/// <summary>
/// Reads a NeatGenome from XML.
/// </summary>
/// <param name="xr">The XmlReader to read from.</param>
/// <param name="nodeFnIds">Indicates if node activation function IDs
/// should be read. They are required for HyperNEAT genomes but not for NEAT</param>
public static NeatGenome ReadGenome(XmlReader xr, bool nodeFnIds)
{
// Find <Network>.
XmlIoUtils.MoveToElement(xr, false, __ElemNetwork);
int initialDepth = xr.Depth;
// Read genome ID attribute if present. Otherwise default to zero;
// it's the caller's responsibility to check IDs are unique and
// in-line with the genome factory's ID generators.
string genomeIdStr = xr.GetAttribute(__AttrId);
uint genomeId;
uint.TryParse(genomeIdStr, out genomeId);
// Read birthGeneration attribute if present. Otherwise default to zero.
string birthGenStr = xr.GetAttribute(__AttrBirthGeneration);
uint birthGen;
uint.TryParse(birthGenStr, out birthGen);
// Read fitness attribute if present. Otherwise default to zero.
string fitnessStr = xr.GetAttribute(__AttrFitness);
double fitness;
double.TryParse(fitnessStr, out fitness);
// Find <Nodes>.
XmlIoUtils.MoveToElement(xr, true, __ElemNodes);
// Create a reader over the <Nodes> sub-tree.
int inputNodeCount = 0;
int outputNodeCount = 0;
int regulatoryCount = 0;
int localInCount = 0;
int localOutCount = 0;
// Used to count local input and output neurons (which are not
// found in the base module = 0)
int activeModule = 1;
NeuronGeneList nGeneList = new NeuronGeneList();
using (XmlReader xrSubtree = xr.ReadSubtree())
{
// Re-scan for the root <Nodes> element.
XmlIoUtils.MoveToElement(xrSubtree, false);
// Move to first node elem.
XmlIoUtils.MoveToElement(xrSubtree, true, __ElemNode);
// Read node elements.
do
{
NodeType neuronType =
NetworkXmlIO.ReadAttributeAsNodeType(xrSubtree, __AttrType);
uint id = XmlIoUtils.ReadAttributeAsUInt(xrSubtree, __AttrId);
int functionId = GetFunctionId(neuronType);
int module = XmlIoUtils.ReadAttributeAsInt(xrSubtree, __AttrModule);
int pandemonium;
// If we have a regulatory neuron, we read its pandemonium label
if (neuronType == NodeType.Regulatory)
{
pandemonium = XmlIoUtils.ReadAttributeAsInt(xrSubtree, __AttrPandemonium);
}
// Otherwise it is simply -1
else
{
pandemonium = -1;
}
double[] auxState = null;
if (nodeFnIds)
{ // Read activation fn ID.
functionId = XmlIoUtils.ReadAttributeAsInt(xrSubtree,
__AttrActivationFunctionId);
// Read aux state as comma seperated list of real values.
auxState = XmlIoUtils.ReadAttributeAsDoubleArray(xrSubtree,
__AttrAuxState);
}
NeuronGene nGene = new NeuronGene(id, neuronType, functionId,
module, pandemonium, auxState);
nGeneList.Add(nGene);
// Track the number of input and output nodes.
switch (neuronType)
{
case NodeType.Input:
++inputNodeCount;
break;
case NodeType.Output:
++outputNodeCount;
break;
case NodeType.Regulatory:
++regulatoryCount;
break;
case NodeType.Local_Input:
if (module == activeModule)
{
++localInCount;
}
else
{
// Found a new module, discard previous count
activeModule = module;
localInCount = 1;
localOutCount = 0;
}
break;
case NodeType.Local_Output:
// Here we do not care about the correct module,
// because that has been considered in the local input
// count (and local input always comes first).
++localOutCount;
break;
}
}while(xrSubtree.ReadToNextSibling(__ElemNode));
}
// Find <Connections>.
XmlIoUtils.MoveToElement(xr, false, __ElemConnections);
// Create a reader over the <Connections> sub-tree.
ConnectionGeneList cGeneList = new ConnectionGeneList();
using (XmlReader xrSubtree = xr.ReadSubtree())
{
// Re-scan for the root <Connections> element.
XmlIoUtils.MoveToElement(xrSubtree, false);
// Move to first connection elem.
string localName = XmlIoUtils.MoveToElement(xrSubtree, true);
if (localName == __ElemConnection)
{ // We have at least one connection.
// Read connection elements.
do
{
uint id = XmlIoUtils.ReadAttributeAsUInt(xrSubtree, __AttrId);
uint srcId = XmlIoUtils.ReadAttributeAsUInt(xrSubtree, __AttrSourceId);
uint tgtId = XmlIoUtils.ReadAttributeAsUInt(xrSubtree, __AttrTargetId);
double weight = XmlIoUtils.ReadAttributeAsDouble(xrSubtree, __AttrWeight);
int module = XmlIoUtils.ReadAttributeAsInt(xrSubtree, __AttrModule);
bool protect = XmlIoUtils.ReadAttributeAsBool(xrSubtree, __AttrProtected);
ConnectionGene cGene = new ConnectionGene(id, srcId, tgtId,
weight, module,
protect);
cGeneList.Add(cGene);
}while(xrSubtree.ReadToNextSibling(__ElemConnection));
}
}
// Move the reader beyond the closing tags </Connections> and </Network>.
do
{
if (xr.Depth <= initialDepth)
{
break;
}
}while(xr.Read());
// Construct and return loaded NeatGenome. We construct it first
// so we can access its properties before leaving.
bool rebuildConnectivity = true;
// Integrity will fail if we attempt to create the genome before
// updating some of the statistics (counts for each type of neurons,
// etc). It can be done after that step!
bool shouldAssertIntegrity = false;
NeatGenome genome = new NeatGenome(null, genomeId, birthGen, nGeneList,
cGeneList, rebuildConnectivity,
shouldAssertIntegrity);
if (genomeFactory != null)
{
// Note genomeFactory is not fully initialized yet, but it is needed to create
// an EvaluationInfo structure.
genome.GenomeFactory = genomeFactory;
genome.EvaluationInfo.SetFitness(fitness);
}
// We update count variables. While it is true most are static
// variables, loading genomes is done only once, so we can afford
// to count them for each genome.
genome.Input = inputNodeCount;
genome.Output = outputNodeCount;
genome.Regulatory = regulatoryCount;
genome.LocalIn = localInCount;
genome.LocalOut = localOutCount;
// We use base for neurons InHiddenModules
genome.NeuronGeneList.LocateLastBase();
genome.InHiddenModulesFromLoad();
genome.ActiveConnectionsFromLoad();
// Before this was done only once after creating all genomes. However,
// we need these values if we want to perform an integrity check.
// The performance overhead is negligible (specially in a one-time method)
// and reliability is increased this way.
genome.NeuronGeneList.LocateLastBase();
genome.NeuronGeneList.LocateFirstIndex();
genome.ConnectionGeneList.LocateFirstId();
Debug.Assert(genome.PerformIntegrityCheck());
return(genome);
}
/// <summary>
/// Reads a NeatGenome from XML.
/// </summary>
/// <param name="xr">The XmlReader to read from.</param>
/// <param name="nodeFnIds">Indicates if node activation function IDs should be read. They are required
/// for HyperNEAT genomes but not for NEAT</param>
public static NeatGenome ReadGenome(XmlReader xr, bool nodeFnIds)
{
// Find <Network>.
XmlIoUtils.MoveToElement(xr, false, __ElemNetwork);
int initialDepth = xr.Depth;
// Read genome ID attribute if present. Otherwise default to zero; it's the caller's responsibility to
// check IDs are unique and in-line with the genome factory's ID generators.
string genomeIdStr = xr.GetAttribute(__AttrId);
uint genomeId;
uint.TryParse(genomeIdStr, out genomeId);
// Read birthGeneration attribute if present. Otherwise default to zero.
string birthGenStr = xr.GetAttribute(__AttrBirthGeneration);
uint birthGen;
uint.TryParse(birthGenStr, out birthGen);
// Find <Nodes>.
XmlIoUtils.MoveToElement(xr, true, __ElemNodes);
// Create a reader over the <Nodes> sub-tree.
int inputNodeCount = 0;
int outputNodeCount = 0;
NeuronGeneList nGeneList = new NeuronGeneList();
using (XmlReader xrSubtree = xr.ReadSubtree())
{
// Re-scan for the root <Nodes> element.
XmlIoUtils.MoveToElement(xrSubtree, false);
// Move to first node elem.
XmlIoUtils.MoveToElement(xrSubtree, true, __ElemNode);
// Read node elements.
do
{
NodeType neuronType = NetworkXmlIO.ReadAttributeAsNodeType(xrSubtree, __AttrType);
uint id = XmlIoUtils.ReadAttributeAsUInt(xrSubtree, __AttrId);
int functionId = 0;
double[] auxState = null;
if (nodeFnIds)
{ // Read activation fn ID.
functionId = XmlIoUtils.ReadAttributeAsInt(xrSubtree, __AttrActivationFunctionId);
// Read aux state as comma separated list of real values.
auxState = XmlIoUtils.ReadAttributeAsDoubleArray(xrSubtree, __AttrAuxState);
}
NeuronGene nGene = new NeuronGene(id, neuronType, functionId, auxState);
nGeneList.Add(nGene);
// Track the number of input and output nodes.
switch (neuronType)
{
case NodeType.Input:
inputNodeCount++;
break;
case NodeType.Output:
outputNodeCount++;
break;
}
}while(xrSubtree.ReadToNextSibling(__ElemNode));
}
// Find <Connections>.
XmlIoUtils.MoveToElement(xr, false, __ElemConnections);
// Create a reader over the <Connections> sub-tree.
ConnectionGeneList cGeneList = new ConnectionGeneList();
using (XmlReader xrSubtree = xr.ReadSubtree())
{
// Re-scan for the root <Connections> element.
XmlIoUtils.MoveToElement(xrSubtree, false);
// Move to first connection elem.
string localName = XmlIoUtils.MoveToElement(xrSubtree, true);
if (localName == __ElemConnection)
{ // We have at least one connection.
// Read connection elements.
do
{
uint id = XmlIoUtils.ReadAttributeAsUInt(xrSubtree, __AttrId);
uint srcId = XmlIoUtils.ReadAttributeAsUInt(xrSubtree, __AttrSourceId);
uint tgtId = XmlIoUtils.ReadAttributeAsUInt(xrSubtree, __AttrTargetId);
double weight = XmlIoUtils.ReadAttributeAsDouble(xrSubtree, __AttrWeight);
ConnectionGene cGene = new ConnectionGene(id, srcId, tgtId, weight);
cGeneList.Add(cGene);
}while(xrSubtree.ReadToNextSibling(__ElemConnection));
}
}
// Move the reader beyond the closing tags </Connections> and </Network>.
do
{
if (xr.Depth <= initialDepth)
{
break;
}
}while(xr.Read());
// Construct and return loaded NeatGenome.
return(new NeatGenome(null, genomeId, birthGen, nGeneList, cGeneList, inputNodeCount, outputNodeCount, true));
}