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Developed the new genetic algorithm module following the JIRA MATH-1563.
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‎commons-math-examples/examples-ga/examples-ga-math-functions/pom.xml

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<?xml version="1.0"?>
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<!--
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Licensed to the Apache Software Foundation (ASF) under one or more
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contributor license agreements. See the NOTICE file distributed with
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this work for additional information regarding copyright ownership.
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The ASF licenses this file to You under the Apache License, Version 2.0
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(the "License"); you may not use this file except in compliance with
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the License. You may obtain a copy of the License at
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http://www.apache.org/licenses/LICENSE-2.0
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Unless required by applicable law or agreed to in writing, software
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distributed under the License is distributed on an "AS IS" BASIS,
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WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
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See the License for the specific language governing permissions and
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limitations under the License.
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-->
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<project xmlns="http://maven.apache.org/POM/4.0.0"
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xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
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xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 https://maven.apache.org/xsd/maven-4.0.0.xsd">
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<modelVersion>4.0.0</modelVersion>
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<parent>
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<groupId>org.apache.commons</groupId>
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<artifactId>examples-ga</artifactId>
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<version>4.0-SNAPSHOT</version>
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</parent>
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<artifactId>examples-ga-math-functions</artifactId>
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<properties>
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<maven.compiler.source>1.8</maven.compiler.source>
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<maven.compiler.target>1.8</maven.compiler.target>
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<!-- OSGi -->
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<commons.osgi.symbolicName>org.apache.commons.math4.examples.ga.mathfunctions</commons.osgi.symbolicName>
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<commons.osgi.export>org.apache.commons.math4.examples.ga.mathfunctions</commons.osgi.export>
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<!-- Java 9+ -->
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<commons.automatic.module.name>org.apache.commons.math4.examples.ga.mathfunctions</commons.automatic.module.name>
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<!-- Workaround to avoid duplicating config files. -->
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<math.parent.dir>${basedir}/../../..</math.parent.dir>
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<uberjar.name>examples-ga-mathfunctions</uberjar.name>
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<project.mainClass>org.apache.commons.math4.examples.ga.mathfunctions.Dimension2FunctionOptimizer</project.mainClass>
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</properties>
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</project>

‎commons-math-examples/examples-ga/examples-ga-math-functions/src/main/java/org/apache/commons/math4/examples/ga/mathfunctions/dimension2/Dim2GraphPlotter.java

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/*
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* Licensed to the Apache Software Foundation (ASF) under one or more
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* contributor license agreements. See the NOTICE file distributed with
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* this work for additional information regarding copyright ownership.
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* The ASF licenses this file to You under the Apache License, Version 2.0
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* (the "License"); you may not use this file except in compliance with
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* the License. You may obtain a copy of the License at
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*
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* http://www.apache.org/licenses/LICENSE-2.0
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*
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* Unless required by applicable law or agreed to in writing, software
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* distributed under the License is distributed on an "AS IS" BASIS,
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* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
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* See the License for the specific language governing permissions and
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* limitations under the License.
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*/
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package org.apache.commons.math4.examples.ga.mathfunctions.dimension2;
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import java.awt.BorderLayout;
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import java.util.List;
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import javax.swing.JFrame;
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import javax.swing.JPanel;
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import org.apache.commons.math4.ga.internal.stats.PopulationStatisticalSummaryImpl;
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import org.apache.commons.math4.ga.listener.ConvergenceListener;
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import org.apache.commons.math4.ga.population.Population;
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import org.apache.commons.math4.ga.stats.PopulationStatisticalSummary;
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import org.jfree.chart.ChartFactory;
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import org.jfree.chart.ChartPanel;
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import org.jfree.chart.JFreeChart;
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import org.jfree.chart.plot.PlotOrientation;
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import org.jfree.chart.plot.XYPlot;
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import org.jfree.chart.renderer.xy.XYLineAndShapeRenderer;
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import org.jfree.data.xy.XYSeries;
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import org.jfree.data.xy.XYSeriesCollection;
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/**
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* This class represents the graph plotter during optimization.
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*/
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public class Dim2GraphPlotter extends JFrame implements ConvergenceListener<Dimension2Coordinate> {
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/**
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* Generated serialversionId.
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*/
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private static final long serialVersionUID = -5683904006424006584L;
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/** collection of 2-D series. **/
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private final XYSeriesCollection dataset = new XYSeriesCollection();
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/**
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* constructor.
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* @param plotSubject subject of plot
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* @param xAxisLabel x axis label
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* @param yAxisLabel y axis label
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*/
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public Dim2GraphPlotter(String plotSubject, String xAxisLabel, String yAxisLabel) {
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super(plotSubject);
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final JPanel chartPanel = createChartPanel(plotSubject, xAxisLabel, yAxisLabel);
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add(chartPanel, BorderLayout.CENTER);
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setSize(640, 480);
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setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);
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setLocationRelativeTo(null);
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setVisible(true);
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}
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/**
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* Adds data point to graph.
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* @param graphName name of graph
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* @param generation generation, to be plotted along x axis
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* @param value value, to be plotted along y axis
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*/
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private void addDataPoint(String graphName, int generation, double value) {
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XYSeries series = null;
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if (!containsGraph(graphName)) {
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series = new XYSeries(graphName);
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dataset.addSeries(series);
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} else {
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series = dataset.getSeries(graphName);
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}
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series.add(generation, value);
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setVisible(true);
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}
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/**
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* Checks if the graph with the given name already exists.
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* @param graphName name of the graph
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* @return true/false
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*/
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@SuppressWarnings("unchecked")
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private boolean containsGraph(String graphName) {
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final List<XYSeries> seriesList = dataset.getSeries();
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if (seriesList == null || seriesList.isEmpty()) {
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return false;
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}
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for (XYSeries series : seriesList) {
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if (series.getKey().compareTo(graphName) == 0) {
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return true;
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}
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}
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return false;
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}
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/**
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* Creates chart panel.
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* @param chartTitle chart title
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* @param xAxisLabel x axis label
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* @param yAxisLabel y axis label
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* @return panel
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*/
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private JPanel createChartPanel(String chartTitle, String xAxisLabel, String yAxisLabel) {
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final boolean showLegend = true;
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final boolean createURL = false;
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final boolean createTooltip = false;
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final JFreeChart chart = ChartFactory.createXYLineChart(chartTitle, xAxisLabel, yAxisLabel, dataset,
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PlotOrientation.VERTICAL, showLegend, createTooltip, createURL);
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final XYPlot plot = chart.getXYPlot();
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final XYLineAndShapeRenderer renderer = new XYLineAndShapeRenderer();
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plot.setRenderer(renderer);
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return new ChartPanel(chart);
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}
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/**
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* {@inheritDoc}
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*/
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@Override
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public void notify(int generation, Population<Dimension2Coordinate> population) {
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PopulationStatisticalSummary<Dimension2Coordinate> populationStatisticalSummary =
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new PopulationStatisticalSummaryImpl<>(population);
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this.addDataPoint("Average", generation, populationStatisticalSummary.getMeanFitness());
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this.addDataPoint("Best", generation, populationStatisticalSummary.getMaxFitness());
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}
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}

‎commons-math-examples/examples-ga/examples-ga-math-functions/src/main/java/org/apache/commons/math4/examples/ga/mathfunctions/dimension2/Dimension2Coordinate.java

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/*
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* Licensed to the Apache Software Foundation (ASF) under one or more
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* contributor license agreements. See the NOTICE file distributed with
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* this work for additional information regarding copyright ownership.
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* The ASF licenses this file to You under the Apache License, Version 2.0
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* (the "License"); you may not use this file except in compliance with
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* the License. You may obtain a copy of the License at
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*
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* http://www.apache.org/licenses/LICENSE-2.0
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*
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* Unless required by applicable law or agreed to in writing, software
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* distributed under the License is distributed on an "AS IS" BASIS,
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* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
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* See the License for the specific language governing permissions and
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* limitations under the License.
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*/
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package org.apache.commons.math4.examples.ga.mathfunctions.dimension2;
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/**
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* This class represents the coordinate of the problem domain i.e. the phenotype of chromosome.
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*/
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public class Dimension2Coordinate {
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/** coordinate of first dimension. **/
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private final double x;
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/** coordinate of second dimension. **/
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private final double y;
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/**
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* constructor.
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* @param x coordinate of first dimension
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* @param y coordinate of second dimension
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*/
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public Dimension2Coordinate(double x, double y) {
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this.x = x;
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this.y = y;
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}
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/**
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* returns the coordinate of first dimension.
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* @return coordinate of first dimension
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*/
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public double getX() {
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return x;
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}
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/**
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* returns the coordinate of second dimension.
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* @return coordinate of second dimension
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*/
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public double getY() {
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return y;
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}
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/**
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* Returns a string representation of coordinate.
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*/
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@Override
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public String toString() {
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return "Coordinate [x=" + x + ", y=" + y + "]";
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}
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}

‎commons-math-examples/examples-ga/examples-ga-math-functions/src/main/java/org/apache/commons/math4/examples/ga/mathfunctions/dimension2/Dimension2Decoder.java

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/*
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* Licensed to the Apache Software Foundation (ASF) under one or more
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* contributor license agreements. See the NOTICE file distributed with
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* this work for additional information regarding copyright ownership.
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* The ASF licenses this file to You under the Apache License, Version 2.0
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* (the "License"); you may not use this file except in compliance with
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* the License. You may obtain a copy of the License at
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*
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* http://www.apache.org/licenses/LICENSE-2.0
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*
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* Unless required by applicable law or agreed to in writing, software
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* distributed under the License is distributed on an "AS IS" BASIS,
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* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
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* See the License for the specific language governing permissions and
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* limitations under the License.
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*/
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package org.apache.commons.math4.examples.ga.mathfunctions.dimension2;
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import java.util.List;
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import org.apache.commons.math4.ga.chromosome.AbstractListChromosome;
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import org.apache.commons.math4.ga.chromosome.BinaryChromosome;
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import org.apache.commons.math4.ga.decoder.AbstractListChromosomeDecoder;
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/**
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* Decoder to convert chromosome's binary genotype to phenotype
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* {@link Dimension2Coordinate}.
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*/
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public class Dimension2Decoder extends AbstractListChromosomeDecoder<Integer, Dimension2Coordinate> {
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/**
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* decode the binary representation of chromosome to
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* {@link Dimension2Coordinate}.
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* @param chromosome The {@link AbstractListChromosome}
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*/
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@Override
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protected Dimension2Coordinate decode(AbstractListChromosome<Integer, Dimension2Coordinate> chromosome) {
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final BinaryChromosome<Dimension2Coordinate> binaryChromosome =
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(BinaryChromosome<Dimension2Coordinate>) chromosome;
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final List<Integer> alleles = binaryChromosome.getRepresentation();
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final StringBuilder allelesStr = new StringBuilder();
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for (Integer allele : alleles) {
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allelesStr.append(Integer.toBinaryString(allele));
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}
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final double x = Integer.parseInt(allelesStr.substring(0, 12), 2) / 100.0;
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final double y = Integer.parseInt(allelesStr.substring(12, 24), 2) / 100.0;
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return new Dimension2Coordinate(x, y);
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}
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}

‎commons-math-examples/examples-ga/examples-ga-math-functions/src/main/java/org/apache/commons/math4/examples/ga/mathfunctions/dimension2/Dimension2FitnessFunction.java

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/*
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* Licensed to the Apache Software Foundation (ASF) under one or more
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* contributor license agreements. See the NOTICE file distributed with
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* this work for additional information regarding copyright ownership.
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* The ASF licenses this file to You under the Apache License, Version 2.0
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* (the "License"); you may not use this file except in compliance with
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* the License. You may obtain a copy of the License at
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*
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* http://www.apache.org/licenses/LICENSE-2.0
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*
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* Unless required by applicable law or agreed to in writing, software
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* distributed under the License is distributed on an "AS IS" BASIS,
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* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
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* See the License for the specific language governing permissions and
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* limitations under the License.
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*/
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package org.apache.commons.math4.examples.ga.mathfunctions.dimension2;
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import org.apache.commons.math4.ga.fitness.FitnessFunction;
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/**
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* This class represents the mathematical fitness function for optimizing a 2
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* dimension mathematical function.
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*/
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public class Dimension2FitnessFunction implements FitnessFunction<Dimension2Coordinate> {
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/**
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* Computes the fitness value based on the decoded chromosome.
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* @param coordinate The {@link Dimension2Coordinate}
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* @return the fitness value
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*/
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@Override
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public double compute(Dimension2Coordinate coordinate) {
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return -Math.pow(Math.pow(coordinate.getX(), 2) + Math.pow(coordinate.getY(), 2), .25) *
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(Math.pow(Math.sin(50 * Math.pow(Math.pow(coordinate.getX(), 2) + Math.pow(coordinate.getY(), 2), .1)),
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2) + 1);
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}
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}

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