private void RandomizeWeights(NetworkGenome temp)
{
foreach (LinkGene LinkGenes in temp.Links)
{
LinkGenes.Weight = Utilities.Rnd.NextDouble(-this.Mutate.WeightRange / 2.0, this.Mutate.WeightRange / 2.0);
}
}
private void DetermineSpecies(NetworkGenome temp)
{
int index1 = -1;
double num1 = 100000.0;
for (int index2 = 0; index2 < this.species.Count; ++index2)
{
if (!this.species[index2].Extinct)
{
double num2 = this.species[index2].GenomeCompatibility(temp);
if (num2 < num1)
{
num1 = num2;
index1 = index2;
}
}
}
if (num1 <= this.Speciate.Threshold || (double)Enumerable.Count <Species>((IEnumerable <Species>) this.species, (Func <Species, bool>)(g => !g.Extinct)) > (double)this.Speciate.SpeciesCount * 1.5)
{
temp.Species = index1;
this.species[index1].Genomes.Add(temp);
}
else
{
temp.Species = this.species.Count;
this.species.Add(new Species(this.Generation, this.Generation, 0.0, temp));
}
}
private NetworkGenome SelectGenome(List <NetworkGenome> list, NetworkGenome parent1)
{
List <NetworkGenome> list1 = new List <NetworkGenome>((IEnumerable <NetworkGenome>)list);
list1.Remove(parent1);
return(this.SelectGenome(list1));
}
private bool AddNode(NetworkGenome temp)
{
List <LinkGene> list = new List <LinkGene>(temp.MutatableLinks);
if (list.Count < 1)
{
return(false);
}
LinkGene split = list[(int)(Utilities.Rnd.NextDouble() * (double)list.Count)];
NodeGene NodeGenes1 = temp.Nodes.Find((Predicate <NodeGene>)(g => g.Id == split.Source));
NodeGene NodeGenes2 = temp.Nodes.Find((Predicate <NodeGene>)(g => g.Id == split.Target));
if (Math.Abs(NodeGenes1.Layer - NodeGenes2.Layer) <= 1)
{
return(false);
}
NodeGene NodeGenes3 = new NodeGene("Identity", 0, Utilities.Rnd.Next(Math.Min(NodeGenes1.Layer, NodeGenes2.Layer) + 1, Math.Max(NodeGenes1.Layer, NodeGenes2.Layer)), NodeType.Hidden);
NodeGenes3.Id = HistoricalMarkings.GetNodeMarking(split.Id, NodeGenes3.Layer, this.Generation);
NodeGenes3.Function = this.SelectFunction();
LinkGene LinkGenes1 = new LinkGene(HistoricalMarkings.GetLinkMarking(NodeGenes1.Id, NodeGenes3.Id, this.Generation), NodeGenes1.Id, NodeGenes3.Id, split.Weight);
LinkGene LinkGenes2 = new LinkGene(HistoricalMarkings.GetLinkMarking(NodeGenes3.Id, NodeGenes2.Id, this.Generation), NodeGenes3.Id, NodeGenes2.Id, Math.Max(-this.Mutate.WeightRange / 2.0, Math.Min(this.Mutate.WeightRange / 2.0, Utilities.Rnd.NextGuassian(0.0, 0.2) * this.Mutate.WeightRange / 2.0)));
temp.Nodes.Add(NodeGenes3);
temp.Links.Add(LinkGenes1);
temp.Links.Add(LinkGenes2);
if (Utilities.Rnd.NextDouble() > this.Mutate.KeepLinkOnAddNode)
{
temp.Links.Remove(split);
}
return(true);
}
private void Save()
{
this.Current.Genomes.Sort((Comparison <NetworkGenome>)((b, a) => a.Fitness.CompareTo(b.Fitness)));
NetworkGenome genome = this.Current.Genomes[0];
this.Champions.Add(genome);
this.Current.Genomes.Sort((Comparison <NetworkGenome>)((a, b) => a.Species.CompareTo(b.Species)));
if (this.Saves.Champions.save && this.Generation % this.Saves.Champions.inteval == 0)
{
NetworkGenome.SaveToFile(genome, this.Saves.Champions.path + "G" + this.Generation.ToString("0000") + "Champ.xml");
}
if (this.Saves.Populations.save && this.Generation % this.Saves.Populations.inteval == 0)
{
Population.SaveToXml(this.Saves.Populations.path + "G" + this.Generation.ToString("0000") + "Pop.xml", this.Current);
}
if (this.Saves.PopulationStatistics.save && (this.Generation % this.Saves.PopulationStatistics.inteval == 0 || this.Generation == 1))
{
this.PopulationStatsFile.WriteLine((string)(object)this.Current.Generation + (object)"\t" + (string)(object)this.Current.MeanFitness + "\t" + (string)(object)this.Current.MaxFitness);
}
if (this.Saves.Species.save && this.Generation % this.Saves.Species.inteval == 0)
{
for (int index = 0; index < this.species.Count; ++index)
{
Species.SaveToXml(this.Saves.Species.path + "G" + this.Generation.ToString("0000") + "Species" + index.ToString("0000") + ".xml", this.species[index]);
}
}
if (!this.Saves.SpeciesStatistics.save || this.Generation % this.Saves.SpeciesStatistics.inteval != 0)
{
return;
}
this.WriteSpeciesStats();
}
public static bool SaveToFile(NetworkGenome genome, string file)
{
using (StreamWriter streamWriter = new StreamWriter(file))
{
NetworkGenome.serializer.Serialize((TextWriter)streamWriter, (object)genome);
return(true);
}
}
public static void subXor(NetworkGenome cppn)
{
DecodedNetworks decodedNetwork = (DecodedNetworks)null;
double[] inputs = new double[4];
bool flag1 = true;
inputs[0] = 1.0;
inputs[1] = 0.0;
inputs[2] = 0.0;
inputs[3] = 0.0;
decodedNetwork.SetInputs(inputs);
decodedNetwork.ActivateNetwork(2);
double[] outputs1 = decodedNetwork.GetOutputs();
cppn.Fitness = 0.0;
cppn.Fitness += Math.Min(1.0, Math.Max(0.0, 1.0 - outputs1[0]));
bool flag2 = flag1 && outputs1[0] < 0.5;
decodedNetwork.Flush();
inputs[0] = 0.0;
inputs[1] = 0.0;
inputs[2] = 0.0;
inputs[3] = 1.0;
decodedNetwork.SetInputs(inputs);
decodedNetwork.ActivateNetwork(2);
double[] outputs2 = decodedNetwork.GetOutputs();
cppn.Fitness += Math.Min(1.0, Math.Max(0.0, 1.0 - outputs2[0]));
bool flag3 = flag2 && outputs2[0] < 0.5;
decodedNetwork.Flush();
inputs[0] = 0.0;
inputs[1] = 1.0;
inputs[2] = 0.0;
inputs[3] = 0.0;
decodedNetwork.SetInputs(inputs);
decodedNetwork.ActivateNetwork(2);
double[] outputs3 = decodedNetwork.GetOutputs();
cppn.Fitness += Math.Min(1.0, Math.Max(0.0, outputs3[0]));
bool flag4 = flag3 && outputs3[0] >= 0.5;
decodedNetwork.Flush();
inputs[0] = 0.0;
inputs[1] = 0.0;
inputs[2] = 1.0;
inputs[3] = 0.0;
decodedNetwork.SetInputs(inputs);
decodedNetwork.ActivateNetwork(2);
double[] outputs4 = decodedNetwork.GetOutputs();
cppn.Fitness += Math.Min(1.0, Math.Max(0.0, outputs4[0]));
bool flag5 = flag4 && outputs4[0] >= 0.5;
decodedNetwork.Flush();
if (!flag5)
{
return;
}
cppn.Fitness = 4.0;
}
private bool LoadSeedInit()
{
NetworkGenome genome = NetworkGenome.LoadFromFile(this.Init.Seed.file);
if (genome == null)
{
return(false);
}
genome.Fitness = 0.0;
genome.Age = 0;
genome.Species = 0;
genome.Id = 0;
this.Current.Genomes.Add(genome);
this.species.Add(new Species(0, 0, 0.0, genome));
this.Init.MaxLayers = Enumerable.First <NodeGene>((IEnumerable <NodeGene>)genome.Nodes, (Func <NodeGene, bool>)(g => g.Type == NodeType.Output)).Layer + 1;
this.Init.Inputs = Enumerable.Count <NodeGene>((IEnumerable <NodeGene>)genome.Nodes, (Func <NodeGene, bool>)(g => g.Type == NodeType.Input));
this.Init.Outputs = Enumerable.Count <NodeGene>((IEnumerable <NodeGene>)genome.Nodes, (Func <NodeGene, bool>)(g => g.Type == NodeType.Output));
NetworkGenome.NextId = 1;
foreach (LinkGene LinkGenes in genome.Links)
{
LinkGene.NextId = Math.Max(LinkGene.NextId, LinkGenes.Id);
}
foreach (NodeGene NodeGenes in genome.Nodes)
{
NodeGene.NextId = Math.Max(NodeGene.NextId, NodeGenes.Id);
}
while (this.Current.Genomes.Count < this.Init.PopulationSize)
{
NetworkGenome networkGenomes = genome.Clone() as NetworkGenome;
networkGenomes.Id = NetworkGenome.NextId;
networkGenomes.Parent1 = 0;
networkGenomes.Parent2 = -1;
this.RandomizeWeights(networkGenomes);
double num1 = 1000000.0;
int index1 = 0;
for (int index2 = 0; index2 < this.species.Count; ++index2)
{
double num2 = this.species[index2].GenomeCompatibility(networkGenomes);
if (num2 < num1)
{
num1 = num2;
index1 = index2;
}
}
if (num1 <= this.Speciate.Threshold)
{
this.species[index1].Genomes.Add(networkGenomes);
networkGenomes.Species = index1;
}
else
{
this.species.Add(new Species(0, 0, 0.0, networkGenomes));
networkGenomes.Species = this.species.Count - 1;
}
this.Current.Genomes.Add(networkGenomes);
}
return(true);
}
public int CompareTo(object obj)
{
NetworkGenome networkGenome = obj as NetworkGenome;
if (networkGenome == null)
{
throw new InvalidOperationException("Object being compared to is not a Network Genome!");
}
return(this.Id.CompareTo(networkGenome.Id));
}
private bool DelectConnection(NetworkGenome temp)
{
List <LinkGene> list = new List <LinkGene>(temp.MutatableLinks);
if (list.Count < 1)
{
return(false);
}
LinkGene LinkGenes = list[(int)(Utilities.Rnd.NextDouble() * (double)list.Count)];
temp.Links.Remove(LinkGenes);
return(true);
}
public static void Xor(object target)
{
NetworkGenome genome = target as NetworkGenome;
double[] inputs = new double[2];
bool flag1 = true;
DecodedNetworks decodedNetwork = DecodedNetworks.DecodeGenome(genome);
inputs[0] = 0.0;
inputs[1] = 0.0;
decodedNetwork.SetInputs(inputs);
decodedNetwork.ActivateNetwork(6);
double[] outputs1 = decodedNetwork.GetOutputs();
genome.Fitness = 0.0;
genome.Fitness += Math.Min(1.0, Math.Max(0.0, 1.0 - outputs1[0]));
bool flag2 = flag1 && outputs1[0] < 0.5;
decodedNetwork.Flush();
inputs[0] = 1.0;
inputs[1] = 1.0;
decodedNetwork.SetInputs(inputs);
decodedNetwork.ActivateNetwork(6);
double[] outputs2 = decodedNetwork.GetOutputs();
genome.Fitness += Math.Min(1.0, Math.Max(0.0, 1.0 - outputs2[0]));
bool flag3 = flag2 && outputs2[0] < 0.5;
decodedNetwork.Flush();
inputs[0] = 0.0;
inputs[1] = 1.0;
decodedNetwork.SetInputs(inputs);
decodedNetwork.ActivateNetwork(6);
double[] outputs3 = decodedNetwork.GetOutputs();
genome.Fitness += Math.Min(1.0, Math.Max(0.0, outputs3[0]));
bool flag4 = flag3 && outputs3[0] >= 0.5;
decodedNetwork.Flush();
inputs[0] = 1.0;
inputs[1] = 0.0;
decodedNetwork.SetInputs(inputs);
decodedNetwork.ActivateNetwork(6);
double[] outputs4 = decodedNetwork.GetOutputs();
genome.Fitness += Math.Min(1.0, Math.Max(0.0, outputs4[0]));
bool flag5 = flag4 && outputs4[0] >= 0.5;
decodedNetwork.Flush();
if (!flag5)
{
return;
}
genome.Fitness = 4.0;
}
//by phillip
static void MapWeights(NetworkGenome genome, DecodedNetworks cppn)
{
double[] coords = new double[4];
double[] output;
LinkGene temp;
SubstrateNodes source;
SubstrateNodes target;
int linkId = 0;
for (int i = 1; i < genome.Links.Count; i++)
{
temp = genome.Links[i];
source = (SubstrateNodes)genome.Nodes[temp.Source];
target = (SubstrateNodes)genome.Nodes[temp.Target];
if (temp.Source != 0)
{
coords[0] = source.Coordinate[0];
coords[1] = source.Coordinate[1];
}
else
{
coords[0] = target.Coordinate[0];
coords[1] = target.Coordinate[1];
}
coords[2] = target.Coordinate[0];
coords[3] = target.Coordinate[1];
cppn.Flush();
cppn.SetInputs(coords);
cppn.ActivateNetwork(5);
output = cppn.GetOutputs();
if (source.Id != 0)
{
temp.Weight = output[0];
}
else
{
temp.Weight = output[1];
}
}
if (saveSub)
{
NetworkGenome.SaveToFile(genome, "Sub.xml");
saveSub = false;
}
}
public NetworkGenome(NetworkGenome copy)
: this(copy.Id, copy.Age, copy.Parent1, copy.Parent2, copy.Species, copy.Fitness, copy.Novelty, copy.RealFitness, copy.Genotypic_Diversity)
{
foreach (NodeGene nodeGene in copy.Nodes)
{
this.Nodes.Add(nodeGene.Clone() as NodeGene);
}
foreach (LinkGene linkGene in copy.Links)
{
this.Links.Add(linkGene.Clone() as LinkGene);
}
this.Complexity = this.Links.Count + this.Nodes.Count;
//this.BehaviorType = copy.BehaviorType;
//this.GenomeDiversity = copy.GenomeDiversity;
}
private bool ChangeNode(NetworkGenome temp)
{
List <NodeGene> list = new List <NodeGene>(temp.MutatableNodes);
if (list.Count < 1)
{
return(false);
}
NodeGene NodeGenes = list[(int)(Utilities.Rnd.NextDouble() * (double)list.Count)];
string str = NodeGenes.Function;
for (int index = 0; NodeGenes.Function == str && index < 7; ++index)
{
NodeGenes.Function = this.SelectFunction();
}
return(!(NodeGenes.Function == str));
}
private NetworkGenome SelectGenome(List <NetworkGenome> list)
{
if (list.Count < 2)
{
return(list[0]);
}
if (list.Count < 3)
{
NetworkGenome NetworkGenomes1 = list[0].Fitness > list[1].Fitness ? list[0] : list[1];
NetworkGenome NetworkGenomes2 = list[0].Fitness > list[1].Fitness ? list[1] : list[0];
if (Utilities.Rnd.NextDouble() < this.Reprod.SelectFitterGenome)
{
return(NetworkGenomes1);
}
return(NetworkGenomes2);
}
List <NetworkGenome> list1 = new List <NetworkGenome>(3);
int index1 = (int)(Utilities.Rnd.NextDouble() * (double)list.Count);
list1.Add(list[index1]);
int index2 = (int)(Utilities.Rnd.NextDouble() * (double)list.Count);
if (list1.Contains(list[index2]))
{
index2 = (index2 + 1) % list.Count;
}
list1.Add(list[index2]);
int index3 = (int)(Utilities.Rnd.NextDouble() * (double)list.Count);
while (list1.Contains(list[index3]))
{
index3 = (index3 + 1) % list.Count;
}
list1.Add(list[index3]);
list1.Sort((Comparison <NetworkGenome>)((g, e) => e.Fitness.CompareTo(g.Fitness)));
if (Utilities.Rnd.NextDouble() < this.Reprod.SelectFitterGenome)
{
return(list[0]);
}
if (Utilities.Rnd.NextDouble() > this.Reprod.SelectFitterGenome)
{
return(list[1]);
}
return(list[2]);
}
/// <summary>
/// Computes the genome average novelty
/// based on k nearest neighbors and against the archive
/// </summary>
/// <param name="neatGenome"></param>
/// <param name="genomeList"></param>
/// <returns></returns>
public double computeNovelty(NetworkGenome neatGenome, List <NetworkGenome> genomeList)
{
config = KeepawayConfig.Load("KeepawayConfig.xml");
double novelty = 0.0;
//double dist = 0.0;
List <NetworkGenome> Genomes = genomeList;
int len = Genomes.Count + archive.Count;
NetworkGenome neatgenomes;
List <Pair <double, NetworkGenome> > noveltyList = new List <Pair <double, NetworkGenome> >();
//if (genomeList.Count == 0) novelty = 0.002;
foreach (NetworkGenome genome in genomeList)
{
//add a list of behaviors
if (neatGenome != genome)
{
noveltyList.Add(new Pair <double, NetworkGenome>(Behavior.BehaviorDistance(((NetworkGenome)genome).BehaviorType, neatGenome.BehaviorType), ((NetworkGenome)genome)));
}
}
//noveltyList.Sort(CompareFirst);
//easy break tires
noveltyList = noveltyList.OrderBy(o => o.First).ThenBy(o => o.Second.Fitness).ToList();
int neighbors = config.nearestNeighbors;
if (noveltyList.Count < config.nearestNeighbors)
{
neighbors = noveltyList.Count;
}
//test against k nearest neighbors
for (int i = 0; i < neighbors; i++)
{
novelty += noveltyList[i].First;
neatGenome.nearestNeighbors++;
}
//test against the archive
foreach (NetworkGenome inArchive in archive)
{
novelty += Behavior.BehaviorDistance(neatGenome.BehaviorType, inArchive.BehaviorType);
}
//average novelty of genome x
novelty /= (neighbors + archive.Count());
return(novelty);
}
private bool FreshInit()
{
NetworkGenome NetworkGenomes1 = new NetworkGenome(-1, 0, -1, -1, -1);
NetworkGenomes1.Nodes.Add(new NodeGene("Identity", NodeGene.NextId, 0, NodeType.Bias));
for (int index = 0; index < this.Init.Inputs; ++index)
{
NetworkGenomes1.Nodes.Add(new NodeGene("Identity", NodeGene.NextId, 0, NodeType.Input));
}
for (int index = 0; index < this.Init.Outputs; ++index)
{
NetworkGenomes1.Nodes.Add(new NodeGene("BipolarSigmoid", NodeGene.NextId, this.Init.MaxLayers - 1, NodeType.Output));
}
while (this.Current.Genomes.Count < this.Init.PopulationSize)
{
NetworkGenome NetworkGenomes2 = NetworkGenomes1.Clone() as NetworkGenome;
NetworkGenomes2.Id = NetworkGenome.NextId;
this.InitLinks(NetworkGenomes2);
double num1 = 1000000.0;
int index1 = 0;
for (int index2 = 0; index2 < this.species.Count; ++index2)
{
double num2 = this.species[index2].GenomeCompatibility(NetworkGenomes2);
if (num2 < num1)
{
num1 = num2;
index1 = index2;
}
}
if (num1 <= this.Speciate.Threshold)
{
this.species[index1].Genomes.Add(NetworkGenomes2);
NetworkGenomes2.Species = index1;
}
else
{
this.species.Add(new Species(0, 0, 0.0, NetworkGenomes2));
NetworkGenomes2.Species = this.species.Count - 1;
}
this.Current.Genomes.Add(NetworkGenomes2);
}
return(true);
}
private void InitLinks(NetworkGenome temp)
{
foreach (NodeGene NodeGenes1 in Enumerable.Where <NodeGene>((IEnumerable <NodeGene>)temp.Nodes, (Func <NodeGene, bool>)(nodes =>
{
if (nodes.Type != NodeType.Bias)
{
return(nodes.Type == NodeType.Input);
}
return(true);
})))
{
foreach (NodeGene NodeGenes2 in Enumerable.Where <NodeGene>((IEnumerable <NodeGene>)temp.Nodes, (Func <NodeGene, bool>)(nodes => nodes.Type == NodeType.Output)))
{
if (Utilities.Rnd.NextDouble() < this.Init.InitalConnectionPercentage)
{
temp.Links.Add(new LinkGene(HistoricalMarkings.GetLinkMarking(NodeGenes1.Id, NodeGenes2.Id, 0), NodeGenes1.Id, NodeGenes2.Id, Utilities.Rnd.NextDouble(-this.Mutate.WeightRange / 2.0, this.Mutate.WeightRange / 2.0)));
}
}
}
}
/// <summary>
/// returns the genome diversity
/// considers the k-nearest neighbors and the archive
/// </summary>
/// <param name="GenomesList"></param>
/// <param name="genomes"></param>
/// <returns></returns>
public double DiversityDistance(List <NetworkGenome> GenomesList, NetworkGenome genomes)
{
config = KeepawayConfig.Load("KeepawayConfig.xml");
List <NetworkGenome> Genomes = GenomesList;
double diversity_dist = 0;
List <Pair <double, NetworkGenome> > diversityList = new List <Pair <double, NetworkGenome> >();
foreach (NetworkGenome networkGenomes in Genomes)
{
if (networkGenomes != genomes)
{
diversityList.Add(new Pair <double, NetworkGenome>(this.GenomeCompatibility(genomes, networkGenomes), networkGenomes));
}
}
//diversityList.Sort(CompareFirstFirst);
//sort order
diversityList = diversityList.OrderBy(o => o.First).ThenBy(o => o.Second.Fitness).ToList();
int neighbors = config.nearestNeighbors;
//if list less than k nearestneighbors
if (diversityList.Count < config.nearestNeighbors)
{
neighbors = diversityList.Count;
}
//compute a sum of the first k nearestneighbors distances of genome x
for (int i = 0; i < neighbors; i++)
{
diversity_dist += diversityList[i].First;
genomes.nearestNeighbors++;
}
//test against the archive
foreach (NetworkGenome inArchive in archiveGD)
{
diversity_dist += this.GenomeCompatibility(genomes, inArchive);
}
//compute average diversity
genotype_Diversity = diversity_dist / ((neighbors + archiveGD.Count));
return(genotype_Diversity);
}
private bool TestInit()
{
this.TestRun = true;
if (this.Tests.Directory.test)
{
DirectoryInfo directoryInfo = new DirectoryInfo(this.Tests.Directory.path);
foreach (FileSystemInfo fileSystemInfo in directoryInfo.GetFiles("*.xml"))
{
NetworkGenome networkGenomes = NetworkGenome.LoadFromFile(fileSystemInfo.FullName);
if (networkGenomes != null)
{
this.Current.Genomes.Add(networkGenomes);
}
}
}
else
{
this.Current.Genomes.Add(NetworkGenome.LoadFromFile(this.Tests.Genome.path));
}
return(true);
}
public static void XorCreate(NetworkGenome sub, DecodedNetworks cppn)
{
SubstrateNodes substrateNode1 = sub.Nodes.Find((Predicate <NodeGene>)(n => n.Type == NodeType.Output)) as SubstrateNodes;
double[] inputs = new double[4];
int id = 0;
for (int index = 0; index < sub.Nodes.Count - 1; ++index)
{
SubstrateNodes substrateNode2 = sub.Nodes[index] as SubstrateNodes;
cppn.Flush();
inputs[0] = substrateNode2.Coordinate[0];
inputs[1] = substrateNode2.Coordinate[1];
inputs[2] = substrateNode1.Coordinate[0];
inputs[3] = substrateNode1.Coordinate[1];
cppn.SetInputs(inputs);
cppn.ActivateNetwork(5);
double[] outputs = cppn.GetOutputs();
sub.Links.Add(new LinkGene(id, substrateNode2.Id, substrateNode1.Id, outputs[0]));
}
}
private bool AddConnection(NetworkGenome temp)
{
List <NodeGene> list1 = new List <NodeGene>((IEnumerable <NodeGene>)temp.Nodes);
NodeGene source = list1[(int)(Utilities.Rnd.NextDouble() * (double)list1.Count)];
List <NodeGene> list2 = new List <NodeGene>(Enumerable.Where <NodeGene>((IEnumerable <NodeGene>)temp.Nodes, (Func <NodeGene, bool>)(nodes =>
{
if (nodes.Type == NodeType.Bias || nodes.Type == NodeType.Input)
{
return(false);
}
if (!this.Mutate.Recurrence)
{
return(nodes.Layer > source.Layer);
}
return(true);
})));
if (list2.Count < 1)
{
return(false);
}
NodeGene target = list2[(int)(Utilities.Rnd.NextDouble() * (double)list2.Count)];
if (Enumerable.Any <LinkGene>((IEnumerable <LinkGene>)temp.Links, (Func <LinkGene, bool>)(l =>
{
if (l.Source == source.Id)
{
return(l.Target == target.Id);
}
return(false);
})))
{
return(false);
}
temp.Links.Add(new LinkGene(0, source.Id, target.Id, Math.Max(-this.Mutate.WeightRange / 2.0, Math.Min(this.Mutate.WeightRange / 2.0, Utilities.Rnd.NextGuassian(0.0, 0.1) * this.Mutate.WeightRange / 2.0)))
{
Id = HistoricalMarkings.GetLinkMarking(source.Id, target.Id, this.Generation)
});
return(true);
}
//phillip
static void LinkCreation(NetworkGenome sub)
{
LinkGene temp;
int linkId = 0;
for (int i = 0; i < sub.Nodes.Count; i++)
{
for (int j = 0; j < sub.Nodes.Count && sub.Nodes[i].Layer > sub.Nodes[j].Layer; j++)
{
if (sub.Nodes[i].Layer - sub.Nodes[j].Layer == 1)
{
temp = new LinkGene();
temp.Id = linkId;
linkId++;
temp.Source = sub.Nodes[j].Id;
temp.Target = sub.Nodes[i].Id;
temp.Weight = 0;
sub.Links.Add(temp);
}
}
}
}
private void MutateGenome(NetworkGenome temp)
{
double num1 = Utilities.Rnd.NextDouble() * (this.Mutate.AddConnection + this.Mutate.AddNode + this.Mutate.ChangeNodeFunction + this.Mutate.DeleteConnection + this.Mutate.MutateWeights) - this.Mutate.DeleteConnection;
if (num1 <= 0.0 && this.DelectConnection(temp))
{
return;
}
double num2 = num1 - this.Mutate.ChangeNodeFunction;
if (num2 <= 0.0 && this.ChangeNode(temp))
{
return;
}
double num3 = num2 - this.Mutate.AddNode;
if (num3 <= 0.0 && this.AddNode(temp) || num3 - this.Mutate.AddConnection <= 0.0 && this.AddConnection(temp))
{
return;
}
this.MutateWeights(temp);
}
private NetworkGenome CreateOneOffspringFromSpecies(List <NetworkGenome> list)
{
NetworkGenome parent1 = this.SelectGenome(list);
NetworkGenome temp;
if (Utilities.Rnd.NextDouble() < this.Reprod.AsexualProbability || list.Count < 2)
{
temp = parent1.Clone() as NetworkGenome;
temp.Age = 0;
temp.Fitness = 0.0;
temp.Id = NetworkGenome.NextId;
temp.Parent1 = parent1.Id;
temp.Parent2 = -1;
this.MutateGenome(temp);
}
else
{
NetworkGenome parent2 = this.SelectGenome(list, parent1);
temp = this.Recombine(parent1, parent2);
}
this.DetermineSpecies(temp);
return(temp);
}
private void PerformTest()
{
if (this.Tests.Directory.test || this.Tests.Genome.test)
{
int num = this.Evaluator(this.Current.Genomes, true) ? 1 : 0;
if (this.Tests.Genome.test)
{
NetworkGenome.SaveToFile(this.Current.Genomes[0], this.Tests.Genome.path);
}
else
{
using (StreamWriter streamWriter = new StreamWriter(this.Tests.Directory.path + "Results.txt"))
{
for (int index = 0; index < this.Current.Genomes.Count; ++index)
{
streamWriter.WriteLine(this.Current.Genomes[index].Fitness);
}
}
}
}
else
{
if (!this.Tests.ChampionsAtEnd.test)
{
return;
}
int num = this.Evaluator(this.Champions, true) ? 1 : 0;
using (StreamWriter streamWriter = new StreamWriter(this.Tests.ChampionsAtEnd.path + "ChampResults.txt"))
{
for (int index = 0; index < this.Champions.Count; ++index)
{
streamWriter.WriteLine(this.Champions[index].Fitness);
}
}
}
}
private NetworkGenome Recombine(NetworkGenome parent1, NetworkGenome parent2)
{
NetworkGenome NetworkGenomes1 = parent1;
if (parent1.Fitness < parent2.Fitness)
{
parent1 = parent2;
parent2 = NetworkGenomes1;
}
NetworkGenome NetworkGenomes2 = new NetworkGenome();
NetworkGenomes2.Id = NetworkGenome.NextId;
NetworkGenomes2.Parent1 = parent1.Id;
NetworkGenomes2.Parent2 = parent2.Id;
List <NodeGene> list1 = new List <NodeGene>(Enumerable.Where <NodeGene>((IEnumerable <NodeGene>)parent1.Nodes, (Func <NodeGene, bool>)(genes => parent2.Nodes.Contains(genes))));
list1.Sort();
List <NodeGene> list2 = new List <NodeGene>(Enumerable.Where <NodeGene>((IEnumerable <NodeGene>)parent2.Nodes, (Func <NodeGene, bool>)(genes => parent1.Nodes.Contains(genes))));
list2.Sort();
List <LinkGene> list3 = new List <LinkGene>(Enumerable.Where <LinkGene>((IEnumerable <LinkGene>)parent1.Links, (Func <LinkGene, bool>)(genes => parent2.Links.Contains(genes))));
list3.Sort();
List <LinkGene> list4 = new List <LinkGene>(Enumerable.Where <LinkGene>((IEnumerable <LinkGene>)parent2.Links, (Func <LinkGene, bool>)(genes => parent1.Links.Contains(genes))));
list4.Sort();
bool flag = Utilities.Rnd.NextDouble() < this.Reprod.RecombineExcessFromLessFit;
NetworkGenome NetworkGenomes3 = parent1;
NetworkGenome notChoice = parent2;
if (flag)
{
NetworkGenomes3 = parent2;
notChoice = parent1;
}
List <NodeGene> list5 = new List <NodeGene>(Enumerable.Where <NodeGene>((IEnumerable <NodeGene>)NetworkGenomes3.Nodes, (Func <NodeGene, bool>)(genes => !notChoice.Nodes.Contains(genes))));
list5.Sort();
List <LinkGene> list6 = new List <LinkGene>(Enumerable.Where <LinkGene>((IEnumerable <LinkGene>)NetworkGenomes3.Links, (Func <LinkGene, bool>)(genes => !notChoice.Links.Contains(genes))));
list6.Sort();
for (int index = 0; index < list1.Count; ++index)
{
if (Utilities.Rnd.NextDouble() < this.Reprod.SelectFitterGene)
{
NetworkGenomes2.Nodes.Add(list1[index]);
}
else
{
NetworkGenomes2.Nodes.Add(list2[index]);
}
}
for (int index = 0; index < list3.Count; ++index)
{
if (Utilities.Rnd.NextDouble() < this.Reprod.SelectFitterGene)
{
NetworkGenomes2.Links.Add(list3[index]);
}
else
{
NetworkGenomes2.Links.Add(list4[index]);
}
}
NetworkGenomes2.Nodes.AddRange((IEnumerable <NodeGene>)list5);
NetworkGenomes2.Links.AddRange((IEnumerable <LinkGene>)list6);
return(NetworkGenomes2);
}
/// <summary>
/// compute the distance measure
/// </summary>
/// <param name="genome1"></param>
/// <param name="genome2"></param>
/// <returns></returns>
internal double GenomeCompatibility(NetworkGenome genome1, NetworkGenome genome2)
{
double num1 = 0.0;
List <LinkGene> list1 = new List <LinkGene>();
List <NodeGene> list2 = new List <NodeGene>();
List <LinkGene> list3 = new List <LinkGene>();
List <NodeGene> list4 = new List <NodeGene>();
genome1.Nodes.Sort();
genome1.Links.Sort();
int num3 = 0;
genome2.Nodes.Sort();
genome2.Links.Sort();
list1.Clear();
list2.Clear();
list3.Clear();
list4.Clear();
int index1 = 0;
int index2 = 0;
//finding the last nodes ids
while (index1 < genome1.Nodes.Count && index2 < genome2.Nodes.Count)
{
if (genome1.Nodes[index1].Id == genome2.Nodes[index2].Id) // common nodes between genomes
{
list2.Add(genome1.Nodes[index1]); //add nodes of genome 1 to list2
list4.Add(genome2.Nodes[index2]); // add nodes of genome 2 to list4
++index1; //increase index of nodes of genome 1
++index2; //increase index of nodes of genome 2
}
else if (genome1.Nodes[index1].Id > genome2.Nodes[index2].Id) //genome 1 id greater than genome 2 id , checking if its a disjoint or excess
{
++num3;
++index2;
}
else
{
++num3;
++index1;
}
}
num1 += Species.Compatible.Disjoint * (double)(num3 + genome1.Nodes.Count + genome2.Nodes.Count - (index1 + index2));
int index3 = 0;
int index4 = 0;
int num4 = 0;
while (index3 < genome1.Links.Count && index4 < genome2.Links.Count)
{
if (genome1.Links[index3].Id == genome2.Links[index4].Id)
{
list1.Add(genome1.Links[index3]);
list3.Add(genome2.Links[index4]);
++index3;
++index4;
}
else if (genome1.Links[index3].Id > genome2.Links[index4].Id)
{
++num4;
++index4;
}
else
{
++num4;
++index3;
}
}
num1 += Species.Compatible.Disjoint * (double)(num4 + genome1.Links.Count + genome2.Links.Count - (index3 + index4));
for (int index5 = 0; index5 < list1.Count; ++index5)
{
num1 += Math.Abs(list1[index5].Weight - list3[index5].Weight) * Species.Compatible.Weight;
}
for (int index5 = 0; index5 < list2.Count; ++index5)
{
num1 += list2[index5].Function == list4[index5].Function ? 0.0 : Species.Compatible.Function;
}
return(num1);
}
private void button1_Click(object sender, EventArgs e)
{
OpenFileDialog openFileDialog = new OpenFileDialog();
if (openFileDialog.ShowDialog() != DialogResult.OK)
{
return;
}
NetworkGenome networkGenome = NetworkGenome.LoadFromFile(openFileDialog.FileName);
Graph graph = new Graph("Genome: " + (object)networkGenome.Id);
graph.GraphAttr.LayerDirection = LayerDirection.BT;
graph.Directed = true;
graph.GraphAttr.LayerSep = 10.0;
graph.BuildNodeHierarchy = true;
graph.GraphAttr.OptimizeLabelPositions = true;
graph.GraphAttr.NodeAttr.Padding = 1.0;
int num = networkGenome.Nodes.Find((Predicate <NodeGene>)(n => n.Type == NodeType.Output)).Layer;
ArrayList arrayList1 = new ArrayList();
for (int i = 0; i < num + 1; ++i)
{
ArrayList arrayList2 = new ArrayList();
foreach (NodeGene nodeGene in Enumerable.Where <NodeGene>((IEnumerable <NodeGene>)networkGenome.Nodes, (Func <NodeGene, bool>)(node => node.Layer == i)))
{
arrayList2.Add((object)nodeGene.Id.ToString());
}
graph.AddSameLayer((IEnumerable)arrayList2);
}
graph.GraphAttr.Orientation = Microsoft.Glee.Drawing.Orientation.Landscape;
graph.NeedCalculateLayout = true;
graph.GraphAttr.Fontsize = 8;
graph.GraphAttr.EdgeAttr.Fontsize = 7;
graph.Cluster = true;
graph.GraphAttr.LabelFloat = LabelFloat.Float;
using (List <LinkGene> .Enumerator enumerator = networkGenome.Links.GetEnumerator())
{
while (enumerator.MoveNext())
{
LinkGene link = enumerator.Current;
if (link.Weight != 0.0 && link.Source != -1)
{
//Edge edge = graph.AddEdge(link.Source.ToString(), link.Id.ToString(), link.Target.ToString());
Edge edge = graph.AddEdge(link.Source.ToString(), link.Weight.ToString("0.##"), link.Target.ToString());
edge.Attr.Fontsize = 7;
edge.EdgeAttr.Fontsize = 7;
if (link.Weight <= 0.0)
{
edge.Attr.Color = Microsoft.Glee.Drawing.Color.Red;
}
NodeGene nodeGene1 = networkGenome.Nodes.Find((Predicate <NodeGene>)(n => n.Id == link.Source));
NodeGene nodeGene2 = networkGenome.Nodes.Find((Predicate <NodeGene>)(n => n.Id == link.Target));
edge.Attr.Weight = Math.Max(nodeGene1.Layer - nodeGene2.Layer, 0);
edge.UserData = (object)link;
}
}
}
for (int index = 0; index < networkGenome.Nodes.Count; ++index)
{
(graph.FindNode(networkGenome.Nodes[index].Id.ToString()) ?? graph.AddNode(networkGenome.Nodes[index].Id.ToString())).UserData = (object)networkGenome.Nodes[index];
}
foreach (NodeGene nodeGene in networkGenome.Nodes)
{
if (nodeGene.Layer == 0)
{
Visualizers.CreateSourceNode(graph.FindNode(nodeGene.Id.ToString()));
}
else if (nodeGene.Layer == num)
{
this.CreateTargetNode(graph.FindNode(nodeGene.Id.ToString()));
}
else
{
this.CreateHiddenNode(graph.FindNode(nodeGene.Id.ToString()));
}
}
this.gViewer.Graph = graph;
}
private void MutateWeights(NetworkGenome temp)
{
double num1 = 0.0;
for (int index = 0; index < this.Mutate.WeightProbabilities.Count; ++index)
{
num1 += this.Mutate.WeightProbabilities[index].Probability;
}
double num2 = Utilities.Rnd.NextDouble() * num1;
Mutation.WeightMutation weightMutation = new Mutation.WeightMutation();
for (int index = 0; index < this.Mutate.WeightProbabilities.Count; ++index)
{
num2 -= this.Mutate.WeightProbabilities[index].Probability;
if (num2 <= 0.0)
{
weightMutation = this.Mutate.WeightProbabilities[index];
break;
}
}
if (weightMutation.Proportional)
{
List <LinkGene> list = new List <LinkGene>(temp.MutatableLinks);
for (int index = 0; index < list.Count; ++index)
{
if (Utilities.Rnd.NextDouble() < weightMutation.Amount)
{
if (weightMutation.Delta)
{
list[index].Weight += weightMutation.Normal ? Utilities.Rnd.NextGuassian(0.0, 0.3) * this.Mutate.WeightRange / 10.0 : Utilities.Rnd.NextDouble(-this.Mutate.WeightRange / 10.0, this.Mutate.WeightRange / 10.0);
}
else
{
list[index].Weight = weightMutation.Normal ? Utilities.Rnd.NextGuassian(0.0, 0.3) * this.Mutate.WeightRange / 2.0 : Utilities.Rnd.NextDouble(-this.Mutate.WeightRange / 2.0, this.Mutate.WeightRange / 2.0);
}
list[index].Weight = Math.Max(-this.Mutate.WeightRange / 2.0, Math.Min(this.Mutate.WeightRange / 2.0, list[index].Weight));
}
}
}
else
{
for (int index1 = 0; (double)index1 < weightMutation.Amount && Enumerable.Count <LinkGene>(temp.MutatableLinks) > 0; ++index1)
{
int index2 = Utilities.Rnd.Next(Enumerable.Count <LinkGene>(temp.MutatableLinks));
LinkGene LinkGenes = Enumerable.ElementAt <LinkGene>(temp.MutatableLinks, index2);
LinkGenes.Mutated = true;
if (weightMutation.Delta)
{
LinkGenes.Weight += weightMutation.Normal ? Utilities.Rnd.NextGuassian(0.0, 1.0) * this.Mutate.WeightRange / 4.0 : Utilities.Rnd.NextDouble(-this.Mutate.WeightRange / 8.0, this.Mutate.WeightRange / 8.0);
}
else
{
LinkGenes.Weight = weightMutation.Normal ? Utilities.Rnd.NextGuassian(0.0, 0.3) * this.Mutate.WeightRange / 2.0 : Utilities.Rnd.NextDouble(-this.Mutate.WeightRange / 2.0, this.Mutate.WeightRange / 2.0);
}
LinkGenes.Weight = Math.Max(-this.Mutate.WeightRange / 2.0, Math.Min(this.Mutate.WeightRange / 2.0, LinkGenes.Weight));
}
for (int index = 0; index < temp.Links.Count; ++index)
{
temp.Links[index].Mutated = false;
}
}
}
