<commit_before>//  NSGAIIRunner.java
//
//  Author:
//       <NAME> <<EMAIL>>
//
//  Copyright (c) 2014 <NAME>
//
//  This program is free software: you can redistribute it and/or modify
//  it under the terms of the GNU Lesser General Public License as published by
//  the Free Software Foundation, either version 3 of the License, or
//  (at your option) any later version.
//
//  This program is distributed in the hope that it will be useful,
//  but WITHOUT ANY WARRANTY; without even the implied warranty of
//  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
//  GNU Lesser General Public License for more details.
// 
//  You should have received a copy of the GNU Lesser General Public License
//  along with this program.  If not, see <http://www.gnu.org/licenses/>.

package org.uma.jmetal.runner.multiobjective;

import org.uma.jmetal.algorithm.Algorithm;
import org.uma.jmetal.algorithm.multiobjective.nsgaii.NSGAIIBuilder;
import org.uma.jmetal.operator.CrossoverOperator;
import org.uma.jmetal.operator.MutationOperator;
import org.uma.jmetal.operator.SelectionOperator;
import org.uma.jmetal.operator.impl.crossover.SBXCrossover;
import org.uma.jmetal.operator.impl.mutation.PolynomialMutation;
import org.uma.jmetal.operator.impl.selection.BinaryTournamentSelection;
import org.uma.jmetal.problem.DoubleProblem;
import org.uma.jmetal.solution.DoubleSolution;
import org.uma.jmetal.util.AlgorithmRunner;
import org.uma.jmetal.util.JMetalException;
import org.uma.jmetal.util.JMetalLogger;
import org.uma.jmetal.util.ProblemUtils;
import org.uma.jmetal.util.comparator.RankingAndCrowdingDistanceComparator;
import org.uma.jmetal.util.fileoutput.SolutionSetOutput;
import org.uma.jmetal.util.fileoutput.impl.DefaultFileOutputContext;

import java.util.List;

/**
 * Class to configure and run the NSGA-II algorithm
 *
 * @author <NAME> <<EMAIL>>
 */
public class NSGAIIRunner {
  /**
   * @param args Command line arguments.
   * @throws java.io.IOException
   * @throws SecurityException
   * @throws ClassNotFoundException
   * Usage: two options
   *        - org.uma.jmetal.runner.multiobjective.NSGAIIRunner
   *        - org.uma.jmetal.runner.multiobjective.NSGAIIRunner problemName
   */
  public static void main(String[] args) throws JMetalException {
    DoubleProblem problem;
    Algorithm<List<DoubleSolution>> algorithm;
    CrossoverOperator<DoubleSolution> crossover;
    MutationOperator<DoubleSolution> mutation;
    SelectionOperator<List<DoubleSolution>, DoubleSolution> selection;

    String problemName ;
    if (args.length == 1) {
      problemName = args[0] ;
    } else {
      problemName = "org.uma.jmetal.problem.multiobjective.zdt.ZDT1";
    }

    problem = (DoubleProblem)ProblemUtils.<DoubleSolution> loadProblem(problemName);

    double crossoverProbability = 0.9 ;
    double crossoverDistributionIndex = 20.0 ;
    crossover = new SBXCrossover(crossoverProbability, crossoverDistributionIndex) ;

    double mutationProbability = 1.0 / problem.getNumberOfVariables() ;
    double mutationDistributionIndex = 20.0 ;
    mutation = new PolynomialMutation(mutationProbability, mutationDistributionIndex) ;

    selection = new BinaryTournamentSelection<DoubleSolution>(new RankingAndCrowdingDistanceComparator<DoubleSolution>());

    algorithm = new NSGAIIBuilder<DoubleSolution>(problem, crossover, mutation)
            .setSelectionOperator(selection)
            .setMaxIterations(250)
            .setPopulationSize(100)
            .build() ;

    AlgorithmRunner algorithmRunner = new AlgorithmRunner.Executor(algorithm)
            .execute() ;

    List<DoubleSolution> population = algorithm.getResult() ;
    long computingTime = algorithmRunner.getComputingTime() ;

    new SolutionSetOutput.Printer(population)
            .setSeparator("\t")
            .setVarFileOutputContext(new DefaultFileOutputContext("VAR.tsv"))
            .setFunFileOutputContext(new DefaultFileOutputContext("FUN.tsv"))
            .print();

    JMetalLogger.logger.info("Total execution time: " + computingTime + "ms");
    JMetalLogger.logger.info("Objectives values have been written to file FUN.tsv");
    JMetalLogger.logger.info("Variables values have been written to file VAR.tsv");
  }
}<commit_msg>Adding an example in class NSGAIIRunner of using quality indicators<commit_after>//  NSGAIIRunner.java
//
//  Author:
//       <NAME> <<EMAIL>>
//
//  Copyright (c) 2014 <NAME>
//
//  This program is free software: you can redistribute it and/or modify
//  it under the terms of the GNU Lesser General Public License as published by
//  the Free Software Foundation, either version 3 of the License, or
//  (at your option) any later version.
//
//  This program is distributed in the hope that it will be useful,
//  but WITHOUT ANY WARRANTY; without even the implied warranty of
//  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
//  GNU Lesser General Public License for more details.
// 
//  You should have received a copy of the GNU Lesser General Public License
//  along with this program.  If not, see <http://www.gnu.org/licenses/>.

package org.uma.jmetal.runner.multiobjective;

import org.uma.jmetal.algorithm.Algorithm;
import org.uma.jmetal.algorithm.multiobjective.nsgaii.NSGAIIBuilder;
import org.uma.jmetal.operator.CrossoverOperator;
import org.uma.jmetal.operator.MutationOperator;
import org.uma.jmetal.operator.SelectionOperator;
import org.uma.jmetal.operator.impl.crossover.SBXCrossover;
import org.uma.jmetal.operator.impl.mutation.PolynomialMutation;
import org.uma.jmetal.operator.impl.selection.BinaryTournamentSelection;
import org.uma.jmetal.problem.DoubleProblem;
import org.uma.jmetal.qualityindicator.QualityIndicator;
import org.uma.jmetal.qualityindicator.impl.Epsilon;
import org.uma.jmetal.qualityindicator.impl.Hypervolume;
import org.uma.jmetal.solution.DoubleSolution;
import org.uma.jmetal.util.AlgorithmRunner;
import org.uma.jmetal.util.JMetalException;
import org.uma.jmetal.util.JMetalLogger;
import org.uma.jmetal.util.ProblemUtils;
import org.uma.jmetal.util.comparator.RankingAndCrowdingDistanceComparator;
import org.uma.jmetal.util.fileoutput.SolutionSetOutput;
import org.uma.jmetal.util.fileoutput.impl.DefaultFileOutputContext;
import org.uma.jmetal.util.front.Front;
import org.uma.jmetal.util.front.imp.ArrayFront;

import java.io.FileNotFoundException;
import java.util.List;

/**
 * Class to configure and run the NSGA-II algorithm
 *
 * @author <NAME> <<EMAIL>>
 */
public class NSGAIIRunner {
  /**
   * @param args Command line arguments.
   * @throws java.io.IOException
   * @throws SecurityException
   * @throws ClassNotFoundException
   * Usage: two options
   *        - org.uma.jmetal.runner.multiobjective.NSGAIIRunner
   *        - org.uma.jmetal.runner.multiobjective.NSGAIIRunner problemName
   */
  public static void main(String[] args) throws JMetalException, FileNotFoundException {
    DoubleProblem problem;
    Algorithm<List<DoubleSolution>> algorithm;
    CrossoverOperator<DoubleSolution> crossover;
    MutationOperator<DoubleSolution> mutation;
    SelectionOperator<List<DoubleSolution>, DoubleSolution> selection;

    String problemName ;
    if (args.length == 1) {
      problemName = args[0] ;
    } else {
      problemName = "org.uma.jmetal.problem.multiobjective.zdt.ZDT1";
    }

    problem = (DoubleProblem) ProblemUtils.<DoubleSolution> loadProblem(problemName);

    double crossoverProbability = 0.9 ;
    double crossoverDistributionIndex = 20.0 ;
    crossover = new SBXCrossover(crossoverProbability, crossoverDistributionIndex) ;

    double mutationProbability = 1.0 / problem.getNumberOfVariables() ;
    double mutationDistributionIndex = 20.0 ;
    mutation = new PolynomialMutation(mutationProbability, mutationDistributionIndex) ;

    selection = new BinaryTournamentSelection<DoubleSolution>(new RankingAndCrowdingDistanceComparator<DoubleSolution>());

    algorithm = new NSGAIIBuilder<DoubleSolution>(problem, crossover, mutation)
            .setSelectionOperator(selection)
            .setMaxIterations(250)
            .setPopulationSize(100)
            .build() ;

    AlgorithmRunner algorithmRunner = new AlgorithmRunner.Executor(algorithm)
            .execute() ;

    List<DoubleSolution> population = algorithm.getResult() ;
    long computingTime = algorithmRunner.getComputingTime() ;

    new SolutionSetOutput.Printer(population)
            .setSeparator("\t")
            .setVarFileOutputContext(new DefaultFileOutputContext("VAR.tsv"))
            .setFunFileOutputContext(new DefaultFileOutputContext("FUN.tsv"))
            .print();

    Front referenceFront = new ArrayFront() ;
    referenceFront.readFrontFromFile("jmetal-problem/src/test/resources/pareto_fronts/ZDT1.pf");

    QualityIndicator hypervolume = new Hypervolume() ;
    QualityIndicator epsilon = new Epsilon() ;
    double hvValue = hypervolume.execute(new ArrayFront(population), referenceFront) ;
    double epsilonValue = epsilon.execute(new ArrayFront(population), referenceFront) ;

    JMetalLogger.logger.info("Total execution time: " + computingTime + "ms");
    JMetalLogger.logger.info("Hypervolume: " + hvValue);
    JMetalLogger.logger.info("Epsilon    : " + epsilonValue);
    JMetalLogger.logger.info("Objectives values have been written to file FUN.tsv");
    JMetalLogger.logger.info("Variables values have been written to file VAR.tsv");
  }
}
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