/*
* Encog(tm) Core v2.5 - Java Version
* http://www.heatonresearch.com/encog/
* http://code.google.com/p/encog-java/
* Copyright 2008-2010 Heaton Research, Inc.
*
* Licensed 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.
*
* For more information on Heaton Research copyrights, licenses
* and trademarks visit:
* http://www.heatonresearch.com/copyright
*/
package org.encog.neural.networks.training.genetic;
import org.encog.neural.networks.BasicNetwork;
import org.encog.neural.networks.structure.NetworkCODEC;
import org.encog.solve.genetic.genes.DoubleGene;
import org.encog.solve.genetic.genes.Gene;
import org.encog.solve.genetic.genome.BasicGenome;
import org.encog.solve.genetic.genome.Chromosome;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
/**
* Implements a genome that allows a feedforward neural network to be trained
* using a genetic algorithm. The chromosome for a feed forward neural network
* is the weight and bias matrix.
*/
public class NeuralGenome extends BasicGenome {
/**
* The chromosome.
*/
private final Chromosome networkChromosome;
/**
* The logging object.
*/
@SuppressWarnings("unused")
private final Logger logger = LoggerFactory.getLogger(this.getClass());
/**
* Construct a neural genome.
* @param nga The NeuralGeneticAlgorithm class to use.
* @param network The network to use.
*/
public NeuralGenome(final NeuralGeneticAlgorithm nga,
final BasicNetwork network) {
super(nga.getGenetic());
setOrganism(network);
this.networkChromosome = new Chromosome();
// create an array of "double genes"
final int size = network.getStructure().calculateSize();
for (int i = 0; i < size; i++) {
final Gene gene = new DoubleGene();
this.networkChromosome.getGenes().add(gene);
}
getChromosomes().add(this.networkChromosome);
encode();
}
/**
* Decode the genomes into a neural network.
*/
public void decode() {
final double[] net = new double[this.networkChromosome.getGenes()
.size()];
for (int i = 0; i < net.length; i++) {
final DoubleGene gene = (DoubleGene) this.networkChromosome
.getGenes().get(i);
net[i] = gene.getValue();
}
NetworkCODEC.arrayToNetwork(net, (BasicNetwork) getOrganism());
}
/**
* Encode the neural network into genes.
*/
public void encode() {
final double[] net = NetworkCODEC
.networkToArray((BasicNetwork) getOrganism());
for (int i = 0; i < net.length; i++) {
((DoubleGene) this.networkChromosome.getGene(i)).setValue(net[i]);
}
}
}