diff --git a/src/main/java/org/apache/commons/math3/genetics/NPointCrossover.java b/src/main/java/org/apache/commons/math3/genetics/NPointCrossover.java new file mode 100644 index 000000000..7d43abaab --- /dev/null +++ b/src/main/java/org/apache/commons/math3/genetics/NPointCrossover.java @@ -0,0 +1,178 @@ +/* + * 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.math3.genetics; + +import java.util.ArrayList; +import java.util.List; + +import org.apache.commons.math3.exception.DimensionMismatchException; +import org.apache.commons.math3.exception.MathIllegalArgumentException; +import org.apache.commons.math3.exception.NotStrictlyPositiveException; +import org.apache.commons.math3.exception.NumberIsTooLargeException; +import org.apache.commons.math3.exception.util.LocalizedFormats; +import org.apache.commons.math3.random.RandomGenerator; + +/** + * N-point crossover policy. For each iteration a random crossover point is + * selected and the first part from each parent is copied to the corresponding + * child, and the second parts are copied crosswise. + * + * Example (2-point crossover): + *
+ * -C- denotes a crossover point
+ *           -C-       -C-                         -C-        -C-
+ * p1 = (1 0  | 1 0 0 1 | 0 1 1)    X    p2 = (0 1  | 1 0 1 0  | 1 1 1)
+ *      \----/ \-------/ \-----/              \----/ \--------/ \-----/
+ *        ||      (*)       ||                  ||      (**)       ||
+ *        VV      (**)      VV                  VV      (*)        VV
+ *      /----\ /--------\ /-----\             /----\ /--------\ /-----\
+ * c1 = (1 0  | 1 0 1 0  | 0 1 1)    X   c2 = (0 1  | 1 0 0 1  | 0 1 1)
+ * 
+ * + * This policy works only on {@link AbstractListChromosome}, and therefore it + * is parameterized by T. Moreover, the chromosomes must have same lengths. + * + * @param generic type of the {@link AbstractListChromosome}s for crossover + * @since 3.1 + * @version $Id$ + */ +public class NPointCrossover implements CrossoverPolicy { + + /** The number of crossover points. */ + private final int crossoverPoints; + + /** + * Creates a new {@link NPointCrossover} policy using the given number of points. + * + *

Note: the number of crossover points must be < chromosome length - 1. + * This condition can only be checked at runtime, as the chromosome length is not known in advance. + *

+ * + * @param crossoverPoints the number of crossover points + * @throws NotStrictlyPositiveException if the number of {@code crossoverPoints} is not + * strictly positive + */ + public NPointCrossover(final int crossoverPoints) { + if (crossoverPoints <= 0) { + throw new NotStrictlyPositiveException(crossoverPoints); + } + this.crossoverPoints = crossoverPoints; + } + + /** + * Returns the number of crossover points used by this {@link CrossoverPolicy}. + * + * @return the number of crossover points + */ + public int getCrossoverPoints() { + return crossoverPoints; + } + + /** + * Performs a N-point crossover. N random crossover points are selected and are used + * to divide the parent chromosomes into segments. The segments are copied in alternate + * order from the two parents to the corresponding child chromosomes. + * + * Example (2-point crossover): + *
+     * -C- denotes a crossover point
+     *           -C-       -C-                         -C-        -C-
+     * p1 = (1 0  | 1 0 0 1 | 0 1 1)    X    p2 = (0 1  | 1 0 1 0  | 1 1 1)
+     *      \----/ \-------/ \-----/              \----/ \--------/ \-----/
+     *        ||      (*)       ||                  ||      (**)       ||
+     *        VV      (**)      VV                  VV      (*)        VV
+     *      /----\ /--------\ /-----\             /----\ /--------\ /-----\
+     * c1 = (1 0  | 1 0 1 0  | 0 1 1)    X   c2 = (0 1  | 1 0 0 1  | 0 1 1)
+     * 
+ * + * @param first first parent (p1) + * @param second second parent (p2) + * @return pair of two children (c1,c2) + * @throws MathIllegalArgumentException iff one of the chromosomes is + * not an instance of {@link AbstractListChromosome} + * @throws DimensionMismatchException if the length of the two chromosomes is different + */ + @SuppressWarnings("unchecked") // OK because of instanceof checks + public ChromosomePair crossover(final Chromosome first, final Chromosome second) { + if (!(first instanceof AbstractListChromosome && second instanceof AbstractListChromosome)) { + throw new MathIllegalArgumentException(LocalizedFormats.INVALID_FIXED_LENGTH_CHROMOSOME); + } + return mate((AbstractListChromosome) first, (AbstractListChromosome) second); + } + + /** + * Helper for {@link #crossover(Chromosome, Chromosome)}. Performs the actual crossover. + * + * @param first the first chromosome + * @param second the second chromosome + * @return the pair of new chromosomes that resulted from the crossover + * @throws DimensionMismatchException if the length of the two chromosomes is different + * @throws NumberIsTooLargeException if the number of crossoverPoints is too large for the + * actual chromosomes + */ + private ChromosomePair mate(final AbstractListChromosome first, + final AbstractListChromosome second) { + final int length = first.getLength(); + if (length != second.getLength()) { + throw new DimensionMismatchException(second.getLength(), length); + } + if (crossoverPoints >= length) { + throw new NumberIsTooLargeException(crossoverPoints, length, false); + } + + // array representations of the parents + final List parent1Rep = first.getRepresentation(); + final List parent2Rep = second.getRepresentation(); + // and of the children + final ArrayList child1Rep = new ArrayList(first.getLength()); + final ArrayList child2Rep = new ArrayList(second.getLength()); + + final RandomGenerator random = GeneticAlgorithm.getRandomGenerator(); + + ArrayList c1 = child1Rep; + ArrayList c2 = child2Rep; + + int remainingPoints = crossoverPoints; + int lastIndex = 0; + for (int i = 0; i < crossoverPoints; i++, remainingPoints--) { + // select the next crossover point at random + final int crossoverIndex = 1 + lastIndex + random.nextInt(length - lastIndex - remainingPoints); + + // copy the current segment + for (int j = lastIndex; j < crossoverIndex; j++) { + c1.add(parent1Rep.get(j)); + c2.add(parent2Rep.get(j)); + } + + // swap the children for the next segment + ArrayList tmp = c1; + c1 = c2; + c2 = tmp; + + lastIndex = crossoverIndex; + } + + // copy the last segment + for (int j = lastIndex; j < length; j++) { + c1.add(parent1Rep.get(j)); + c2.add(parent2Rep.get(j)); + } + + return new ChromosomePair(first.newFixedLengthChromosome(child1Rep), + second.newFixedLengthChromosome(child2Rep)); + } +} diff --git a/src/test/java/org/apache/commons/math3/genetics/NPointCrossoverTest.java b/src/test/java/org/apache/commons/math3/genetics/NPointCrossoverTest.java new file mode 100644 index 000000000..87ac21d7a --- /dev/null +++ b/src/test/java/org/apache/commons/math3/genetics/NPointCrossoverTest.java @@ -0,0 +1,113 @@ +package org.apache.commons.math3.genetics; + +import java.util.List; + +import org.apache.commons.math3.exception.DimensionMismatchException; +import org.apache.commons.math3.exception.MathIllegalArgumentException; +import org.apache.commons.math3.exception.NumberIsTooLargeException; +import org.junit.Assert; +import org.junit.Test; + +public class NPointCrossoverTest { + + @Test(expected = DimensionMismatchException.class) + public void testCrossoverDimensionMismatchException() { + final Integer[] p1 = new Integer[] {1,0,1,0,0,1,0,1,1}; + final Integer[] p2 = new Integer[] {0,1,1,0,1}; + + final BinaryChromosome p1c = new DummyBinaryChromosome(p1); + final BinaryChromosome p2c = new DummyBinaryChromosome(p2); + + final CrossoverPolicy cp = new NPointCrossover(1); + cp.crossover(p1c,p2c); + } + + @Test(expected = NumberIsTooLargeException.class) + public void testNumberIsTooLargeException() { + final Integer[] p1 = new Integer[] {1,0,1,0,0,1,0,1,1}; + final Integer[] p2 = new Integer[] {0,1,1,0,1,0,1,1,1}; + + final BinaryChromosome p1c = new DummyBinaryChromosome(p1); + final BinaryChromosome p2c = new DummyBinaryChromosome(p2); + + final CrossoverPolicy cp = new NPointCrossover(15); + cp.crossover(p1c,p2c); + } + + @Test(expected = MathIllegalArgumentException.class) + public void testCrossoverInvalidFixedLengthChromosomeFirst() { + final Integer[] p1 = new Integer[] {1,0,1,0,0,1,0,1,1}; + final BinaryChromosome p1c = new DummyBinaryChromosome(p1); + final Chromosome p2c = new Chromosome() { + public double fitness() { + // Not important + return 0; + } + }; + + final CrossoverPolicy cp = new NPointCrossover(1); + cp.crossover(p1c,p2c); + } + + @Test(expected = MathIllegalArgumentException.class) + public void testCrossoverInvalidFixedLengthChromosomeSecond() { + final Integer[] p1 = new Integer[] {1,0,1,0,0,1,0,1,1}; + final BinaryChromosome p2c = new DummyBinaryChromosome(p1); + final Chromosome p1c = new Chromosome() { + public double fitness() { + // Not important + return 0; + } + }; + + final CrossoverPolicy cp = new NPointCrossover(1); + cp.crossover(p1c,p2c); + } + + @Test + public void testCrossover() { + Integer[] p1 = new Integer[] {1,0,1,0,1,0,1,0,1}; + Integer[] p2 = new Integer[] {0,1,0,1,0,1,0,1,0}; + + BinaryChromosome p1c = new DummyBinaryChromosome(p1); + BinaryChromosome p2c = new DummyBinaryChromosome(p2); + + final int order = 3; + NPointCrossover npc = new NPointCrossover(order); + + // the two parent chromosomes are different at each position, so it is easy to detect + // the number of crossovers that happened for each child + for (int i=0; i<20; i++) { + ChromosomePair pair = npc.crossover(p1c,p2c); + + Integer[] c1 = new Integer[p1.length]; + Integer[] c2 = new Integer[p2.length]; + + c1 = ((BinaryChromosome) pair.getFirst()).getRepresentation().toArray(c1); + c2 = ((BinaryChromosome) pair.getSecond()).getRepresentation().toArray(c2); + + Assert.assertEquals(order, detectCrossoverPoints(p1c, p2c, (BinaryChromosome) pair.getFirst())); + Assert.assertEquals(order, detectCrossoverPoints(p2c, p1c, (BinaryChromosome) pair.getSecond())); + } + } + + private int detectCrossoverPoints(BinaryChromosome p1, BinaryChromosome p2, BinaryChromosome c) { + int crossovers = 0; + final int length = p1.getLength(); + + final List p1Rep = p1.getRepresentation(); + final List p2Rep = p2.getRepresentation(); + final List cRep = c.getRepresentation(); + + List rep = p1Rep; + for (int i = 0; i < length; i++) { + if (rep.get(i) != cRep.get(i)) { + crossovers++; + rep = rep == p1Rep ? p2Rep : p1Rep; + } + } + + return crossovers; + } + +}