private static void AssertConnections(
ConnectionGenes <T> connGenes,
DirectedGraph digraph,
INodeIdMap nodeIndexByIdMap,
int[]?connectionIndexMap)
{
// Connection counts.
Debug.Assert(connGenes._connArr.Length == digraph.ConnectionIdArrays.Length);
// Connection order.
Debug.Assert(SortUtils.IsSortedAscending(connGenes._connArr));
Debug.Assert(IsSortedAscending(digraph.ConnectionIdArrays));
// Connection node ID mappings.
DirectedConnection[] connArr = connGenes._connArr;
int[] srcIdArr = digraph.ConnectionIdArrays._sourceIdArr;
int[] tgtIdArr = digraph.ConnectionIdArrays._targetIdArr;
for (int i = 0; i < connGenes._connArr.Length; i++)
{
// Determine the index of the equivalent connection in the digraph.
int genomeConnIdx = (connectionIndexMap is null) ? i : connectionIndexMap[i];
Debug.Assert(nodeIndexByIdMap.Map(connArr[genomeConnIdx].SourceId) == srcIdArr[i]);
Debug.Assert(nodeIndexByIdMap.Map(connArr[genomeConnIdx].TargetId) == tgtIdArr[i]);
}
}
public static DirectedGraph CreateDirectedGraph <T>(
MetaNeatGenome <T> metaNeatGenome,
ConnectionGenes <T> connGenes,
INodeIdMap nodeIndexByIdMap)
where T : struct
{
// Extract/copy the neat genome connectivity graph into an array of DirectedConnection.
// Notes.
// The array contents will be manipulated, so copying this avoids modification of the genome's
// connection gene list.
// The IDs are substituted for node indexes here.
CopyAndMapIds(
connGenes._connArr,
nodeIndexByIdMap,
out ConnectionIdArrays connIdArrays);
// Construct a new DirectedGraph.
var digraph = new DirectedGraph(
connIdArrays,
metaNeatGenome.InputNodeCount,
metaNeatGenome.OutputNodeCount,
nodeIndexByIdMap.Count);
return(digraph);
}
public static void AssertIsValid(
MetaNeatGenome <T> metaNeatGenome,
int id,
int birthGeneration,
ConnectionGenes <T> connGenes,
int[] hiddenNodeIdArr,
INodeIdMap nodeIndexByIdMap,
DirectedGraph digraph,
int[] connectionIndexMap)
{
// Mandatory ref tests.
Debug.Assert(null != metaNeatGenome);
Debug.Assert(null != connGenes);
Debug.Assert(null != hiddenNodeIdArr);
Debug.Assert(null != nodeIndexByIdMap);
Debug.Assert(null != digraph);
// Acyclic graph checks.
if (metaNeatGenome.IsAcyclic)
{
AssertAcyclicGraph(metaNeatGenome, digraph, connectionIndexMap);
}
// Node counts.
AssertNodeCounts(metaNeatGenome, hiddenNodeIdArr, nodeIndexByIdMap, digraph);
// Hidden node IDs.
Debug.Assert(ConnectionGenesUtils.ValidateHiddenNodeIds(hiddenNodeIdArr, connGenes._connArr, metaNeatGenome.InputOutputNodeCount));
// Connections.
AssertConnections(connGenes, digraph, nodeIndexByIdMap, connectionIndexMap);
}
/// <summary>
/// Constructs with the provided ID, birth generation and gene arrays.
/// </summary>
internal NeatGenome(
MetaNeatGenome <T> metaNeatGenome,
int id,
int birthGeneration,
ConnectionGenes <T> connGenes,
int[] hiddenNodeIdArr,
INodeIdMap nodeIndexByIdMap,
DirectedGraph digraph,
int[] connectionIndexMap)
{
#if DEBUG
NeatGenomeAssertions <T> .AssertIsValid(
metaNeatGenome, id, birthGeneration,
connGenes, hiddenNodeIdArr, nodeIndexByIdMap,
digraph, connectionIndexMap);
#endif
this.MetaNeatGenome = metaNeatGenome;
this.Id = id;
this.BirthGeneration = birthGeneration;
this.ConnectionGenes = connGenes;
this.HiddenNodeIdArray = hiddenNodeIdArr;
this.NodeIndexByIdMap = nodeIndexByIdMap;
this.DirectedGraph = digraph;
this.ConnectionIndexMap = connectionIndexMap;
}
/// <summary>
/// Create a NeatGenome with the given meta data and connection genes.
/// </summary>
/// <param name="id">Genome ID.</param>
/// <param name="birthGeneration">Birth generation.</param>
/// <param name="connGenes">Connection genes.</param>
/// <returns>A new NeatGenome instance.</returns>
public NeatGenome <T> Create(
int id,
int birthGeneration,
ConnectionGenes <T> connGenes)
{
// Determine the set of node IDs, and create a mapping from node IDs to node indexes.
int[] hiddenNodeIdArr = ConnectionGenesUtils.CreateHiddenNodeIdArray(connGenes._connArr, _metaNeatGenome.InputOutputNodeCount, _workingIdSet);
return(Create(id, birthGeneration, connGenes, hiddenNodeIdArr));
}
/// <summary>
/// Create a NeatGenome with the given meta data, connection genes and supplementary data.
/// </summary>
/// <param name="id">Genome ID.</param>
/// <param name="birthGeneration">Birth generation.</param>
/// <param name="connGenes">Connection genes.</param>
/// <param name="hiddenNodeIdArr">An array of the hidden node IDs in the genome, in ascending order.</param>
/// <param name="digraph">A DirectedGraph that mirrors the structure described by the connection genes.</param>
/// <param name="acyclicInfoCache">Cached info related to acyclic digraphs only.</param>
/// <returns>A new NeatGenome instance.</returns>
public NeatGenome <T> Create(
int id, int birthGeneration,
ConnectionGenes <T> connGenes,
int[] hiddenNodeIdArr,
INodeIdMap nodeIndexByIdMap,
DirectedGraph digraph,
int[] connectionIndexMap)
{
return(new NeatGenome <T>(_metaNeatGenome, id, birthGeneration, connGenes, hiddenNodeIdArr, nodeIndexByIdMap, digraph, connectionIndexMap));
}
/// <summary>
/// Create a NeatGenome with the given meta data, connection genes and supplementary data.
/// </summary>
/// <param name="id">Genome ID.</param>
/// <param name="birthGeneration">Birth generation.</param>
/// <param name="connGenes">Connection genes.</param>
/// <param name="hiddenNodeIdArr">An array of the hidden node IDs in the genome, in ascending order.</param>
/// <returns>A new NeatGenome instance.</returns>
public NeatGenome <T> Create(
int id, int birthGeneration,
ConnectionGenes <T> connGenes,
int[] hiddenNodeIdArr)
{
int inputCount = _metaNeatGenome.InputNodeCount;
int outputCount = _metaNeatGenome.OutputNodeCount;
int inputOutputCount = _metaNeatGenome.InputOutputNodeCount;
// Create a mapping from node IDs to node indexes.
Dictionary <int, int> nodeIdxById = BuildNodeIndexById(hiddenNodeIdArr);
// Create a DictionaryNodeIdMap.
DictionaryNodeIdMap nodeIndexByIdMap = new DictionaryNodeIdMap(inputCount, nodeIdxById);
// Create a digraph from the genome.
DirectedGraph digraph = NeatGenomeBuilderUtils.CreateDirectedGraph(
_metaNeatGenome, connGenes, nodeIndexByIdMap);
// Calc the depth of each node in the digraph.
GraphDepthInfo depthInfo = _graphDepthAnalysis.CalculateNodeDepths(digraph);
// Create a weighted acyclic digraph.
// Note. This also outputs connectionIndexMap. For each connection in the acyclic graph this gives
// the index of the same connection in the genome; this is because connections are re-ordered based
// on node depth in the acyclic graph.
AcyclicDirectedGraph acyclicDigraph = AcyclicDirectedGraphBuilderUtils.CreateAcyclicDirectedGraph(
digraph,
depthInfo,
out int[] newIdByOldId,
out int[] connectionIndexMap,
ref _timesortWorkArr,
ref _timesortWorkVArr);
// TODO: Write unit tests to cover this!
// Update nodeIdxById with the new depth based node index allocations.
// Notes.
// The current nodeIndexByIdMap maps node IDs (also know as innovation IDs in NEAT) to a compact
// ID space in which any gaps have been removed, i.e. a compacted set of IDs that can be used as indexes,
// i.e. if there are N nodes in total then the highest node ID will be N-1.
//
// Here we map the new compact IDs to an alternative ID space that is also compact, but ensures that nodeIDs
// reflect the depth of a node in the acyclic graph.
UpdateNodeIndexById(nodeIdxById, hiddenNodeIdArr, newIdByOldId);
// Create the neat genome.
return(new NeatGenome <T>(
_metaNeatGenome, id, birthGeneration,
connGenes,
hiddenNodeIdArr,
nodeIndexByIdMap,
acyclicDigraph,
connectionIndexMap));
}
/// <summary>
/// Create a NeatGenome with the given meta data, connection genes and supplementary data.
/// </summary>
/// <param name="id">Genome ID.</param>
/// <param name="birthGeneration">Birth generation.</param>
/// <param name="connGenes">Connection genes.</param>
/// <param name="hiddenNodeIdArr">An array of the hidden node IDs in the genome, in ascending order.</param>
/// <returns>A new NeatGenome instance.</returns>
public NeatGenome <T> Create(
int id, int birthGeneration,
ConnectionGenes <T> connGenes,
int[] hiddenNodeIdArr,
INodeIdMap nodeIndexByIdMap)
{
// Note. Not required for acyclic graphs.
// In acyclic graphs nodeIndexByIdMap is so closely related/tied to digraph and connectionIndexMap that
// these three objects exist as a logical unit, i.e. we get all three or none at all.
throw new NotImplementedException();
}
/// <summary>
/// Create a NeatGenome with the given meta data, connection genes and supplementary data.
/// </summary>
/// <param name="id">Genome ID.</param>
/// <param name="birthGeneration">Birth generation.</param>
/// <param name="connGenes">Connection genes.</param>
/// <param name="hiddenNodeIdArr">An array of the hidden node IDs in the genome, in ascending order.</param>
/// <returns>A new NeatGenome instance.</returns>
public NeatGenome <T> Create(
int id, int birthGeneration,
ConnectionGenes <T> connGenes,
int[] hiddenNodeIdArr)
{
// Create a mapping from node IDs to node indexes.
INodeIdMap nodeIndexByIdMap = DirectedGraphUtils.CompileNodeIdMap_InputOutputCount_HiddenNodeIdArr(
_metaNeatGenome.InputOutputNodeCount, hiddenNodeIdArr);
return(Create(id, birthGeneration, connGenes, hiddenNodeIdArr, nodeIndexByIdMap));
}
/// <summary>
/// Create a NeatGenome with the given meta data, connection genes and supplementary data.
/// </summary>
/// <param name="id">Genome ID.</param>
/// <param name="birthGeneration">Birth generation.</param>
/// <param name="connGenes">Connection genes.</param>
/// <param name="hiddenNodeIdArr">An array of the hidden node IDs in the genome, in ascending order.</param>
/// <returns>A new NeatGenome instance.</returns>
public NeatGenome <T> Create(
int id, int birthGeneration,
ConnectionGenes <T> connGenes,
int[] hiddenNodeIdArr,
INodeIdMap nodeIndexByIdMap)
{
// Create a digraph from the genome.
DirectedGraph digraph = NeatGenomeBuilderUtils.CreateDirectedGraph(
_metaNeatGenome, connGenes, nodeIndexByIdMap);
return(new NeatGenome <T>(_metaNeatGenome, id, birthGeneration, connGenes, hiddenNodeIdArr, nodeIndexByIdMap, digraph, null));
}
/// <summary>
/// Create a NeatGenome with the given meta data, connection genes and supplementary data.
/// </summary>
/// <param name="id">Genome ID.</param>
/// <param name="birthGeneration">Birth generation.</param>
/// <param name="connGenes">Connection genes.</param>
/// <param name="hiddenNodeIdArr">An array of the hidden node IDs in the genome, in ascending order.</param>
/// <param name="digraph">A DirectedGraph that mirrors the structure described by the connection genes.</param>
/// <param name="connectionIndexMap">Mapping from genome connection indexes (in NeatGenome.ConnectionGenes) to reordered connections, based on depth based
/// node index allocations.</param>
/// <returns>A new NeatGenome instance.</returns>
public NeatGenome <T> Create(
int id, int birthGeneration,
ConnectionGenes <T> connGenes,
int[] hiddenNodeIdArr,
INodeIdMap nodeIndexByIdMap,
DirectedGraph digraph,
int[] connectionIndexMap)
{
// This should always be null when evolving cyclic genomes/graphs.
Debug.Assert(null == connectionIndexMap);
return(new NeatGenome <T>(_metaNeatGenome, id, birthGeneration, connGenes, hiddenNodeIdArr, nodeIndexByIdMap, digraph, null));
}
private static bool ValidateConnections(
ConnectionGenes <T> connGenes,
DirectedGraph digraph,
INodeIdMap nodeIndexByIdMap,
int[] connectionIndexMap)
{
// Connection counts.
if (connGenes._connArr.Length != digraph.ConnectionIdArrays.Length)
{
return(false);
}
// Connection order.
if (!SortUtils.IsSortedAscending(connGenes._connArr) ||
!IsSortedAscending(digraph.ConnectionIdArrays))
{
return(false);
}
// Connection node ID mappings.
DirectedConnection[] connArr = connGenes._connArr;
int[] srcIdArr = digraph.ConnectionIdArrays._sourceIdArr;
int[] tgtIdArr = digraph.ConnectionIdArrays._targetIdArr;
for (int i = 0; i < connGenes._connArr.Length; i++)
{
DirectedConnection connGene = connArr[i];
// Determine the index of he equivalent connection in the digraph.
int genomeConnIdx = (null == connectionIndexMap) ? i : connectionIndexMap[i];
if (nodeIndexByIdMap.Map(connArr[genomeConnIdx].SourceId) != srcIdArr[i] ||
nodeIndexByIdMap.Map(connArr[genomeConnIdx].TargetId) != tgtIdArr[i])
{
return(false);
}
}
return(true);
}
public static void AssertIsValid(
MetaNeatGenome <T> metaNeatGenome,
int id,
int birthGeneration,
ConnectionGenes <T> connGenes,
int[] hiddenNodeIdArr,
INodeIdMap nodeIndexByIdMap,
DirectedGraph digraph,
int[]?connectionIndexMap)
{
// Check for mandatory object references.
Debug.Assert(metaNeatGenome is object);
Debug.Assert(connGenes is object);
Debug.Assert(hiddenNodeIdArr is object);
Debug.Assert(nodeIndexByIdMap is object);
Debug.Assert(digraph is object);
// Basic check on ID and birth generation.
Debug.Assert(id >= 0);
Debug.Assert(birthGeneration >= 0);
// Acyclic graph checks.
if (metaNeatGenome.IsAcyclic)
{
AssertAcyclicGraph(metaNeatGenome, digraph, connectionIndexMap);
}
// Node counts.
AssertNodeCounts(metaNeatGenome, hiddenNodeIdArr, nodeIndexByIdMap, digraph);
// Hidden node IDs.
Debug.Assert(ConnectionGenesUtils.ValidateHiddenNodeIds(hiddenNodeIdArr, connGenes._connArr, metaNeatGenome.InputOutputNodeCount));
// Connections.
AssertConnections(connGenes, digraph, nodeIndexByIdMap, connectionIndexMap);
}
public static bool IsValid(
MetaNeatGenome <T> metaNeatGenome,
int id,
int birthGeneration,
ConnectionGenes <T> connGenes,
int[] hiddenNodeIdArr,
INodeIdMap nodeIndexByIdMap,
DirectedGraph digraph,
int[] connectionIndexMap)
{
// Mandatory ref tests.
if (null == metaNeatGenome ||
null == connGenes ||
null == hiddenNodeIdArr ||
null == nodeIndexByIdMap ||
null == digraph)
{
return(false);
}
// Acyclic/cyclic specific checks.
if (metaNeatGenome.IsAcyclic)
{
if (digraph.GetType() != typeof(AcyclicDirectedGraph) || null == connectionIndexMap)
{
return(false);
}
}
else
{
if (digraph.GetType() != typeof(DirectedGraph))
{
return(false);
}
}
// DepthInfo relates to acyclic graphs only, and is mandatory for acyclic graphs.
// TODO: Enable once NeatGenomeAcyclicBuilder is finished.
//if(metaNeatGenome.IsAcyclic)
//{
// if(!IsValid_Acyclic(metaNeatGenome, depthInfo)) {
// return false;
// }
//}
// Node counts.
if (!ValidateNodeCounts(metaNeatGenome, hiddenNodeIdArr, nodeIndexByIdMap, digraph))
{
return(false);
}
// Hidden node IDs.
if (!ConnectionGenesUtils.ValidateHiddenNodeIds(hiddenNodeIdArr, connGenes._connArr, metaNeatGenome.InputOutputNodeCount))
{
return(false);
}
// Connections.
if (!ValidateConnections(connGenes, digraph, nodeIndexByIdMap, connectionIndexMap))
{
return(false);
}
// All tests passed.
return(true);
}
