/// <summary>
///
/// </summary>
/// <param name="doc"></param>
/// <param name="genome"></param>
/// <param name="activationFn">Not strictly part of a genome. But it is useful to document which function
/// the genome is supposed to run against when decoded into a network.</param>
public static void Write(XmlNode parentNode, NeatGenome genome, IActivationFunction activationFn)
{
//----- Start writing. Create document root node.
XmlElement xmlGenome = XmlUtilities.AddElement(parentNode, "genome");
XmlUtilities.AddAttribute(xmlGenome, "id", genome.GenomeId.ToString());
XmlUtilities.AddAttribute(xmlGenome, "species-id", genome.SpeciesId.ToString());
XmlUtilities.AddAttribute(xmlGenome, "age", genome.GenomeAge.ToString());
XmlUtilities.AddAttribute(xmlGenome, "fitness", genome.Fitness.ToString("0.00"));
XmlUtilities.AddAttribute(xmlGenome, "objective-fitness", genome.ObjectiveFitness.ToString("0.00"));
XmlUtilities.AddAttribute(xmlGenome, "activation-fn-id", activationFn.FunctionId);
//----- Write neurons.
XmlElement xmlNeurons = XmlUtilities.AddElement(xmlGenome, "neurons");
foreach (NeuronGene neuronGene in genome.NeuronGeneList)
{
WriteNeuron(xmlNeurons, neuronGene);
}
//----- Write Connections.
XmlElement xmlConnections = XmlUtilities.AddElement(xmlGenome, "connections");
foreach (ConnectionGene connectionGene in genome.ConnectionGeneList)
{
WriteConnectionGene(xmlConnections, connectionGene);
}
}
//public static void Write(XmlNode parentNode, ModularNetwork network, IActivationFunction activationFn)
//{
// //----- Start writing. Create document root node.
// XmlElement xmlNetwork = XmlUtilities.AddElement(parentNode, "network");
// if (activationFn != null)
// {
// XmlUtilities.AddAttribute(xmlNetwork, "activation-fn-id", activationFn.FunctionId);
// }
// //----- Write neurons.
// XmlElement xmlNeurons = XmlUtilities.AddElement(xmlNetwork, "neurons");
// foreach (NeuronGene neuronGene in genome.NeuronGeneList)
// WriteNeuron(xmlNeurons, neuronGene);
// //----- Write Connections.
// XmlElement xmlConnections = XmlUtilities.AddElement(xmlNetwork, "connections");
// foreach (FloatFastConnection connectionGene in network.connections)
// WriteConnection(xmlConnections, connectionGene);
//}
public static void Write(XmlNode parentNode, NeatGenome.NeatGenome genome, IActivationFunction activationFn)
{
//----- Start writing. Create document root node.
XmlElement xmlNetwork = XmlUtilities.AddElement(parentNode, "network");
if (activationFn != null)
{
XmlUtilities.AddAttribute(xmlNetwork, "activation-fn-id", activationFn.FunctionId);
XmlUtilities.AddAttribute(xmlNetwork, "adaptable", "false");
}
//----- Write neurons.
XmlElement xmlNeurons = XmlUtilities.AddElement(xmlNetwork, "neurons");
foreach (NeuronGene neuronGene in genome.NeuronGeneList)
{
WriteNeuron(xmlNeurons, neuronGene);
}
//----- Write Connections.
XmlElement xmlConnections = XmlUtilities.AddElement(xmlNetwork, "connections");
foreach (ConnectionGene connectionGene in genome.ConnectionGeneList)
{
WriteConnection(xmlConnections, connectionGene);
}
}
/// <param name="activationFn">Not strictly part of a genome. But it is useful to document which function
/// the genome is supposed to run against when decoded into a network.</param>
public static void Write(XmlNode parentNode, NeatGenome genome, IActivationFunction activationFn)
{
//----- Start writing. Create document root node.
XmlElement xmlGenome = XmlUtilities.AddElement(parentNode, "genome");
XmlUtilities.AddAttribute(xmlGenome, "id", genome.GenomeId.ToString());
XmlUtilities.AddAttribute(xmlGenome, "species-id", genome.SpeciesId.ToString());
XmlUtilities.AddAttribute(xmlGenome, "age", genome.GenomeAge.ToString());
XmlUtilities.AddAttribute(xmlGenome, "fitness", genome.Fitness.ToString("0.00"));
XmlUtilities.AddAttribute(xmlGenome, "activation-fn-id", activationFn.FunctionId);
//----- Write neurons.
XmlElement xmlNeurons = XmlUtilities.AddElement(xmlGenome, "neurons");
foreach (NeuronGene neuronGene in genome.NeuronGeneList)
{
WriteNeuron(xmlNeurons, neuronGene);
}
//----- Write modules.
XmlElement xmlModules = XmlUtilities.AddElement(xmlGenome, "modules");
foreach (ModuleGene moduleGene in genome.ModuleGeneList)
{
WriteModule(xmlModules, moduleGene);
}
//----- Write Connections.
XmlElement xmlConnections = XmlUtilities.AddElement(xmlGenome, "connections");
foreach (ConnectionGene connectionGene in genome.ConnectionGeneList)
{
WriteConnectionGene(xmlConnections, connectionGene);
}
//----- Write beahavior
if (genome.Behavior != null)
{
if (genome.Behavior.behaviorList != null)
{
XmlElement xmlBehavior = XmlUtilities.AddElement(xmlGenome, "behavior");
WriteBehavior(xmlBehavior, genome.objectives, genome.Behavior);
}
}
//----- JUSTIN: Write grid coords
if (genome.GridCoords != null)
{
XmlElement xmlGridCoords = XmlUtilities.AddElement(xmlGenome, "grid");
WriteGridCoords(xmlGridCoords, genome.GridCoords);
}
//----- JUSTIN: Write trajectory
if (genome.Behavior.trajectory != null && genome.Behavior.trajectory.Count > 0)
{
XmlElement xmlTrajectory = XmlUtilities.AddElement(xmlGenome, "trajectory");
WriteTrajectory(xmlTrajectory, genome.Behavior.trajectory);
}
}
private static void WriteConnection(XmlElement xmlConnections, FloatFastConnection connectionGene)
{
XmlElement xmlConnection = XmlUtilities.AddElement(xmlConnections, "connection");
XmlUtilities.AddAttribute(xmlConnection, "src-id", connectionGene.sourceNeuronIdx.ToString());
XmlUtilities.AddAttribute(xmlConnection, "tgt-id", connectionGene.targetNeuronIdx.ToString());
XmlUtilities.AddAttribute(xmlConnection, "weight", connectionGene.weight.ToString());
}
private static void WriteNeuron(XmlElement xmlNeurons, NeuronGene neuronGene)
{
XmlElement xmlNeuron = XmlUtilities.AddElement(xmlNeurons, "neuron");
XmlUtilities.AddAttribute(xmlNeuron, "id", neuronGene.InnovationId.ToString());
XmlUtilities.AddAttribute(xmlNeuron, "type", XmlUtilities.GetNeuronTypeString(neuronGene.NeuronType));
XmlUtilities.AddAttribute(xmlNeuron, "activationFunction", neuronGene.ActivationFunction.FunctionId);
}
private static void WriteConnection(XmlElement xmlConnections, ConnectionGene connectionGene)
{
XmlElement xmlConnection = XmlUtilities.AddElement(xmlConnections, "connection");
XmlUtilities.AddAttribute(xmlConnection, "src-id", connectionGene.SourceNeuronId.ToString());
XmlUtilities.AddAttribute(xmlConnection, "tgt-id", connectionGene.TargetNeuronId.ToString());
XmlUtilities.AddAttribute(xmlConnection, "weight", connectionGene.Weight.ToString("R"));
}
public static void WriteGenomeList(XmlNode parentNode, GenomeList g)
{
XmlElement xmlPopulation = XmlUtilities.AddElement(parentNode, "population");
foreach (IGenome genome in g)
{
genome.Write(xmlPopulation);
}
}
private static void WriteNeuron(XmlElement xmlNeurons, NeuronGene neuronGene)
{
XmlElement xmlNeuron = XmlUtilities.AddElement(xmlNeurons, "neuron");
XmlUtilities.AddAttribute(xmlNeuron, "id", neuronGene.InnovationId.ToString());
XmlUtilities.AddAttribute(xmlNeuron, "type", XmlUtilities.GetNeuronTypeString(neuronGene.NeuronType));
XmlUtilities.AddAttribute(xmlNeuron, "activationFunction", neuronGene.ActivationFunction.FunctionId);
XmlUtilities.AddAttribute(xmlNeuron, "bias", neuronGene.Bias.ToString());
XmlUtilities.AddAttribute(xmlNeuron, "layer", neuronGene.Layer.ToString());
// newNode.attributes["layer"] = neuronGene.Layer;
}
public static void Write(XmlNode parentNode, Population p, IActivationFunction activationFn)
{
XmlElement xmlPopulation = XmlUtilities.AddElement(parentNode, "population");
XmlUtilities.AddAttribute(xmlPopulation, "activation-fn-id", activationFn.FunctionId);
foreach (IGenome genome in p.GenomeList)
{
genome.Write(xmlPopulation);
}
}
private static void WriteConnectionGene(XmlElement xmlConnections, ConnectionGene connectionGene)
{
XmlElement xmlConnectionGene = XmlUtilities.AddElement(xmlConnections, "connection");
XmlUtilities.AddAttribute(xmlConnectionGene, "innov-id", connectionGene.InnovationId.ToString());
XmlUtilities.AddAttribute(xmlConnectionGene, "src-id", connectionGene.SourceNeuronId.ToString());
XmlUtilities.AddAttribute(xmlConnectionGene, "tgt-id", connectionGene.TargetNeuronId.ToString());
XmlUtilities.AddAttribute(xmlConnectionGene, "weight", connectionGene.Weight.ToString("R"));
XmlUtilities.AddAttribute(xmlConnectionGene, "learningrate", connectionGene.learningRate.ToString("R"));
XmlUtilities.AddAttribute(xmlConnectionGene, "A", connectionGene.A.ToString("R"));
XmlUtilities.AddAttribute(xmlConnectionGene, "B", connectionGene.B.ToString("R"));
XmlUtilities.AddAttribute(xmlConnectionGene, "C", connectionGene.C.ToString("R"));
XmlUtilities.AddAttribute(xmlConnectionGene, "D", connectionGene.D.ToString("R"));
}
public static void Write(XmlNode parentNode, NeatGenome genome)
{
//----- Start writing. Create document root node.
XmlElement xmlGenome = XmlUtilities.AddElement(parentNode, "genome");
XmlUtilities.AddAttribute(xmlGenome, "id", genome.GenomeId.ToString());
XmlUtilities.AddAttribute(xmlGenome, "species-id", genome.SpeciesId.ToString());
XmlUtilities.AddAttribute(xmlGenome, "age", genome.GenomeAge.ToString());
XmlUtilities.AddAttribute(xmlGenome, "fitness", genome.Fitness.ToString("0.00"));
XmlUtilities.AddAttribute(xmlGenome, "realfitness", genome.RealFitness.ToString("0.00"));
XmlUtilities.AddAttribute(xmlGenome, "adaptable", genome.networkAdaptable.ToString());
XmlUtilities.AddAttribute(xmlGenome, "modulated", genome.networkModulatory.ToString());
// Schrum: Extra properties necessary for multimodal networks to make sense
XmlUtilities.AddAttribute(xmlGenome, "outputsperpolicy", genome.OutputsPerPolicy.ToString());
//----- Write neurons.
XmlElement xmlNeurons = XmlUtilities.AddElement(xmlGenome, "neurons");
foreach (NeuronGene neuronGene in genome.NeuronGeneList)
{
WriteNeuron(xmlNeurons, neuronGene);
}
//----- Write modules.
XmlElement xmlModules = XmlUtilities.AddElement(xmlGenome, "modules");
foreach (ModuleGene moduleGene in genome.ModuleGeneList)
{
WriteModule(xmlModules, moduleGene);
}
//----- Write connections.
XmlElement xmlConnections = XmlUtilities.AddElement(xmlGenome, "connections");
foreach (ConnectionGene connectionGene in genome.ConnectionGeneList)
{
WriteConnectionGene(xmlConnections, connectionGene);
}
//----- Write beahavior
if (genome.Behavior != null)
{
if (genome.Behavior.behaviorList != null)
{
XmlElement xmlBehavior = XmlUtilities.AddElement(xmlGenome, "behavior");
WriteBehavior(xmlBehavior, genome.Behavior);
}
}
}
public static void Write(XmlNode parentNode, FloatFastConcurrentNetwork network, IActivationFunction activationFn)
{
//----- Start writing. Create document root node.
XmlElement xmlNetwork = XmlUtilities.AddElement(parentNode, "network");
XmlUtilities.AddAttribute(xmlNetwork, "activation-fn-id", activationFn.FunctionId);
//----- Write Connections.
XmlElement xmlConnections = XmlUtilities.AddElement(xmlNetwork, "connections");
foreach (FloatFastConnection connectionGene in network.connectionArray)
{
WriteConnection(xmlConnections, connectionGene);
}
}
private static void WriteModule(XmlElement xmlModules, ModuleGene moduleGene)
{
XmlElement xmlModule = XmlUtilities.AddElement(xmlModules, "module");
XmlUtilities.AddAttribute(xmlModule, "id", moduleGene.InnovationId.ToString());
XmlUtilities.AddAttribute(xmlModule, "function", moduleGene.Function.FunctionId);
int index = 0;
foreach (uint inputId in moduleGene.InputIds)
{
XmlElement inputGene = XmlUtilities.AddElement(xmlModule, "input");
XmlUtilities.AddAttribute(inputGene, "id", inputId.ToString());
XmlUtilities.AddAttribute(inputGene, "order", (index++).ToString());
}
index = 0;
foreach (uint outputId in moduleGene.OutputIds)
{
XmlElement outputGene = XmlUtilities.AddElement(xmlModule, "output");
XmlUtilities.AddAttribute(outputGene, "id", outputId.ToString());
XmlUtilities.AddAttribute(outputGene, "order", (index++).ToString());
}
}
