Merge 4b094b2 into 3a5cf27

commons-math-examples/examples-ga/examples-ga-math-functions/pom.xml

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+<!--
+   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.
+-->
+<project xmlns="http://maven.apache.org/POM/4.0.0"
+	xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+	xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 https://maven.apache.org/xsd/maven-4.0.0.xsd">
+	<modelVersion>4.0.0</modelVersion>
+	<parent>
+		<groupId>org.apache.commons</groupId>
+		<artifactId>examples-ga</artifactId>
+		<version>4.0-SNAPSHOT</version>
+	</parent>
+	<artifactId>examples-ga-math-functions</artifactId>
+
+	<properties>
+		<maven.compiler.source>1.8</maven.compiler.source>
+		<maven.compiler.target>1.8</maven.compiler.target>
+
+		<!-- OSGi -->
+		<commons.osgi.symbolicName>org.apache.commons.math4.examples.ga.mathfunctions</commons.osgi.symbolicName>
+		<commons.osgi.export>org.apache.commons.math4.examples.ga.mathfunctions</commons.osgi.export>
+		<!-- Java 9+ -->
+		<commons.automatic.module.name>org.apache.commons.math4.examples.ga.mathfunctions</commons.automatic.module.name>
+		<!-- Workaround to avoid duplicating config files. -->
+		<math.parent.dir>${basedir}/../../..</math.parent.dir>
+
+		<uberjar.name>examples-ga-mathfunctions</uberjar.name>
+		<project.mainClass>org.apache.commons.math4.examples.ga.mathfunctions.Dimension2FunctionOptimizer</project.mainClass>
+	</properties>
+
+</project>

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

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+/*
+ * 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.math4.examples.ga.mathfunctions;
+
+/**
+ * This class represents the coordinate of the problem domain i.e. the phenotype of chromosome.
+ */
+public class Coordinate {
+
+    /** coordinate of first dimension. **/
+    private final double x;
+
+    /** coordinate of second dimension. **/
+    private final double y;
+
+    /**
+     * constructor.
+     * @param x coordinate of first dimension
+     * @param y coordinate of second dimension
+     */
+    public Coordinate(double x, double y) {
+        this.x = x;
+        this.y = y;
+    }
+
+    /**
+     * returns the coordinate of first dimension.
+     * @return coordinate of first dimension
+     */
+    public double getX() {
+        return x;
+    }
+
+    /**
+     * returns the coordinate of second dimension.
+     * @return coordinate of second dimension
+     */
+    public double getY() {
+        return y;
+    }
+
+    /**
+     * Returns a string representation of coordinate.
+     */
+    @Override
+    public String toString() {
+        return "Coordinate [x=" + x + ", y=" + y + "]";
+    }
+
+}

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

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+/*
+ * 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.math4.examples.ga.mathfunctions;
+
+import java.util.List;
+
+import org.apache.commons.math4.ga.chromosome.AbstractListChromosome;
+import org.apache.commons.math4.ga.chromosome.BinaryChromosome;
+import org.apache.commons.math4.ga.decoder.AbstractListChromosomeDecoder;
+
+/**
+ * Decoder to convert chromosome's binary genotype to phenotype
+ * {@link Coordinate}.
+ */
+public class Dimension2Decoder extends AbstractListChromosomeDecoder<Integer, Coordinate> {
+
+    /**
+     * decode the binary representation of chromosome to {@link Coordinate}.
+     * @param chromosome The {@link AbstractListChromosome}
+     */
+    @Override
+    protected Coordinate decode(AbstractListChromosome<Integer, Coordinate> chromosome) {
+        final BinaryChromosome<Coordinate> binaryChromosome = (BinaryChromosome<Coordinate>) chromosome;
+        final List<Integer> alleles = binaryChromosome.getRepresentation();
+
+        final StringBuilder allelesStr = new StringBuilder();
+        for (Integer allele : alleles) {
+            allelesStr.append(Integer.toBinaryString(allele));
+        }
+
+        final double x = Integer.parseInt(allelesStr.substring(0, 12), 2) / 100.0;
+        final double y = Integer.parseInt(allelesStr.substring(12, 24), 2) / 100.0;
+
+        return new Coordinate(x, y);
+    }
+
+}

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

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+/*
+ * 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.math4.examples.ga.mathfunctions;
+
+import org.apache.commons.math4.ga.fitness.FitnessFunction;
+
+/**
+ * This class represents the mathematical fitness function for optimizing a 2
+ * dimension mathematical function.
+ */
+public class Dimension2FitnessFunction implements FitnessFunction<Coordinate> {
+
+    /**
+     * Computes the fitness value based on the decoded chromosome.
+     * @param coordinate The {@link Coordinate}
+     * @return the fitness value
+     */
+    @Override
+    public double compute(Coordinate coordinate) {
+        return -Math.pow(Math.pow(coordinate.getX(), 2) + Math.pow(coordinate.getY(), 2), .25) *
+                (Math.pow(Math.sin(50 * Math.pow(Math.pow(coordinate.getX(), 2) + Math.pow(coordinate.getY(), 2), .1)),
+                        2) + 1);
+    }
+
+}

commons-math-examples/examples-ga/examples-ga-math-functions/src/main/java/org/apache/commons/math4/examples/ga/mathfunctions/Dimension2FunctionOptimizer.java

@@ -0,0 +1,104 @@
+/*
+ * 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.math4.examples.ga.mathfunctions;
+
+import org.apache.commons.math4.ga.crossover.OnePointCrossover;
+import org.apache.commons.math4.ga.convergencecond.UnchangedBestFitness;
+import org.apache.commons.math4.examples.ga.mathfunctions.utils.Constants;
+import org.apache.commons.math4.examples.ga.mathfunctions.utils.GraphPlotter;
+import org.apache.commons.math4.ga.GeneticAlgorithm;
+import org.apache.commons.math4.ga.chromosome.BinaryChromosome;
+import org.apache.commons.math4.ga.chromosome.Chromosome;
+import org.apache.commons.math4.ga.convergencecond.StoppingCondition;
+import org.apache.commons.math4.ga.listener.ConvergenceListenerRegistry;
+import org.apache.commons.math4.ga.listener.PopulationStatisticsLogger;
+import org.apache.commons.math4.ga.mutation.BinaryMutation;
+import org.apache.commons.math4.ga.population.ListPopulation;
+import org.apache.commons.math4.ga.population.Population;
+import org.apache.commons.math4.ga.selection.TournamentSelection;
+import org.apache.commons.math4.ga.utils.ConsoleLogger;
+
+/**
+ * This class represents an optimizer for a 2-dimensional math function using
+ * genetic algorithm.
+ */
+public class Dimension2FunctionOptimizer {
+
+    /**
+     * Optimizes the 2-dimension fitness function.
+     * @param args arguments
+     */
+    public static void main(String[] args) {
+        final Population<Coordinate> initPopulation = getInitialPopulation();
+
+        final Dimension2FunctionOptimizer optimizer = new Dimension2FunctionOptimizer();
+
+        final ConvergenceListenerRegistry<Coordinate> convergenceListenerRegistry = ConvergenceListenerRegistry
+                .getInstance();
+        convergenceListenerRegistry
+                .addConvergenceListener(new PopulationStatisticsLogger<Coordinate>(Constants.ENCODING));
+        convergenceListenerRegistry
+                .addConvergenceListener(new GraphPlotter("Convergence Stats", "generation", "fitness"));
+
+        optimizer.optimize(initPopulation);
+    }
+
+    /**
+     * Optimizes the population.
+     * @param initial The {@link Population}
+     */
+    public void optimize(Population<Coordinate> initial) {
+
+        // initialize a new genetic algorithm
+        final GeneticAlgorithm<Coordinate> ga = new GeneticAlgorithm<>(new OnePointCrossover<Integer, Coordinate>(),
+                Constants.CROSSOVER_RATE, new BinaryMutation<Coordinate>(), Constants.AVERAGE_MUTATION_RATE,
+                new TournamentSelection<Coordinate>(Constants.TOURNAMENT_SIZE), Constants.ELITISM_RATE);
+
+        // stopping condition
+        final StoppingCondition<Coordinate> stopCond = new UnchangedBestFitness<>(
+                Constants.GENERATION_COUNT_WITH_UNCHANGED_BEST_FUTNESS);
+
+        // run the algorithm
+        final Population<Coordinate> finalPopulation = ga.evolve(initial, stopCond);
+
+        // best chromosome from the final population
+        final Chromosome<Coordinate> bestFinal = finalPopulation.getFittestChromosome();
+        final ConsoleLogger consoleLogger = ConsoleLogger.getInstance(Constants.ENCODING);
+        consoleLogger.log("*********************************************");
+        consoleLogger.log("***********Optimization Result***************");
+
+        consoleLogger.log(bestFinal.toString());
+
+    }
+
+    /**
+     * Generates an initial population.
+     * @return initial population
+     */
+    private static Population<Coordinate> getInitialPopulation() {
+        final Population<Coordinate> population = new ListPopulation<>(Constants.POPULATION_SIZE);
+        final Dimension2FitnessFunction fitnessFunction = new Dimension2FitnessFunction();
+        final Dimension2Decoder decoder = new Dimension2Decoder();
+        for (int i = 0; i < Constants.POPULATION_SIZE; i++) {
+            population.addChromosome(BinaryChromosome.<Coordinate>randomChromosome(Constants.CHROMOSOME_LENGTH,
+                    fitnessFunction, decoder));
+        }
+        return population;
+    }
+
+}