Added fields for activation scheme and fixed issue with navigation ev…

…aluation code being hard-coded to acyclic networks.

ExperimentEntities/ExperimentDictionary.cs

@@ -165,6 +165,9 @@ public ExperimentDictionary()
         public Nullable<double> Primary_Maze_VerticalWallBias { get; set; }
         public Nullable<int> Primary_Maze_QuadrantHeight { get; set; }
         public Nullable<int> Primary_Maze_QuadrantWidth { get; set; }
+        public string Primary_ActivationScheme { get; set; }
+        public Nullable<int> Primary_ActivationIters { get; set; }
+        public Nullable<double> Primary_ActivationDeltaThreshold { get; set; }
 
         [System.Diagnostics.CodeAnalysis.SuppressMessage("Microsoft.Usage", "CA2227:CollectionPropertiesShouldBeReadOnly")]
         public virtual ICollection<NoveltyExperimentOrganismStateData> NoveltyExperimentOrganismStateDatas { get; set; }

ExperimentEntities/ExperimentModel.edmx

@@ -56,6 +56,12 @@
           <Property Name="MinWidth" Type="int" />
           <Property Name="MaxWidth" Type="int" />
           <Property Name="MeanWidth" Type="float" />
+          <Property Name="MinJunctures" Type="int" />
+          <Property Name="MaxJunctures" Type="int" />
+          <Property Name="MeanJunctures" Type="float" />
+          <Property Name="MinTrajectoryFacingOpenings" Type="int" />
+          <Property Name="MaxTrajectoryFacingOpenings" Type="int" />
+          <Property Name="MeanTrajectoryFacingOpenings" Type="float" />
           <Property Name="TotalEvaluations" Type="int" Nullable="false" />
           <Property Name="EvaluationsPerSecond" Type="int" />
         </EntityType>
@@ -283,6 +289,7 @@ warning 6002: The table/view 'ExperimentData.dbo.ExperimentDictionary_vw' does n
 
 
 
+
 
 
           </Key>
@@ -327,6 +334,9 @@ warning 6002: The table/view 'ExperimentData.dbo.ExperimentDictionary_vw' does n
           <Property Name="Primary_ConnectionProportion" Type="float" Nullable="false" />
           <Property Name="Primary_ConnectionWeightRange" Type="int" Nullable="false" />
           <Property Name="Primary_SpecieSizeFixed" Type="bit" Nullable="false" />
+          <Property Name="Primary_ActivationScheme" Type="varchar" MaxLength="50" Nullable="false" />
+          <Property Name="Primary_ActivationIters" Type="int" />
+          <Property Name="Primary_ActivationDeltaThreshold" Type="float" />
           <Property Name="Primary_Maze_PopulationSize" Type="int" Nullable="false" />
           <Property Name="Primary_Maze_NumSpecies" Type="int" Nullable="false" />
           <Property Name="Primary_Maze_MutateWallLocationProbability" Type="float" />
@@ -550,6 +560,9 @@ warning 6002: The table/view 'ExperimentData.dbo.ExperimentDictionary_vw' does n
     [ExperimentDictionary_vw].[Primary_ConnectionProportion] AS [Primary_ConnectionProportion], 
     [ExperimentDictionary_vw].[Primary_ConnectionWeightRange] AS [Primary_ConnectionWeightRange], 
     [ExperimentDictionary_vw].[Primary_SpecieSizeFixed] AS [Primary_SpecieSizeFixed], 
+    [ExperimentDictionary_vw].[Primary_ActivationScheme] AS [Primary_ActivationScheme], 
+    [ExperimentDictionary_vw].[Primary_ActivationIters] AS [Primary_ActivationIters], 
+    [ExperimentDictionary_vw].[Primary_ActivationDeltaThreshold] AS [Primary_ActivationDeltaThreshold], 
     [ExperimentDictionary_vw].[Primary_Maze_PopulationSize] AS [Primary_Maze_PopulationSize], 
     [ExperimentDictionary_vw].[Primary_Maze_NumSpecies] AS [Primary_Maze_NumSpecies], 
     [ExperimentDictionary_vw].[Primary_Maze_MutateWallLocationProbability] AS [Primary_Maze_MutateWallLocationProbability], 
@@ -916,6 +929,9 @@ warning 6002: The table/view 'ExperimentData.dbo.ExperimentDictionary_vw' does n
           <NavigationProperty Name="MCCExperimentExtantNavigatorPopulations" Relationship="ExperimentDataModel.MCCExperimentExtantNavigatorPopulationExperimentDictionary" FromRole="ExperimentDictionary" ToRole="MCCExperimentExtantNavigatorPopulation" />
           <Property Name="Primary_Maze_QuadrantHeight" Type="Int32" />
           <Property Name="Primary_Maze_QuadrantWidth" Type="Int32" />
+          <Property Name="Primary_ActivationScheme" Type="String" Nullable="false" MaxLength="50" FixedLength="false" Unicode="false" />
+          <Property Name="Primary_ActivationIters" Type="Int32" />
+          <Property Name="Primary_ActivationDeltaThreshold" Type="Double" />
         </EntityType>
         <EntityType Name="NoveltyExperimentOrganismStateData">
           <Key>
@@ -1178,6 +1194,12 @@ warning 6002: The table/view 'ExperimentData.dbo.ExperimentDictionary_vw' does n
           <Property Name="TotalEvaluations" Type="Int32" Nullable="false" />
           <Property Name="EvaluationsPerSecond" Type="Int32" />
           <NavigationProperty Name="ExperimentDictionary" Relationship="ExperimentDataModel.MCCExperimentMazeEvaluationDataExperimentDictionary" FromRole="MCCExperimentMazeEvaluationData" ToRole="ExperimentDictionary" />
+          <Property Name="MinJunctures" Type="Int32" />
+          <Property Name="MaxJunctures" Type="Int32" />
+          <Property Name="MeanJunctures" Type="Double" />
+          <Property Name="MinTrajectoryFacingOpenings" Type="Int32" />
+          <Property Name="MaxTrajectoryFacingOpenings" Type="Int32" />
+          <Property Name="MeanTrajectoryFacingOpenings" Type="Double" />
         </EntityType>
         <Association Name="MCCExperimentMazeEvaluationDataExperimentDictionary">
           <End Type="ExperimentDataModel.MCCExperimentMazeEvaluationData" Role="MCCExperimentMazeEvaluationData" Multiplicity="*" />
@@ -1431,7 +1453,10 @@ warning 6002: The table/view 'ExperimentData.dbo.ExperimentDictionary_vw' does n
           <EntitySetMapping Name="ExperimentDictionaries">
             <EntityTypeMapping TypeName="ExperimentDataModel.ExperimentDictionary">
               <MappingFragment StoreEntitySet="ExperimentDictionary_vw">
-                <ScalarProperty Name="Primary_MazeQuadrant_Width" ColumnName="Primary_Maze_QuadrantWidth" />
+                <ScalarProperty Name="Primary_ActivationDeltaThreshold" ColumnName="Primary_ActivationDeltaThreshold" />
+                <ScalarProperty Name="Primary_ActivationIters" ColumnName="Primary_ActivationIters" />
+                <ScalarProperty Name="Primary_ActivationScheme" ColumnName="Primary_ActivationScheme" />
+                <ScalarProperty Name="Primary_Maze_QuadrantWidth" ColumnName="Primary_Maze_QuadrantWidth" />
                 <ScalarProperty Name="Primary_Maze_QuadrantHeight" ColumnName="Primary_Maze_QuadrantHeight" />
                 <ScalarProperty Name="Primary_Maze_VerticalWallBias" ColumnName="Primary_Maze_VerticalWallBias" />
                 <ScalarProperty Name="Primary_Maze_MutateExpandMazeProbability" ColumnName="Primary_Maze_MutateExpandMazeProbability" />
@@ -1693,6 +1718,12 @@ warning 6002: The table/view 'ExperimentData.dbo.ExperimentDictionary_vw' does n
           <EntitySetMapping Name="MCCExperimentMazeEvaluationDatas">
             <EntityTypeMapping TypeName="ExperimentDataModel.MCCExperimentMazeEvaluationData">
               <MappingFragment StoreEntitySet="MCCExperimentMazeEvaluationData">
+                <ScalarProperty Name="MeanTrajectoryFacingOpenings" ColumnName="MeanTrajectoryFacingOpenings" />
+                <ScalarProperty Name="MaxTrajectoryFacingOpenings" ColumnName="MaxTrajectoryFacingOpenings" />
+                <ScalarProperty Name="MinTrajectoryFacingOpenings" ColumnName="MinTrajectoryFacingOpenings" />
+                <ScalarProperty Name="MeanJunctures" ColumnName="MeanJunctures" />
+                <ScalarProperty Name="MaxJunctures" ColumnName="MaxJunctures" />
+                <ScalarProperty Name="MinJunctures" ColumnName="MinJunctures" />
                 <ScalarProperty Name="EvaluationsPerSecond" ColumnName="EvaluationsPerSecond" />
                 <ScalarProperty Name="TotalEvaluations" ColumnName="TotalEvaluations" />
                 <ScalarProperty Name="MeanWidth" ColumnName="MeanWidth" />

ExperimentEntities/ExperimentModel.edmx.diagram

@@ -13,6 +13,9 @@
         <EntityTypeShape EntityType="ExperimentDataModel.RunPhase" Width="1.5" PointX="0.75" PointY="11.875" />
         <AssociationConnector Association="ExperimentDataModel.FK_MCSExperimentEvaluationData_RunPhase" />
         <AssociationConnector Association="ExperimentDataModel.FK_MCSExperimentOrganismStateData_RunPhase" />
+        <EntityTypeShape EntityType="ExperimentDataModel.MCCExperimentExtantNavigatorPopulation" Width="1.5" PointX="3" PointY="11.875" />
+        <AssociationConnector Association="ExperimentDataModel.FK_MCCExperimentExtantNavigatorPopulation_RunPhase" />
+        <AssociationConnector Association="ExperimentDataModel.MCCExperimentExtantNavigatorPopulationExperimentDictionary" />
       </Diagram>
       <Diagram DiagramId="f3bab535c2fa4fa6ba0a74e76d67658f" Name="Coevolution MCS Experiment Model" ZoomLevel="83" >
         <EntityTypeShape EntityType="ExperimentDataModel.ExperimentDictionary" Width="4.375" PointX="6.75" PointY="8.5" IsExpanded="true" />

ExperimentEntities/MCCExperimentMazeEvaluationData.cs

@@ -33,6 +33,12 @@ public partial class MCCExperimentMazeEvaluationData
         public Nullable<double> MeanWidth { get; set; }
         public int TotalEvaluations { get; set; }
         public Nullable<int> EvaluationsPerSecond { get; set; }
+        public Nullable<int> MinJunctures { get; set; }
+        public Nullable<int> MaxJunctures { get; set; }
+        public Nullable<double> MeanJunctures { get; set; }
+        public Nullable<int> MinTrajectoryFacingOpenings { get; set; }
+        public Nullable<int> MaxTrajectoryFacingOpenings { get; set; }
+        public Nullable<double> MeanTrajectoryFacingOpenings { get; set; }
 
         public virtual ExperimentDictionary ExperimentDictionary { get; set; }
     }

MCC_Domains/MazeNavigation/BaseMCCMazeNavigationExperiment.cs

@@ -308,8 +308,8 @@ public virtual void Initialize(string name, XmlElement xmlConfig,
 
             // Setup initialization algorithm
             _mazeNavigationInitializer.SetAlgorithmParameters(
-                xmlConfig.GetElementsByTagName("InitializationAlgorithmConfig", "")[0] as XmlElement, AnnInputCount,
-                AnnOutputCount, NumAgentSuccessCriteria, 0);
+                xmlConfig.GetElementsByTagName("InitializationAlgorithmConfig", "")[0] as XmlElement,
+                ActivationScheme.AcyclicNetwork, NumAgentSuccessCriteria, 0);
 
             // Pass in maze experiment specific parameters 
             // (note that a new maze structure is created here for the sole purpose of extracting the maze dimensions and calculating max distance to target)

MCC_Domains/MazeNavigation/Bootstrappers/MCCMazeNavigationInitializer.cs

@@ -48,17 +48,16 @@ public void SetDataLoggers(IDataLogger navigatorEvolutionDataLogger,
         /// <summary>
         ///     Constructs and initializes the maze navigator initialization algorithm (fitness using generational selection).
         /// </summary>
-        /// <param name="xmlConfig">The XML configuration for the initialization algorithm.</param>
-        /// <param name="inputCount">The number of input neurons.</param>
-        /// <param name="outputCount">The number of output neurons.</param>
+        /// <param name="xmlConfig">The XML configuration for the initialization algorithm.</param>        
+        /// <param name="isAcyclic">Flag indicating whether the network is acyclic (i.e. does not have recurrent connections).</param>
         /// <param name="numSuccessfulAgents">The minimum number of successful maze navigators that must be produced.</param>
         /// <param name="numUnsuccessfulAgents">The minimum number of unsuccessful maze navigators that must be produced.</param>
         /// <returns>The constructed initialization algorithm.</returns>
-        public virtual void SetAlgorithmParameters(XmlElement xmlConfig, int inputCount, int outputCount,
-            int numSuccessfulAgents, int numUnsuccessfulAgents)
+        public virtual void SetAlgorithmParameters(XmlElement xmlConfig, bool isAcyclic, int numSuccessfulAgents,
+            int numUnsuccessfulAgents)
         {
             // Set the boiler plate parameters
-            base.SetAlgorithmParameters(xmlConfig, inputCount, outputCount);
+            base.SetAlgorithmParameters(xmlConfig, isAcyclic);
 
             // Set the static population size
             PopulationSize = XmlUtils.GetValueAsInt(xmlConfig, "PopulationSize");

MCC_Domains/MazeNavigation/Bootstrappers/MazeNavigationInitializer.cs

@@ -40,16 +40,15 @@ protected MazeNavigationInitializer()
         ///     Constructs and initializes the initialization algorithm.
         /// </summary>
         /// <param name="xmlConfig">The XML configuration for the initialization algorithm.</param>
-        /// <param name="inputCount">The number of input neurons.</param>
-        /// <param name="outputCount">The number of output neurons.</param>
+        /// <param name="isAcyclic">Flag indicating whether the network is acyclic (i.e. does not have recurrent connections).</param>
         /// <returns>The constructed initialization algorithm.</returns>
-        public virtual void SetAlgorithmParameters(XmlElement xmlConfig, int inputCount, int outputCount)
+        public virtual void SetAlgorithmParameters(XmlElement xmlConfig, bool isAcyclic)
         {
             // Read NEAT genome parameters
             // Save off genome parameters specifically for the initialization algorithm 
             // (this is primarily because the initialization algorithm will quite likely have different NEAT parameters)
             NeatGenomeParameters = ExperimentUtils.ReadNeatGenomeParameters(xmlConfig);
-            NeatGenomeParameters.FeedforwardOnly = NetworkActivationScheme.CreateAcyclicScheme().AcyclicNetwork;
+            NeatGenomeParameters.FeedforwardOnly = isAcyclic;
 
             // Read NEAT evolution parameters
             EvolutionAlgorithmParameters = ExperimentUtils.ReadNeatEvolutionAlgorithmParameters(xmlConfig);
@@ -156,7 +155,7 @@ protected void InitializeAlgorithm(ParallelOptions parallelOptions, List<NeatGen
         ///     The maximum distance to the target possible.
         /// </summary>
         protected int MaxDistanceToTarget;
-        
+
         /// <summary>
         ///     The minimum distance to the target permitted for the navigator to have successfully solved the maze.
         /// </summary>

MCC_Domains/MazeNavigation/Bootstrappers/NoveltySearchMCCMazeNavigationInitializer.cs

@@ -43,16 +43,15 @@ public class NoveltySearchMCCMazeNavigationInitializer : MCCMazeNavigationInitia
         ///     particular, this sets additional novelty search configuration parameters.
         /// </summary>
         /// <param name="xmlConfig">The XML configuration for the initialization algorithm.</param>
-        /// <param name="inputCount">The number of input neurons.</param>
-        /// <param name="outputCount">The number of output neurons.</param>
+        /// <param name="isAcyclic">Flag indicating whether the network is acyclic (i.e. does not have recurrent connections).</param>
         /// <param name="numSuccessfulAgents">The minimum number of successful maze navigators that must be produced.</param>
         /// <param name="numUnsuccessfulAgents">The minimum number of unsuccessful maze navigators that must be produced.</param>
         /// <returns>The constructed initialization algorithm.</returns>
-        public override void SetAlgorithmParameters(XmlElement xmlConfig, int inputCount, int outputCount,
-            int numSuccessfulAgents, int numUnsuccessfulAgents)
+        public override void SetAlgorithmParameters(XmlElement xmlConfig, bool isAcyclic, int numSuccessfulAgents,
+            int numUnsuccessfulAgents)
         {
             // Set the boiler plate MCC parameters and minimal criterions
-            base.SetAlgorithmParameters(xmlConfig, inputCount, outputCount, numSuccessfulAgents, numUnsuccessfulAgents);
+            base.SetAlgorithmParameters(xmlConfig, isAcyclic, numSuccessfulAgents, numUnsuccessfulAgents);
 
             // Read in the behavior characterization
             _behaviorCharacterizationFactory = ExperimentUtils.ReadBehaviorCharacterizationFactory(xmlConfig,
@@ -109,7 +108,8 @@ public override void InitializeAlgorithm(ParallelOptions parallelOptions, List<N
 
             // Create the genome evaluator
             IGenomeEvaluator<NeatGenome> fitnessEvaluator =
-                new ParallelGenomeBehaviorEvaluator<NeatGenome, IBlackBox>(genomeDecoder, mazeNavigatorEvaluator, SearchType.NoveltySearch, _nearestNeighbors);
+                new ParallelGenomeBehaviorEvaluator<NeatGenome, IBlackBox>(genomeDecoder, mazeNavigatorEvaluator,
+                    SearchType.NoveltySearch, _nearestNeighbors);
 
             // Only pull the number of genomes from the list equivalent to the initialization algorithm population size
             // (this is to handle the case where the list was created in accordance with the primary algorithm 
@@ -182,9 +182,9 @@ public override List<NeatGenome> RunEvolution(out ulong totalEvaluations, uint?
                 // Add all of the genomes that have solved the maze
                 viableGenomes.AddRange(
                     InitializationEa.GenomeList.Where(
-                        genome =>
-                            genome.EvaluationInfo != null &&
-                            genome.EvaluationInfo.ObjectiveDistance < MinSuccessDistance)
+                            genome =>
+                                genome.EvaluationInfo != null &&
+                                genome.EvaluationInfo.ObjectiveDistance < MinSuccessDistance)
                         .Take(MinSuccessfulAgentCount));
 
                 Console.Out.WriteLine("Extracted [{0}] of [{1}] viable genomes in [{2}] evaluations",
@@ -195,8 +195,9 @@ public override List<NeatGenome> RunEvolution(out ulong totalEvaluations, uint?
             // (note that the intuition for doing this after the loop is that most will not have solved)
             viableGenomes.AddRange(
                 InitializationEa.GenomeList.Where(
-                    genome =>
-                        genome.EvaluationInfo != null && genome.EvaluationInfo.ObjectiveDistance > MinSuccessDistance)
+                        genome =>
+                            genome.EvaluationInfo != null &&
+                            genome.EvaluationInfo.ObjectiveDistance > MinSuccessDistance)
                     .Take(MinUnsuccessfulAgentCount));
 
             // Ensure that the above statement was able to get the required number of unsuccessful agent genomes

MCC_Executor/MazeNavigation/ExperimentConfigurations/MCC-PathEvolution-1.config.xml

@@ -12,7 +12,8 @@
   <AgentSpecieSizeFixed>True</AgentSpecieSizeFixed>
   <MazeSpecieSizeFixed>True</MazeSpecieSizeFixed>
   <Activation>
-    <Scheme>Acyclic</Scheme>
+    <Scheme>CyclicFixedIters</Scheme>
+    <Iters>5</Iters>
   </Activation>
   <GenomeConfig>
     <InitialConnectionProportion>1</InitialConnectionProportion>