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From er...@apache.org
Subject [06/10] [math] MATH-1270
Date Fri, 11 Sep 2015 09:42:18 GMT
MATH-1270

SOFM visualization: Topographic error.


Project: http://git-wip-us.apache.org/repos/asf/commons-math/repo
Commit: http://git-wip-us.apache.org/repos/asf/commons-math/commit/d7f6c8da
Tree: http://git-wip-us.apache.org/repos/asf/commons-math/tree/d7f6c8da
Diff: http://git-wip-us.apache.org/repos/asf/commons-math/diff/d7f6c8da

Branch: refs/heads/MATH_3_X
Commit: d7f6c8da9512af55c04a86984f56ab6f9e2da126
Parents: afac1f0
Author: Gilles <erans@apache.org>
Authored: Fri Sep 11 00:54:36 2015 +0200
Committer: Gilles <erans@apache.org>
Committed: Fri Sep 11 00:54:36 2015 +0200

----------------------------------------------------------------------
 .../twod/util/TopographicErrorHistogram.java    | 90 ++++++++++++++++++++
 1 file changed, 90 insertions(+)
----------------------------------------------------------------------


http://git-wip-us.apache.org/repos/asf/commons-math/blob/d7f6c8da/src/main/java/org/apache/commons/math3/ml/neuralnet/twod/util/TopographicErrorHistogram.java
----------------------------------------------------------------------
diff --git a/src/main/java/org/apache/commons/math3/ml/neuralnet/twod/util/TopographicErrorHistogram.java
b/src/main/java/org/apache/commons/math3/ml/neuralnet/twod/util/TopographicErrorHistogram.java
new file mode 100644
index 0000000..b337c0a
--- /dev/null
+++ b/src/main/java/org/apache/commons/math3/ml/neuralnet/twod/util/TopographicErrorHistogram.java
@@ -0,0 +1,90 @@
+/*
+ * Licensed to the Apache Software Foundation (ASF) under one or more
+ * contributor license agreements.  See the NOTICE file distributed with
+ * this work for additional information regarding copyright ownership.
+ * The ASF licenses this file to You under the Apache License, Version 2.0
+ * (the "License"); you may not use this file except in compliance with
+ * the License.  You may obtain a copy of the License at
+ *
+ *      http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package org.apache.commons.math3.ml.neuralnet.twod.util;
+
+import org.apache.commons.math3.ml.neuralnet.MapUtils;
+import org.apache.commons.math3.ml.neuralnet.Neuron;
+import org.apache.commons.math3.ml.neuralnet.Network;
+import org.apache.commons.math3.ml.neuralnet.twod.NeuronSquareMesh2D;
+import org.apache.commons.math3.ml.distance.DistanceMeasure;
+import org.apache.commons.math3.util.Pair;
+
+/**
+ * Computes the topographic error histogram.
+ * Each bin will contain the number of data for which the first and
+ * second best matching units are not adjacent in the map.
+ */
+public class TopographicErrorHistogram implements MapDataVisualization {
+    /** Distance. */
+    private final DistanceMeasure distance;
+    /** Whether to compute relative bin counts. */
+    private final boolean relativeCount;
+
+    /**
+     * @param relativeCount Whether to compute relative bin counts.
+     * If {@code true}, the data count in each bin will be divided by the total
+     * number of samples mapped to the neuron represented by that bin.
+     * @param distance Distance.
+     */
+    public TopographicErrorHistogram(boolean relativeCount,
+                                     DistanceMeasure distance) {
+        this.relativeCount = relativeCount;
+        this.distance = distance;
+    }
+
+    /** {@inheritDoc} */
+    public double[][] computeImage(NeuronSquareMesh2D map,
+                                   Iterable<double[]> data) {
+        final int nR = map.getNumberOfRows();
+        final int nC = map.getNumberOfColumns();
+
+        final Network net = map.getNetwork();
+        final LocationFinder finder = new LocationFinder(map);
+
+        // Hit bins.
+        final int[][] hit = new int[nR][nC];
+        // Error bins.
+        final double[][] error = new double[nR][nC];
+
+        for (double[] sample : data) {
+            final Pair<Neuron, Neuron> p = MapUtils.findBestAndSecondBest(sample, map,
distance);
+            final Neuron best = p.getFirst();
+            
+            final LocationFinder.Location loc = finder.getLocation(best);
+            final int row = loc.getRow();
+            final int col = loc.getColumn();
+            hit[row][col] += 1;
+
+            if (!net.getNeighbours(best).contains(p.getSecond())) {
+                // Increment count if first and second best matching units
+                // are not neighbours.
+                error[row][col] += 1;
+            }
+        }
+
+        if (relativeCount) {
+            for (int r = 0; r < nR; r++) {
+                for (int c = 0; c < nC; c++) {
+                    error[r][c] /= hit[r][c];
+                }
+            }
+        }
+
+        return error;
+    }
+}


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