private void saveSpecies(final EncogWriteHelper out, final Species species) {
out.addColumn("s");
out.addColumn(species.getAge());
out.addColumn(species.getBestScore());
out.addColumn(species.getGensNoImprovement());
out.writeLine();
for (final Genome genome : species.getMembers()) {
final NEATGenome neatGenome = (NEATGenome) genome;
out.addColumn("g");
out.addColumn(neatGenome.getAdjustedScore());
out.addColumn(neatGenome.getScore());
out.addColumn(neatGenome.getBirthGeneration());
out.writeLine();
for (final NEATNeuronGene neatNeuronGene : neatGenome.getNeuronsChromosome()) {
out.addColumn("n");
out.addColumn(neatNeuronGene.getId());
out.addColumn(neatNeuronGene.getActivationFunction());
out.addColumn(PersistNEATPopulation.neuronTypeToString(neatNeuronGene.getNeuronType()));
out.addColumn(neatNeuronGene.getInnovationId());
out.writeLine();
}
for (final NEATLinkGene neatLinkGene : neatGenome.getLinksChromosome()) {
out.addColumn("l");
out.addColumn(neatLinkGene.getId());
out.addColumn(neatLinkGene.isEnabled());
out.addColumn(neatLinkGene.getFromNeuronID());
out.addColumn(neatLinkGene.getToNeuronID());
out.addColumn(neatLinkGene.getWeight());
out.addColumn(neatLinkGene.getInnovationId());
out.writeLine();
}
}
}
@Override
public Object read(final InputStream is) {
long nextInnovationID = 0;
long nextGeneID = 0;
final NEATPopulation result = new NEATPopulation();
final NEATInnovationList innovationList = new NEATInnovationList();
innovationList.setPopulation(result);
result.setInnovations(innovationList);
final EncogReadHelper in = new EncogReadHelper(is);
EncogFileSection section;
while ((section = in.readNextSection()) != null) {
if (section.getSectionName().equals("NEAT-POPULATION")
&& section.getSubSectionName().equals("INNOVATIONS")) {
for (final String line : section.getLines()) {
final List<String> cols = EncogFileSection.splitColumns(line);
final NEATInnovation innovation = new NEATInnovation();
final int innovationID = Integer.parseInt(cols.get(1));
innovation.setInnovationID(innovationID);
innovation.setNeuronID(Integer.parseInt(cols.get(2)));
result.getInnovations().getInnovations().put(cols.get(0), innovation);
nextInnovationID = Math.max(nextInnovationID, innovationID + 1);
}
} else if (section.getSectionName().equals("NEAT-POPULATION")
&& section.getSubSectionName().equals("SPECIES")) {
NEATGenome lastGenome = null;
BasicSpecies lastSpecies = null;
for (final String line : section.getLines()) {
final List<String> cols = EncogFileSection.splitColumns(line);
if (cols.get(0).equalsIgnoreCase("s")) {
lastSpecies = new BasicSpecies();
lastSpecies.setPopulation(result);
lastSpecies.setAge(Integer.parseInt(cols.get(1)));
lastSpecies.setBestScore(CSVFormat.EG_FORMAT.parse(cols.get(2)));
lastSpecies.setGensNoImprovement(Integer.parseInt(cols.get(3)));
result.getSpecies().add(lastSpecies);
} else if (cols.get(0).equalsIgnoreCase("g")) {
final boolean isLeader = lastGenome == null;
lastGenome = new NEATGenome();
lastGenome.setInputCount(result.getInputCount());
lastGenome.setOutputCount(result.getOutputCount());
lastGenome.setSpecies(lastSpecies);
lastGenome.setAdjustedScore(CSVFormat.EG_FORMAT.parse(cols.get(1)));
lastGenome.setScore(CSVFormat.EG_FORMAT.parse(cols.get(2)));
lastGenome.setBirthGeneration(Integer.parseInt(cols.get(3)));
lastSpecies.add(lastGenome);
if (isLeader) {
lastSpecies.setLeader(lastGenome);
}
} else if (cols.get(0).equalsIgnoreCase("n")) {
final NEATNeuronGene neuronGene = new NEATNeuronGene();
final int geneID = Integer.parseInt(cols.get(1));
neuronGene.setId(geneID);
final ActivationFunction af = EncogFileSection.parseActivationFunction(cols.get(2));
neuronGene.setActivationFunction(af);
neuronGene.setNeuronType(PersistNEATPopulation.stringToNeuronType(cols.get(3)));
neuronGene.setInnovationId(Integer.parseInt(cols.get(4)));
lastGenome.getNeuronsChromosome().add(neuronGene);
nextGeneID = Math.max(geneID + 1, nextGeneID);
} else if (cols.get(0).equalsIgnoreCase("l")) {
final NEATLinkGene linkGene = new NEATLinkGene();
linkGene.setId(Integer.parseInt(cols.get(1)));
linkGene.setEnabled(Integer.parseInt(cols.get(2)) > 0);
linkGene.setFromNeuronID(Integer.parseInt(cols.get(3)));
linkGene.setToNeuronID(Integer.parseInt(cols.get(4)));
linkGene.setWeight(CSVFormat.EG_FORMAT.parse(cols.get(5)));
linkGene.setInnovationId(Integer.parseInt(cols.get(6)));
lastGenome.getLinksChromosome().add(linkGene);
}
}
} else if (section.getSectionName().equals("NEAT-POPULATION")
&& section.getSubSectionName().equals("CONFIG")) {
final Map<String, String> params = section.parseParams();
final String afStr = params.get(NEATPopulation.PROPERTY_NEAT_ACTIVATION);
if (afStr.equalsIgnoreCase(PersistNEATPopulation.TYPE_CPPN)) {
HyperNEATGenome.buildCPPNActivationFunctions(result.getActivationFunctions());
} else {
result.setNEATActivationFunction(
EncogFileSection.parseActivationFunction(
params, NEATPopulation.PROPERTY_NEAT_ACTIVATION));
}
result.setActivationCycles(
EncogFileSection.parseInt(params, PersistConst.ACTIVATION_CYCLES));
result.setInputCount(EncogFileSection.parseInt(params, PersistConst.INPUT_COUNT));
result.setOutputCount(EncogFileSection.parseInt(params, PersistConst.OUTPUT_COUNT));
result.setPopulationSize(
EncogFileSection.parseInt(params, NEATPopulation.PROPERTY_POPULATION_SIZE));
result.setSurvivalRate(
EncogFileSection.parseDouble(params, NEATPopulation.PROPERTY_SURVIVAL_RATE));
result.setActivationCycles(
EncogFileSection.parseInt(params, NEATPopulation.PROPERTY_CYCLES));
}
}
// set factories
if (result.isHyperNEAT()) {
result.setGenomeFactory(new FactorHyperNEATGenome());
result.setCODEC(new HyperNEATCODEC());
} else {
result.setGenomeFactory(new FactorNEATGenome());
result.setCODEC(new NEATCODEC());
}
// set the next ID's
result.getInnovationIDGenerate().setCurrentID(nextInnovationID);
result.getGeneIDGenerate().setCurrentID(nextGeneID);
// find first genome, which should be the best genome
if (result.getSpecies().size() > 0) {
final Species species = result.getSpecies().get(0);
if (species.getMembers().size() > 0) {
result.setBestGenome(species.getMembers().get(0));
}
}
return result;
}