/// <summary>
/// Create a sandwich substrate. A sandwich has an input layer connected
/// directly to an output layer, both are square.
/// </summary>
/// <param name="inputEdgeSize">The input edge size.</param>
/// <param name="outputEdgeSize">The output edge size.</param>
/// <returns>The substrate.</returns>
public static Substrate factorSandwichSubstrate(int inputEdgeSize,
int outputEdgeSize)
{
Substrate result = new Substrate(3);
double inputTick = 2.0 / inputEdgeSize;
double outputTick = 2.0 / inputEdgeSize;
double inputOrig = -1.0 + (inputTick / 2.0);
double outputOrig = -1.0 + (inputTick / 2.0);
// create the input layer
for (int row = 0; row < inputEdgeSize; row++)
{
for (int col = 0; col < inputEdgeSize; col++)
{
SubstrateNode inputNode = result.CreateInputNode();
inputNode.Location[0] = -1;
inputNode.Location[1] = inputOrig + (row * inputTick);
inputNode.Location[2] = inputOrig + (col * inputTick);
}
}
// create the output layer (and connect to input layer)
for (int orow = 0; orow < outputEdgeSize; orow++)
{
for (int ocol = 0; ocol < outputEdgeSize; ocol++)
{
SubstrateNode outputNode = result.CreateOutputNode();
outputNode.Location[0] = 1;
outputNode.Location[1] = outputOrig + (orow * outputTick);
outputNode.Location[2] = outputOrig + (ocol * outputTick);
// link this output node to every input node
foreach (SubstrateNode inputNode in result.InputNodes)
{
result.CreateLink(inputNode, outputNode);
}
}
}
return(result);
}
/// <inheritdoc/>
public IMLMethod Decode(NEATPopulation pop, Substrate.Substrate substrate,
IGenome genome)
{
// obtain the CPPN
NEATCODEC neatCodec = new NEATCODEC();
NEATNetwork cppn = (NEATNetwork)neatCodec.Decode(genome);
List <NEATLink> linkList = new List <NEATLink>();
IActivationFunction[] afs = new IActivationFunction[substrate.NodeCount];
IActivationFunction af = new ActivationSteepenedSigmoid();
// all activation functions are the same
for (int i = 0; i < afs.Length; i++)
{
afs[i] = af;
}
double c = this.MaxWeight / (1.0 - this.MinWeight);
BasicMLData input = new BasicMLData(cppn.InputCount);
// First create all of the non-bias links.
foreach (SubstrateLink link in substrate.Links)
{
SubstrateNode source = link.Source;
SubstrateNode target = link.Target;
int index = 0;
foreach (double d in source.Location)
{
input.Data[index++] = d;
}
foreach (double d in target.Location)
{
input.Data[index++] = d;
}
IMLData output = cppn.Compute(input);
double weight = output[0];
if (Math.Abs(weight) > this.MinWeight)
{
weight = (Math.Abs(weight) - this.MinWeight) * c
* Math.Sign(weight);
linkList.Add(new NEATLink(source.ID, target.ID,
weight));
}
}
// now create biased links
input.Clear();
int d2 = substrate.Dimensions;
IList <SubstrateNode> biasedNodes = substrate.GetBiasedNodes();
foreach (SubstrateNode target in biasedNodes)
{
for (int i = 0; i < d2; i++)
{
input.Data[d2 + i] = target.Location[i];
}
IMLData output = cppn.Compute(input);
double biasWeight = output[1];
if (Math.Abs(biasWeight) > this.MinWeight)
{
biasWeight = (Math.Abs(biasWeight) - this.MinWeight) * c
* Math.Sign(biasWeight);
linkList.Add(new NEATLink(0, target.ID, biasWeight));
}
}
// check for invalid neural network
if (linkList.Count == 0)
{
return(null);
}
linkList.Sort();
NEATNetwork network = new NEATNetwork(substrate.InputCount,
substrate.OutputCount, linkList, afs);
network.ActivationCycles = substrate.ActivationCycles;
return(network);
}
/// <summary>
/// Constructs with the specified source and target substrate nodes.
/// </summary>
public SubstrateConnection(SubstrateNode srcNode, SubstrateNode tgtNode)
{
_srcNode = srcNode;
_tgtNode = tgtNode;
}
/// <summary>
/// Constructs with the specified source and target substrate nodes.
/// </summary>
public SubstrateConnection(SubstrateNode srcNode, SubstrateNode tgtNode)
{
_srcNode = srcNode;
_tgtNode = tgtNode;
}
/// <summary>
///
/// </summary>
/// <param name="substrateXml"></param>
/// <param name="substrateSettingsXml"></param>
/// <param name="multispatial"></param>
/// <returns></returns>
public static ISubstrate ReadSubstrateFromXml(XmlElement substrateXml, XmlElement substrateSettingsXml)
{
var activationFunction = CreateActivationFunctionFromString(XmlUtils.GetValueAsString(substrateSettingsXml, "Function"));
var weightThreshold = XmlUtils.TryGetValueAsDouble(substrateSettingsXml, "WeightThreshold") ?? 0.2;
var maxWeight = XmlUtils.TryGetValueAsDouble(substrateSettingsXml, "MaxWeight") ?? 5.0;
bool multispatial = XmlUtils.TryGetValueAsBool(substrateSettingsXml, "Multispatial") ?? false;
bool leo = XmlUtils.TryGetValueAsBool(substrateSettingsXml, "Leo") ?? false;
var layerlist = new List <SubstrateNodeSet>();
var nodes = new Dictionary <uint, SubstrateNode>();
uint nodeid = 1;
foreach (XmlElement layer in substrateXml.GetElementsByTagName("Layer"))
{
SubstrateNodeSet.LayerType type;
if (!Enum.TryParse(layer.GetAttribute("type"), out type))
{
throw new Exception("Layer type must be defined as Input/Output/Hidden");
}
var tmp = new SubstrateNodeSet(layer.ChildNodes.Count, type);
foreach (XmlNode n in layer.ChildNodes)
{
if (n is XmlComment)
{
continue;
}
var node = (XmlElement)n;
var tmpNode = new SubstrateNode(nodeid, Array.ConvertAll(node.InnerText.Split(','), double.Parse));
tmp.NodeList.Add(tmpNode);
nodes.Add(nodeid, tmpNode);
nodeid++;
}
layerlist.Add(tmp);
}
XmlNodeList mappings = substrateXml.GetElementsByTagName("Mapping");
XmlNodeList connections = substrateXml.GetElementsByTagName("Connection");
ISubstrate retval;
if (connections.Count > 0)
{
var connectionList = new List <SubstrateConnection>();
foreach (XmlElement connection in connections)
{
var ids = Array.ConvertAll(connection.InnerText.Split(','), uint.Parse);
connectionList.Add(new SubstrateConnection(nodes[ids[0]], nodes[ids[1]]));
}
retval = multispatial ? (ISubstrate) new MultiSpatialSubstrate(layerlist, activationFunction, 0,
weightThreshold, maxWeight, connectionList) : new Substrate(layerlist, activationFunction, 0,
weightThreshold, maxWeight, connectionList);
}
else if (mappings.Count > 0)
{
var mappingList = new List <NodeSetMapping>();
foreach (XmlElement mapping in mappings)
{
var ids = Array.ConvertAll(mapping.InnerText.Split(','), int.Parse);
double maxDist;
double?maxDistN = null;
if (double.TryParse(mapping.GetAttribute("maxDist"), out maxDist))
{
maxDistN = maxDist;
}
mappingList.Add(NodeSetMapping.Create(ids[0], ids[1], maxDistN));
}
retval = multispatial ? (ISubstrate) new MultiSpatialSubstrate(layerlist, activationFunction, 0,
weightThreshold, maxWeight, mappingList) : new Substrate(layerlist, activationFunction, 0,
weightThreshold, maxWeight, mappingList);
}
else
{
throw new XmlException("Faulty substrate definition, at least one Mapping or Connection element must be defined.");
}
retval.Leo = leo;
return(retval);
}
