/// <summary>
/// Merge new genomes into an existing set of species.
/// </summary>
/// <param name="genomeList">A list of genomes that have not yet been assigned a species.</param>
/// <param name="speciesArr">An array of pre-existing species</param>
/// <param name="rng">Random source.</param>
public void SpeciateAdd(IList <NeatGenome <T> > genomeList, Species <T>[] speciesArr, IRandomSource rng)
{
// Create a temporary working array of species modification bits.
var updateBits = new bool[speciesArr.Length];
// Allocate the new genomes to the species centroid they are nearest too.
Parallel.ForEach(genomeList, _parallelOptions, (genome) =>
{
var nearestSpeciesIdx = SpeciationUtils.GetNearestSpecies(_distanceMetric, genome, speciesArr);
var nearestSpecies = speciesArr[nearestSpeciesIdx];
lock (nearestSpecies.GenomeList) {
nearestSpecies.GenomeList.Add(genome);
}
// Set the modification bit for the species.
updateBits[nearestSpeciesIdx] = true;
});
// Recalc the species centroids for species that have been modified.
RecalcCentroids_GenomeList(speciesArr, updateBits);
// Run the k-means algorithm.
RunKMeans(speciesArr);
}
private int KMeansIteration(Species <T>[] speciesArr, bool[] updateBits)
{
int reallocCount = 0;
Array.Clear(updateBits, 0, updateBits.Length);
// Loop species.
// Note. The nested parallel loop here is intentional and should give good thread concurrency in the general case.
// For more info see: "Is it OK to use nested Parallel.For loops?"
// https://blogs.msdn.microsoft.com/pfxteam/2012/03/14/is-it-ok-to-use-nested-parallel-for-loops/
Parallel.For(0, speciesArr.Length, _parallelOptions, (speciesIdx) =>
{
var species = speciesArr[speciesIdx];
// Loop genomes in the current species.
Parallel.ForEach(species.GenomeById.Values, _parallelOptions, (genome) =>
{
// Determine the species centroid the genome is nearest to.
var nearestSpeciesIdx = SpeciationUtils.GetNearestSpecies(_distanceMetric, genome, speciesArr);
// If the nearest species is not the species the genome is currently in then move the genome.
if (nearestSpeciesIdx != speciesIdx)
{
// Move genome.
// Note. We can't modify species.GenomeById while we are enumerating through it, therefore we record the IDs
// of the genomes to be removed and remove them once we leave the enumeration loop.
lock (species.PendingRemovesList)
{
species.PendingRemovesList.Add(genome.Id);
}
var nearestSpecies = speciesArr[nearestSpeciesIdx];
lock (nearestSpecies.PendingAddsList)
{
nearestSpecies.PendingAddsList.Add(genome);
}
// Set the modification bits for the two species.
updateBits[speciesIdx] = true;
updateBits[nearestSpeciesIdx] = true;
// Track the number of re-allocations.
Interlocked.Increment(ref reallocCount);
}
});
});
// Complete moving of genomes to their new species.
Parallel.ForEach(speciesArr, _parallelOptions, (species) => species.CompletePendingMoves());
// Recalc the species centroids for species that have been modified.
RecalcCentroids_GenomeById(speciesArr, updateBits);
return(reallocCount);
}
private void KMeansComplete(Species <T>[] speciesArr)
{
// Check for empty species (this can happen with k-means), and if there are any then
// move genomes into those empty species.
var emptySpeciesArr = speciesArr.Where(x => x.GenomeById.Count == 0).ToArray();
if (emptySpeciesArr.Length != 0)
{
SpeciationUtils.PopulateEmptySpecies(_distanceMetric, emptySpeciesArr, speciesArr);
}
// Transfer all genomes from GenomeById to GenomeList.
Parallel.ForEach(speciesArr, _parallelOptions, species => species.FlushWorkingDictionary());
}
private void RecalcCentroids_GenomeList(Species <T>[] speciesArr, bool[] updateBits)
{
Parallel.ForEach(
Enumerable.Range(0, speciesArr.Length).Where(i => updateBits[i]),
_parallelOptions,
() => new List <ConnectionGenes <T> >(),
(speciesIdx, loopState, connGenesList) =>
{
var species = speciesArr[speciesIdx];
SpeciationUtils.ExtractConnectionGenes(connGenesList, species.GenomeList);
species.Centroid = _distanceMetric.CalculateCentroid(connGenesList);
return(connGenesList);
},
(connGenesList) => connGenesList.Clear());
}
private int KMeansIteration(Species <T>[] speciesArr, bool[] updateBits)
{
int reallocCount = 0;
Array.Clear(updateBits, 0, updateBits.Length);
// Loop species.
for (int speciesIdx = 0; speciesIdx < speciesArr.Length; speciesIdx++)
{
var species = speciesArr[speciesIdx];
// Loop genomes in the current species.
foreach (var genome in species.GenomeById.Values)
{
// Determine the species centroid the genome is nearest to.
var nearestSpeciesIdx = SpeciationUtils.GetNearestSpecies(_distanceMetric, genome, speciesArr);
// If the nearest species is not the species the genome is currently in then move the genome.
if (nearestSpeciesIdx != speciesIdx)
{
// Move genome.
// Note. We can't modify species.GenomeById while we are enumerating through it, therefore we record the IDs
// of the genomes to be removed and remove them once we leave the enumeration loop.
species.PendingRemovesList.Add(genome.Id);
speciesArr[nearestSpeciesIdx].PendingAddsList.Add(genome);
// Set the modification bits for the two species.
updateBits[speciesIdx] = true;
updateBits[nearestSpeciesIdx] = true;
// Track the number of re-allocations.
reallocCount++;
}
}
}
// Complete moving of genomes to their new species.
foreach (var species in speciesArr)
{
species.CompletePendingMoves();
}
// Recalc the species centroids for species that have been modified.
RecalcCentroids_GenomeById(speciesArr, updateBits);
return(reallocCount);
}
private void RecalcCentroids_GenomeById(Species <T>[] speciesArr, bool[] updateBits)
{
Parallel.ForEach(
Enumerable.Range(0, speciesArr.Length).Where(i => updateBits[i]),
_parallelOptions,
() => new List <ConnectionGenes <T> >(),
(speciesIdx, loopState, connGenesList) =>
{
var species = speciesArr[speciesIdx];
// Extract the ConnectionGenes<T> object from each genome in the GenomeById dictionary.
SpeciationUtils.ExtractConnectionGenes(connGenesList, species.GenomeById);
// Calculate the centroid for the extracted connection genes.
species.Centroid = _distanceMetric.CalculateCentroid(connGenesList);
return(connGenesList);
},
(connGenesList) => connGenesList.Clear());
}
private void RecalcCentroids_GenomeList(
Species <T>[] speciesArr,
bool[] updateBits)
{
// Create a temporary, reusable, working list.
var tmpConnGenes = new List <ConnectionGenes <T> >();
for (int i = 0; i < speciesArr.Length; i++)
{
if (updateBits[i])
{
var species = speciesArr[i];
// Extract the ConnectionGenes<T> object from each genome in GenomeList.
SpeciationUtils.ExtractConnectionGenes(tmpConnGenes, species.GenomeList);
// Calculate the centroid for the extracted connection genes.
species.Centroid = _distanceMetric.CalculateCentroid(tmpConnGenes);
}
}
tmpConnGenes.Clear();
}
