package net.bmahe.genetics4j.samples.symbolicregression;
   
   import static net.bmahe.genetics4j.core.termination.Terminations.ofFitnessAtMost;
   import static net.bmahe.genetics4j.core.termination.Terminations.ofMaxGeneration;
   import static net.bmahe.genetics4j.core.termination.Terminations.or;
   
   import java.io.File;
   import java.io.IOException;
   import java.util.Comparator;
  import java.util.Random;
  
  import org.apache.commons.cli.CommandLine;
  import org.apache.commons.cli.CommandLineParser;
  import org.apache.commons.cli.DefaultParser;
  import org.apache.commons.cli.HelpFormatter;
  import org.apache.commons.cli.Options;
  import org.apache.commons.cli.ParseException;
  import org.apache.commons.io.FileUtils;
  import org.apache.commons.lang3.StringUtils;
  import org.apache.commons.lang3.Validate;
  import org.apache.logging.log4j.LogManager;
  import org.apache.logging.log4j.Logger;
  
  import net.bmahe.genetics4j.core.EASystem;
  import net.bmahe.genetics4j.core.EASystemFactory;
  import net.bmahe.genetics4j.core.Fitness;
  import net.bmahe.genetics4j.core.Genotype;
  import net.bmahe.genetics4j.core.Individual;
  import net.bmahe.genetics4j.core.chromosomes.TreeChromosome;
  import net.bmahe.genetics4j.core.chromosomes.TreeNode;
  import net.bmahe.genetics4j.core.evolutionlisteners.EvolutionListeners;
  import net.bmahe.genetics4j.core.spec.EAConfiguration;
  import net.bmahe.genetics4j.core.spec.EAExecutionContext;
  import net.bmahe.genetics4j.core.spec.EAExecutionContexts;
  import net.bmahe.genetics4j.core.spec.EvolutionResult;
  import net.bmahe.genetics4j.core.spec.Optimization;
  import net.bmahe.genetics4j.core.spec.replacement.Elitism;
  import net.bmahe.genetics4j.core.spec.selection.Tournament;
  import net.bmahe.genetics4j.gp.Operation;
  import net.bmahe.genetics4j.gp.math.SimplificationRules;
  import net.bmahe.genetics4j.gp.program.Program;
  import net.bmahe.genetics4j.gp.spec.GPEAExecutionContexts;
  import net.bmahe.genetics4j.gp.spec.chromosome.ProgramTreeChromosomeSpec;
  import net.bmahe.genetics4j.gp.spec.combination.ProgramRandomCombine;
  import net.bmahe.genetics4j.gp.spec.mutation.NodeReplacement;
  import net.bmahe.genetics4j.gp.spec.mutation.ProgramApplyRules;
  import net.bmahe.genetics4j.gp.spec.mutation.ProgramRandomMutate;
  import net.bmahe.genetics4j.gp.spec.mutation.ProgramRandomPrune;
  import net.bmahe.genetics4j.gp.spec.selection.DoubleTournament;
  import net.bmahe.genetics4j.gp.utils.ProgramUtils;
  import net.bmahe.genetics4j.gp.utils.TreeNodeUtils;
  
  public class SymbolicRegressionWithDoubleTournament {
  	final static public Logger logger = LogManager.getLogger(SymbolicRegressionWithDoubleTournament.class);
  
  	final static public String PARAM_DEST_CSV = "d";
  	final static public String LONG_PARAM_DEST_CSV = "csv-dest";
  
  	final static public String PARAM_POPULATION_SIZE = "p";
  	final static public String LONG_PARAM_POPULATION_SIZE = "population-size";
  
  	final static public String DEFAULT_DEST_CSV = SymbolicRegressionWithDoubleTournament.class.getSimpleName() + ".csv";
  
  	final static public int DEFAULT_POPULATION_SIZE = 500;
  
  	public static void cliError(final Options options, final String errorMessage) {
  		final HelpFormatter formatter = new HelpFormatter();
  		logger.error(errorMessage);
  		formatter.printHelp(SymbolicRegressionWithDoubleTournament.class.getSimpleName(), options);
  		System.exit(-1);
  	}
  
  	@SuppressWarnings("unchecked")
  	public void run(String csvFilename, int populationSize) {
  		Validate.isTrue(StringUtils.isNotBlank(csvFilename));
  		Validate.isTrue(populationSize > 0);
  
  		final Random random = new Random();
  
  		final Program program = SymbolicRegressionUtils.buildProgram(random);
  
  		// tag::compute_fitness[]
  		final Double[][] inputs = new Double[100][1];
  		for (int i = 0; i < 100; i++) {
  			inputs[i][0] = (i - 50) * 1.2;
  		}
  
  		final Fitness<Double> computeFitness = (genoType) -> {
  			final TreeChromosome<Operation<?>> chromosome = (TreeChromosome<Operation<?>>) genoType.getChromosome(0);
  
  			double mse = 0;
  			for (final Double[] input : inputs) {
  
  				final double x = input[0];
  				final double expected = SymbolicRegressionUtils.evaluate(x);
  				final Object result = ProgramUtils.execute(chromosome, input);
  
  				if (Double.isFinite(expected)) {
  					final Double resultDouble = (Double) result;
 					mse += Double.isFinite(resultDouble) ? (expected - resultDouble) * (expected - resultDouble)
 							: 1_000_000_000;
 				}
 			}
 			return Double.isFinite(mse) ? mse / 100.0d : Double.MAX_VALUE;
 		};
 		// end::compute_fitness[]
 
 		// tag::double_tournament[]
 		final Comparator<Individual<Double>> parsimonyComparator = (a, b) -> {
 			final var treeChromosomeA = a.genotype().getChromosome(0, TreeChromosome.class);
 			final var treeChromosomeB = b.genotype().getChromosome(0, TreeChromosome.class);
 
 			return Integer.compare(treeChromosomeA.getSize(), treeChromosomeB.getSize());
 		};
 
 		final DoubleTournament<Double> doubleTournament = DoubleTournament
 				.of(Tournament.of(3), parsimonyComparator, 1.3d);
 		// end::double_tournament[]
 
 		// tag::ea_config[]
 		final var eaConfigurationBuilder = new EAConfiguration.Builder<Double>();
 		eaConfigurationBuilder.chromosomeSpecs(ProgramTreeChromosomeSpec.of(program)) // <1>
 				.parentSelectionPolicy(doubleTournament)
 				.replacementStrategy(
 						Elitism.builder() // <2>
 								.offspringRatio(0.99)
 								.offspringSelectionPolicy(doubleTournament)
 								.survivorSelectionPolicy(doubleTournament)
 								.build())
 				.combinationPolicy(ProgramRandomCombine.build())
 				.mutationPolicies(
 						ProgramRandomMutate.of(0.10),
 							ProgramRandomPrune.of(0.12),
 							NodeReplacement.of(0.05),
 							ProgramApplyRules.of(SimplificationRules.SIMPLIFY_RULES))
 				.optimization(Optimization.MINIMIZE) // <3>
 				.termination(or(ofMaxGeneration(200), ofFitnessAtMost(0.00001)))
 				.fitness(computeFitness);
 		final EAConfiguration<Double> eaConfiguration = eaConfigurationBuilder.build();
 		// end::ea_config[]
 
 		final var eaExecutionContextBuilder = GPEAExecutionContexts.<Double>forGP(random);
 		EAExecutionContexts.enrichForScalarFitness(eaExecutionContextBuilder);
 
 		eaExecutionContextBuilder.populationSize(populationSize);
 		eaExecutionContextBuilder.numberOfPartitions(Math.max(1, Runtime.getRuntime().availableProcessors() - 1));
 
 		eaExecutionContextBuilder.addEvolutionListeners(
 				EvolutionListeners.ofLogTopN(logger, 5, Comparator.<Double>reverseOrder(), (genotype) -> {
 					final TreeChromosome<Operation<?>> chromosome = (TreeChromosome<Operation<?>>) genotype.getChromosome(0);
 					final TreeNode<Operation<?>> root = chromosome.getRoot();
 
 					return TreeNodeUtils.toStringTreeNode(root);
 				}),
 					SymbolicRegressionUtils.csvLoggerDouble(
 							csvFilename,
 								evolutionStep -> evolutionStep.fitness(),
 								evolutionStep -> (double) evolutionStep.individual()
 										.getChromosome(0, TreeChromosome.class)
 										.getSize()));
 
 		final EAExecutionContext<Double> eaExecutionContext = eaExecutionContextBuilder.build();
 		final EASystem<Double> eaSystem = EASystemFactory.from(eaConfiguration, eaExecutionContext);
 
 		final EvolutionResult<Double> evolutionResult = eaSystem.evolve();
 		final Genotype bestGenotype = evolutionResult.bestGenotype();
 		final TreeChromosome<Operation<?>> bestChromosome = (TreeChromosome<Operation<?>>) bestGenotype.getChromosome(0);
 		logger.info("Best genotype: {}", bestChromosome.getRoot());
 		logger.info("Best genotype - pretty print: {}", TreeNodeUtils.toStringTreeNode(bestChromosome.getRoot()));
 	}
 
 	public static void main(String[] args) throws IOException {
 
 		/**
 		 * Parse CLI
 		 */
 
 		final CommandLineParser parser = new DefaultParser();
 
 		final Options options = new Options();
 		options.addOption(PARAM_DEST_CSV, LONG_PARAM_DEST_CSV, true, "destination csv file");
 
 		options.addOption(PARAM_POPULATION_SIZE, LONG_PARAM_POPULATION_SIZE, true, "Population size");
 
 		String csvFilename = DEFAULT_DEST_CSV;
 		int populationSize = DEFAULT_POPULATION_SIZE;
 		try {
 			final CommandLine line = parser.parse(options, args);
 
 			if (line.hasOption(PARAM_DEST_CSV)) {
 				csvFilename = line.getOptionValue(PARAM_DEST_CSV);
 			}
 
 			if (line.hasOption(PARAM_POPULATION_SIZE)) {
 				populationSize = Integer.parseInt(line.getOptionValue(PARAM_POPULATION_SIZE));
 			}
 
 		} catch (ParseException exp) {
 			cliError(options, "Unexpected exception:" + exp.getMessage());
 		}
 
 		logger.info("Population size: {}", populationSize);
 
 		logger.info("CSV output located at {}", csvFilename);
 		FileUtils.forceMkdirParent(new File(csvFilename));
 
 		final var symbolicRegression = new SymbolicRegressionWithDoubleTournament();
 		symbolicRegression.run(csvFilename, populationSize);
 	}
 }