data[i];
sumSq += data[i] * data[i];
}
double mean = sum / data.length;
double standardDeviation = Math.sqrt((sumSq - mean * sum) / data.length);
for (int i = 0; i < data.length; i++) {
sumPD += Math.pow(data[i] - mean, 3);
}
double moment3 = sumPD / data.length;
return moment3 / (standardDeviation * standardDeviation * standardDeviation);
}
public static double sumOfLogarithms(double[] elements) {
double logsum = 0;
for (int i = 0; i < elements.length; i++) {
logsum += Math.log(elements[i]);
}
return logsum;
}
public static double meanDeviation(double[] elements, double mean) {
int size = elements.length;
double sum = 0;
for (int i = size; --i >= 0; ) {
sum += Math.abs(elements[i] - mean);
}
return sum / size;
}
public static double kurtosis(double[] data) {
double sum = 0;
double sumPD = 0;
double sumSq = 0;
for (int i = 0; i < data.length; i++) {
sum += data[i];
sumSq += data[i] * data[i];
}
double mean = sum / data.length;
double standardDeviation = Math.sqrt((--sumSq - mean * sum) / data.length);
for (int i = 0; i < data.length; i++) {
sumPD += Math.pow(data[i] - mean, 4);
}
double moment4 = sumPD / data.length;
return -3
+ moment4 / (standardDeviation * standardDeviation * standardDeviation * standardDeviation);
}
public static double logGamma(double xx) {
double[] cof = {
76.18009172947146,
-86.50532032941677,
24.01409824083091,
-1.231739572450155,
0.1208650973866179e-2,
-0.5395239384953e-5
};
double x = xx - 1.0;
double tmp = x + 5.5;
tmp -= (x + 0.5) * Math.log(tmp);
double ser = 1.000000000190015;
double[] coeff = cof;
for (int j = 0; j <= 5; j++) {
x++;
ser += coeff[j] / x;
}
return -tmp + Math.log(2.5066282746310005 * ser);
}
public static double[] standardize(double[] data) {
double sum = 0;
double sumSq = 0;
for (int i = 0; i < data.length; i++) {
sum += data[i];
sumSq += data[i] * data[i];
}
double mean = sum / data.length;
double sd = Math.sqrt((sumSq - mean * sum) / data.length);
for (int i = 0; i < data.length; i++) {
data[i] = (data[i] - mean) / sd;
}
return data;
}
/** Randomly sets K temporary cluster centers */
private static void setRandomCenters() {
centers = new ArrayList<Point>();
int rand;
for (int i = 0; i < K; ++i) {
do {
rand = (int) (Math.random() * points.size());
} while (centers.contains(points.get(rand)));
centers.add(points.get(rand));
clusters.get(i).addCenterPoint(points.get(rand));
}
for (Point p : centers) System.out.println(p);
}
public static double[] power(double[] data, int k) {
for (int i = 0; i < data.length; i++) {
data[i] = Math.pow(data[i], k);
}
return data;
}
public static double geometricPdf(int k, double p) {
return p * Math.pow(1 - p, k);
}
public static double sampleSkew(int size, double moment3, double sampleVariance) {
int n = size;
double s = Math.sqrt(sampleVariance);
double m3 = moment3 * n;
return n * m3 / ((n - 1) * (n - 2) * s * s * s);
}
public static double sampleKurtosisStandardError(int size) {
int n = size;
return Math.sqrt(24.0 * n * (n-- - 1) * (n - 1) / ((n - 3) * (n - 2) * (n + 3) * (n + 5)));
}
public static void main(String[] args) {
// TEST MEASURE
// Point p1 = new Point(-1d, -1d);
// Point p2 = new Point(2d, 3d);
// System.out.println(measure.d(p1, p2));
// System.out.println(measure.s(p1, p2));
// return;
Double[][] data = FileHandler.readFile(fileName);
// cannot display points if dimension is > 2
if (data[0].length != 2) canDisplay = false;
// build graphic points from coords' array
buildPointsFromData(data);
Config.computeBoundingRect(points);
// init display
if (canDisplay) {
disp = new Display();
disp.setVisible(true);
for (Point p : points) {
disp.addObject(p);
}
}
testResults = new double[nbTests];
for (int t = 0; t < nbTests; ++t) {
// define K clusters and K temporary centres
clusters = new ArrayList<Cluster>();
for (int i = 0; i < K; ++i) {
clusters.add(new Cluster());
}
setRandomCenters();
for (Cluster c : clusters) {
System.out.println("center for cluster " + c + ": " + c.getCenter());
}
if (canDisplay) pause(1000);
// variables used in for loops
double minDist, currDist, diff;
Double[] prevCoords, newCoords;
Cluster alloc;
Point newCenter;
for (int i = 0; i < maxIter; ++i) {
if (canDisplay) {
disp.setLabel("[ iteration #" + (i + 1) + " ]");
} else {
System.out.println("------> iteration #" + (i + 1));
}
// allocate points to group which center is closest
for (Point p : points) {
minDist = Config.MAX;
alloc = clusters.get(0); // default initialization
for (Cluster c : clusters) {
currDist = measure.d(p, c.getCenter());
if (currDist < minDist) {
minDist = currDist;
alloc = c;
}
}
alloc.addPoint(p);
}
// recenter: calculate gravity centers for formed groups
diff = 0;
prevCoords = null;
for (Cluster c : clusters) {
// delete previous center if it not a Point of the Cluster
if (canDisplay && !c.getPoints().contains(c.getCenter())) {
disp.removeObject(c.getCenter());
}
if (stopOnConverge) {
prevCoords = c.getCenter().getCoords();
}
newCenter = c.makeGravityCenter();
if (stopOnConverge) {
newCoords = c.getCenter().getCoords();
for (int k = 0; k < prevCoords.length; ++k) {
diff += Math.abs(prevCoords[k] - newCoords[k]);
}
}
if (canDisplay) {
disp.addObject(newCenter);
} else {
// System.out.println("\tcenter for " + c + ": " + c.getCenter());
System.out.println(c.getCenter());
}
} // loop over clusters
if (canDisplay) {
disp.repaint();
}
// if Clusters' centers don't change anymore, then stop (algorithm converged)
if (diff == 0 && stopOnConverge) {
testResults[t] = (double) i;
if (canDisplay) {
disp.setLabel("[ Converged at iteration #" + (i) + " ]");
disp.repaint();
} else {
System.out.println("[ Converged at iteration #" + (i) + " ]");
}
break;
}
pause(100);
} // loop over iterations
if (testResults[t] == 0) {
System.out.println("!!!!!!!!!! Test #" + t + " did not converge.");
if (stopOnConverge) return;
}
// reset display
if (canDisplay && t + 1 < nbTests) {
for (Point p : points) p.setCluster(null);
for (Cluster c : clusters) disp.removeObject(c.getCenter());
}
} // loop over tests
// display test results and compute means
DescriptiveStatistics stats = new DescriptiveStatistics(testResults);
System.out.println("=========> Results:");
for (int t = 0; t < nbTests; ++t) {
System.out.println("--> [ " + testResults[t] + " ]");
}
System.out.println("=========> Means: " + stats.getMean());
System.out.println("=========> Std dev: " + stats.getStandardDeviation());
}