@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; }