Changeset 10097 for branches/HeuristicLab.Analysis.AlgorithmBehavior/HeuristicLab.Analysis.AlgorithmBehavior.Analyzers/3.3/DistanceMatrixToPoints.cs

Timestamp:

10/30/13 21:49:27 (11 years ago)

Author:

ascheibe

Message:

#1886 added metric mds for testing purposes

File:

• branches/HeuristicLab.Analysis.AlgorithmBehavior/HeuristicLab.Analysis.AlgorithmBehavior.Analyzers/3.3/DistanceMatrixToPoints.cs (modified) (1 diff)

branches/HeuristicLab.Analysis.AlgorithmBehavior/HeuristicLab.Analysis.AlgorithmBehavior.Analyzers/3.3/DistanceMatrixToPoints.cs

@@ -61 +61 @@
       int pi = 0;
       for (int i = 0; i < dm.Length; i++) {
-        if (!q[i].IsAlmost(0) && q[i] > 0.0) {
+        if (!q[i].IsAlmost(0.0) && q[i] > 0.0) {
+          for (int j = 0; j < dm.Length; j++) {
+            points[j][pi] = Math.Sqrt(q[i]) * v[j, i];
+          }
+          pi++;
+        }
+      }
+
+      return points;
+    }
+
+    public static double[][] MetricMDS(double[][] dm) {
+      double[][] points = new double[dm.Length][];
+      double[,] a = new double[dm.Length, dm.Length];
+      double[,] b = new double[dm.Length, dm.Length];
+      double[] ai = new double[dm.Length];
+      double[] aj = new double[dm.Length];
+      double aavg = 0.0;
+      double[] q = new double[dm.Length];
+      double[,] v = new double[dm.Length, dm.Length];
+
+
+      for (int i = 0; i < dm.Length; i++) {
+        for (int j = 0; j < dm.Length; j++) {
+          a[i, j] = -0.5 * Math.Pow(dm[i][j], 2);
+          aavg += a[i, j];
+        }
+      }
+
+      aavg /= dm.Length * dm.Length;
+
+      for (int i = 0; i < dm.Length; i++) {
+        ai[i] = dm[i].Average();
+      }
+
+      for (int i = 0; i < dm.Length; i++) {
+        for (int j = 0; j < dm.Length; j++) {
+          aj[i] += dm[j][i];
+        }
+        aj[i] /= dm.Length;
+      }
+
+      for (int i = 0; i < dm.Length; i++) {
+        for (int j = 0; j < dm.Length; j++) {
+          b[i, j] = a[i, j] - ai[i] - aj[j] + aavg;
+        }
+      }
+
+      //TODO: check b for negative values and make it positiv
+
+      double[] tau;
+      double[,] r;
+      alglib.rmatrixqr(ref b, dm.Length, dm.Length, out tau);
+      alglib.rmatrixqrunpackr(b, dm.Length, dm.Length, out r);
+
+      bool res = alglib.smatrixevd(r, dm.Length, 1, true, out q, out v);
+      if (!res) throw new Exception("Eigenvalue computation did not converge!");
+
+      int zeroCnt = q.Count(x => x.IsAlmost(0) || x < 0.0);
+      for (int i = 0; i < dm.Length; i++) {
+        points[i] = new double[dm.Length - zeroCnt];
+      }
+
+      int pi = 0;
+      for (int i = 0; i < dm.Length; i++) {
+        if (!q[i].IsAlmost(0.0) && q[i] > 0.0) {
           for (int j = 0; j < dm.Length; j++) {
             points[j][pi] = Math.Sqrt(q[i]) * v[j, i];