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Java example source code file (TopographicErrorHistogram.java)

This example Java source code file (TopographicErrorHistogram.java) is included in the alvinalexander.com "Java Source Code Warehouse" project. The intent of this project is to help you "Learn Java by Example" TM.

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Java - Java tags/keywords

distancemeasure, iterable, locationfinder, mapdatavisualization, network, neuron, pair, topographicerrorhistogram

The TopographicErrorHistogram.java Java example source code

 * 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,
 * 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.
 * @since 3.6
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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