public static GenomeList CreateGenomeList(NeatGenome seedGenome, int length, NeatParameters neatParameters, IdGenerator idGenerator)
{
//Build the list.
GenomeList genomeList = new GenomeList();
// Use the seed directly just once.
NeatGenome newGenome = new NeatGenome(seedGenome, idGenerator.NextGenomeId);
genomeList.Add(newGenome);
// For the remainder we alter the weights.
for (int i = 1; i < length; i++)
{
newGenome = new NeatGenome(seedGenome, idGenerator.NextGenomeId);
// Reset the connection weights
foreach (ConnectionGene connectionGene in newGenome.ConnectionGeneList)
{
connectionGene.Weight += (Utilities.NextDouble() * neatParameters.connectionWeightRange) - neatParameters.connectionWeightRange / 2.0;
}
//newGenome.ConnectionGeneList.Add(new ConnectionGene(idGenerator.NextInnovationId,5,newGenome.NeuronGeneList[Utilities.Next(newGenome.NeuronGeneList.Count-7)+7].InnovationId ,(Utilities.NextDouble() * neatParameters.connectionWeightRange) - neatParameters.connectionWeightRange/2.0));
//newGenome.ConnectionGeneList.Add(new ConnectionGene(idGenerator.NextInnovationId, 6, newGenome.NeuronGeneList[Utilities.Next(newGenome.NeuronGeneList.Count - 7) + 7].InnovationId, (Utilities.NextDouble() * neatParameters.connectionWeightRange) - neatParameters.connectionWeightRange / 2.0));
genomeList.Add(newGenome);
}
//
return(genomeList);
}
public void initalizeEvoManager(int cInputs, int cOuputs, NeatParameters np, IPopulationEvaluator popEval)
{
cppnInputs = cInputs;
cppnOutputs = cOuputs;
neatParams = np;
populationEval = popEval;
}
public static GenomeList CreateGenomeListPreserveIDs(NeatParameters neatParameters, IdGenerator idGenerator,
int inputNeuronCount, int outputNeuronCount, float connectionProportion, int length, AssessGenotypeFunction assess)
{
GenomeList genomeList = new GenomeList();
int testCount = 0; int maxTests = 5;
//for (int i = 0; i < length; i++)
while (genomeList.Count < length)
{
IGenome genome = CreateGenomePreserveID(neatParameters, idGenerator, inputNeuronCount, outputNeuronCount, connectionProportion);
if (assess != null && assess(genome) && testCount++ < maxTests)
{
//after adding the genome, reset test count
genomeList.Add(genome);
testCount = 0;
}
else if (assess == null)
{
genomeList.Add(genome);
}
else if (testCount >= maxTests)
{
genomeList.Add(genome);
testCount = 0;
}
}
return(genomeList);
}
public Multiobjective(NeatParameters _np)
{
np = _np;
population = new GenomeList();
ranks = new List <RankInformation>();
nov = new noveltyfixed(10.0);
doNovelty = false;
generation = 0;
}
public Multiobjective(NeatParameters _np)
{
np = _np;
population = new GenomeList();
ranks = new List <RankInformation>();
nov = new noveltyfixed(10.0);
doNovelty = _np.noveltySearch;
Console.WriteLine("multiobjective novelty " + doNovelty);
generation = 0;
}
/// <summary>
/// Construct a GenomeList. This can be used to construct a new Population object.
/// </summary>
/// <param name="evolutionAlgorithm"></param>
/// <param name="inputNeuronCount"></param>
/// <param name="outputNeuronCount"></param>
/// <param name="length"></param>
/// <returns></returns>
public static GenomeList CreateGenomeList(NeatParameters neatParameters, IdGenerator idGenerator, int inputNeuronCount, int outputNeuronCount, float connectionProportion, int length, bool neatBrain = false)
{
GenomeList genomeList = new GenomeList();
for (int i = 0; i < length; i++)
{
idGenerator.ResetNextInnovationNumber();
genomeList.Add(CreateGenome(neatParameters, idGenerator, inputNeuronCount, outputNeuronCount, connectionProportion, neatBrain));
}
return(genomeList);
}
/// <summary>
/// Construct a GenomeList. This can be used to construct a new Population object.
/// </summary>
/// <param name="evolutionAlgorithm"></param>
/// <param name="inputNeuronCount"></param>
/// <param name="outputNeuronCount"></param>
/// <param name="length"></param>
/// <returns></returns>
// Schrum: Added outputsPerPolicy
public static GenomeList CreateGenomeList(NeatParameters neatParameters, IdGenerator idGenerator, int inputNeuronCount, int outputNeuronCount, int outputsPerPolicy, float connectionProportion, int length)
{
GenomeList genomeList = new GenomeList();
for (int i = 0; i < length; i++)
{
idGenerator.ResetNextInnovationNumber();
// Schrum: Added outputsPerPolicy
genomeList.Add(CreateGenome(neatParameters, idGenerator, inputNeuronCount, outputNeuronCount, outputsPerPolicy, connectionProportion));
}
return(genomeList);
}
EvolutionManager()
{
//generic neat params, if need to change, just create a function that swaps them in
neatParams = new NeatParameters();
//neatParams.noveltySearch = true;
//neatParams.noveltyFloat = true;
neatParams.multiobjective = true;
neatParams.archiveThreshold = 0.5;
//neatParams.archiveThreshold = 300000.0;
//maybe we load this idgenerator from server or local database, just keep that in mind
idgen = new IdGenerator();
//we just default to this, but it doesn't have to be so
this.setDefaultCPPNs(4, 3);
genomeListDictionary.Add(CurrentGenomePool, new GenomeList());
}
public static GenomeList CreateGenomeList(Population seedPopulation, int length, NeatParameters neatParameters, IdGenerator idGenerator)
{
//Build the list.
GenomeList genomeList = new GenomeList();
int seedIdx = 0;
for (int i = 0; i < length; i++)
{
NeatGenome newGenome = new NeatGenome((NeatGenome)seedPopulation.GenomeList[seedIdx], idGenerator.NextGenomeId);
// Reset the connection weights
foreach (ConnectionGene connectionGene in newGenome.ConnectionGeneList)
{
connectionGene.Weight = (Utilities.NextDouble() * neatParameters.connectionWeightRange) - neatParameters.connectionWeightRange / 2.0;
}
genomeList.Add(newGenome);
if (++seedIdx >= seedPopulation.GenomeList.Count)
{ // Back to first genome.
seedIdx = 0;
}
}
return(genomeList);
}
/// <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));
}
/// <summary>
/// CPPNGenomeFactory constructor. Used to generate a minimal CPPN
/// </summary>
/// <param name="neatParameters"></param>
/// <param name="idGenerator"></param>
/// <param name="inputNeuronCount"></param>
/// <param name="outputNeuronCount"></param>
/// <param name="connectionProportion"></param>
public CPPNGenomeFactory(NeatParameters neatParameters, IdGenerator idGenerator, int inputNeuronCount, int outputNeuronCount, float connectionProportion)
{
cppnGenerator = new GenomeFactory();
listOfCppnGenomes = cppnGenerator.CreateGenomeList(neatParameters, idGenerator, inputNeuronCount, outputNeuronCount, connectionProportion, Chromaria.Simulator.populationSize);
}
/// <summary>
/// This function contains all of the pre-run logic that doesn't involve graphics.
/// </summary>
protected override void Initialize()
{
base.Initialize();
// Create the world / region system
// Note: The morphology must be generated in advance of the Load
INetwork morphologyCPPN = loadCPPNFromXml(initialMorphologyFilename).Decode(ActivationFunctionFactory.GetActivationFunction("BipolarSigmoid"));
morphology = generateMorphology(morphologyCPPN);
redTexture = generateSolidMorphology(morphology);
InitializeRegions();
// Initialize a log to track some instance-specific data
using (System.IO.StreamWriter file = new System.IO.StreamWriter("RunInfo.txt", true))
{
file.WriteLine("Novelty search run");
file.WriteLine("Start time: " + DateTime.Now.ToString("HH:mm:ss tt"));
if (freezeAfterPlanting)
{
file.WriteLine("Individuals are immobilized once they attempt to plant.");
}
else
{
file.WriteLine("Individuals are allowed to keep moving even if/after they attempt to plant.");
}
file.WriteLine("Morphology genome XML filename: " + initialControllerFilename);
file.WriteLine("Behavior update interval: " + behaviorUpdateInterval);
file.WriteLine("Planting weight: " + plantingWeight);
file.WriteLine("Position weight: " + positionWeight);
file.WriteLine("Population size: " + populationSize);
file.WriteLine("Archive threshold: " + archiveThreshold);
}
// Initialize some static variables for the simulation
numBidirectionalPlanters = 0;
numFirstTrialPlanters = 0;
numSecondTrialPlanters = 0;
numBidirectionalMisplanters = 0;
numFirstTrialMisplanters = 0;
numSecondTrialMisplanters = 0;
firstTrial = true;
// Set the NEAT parameters
neatParams = new NeatParameters();
neatParams.archiveThreshold = archiveThreshold;
neatParams.noveltyFixed = true;
neatParams.noveltySearch = true;
// Configure the HyperNEAT substrate
controllerSubstrate = new ControllerSubstrate(308, 4, 108, new BipolarSigmoid());
controllerSubstrate.weightRange = 5.0;
controllerSubstrate.threshold = 0.2;
// Create a genome factory to generate a list of CPPN genomes
cppnGenerator = new GenomeFactory();
idGen = new IdGenerator();
cppnGenomeList = cppnGenerator.CreateGenomeList(neatParams, idGen, 4, 8, 1.0f, populationSize);
GenomeIndexOfCurrentCreature = 0;
// Initialize the folders for storing the archive and planters
noveltyLogsFolder = Directory.GetCurrentDirectory() + "\\archive\\" + GenomeIndexOfCurrentCreature + "\\";
if (!Directory.Exists(noveltyLogsFolder))
{
Directory.CreateDirectory(noveltyLogsFolder);
}
plantersFolder = Directory.GetCurrentDirectory() + "\\planters\\" + GenomeIndexOfCurrentCreature + "\\";
if (!Directory.Exists(plantersFolder))
{
Directory.CreateDirectory(plantersFolder);
}
// Create an initial population based on the genome list
popn = new Population(idGen, cppnGenomeList);
// Set the generation counter
// Note: This must be kept seperately from the EA generation counter because novelty search here does't follow the traditional loop.
generation = 1;
// Create the EA
// (Don't run the EA until the first generation has had a chance to go through the simulation.
// The EA call happens in Simulator.NewGeneration().)
ea = new EvolutionAlgorithm(popn, new ChromariaPopulationEvaluator(new ChromariaNetworkEvaluator()), neatParams);
// Initialize the behavior trackers for this individual
ea.Population.GenomeList[GenomeIndexOfCurrentCreature].Behavior = new BehaviorType();
ea.Population.GenomeList[GenomeIndexOfCurrentCreature].Behavior.behaviorList = new List <double>();
// Generate the initial creature
int x = initialBoardWidth / 2;
int y = initialBoardHeight / 2;
INetwork newController = controllerSubstrate.generateGenome(ea.Population.GenomeList[GenomeIndexOfCurrentCreature].Decode(ActivationFunctionFactory.GetActivationFunction("BipolarSigmoid"))).Decode(ActivationFunctionFactory.GetActivationFunction("BipolarSigmoid"));
if (bidirectionalTrials)
{
currentCreature = new NNControlledCreature(morphology, x, y, initialHeading + (float)(Math.PI / 2.0), newController, this, drawSensorField, trackPlanting, defaultNumSensors, freezeAfterPlanting);
}
else
{
currentCreature = new NNControlledCreature(morphology, x, y, initialHeading, newController, this, drawSensorField, trackPlanting, defaultNumSensors, freezeAfterPlanting);
}
currentCreature.DrawOrder = 1;
indexOfCurrentCreature = Components.Count - 1;
// Add the creature to the simulator's region lists
int currentPointer = Components.Count - 1;
regions[y / regionHeight, x / regionWidth].Add(currentPointer);
if ((x % regionWidth > (x + morphology.Width) % regionWidth) && (y % regionHeight > (y + morphology.Height) % regionHeight) && !regions[(y + morphology.Height) / regionHeight, (x + morphology.Width) / regionWidth].Contains(currentPointer))
{
regions[(y + morphology.Height) / regionHeight, (x + morphology.Width) / regionWidth].Add(currentPointer);
}
if (x % regionWidth > (x + morphology.Width) % regionWidth && !regions[(y / regionHeight), (x + morphology.Width) / regionWidth].Contains(currentPointer))
{
regions[(y / regionHeight), (x + morphology.Width) / regionWidth].Add(currentPointer);
}
if (y % regionHeight > (y + morphology.Height) % regionHeight && !(regions[(y + morphology.Height) / regionHeight, x / regionWidth].Contains(currentPointer)))
{
regions[(y + morphology.Height) / regionHeight, x / regionWidth].Add(currentPointer);
}
// Preliminarily update the creature's sensors so its first movements are actually based on what's underneath its starting position
currentCreature.InitializeSensor();
plantedInColoredSpace1 = false;
plantedInColoredSpace2 = false;
plantedInWhiteSpace1 = false;
plantedInWhiteSpace2 = false;
numUpdates = 0;
}
public static IGenome CreateGenomePreserveID(NeatParameters neatParameters, IdGenerator idGenerator, int inputNeuronCount, int outputNeuronCount, float connectionProportion)
{
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();
int nodeCount = 0;
WINManager win = WINManager.SharedWIN;
// 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);
WINNode neuronNode = win.findOrInsertNodeWithProperties(idGenerator,
WINNode.NodeWithProperties(nodeCount++, NeuronType.Bias)
);
neuronGene = new NeuronGene(null, neuronNode.UniqueID, NeuronGene.INPUT_LAYER, NeuronType.Bias, actFunct);
inputNeuronGeneList.Add(neuronGene);
neuronGeneList.Add(neuronGene);
// Create input neuron genes.
actFunct = ActivationFunctionFactory.GetActivationFunction("NullFn");
for (int i = 0; i < inputNeuronCount; i++)
{
//TODO: DAVID proper activation function change to NULL?
//neuronGene = new NeuronGene(idGenerator.NextInnovationId, NeuronType.Input, actFunct);
neuronNode = win.findOrInsertNodeWithProperties(idGenerator, WINNode.NodeWithProperties(nodeCount++, NeuronType.Input));
neuronGene = new NeuronGene(null, neuronNode.UniqueID, NeuronGene.INPUT_LAYER, NeuronType.Input, actFunct);
inputNeuronGeneList.Add(neuronGene);
neuronGeneList.Add(neuronGene);
}
// Create output neuron genes.
//actFunct = ActivationFunctionFactory.GetActivationFunction("NullFn");
for (int i = 0; i < outputNeuronCount; i++)
{
actFunct = ActivationFunctionFactory.GetActivationFunction("BipolarSigmoid");
//actFunct = ActivationFunctionFactory.GetRandomActivationFunction(neatParameters);
//TODO: DAVID proper activation function
//neuronGene = new NeuronGene(idGenerator.NextInnovationId, NeuronType.Output, actFunct);
neuronNode = win.findOrInsertNodeWithProperties(idGenerator, WINNode.NodeWithProperties(nodeCount++, NeuronType.Output));
neuronGene = new NeuronGene(null, neuronNode.UniqueID, NeuronGene.OUTPUT_LAYER, NeuronType.Output, actFunct);
outputNeuronGeneList.Add(neuronGene);
neuronGeneList.Add(neuronGene);
}
int currentConnCount = 0;
WINConnection winConn;
// 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.
//PAUL NOTE:
//instead of generating and not using and id, we use the target and connection properties to uniquely identify a connection in WIN
//uint connectionInnovationId = idGenerator.NextInnovationId;
if (Utilities.NextDouble() < connectionProportion)
{
// Ok lets create a connection.
//first we search or create the winconnection object
winConn = win.findOrInsertConnectionWithProperties(idGenerator,
WINConnection.ConnectionWithProperties(currentConnCount, sourceNeuronGene.InnovationId, targetNeuronGene.InnovationId));
//our winconn will have our innovationID, and our weight like normal
//this will also respect the idgenerator, since it gets sent in as well, for legacy purposes
connectionGeneList.Add(new ConnectionGene(winConn.UniqueID,
sourceNeuronGene.InnovationId,
targetNeuronGene.InnovationId,
(Utilities.NextDouble() * neatParameters.connectionWeightRange) - neatParameters.connectionWeightRange / 2.0)
);
//(Utilities.NextDouble() * neatParameters.connectionWeightRange) - neatParameters.connectionWeightRange / 2.0)); // Weight 0 +-5
}
currentConnCount++;
}
}
//WIN will eventually be in control of all the genomes that are created as well, but not quite yet!
//TODO: WIN should be generating genomeIDs explicitly
// 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));
}
public static GenomeList CreateGenomeListPreserveIDs(GenomeList seedGenomes, int length, NeatParameters neatParameters, IdGenerator idGenerator, AssessGenotypeFunction assess)
{
//Eventually, WIN will be brought in to maintain the genomes, for now, no need
//Build the list.
GenomeList genomeList = new GenomeList();
if (length < seedGenomes.Count)
{
throw new Exception("Attempting to generate a population that is smaller than the number of seeds (i.e. some seeds will be lost). Please change pop size to accomodate for all seeds.");
}
NeatGenome newGenome;
for (int i = 0; i < seedGenomes.Count; i++)
{
// Use each seed directly just once.
newGenome = new NeatGenome((NeatGenome)seedGenomes[i], idGenerator.NextGenomeId);
genomeList.Add(newGenome);
}
int testCount = 0; int maxTests = 5;
// For the remainder we alter the weights.
//for (int i = 1; i < length; i++)
//{
while (genomeList.Count < length)
{
newGenome = new NeatGenome((NeatGenome)seedGenomes[Utilities.Next(seedGenomes.Count)], idGenerator.NextGenomeId);
// Reset the connection weights
//in this particular instance, we would take a snapshot of the genome AFTER mutation for WIN purposes. But we don't track genomes yet
foreach (ConnectionGene connectionGene in newGenome.ConnectionGeneList)
{
connectionGene.Weight += (0.1 - Utilities.NextDouble() * 0.2);
}
//!connectionGene.Weight = (Utilities.NextDouble() * neatParameters.connectionWeightRange) - neatParameters.connectionWeightRange/2.0;
//Console.WriteLine((0.1 - Utilities.NextDouble() * 0.2));
//newGenome.ConnectionGeneList.Add(new ConnectionGene(idGenerator.NextInnovationId,5,newGenome.NeuronGeneList[Utilities.Next(newGenome.NeuronGeneList.Count-7)+7].InnovationId ,(Utilities.NextDouble() * neatParameters.connectionWeightRange) - neatParameters.connectionWeightRange/2.0));
//newGenome.ConnectionGeneList.Add(new ConnectionGene(idGenerator.NextInnovationId, 6, newGenome.NeuronGeneList[Utilities.Next(newGenome.NeuronGeneList.Count - 7) + 7].InnovationId, (Utilities.NextDouble() * neatParameters.connectionWeightRange) - neatParameters.connectionWeightRange / 2.0));
//if we have an assess function, it should be used for generating this individual!
if (assess != null && assess(newGenome) && testCount++ < maxTests)
{
//after adding the genome, reset test count
genomeList.Add(newGenome);
testCount = 0;
}
else if (assess == null)
{
genomeList.Add(newGenome);
}
else if (testCount >= maxTests)
{
genomeList.Add(newGenome);
testCount = 0;
}
}
//
return(genomeList);
}
void generateSampleCPPNs()
{
NeatParameters np = new NeatParameters();
IdGenerator idGen = new IdGenerator();
idGen.ResetNextInnovationNumber();
Random r = new Random();
JObject root = new JObject();
JObject meta = new JObject();
JArray networkArray = new JArray();
//how many random input tests?
int testCount = 100;
int networkCount = 20;
meta.Add("networkCount", networkCount);
meta.Add("sampleCount", testCount);
Console.WriteLine("All Networks start will run:" + networkCount * testCount);
for (int n = 0; n < networkCount; n++)
{
Console.WriteLine("Network start:" + n);
JObject networkJSON = new JObject();
//create our genome
var inputCount = r.Next(4) + 3;
var outputCount = r.Next(3) + 1;
//radnom inputs 3-6, random outputs 1-3
var genome = GenomeFactory.CreateGenome(np, idGen, inputCount, outputCount, 1);
Console.WriteLine("Genoem created:" + n);
Hashtable nodeHT = new Hashtable();
Hashtable connHT = new Hashtable();
//mutate our genome
for (int m = 0; m < 20; m++)
{
((NeatGenome)genome).Mutate(np, idGen, nodeHT, connHT);
Console.WriteLine("Mutation done: " + m);
}
Console.WriteLine("Mutations done:" + n);
//now turn genome into a network
var network = genome.Decode(null);
Console.WriteLine("genome decoded:" + n);
//turn network into JSON, and save as the network object
networkJSON.Add("network", JObject.FromObject(network));
JArray inputsAndOutputs = new JArray();
Console.WriteLine("starting tests:" + n);
for (var t = 0; t < testCount; t++)
{
Console.WriteLine("Test " + t + " :" + "for" + n);
JArray inputSamples = new JArray();
JArray outputSamples = new JArray();
network.ClearSignals();
Console.WriteLine("Testclear " + t + " :" + "for" + n);
//var saveInputs = new float[inputCount];
for (int ins = 0; ins < inputCount; ins++)
{
//inputs from -1,1
var inF = (float)(2 * r.NextDouble() - 1);
//saveInputs[ins] = inF;
network.SetInputSignal(ins, inF);
//add our random input
inputSamples.Add(JToken.FromObject(inF));
}
Console.WriteLine("Testrecursive next" + t + " :" + "for" + n);
//run our network, and save the response
((ModularNetwork)network).RecursiveActivation();
//network.MultipleSteps(30);
Console.WriteLine("recursive done " + t + " :" + "for" + n);
//var saveOuts = new float[outputCount];
for (var outs = 0; outs < outputCount; outs++)
{
//saveOuts[outs] = network.GetOutputSignal(outs);
//keep our outputs in an output array
outputSamples.Add(JToken.FromObject(network.GetOutputSignal(outs)));
}
//network.ClearSignals();
//network.SetInputSignals(saveInputs);
//network.MultipleSteps(30);
////((ModularNetwork)network).RecursiveActivation();
//for (var outs = 0; outs < outputCount; outs++)
//{
// Console.WriteLine("Difference in activation: " + Math.Abs(network.GetOutputSignal(outs) - saveOuts[outs]));
//}
Console.WriteLine("test reached past outputs " + t + " :" + "for" + n);
JObject test = new JObject();
test.Add("inputs", inputSamples);
test.Add("outputs", outputSamples);
inputsAndOutputs.Add(test);
Console.WriteLine("Ins/outs done " + t + " :" + "for" + n);
}
Console.WriteLine("tests ended:" + n);
//we add our inputs/outs for this json network
networkJSON.Add("tests", inputsAndOutputs);
//finally, we add our network json to the network array
networkArray.Add(networkJSON);
Console.WriteLine("Network finished:" + n);
}
Console.WriteLine("All newtorks finished, cleaning up");
//add our networks, and add our meta information
root.Add("networks", networkArray);
root.Add("meta", meta);
//and away we go! Let's save to file!
using (System.IO.StreamWriter file = new System.IO.StreamWriter("testgenomes.json"))
{
file.WriteLine(root.ToString());
}
}
void buildBodyExamples()
{
//we need to create random genomes, then save their generated bodies!
NeatParameters np = new NeatParameters();
IdGenerator idGen = new IdGenerator();
idGen.ResetNextInnovationNumber();
Random r = new Random();
JObject root = new JObject();
JObject meta = new JObject();
JArray genomeArray = new JArray();
//how many random input tests?
int genomeCount = 20;
meta.Add("genomeCount", genomeCount);
meta.Add("weightRange", HyperNEATParameters.weightRange);
NeatGenome seed = EvolutionManager.SharedEvolutionManager.getSeed();
int tEmpty = 0;
int emptyCount = genomeCount / 4;
for (int n = genomeArray.Count; n < genomeCount; n = genomeArray.Count)
{
//create our genome
var inputCount = r.Next(4) + 3;
var outputCount = r.Next(3) + 1;
//radnom inputs 3-6, random outputs 1-3
var genome = GenomeFactory.CreateGenomePreserveID(seed, idGen);//np, idGen, inputCount, outputCount, 1);
Hashtable nodeHT = new Hashtable();
Hashtable connHT = new Hashtable();
//mutate our genome
for (int m = 0; m < 20; m++)
{
((NeatGenome)genome).Mutate(np, idGen, nodeHT, connHT);
}
//now turn genome into a network
var network = genome.Decode(null);
//turn network into JSON, and save as the network object
//genomeJSON.Add("network", JObject.FromObject(network));
//now we need a body
bool isEmptyBody;
//convert to body object
var bodyObject = simpleCom.simpleExperiment.genomeIntoBodyObject(genome, out isEmptyBody);
if ((isEmptyBody && tEmpty++ < emptyCount) || (!isEmptyBody))
{
//create object and add body info to it, then save it in our array
JObject genomeJSON = new JObject();
genomeJSON.Add("genome", JObject.FromObject(genome, new JsonSerializer()
{
ReferenceLoopHandling = ReferenceLoopHandling.Ignore
}));
genomeJSON.Add("network", JObject.FromObject(network, new JsonSerializer()
{
ReferenceLoopHandling = ReferenceLoopHandling.Ignore
}));
//save our body object from test
genomeJSON.Add("body", JObject.FromObject(bodyObject));
genomeJSON.Add("isEmpty", isEmptyBody.ToString());
//finally, we add our network json to the body array
genomeArray.Add(genomeJSON);
}
}
//add our networks, and add our meta information
root.Add("genomeCount", genomeArray.Count);
root.Add("genomes", genomeArray);
root.Add("meta", meta);
//and away we go! Let's save to file!
using (System.IO.StreamWriter file = new System.IO.StreamWriter("testgenomebodies.json"))
{
file.WriteLine(root.ToString());
}
}