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Posted to commits@commons.apache.org by tn...@apache.org on 2012/08/05 20:46:54 UTC
svn commit: r1369637 - in /commons/proper/math/trunk/src:
main/java/org/apache/commons/math3/genetics/CycleCrossover.java
test/java/org/apache/commons/math3/genetics/CycleCrossoverTest.java
Author: tn
Date: Sun Aug 5 18:46:54 2012
New Revision: 1369637
URL: http://svn.apache.org/viewvc?rev=1369637&view=rev
Log:
[MATH-777] Added CycleCrossover policy.
Added:
commons/proper/math/trunk/src/main/java/org/apache/commons/math3/genetics/CycleCrossover.java (with props)
commons/proper/math/trunk/src/test/java/org/apache/commons/math3/genetics/CycleCrossoverTest.java (with props)
Added: commons/proper/math/trunk/src/main/java/org/apache/commons/math3/genetics/CycleCrossover.java
URL: http://svn.apache.org/viewvc/commons/proper/math/trunk/src/main/java/org/apache/commons/math3/genetics/CycleCrossover.java?rev=1369637&view=auto
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--- commons/proper/math/trunk/src/main/java/org/apache/commons/math3/genetics/CycleCrossover.java (added)
+++ commons/proper/math/trunk/src/main/java/org/apache/commons/math3/genetics/CycleCrossover.java Sun Aug 5 18:46:54 2012
@@ -0,0 +1,160 @@
+package org.apache.commons.math3.genetics;
+
+import java.util.ArrayList;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Set;
+
+import org.apache.commons.math3.exception.DimensionMismatchException;
+import org.apache.commons.math3.exception.MathIllegalArgumentException;
+import org.apache.commons.math3.exception.util.LocalizedFormats;
+
+/**
+ * Cycle Crossover [CX] builds offspring from <b>ordered</b> chromosomes by identifying cycles
+ * between two parent chromosomes. To form the children, the cycles are copied from the
+ * respective parents.
+ * <p>
+ * To form a cycle the following procedure is applied:
+ * <ol>
+ * <li>start with the first gene of parent 1</li>
+ * <li>look at the gene at the same position of parent 2</li>
+ * <li>go to the position with the same gene in parent 1</li>
+ * <li>add this gene index to the cycle</li>
+ * <li>repeat the steps 2-5 until we arrive at the starting gene of this cycle</li>
+ * </ol>
+ * The indices that form a cycle are then used to form the children in alternating order, i.e.
+ * in cycle 1, the genes of parent 1 are copied to child 1, while in cycle 2 the genes of parent 1
+ * are copied to child 2, and so forth ...
+ * </p>
+ *
+ * Example (zero-start cycle):
+ * <pre>
+ * p1 = (8 4 7 3 6 2 5 1 9 0) X c1 = (8 1 2 3 4 5 6 7 9 0)
+ * p2 = (0 1 2 3 4 5 6 7 8 9) X c2 = (0 4 7 3 6 2 5 1 8 9)
+ *
+ * cycle 1: 8 0 9
+ * cycle 2: 4 1 7 2 5 6
+ * cycle 3: 3
+ * </pre>
+ *
+ * This policy works only on {@link AbstractListChromosome}, and therefore it
+ * is parameterized by T. Moreover, the chromosomes must have same lengths.
+ *
+ * @see <a href="http://www.rubicite.com/Tutorials/GeneticAlgorithms/CrossoverOperators/CycleCrossoverOperator.aspx"
+ * Cycle Crossover Operator</a>
+ *
+ * @param <T> generic type of the {@link AbstractListChromosome}s for crossover
+ * @since 3.1
+ * @version $Id$
+ */
+public class CycleCrossover<T> implements CrossoverPolicy {
+
+ /** If the start index shall be chosen randomly. */
+ private final boolean randomStart;
+
+ /**
+ * Creates a new {@link CycleCrossover} policy.
+ */
+ public CycleCrossover() {
+ this(false);
+ }
+
+ /**
+ * Creates a new {@link CycleCrossover} policy using the given {@code randomStart} behavior.
+ *
+ * @param randomStart whether the start index shall be chosen randomly or be set to 0
+ */
+ public CycleCrossover(final boolean randomStart) {
+ this.randomStart = randomStart;
+ }
+
+ /**
+ * Returns whether the starting index is chosen randomly or set to zero.
+ *
+ * @return {@code true} if the starting index is chosen randomly, {@code false} otherwise
+ */
+ public boolean isRandomStart() {
+ return randomStart;
+ }
+
+ /**
+ * {@inheritDoc}
+ */
+ @SuppressWarnings("unchecked")
+ 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<T>) first, (AbstractListChromosome<T>) 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
+ */
+ protected ChromosomePair mate(final AbstractListChromosome<T> first, final AbstractListChromosome<T> second) {
+ final int length = first.getLength();
+ if (length != second.getLength()) {
+ throw new DimensionMismatchException(second.getLength(), length);
+ }
+
+ // array representations of the parents
+ final List<T> parent1Rep = first.getRepresentation();
+ final List<T> parent2Rep = second.getRepresentation();
+ // and of the children: do a crossover copy to simplify the later processing
+ final List<T> child1Rep = new ArrayList<T>(second.getRepresentation());
+ final List<T> child2Rep = new ArrayList<T>(first.getRepresentation());
+
+ // the set of all visited indices so far
+ final Set<Integer> visitedIndices = new HashSet<Integer>(length);
+ // the indices of the current cycle
+ final List<Integer> indices = new ArrayList<Integer>(length);
+
+ // determine the starting index
+ int idx = randomStart ? GeneticAlgorithm.getRandomGenerator().nextInt(length) : 0;
+ int cycle = 1;
+
+ while (visitedIndices.size() < length) {
+ indices.add(idx);
+
+ T item = parent2Rep.get(idx);
+ idx = parent1Rep.indexOf(item);
+
+ while (idx != indices.get(0)) {
+ // add that index to the cycle indices
+ indices.add(idx);
+ // get the item in the second parent at that index
+ item = parent2Rep.get(idx);
+ // get the index of that item in the first parent
+ idx = parent1Rep.indexOf(item);
+ }
+
+ // for even cycles: swap the child elements on the indices found in this cycle
+ if (cycle++ % 2 != 0) {
+ for (int i : indices) {
+ T tmp = child1Rep.get(i);
+ child1Rep.set(i, child2Rep.get(i));
+ child2Rep.set(i, tmp);
+ }
+ }
+
+ visitedIndices.addAll(indices);
+ // find next starting index: last one + 1 until we find an unvisited index
+ idx = (indices.get(0) + 1) % length;
+ while (visitedIndices.contains(idx) && visitedIndices.size() < length) {
+ idx++;
+ if (idx >= length) {
+ idx = 0;
+ }
+ }
+ indices.clear();
+ }
+
+ return new ChromosomePair(first.newFixedLengthChromosome(child1Rep),
+ second.newFixedLengthChromosome(child2Rep));
+ }
+}
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Added: commons/proper/math/trunk/src/test/java/org/apache/commons/math3/genetics/CycleCrossoverTest.java
URL: http://svn.apache.org/viewvc/commons/proper/math/trunk/src/test/java/org/apache/commons/math3/genetics/CycleCrossoverTest.java?rev=1369637&view=auto
==============================================================================
--- commons/proper/math/trunk/src/test/java/org/apache/commons/math3/genetics/CycleCrossoverTest.java (added)
+++ commons/proper/math/trunk/src/test/java/org/apache/commons/math3/genetics/CycleCrossoverTest.java Sun Aug 5 18:46:54 2012
@@ -0,0 +1,133 @@
+package org.apache.commons.math3.genetics;
+
+import org.apache.commons.math3.exception.DimensionMismatchException;
+import org.apache.commons.math3.exception.MathIllegalArgumentException;
+import org.junit.Assert;
+import org.junit.Test;
+
+public class CycleCrossoverTest {
+
+ @Test
+ public void testCrossoverExample() {
+ // taken from http://www.rubicite.com/Tutorials/GeneticAlgorithms/CrossoverOperators/CycleCrossoverOperator.aspx
+ final Integer[] p1 = new Integer[] { 8, 4, 7, 3, 6, 2, 5, 1, 9, 0 };
+ final Integer[] p2 = new Integer[] { 0, 1, 2, 3, 4, 5, 6, 7, 8, 9 };
+ final DummyListChromosome p1c = new DummyListChromosome(p1);
+ final DummyListChromosome p2c = new DummyListChromosome(p2);
+
+ final CrossoverPolicy cp = new CycleCrossover<Integer>();
+ final ChromosomePair pair = cp.crossover(p1c, p2c);
+
+ final Integer[] c1 = ((DummyListChromosome) pair.getFirst()).getRepresentation().toArray(new Integer[p1.length]);
+ final Integer[] c2 = ((DummyListChromosome) pair.getSecond()).getRepresentation().toArray(new Integer[p2.length]);
+
+ final Integer[] c1e = new Integer[] { 8, 1, 2, 3, 4, 5, 6, 7, 9, 0 };
+ final Integer[] c2e = new Integer[] { 0, 4, 7, 3, 6, 2, 5, 1, 8, 9 };
+
+ Assert.assertArrayEquals(c1e, c1);
+ Assert.assertArrayEquals(c2e, c2);
+ }
+
+ @Test
+ public void testCrossoverExample2() {
+ // taken from http://www.scribd.com/doc/54206412/32/Cycle-crossover
+ final Integer[] p1 = new Integer[] { 1, 2, 3, 4, 5, 6, 7, 8, 9 };
+ final Integer[] p2 = new Integer[] { 9, 3, 7, 8, 2, 6, 5, 1, 4};
+ final DummyListChromosome p1c = new DummyListChromosome(p1);
+ final DummyListChromosome p2c = new DummyListChromosome(p2);
+
+ final CrossoverPolicy cp = new CycleCrossover<Integer>();
+ final ChromosomePair pair = cp.crossover(p1c, p2c);
+
+ final Integer[] c1 = ((DummyListChromosome) pair.getFirst()).getRepresentation().toArray(new Integer[p1.length]);
+ final Integer[] c2 = ((DummyListChromosome) pair.getSecond()).getRepresentation().toArray(new Integer[p2.length]);
+
+ final Integer[] c1e = new Integer[] { 1, 3, 7, 4, 2, 6, 5, 8, 9 };
+ final Integer[] c2e = new Integer[] { 9, 2, 3, 8, 5, 6, 7, 1, 4 };
+
+ Assert.assertArrayEquals(c1e, c1);
+ Assert.assertArrayEquals(c2e, c2);
+ }
+
+ @Test
+ public void testCrossover() {
+ final Integer[] p1 = new Integer[] { 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 };
+ final Integer[] p2 = new Integer[] { 10, 9, 8, 7, 6, 5, 4, 3, 2, 1 };
+ final DummyListChromosome p1c = new DummyListChromosome(p1);
+ final DummyListChromosome p2c = new DummyListChromosome(p2);
+
+ final CrossoverPolicy cp = new CycleCrossover<Integer>(true);
+
+ for (int i = 0; i < 20; i++) {
+ final ChromosomePair pair = cp.crossover(p1c, p2c);
+
+ final Integer[] c1 = ((DummyListChromosome) pair.getFirst()).getRepresentation().toArray(new Integer[p1.length]);
+ final Integer[] c2 = ((DummyListChromosome) pair.getSecond()).getRepresentation().toArray(new Integer[p2.length]);
+
+ int index = 0;
+ // Determine if it is in the same spot as in the first parent, if
+ // not it comes from the second parent.
+ for (final Integer j : c1) {
+ if (!p1[index].equals(j)) {
+ Assert.assertEquals(j, p2[index]);
+ } else {
+ Assert.assertEquals(j, p1[index]);
+ }
+ index++;
+ }
+
+ // Same as above only for the second parent.
+ index = 0;
+ for (final Integer k : c2) {
+ if (p2[index] != k) {
+ Assert.assertEquals(k, p1[index]);
+ } else {
+ Assert.assertEquals(k, p2[index]);
+ }
+ index++;
+ }
+ }
+ }
+
+ @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 CycleCrossover<Integer>();
+ 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 CycleCrossover<Integer>();
+ 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 CycleCrossover<Integer>();
+ cp.crossover(p1c, p2c);
+ }
+}
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