Examples of jcgp.backend.population.Chromosome

jcgp.backend.population.Chromosome
This class encapsulates a CGP chromosome.

A chromosome contains a matrix of nodes and arrays of inputs and outputs. These elements are all interconnected, and actually form the chromosome network itself. Individual nodes can be retrieved using {@code getNode()}which requires the row and column to be specified. The same works for inputs and outputs using the associated getters, in which case only the index is necessary.

In evolutionary computation it is often necessary to make copies of chromosomes; this can be accomplished in JCGP in two ways. The recommended way to do this is using {@code copyChromosome()} in {@code Population}, but alternatively it can be done by using the {@code Chromosome} copy constructor and specifying theobject to copy from, or by using the {@code copyGenes()} method.

To illustrate this, given two chromosomes, chr1 and chr2, the following code:

chr1.copyGenes(chr2);

will modify all of chr1's connections and functions to match those of chr2, without creating a new instance. In contrast,

chr1 = new Chromosome(chr2);

creates a new instance of chromosome which is identical to chr2 and assigns it to chr1, meaning any old references to chr1 that are not updated will still refer to a chromosome that is not identical to chr2. In practice, the most reliable way is to use the copy method in {@code Population}. Assuming chr1 and chr2 are indexed 1 and 2 in {@code population} respectively,

population.copyChromosome(2, 1);

will copy chr2 into chr1 without creating new instances or requiring access to the underlying chromosome array. {@code Chromosome} offers a variety of methods to compare chromosomes as well, such as {@code compareGenesTo()} and {@code compareActiveGenesTo()}. {@code Comparable} is implementedto compare fitness value, meaning {@code compareTo()} returns a value depending the relative fitnessof the compared chromosomes.

In order to set the chromosome's input values for decoding, {@code setInputs()} should be used. A few utility methods are provided in order to retrieve random elements from the chromosome, which are used internally to initialise with random connections but also externally by mutators when performing mutations. @author Eduardo Pedroni

  }
  
  @Test
  public void preinitialisedChromosomeTest() {
    // the original chromosome that will be cloned
    Chromosome oc = new Chromosome(resources);


    // initialise a population with a copy of it
    population = new Population(oc, resources);
    // check that the first parent chromosome is identical to, but not the same instance as, the one given
    assertTrue("Incorrect chromosome in population.", population.get(0).compareGenesTo(oc) && population.get(0) != oc);

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      }
      if (report.get()) getResources().reportln("[ES] Selected contenders: " + Arrays.toString(contenders));
      Arrays.sort(contenders);
      if (report.get()) getResources().reportln("[ES] Chr " + contenders[contenders.length - 1] + " wins the tournament, copying and mutating...");
      // create a copy of the selected chromosome and mutate it
      newPopulation[i] = new Chromosome(population.get(contenders[contenders.length - 1]));
      mutator.mutate(newPopulation[i]);
    }
    if (report.get()) getResources().reportln("[ES] Tournaments are finished, copying new chromosomes into population");
    // newPopulation has been generated, copy into the population
    for (int c = 0; c < getResources().populationSize(); c++) {

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  @BeforeClass
  public static void setUpBeforeClass() {
    
    resources = new ModifiableResources();
    resources.setFunctionSet(new TestFunctionSet());
    chromosome = new Chromosome(resources);
  }

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  @BeforeClass
  public static void setUpBeforeClass() {
    resources = new ModifiableResources();
    resources.setFunctionSet(new SymbolicRegressionFunctions());
    chromosome = new Chromosome(resources);
  }

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    resources.setFunctionSet(new TestFunctionSet());
  }


  @Before
  public void setUp() throws Exception {
    chromosome = new Chromosome(resources);
  }

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   * 
   */
  @Test
  public void cloneTest() {
    // create a clone, check to see if it really is a clone
    Chromosome clone = new Chromosome(chromosome);


    // compare all elements, one by one
    // check outputs
    for (int o = 0; o < resources.outputs(); o++) {
      // check that no cross-references exist between chromosomes
      assertTrue("Cloned chromosome contains a reference to a member of the original chromosome.",
          clone.getOutput(o) != chromosome.getOutput(o) && 
          clone.getOutput(o).getSource() != chromosome.getOutput(o).getSource());
      // check that the connections are equivalent
      if (clone.getOutput(o).getSource() instanceof Input && chromosome.getOutput(o).getSource() instanceof Input) {
        assertTrue("Outputs did not connect to equivalent inputs.", 
            ((Input) clone.getOutput(o).getSource()).getIndex() == ((Input) chromosome.getOutput(o).getSource()).getIndex());
      } else if (clone.getOutput(o).getSource() instanceof Node && chromosome.getOutput(o).getSource() instanceof Node) {
        assertTrue("Outputs did not connect to equivalent nodes.", 
            ((Node) clone.getOutput(o).getSource()).getRow() == ((Node) chromosome.getOutput(o).getSource()).getRow() && 
            ((Node) clone.getOutput(o).getSource()).getColumn() == ((Node) chromosome.getOutput(o).getSource()).getColumn());
      } else {
        fail("Output source types did not match.");
      }
    }
    // check nodes, rows first
    for (int row = 0; row < resources.rows(); row++) {
      for (int column = 0; column < resources.columns(); column++) {
        // check that nodes are not pointers to the same instance
        assertTrue("Both chromosomes contain a reference to the same node.", clone.getNode(row, column) != chromosome.getNode(row, column));
        // check that both nodes reference their own position in the grid correctly
        assertTrue("Equivalent nodes self-reference differently.", clone.getNode(row, column).getRow() == chromosome.getNode(row, column).getRow() &&
            clone.getNode(row, column).getColumn() == chromosome.getNode(row, column).getColumn());
        // check that the two nodes have the same function
        assertTrue("Equivalent nodes have different functions.", clone.getNode(row, column).getFunction() == chromosome.getNode(row, column).getFunction());


        // compare each connection
        for (int connection = 0; connection < resources.arity(); connection++) {
          // first look at whether they are actually the same instance
          assertTrue("Nodes are connected to the same connection instance.", 
              clone.getNode(row, column).getConnection(connection) !=  chromosome.getNode(row, column).getConnection(connection));


          // if the connections aren't the same instance, check that their addresses are the same
          if (clone.getNode(row, column).getConnection(connection) instanceof Input && 
              chromosome.getNode(row, column).getConnection(connection) instanceof Input) {


            assertTrue("Nodes did not connect to equivalent inputs.", 
                ((Input) clone.getNode(row, column).getConnection(connection)).getIndex() ==
                ((Input) chromosome.getNode(row, column).getConnection(connection)).getIndex());


          } else if (clone.getNode(row, column).getConnection(connection) instanceof Node && 
              chromosome.getNode(row, column).getConnection(connection) instanceof Node) {


            assertTrue("Nodes did not connect to equivalent nodes.", 
                ((Node) clone.getNode(row, column).getConnection(connection)).getRow() ==
                ((Node) chromosome.getNode(row, column).getConnection(connection)).getRow() &&


                ((Node) clone.getNode(row, column).getConnection(connection)).getColumn() ==
                ((Node) chromosome.getNode(row, column).getConnection(connection)).getColumn());


          } else {
            fail("Connection types did not match.");
          }
        }
      }
    }


    // check cloning given a known topology
    chromosome = createKnownConfiguration();
    clone = new Chromosome(chromosome);
    
    Integer[] testInputs = new Integer[] {5, 8, 4};
    chromosome.setInputs((Object[]) testInputs);
    clone.setInputs((Object[]) testInputs);


    // check that both chromosomes have the same outputs
    for (int i = 0; i < resources.outputs(); i++) {
      assertTrue("Incorrect output returned", ((Integer) chromosome.getOutput(i).calculate()) == ((Integer) clone.getOutput(i).calculate()));
    }


    // mutate an output in clone, check that the same node in chromosome produces a different output
    clone.getOutput(1).setSource(clone.getInput(2));


    assertTrue("Mutation affected nodes in both chromosomes.",
        clone.getOutput(1).calculate() != chromosome.getOutput(1).calculate());


  }

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   * 
   */
  @Test
  public void compareActiveTest() {
    // create a clone of the chromosome, compare active nodes - should return true
    Chromosome c = new Chromosome(chromosome);
    assertTrue("Active nodes did not match.", chromosome.compareActiveGenesTo(c));
    assertTrue("Symmetry not obeyed.", c.compareActiveGenesTo(chromosome));


    // create a new random chromosome, this time they should not match
    c = new Chromosome(resources);
    assertTrue("Active nodes did match.", !chromosome.compareActiveGenesTo(c));
  }

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   * 
   */
  @Test
  public void compareTest() {
    // create a clone of the chromosome, compare - should return true
    Chromosome c = new Chromosome(chromosome);
    assertTrue("Chromosomes did not match.", chromosome.compareGenesTo(c));
    assertTrue("Symmetry not obeyed.", c.compareGenesTo(chromosome));


    // create a new random chromosome, this time they should not match
    c = new Chromosome(resources);
    assertTrue("Chromosomes did match.", !chromosome.compareGenesTo(c));
  }

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    resources.setRows(3);
    resources.setInputs(3);
    resources.setOutputs(2);
    resources.setLevelsBack(3);


    Chromosome c = new Chromosome(resources);


    c.getNode(0, 0).initialise(resources.getFunction(0), c.getInput(0), c.getInput(1));
    c.getNode(1, 1).initialise(resources.getFunction(0), c.getNode(0, 0), c.getInput(1));
    c.getNode(1, 2).initialise(resources.getFunction(0), c.getNode(1, 1), c.getInput(2));


    c.getOutput(0).setSource(c.getNode(0, 0));
    c.getOutput(1).setSource(c.getNode(1, 2));
    
    return c;
  }

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Related Classes of jcgp.backend.population.Chromosome

jcgp.backend.modules.es.TournamentSelection

jcgp.backend.tests.ChromosomeTests

jcgp.backend.tests.NodeTests

jcgp.backend.tests.OutputTests

jcgp.backend.tests.PopulationTests

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