public void addSynapse(Synapse synapse, Genome parent1, Genome parent2)
{
if (this.fitness != -1)
{
return;
}
if (this.synapses.ContainsKey(synapse.innovationNumber))
{
return;
}
synapse = synapse.clone();
if (parent1 != null && parent2 != null)
{
if (parent1.hasSynapse(synapse.innovationNumber) && parent2.hasSynapse(synapse.innovationNumber))
{
bool dis1 = !parent1.synapses[synapse.innovationNumber].enabled;
bool dis2 = !parent2.synapses[synapse.innovationNumber].enabled;
if ((dis1 && !dis2) || (!dis1 && dis2))
{
bool disabled = RandomUtil.success(Config.NEURON_DISABLE_CHANCE);
synapse.enabled = !disabled;
}
}
}
this.synapses.Add(synapse.innovationNumber, synapse);
}
public void removeDuplicateSynapses()
{
if (this.fitness != -1)
{
throw new Exception("Can't remove duplicate of a untested Genome");
}
foreach (Species species in this.neat.popManager.currentPop.species)
{
foreach (Genome genome in species.genomes)
{
List <ZeroSynapse> conA = this.getAllSynapses();
List <ZeroSynapse> conB = genome.getAllSynapses();
if (ListUtil.equals(conB, conA))
{
List <Synapse> toCloneFrom = new List <Synapse>(genome.synapses.Values);
List <Synapse> toReplace = new List <Synapse>(this.synapses.Values);
for (int i = 0; i < toCloneFrom.Count; i++)
{
if (toCloneFrom[i] == null || toReplace[i] == null)
{
return;
}
Synapse from = toCloneFrom[i];
Synapse to = toReplace[i];
int oldInno = to.innovationNumber;
int changeTo = from.innovationNumber;
Synapse old = this.synapses[oldInno];
if (!this.synapses.Remove(oldInno))
{
new Exception("Synapse could not be removed " + old.toString());
}
old.innovationNumber = changeTo;
this.synapses.Add(old.innovationNumber, old);
}
}
}
}
}
// REF: [GITHUB] SanderGielisse logic for distance
// between genomes (eg compatibility)
// (https://github.com/SanderGielisse/Mythan)
public static double distance(Genome a, Genome b)
{
int aLength = a.getHighestInnovationNumber();
int bLength = b.getHighestInnovationNumber();
Genome longest;
Genome shortest;
if (aLength > bLength)
{
longest = a;
shortest = b;
}
else
{
longest = b;
shortest = a;
}
int shortestLength = shortest.getHighestInnovationNumber();
int longestLength = longest.getHighestInnovationNumber();
double disjoint = 0;
double excess = 0;
List <double> weights = new List <double>();
for (int i = 0; i < longestLength; i++)
{
Synapse aa = longest.getSynapse(i);
Synapse bb = shortest.getSynapse(i);
if ((aa == null && bb != null) || (aa != null && bb == null))
{
// only present in one of them
if (i <= shortestLength)
{
disjoint++;
}
else if (i > shortestLength)
{
excess++;
}
}
if (aa != null && bb != null)
{
double distance = Math.Abs(aa.weight - bb.weight);
weights.Add(distance);
}
}
double total = 0;
double size = 0;
foreach (double w in weights)
{
total += w;
size++;
}
double averageWeightDistance = total / size;
double n = longest.synapses.Count;
double c1 = Config.DISTANCE_EXCESS_WEIGHT;
double c2 = Config.DISTANCE_DISJOINT_WEIGHT;
double c3 = Config.DISTANCE_WEIGHTS_WEIGHT;
double d = ((c1 * excess) / n) + ((c2 * disjoint) / n) + (c3 * averageWeightDistance);
return(d);
}