/// <summary>
/// Sorts next generation into their respective species.
/// </summary>
/// <param name="nextGen">The next generation.</param>
private void SpeciateNewGeneration(List <Genome> nextGen)
{
foreach (var child in nextGen)
{
bool speciesFound = false;
foreach (var spec in Species)
{
if (GenomeCompatibility.Compatibility(spec.Template, child) <= GenomeCompatibility.SpeciesCompatibilityThreshold)
{
spec.Genomes.Add(child);
speciesFound = true;
break;
}
}
if (!speciesFound)
{
//TODO: Find a better way of doing age.
Species spec = new Species(child);
spec.Age = -1;
Species.Add(spec);
}
}
}
public void Speciate(IGenome genome)
{
bool newSpecies = true;
// Remove from current species
if (genome.SpeciesId.HasValue)
{
Species.First(s => s.Id == genome.SpeciesId).Genomes.Remove(genome);
}
foreach (ISpecies species in Species.Where(s => s.Genomes.Any()))
{
IGenome representative = species.Genomes.First();
if (genome.IsCompatible(representative))
{
species.Genomes.Add(genome);
genome.SpeciesId = species.Id;
newSpecies = false;
break;
}
}
;
if (newSpecies)
{
ISpecies species = new Species();
species.Genomes.Add(genome);
genome.SpeciesId = species.Id;
Species.Add(species);
}
}
/// <summary>
/// Reproduces the surviving species based on their fitness scores. Chooses the organisms in the species to mate based on fitness scores as well. Replaces the previous generation
/// with the newly created organisms. Removes extinct species if necessary. Adjusts compatibility distance after replacement.
/// See <see cref="NEAT.NEATClient.Evolve"/> before using!
/// </summary>
/// <remarks>
/// Decides the amount of offspring (nk) each species (k) should be allotted via the following equation:
/// <para/>
/// nk = P * (Fk / Ft)
/// <para/>
/// Where:
/// <list type="bullet">
/// <item>k: The species.</item>
/// <item>nk: The number of new organisms for species k in the next generation.</item>
/// <item>P: The desired new population count.</item>
/// <item>Fk: The average fitness score of the species.</item>
/// <item>Ft: The sum of all fitness score averages of every species.</item>
/// </list>
/// </remarks>
public void ReproduceAndReplace()
{
double total_speciesFitness = Species.Sum(x => x.AverageFitnessScore);
Dictionary <Species, ReproduceAndReplace_Node> stored_distributionsSpecies = new Dictionary <Species, ReproduceAndReplace_Node>(Species.Count);
List <Organism> next_generation = new List <Organism>(NumOrganisms); //All of the new organisms.
HashSet <Species> next_species = new HashSet <Species>(Species.Count);
#region Reproduction
foreach (Species species in Species)
{
//Calculate the number of organisms every species will have:
int num_alloted_offspring = (int)(NumOrganisms * (species.AverageFitnessScore / total_speciesFitness));
//Prepare new species for placement:
Species creation_species = new Species();
next_species.Add(creation_species);
//Prepare ScoredDistribution for selecting organisms to mate:
ScoredDistribution <Organism> internal_organisms = new ScoredDistribution <Organism>(species.Size, Pedigree.Random);
foreach (Organism organism in species)
{
internal_organisms.Add(organism, organism.FitnessScore);
}
stored_distributionsSpecies.Add(species, new ReproduceAndReplace_Node(internal_organisms, creation_species));
//Actaully mate the organisms:
for (int i = 0; i < num_alloted_offspring; ++i)
{
Organism random_organism_1 = internal_organisms.ChooseValue();
Organism random_organism_2 = internal_organisms.ChooseValue(random_organism_1); //We don't want any self-replication...
if (random_organism_2 == null)
{
random_organism_2 = random_organism_1; //Unless that's the only option ;) Only happens when the organism is the only one in the species.
}
Organism baby = new Organism(random_organism_1.Genome.Crossover(random_organism_1.FitnessScore, random_organism_2.Genome, random_organism_2.FitnessScore,
Pedigree.Random));
next_generation.Add(baby);
creation_species.AddOrganism(baby);
}
}
while (next_generation.Count < NumOrganisms) //We need more organisms, give it to some random species. Super rare that this doesn't happen.
{
ReproduceAndReplace_Node chosen_last_node = stored_distributionsSpecies[Species.RandomValue(Pedigree.Random)];
ScoredDistribution <Organism> last_round_distribution = chosen_last_node.scoredDistribution_organisms;
Species last_round_species = chosen_last_node.new_species;
Organism random_organism_1 = last_round_distribution.ChooseValue();
Organism random_organism_2 = last_round_distribution.ChooseValue(random_organism_1); //We don't want any self-replication...
if (random_organism_2 == null)
{
random_organism_2 = random_organism_1; //Unless that's the only option ;) Only happens when the organism is the only one in the species.
}
Organism baby = new Organism(random_organism_1.Genome.Crossover(random_organism_1.FitnessScore, random_organism_2.Genome, random_organism_2.FitnessScore,
Pedigree.Random));
next_generation.Add(baby);
last_round_species.AddOrganism(baby);
}
#endregion Reproduction
#region Replacement
//Organisms:
Organisms.Clear();
Organisms.AddRange(next_generation);
//Species:
Species.Clear();
foreach (Species species in next_species)
{
Species.Add(species);
}
#endregion Replacement
RemoveExtinctions();
CompatibilityDistance += CD_function.Invoke(Species.Count);
}
/// <summary>
/// Separates the current organisms into the correct species. Makes new species and deletes extinct species as needed. See <see cref="NEAT.NEATClient.Evolve"/> before using!
/// </summary>
public void Speciate()
{
foreach (Organism organism in Organisms)
{
bool found_species = false;
foreach (Species species in Species)
{
Organism random_organism = species.GetRandomOrganism(Pedigree.Random, organism);
if (random_organism == null) //The organism we're at is the only organism in the species we're at. See if we should leave it in this species.
{
bool kill_species = false;
IEnumerable <Species> all_other_species = Species.Where(x => x != species);
foreach (Species other_species in all_other_species)
{
Organism other_random_organism = other_species.GetRandomOrganism(Pedigree.Random); //No need to exclude the organism because it can't be here.
if (organism.Genome.Distance(other_random_organism.Genome) < CompatibilityDistance) //The organism can fit in another species, put it there.
{
organism.Species.RemoveOrganism(organism);
other_species.AddOrganism(organism);
kill_species = true;
break;
}
}
if (kill_species) //This species no longer has any organisms, it is now extinct.
{
Species.Remove(species);
}
found_species = true;
break;
}
if (organism.Genome.Distance(random_organism.Genome) < CompatibilityDistance)
{
if (organism.Species != random_organism.Species) //If the species to set is actually different.
{
Species original_species = organism.Species;
original_species?.RemoveOrganism(organism);
species.AddOrganism(organism);
if (original_species?.Size == 0) //This species just went extinct.
{
Species.Remove(original_species);
}
}
found_species = true;
break;
}
}
if (!found_species)
{
Species original_species = organism.Species;
original_species?.RemoveOrganism(organism);
Species new_species = new Species();
Species.Add(new_species);
new_species.AddOrganism(organism);
if (original_species?.Size == 0) //This species just went extinct.
{
Species.Remove(original_species);
}
}
}
}