public GeomPlayerSubstrate(bool useBias,
IActivationFunction activationFunction, int cppnOutIndex)
{
m_delta = 2.0f / 5.0f;
m_start = -1.0f + (m_delta * 0.5f);
m_activationFunction = activationFunction;
m_neurons = new NeuronGeneList(m_inputsCount + m_outputsCount + (m_useBias ? 1 : 0));
uint curNeurId = 0;
if (m_useBias)
{
m_neurons.Add(new NeuronGene(curNeurId++, NeuronType.Bias, ActivationFunctionFactory.GetActivationFunction("NullFn")));
}
for (int i = 0; i < m_inputsCount; i++)
{
m_neurons.Add(new NeuronGene(curNeurId++, NeuronType.Input, ActivationFunctionFactory.GetActivationFunction("NullFn")));
}
for (int i = 0; i < m_outputsCount; i++)
{
m_neurons.Add(new NeuronGene(curNeurId++, NeuronType.Output, m_activationFunction));
}
}
// ControllerSubstrate constructor
public ControllerSubstrate(uint input, uint output, uint hidden, IActivationFunction function, uint rgbSize = 10) : base(input, output, hidden, function)
{
rgbOneDimension = rgbSize;
colorArraySize = rgbOneDimension * rgbOneDimension;
headingArraySize = 8;
neurons.Clear();
// SharpNEAT requires that the neuron list be in this order: bias|input|output|hidden
neurons = new NeuronGeneList((int)(inputCount + outputCount + hiddenCount));
// set up the bias nodes
for (uint a = 0; a < biasCount; a++)
{
neurons.Add(new NeuronGene(a, NeuronType.Bias, ActivationFunctionFactory.GetActivationFunction("Linear"), 0.0f));
}
// set up the input nodes
for (uint a = 0; a < inputCount; a++)
{
neurons.Add(new NeuronGene(a + biasCount, NeuronType.Input, ActivationFunctionFactory.GetActivationFunction("Linear"), 0.0f));
}
// set up the output nodes
for (uint a = 0; a < outputCount; a++)
{
neurons.Add(new NeuronGene(a + biasCount + inputCount, NeuronType.Output, ActivationFunctionFactory.GetActivationFunction("BipolarSigmoid"), 1.0f));
}
// set up the hidden nodes
for (uint a = 0; a < hiddenCount; a++)
{
neurons.Add(new NeuronGene(a + biasCount + inputCount + outputCount, NeuronType.Hidden, ActivationFunctionFactory.GetActivationFunction("BipolarSigmoid"), 0.5f));
}
}
public BallOwnerAwareSubstrate(int rows, int cols, IActivationFunction activationFunction)
{
m_rows = rows;
m_cols = cols;
m_rowDelta = 2.0f / m_rows;
m_colDelta = 2.0f / m_cols;
m_activationFunction = activationFunction;
m_neurons = new NeuronGeneList(2 * (m_rows * m_cols) + (m_useBias ? 1 : 0));
uint curNeurId = 0;
if (m_useBias)
{
m_neurons.Add(new NeuronGene(curNeurId++, NeuronType.Bias, ActivationFunctionFactory.GetActivationFunction("NullFn")));
}
for (int i = 0, len = m_rows * m_cols; i < len; i++)
{
m_neurons.Add(new NeuronGene(curNeurId++, NeuronType.Input, ActivationFunctionFactory.GetActivationFunction("NullFn")));
}
m_neurons.Add(new NeuronGene(curNeurId++, NeuronType.Input, ActivationFunctionFactory.GetActivationFunction("NullFn")));
for (int i = 0, len = m_rows * m_cols; i < len; i++)
{
m_neurons.Add(new NeuronGene(curNeurId++, NeuronType.Output, m_activationFunction));
}
}
/// <summary>
/// Performs multiple generations of the evolutionary algorithm.
/// </summary>
public void evolve(int generations)
{
for (int j = 0; j < generations; j++)
{
oneGeneration(j);
}
LogOutput.Close();
XmlDoc = new XmlDocument();
XmlGenomeWriterStatic.Write(XmlDoc, (NeatGenome)EA.BestGenome, ActivationFunctionFactory.GetActivationFunction("NullFn"));
OutputFileInfo = new FileInfo(Path.Combine(OutputFolder, "bestGenome.xml"));
XmlDoc.Save(OutputFileInfo.FullName);
//if doing novelty search, write out archive
if (experiment.DefaultNeatParameters.noveltySearch)
{
XmlDocument archiveout = new XmlDocument();
XmlPopulationWriter.WriteGenomeList(archiveout, EA.noveltyFixed.archive);
OutputFileInfo = new FileInfo(Path.Combine(OutputFolder, "archive.xml"));
archiveout.Save(OutputFileInfo.FullName);
}
// dump the MapElites grid contents (empty if we aren'type doing ME and we aren'type tracking ME-style-grid for some other algorithm)
XmlDocument gridout = new XmlDocument();
XmlPopulationWriter.WriteGenomeList(gridout, EA.meDumpGrid());
OutputFileInfo = new FileInfo(Path.Combine(OutputFolder, "finalgrid.xml"));
gridout.Save(OutputFileInfo.FullName);
}
public TwoLayerSandwichSubstrate(int rows, int cols, bool useBias,
IActivationFunction activationFunction, int cppnOutIndex)
{
m_rows = rows;
m_cols = cols;
m_useBias = useBias;
m_cppnOutIndex = cppnOutIndex;
m_rowDelta = 2.0f / m_rows;
m_colDelta = 2.0f / m_cols;
m_activationFunction = activationFunction;
m_neurons = new NeuronGeneList(2 * (m_rows * m_cols) + (m_useBias ? 1 : 0));
uint curNeurId = 0;
if (m_useBias)
{
m_neurons.Add(new NeuronGene(curNeurId++, NeuronType.Bias, ActivationFunctionFactory.GetActivationFunction("NullFn")));
}
for (int i = 0, len = m_rows * m_cols; i < len; i++)
{
m_neurons.Add(new NeuronGene(curNeurId++, NeuronType.Input, ActivationFunctionFactory.GetActivationFunction("NullFn")));
}
for (int i = 0, len = m_rows * m_cols; i < len; i++)
{
m_neurons.Add(new NeuronGene(curNeurId++, NeuronType.Output, m_activationFunction));
}
}
public void ZeroInputTest()
{
var function = ActivationFunctionFactory.Get(EActivationFunctionType.Sum);
var result = function.Impuls(0);
Assert.AreEqual(0, result);
}
private static Neuron ReadNeuron(XmlElement xmlNeuron)
{
uint id = uint.Parse(XmlUtilities.GetAttributeValue(xmlNeuron, "id"));
NeuronType neuronType = XmlUtilities.GetNeuronType(XmlUtilities.GetAttributeValue(xmlNeuron, "type"));
string activationFn = XmlUtilities.GetAttributeValue(xmlNeuron, "activationFunction");
return(new Neuron(ActivationFunctionFactory.GetActivationFunction(activationFn), neuronType, id));
}
public void NegativeInputTest()
{
var function = ActivationFunctionFactory.Get(EActivationFunctionType.Sum);
var result = function.Impuls(-1);
Assert.AreEqual(-1, result);
}
private static NeuronGene ReadNeuronGene(XmlElement xmlNeuronGene)
{
uint id = uint.Parse(XmlUtilities.GetAttributeValue(xmlNeuronGene, "id"));
NeuronType neuronType = XmlUtilities.GetNeuronType(XmlUtilities.GetAttributeValue(xmlNeuronGene, "type"));
string activationFn = XmlUtilities.GetAttributeValue(xmlNeuronGene, "activationFunction");
double layer = double.Parse(XmlUtilities.GetAttributeValue(xmlNeuronGene, "layer"));
return(new NeuronGene(null, id, layer, neuronType, ActivationFunctionFactory.GetActivationFunction(activationFn)));
}
private static void setSubstrateActivationFunction()
{
string parameter = getParameter("substrateactivationfunction");
if (parameter != null)
{
substrateActivationFunction = ActivationFunctionFactory.GetActivationFunction(parameter);
}
}
private static NeuronGene ReadNeuronGene(XmlElement xmlNeuronGene)
{
uint id = uint.Parse(XmlUtilities.GetAttributeValue(xmlNeuronGene, "id"));
float layer = (float)Convert.ToDouble(XmlUtilities.GetAttributeValue(xmlNeuronGene, "layer"));
NeuronType neuronType = XmlUtilities.GetNeuronType(XmlUtilities.GetAttributeValue(xmlNeuronGene, "type"));
string activationFn = XmlUtilities.GetAttributeValue(xmlNeuronGene, "activationFunction");
return(new NeuronGene(id, neuronType, ActivationFunctionFactory.GetActivationFunction(activationFn), layer));
}
public Neuron(int index, float biasWeight)
{
Index = index;
BiasWeight = biasWeight;
Inputs = new List <Synapse>();
// Default activation function shall be sigmoid
ActivationFunction = ActivationFunctionFactory.CreateDefaultFunction();
}
/// <summary>
/// Constructor that manually generates a NN controller (used mostly for debugging).
/// </summary>
/// <param name="x">X coordinate of initial position.</param>
/// <param name="y">Y coordinate of intial position.</param>
/// <param name="numSensors">Number of sensor components. Each agent has one sensor composed of at least 3 components.</param>
public NNControlledCreature(Texture2D bodyTexture, float x, float y, float headingInRadians, Simulator sim, bool drawSensorField_in, bool trackPlanting_in, int numSensors, bool freezeAfterPlanting_in)
: base(bodyTexture, x, y, headingInRadians, sim, drawSensorField_in, trackPlanting_in, numSensors)
{
PlanterSubstrate substrate = new PlanterSubstrate(308, 4, 108, new BipolarSigmoid());
NeatGenome genome = substrate.generateGenome();
Controller = genome.Decode(ActivationFunctionFactory.GetActivationFunction("BipolarSigmoid"));
freezeAfterPlanting = freezeAfterPlanting_in;
frozen = false;
}
public NeuralNet(NeuralNetParameters parameters)
{
wagesBetweenInputAndFirstHiddenLayer = ArrayAllocatorUtils.Allocate <double>(parameters.InputLayerSize, parameters.HiddenLayerSize);
wagesBetweenHiddenLayers = ArrayAllocatorUtils.Allocate <double>(parameters.NumberOfHiddenLayers - 1, parameters.HiddenLayerSize, parameters.HiddenLayerSize);
wagesBetweenLastHiddenAndOutputLayer = ArrayAllocatorUtils.Allocate <double>(parameters.HiddenLayerSize, parameters.OutputLayerSize);
biasesInHiddenLayers = ArrayAllocatorUtils.Allocate <double>(parameters.NumberOfHiddenLayers, parameters.HiddenLayerSize);
biasesInOutputLayer = ArrayAllocatorUtils.Allocate <double>(parameters.OutputLayerSize);
this.activationFunctionType = parameters.ActivationFunctionType;
activationFunction = ActivationFunctionFactory.Get(activationFunctionType);
}
public Substrate(uint biasCount, uint inputCount, uint outputCount, uint hiddenCount, IActivationFunction function)
{
this.biasCount = biasCount;
this.inputCount = inputCount;
this.outputCount = outputCount;
this.hiddenCount = hiddenCount;
this.activationFunction = function;
weightRange = HyperNEATParameters.weightRange;
threshold = HyperNEATParameters.threshold;
if (inputCount != 0)
{
inputDelta = 2.0f / (inputCount);
}
if (hiddenCount != 0)
{
hiddenDelta = 2.0f / (hiddenCount);
}
if (outputCount != 0)
{
outputDelta = 2.0f / (outputCount);
}
// SharpNEAT requires that the neuron list be in this order: bias|input|output|hidden
neurons = new NeuronGeneList((int)(inputCount + outputCount + hiddenCount));
// set up the bias nodes
for (uint a = 0; a < biasCount; a++)
{
neurons.Add(new NeuronGene(a, NeuronType.Bias, ActivationFunctionFactory.GetActivationFunction("NullFn"), 0.0f));
}
// set up the input nodes
for (uint a = 0; a < inputCount; a++)
{
neurons.Add(new NeuronGene(a + biasCount, NeuronType.Input, ActivationFunctionFactory.GetActivationFunction("NullFn"), 0.0f));
}
// set up the output nodes
for (uint a = 0; a < outputCount; a++)
{
neurons.Add(new NeuronGene(a + biasCount + inputCount, NeuronType.Output, activationFunction, 1.0f));
}
// set up the hidden nodes
for (uint a = 0; a < hiddenCount; a++)
{
neurons.Add(new NeuronGene(a + biasCount + inputCount + outputCount, NeuronType.Hidden, activationFunction, 0.5f));
}
}
public void oneGeneration(int currentGeneration)
{
DateTime dt = DateTime.Now;
ea.PerformOneGeneration();
if (ea.BestGenome.RealFitness > maxFitness)
{
simExperiment.bestGenomeSoFar = (NeatGenome)ea.BestGenome;
maxFitness = ea.BestGenome.RealFitness;
doc = new XmlDocument();
XmlGenomeWriterStatic.Write(doc, (NeatGenome)ea.BestGenome);
oFileInfo = new FileInfo(outputFolder + "bestGenome" + currentGeneration.ToString() + ".xml");
doc.Save(oFileInfo.FullName);
}
//Console.WriteLine(ea.Generation.ToString() + " " + ea.BestGenome.RealFitness + " " + ea.Population.GenomeList.Count + " " + (DateTime.Now.Subtract(dt)));
// Schrum: Changed this to include fitness values from each environment: Mainly for FourTasks
Console.WriteLine(ea.Generation.ToString() + " " + ea.BestGenome.RealFitness + " " + ea.Population.GenomeList.Count + " (" + string.Join(",", ea.BestGenome.Behavior.objectives) + ") " + (DateTime.Now.Subtract(dt)) + " " + ea.BestGenome.Behavior.modules + " " + ea.BestGenome.Behavior.cppnLinks + " " + ea.BestGenome.Behavior.substrateLinks);
int gen_mult = 200;
if (logging)
{
if (experiment.DefaultNeatParameters.noveltySearch && currentGeneration % gen_mult == 0)
{
XmlDocument archiveout = new XmlDocument();
XmlPopulationWriter.WriteGenomeList(archiveout, ea.noveltyFixed.archive);
oFileInfo = new FileInfo(outputFolder + "archive.xml");
archiveout.Save(oFileInfo.FullName);
}
if ((experiment.DefaultNeatParameters.noveltySearch || experiment.DefaultNeatParameters.multiobjective) && currentGeneration % gen_mult == 0)
{
XmlDocument popout = new XmlDocument();
if (!experiment.DefaultNeatParameters.multiobjective)
{
XmlPopulationWriter.Write(popout, ea.Population, ActivationFunctionFactory.GetActivationFunction("NullFn"));
}
else
{
XmlPopulationWriter.WriteGenomeList(popout, ea.multiobjective.population);
}
oFileInfo = new FileInfo(outputFolder + "population" + currentGeneration.ToString() + ".xml");
popout.Save(oFileInfo.FullName);
}
// Schrum: Added contents of objective array to log so individual environment scores can be seen in FourTasks domain
// Also always print modules, cppn links, and substrate links
logOutput.WriteLine(ea.Generation.ToString() + " " + (maxFitness).ToString() + " " + string.Join(" ", ea.BestGenome.Behavior.objectives) + " " + ea.BestGenome.Behavior.modules + " " + ea.BestGenome.Behavior.cppnLinks + " " + ea.BestGenome.Behavior.substrateLinks);
}
}
public NeuralNet Crossover(NeuralNet other)
{
if (other is NeuralNet == false)
{
throw new ArgumentException();
}
var parsedOther = other as NeuralNet;
var child = new NeuralNet(
new NeuralNetParameters()
{
ActivationFunctionType = activationFunctionType,
InputLayerSize = wagesBetweenInputAndFirstHiddenLayer.Length,
HiddenLayerSize = wagesBetweenLastHiddenAndOutputLayer[0].Length,
NumberOfHiddenLayers = wagesBetweenHiddenLayers.Length + 1,
OutputLayerSize = biasesInOutputLayer.Length
});
child.wagesBetweenInputAndFirstHiddenLayer =
CrossoverUtils.Crossover(wagesBetweenInputAndFirstHiddenLayer, parsedOther.wagesBetweenInputAndFirstHiddenLayer);
for (int i = 0; i < wagesBetweenHiddenLayers.Length; i++)
{
child.wagesBetweenHiddenLayers[i] =
CrossoverUtils.Crossover(wagesBetweenHiddenLayers[i], parsedOther.wagesBetweenHiddenLayers[i]);
}
for (int i = 0; i < biasesInHiddenLayers.Length; i++)
{
child.biasesInHiddenLayers[i] =
CrossoverUtils.Crossover(biasesInHiddenLayers[i], parsedOther.biasesInHiddenLayers[i]);
}
child.wagesBetweenLastHiddenAndOutputLayer =
CrossoverUtils.Crossover(wagesBetweenLastHiddenAndOutputLayer, parsedOther.wagesBetweenLastHiddenAndOutputLayer);
child.biasesInOutputLayer =
CrossoverUtils.Crossover(biasesInOutputLayer, parsedOther.biasesInOutputLayer);
if (StaticRandom.R.NextDouble() < 0.5)
{
child.activationFunctionType = other.activationFunctionType;
}
child.activationFunction = ActivationFunctionFactory.Get(child.activationFunctionType);
return(child);
}
public void oneGeneration(int currentGeneration)
{
DateTime dt = DateTime.Now;
ea.PerformOneGeneration();
if (ea.BestGenome.RealFitness > maxFitness)
{
//simExperiment.bestGenomeSoFar = (NeatGenome)ea.BestGenome;
maxFitness = ea.BestGenome.RealFitness;
doc = new XmlDocument();
XmlGenomeWriterStatic.Write(doc, (NeatGenome)ea.BestGenome);
oFileInfo = new FileInfo(outputFolder + "bestGenome" + currentGeneration.ToString() + ".xml");
doc.Save(oFileInfo.FullName);
}
Console.WriteLine(ea.Generation.ToString() + " " + ea.BestGenome.RealFitness + " " + ea.Population.GenomeList.Count + " " + (DateTime.Now.Subtract(dt)));
int gen_mult = 200;
if (logging)
{
if (neatParams.noveltySearch && currentGeneration % gen_mult == 0)
{
XmlDocument archiveout = new XmlDocument();
XmlPopulationWriter.WriteGenomeList(archiveout, ea.noveltyFixed.archive);
oFileInfo = new FileInfo(outputFolder + "archive.xml");
archiveout.Save(oFileInfo.FullName);
}
if ((neatParams.noveltySearch || neatParams.multiobjective) && currentGeneration % gen_mult == 0)
{
XmlDocument popout = new XmlDocument();
if (!neatParams.multiobjective)
{
XmlPopulationWriter.Write(popout, ea.Population, ActivationFunctionFactory.GetActivationFunction("NullFn"));
}
else
{
XmlPopulationWriter.WriteGenomeList(popout, ea.multiobjective.population);
}
oFileInfo = new FileInfo(outputFolder + "population" + currentGeneration.ToString() + ".xml");
popout.Save(oFileInfo.FullName);
}
logOutput.WriteLine(ea.Generation.ToString() + " " + (maxFitness).ToString());
}
}
public static void loadParameterFile()
{
try
{
System.IO.StreamReader input = new System.IO.StreamReader(@"params.txt");
string[] line;
double probability;
bool readingActivation = false;
while (!input.EndOfStream)
{
line = input.ReadLine().Split(' ');
if (line[0].Equals("StartActivationFunctions"))
{
readingActivation = true;
}
else if (line[0].Equals("EndActivationFunctions"))
{
readingActivation = false;
}
else
{
if (readingActivation)
{
double.TryParse(line[1], out probability);
activationFunctions.Add(line[0], probability);
}
else
{
parameters.Add(line[0].ToLower(), line[1]);
}
}
}
}
catch (Exception e)
{
System.Console.WriteLine(e.Message);
System.Console.WriteLine("Error reading config file, check file location and formation. Using default parameters");
loadDefaultParameters();
}
ActivationFunctionFactory.setProbabilities(activationFunctions);
setParameterDouble("threshold", ref threshold);
setParameterDouble("weightrange", ref weightRange);
setParameterInt("numberofthreads", ref numThreads);
setSubstrateActivationFunction();
}
public MultiLayerSandwichSubstrate(int rows, int cols, int numLayers, bool useBias, IActivationFunction activationFunction)
{
m_rows = rows;
m_cols = cols;
m_numLayers = numLayers;
m_useBias = useBias;
m_rowDelta = 2.0f / m_rows;
m_colDelta = 2.0f / m_cols;
m_activationFunction = activationFunction;
// add only one bias
m_neurons = new NeuronGeneList(m_numLayers * (m_rows * m_cols) + (m_useBias ? 1 : 0));
uint curNeurId = 0;
// inserting the bias if needed
if (m_useBias)
{
m_neurons.Add(new NeuronGene(curNeurId++, NeuronType.Bias, ActivationFunctionFactory.GetActivationFunction("NullFn")));
}
// inserting input layer neurons
for (int i = 0, len = m_rows * m_cols; i < len; i++)
{
m_neurons.Add(new NeuronGene(curNeurId++, NeuronType.Input, ActivationFunctionFactory.GetActivationFunction("NullFn")));
}
// inserting output layer neurons
for (int i = 0, len = m_rows * m_cols; i < len; i++)
{
m_neurons.Add(new NeuronGene(curNeurId++, NeuronType.Output, m_activationFunction));
}
// inserting hidden layer neurons
for (int li = 0; li < m_numLayers - 2; li++)
{
for (int i = 0, len = m_rows * m_cols; i < len; i++)
{
m_neurons.Add(new NeuronGene(curNeurId++, NeuronType.Hidden, m_activationFunction));
}
}
}
public void evolve(int generations)
{
for (int j = 0; j < generations; j++)
{
oneGeneration(j);
}
logOutput.Close();
doc = new XmlDocument();
XmlGenomeWriterStatic.Write(doc, (NeatGenome)ea.BestGenome, ActivationFunctionFactory.GetActivationFunction("NullFn"));
oFileInfo = new FileInfo(outputFolder + "bestGenome.xml");
doc.Save(oFileInfo.FullName);
//if doing novelty search, write out archive
if (neatParams.noveltySearch)
{
XmlDocument archiveout = new XmlDocument();
XmlPopulationWriter.WriteGenomeList(archiveout, ea.noveltyFixed.archive);
oFileInfo = new FileInfo(outputFolder + "archive.xml");
archiveout.Save(oFileInfo.FullName);
}
}
protected override void Initialize()
{
int divider = (int)Math.Ceiling((double)(256.0 / numDimsPerRGBAxis));
// Iterate through each snapshot (each subdirectory of logsfolder)
List <String> dirEnum = new List <String>(Directory.EnumerateDirectories(logsFolder));
foreach (string snapshotNum in dirEnum)
{
if (!analyzePlantingRatesOnly)
{
// First, get bins for single snapshot of the world
activatedNodes = new List <GraphNode>();
disjointSets = new List <List <GraphNode> >();
numNonTransparentPixels = 0;
// Populate the components list
if (File.Exists(snapshotNum + "\\Components.txt"))
{
using (System.IO.StreamReader reader = new System.IO.StreamReader(snapshotNum + "\\Components.txt"))
{
// The first line is the current creature's ID; skip it
reader.ReadLine();
int genomeID, folderNumber;
String nextLine;
NeatGenome morphologyCPPNGenome;
INetwork morphologyCPPN;
Texture2D newMorphology;
NNControlledCreature newCreature;
while ((nextLine = reader.ReadLine()) != null)
{
// First get the ID of the morphology
genomeID = Convert.ToInt32(nextLine);
// Then go find the genome corresponding to that ID
folderNumber = (genomeID - 1) / numCreaturesPerFolder;
// Load the creature's morphology CPPN
morphologyCPPNGenome = loadCPPNFromXml(logsFolder + folderNumber.ToString() + "\\" + morphologyXMLprefix + genomeID.ToString() + ".xml");
morphologyCPPN = morphologyCPPNGenome.Decode(ActivationFunctionFactory.GetActivationFunction("BipolarSigmoid"));
newMorphology = generateMorphology(morphologyCPPN);
// Create a new creature, which will automatically add it to the components list
newCreature = new NNControlledCreature(newMorphology, initialBoardWidth / 2, initialBoardWidth / 2, 0.0f, null, this, drawSensorField, trackPlanting, defaultNumSensors, freezeAfterPlanting, null, morphologyCPPNGenome);
newCreature.Genome.fileNumber = genomeID;
}
}
}
// Loop through the parent list and find the number of pixels that belong in each bin
numNonTransparentPixels = 0;
parentQueueGraph = new GraphNode[numDimsPerRGBAxis, numDimsPerRGBAxis, numDimsPerRGBAxis];
if (File.Exists(snapshotNum + "\\ParentList.txt"))
{
using (System.IO.StreamReader reader = new System.IO.StreamReader(snapshotNum + "\\ParentList.txt")) //parent list contains index into components list
{
// Skip first line, then read the rest
reader.ReadLine();
while ((nextLine = reader.ReadLine()) != null)
{
// Find the decoded individual (index into components list)
NNControlledCreature currentCreature = (NNControlledCreature)(Components[Convert.ToInt32(nextLine) - 1]);
summedR = 0;
summedG = 0;
summedB = 0;
numNonTransparentPixels = 0;
// calculate the RGB ratios
foreach (Color pixel in currentCreature.TextureAsColorArray)
{
if (pixel.A != 0)
{
numNonTransparentPixels++;
summedR += pixel.R;
summedG += pixel.G;
summedB += pixel.B;
}
}
// Add individual to one bin based on R, G, B ratios
// To get ratios, just sum the R, G, B values divided by number of nontransparent pixels
if (parentQueueGraph[summedR / (divider * numNonTransparentPixels), summedG / (divider * numNonTransparentPixels), summedB / (divider * numNonTransparentPixels)] == null)
{
parentQueueGraph[summedR / (divider * numNonTransparentPixels), summedG / (divider * numNonTransparentPixels), summedB / (divider * numNonTransparentPixels)] = new GraphNode();
parentQueueGraph[summedR / (divider * numNonTransparentPixels), summedG / (divider * numNonTransparentPixels), summedB / (divider * numNonTransparentPixels)].representativeID = currentCreature.Genome.fileNumber;
}
parentQueueGraph[summedR / (divider * numNonTransparentPixels), summedG / (divider * numNonTransparentPixels), summedB / (divider * numNonTransparentPixels)].r = summedR / (divider * numNonTransparentPixels);
parentQueueGraph[summedR / (divider * numNonTransparentPixels), summedG / (divider * numNonTransparentPixels), summedB / (divider * numNonTransparentPixels)].g = summedG / (divider * numNonTransparentPixels);
parentQueueGraph[summedR / (divider * numNonTransparentPixels), summedG / (divider * numNonTransparentPixels), summedB / (divider * numNonTransparentPixels)].b = summedB / (divider * numNonTransparentPixels);
}
}
// After all individuals have been read, append the counts to an external text file
using (System.IO.StreamWriter file = new System.IO.StreamWriter(logsFolder + "parent-queue-visualization.txt", true))
{
// Then, loop through each bin and record the count for each
for (int r = 0; r < numDimsPerRGBAxis; r++)
{
for (int g = 0; g < numDimsPerRGBAxis; g++)
{
for (int b = 0; b < numDimsPerRGBAxis; b++)
{
if (parentQueueGraph[r, g, b] == null)
{
file.Write("0,");
}
else
{
file.Write("1,");
}
}
}
}
file.WriteLine();
}
// Connect all adjacent neighbors in the parent queue graph
for (int r = 0; r < numDimsPerRGBAxis; r++)
{
for (int g = 0; g < numDimsPerRGBAxis; g++)
{
for (int b = 0; b < numDimsPerRGBAxis; b++)
{
if (parentQueueGraph[r, g, b] != null)
{
activatedNodes.Add(parentQueueGraph[r, g, b]);
for (int rmod = -1; rmod < 2; rmod++)
{
for (int gmod = -1; gmod < 2; gmod++)
{
for (int bmod = -1; bmod < 2; bmod++)
{
if (!(rmod == 0 && bmod == 0 && gmod == 0) && (r + rmod > -1) && (r + rmod < numDimsPerRGBAxis) && (g + gmod > -1) && (g + gmod < numDimsPerRGBAxis) && (b + bmod > -1) && (b + bmod < numDimsPerRGBAxis))
{
if (parentQueueGraph[r + rmod, g + gmod, b + bmod] != null)
{
parentQueueGraph[r, g, b].connections.Add(parentQueueGraph[r + rmod, g + gmod, b + bmod]);
}
}
}
}
}
}
}
}
}
// Now that all nodes have been connected, identify the connected components.
// To find all the connected components of a graph, loop through its vertices,
// starting a new breadth first or depth first search whenever the loop reaches
// a vertex that has not already been included in a previously found connected component.
while (activatedNodes.Count > 0)
{
if (activatedNodes[0].parent == null)
{
// Create a new disjoint set and add the current parent (it will be the root)
disjointSets.Add(new List <GraphNode>());
disjointSets[disjointSets.Count - 1].Add(activatedNodes[0]);
}
else
{
// Add the node to the correct disjoint set (containing the parent)
foreach (List <GraphNode> set in disjointSets)
{
if (set.Contains(activatedNodes[0].parent))
{
set.Add(activatedNodes[0]);
break;
}
}
}
// Find all of the current node's children and set the current node as the parent
foreach (GraphNode connectedNode in activatedNodes[0].connections)
{
connectedNode.parent = activatedNodes[0];
}
activatedNodes.RemoveAt(0);
}
using (System.IO.StreamWriter file = new System.IO.StreamWriter(logsFolder + "disjointsets.txt", true))
{
file.WriteLine(disjointSets.Count);
}
// Print out connected component information
using (System.IO.StreamWriter file = new System.IO.StreamWriter(logsFolder + "parent-queue-connected-components.txt", true))
{
file.WriteLine(disjointSets.Count);
foreach (List <GraphNode> set in disjointSets)
{
for (int i = 0; i < set.Count; i++)
{
file.Write(set[i].r + " " + set[i].g + " " + set[i].b + " " + set[i].representativeID + ", ");
}
file.WriteLine();
set.Clear();
}
}
activatedNodes.Clear();
disjointSets.Clear();
}
else
{
throw new Exception(logsFolder + "ParentList.txt not found.");
}
// Finally, reset the components list and free the textures for each individual
for (int i = 0; i < Components.Count; i++)
{
((Creature)(Components[i])).Texture.Dispose();
}
Components.Clear();
}
numPlanters = 0;
if (File.Exists(snapshotNum + "\\RunInfo.txt"))
{
using (System.IO.StreamReader reader = new System.IO.StreamReader(snapshotNum + "\\RunInfo.txt"))
{
// Skip first line, then read the rest
while ((nextLine = reader.ReadLine()) != null)
{
if (nextLine.Contains("planted successfully"))
{
numPlanters++;
}
}
}
}
using (System.IO.StreamWriter file = new System.IO.StreamWriter(logsFolder + "planters.txt", true))
{
file.WriteLine(numPlanters);
}
}
}
static public NetworkModel DecodeToNetworkModel(ConcurrentNetwork network)
{
ModelNeuronList masterNeuronList = new ModelNeuronList();
// loop all neurons and build a table keyed on id.
Hashtable neuronTable = new Hashtable(network.MasterNeuronList.Count);
foreach (Neuron neuron in network.MasterNeuronList)
{
ModelNeuron modelNeuron = new ModelNeuron(neuron.NeuronType, neuron.Id, ActivationFunctionFactory.GetActivationFunction("NullFn"));
neuronTable.Add(modelNeuron.Id, modelNeuron);
masterNeuronList.Add(modelNeuron);
}
// Loop through all of the connections (within the neurons)
// Now we have a neuron table keyed on id we can attach the connections
// to their source and target neurons.
foreach (Neuron neuron in network.MasterNeuronList)
{
foreach (Connection connection in neuron.ConnectionList)
{
ModelConnection modelConnection = new ModelConnection();
modelConnection.Weight = connection.Weight;
modelConnection.SourceNeuron = (ModelNeuron)neuronTable[connection.SourceNeuronId];
modelConnection.TargetNeuron = (ModelNeuron)neuronTable[connection.TargetNeuronId];
modelConnection.SourceNeuron.OutConnectionList.Add(modelConnection);
modelConnection.TargetNeuron.InConnectionList.Add(modelConnection);
}
}
return(new NetworkModel(masterNeuronList));
}
private static ConcurrentNetwork ReadNetwork(XmlElement xmlNetwork)
{
//--- Read the activation function id.
string activationFnId = XmlUtilities.GetAttributeValue(xmlNetwork, "activation-fn-id");
IActivationFunction activationFn = ActivationFunctionFactory.GetActivationFunction(activationFnId);
// Read the neurons into a list and also into a table keyed on id.
Hashtable neuronTable = new Hashtable();
NeuronList biasNeuronList = new NeuronList();
NeuronList inputNeuronList = new NeuronList();
NeuronList hiddenNeuronList = new NeuronList();
NeuronList outputNeuronList = new NeuronList();
NeuronList masterNeuronList = new NeuronList();
XmlNodeList listNeurons = xmlNetwork.SelectNodes("neurons/neuron");
foreach (XmlElement xmlNeuron in listNeurons)
{
Neuron neuron = ReadNeuron(xmlNeuron);
neuronTable.Add(neuron.Id, neuron);
switch (neuron.NeuronType)
{
case NeuronType.Bias:
biasNeuronList.Add(neuron);
break;
case NeuronType.Input:
inputNeuronList.Add(neuron);
break;
case NeuronType.Hidden:
hiddenNeuronList.Add(neuron);
break;
case NeuronType.Output:
outputNeuronList.Add(neuron);
break;
}
}
//----- Build a master list of neurons. Neurons must be ordered by type - bias,input,hidden,output.
if (biasNeuronList.Count != 1)
{
throw new SharpNeatLib.Xml.XmlException("Neural Network XML must contain exactly 1 bias node.");
}
foreach (Neuron neuron in biasNeuronList)
{
masterNeuronList.Add(neuron);
}
foreach (Neuron neuron in inputNeuronList)
{
masterNeuronList.Add(neuron);
}
foreach (Neuron neuron in hiddenNeuronList)
{
masterNeuronList.Add(neuron);
}
foreach (Neuron neuron in outputNeuronList)
{
masterNeuronList.Add(neuron);
}
//----- Read Connections and store against target neurons.
XmlNodeList listConnections = xmlNetwork.SelectNodes("connections/connection");
foreach (XmlElement xmlConnection in listConnections)
{
Connection connection = ReadConnection(xmlConnection);
// Store the connection with it's target neuron.
((Neuron)neuronTable[connection.TargetNeuronId]).ConnectionList.Add(connection);
// Bind the connection to it's source neuron.
connection.SetSourceNeuron((Neuron)neuronTable[connection.SourceNeuronId]);
}
return(new ConcurrentNetwork(masterNeuronList));
}
protected override void Initialize()
{
base.Initialize();
string backgroundFileName = (logsFolder + "0\\background.dat");
backgroundImage = new StaticImage("Background", 0, 0, ReadBackgroundFromFile(backgroundFileName), this);
// Create the world / region system
// Note: The morphology must be generated in advance of the Load
int folderNumber = (Simulator.replayIndividualNumber - 1) / numCreaturesPerFolder;
initialMorphologyFilename = logsFolder + folderNumber.ToString() + "\\" + morphologyXMLprefix + Simulator.replayIndividualNumber.ToString() + ".xml";
INetwork morphologyCPPN = loadCPPNFromXml(initialMorphologyFilename).Decode(ActivationFunctionFactory.GetActivationFunction("BipolarSigmoid"));
morphology = generateMorphology(morphologyCPPN);
StaticImage demoCreature = new StaticImage("Creature", initialBoardWidth / 2, initialBoardHeight / 2, morphology, this);
}
public NeatGenome.NeatGenome generateGenomeStackSituationalPolicy(INetwork network, List <float> stackCoordinates, bool normalizeWeights, bool adaptiveNetwork, bool modulatoryNet, float signal)
{
// Schrum: For debugging
//Console.WriteLine("generateGenomeStackSituationalPolicy:signal=" + signal);
//Console.WriteLine("CPPN inputs = " + network.InputNeuronCount);
uint numberOfAgents = (uint)stackCoordinates.Count;
IActivationFunction activationFunction = HyperNEATParameters.substrateActivationFunction;
ConnectionGeneList connections = new ConnectionGeneList((int)(numberOfAgents * (InputCount * HiddenCount) + numberOfAgents * (HiddenCount * OutputCount)));
// Schrum: Too many inputs: Only store those that are needed
//float[] coordinates = new float[5 + 1]; // <-- Schrum: bit sloppy: frequently results in unused CPPN inputs. Should make more precise
float[] coordinates = new float[network.InputNeuronCount]; // Schrum: CPPN tracks how many inputs it needs
float output;
uint connectionCounter = 0;
float agentDelta = 2.0f / (numberOfAgents - 1);
int iterations = 2 * (network.TotalNeuronCount - (network.InputNeuronCount + network.OutputNeuronCount)) + 1;
uint totalOutputCount = OutputCount * numberOfAgents;
uint totalInputCount = InputCount * numberOfAgents;
uint totalHiddenCount = HiddenCount * numberOfAgents;
uint sourceCount, targetCout;
double weightRange = HyperNEATParameters.weightRange;
double threshold = HyperNEATParameters.threshold;
bool[] biasCalculated = new bool[totalHiddenCount + totalOutputCount + totalInputCount];
// Schrum: If we are inside this function, then we either have a heterogeneous team
// of a single agent (not sure why that ended up being the case; odd use of homogeneousTeam).
// Therefore, numberOfAgents tells us whether we need to save space for a Z-coordinate,
// and whether we are expecting a Situation input.
if (numberOfAgents == 1 && coordinates.Length > 4)
{
coordinates[4] = signal; // No Z coord, but save situation
}
else if (coordinates.Length > 5)
{
coordinates[5] = signal; // Both Z coord and situation
}
NeuronGeneList neurons;
// SharpNEAT requires that the neuron list be in thisorder: bias|input|output|hidden
neurons = new NeuronGeneList((int)(InputCount * numberOfAgents + OutputCount * numberOfAgents + HiddenCount * numberOfAgents));
// set up the input nodes
for (uint a = 0; a < totalInputCount; a++)
{
neurons.Add(new NeuronGene(a, NeuronType.Input, ActivationFunctionFactory.GetActivationFunction("NullFn")));
}
// set up the output nodes
for (uint a = 0; a < totalOutputCount; a++)
{
neurons.Add(new NeuronGene(a + InputCount * numberOfAgents, NeuronType.Output, activationFunction));
}
// set up the hidden nodes
for (uint a = 0; a < totalHiddenCount; a++)
{
neurons.Add(new NeuronGene(a + InputCount * numberOfAgents + OutputCount * numberOfAgents, NeuronType.Hidden, activationFunction));
}
uint agent = 0;
float A = 0.0f, B = 0.0f, C = 0.0f, D = 0.0f, learningRate = 0.0f, modConnection;
foreach (float stackCoordinate in stackCoordinates)
{
// Schrum: Only include Z-coord as input if there are multiple team members
if (numberOfAgents > 1)
{
coordinates[4] = stackCoordinate; // Schrum: z-coord will always be at index 4
}
// Schrum: Debug
//Console.WriteLine("CPPN inputs (first 4 blank): " + string.Join(",", coordinates));
uint sourceID = uint.MaxValue, targetID = uint.MaxValue;
NeuronGroup connectedNG;
foreach (NeuronGroup ng in neuronGroups)
{
foreach (uint connectedTo in ng.ConnectedTo)
{
connectedNG = getNeuronGroup(connectedTo);
sourceCount = 0;
foreach (PointF source in ng.NeuronPositions)
{
//----------------------------
targetCout = 0;
foreach (PointF target in connectedNG.NeuronPositions)
{
switch (ng.GroupType)
{
case 0: sourceID = (agent * InputCount) + ng.GlobalID + sourceCount; break;
//Input
case 1: sourceID = totalInputCount + (agent * OutputCount) + ng.GlobalID + sourceCount; break;
//Output
case 2: sourceID = totalInputCount + totalOutputCount + (agent * HiddenCount) + ng.GlobalID + sourceCount; break; //Hidden
}
switch (connectedNG.GroupType)
{
case 0: targetID = (agent * InputCount) + connectedNG.GlobalID + targetCout; break;
case 1: targetID = totalInputCount + (agent * OutputCount) + connectedNG.GlobalID + targetCout; break;
case 2: targetID = totalInputCount + totalOutputCount + (agent * HiddenCount) + connectedNG.GlobalID + targetCout; break;
}
//--- bias
//-----------------Get the bias of the target node
if (!biasCalculated[targetID])
{
coordinates[0] = 0.0f; coordinates[1] = 0.0f; coordinates[2] = target.X; coordinates[3] = target.Y;
network.ClearSignals();
network.SetInputSignals(coordinates);
((ModularNetwork)network).RecursiveActivation();
neurons[(int)targetID].Bias = (float)(network.GetOutputSignal(1) * weightRange);
biasCalculated[targetID] = true;
}
//--bias
coordinates[0] = source.X;
coordinates[1] = source.Y;
coordinates[2] = target.X;
coordinates[3] = target.Y;
// Schrum: Debug
//Console.WriteLine("CPPN inputs: " + string.Join(",", coordinates));
network.ClearSignals();
network.SetInputSignals(coordinates);
((ModularNetwork)network).RecursiveActivation();
//network.MultipleSteps(iterations);
output = network.GetOutputSignal(0);
double leo = 0.0;
// Schrum: Observation: It seems impossible to use both LEO and adaptive networks because of these hardcoded magic numbers
if (adaptiveNetwork)
{
A = network.GetOutputSignal(2);
B = network.GetOutputSignal(3);
C = network.GetOutputSignal(4);
D = network.GetOutputSignal(5);
learningRate = network.GetOutputSignal(6);
}
if (modulatoryNet)
{
modConnection = network.GetOutputSignal(7);
}
else
{
modConnection = 0.0f;
}
// Schrum: Observation: In long run, might be desirable to use LEO, but incompatible with special preference neuron output
if (useLeo)
{
threshold = 0.0;
leo = network.GetOutputSignal(2);
}
// Schrum: This is a horrible hack, but it gets the job done for now.
// The reason this works is that it makes the following assumptions that could easily be broken in the future:
// 1) It is assumed that the only reason a CPPN would have 3 outputs per policy is if the third is for preference links
// 2) It is assumed that in a substrate with a preference neuron, the y-coord will always be 0.8, and no other neuron will have
// that y-coord.
//Console.WriteLine("output:" + coordinates[0] + "," + coordinates[1] + ":" + coordinates[2] + "," + coordinates[3]);
//Console.WriteLine("network.OutputsPerPolicy == 3" + (network.OutputsPerPolicy == 3));
//Console.WriteLine("target.Y == 0.8" + (target.Y == 0.8f));
if (network.OutputsPerPolicy == 3 && target.Y == 0.8f)
{
// The output from the link for the preference neuron replaces the standard output.
// Because the link weight is defined by a totally different CPPN output, the preference
// neuron is more free to behave very differently.
output = network.GetOutputSignal(2);
//Console.WriteLine("Preference output:" + coordinates[0] + "," + coordinates[1] + ":" + coordinates[2] + "," + coordinates[3]);
}
if (!useLeo || leo > 0.0)
{
if (Math.Abs(output) > threshold)
{
float weight =
(float)(((Math.Abs(output) - (threshold)) / (1 - threshold)) *
weightRange * Math.Sign(output));
//if (adaptiveNetwork)
//{
// //If adaptive networkset weight to small value
// weight = 0.1f;
//}
connections.Add(new
ConnectionGene(connectionCounter++, sourceID, targetID, weight, ref
coordinates, A, B, C, D, modConnection, learningRate));
}
}
//else
//{
// Console.WriteLine("Not connected");
//}
targetCout++;
}
sourceCount++;
}
}
}
agent++;
}
if (normalizeWeights)
{
normalizeWeightConnections(ref connections, neurons.Count);
}
SharpNeatLib.NeatGenome.NeatGenome sng = new SharpNeatLib.NeatGenome.NeatGenome(0, neurons, connections, (int)(totalInputCount), (int)(totalOutputCount));
sng.networkAdaptable = adaptiveNetwork;
sng.networkModulatory = modulatoryNet;
// Schrum: Debugging
// Looking at the control networks has revealed that the order of details in the substrate
// description is important. The layer with the preference neuron has to be defined last
// if it is to be the final neuron in the linearly organized output layer.
//XmlDocument doc = new XmlDocument();
//SharpNeatLib.NeatGenome.Xml.XmlGenomeWriterStatic.Write(doc, sng);
//System.IO.FileInfo oFileInfo = new System.IO.FileInfo("temp.xml");
//doc.Save(oFileInfo.FullName);
return(sng);
}
public NeatGenome.NeatGenome generateMultiGenomeStack(INetwork network, List <float> stackCoordinates, bool normalizeWeights, bool adaptiveNetwork, bool modulatoryNet)
{
uint numberOfAgents = (uint)stackCoordinates.Count;
IActivationFunction activationFunction = HyperNEATParameters.substrateActivationFunction;
ConnectionGeneList connections = new ConnectionGeneList((int)(numberOfAgents * (InputCount * HiddenCount) + numberOfAgents * (HiddenCount * OutputCount)));
float[] coordinates = new float[5];
float output;
uint connectionCounter = 0;
float agentDelta = 2.0f / (numberOfAgents - 1);
int iterations = 2 * (network.TotalNeuronCount - (network.InputNeuronCount + network.OutputNeuronCount)) + 1;
uint totalOutputCount = OutputCount * numberOfAgents;
uint totalInputCount = InputCount * numberOfAgents;
uint totalHiddenCount = HiddenCount * numberOfAgents;
// Schrum: debugging
/*
* Console.WriteLine("generateMultiGenomeStack");
* Console.WriteLine("numberOfAgents:" + numberOfAgents);
* Console.WriteLine("totalOutputCount:" + totalOutputCount);
* Console.WriteLine("totalInputCount:" + totalInputCount);
*/
uint sourceCount, targetCout;
double weightRange = HyperNEATParameters.weightRange;
double threshold = HyperNEATParameters.threshold;
NeuronGeneList neurons;
// SharpNEAT requires that the neuron list be in this order: bias|input|output|hidden
neurons = new NeuronGeneList((int)(InputCount * numberOfAgents + OutputCount * numberOfAgents + HiddenCount * numberOfAgents));
// set up the input nodes
for (uint a = 0; a < totalInputCount; a++)
{
neurons.Add(new NeuronGene(a, NeuronType.Input, ActivationFunctionFactory.GetActivationFunction("NullFn")));
}
// set up the output nodes
for (uint a = 0; a < totalOutputCount; a++)
{
neurons.Add(new NeuronGene(a + InputCount * numberOfAgents, NeuronType.Output, activationFunction));
}
// set up the hidden nodes
for (uint a = 0; a < totalHiddenCount; a++)
{
neurons.Add(new NeuronGene(a + InputCount * numberOfAgents + OutputCount * numberOfAgents, NeuronType.Hidden, activationFunction));
}
bool[] biasCalculated = new bool[totalHiddenCount + totalOutputCount + totalInputCount];
uint agent = 0;
float A = 0.0f, B = 0.0f, C = 0.0f, D = 0.0f, learningRate = 0.0f, modConnection;
foreach (float stackCoordinate in stackCoordinates)
{
coordinates[4] = stackCoordinate;
uint sourceID = uint.MaxValue, targetID = uint.MaxValue;
NeuronGroup connectedNG;
foreach (NeuronGroup ng in neuronGroups)
{
foreach (uint connectedTo in ng.ConnectedTo)
{
connectedNG = getNeuronGroup(connectedTo);
sourceCount = 0;
foreach (PointF source in ng.NeuronPositions)
{
targetCout = 0;
foreach (PointF target in connectedNG.NeuronPositions)
{
switch (ng.GroupType)
{
case 0: sourceID = (agent * InputCount) + ng.GlobalID + sourceCount; break; //Input
case 1: sourceID = totalInputCount + (agent * OutputCount) + ng.GlobalID + sourceCount; break; //Output
case 2: sourceID = totalInputCount + totalOutputCount + (agent * HiddenCount) + ng.GlobalID + sourceCount; break; //Hidden
}
switch (connectedNG.GroupType)
{
case 0: targetID = (agent * InputCount) + connectedNG.GlobalID + targetCout; break;
case 1: targetID = totalInputCount + (agent * OutputCount) + connectedNG.GlobalID + targetCout; break;
case 2: targetID = totalInputCount + totalOutputCount + (agent * HiddenCount) + connectedNG.GlobalID + targetCout; break;
}
//target node bias
if (!biasCalculated[targetID])
{
coordinates[0] = 0.0f; coordinates[1] = 0.0f; coordinates[2] = target.X; coordinates[3] = target.Y;
network.ClearSignals();
network.SetInputSignals(coordinates);
((ModularNetwork)network).RecursiveActivation();
neurons[(int)targetID].Bias = (float)(network.GetOutputSignal(1) * weightRange);
biasCalculated[targetID] = true;
}
coordinates[0] = source.X;
coordinates[1] = source.Y;
coordinates[2] = target.X;
coordinates[3] = target.Y;
network.ClearSignals();
network.SetInputSignals(coordinates);
((ModularNetwork)network).RecursiveActivation();
//network.MultipleSteps(iterations);
output = network.GetOutputSignal(0);
double leo = 0.0;
if (adaptiveNetwork)
{
A = network.GetOutputSignal(2);
B = network.GetOutputSignal(3);
C = network.GetOutputSignal(4);
D = network.GetOutputSignal(5);
learningRate = network.GetOutputSignal(6);
}
if (modulatoryNet)
{
modConnection = network.GetOutputSignal(7);
}
else
{
modConnection = 0.0f;
}
if (useLeo)
{
threshold = 0.0;
leo = network.GetOutputSignal(2);
}
if (!useLeo || leo > 0.0)
{
if (Math.Abs(output) > threshold)
{
float weight = (float)(((Math.Abs(output) - (threshold)) / (1 - threshold)) * weightRange * Math.Sign(output));
//if (adaptiveNetwork)
//{
// //If adaptive network set weight to small value
// weight = 0.1f;
//}
connections.Add(new ConnectionGene(connectionCounter++, sourceID, targetID, weight, ref coordinates, A, B, C, D, modConnection, learningRate));
}
}
//else
//{
// Console.WriteLine("Not connected");
//}
targetCout++;
}
sourceCount++;
}
}
}
agent++;
}
if (normalizeWeights)
{
normalizeWeightConnections(ref connections, neurons.Count);
}
SharpNeatLib.NeatGenome.NeatGenome sng = new SharpNeatLib.NeatGenome.NeatGenome(0, neurons, connections, (int)(totalInputCount), (int)(totalOutputCount));
sng.networkAdaptable = adaptiveNetwork;
sng.networkModulatory = modulatoryNet;
// Schrum: debugging
//Console.WriteLine("sng.InputNeuronCount:" + sng.InputNeuronCount);
//Console.WriteLine("sng.OutputNeuronCount:" + sng.OutputNeuronCount);
return(sng);
}
private NeatGenome.NeatGenome generateHomogeneousGenome(INetwork network, bool normalizeWeights, bool adaptiveNetwork, bool modulatoryNet)
{
IActivationFunction activationFunction = HyperNEATParameters.substrateActivationFunction;
ConnectionGeneList connections = new ConnectionGeneList((int)((InputCount * HiddenCount) + (HiddenCount * OutputCount)));
float[] coordinates = new float[4];
float output;
uint connectionCounter = 0;
int iterations = 2 * (network.TotalNeuronCount - (network.InputNeuronCount + network.OutputNeuronCount)) + 1;
uint totalOutputCount = OutputCount;
uint totalInputCount = InputCount;
uint totalHiddenCount = HiddenCount;
uint sourceCount, targetCout;
double weightRange = HyperNEATParameters.weightRange;
double threshold = HyperNEATParameters.threshold;
NeuronGeneList neurons;
// SharpNEAT requires that the neuron list be in this order: bias|input|output|hidden
neurons = new NeuronGeneList((int)(InputCount + OutputCount + HiddenCount));
// set up the input nodes
for (uint a = 0; a < totalInputCount; a++)
{
neurons.Add(new NeuronGene(a, NeuronType.Input, ActivationFunctionFactory.GetActivationFunction("NullFn")));
}
// set up the output nodes
for (uint a = 0; a < totalOutputCount; a++)
{
neurons.Add(new NeuronGene(a + InputCount, NeuronType.Output, activationFunction));
}
// set up the hidden nodes
for (uint a = 0; a < totalHiddenCount; a++)
{
neurons.Add(new NeuronGene(a + InputCount + OutputCount, NeuronType.Hidden, activationFunction));
}
bool[] biasCalculated = new bool[totalHiddenCount + totalOutputCount + totalInputCount];
uint sourceID = uint.MaxValue, targetID = uint.MaxValue;
NeuronGroup connectedNG;
foreach (NeuronGroup ng in neuronGroups)
{
foreach (uint connectedTo in ng.ConnectedTo)
{
connectedNG = getNeuronGroup(connectedTo);
sourceCount = 0;
foreach (PointF source in ng.NeuronPositions)
{
targetCout = 0;
foreach (PointF target in connectedNG.NeuronPositions)
{
switch (ng.GroupType)
{
case 0: sourceID = ng.GlobalID + sourceCount; break; //Input
case 1: sourceID = totalInputCount + ng.GlobalID + sourceCount; break; //Output
case 2: sourceID = totalInputCount + totalOutputCount + ng.GlobalID + sourceCount; break; //Hidden
}
switch (connectedNG.GroupType)
{
case 0: targetID = connectedNG.GlobalID + targetCout; break;
case 1: targetID = totalInputCount + connectedNG.GlobalID + targetCout; break;
case 2: targetID = totalInputCount + totalOutputCount + connectedNG.GlobalID + targetCout; break;
}
//calculate bias of target node
if (!biasCalculated[targetID])
{
coordinates[0] = 0.0f; coordinates[1] = 0.0f; coordinates[2] = target.X; coordinates[3] = target.Y;
network.ClearSignals();
network.SetInputSignals(coordinates);
((ModularNetwork)network).RecursiveActivation();
neurons[(int)targetID].Bias = (float)(network.GetOutputSignal(1) * weightRange);
biasCalculated[targetID] = true;
}
coordinates[0] = source.X;
coordinates[1] = source.Y;
coordinates[2] = target.X;
coordinates[3] = target.Y;
network.ClearSignals();
network.SetInputSignals(coordinates);
((ModularNetwork)network).RecursiveActivation();
//network.MultipleSteps(iterations);
output = network.GetOutputSignal(0);
if (Math.Abs(output) > threshold)
{
float weight = (float)(((Math.Abs(output) - (threshold)) / (1 - threshold)) * weightRange * Math.Sign(output));
connections.Add(new ConnectionGene(connectionCounter++, sourceID, targetID, weight, ref coordinates, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f));
}
//else
//{
// Console.WriteLine("Not connected");
//}
targetCout++;
}
sourceCount++;
}
}
}
if (normalizeWeights)
{
normalizeWeightConnections(ref connections, neurons.Count);
}
NeatGenome.NeatGenome gn = new SharpNeatLib.NeatGenome.NeatGenome(0, neurons, connections, (int)(totalInputCount), (int)(totalOutputCount));
gn.networkAdaptable = adaptiveNetwork;
gn.networkModulatory = modulatoryNet;
return(gn);
}
/// <summary>
/// Create a default minimal genome that describes a NN with the given number of inputs and outputs.
/// </summary>
/// <returns></returns>
public static IGenome CreateGenome(NeatParameters neatParameters, IdGenerator idGenerator, int inputNeuronCount, int outputNeuronCount, float connectionProportion, bool neatBrain)
{
IActivationFunction actFunct;
NeuronGene neuronGene; // temp variable.
NeuronGeneList inputNeuronGeneList = new NeuronGeneList(); // includes bias neuron.
NeuronGeneList outputNeuronGeneList = new NeuronGeneList();
NeuronGeneList neuronGeneList = new NeuronGeneList();
ConnectionGeneList connectionGeneList = new ConnectionGeneList();
// IMPORTANT NOTE: The neurons must all be created prior to any connections. That way all of the genomes
// will obtain the same innovation ID's for the bias,input and output nodes in the initial population.
// Create a single bias neuron.
//TODO: DAVID proper activation function change to NULL?
actFunct = ActivationFunctionFactory.GetActivationFunction("NullFn");
neuronGene = new NeuronGene(idGenerator.NextInnovationId, NeuronType.Bias, actFunct, 0f);
inputNeuronGeneList.Add(neuronGene);
neuronGeneList.Add(neuronGene);
// Create input neuron genes.
for (int i = 0; i < inputNeuronCount; i++)
{
//TODO: DAVID proper activation function change to NULL?
neuronGene = new NeuronGene(idGenerator.NextInnovationId, NeuronType.Input, actFunct, 0f);
inputNeuronGeneList.Add(neuronGene);
neuronGeneList.Add(neuronGene);
}
// Create output neuron genes.
if (neatBrain)
{
actFunct = ActivationFunctionFactory.GetActivationFunction("SteepenedSigmoidApproximation");
}
else
{
actFunct = ActivationFunctionFactory.GetActivationFunction("BipolarSigmoid");
}
for (int i = 0; i < outputNeuronCount; i++)
{
//actFunct = ActivationFunctionFactory.GetRandomActivationFunction(neatParameters);
//TODO: DAVID proper activation function
neuronGene = new NeuronGene(idGenerator.NextInnovationId, NeuronType.Output, actFunct, 1f);
outputNeuronGeneList.Add(neuronGene);
neuronGeneList.Add(neuronGene);
}
// Loop over all possible connections from input to output nodes and create a number of connections based upon
// connectionProportion.
foreach (NeuronGene targetNeuronGene in outputNeuronGeneList)
{
foreach (NeuronGene sourceNeuronGene in inputNeuronGeneList)
{
// Always generate an ID even if we aren't going to use it. This is necessary to ensure connections
// between the same neurons always have the same ID throughout the generated population.
uint connectionInnovationId = idGenerator.NextInnovationId;
if (Utilities.NextDouble() < connectionProportion)
{ // Ok lets create a connection.
connectionGeneList.Add(new ConnectionGene(connectionInnovationId,
sourceNeuronGene.InnovationId,
targetNeuronGene.InnovationId,
(Utilities.NextDouble() * neatParameters.connectionWeightRange) - neatParameters.connectionWeightRange / 2.0)); // Weight 0 +-5
}
}
}
// Don't create any hidden nodes at this point. Fundamental to the NEAT way is to start minimally!
return(new NeatGenome(idGenerator.NextGenomeId, neuronGeneList, connectionGeneList, inputNeuronCount, outputNeuronCount));
}
private NeatGenome.NeatGenome generateHomogeneousGenomeES(INetwork network, bool normalizeWeights, bool adaptiveNetwork, bool modulatoryNet)
{
List <PointF> hiddenNeuronPositions = new List <PointF>();
IActivationFunction activationFunction = HyperNEATParameters.substrateActivationFunction;
ConnectionGeneList connections = new ConnectionGeneList();//(int)((InputCount * HiddenCount) + (HiddenCount * OutputCount)));
List <PointF> outputNeuronPositions = getNeuronGroupByType(1);
List <PointF> inputNeuronPositions = getNeuronGroupByType(0);
EvolvableSubstrate se = new EvolvableSubstrate();
se.generateConnections(inputNeuronPositions, outputNeuronPositions, network,
HyperNEATParameters.initialRes,
(float)HyperNEATParameters.varianceThreshold,
(float)HyperNEATParameters.bandingThreshold,
(int)HyperNEATParameters.ESIterations,
(float)HyperNEATParameters.divisionThreshold,
HyperNEATParameters.maximumRes,
InputCount, OutputCount, -1.0f, -1.0f, 1.0f, 1.0f, ref connections, ref hiddenNeuronPositions);
HiddenCount = (uint)hiddenNeuronPositions.Count;
float[] coordinates = new float[5];
uint connectionCounter = (uint)connections.Count;
NeuronGeneList neurons;
// SharpNEAT requires that the neuron list be in this order: bias|input|output|hidden
neurons = new NeuronGeneList((int)(InputCount + OutputCount + HiddenCount));
// set up the input nodes
for (uint a = 0; a < InputCount; a++)
{
neurons.Add(new NeuronGene(a, NeuronType.Input, ActivationFunctionFactory.GetActivationFunction("NullFn")));
}
// set up the output nodes
for (uint a = 0; a < OutputCount; a++)
{
neurons.Add(new NeuronGene(a + InputCount, NeuronType.Output, activationFunction));
}
// set up the hidden nodes
for (uint a = 0; a < HiddenCount; a++)
{
neurons.Add(new NeuronGene(a + InputCount + OutputCount, NeuronType.Hidden, activationFunction));
}
bool[] visited = new bool[neurons.Count];
List <uint> nodeList = new List <uint>();
bool[] connectedToInput = new bool[neurons.Count];
bool[] isOutput = new bool[neurons.Count];
bool danglingConnection = true;
while (danglingConnection)
{
bool[] hasIncomming = new bool[neurons.Count];
foreach (ConnectionGene co in connections)
{
// if (co.SourceNeuronId != co.TargetNeuronId)
// {
hasIncomming[co.TargetNeuronId] = true;
// }
}
for (int i = 0; i < InputCount; i++)
{
hasIncomming[i] = true;
}
bool[] hasOutgoing = new bool[neurons.Count];
foreach (ConnectionGene co in connections)
{
// if (co.TargetNeuronId != co.SourceNeuronId)
// {
if (co.TargetNeuronId != co.SourceNeuronId) //neurons that only connect to themselfs don't count
{
hasOutgoing[co.SourceNeuronId] = true;
}
// }
}
//Keep output neurons
for (int i = 0; i < OutputCount; i++)
{
hasOutgoing[i + InputCount] = true;
}
danglingConnection = false;
//Check if there are still dangling connections
foreach (ConnectionGene co in connections)
{
if (!hasOutgoing[co.TargetNeuronId] || !hasIncomming[co.SourceNeuronId])
{
danglingConnection = true;
break;
}
}
connections.RemoveAll(delegate(ConnectionGene m) { return(!hasIncomming[m.SourceNeuronId]); });
connections.RemoveAll(delegate(ConnectionGene m) { return(!hasOutgoing[m.TargetNeuronId]); });
}
if (normalizeWeights)
{
normalizeWeightConnections(ref connections, neurons.Count);
}
SharpNeatLib.NeatGenome.NeatGenome gn = new SharpNeatLib.NeatGenome.NeatGenome(0, neurons, connections, (int)(InputCount), (int)(OutputCount));
// SharpNeatLib.NeatGenome.NeatGenome sng = new SharpNeatLib.NeatGenome.NeatGenome(0, neurons, connections, (int)(totalInputCount), (int)(totalOutputCount));
gn.networkAdaptable = adaptiveNetwork;
gn.networkModulatory = modulatoryNet;
return(gn);
}
