/// <summary>
/// Returns an IEnumerable that yields the mappings/connections defined by the mapping function (from the source nodes to
/// the target nodes) as a sequence. The alternative of returning a list would require a very long list in extreme scenarios;
/// this approach minimizes down memory usage.
/// </summary>
public IEnumerable<SubstrateConnection> GenerateConnections(SubstrateNodeSet srcNodeSet, SubstrateNodeSet tgtNodeSet)
{
// Test for scenario where srcNodeSet and tgtNodeSet are the same node set, that is, we are creating
// connections within a nodeset and therefore we need to test (and honour) _allowLocalRecurrentConnections.
if(srcNodeSet == tgtNodeSet)
{
// Mapping between nodes within a single node set.
// Break the inner loop into two. This avoids having to make the local recurrent test connection
// for every node pair - we only test when we actually have the same node as source and target.
IList<SubstrateNode> nodeList = srcNodeSet.NodeList;
int count = nodeList.Count;
for(int i=0; i<count; i++)
{
// Loop over all nodes prior to the i'th.
SubstrateNode srcNode = nodeList[i];
for(int j=0; j<i; j++)
{
if(_testNodePair(srcNode, nodeList[j])) {
yield return new SubstrateConnection(srcNode, nodeList[j]);
}
}
// Test for local recurrent connection.
if(_allowLocalRecurrentConnections && _testNodePair(srcNode, srcNode)) {
yield return new SubstrateConnection(srcNode, srcNode);
}
// Loop over all nodes after the i'th.
for(int j=i+1; j<count; j++)
{
if(_testNodePair(srcNode, nodeList[j])) {
yield return new SubstrateConnection(srcNode, nodeList[j]);
}
}
}
}
else
{
// Mapping between nodes in two distinct node sets.
foreach(SubstrateNode srcNode in srcNodeSet.NodeList)
{
foreach(SubstrateNode tgtNode in tgtNodeSet.NodeList)
{
if(_testNodePair(srcNode, tgtNode)) {
yield return new SubstrateConnection(srcNode, tgtNode);
}
}
}
}
}
/// <summary>
/// Creates a substrate to use to create network defintions/the genome decoder.
/// </summary>
/// <param name="visualFieldResolution">The visual field's pixel resolution, e.g. 11 means 11x11 pixels.</param>
/// <param name="lengthCppnInput">Indicates if the CPPNs being decoded have an extra input for specifying connection length.</param>
public static Substrate CreateSubstrate(int visualFieldResolution, bool lengthCppnInput = false)
{
// Create two layer 'sandwich' substrate.
int pixelCount = visualFieldResolution * visualFieldResolution;
double pixelSize = 2.0 / visualFieldResolution;
double originPixelXY = -1 + (pixelSize / 2.0);
SubstrateNodeSet inputLayer = new SubstrateNodeSet(pixelCount);
SubstrateNodeSet HiddenLayer = new SubstrateNodeSet(pixelCount);
SubstrateNodeSet outputLayer = new SubstrateNodeSet(pixelCount);
// Node IDs start at 1. (bias node is always zero).
uint inputId = 1;
uint outputId = (uint)(pixelCount + 1);
uint hiddenId = (uint)(2 * pixelCount + 2);
double yReal = originPixelXY;
for (int y = 0; y < visualFieldResolution; y++, yReal += pixelSize)
{
double xReal = originPixelXY;
for (int x = 0; x < visualFieldResolution; x++, xReal += pixelSize, inputId++, outputId++, hiddenId++)
{
//CJR: I leave the thrid dimintion in,cause I can ignore it when I'm adding inputs to the CPPN
//but use it to dicate what set of outputs to use
inputLayer.NodeList.Add(new SubstrateNode(inputId, new double[] { xReal, yReal, -1.0 }));
if ((x % 2 == 0 && y % 2 == 0) || ((x + 1) % 2 == 0 && (y + 1) % 2 == 0))
{
HiddenLayer.NodeList.Add(new SubstrateNode(hiddenId, new double[] { xReal, yReal, 0 }));
}
outputLayer.NodeList.Add(new SubstrateNode(outputId, new double[] { xReal, yReal, 1.0 }));
}
}
List<SubstrateNodeSet> nodeSetList = new List<SubstrateNodeSet>(3);
nodeSetList.Add(inputLayer);
nodeSetList.Add(outputLayer);
nodeSetList.Add(HiddenLayer);
//CJR: Fist and second layer must be input/output respectively to be validated by the substrate, so hidden is third
// Define connection mappings between layers/sets.
List<NodeSetMapping> nodeSetMappingList = new List<NodeSetMapping>(3);
nodeSetMappingList.Add(NodeSetMapping.Create(0, 2, (double?)null));
nodeSetMappingList.Add(NodeSetMapping.Create(2, 1, (double?)null));
// Construct substrate.
Substrate substrate = new Substrate(nodeSetList, DefaultActivationFunctionLibrary.CreateLibraryNeat(SteepenedSigmoid.__DefaultInstance), 0, 0.2, 5, nodeSetMappingList);
return substrate;
}
/// <summary>
/// Create a genome decoder for the experiment.
/// </summary>
protected override IGenomeDecoder<NeatGenome, IBlackBox> CreateHyperNeatGenomeDecoder()
{
// Create HyperNEAT network substrate.
uint nodeId = 1;
//-- Create input layer nodes.
var inputLayer = new SubstrateNodeSet(samples.Length);
for (int v = 0; v < samples.GetLength(0); v++) // variables
{
for (int i = 0; i < n; i++)
{
for (int j = 0; j < m; j++)
{
var x = 2 * (double)i / n - 1;
var y = 2 * (double)j / m - 1;
var z = -(double)v / samples.GetLength(0);
inputLayer.NodeList.Add(new SubstrateNode(nodeId++, new double[] { x, y, z }));
}
}
}
//-- Create output layer nodes.
var outputLayers = new SubstrateNodeSet[nbClusters];
for (var c = 0; c < nbClusters; c++) // clusters
{
outputLayers[c] = new SubstrateNodeSet(n * m);
for (int i = 0; i < n; i++)
{
for (int j = 0; j < m; j++)
{
var x = 2 * (double)i / n - 1;
var y = 2 * (double)j / m - 1;
var z = c / nbClusters;
outputLayers[c].NodeList.Add(new SubstrateNode(nodeId++, new double[] { x, y, z }));
}
}
}
// Connect up layers.
List<SubstrateNodeSet> nodeSetList = new List<SubstrateNodeSet>(1 + nbClusters);
nodeSetList.Add(inputLayer);
foreach (var layer in outputLayers)
{
nodeSetList.Add(layer);
}
List<NodeSetMapping> nodeSetMappingList = new List<NodeSetMapping>(nbClusters);
for (int i = 0; i < nbClusters; i++)
{
var inputLayerIdx = 0;
var outputLayerIdx = 1 + i;
nodeSetMappingList.Add(NodeSetMapping.Create(inputLayerIdx, outputLayerIdx, (double?)null));
}
// Construct substrate.
Substrate substrate = new Substrate(nodeSetList,
DefaultActivationFunctionLibrary.CreateLibraryNeat(SteepenedSigmoid.__DefaultInstance),
0, 0.2, 5,
nodeSetMappingList);
// Create genome decoder. Decodes to a neural network packaged with an activation scheme that defines a fixed number of activations per evaluation.
IGenomeDecoder<NeatGenome, IBlackBox> genomeDecoder = new HyperNeatDecoder(substrate, _activationSchemeCppn, _activationScheme, _lengthCppnInput);
return genomeDecoder;
}
/// <summary>
/// Creates a new HyperNEAT genome decoder that can be used to convert
/// a genome into a phenome.
/// </summary>
public IGenomeDecoder<NeatGenome, IBlackBox> CreateHyperNeatGenomeDecoder()
{
var game = Parameters.GameFunction(null, null);
int xTotal = game.Board.GetLength(0);
int yTotal = game.Board.GetLength(1);
// Create an input and an output layer for the HyperNEAT
// substrate. Each layer corresponds to the game board
// with 9 squares.
SubstrateNodeSet inputLayer = new SubstrateNodeSet(Parameters.Inputs);
SubstrateNodeSet outputLayer = new SubstrateNodeSet(Parameters.Outputs);
// Each node in each layer needs a unique ID.
uint uid = 1;
// The game board is represented as a 2-dimensional plane.
// Each square is at [0,...,1] in the x and y axis.
// Thus, the game board for TicTacToe looks like this:
//
// (0,1) | (0.5,1) | (1,1)
// (0,0.5) | (0.5,0.5) | (1,0.5)
// (0,0) | (0.5,0) | (1,0)
//
for (int x = 0; x < xTotal; x++)
for (int y = 0; y < yTotal; y++)
inputLayer.NodeList.Add(new SubstrateNode(uid++, new double[] { x, y }));
for (int x = 0; x < xTotal; x++)
for (int y = 0; y < yTotal; y++)
outputLayer.NodeList.Add(new SubstrateNode(uid++, new double[] { x, y }));
List<SubstrateNodeSet> nodeSetList = new List<SubstrateNodeSet>(2);
nodeSetList.Add(inputLayer);
nodeSetList.Add(outputLayer);
// Define a connection mapping from the input layer to the output layer.
List<NodeSetMapping> nodeSetMappingList = new List<NodeSetMapping>(1);
nodeSetMappingList.Add(NodeSetMapping.Create(0, 1, (double?)null));
// Construct the substrate using a plain sigmoid as the phenome's
// activation function. All weights under 0.2 will not generate
// connections in the final phenome.
List<ActivationFunctionInfo> fnList = new List<ActivationFunctionInfo>(5);
fnList.Add(new ActivationFunctionInfo(0, 0.2, Linear.__DefaultInstance));
fnList.Add(new ActivationFunctionInfo(1, 0.2, BipolarSigmoid.__DefaultInstance));
fnList.Add(new ActivationFunctionInfo(2, 0.2, Gaussian.__DefaultInstance));
fnList.Add(new ActivationFunctionInfo(3, 0.2, Sine.__DefaultInstance));
fnList.Add(new ActivationFunctionInfo(4, 0.2, PlainSigmoid.__DefaultInstance));
var activationFnLib = new DefaultActivationFunctionLibrary(fnList);
Substrate substrate = new Substrate(nodeSetList,
activationFnLib,
4, 0.2, 5, nodeSetMappingList);
// Create genome decoder. Decodes to a neural network packaged with
// an activation scheme that defines a fixed number of activations per evaluation.
IGenomeDecoder<NeatGenome, IBlackBox> genomeDecoder =
new HyperNeatDecoder(substrate,
NetworkActivationScheme.CreateCyclicFixedTimestepsScheme(4),
NetworkActivationScheme.CreateCyclicFixedTimestepsScheme(4),
false);
return genomeDecoder;
}
private void AddNode(SubstrateNodeSet nodeSet, uint id, double x, double y, double z)
{
nodeSet.NodeList.Add(new SubstrateNode(id, new double[] {x, y, z}));
}
/// <summary>
/// Create a genome decoder for the experiment.
/// </summary>
public IGenomeDecoder<NeatGenome,IBlackBox> CreateGenomeDecoder()
{
// Create HyperNEAT network substrate.
//-- Create input layer nodes.
SubstrateNodeSet inputLayer = new SubstrateNodeSet(13);
//-- Hip joint inputs.
// Left hip joint.
AddNode(inputLayer, 1, -1.0, +1.0, -1.0); // Angular velocity.
AddNode(inputLayer, 2, -0.5, +1.0, -1.0); // Angle.
// Right hip joint.
AddNode(inputLayer, 3, +0.5, +1.0, -1.0); // Angle.
AddNode(inputLayer, 4, +1.0, +1.0, -1.0); // Angular velocity.
//-- Knee joint inputs.
// Left knee joint.
AddNode(inputLayer, 5, -1.0, -1.0, -1.0); // Angular velocity.
AddNode(inputLayer, 6, -0.5, -1.0, -1.0); // Angle.
// Right knee joint.
AddNode(inputLayer, 7, +0.5, -1.0, -1.0); // Angular velocity.
AddNode(inputLayer, 8, +1.0, -1.0, -1.0); // Angle.
//-- Torso inputs.
AddNode(inputLayer, 9, 0.0, +1.0, -1.0); // Torso elevation.
AddNode(inputLayer, 10, 0.0, +0.75, -1.0); // Torso angle.
AddNode(inputLayer, 11, 0.0, +0.5, -1.0); // Torso angular velocity.
AddNode(inputLayer, 12, 0.0, +0.25, -1.0); // Velocity X.
AddNode(inputLayer, 13, 0.0, 0.0, -1.0); // Velocity Y.
//-- Output layer nodes.
SubstrateNodeSet outputLayer = new SubstrateNodeSet(4);
AddNode(outputLayer, 14, -1.0, +1.0, +1.0); // Left hip torque.
AddNode(outputLayer, 15, +1.0, +1.0, +1.0); // Right hip torque.
AddNode(outputLayer, 16, -1.0, -1.0, +1.0); // Left knee torque.
AddNode(outputLayer, 17, +1.0, -1.0, +1.0); // Right knee torque.
//-- Hidden layer nodes.
SubstrateNodeSet h1Layer = new SubstrateNodeSet(4);
AddNode(h1Layer, 18, -1.0, +1.0, 0.0);
AddNode(h1Layer, 19, +1.0, +1.0, 0.0);
AddNode(h1Layer, 20, -1.0, -1.0, 0.0);
AddNode(h1Layer, 21, +1.0, -1.0, 0.0);
// Connect up layers.
List<SubstrateNodeSet> nodeSetList = new List<SubstrateNodeSet>(2);
nodeSetList.Add(inputLayer);
nodeSetList.Add(outputLayer);
nodeSetList.Add(h1Layer);
List<NodeSetMapping> nodeSetMappingList = new List<NodeSetMapping>(1);
nodeSetMappingList.Add(NodeSetMapping.Create(0, 1, (double?)null)); // Input -> Output.
nodeSetMappingList.Add(NodeSetMapping.Create(0, 2, (double?)null)); // Input -> Hidden.
nodeSetMappingList.Add(NodeSetMapping.Create(2, 1, (double?)null)); // Hidden -> Output.
nodeSetMappingList.Add(NodeSetMapping.Create(1, 2, (double?)null)); // Output -> Hidden
// Construct substrate.
Substrate substrate = new Substrate(nodeSetList, DefaultActivationFunctionLibrary.CreateLibraryNeat(SteepenedSigmoid.__DefaultInstance), 0, 0.2, 5, nodeSetMappingList);
// Create genome decoder. Decodes to a neural network packaged with an activation scheme that defines a fixed number of activations per evaluation.
IGenomeDecoder<NeatGenome,IBlackBox> genomeDecoder = new HyperNeatDecoder(substrate, _activationSchemeCppn, _activationScheme, _lengthCppnInput);
return genomeDecoder;
}
/// <summary>
/// Creates a genome decoder. We split this code into a separate method so that it can be re-used by the problem domain visualization code
/// (it needs to decode genomes to phenomes in order to create a visualization).
/// </summary>
/// <param name="visualFieldResolution">The visual field's pixel resolution, e.g. 11 means 11x11 pixels.</param>
/// <param name="lengthCppnInput">Indicates if the CPPNs being decoded have an extra input for specifying connection length.</param>
public IGenomeDecoder<NeatGenome,IBlackBox> CreateGenomeDecoder(int visualFieldResolution, bool lengthCppnInput)
{
// Create two layer 'sandwich' substrate.
int pixelCount = visualFieldResolution * visualFieldResolution;
double pixelSize = BoxesVisualDiscriminationEvaluator.VisualFieldEdgeLength / visualFieldResolution;
double originPixelXY = -1 + (pixelSize/2.0);
SubstrateNodeSet inputLayer = new SubstrateNodeSet(pixelCount);
SubstrateNodeSet outputLayer = new SubstrateNodeSet(pixelCount);
// Node IDs start at 1. (bias node is always zero).
uint inputId = 1;
uint outputId = (uint)(pixelCount + 1);
double yReal = originPixelXY;
for(int y=0; y<visualFieldResolution; y++, yReal += pixelSize)
{
double xReal = originPixelXY;
for(int x=0; x<visualFieldResolution; x++, xReal += pixelSize, inputId++, outputId++)
{
inputLayer.NodeList.Add(new SubstrateNode(inputId, new double[] {xReal, yReal, -1.0}));
outputLayer.NodeList.Add(new SubstrateNode(outputId, new double[] {xReal, yReal, 1.0}));
}
}
List<SubstrateNodeSet> nodeSetList = new List<SubstrateNodeSet>(2);
nodeSetList.Add(inputLayer);
nodeSetList.Add(outputLayer);
// Define connection mappings between layers/sets.
List<NodeSetMapping> nodeSetMappingList = new List<NodeSetMapping>(1);
nodeSetMappingList.Add(NodeSetMapping.Create(0, 1,(double?)null));
// Construct substrate.
Substrate substrate = new Substrate(nodeSetList, DefaultActivationFunctionLibrary.CreateLibraryNeat(SteepenedSigmoid.__DefaultInstance), 0, 0.2, 5, nodeSetMappingList);
// Create genome decoder. Decodes to a neural network packaged with an activation scheme that defines a fixed number of activations per evaluation.
IGenomeDecoder<NeatGenome,IBlackBox> genomeDecoder = new HyperNeatDecoder(substrate, _activationSchemeCppn, _activationScheme, lengthCppnInput);
return genomeDecoder;
}
/// <summary>
/// Returns an estimate/hint for the number of connections that would be created between the provided source and target node sets.
/// </summary>
public int GetConnectionCountHint(SubstrateNodeSet srcNodeSet, SubstrateNodeSet tgtNodeSet)
{
if(null == _maximumConnectionDistance) {
return srcNodeSet.NodeList.Count * tgtNodeSet.NodeList.Count;
}
int count = 0;
foreach(SubstrateConnection conn in GenerateConnections(srcNodeSet, tgtNodeSet)) {
count++;
}
return count;
}
/// <summary>
/// Creates a new HyperNEAT genome decoder that can be used to convert a genome into a phenome.
/// </summary>
public IGenomeDecoder<NeatGenome, IBlackBox> CreateGenomeDecoder()
{
// Create an input and an output layer for the HyperNEAT
// substrate. Each layer corresponds to the game board
// with 9 squares.
SubstrateNodeSet inputLayer = new SubstrateNodeSet(9);
SubstrateNodeSet outputLayer = new SubstrateNodeSet(9);
// Each node in each layer needs a unique ID.
// The input nodes use ID range [1,9] and
// the output nodes use [10,18].
uint inputId = 1, outputId = 10;
// The game board is represented as a 2-dimensional plane.
// Each square is at -1, 0, or 1 in the x and y axis.
// Thus, the game board looks like this:
//
// (-1,1) | (0,1) | (1,1)
// (-1,0) | (0,0) | (1,0)
// (-1,-1) | (0,-1) | (1,-1)
//
// Note that the NeatPlayer class orders the board from
// left to right, then top to bottom. So we need to create
// nodes with the following IDs:
//
// 1 | 2 | 3
// 4 | 5 | 6
// 7 | 8 | 9
//
for(int x = -1; x <= 1; x++)
for (int y = 1; y >= -1; y--, inputId++, outputId++)
{
inputLayer.NodeList.Add(new SubstrateNode(inputId, new double[] { x, y }));
outputLayer.NodeList.Add(new SubstrateNode(outputId, new double[] { x, y }));
}
List<SubstrateNodeSet> nodeSetList = new List<SubstrateNodeSet>(2);
nodeSetList.Add(inputLayer);
nodeSetList.Add(outputLayer);
// Define a connection mapping from the input layer to the output layer.
List<NodeSetMapping> nodeSetMappingList = new List<NodeSetMapping>(1);
nodeSetMappingList.Add(NodeSetMapping.Create(0, 1, (double?)null));
// Construct the substrate using a steepened sigmoid as the phenome's
// activation function. All weights under 0.2 will not generate
// connections in the final phenome.
Substrate substrate = new Substrate(nodeSetList,
DefaultActivationFunctionLibrary.CreateLibraryCppn(),
0, 0.2, 5, nodeSetMappingList);
// Create genome decoder. Decodes to a neural network packaged with
// an activation scheme that defines a fixed number of activations per evaluation.
IGenomeDecoder<NeatGenome, IBlackBox> genomeDecoder =
new HyperNeatDecoder(substrate, _activationSchemeCppn, _activationScheme, false);
return genomeDecoder;
}
/// <summary>
/// Create a genome decoder for the experiment.
/// </summary>
protected override IGenomeDecoder<NeatGenome, IBlackBox> CreateHyperNeatGenomeDecoder()
{
// Create HyperNEAT network substrate.
uint nodeId = 1;
//-- Create input layer nodes.
SubstrateNodeSet inputLayer = new SubstrateNodeSet(_dataset.InputCount);
for (var i = 0; i < _dataset.InputCount; i++)
{
inputLayer.NodeList.Add(new SubstrateNode(nodeId++, SetInputNodePosition(i).Extend(-1)));
}
//-- Create output layer nodes.
var outputLayers = new SubstrateNodeSet[nbClusters];
for (var i = 0; i < nbClusters; i++)
{
outputLayers[i] = new SubstrateNodeSet(1);
outputLayers[i].NodeList.Add(new SubstrateNode(nodeId++, SetOutputNodePosition(i).Extend(+1 + i)));
}
//-- Create hidden layer nodes.
SubstrateNodeSet hiddenLayer = null;
if (HiddenNodesCount > 0)
{
hiddenLayer = new SubstrateNodeSet(HiddenNodesCount);
for (var i = 0; i < HiddenNodesCount; i++)
{
hiddenLayer.NodeList.Add(new SubstrateNode(nodeId++, SetHiddenNodePosition(i).Extend(0)));
}
}
// Connect up layers.
List<SubstrateNodeSet> nodeSetList = new List<SubstrateNodeSet>(2 + nbClusters + (HiddenNodesCount > 0 ? 1 : 0));
nodeSetList.Add(inputLayer);
for (var i = 0; i < nbClusters; i++)
{
nodeSetList.Add(outputLayers[i]);
}
if (HiddenNodesCount > 0)
{
nodeSetList.Add(hiddenLayer);
}
List<NodeSetMapping> nodeSetMappingList = new List<NodeSetMapping>(nbClusters * (1 + (HiddenNodesCount > 0 ? 2 : 0)));
var inputIdx = 0;
var hiddenIdx = nbClusters + 1;
for (var i = 0; i < nbClusters; i++)
{
var outputIdx = i + 1;
if (HiddenNodesCount > 0)
{
nodeSetMappingList.Add(NodeSetMapping.Create(inputIdx, hiddenIdx, (double?)null)); // Input -> Hidden.
nodeSetMappingList.Add(NodeSetMapping.Create(hiddenIdx, outputIdx, (double?)null)); // Hidden-> Output.
nodeSetMappingList.Add(NodeSetMapping.Create(inputIdx, outputIdx, (double?)null)); // Input -> Output.
}
else
{
nodeSetMappingList.Add(NodeSetMapping.Create(inputIdx, outputIdx, (double?)null)); // Input -> Output.
}
}
// Construct substrate.
Substrate substrate = new Substrate(nodeSetList,
DefaultActivationFunctionLibrary.CreateLibraryNeat(SteepenedSigmoid.__DefaultInstance),
0, 0.2, 5,
nodeSetMappingList);
// Create genome decoder. Decodes to a neural network packaged with an activation scheme that defines a fixed number of activations per evaluation.
IGenomeDecoder<NeatGenome, IBlackBox> genomeDecoder = new HyperNeatDecoder(substrate, _activationSchemeCppn, _activationScheme, _lengthCppnInput);
return genomeDecoder;
}
/// <summary>
/// Create a genome decoder for the experiment.
/// </summary>
protected override IGenomeDecoder<NeatGenome, IBlackBox> CreateHyperNeatGenomeDecoder()
{
// Create HyperNEAT network substrate.
uint nodeId = 1;
//-- Create input layer nodes.
var inputLayer = new SubstrateNodeSet(nbInputs * f2);
for (var i = 0; i < nbInputs; i++)
{
for (var j = 0; j < f; j++)
{
for (var k = 0; k < f; k++)
{
if (filter[j, k])
{
var x = (double)j / f - 0.5;
var y = (double)k / f - 0.5;
inputLayer.NodeList.Add(new SubstrateNode(nodeId++, new double[] { x, y, -1 - i }));
}
}
}
}
//-- Create hidden layer nodes.
var hiddenLayers = new SubstrateNodeSet[nbClusters];
for (var i = 0; i < nbClusters; i++)
{
hiddenLayers[i] = new SubstrateNodeSet(f2);
for (var j = 0; j < f; j++)
{
for (var k = 0; k < f; k++)
{
if (filter[j, k])
{
var x = (double)j / f - 0.5;
var y = (double)k / f - 0.5;
hiddenLayers[i].NodeList.Add(new SubstrateNode(nodeId++, new double[] { x, y, 0 }));
}
}
}
}
//-- Create output layer nodes.
var outputLayers = new SubstrateNodeSet[nbClusters];
for (var i = 0; i < nbClusters; i++)
{
outputLayers[i] = new SubstrateNodeSet(f2);
for (var j = 0; j < f; j++)
{
for (var k = 0; k < f; k++)
{
if (filter[j, k])
{
var x = (double)j / f - 0.5;
var y = (double)j / f - 0.5;
outputLayers[i].NodeList.Add(new SubstrateNode(nodeId++, new double[] { x, y, +1 + i }));
}
}
}
}
// Connect up layers.
List<SubstrateNodeSet> nodeSetList = new List<SubstrateNodeSet>(1 + 2 * nbClusters);
nodeSetList.Add(inputLayer);
foreach (var layer in hiddenLayers)
{
nodeSetList.Add(layer);
}
foreach (var layer in outputLayers)
{
nodeSetList.Add(layer);
}
List<NodeSetMapping> nodeSetMappingList = new List<NodeSetMapping>(2 * nbClusters);
for (int i = 0; i < nbClusters; i++)
{
var inputLayerIdx = 0;
var hiddenLayerIdx = 1 + i;
var outputLayerIdx = 1 + nbClusters + i;
nodeSetMappingList.Add(NodeSetMapping.Create(inputLayerIdx, hiddenLayerIdx, (double?)null));
nodeSetMappingList.Add(NodeSetMapping.Create(hiddenLayerIdx, outputLayerIdx, (double?)null));
}
// Construct substrate.
Substrate substrate = new Substrate(nodeSetList,
DefaultActivationFunctionLibrary.CreateLibraryNeat(SteepenedSigmoid.__DefaultInstance),
0, 0.2, 5,
nodeSetMappingList);
// Create genome decoder. Decodes to a neural network packaged with an activation scheme that defines a fixed number of activations per evaluation.
IGenomeDecoder<NeatGenome, IBlackBox> genomeDecoder = new HyperNeatDecoder(substrate, _activationSchemeCppn, _activationScheme, _lengthCppnInput);
return genomeDecoder;
}
public IGenomeDecoder<NeatGenome, IBlackBox> CreateGenomeDecoder(bool lengthCppnInput)
{
// Create two layer sandwhich substract substrate. Inputs on bottom of cube and Outputs are on the top.
SubstrateNodeSet inputLayer = new SubstrateNodeSet(Constants.INPUT_SIZE);
SubstrateNodeSet outputLayer = new SubstrateNodeSet(Constants.OUTPUT_SIZE);
for (uint height = 0; height < Constants.INPUT_HEIGHT; height++)
{
for (uint width = 0; width < Constants.INPUT_WIDTH; width++)
{
// start with 1 because of the bias node is 0
uint inputID = (height * Constants.INPUT_WIDTH) + width + 1;
// Get X and Y positions on the hypercube.
double posX = -1.0 + ((width * 1.0D / Constants.INPUT_WIDTH) * 2);
double posY = -1.0 + ((height * 1.0D / Constants.INPUT_HEIGHT) * 2);
// Add nodes to inputs
inputLayer.NodeList.Add(new SubstrateNode(inputID, new double[] { posX, posY, -1.0 }));
}
}
for (uint height = 0; height < Constants.OUTPUT_HEIGHT; height++)
{
for (uint width = 0; width < Constants.OUTPUT_WIDTH; width++)
{
// start with INPUT_SIZE + 1 because id's need to be unique
uint outputID = Constants.INPUT_SIZE + (height * Constants.OUTPUT_WIDTH) + width + 1;
// Get X and Y positions on the hypercube.
double posX = -1.0 + ((width * 1.0D / Constants.OUTPUT_WIDTH) * 2);
double posY = -1.0 + ((height * 1.0D / Constants.OUTPUT_HEIGHT) * 2);
// Add nodes to ouputs
outputLayer.NodeList.Add(new SubstrateNode(outputID, new double[] { posX, posY, 1.0 }));
}
}
List<SubstrateNodeSet> nodeSetList = new List<SubstrateNodeSet>(2);
nodeSetList.Add(inputLayer);
nodeSetList.Add(outputLayer);
// Define connection mappings between layers/sets.
List<NodeSetMapping> nodeSetMappingList = new List<NodeSetMapping>(1);
nodeSetMappingList.Add(NodeSetMapping.Create(0, 1, (double?)null));
// Construct substrate.
Substrate substrate = new Substrate(nodeSetList, GetCppnActivationFunctionLibrary(), 0, Constants.THRESHOLD_WEIGHT, Constants.MAX_WEIGHT, nodeSetMappingList);
// Create genome decoder. Decodes to a neural network packaged with an activation scheme that defines a fixed number of activations per evaluation.
IGenomeDecoder<NeatGenome, IBlackBox> genomeDecoder = new HyperNeatDecoder(substrate, _activationSchemeCppn, _activationScheme, lengthCppnInput);
return genomeDecoder;
}
/// <summary>
/// Creates a genome decoder. We split this code into a separate method so that it can be re-used by the problem domain visualization code
/// (it needs to decode genomes to phenomes in order to create a visualization).
/// </summary>
/// <param name="visualFieldResolution">The visual field's pixel resolution, e.g. 11 means 11x11 pixels.</param>
/// <param name="lengthCppnInput">Indicates if the CPPNs being decoded have an extra input for specifying connection length.</param>
public IGenomeDecoder<NeatGenome,IBlackBox> CreateGenomeDecoder(int visualFieldResolution, bool lengthCppnInput)
{
// Create two layer 'sandwich' substrate.
int pixelCount = visualFieldResolution * visualFieldResolution;
double pixelSize = BoxesVisualDiscriminationEvaluator.VisualFieldEdgeLength / visualFieldResolution;
double originPixelXY = -1 + (pixelSize/2.0);
SubstrateNodeSet inputLayer = new SubstrateNodeSet(pixelCount);
SubstrateNodeSet outputLayer = new SubstrateNodeSet(pixelCount);
// Node IDs start at 1. (bias node is always zero).
uint inputId = 1;
uint outputId = (uint)(pixelCount + 1);
double yReal = originPixelXY;
for(int y=0; y<visualFieldResolution; y++, yReal += pixelSize)
{
double xReal = originPixelXY;
for(int x=0; x<visualFieldResolution; x++, xReal += pixelSize, inputId++, outputId++)
{
inputLayer.NodeList.Add(new SubstrateNode(inputId, new double[] {xReal, yReal, -1.0}));
outputLayer.NodeList.Add(new SubstrateNode(outputId, new double[] {xReal, yReal, 1.0}));
}
}
/*
//////////////////////////////////////////////////////////////////////////////
// Create two layer substrate.
SubstrateNodeSet inputLayer = new SubstrateNodeSet(Constants.INPUT_SIZE);
SubstrateNodeSet outputLayer = new SubstrateNodeSet(Constants.FULLY_CONNECTED_SIZE);
// Inputs to Outputs Mapping
// 1 1 2 2 3 3
// 1 2 3 1 1 2 2 3 3
// 4 5 6 ---> 4 4 5 5 6 6
// 7 8 9 4 4 5 5 6 6
// 7 7 8 8 9 9
// 7 7 8 8 9 9
for (uint width = 0; width < Constants.INPUT_WIDTH; width++)
{
for (uint height = 0; height < Constants.INPUT_HEIGHT; height++)
{
// start + 1 because of bias node
uint inputID = (width * Constants.INPUT_HEIGHT) + height + 1;
inputLayer.NodeList.Add(new SubstrateNode(inputID, new double[] { inputID }));
}
}
// we're fully connected so we will have NEXT_LAYER_SIZE * IMAGE_SIZE weights. This is a lot. yes.
for (uint height = 0; height < Constants.OUTPUT_SIZE; height++)
{
for (uint width = 0; width < Constants.INPUT_SIZE; width++)
{
uint outputID = Constants.INPUT_SIZE + (height * Constants.INPUT_SIZE) + width + 1;
outputLayer.NodeList.Add(new SubstrateNode(outputID, new double[] { outputID }));
}
}
///////////////////////////////////////////////////////////////////////////
*/
List<SubstrateNodeSet> nodeSetList = new List<SubstrateNodeSet>(2);
nodeSetList.Add(inputLayer);
nodeSetList.Add(outputLayer);
// Define connection mappings between layers/sets.
List<NodeSetMapping> nodeSetMappingList = new List<NodeSetMapping>(1);
nodeSetMappingList.Add(NodeSetMapping.Create(0, 1,(double?)null));
// Construct substrate.
//Substrate substrate = new Substrate(nodeSetList, DefaultActivationFunctionLibrary.CreateLibraryNeat(SteepenedSigmoid.__DefaultInstance), 0, 0.2, 5, nodeSetMappingList);
Substrate substrate = new Substrate(nodeSetList, DefaultActivationFunctionLibrary.CreateLibraryCppn(), 0, 0.2, 5, nodeSetMappingList);
// Create genome decoder. Decodes to a neural network packaged with an activation scheme that defines a fixed number of activations per evaluation.
IGenomeDecoder<NeatGenome,IBlackBox> genomeDecoder = new HyperNeatDecoder(substrate, _activationSchemeCppn, _activationScheme, lengthCppnInput);
return genomeDecoder;
}
/// <summary>
/// Returns an IEnumerable that yields the mappings/connections defined by the mapping function (from the source nodes to
/// the target nodes) as a sequence. The alternative of returning a list would require a very long list in extreme scenarios;
/// this approach minimizes down memory usage.
/// </summary>
public IEnumerable <SubstrateConnection> GenerateConnections(SubstrateNodeSet srcNodeSet, SubstrateNodeSet tgtNodeSet)
{
// Test for scenario where srcNodeSet and tgtNodeSet are the same node set, that is, we are creating
// connections within a nodeset and therefore we need to test (and honour) _allowLocalRecurrentConnections.
if (srcNodeSet == tgtNodeSet)
{
// Mapping between nodes within a single node set.
// Break the inner loop into two. This avoids having to make the local recurrent test connection
// for every node pair - we only test when we actually have the same node as source and target.
IList <SubstrateNode> nodeList = srcNodeSet.NodeList;
int count = nodeList.Count;
for (int i = 0; i < count; i++)
{
// Loop over all nodes prior to the i'th.
SubstrateNode srcNode = nodeList[i];
for (int j = 0; j < i; j++)
{
if (_testNodePair(srcNode, nodeList[j]))
{
yield return(new SubstrateConnection(srcNode, nodeList[j]));
}
}
// Test for local recurrent connection.
if (_allowLocalRecurrentConnections && _testNodePair(srcNode, srcNode))
{
yield return(new SubstrateConnection(srcNode, srcNode));
}
// Loop over all nodes after the i'th.
for (int j = i + 1; j < count; j++)
{
if (_testNodePair(srcNode, nodeList[j]))
{
yield return(new SubstrateConnection(srcNode, nodeList[j]));
}
}
}
}
else
{
// Mapping between nodes in two distinct node sets.
foreach (SubstrateNode srcNode in srcNodeSet.NodeList)
{
foreach (SubstrateNode tgtNode in tgtNodeSet.NodeList)
{
if (_testNodePair(srcNode, tgtNode))
{
yield return(new SubstrateConnection(srcNode, tgtNode));
}
}
}
}
}
