Containment works again

Cluster.cs

@@ -39,10 +39,9 @@ public class Cluster : Nucleus {
         Nucleus[] prefabNuclei = this.prefab.nuclei.ToArray();
         // first clone the nuclei without their connections
         foreach (Nucleus nucleus in this.prefab.nuclei) {
-            Debug.Log($"prefab clone {nucleus.name}");
+            // Debug.Log($"prefab clone {nucleus.name}");
             nucleus.ShallowCloneTo(this);
         }
-        Debug.Log(" complete");
         Nucleus[] clonedNuclei = this.clusterNuclei.ToArray();
 
         // Now clone the connections
@@ -57,7 +56,7 @@ public class Cluster : Nucleus {
 
             // Copy the receivers, which will also create the synapses
             // Clusters do not have receivers...
-            foreach (Nucleus receiver in prefabNeuron.receivers) {
+            foreach (Nucleus receiver in prefabNeuron.receivers.ToArray()) {
                 int ix = GetNucleusIndex(prefabNuclei, receiver);
                 if (ix < 0)
                     continue;
@@ -420,10 +419,10 @@ public class Cluster : Nucleus {
         return null;
     }
 
-    public Receptor GetReceptor(string receptorName) {
+    public IReceptor GetReceptor(string receptorName) {
         foreach (Nucleus nucleus in this.clusterNuclei) {
-            if (nucleus is Receptor receptor)
-                if (receptor.name == receptorName)
+            if (nucleus is IReceptor receptor)
+                if (receptor.GetName() == receptorName)
                     return receptor;
         }
         return null;

ClusterReceptor.cs

@@ -15,6 +15,10 @@ public class ClusterReceptor : Cluster, IReceptor {
         this.array = new NucleusArray(this);
     }
 
+    public string GetName() {
+        return this.name;
+    }
+
     public override Nucleus ShallowCloneTo(Cluster parent) {
         ClusterReceptor clone = new(this.prefab, parent, this.name) {
             clusterPrefab = this.clusterPrefab,

Editor/ClusterInspector.cs

@@ -452,10 +452,12 @@ public class ClusterInspector : Editor {
                 Handles.DrawLine(parentPos, pos);
                 Color color = Color.black;
                 if (Application.isPlaying) {
-                    float brightness = length(synapse.nucleus.outputValue) * synapse.weight / maxValue;
+                    if (maxValue == 0 || !float.IsFinite(maxValue))
+                        maxValue = 1;
+                    float brightness = length(synapse.nucleus.outputValue * synapse.weight) / maxValue;
                     color = new Color(brightness, brightness, brightness, 1f);
                 }
-                if (synapse.nucleus.parent != null && synapse.nucleus.parent != this.currentNucleus) {
+                if (synapse.nucleus.parent != null && synapse.nucleus.parent != this.currentNucleus.parent) {
                     // the synapse nucleus is part of a subcluster
                     DrawNucleus(synapse.nucleus.parent, pos, maxValue, size, color);
                 }

IReceptor.cs

@@ -1,5 +1,11 @@
+using UnityEngine;
+
 public interface IReceptor {
+    public string GetName();
+
     public NucleusArray array {
         get; set;
     }
+
+    public void ProcessStimulus(Vector3 inputValue, int thingId = 0, string thingName =null);
 }

Receptor.cs

@@ -4,19 +4,29 @@ using static Unity.Mathematics.math;
 
 [System.Serializable]
 public class Receptor : Neuron, IReceptor {
-    public Receptor(Cluster parent, string name) : base(parent, name) { }
-    public Receptor(ClusterPrefab prefab, string name) : base(prefab, name) { }
+    public Receptor(Cluster parent, string name) : base(parent, name) {
+        this.array ??= new NucleusArray(this);
+    }
+    public Receptor(ClusterPrefab prefab, string name) : base(prefab, name) {
+        this.array ??= new NucleusArray(this);
+    }
+
+    public string GetName() {
+        return this.name;
+    }
 
     public override Nucleus ShallowCloneTo(Cluster parent) {
-        Receptor clone = new(parent, name);
+        Receptor clone = new(parent, name) {
+            //array = this.array
+        };
         CloneFields(clone);
-        clone.array = this.array;
         return clone;
     }
     public override Nucleus Clone(ClusterPrefab prefab) {
-        Receptor clone = new(prefab, name);
+        Receptor clone = new(prefab, name) {
+            //array = this.array
+        };
         CloneFields(clone);
-        clone.array = this.array;
         // Adding receivers will also add synapses to the receivers
         foreach (Nucleus receiver in this.receivers)
             clone.AddReceiver(receiver);
@@ -32,6 +42,7 @@ public class Receptor : Neuron, IReceptor {
 
     public override void UpdateStateIsolated() {
         this.outputValue = this.bias;
+        //Debug.Log($"Receptor {this.name} outputvalue = {this.outputValue}");
     }
 
     public override void UpdateNuclei() {

Scripts/Experimental/SelectorBrain.cs

@@ -1,23 +0,0 @@
-using UnityEngine;
-
-public class SelectorBrain : NanoBrain {
-    public Vector3 input1;
-    public Vector3 input2;
-    public Vector3 output;
-
-    public Receptor receptor;
-    //public Nucleus receptor2;
-
-    protected void Awake() {
-        receptor = this.brain.GetReceptor("Selector");
-        //receptor2 = this.brain.GetNucleus("Selector");
-    }
-
-    protected void Update() {
-        receptor.ProcessStimulus(input1, 0);
-        receptor.ProcessStimulus(input2, 1);
-        output = this.brain.outputValue;
-
-        this.brain.UpdateNuclei();
-    }
-}

Scripts/Experimental/SelectorBrain.cs.meta

@@ -1,2 +0,0 @@
-fileFormatVersion: 2
-guid: 9051408e82b511584998506096af4bf0