private void assignNeuronDepth(Gene[] nodeGenes, int depth, Chromosome mutated) {
int i;
NEATNodeGene node;
// ArrayList nodeGenes = this.findOutputNodes(this.candidateNodes(genes));
for (i = 0; i < nodeGenes.length; i++) {
node = (NEATNodeGene) nodeGenes[i];
if (node.getType() == NEATNodeGene.OUTPUT) {
if (depth == 1) {
node.setDepth(depth);
this.assignNeuronDepth(
this.findSourceNodes(node.id(), mutated.genes()), depth + 1, mutated);
}
} else if (node.getType() == NEATNodeGene.HIDDEN) {
if (node.getDepth() == 0) {
// we have an unassigned depth
node.setDepth(depth);
this.assignNeuronDepth(
this.findSourceNodes(node.id(), mutated.genes()), depth + 1, mutated);
}
} else if (node.getType() == NEATNodeGene.INPUT) {
node.setDepth(Integer.MAX_VALUE);
}
}
}
private Gene mutateNode(NEATNodeGene mutatee) {
double perturbRandVal = perturbRand.nextDouble();
double mutateBias = perturbRand.nextDouble();
NEATNodeGene mutated = mutatee;
double newSF = mutatee.sigmoidFactor();
double newBias = mutatee.bias();
if (perturbRandVal < this.pPerturb) {
newSF = mutatee.sigmoidFactor() + MathUtils.nextClampedDouble(-perturb, perturb);
mutated =
new NEATNodeGene(
mutated.getInnovationNumber(),
mutated.id(),
newSF,
mutated.getType(),
mutated.bias());
}
if (mutateBias < this.pMutateBias) {
newBias += MathUtils.nextClampedDouble(-biasPerturb, biasPerturb);
mutated =
new NEATNodeGene(
mutated.getInnovationNumber(),
mutated.id(),
mutated.sigmoidFactor(),
mutated.getType(),
newBias);
}
return (mutated);
}
private Gene[] findOutputNodes(ArrayList nodes) {
ArrayList outputNodes = new ArrayList();
Gene[] nodeGenes;
NEATNodeGene node;
int i;
for (i = 0; i < nodes.size(); i++) {
node = (NEATNodeGene) nodes.get(i);
if (node.getType() == NEATNodeGene.OUTPUT) {
outputNodes.add(node);
}
}
nodeGenes = new NEATNodeGene[outputNodes.size()];
for (i = 0; i < nodeGenes.length; i++) {
nodeGenes[i] = (NEATNodeGene) outputNodes.get(i);
}
return (nodeGenes);
}
private boolean linkIllegal(NEATNodeGene from, NEATNodeGene to, ArrayList links) {
boolean illegal = false;
int idx = 0;
NEATLinkGene linkGene;
if ((to.getType() == NEATNodeGene.INPUT)) {
illegal = true;
} else {
while (!illegal && (idx < links.size())) {
linkGene = (NEATLinkGene) links.get(idx);
// if ((linkGene.getFromId() == from.id() && linkGene.getToId() == to.id()) ||
// ((to.getDepth() <= from.getDepth()) && !this.recurrencyAllowed)) {
if ((linkGene.getFromId() == from.id() && linkGene.getToId() == to.id())) {
illegal = true;
}
idx++;
}
}
return (illegal);
}
