AnimatedWalkingAnt

Cluster.cs

@@ -1,6 +1,5 @@
 using System;
 using System.Collections.Generic;
-using System.Linq;
 using UnityEngine;
 using Unity.Mathematics;
 using static Unity.Mathematics.math;
@@ -8,6 +7,15 @@ using static Unity.Mathematics.math;
 [Serializable]
 public class Cluster : Nucleus {
 
+    public string baseName {
+        get {
+            int colonPositon = this.name.IndexOf(':');
+            if (colonPositon < 0)
+                return this.name;
+            return this.name[..colonPositon];
+        }
+    }
+
     #region Init
 
     public Cluster(ClusterPrefab prefab, Cluster parent) {
@@ -39,7 +47,6 @@ 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}");
             nucleus.ShallowCloneTo(this);
         }
         Nucleus[] clonedNuclei = this.clusterNuclei.ToArray();
@@ -68,7 +75,7 @@ public class Cluster : Nucleus {
                 float weight = 1;
                 foreach (Synapse synapse in receiver.synapses) {
                     // Find the weight for this synapse
-                    if (synapse.nucleus == prefabNucleus) {
+                    if (synapse.neuron == prefabNucleus) {
                         weight = synapse.weight;
                         break;
                     }
@@ -78,40 +85,46 @@ public class Cluster : Nucleus {
             }
         }
 
-        // Copy nucleus arrays
+        // Copy nucleus arrays for receptors
         for (int nucleusIx = 0; nucleusIx < prefabNuclei.Length; nucleusIx++) {
-            Nucleus prefabReceptor = prefabNuclei[nucleusIx];
-            if (prefabReceptor is not Receptor prefabNucleus)
+            Nucleus prefabNucleus = prefabNuclei[nucleusIx];
+            if (prefabNucleus is not IReceptor prefabReceptor)
                 continue;
 
-            if (prefabNucleus.nucleiArray == null || prefabNucleus.nucleiArray.Length == 0)
+            if (prefabReceptor.nucleiArray == null || prefabReceptor.nucleiArray.Length == 0)
                 continue;
 
-            Receptor clonedNucleus = clonedNuclei[nucleusIx] as Receptor;
-            if (prefabNucleus == prefabNucleus.nucleiArray[0]) {
+            IReceptor clonedNucleus = clonedNuclei[nucleusIx] as IReceptor;
+            if (prefabReceptor == prefabReceptor.nucleiArray[0]) {
                 // We clone the array only for the first entry
-                NucleusArray clonedArray = new(prefabNucleus.nucleiArray.Length, "array");
+                NucleusArray clonedArray = new(prefabReceptor.nucleiArray.Length, "array");
                 int arrayIx = 0;
-                foreach (Nucleus prefabArrayNucleus in prefabNucleus.nucleiArray) {
+                foreach (Nucleus prefabArrayNucleus in prefabReceptor.nucleiArray) {
                     int arrayNucleusIx = GetNucleusIndex(prefabNuclei, prefabArrayNucleus);
                     if (arrayNucleusIx >= 0) {
                         Nucleus clonedArrayNucleus = clonedNuclei[arrayNucleusIx];
                         clonedArray.nuclei[arrayIx] = clonedArrayNucleus;
                     }
                     else {
-                        Debug.LogError($" Could not find prefab nuclues {prefabNucleus.name} in the clones");
+                        Debug.LogError($" Could not find prefab nucleus {prefabNucleus.name} in the clones");
                     }
                     arrayIx++;
                 }
-                clonedNucleus.array = clonedArray;
+                //clonedNucleus.array = clonedArray;
+                clonedNucleus.nucleiArray = clonedArray.nuclei;
             }
             else {
                 // The others will refer to the array created for the first nucleus in the array
-                int firstNucleusIx = GetNucleusIndex(prefabNuclei, prefabNucleus.nucleiArray[0]);
-                Receptor clonedFirstNucleus = clonedNuclei[firstNucleusIx] as Receptor;
+                int firstNucleusIx = GetNucleusIndex(prefabNuclei, prefabReceptor.nucleiArray[0]);
+                IReceptor clonedFirstNucleus = clonedNuclei[firstNucleusIx] as IReceptor;
                 clonedNucleus.nucleiArray = clonedFirstNucleus.nucleiArray;
             }
         }
+
+        foreach (Nucleus nucleus in this.clusterNuclei) {
+            if (nucleus is Cluster clonedSubCluster)
+                RestoreAllExternalReceivers(clonedSubCluster, this.prefab, this);
+        }
     }
 
     // Sort the nuclei in a correct evaluation order
@@ -122,7 +135,11 @@ public class Cluster : Nucleus {
 
         // Calculate in-degrees
         foreach (Nucleus node in nodes) {
-            if (node is Neuron neuron) {
+            if (node is Cluster cluster) {
+                foreach (Nucleus receiver in cluster.CollectReceivers())
+                    inDegree[receiver]++;
+            }
+            else if (node is Neuron neuron) {
                 foreach (Nucleus receiver in neuron.receivers)
                     inDegree[receiver]++;
             }
@@ -147,6 +164,13 @@ public class Cluster : Nucleus {
                         queue.Enqueue(receiver);
                 }
             }
+            else if (current is Cluster cluster) {
+                foreach (Nucleus receiver in cluster.CollectReceivers()) {
+                    inDegree[receiver]--;
+                    if (inDegree[receiver] == 0) // If all dependencies resolved
+                        queue.Enqueue(receiver);
+                }
+            }
         }
 
         // Check for cycles in the graph
@@ -160,7 +184,7 @@ public class Cluster : Nucleus {
         Cluster clone = new(this.prefab, parent);
 
         foreach (Synapse synapse in this.synapses) {
-            Synapse clonedSynapse = clone.AddSynapse(synapse.nucleus);
+            Synapse clonedSynapse = clone.AddSynapse(synapse.neuron);
             clonedSynapse.weight = synapse.weight;
         }
 
@@ -185,48 +209,45 @@ public class Cluster : Nucleus {
             name = this.name,
             clusterPrefab = this.clusterPrefab,
         };
-        // This cloned the prefab with the clusternuclei,
-        // but did not clone the receivers outside the cluster
-        RestoreExternalReceivers(clone, this.clusterPrefab, parent);
 
         return clone;
     }
 
-    protected void RestoreExternalReceivers(Cluster clone, ClusterPrefab prefabParent, Cluster clonedParent) {
-        for (int nucleusIx = 0; nucleusIx < this.clusterNuclei.Count; nucleusIx++) {
-            Nucleus prefabNucleus = this.clusterNuclei[nucleusIx];
-            if (prefabNucleus is not Neuron prefabNeuron)
+    private static void RestoreAllExternalReceivers(Cluster clonedCluster, ClusterPrefab prefabParent, Cluster clonedParent) {
+        int clonedClusterIx = GetNucleusIndex(clonedParent.clusterNuclei, clonedCluster);
+        if (prefabParent.nuclei[clonedClusterIx] is not Cluster sourceCluster)
+            return;
+
+        for (int nucleusIx = 0; nucleusIx < sourceCluster.clusterNuclei.Count; nucleusIx++) {
+            Nucleus sourceNucleus = sourceCluster.clusterNuclei[nucleusIx];
+            if (sourceNucleus is not Neuron sourceNeuron)
                 continue;
 
-            Nucleus clonedNucleus = clone.clusterNuclei[nucleusIx];
-            if (clonedNucleus == null || clonedNucleus is not Neuron clonedNeuron)
+            if (clonedCluster.clusterNuclei[nucleusIx] is not Neuron clonedNeuron)
                 continue;
 
-            // Copy the receivers, which will also create the synapses
-            foreach (Nucleus receiver in prefabNeuron.receivers) {
+            // copy the receivers (and thus synapses) from the source to the clone
+            foreach (Nucleus receiver in sourceNeuron.receivers) {
                 int ix = GetNucleusIndex(prefabParent.nuclei, receiver);
-                if (ix < 0)
+                if (ix < 0 || ix >= clonedParent.clusterNuclei.Count)
                     continue;
 
-                //if (clone.clusterNuclei[ix] is not Nucleus clonedReceiver)
-                if (clonedParent.clusterNuclei[ix] is not Nucleus clonedReceiver)
-                    continue;
+                Nucleus clonedReceiver = clonedParent.clusterNuclei[ix];
 
                 // Find the synapse for the weight
                 float weight = 1;
                 foreach (Synapse synapse in receiver.synapses) {
                     // Find the weight for this synapse
-                    if (synapse.nucleus == prefabNucleus) {
+                    if (synapse.neuron == sourceNucleus) {
                         weight = synapse.weight;
                         break;
                     }
                 }
 
                 clonedNeuron.AddReceiver(clonedReceiver, weight);
+                // Debug.Log($"external: {clonedReceiver.name} receives from {clonedNeuron.name} {clonedNeuron.GetHashCode()}");
             }
         }
-
-
     }
 
     protected int GetNucleusIndex(Nucleus[] nuclei, Nucleus nucleus) {
@@ -237,12 +258,13 @@ public class Cluster : Nucleus {
         return -1;
     }
 
-    protected int GetNucleusIndex(List<Nucleus> nuclei, Nucleus nucleus) {
+    public static int GetNucleusIndex(List<Nucleus> nuclei, Nucleus nucleus) {
         int i = 0;
         foreach (Nucleus nucleiElement in nuclei) {
             //for (int i = 0; i < nuclei.Length; i++) {
             if (nucleus == nucleiElement)
                 return i;
+            i++;
         }
         return -1;
     }
@@ -277,19 +299,17 @@ public class Cluster : Nucleus {
 
     public Dictionary<Nucleus, List<Nucleus>> computeOrders = new();
     private void ComputeOrders() {
-        foreach (Nucleus input in this._inputs) {
+        foreach (Nucleus input in this._inputs)
             computeOrders[input] = TopologicalSort2(input);
-        }
     }
 
     private List<Nucleus> TopologicalSort2(Nucleus startNode) {
-        Dictionary<Nucleus, int> inDegree = new Dictionary<Nucleus, int>();
-        HashSet<Nucleus> visited = new HashSet<Nucleus>();
+        Dictionary<Nucleus, int> inDegree = new();
+        HashSet<Nucleus> visited = new();
 
         // Initialize in-degrees and mark all nodes as unvisited
-        foreach (Nucleus node in this.clusterNuclei) {
+        foreach (Nucleus node in this.clusterNuclei)
             inDegree[node] = 0;
-        }
 
         // Calculate in-degrees for all nodes reachable from the start node
         Queue<Nucleus> queue = new Queue<Nucleus>();
@@ -298,23 +318,28 @@ public class Cluster : Nucleus {
 
         while (queue.Count > 0) {
             Nucleus current = queue.Dequeue();
-            if (current is Neuron neuron) {
-                foreach (Nucleus receiver in neuron.receivers) {
-                    if (!visited.Contains(receiver)) {
-                        visited.Add(receiver);
-                        queue.Enqueue(receiver);
-                    }
-                    inDegree[receiver]++;
+            List<Nucleus> receivers = null;
+            if (current is Neuron neuron)
+                receivers = neuron.receivers;
+            else if (current is Cluster cluster)
+                receivers = cluster.CollectReceivers();
+
+            // if (current is Neuron neuron) {
+            foreach (Nucleus receiver in receivers) {
+                if (!visited.Contains(receiver)) {
+                    visited.Add(receiver);
+                    queue.Enqueue(receiver);
                 }
+                inDegree[receiver]++;
             }
+            // }
         }
 
         // Perform topological sort on all reachable nodes
         queue.Clear();
-        foreach (var node in visited) {
-            if (inDegree[node] == 0) {
+        foreach (Nucleus node in visited) {
+            if (inDegree[node] == 0)
                 queue.Enqueue(node);
-            }
         }
 
         List<Nucleus> sortedOrder = new List<Nucleus>();
@@ -322,58 +347,27 @@ public class Cluster : Nucleus {
             Nucleus current = queue.Dequeue();
             sortedOrder.Add(current); // Process the node
 
-            if (current is Neuron neuron) {
-                foreach (Nucleus receiver in neuron.receivers) {
-                    if (visited.Contains(receiver)) {
-                        inDegree[receiver]--;
-                        if (inDegree[receiver] == 0) // If all dependencies resolved
-                            queue.Enqueue(receiver);
-                    }
-                }
-            }
-        }
+            List<Nucleus> receivers = null;
+            if (current is Neuron neuron)
+                receivers = neuron.receivers;
+            else if (current is Cluster cluster)
+                receivers = cluster.CollectReceivers();
 
-        // Check for cycles in the graph
-        if (sortedOrder.Count != visited.Count)
-            throw new InvalidOperationException("Graph is not a DAG; a cycle exists.");
+            //if (current is Neuron neuron) {
 
-        return sortedOrder;
-    }
-
-    private List<Nucleus> TopologicalSort3(Nucleus startNode) {
-        Dictionary<Nucleus, int> inDegree = new();
-        foreach (Nucleus node in this.clusterNuclei)
-            inDegree[node] = 0; // Initialize in-degree to zero
-
-        // Calculate in-degrees
-        foreach (Nucleus node in this.clusterNuclei) {
-            if (node is Neuron neuron) {
-                foreach (Nucleus receiver in neuron.receivers)
-                    inDegree[receiver]++;
-            }
-        }
-
-        Queue<Nucleus> queue = new();
-        queue.Enqueue(startNode);
-
-        List<Nucleus> sortedOrder = new();
-        while (queue.Count > 0) {
-            Nucleus current = queue.Dequeue();
-            sortedOrder.Add(current); // Process the node
-
-            if (current is Neuron neuron) {
-                foreach (Nucleus receiver in neuron.receivers) {
+            foreach (Nucleus receiver in receivers) {
+                if (visited.Contains(receiver)) {
                     inDegree[receiver]--;
                     if (inDegree[receiver] == 0) // If all dependencies resolved
                         queue.Enqueue(receiver);
                 }
             }
+            //}
         }
 
-        Debug.Log($"Compute order for {startNode.name} length = {sortedOrder.Count}");
         // Check for cycles in the graph
-        // if (sortedOrder.Count != this.nuclei.Count)
-        //     throw new InvalidOperationException("Graph is not a DAG; a cycle exists.");
+        if (sortedOrder.Count != visited.Count)
+            throw new InvalidOperationException("Graph is not a DAG; a cycle exists.");
 
         return sortedOrder;
     }
@@ -412,31 +406,50 @@ public class Cluster : Nucleus {
     }
 
     public Nucleus GetNucleus(string nucleusName) {
-        foreach (Nucleus nucleus in this.clusterNuclei) {
-            if (nucleus.name == nucleusName)
-                return nucleus;
+        int dotPosition = nucleusName.IndexOf('.');
+        if (dotPosition >= 0) {
+            string clusterName = nucleusName[..dotPosition];
+            string clusterName0 = clusterName + ": 0";
+            foreach (Nucleus nucleus in this.clusterNuclei) {
+                if (nucleus is Cluster cluster) {
+                    if (cluster.name == clusterName || cluster.name == clusterName0) {
+                        string subNucleusName = nucleusName[(dotPosition + 1)..];
+                        return cluster.GetNucleus(subNucleusName);
+                    }
+                }
+            }
+            return null;
+        }
+        else {
+            string nucleusName0 = nucleusName + ": 0";
+            foreach (Nucleus nucleus in this.clusterNuclei) {
+                if (nucleus is IReceptor receptor) {
+                    if (nucleus.name == nucleusName | nucleus.name == nucleusName0)
+                        return nucleus;
+                }
+                else if (nucleus.name == nucleusName)
+                    return nucleus;
+            }
+            return null;
         }
-        return null;
     }
 
-    public IReceptor GetReceptor(string receptorName) {
-        string receptorName0 = receptorName + ": 0";
-        foreach (Nucleus nucleus in this.clusterNuclei) {
-            if (nucleus is IReceptor receptor) {
-                if (nucleus.name == receptorName | nucleus.name == receptorName0)
-                //if (receptor.GetName() == receptorName)
-                    return receptor;
-            }
-        }
-        return null;
-    }
+    // [Obsolete("Use GetNucleus instead")]
+    // public IReceptor GetReceptor(string receptorName) {
+    //     return GetNucleus(receptorName) as IReceptor;
+    // }
 
     #region Receivers
 
     public virtual List<Nucleus> CollectReceivers() {
         List<Nucleus> receivers = new();
         foreach (Neuron output in this.outputs) {
-            receivers.AddRange(output.receivers);
+            foreach (Nucleus receiver in output.receivers) {
+                // Only add receivers outside this cluster
+                if (receiver.clusterPrefab != this.prefab)
+                    receivers.Add(receiver);
+                //receivers.AddRange(output.receivers);
+            }
         }
         return receivers;
     }
@@ -448,39 +461,41 @@ public class Cluster : Nucleus {
     public void UpdateFromNucleus(Nucleus startNucleus) {
         // no bias+synapse input state calculation for now...
 
+        if (this.computeOrders.ContainsKey(startNucleus) == false) {
+            //Debug.LogError($"{this.name} compute orders does not contain an order for {startNucleus.name}");
+            return;
+        }
+
         List<Nucleus> computeOrder = this.computeOrders[startNucleus];
         if (startNucleus.trace)
             Debug.Log($"Update from {startNucleus.name}");
         foreach (Nucleus nucleus in computeOrder) {
             nucleus.UpdateStateIsolated();
-            if (startNucleus.trace)
-                Debug.Log($"   {nucleus.name} = {nucleus.outputValue}");
+            if (startNucleus.trace && nucleus is Neuron neuron)
+                Debug.Log($"   {nucleus.name}[{nucleus.GetHashCode()}] = {neuron.outputValue}");
         }
 
-        this.outputValue = this.defaultOutput.outputValue;
-        this.stale = 0;
+        // continue in parent
+        this.parent?.UpdateFromNucleus(this);
 
         UpdateNuclei();
     }
 
     public override void UpdateStateIsolated() {
-        float3 sum = this.bias;
+        throw new Exception("Cluster should not be updated!");
+        // float3 sum = this.bias;
 
-        //Applying the weight factors
-        foreach (Synapse synapse in this.synapses) {
-            if (lengthsq(synapse.nucleus.outputValue) > 0) {
-                sum += synapse.weight * synapse.nucleus.outputValue;
-                this.stale = 0;
-            }
-        }
+        // //Applying the weight factors
+        // foreach (Synapse synapse in this.synapses) {
+        //     if (lengthsq(synapse.neuron.outputValue) > 0) {
+        //         sum += synapse.weight * synapse.neuron.outputValue;
+        //     }
+        // }
 
-        foreach (Nucleus nucleus in this.sortedNuclei)
-            nucleus.UpdateStateIsolated();
+        // foreach (Nucleus nucleus in this.sortedNuclei)
+        //     nucleus.UpdateStateIsolated();
 
-        this.outputValue = this.defaultOutput.outputValue;
-        this.stale = 0;
-
-        UpdateNuclei();
+        // UpdateNuclei();
     }
 
     public override void UpdateNuclei() {

ClusterPrefab.cs

@@ -64,7 +64,6 @@ public class ClusterPrefab : ScriptableObject {
         HashSet<Nucleus> visitedNuclei = new();
         foreach (Nucleus output in this.outputs)
             MarkNuclei(visitedNuclei, output);
-        //MarkNuclei(visitedNuclei, this.output);
         //Debug.Log($"Garbage collection found {visitedNuclei.Count} Nuclei");
         this.nuclei.RemoveAll(nucleus => visitedNuclei.Contains(nucleus) == false);
     }
@@ -80,9 +79,9 @@ public class ClusterPrefab : ScriptableObject {
         if (nucleus.synapses != null) {
             HashSet<Synapse> visitedSynapses = new();
             foreach (Synapse synapse in nucleus.synapses) {
-                if (synapse != null && synapse.nucleus != null) {
+                if (synapse != null && synapse.neuron != null) {
                     visitedSynapses.Add(synapse);
-                    if (synapse.nucleus is Nucleus synapse_nucleus)
+                    if (synapse.neuron is Nucleus synapse_nucleus)
                         MarkNuclei(visitedNuclei, synapse_nucleus);
                 }
             }

ClusterReceptor.cs

@@ -3,14 +3,18 @@ using System.Collections.Generic;
 using UnityEngine;
 using Unity.Mathematics;
 using static Unity.Mathematics.math;
+using System.Linq;
 
 [Serializable]
 public class ClusterReceptor : Cluster, IReceptor {
     public ClusterReceptor(ClusterPrefab prefab, Cluster parent, string name) : base(prefab, parent) {
         this.name = name;
-        this.array ??= new NucleusArray(this);
+        this.array = new NucleusArray(this);
+        if (this.name.IndexOf(":") < 0)
+            this.name += ": 0";
+
     }
-    public ClusterReceptor(ClusterPrefab prefabToInstantiate, ClusterPrefab parent, string name) : base(prefabToInstantiate, parent) {
+    public ClusterReceptor(ClusterPrefab prefab, ClusterPrefab parent, string name) : base(prefab, parent) {
         this.name = name;
         this.array = new NucleusArray(this);
     }
@@ -22,30 +26,21 @@ public class ClusterReceptor : Cluster, IReceptor {
     public override Nucleus ShallowCloneTo(Cluster parent) {
         ClusterReceptor clone = new(this.prefab, parent, this.name) {
             clusterPrefab = this.clusterPrefab,
-            array = this.array
         };
 
-        // This cloned the prefab with the clusternuclei,
-        // but did not clone the receivers outside the cluster
-        RestoreExternalReceivers(clone, this.clusterPrefab, parent);
-
         return clone;
     }
 
     public override Nucleus Clone(ClusterPrefab parent) {
         ClusterReceptor clone = new(prefab, parent, this.name) {
-            array = this.array
+            array = this._array
         };
 
         foreach (Synapse synapse in this.synapses) {
-            Synapse clonedSynapse = clone.AddSynapse(synapse.nucleus);
+            Synapse clonedSynapse = clone.AddSynapse(synapse.neuron);
             clonedSynapse.weight = synapse.weight;
         }
 
-        // foreach (Nucleus receiver in this.receivers) {
-        //     clone.AddReceiver(receiver);
-        // }
-
         this._outputs = null; // Make sure the output are regenerated
         foreach (Neuron output in this.outputs) {
             int ix = GetNucleusIndex(this.clusterNuclei, output);
@@ -58,53 +53,162 @@ public class ClusterReceptor : Cluster, IReceptor {
         return clone;
     }
 
+    public override List<Nucleus> CollectReceivers() {
+        List<Nucleus> receivers = new();
+        foreach (Nucleus element in this.nucleiArray) {
+            if (element is not Cluster clusterElement)
+                continue;
+
+            foreach (Nucleus outputNucleus in clusterElement.clusterNuclei) {
+                if (outputNucleus is not Neuron output)
+                    continue;
+
+                // this should be clusterElement.outputs,
+                // but outputs is not updated when correctly and may contain old data...
+                foreach (Nucleus receiver in output.receivers) {
+                    // Only add receivers outside clusterElement cluster
+                    if (receiver.clusterPrefab != clusterElement.prefab &&
+                        receivers.Contains(receiver) == false)
+                        receivers.Add(receiver);
+                }
+            }
+        }
+        return receivers;
+    }
+
     [SerializeReference]
     private NucleusArray _array;
     public NucleusArray array {
-        get { return _array; }
         set { _array = value; }
     }
 
-    //[SerializeReference]
-    //private Nucleus[] _nucleusArray;
     public Nucleus[] nucleiArray {
         get { return _array.nuclei; }
         set { _array.nuclei = value; }
     }
 
     public void AddReceptorElement(ClusterPrefab prefab) {
-        this.nucleiArray = IReceptorHelpers.AddReceptorElement(this.nucleiArray, prefab);
+        IReceptorHelpers.AddReceptorElement(this, prefab);
     }
 
     public void RemoveReceptorElement() {
-        this.nucleiArray = IReceptorHelpers.RemoveReceptorElement(this.nucleiArray);
+        IReceptorHelpers.RemoveReceptorElement(this);
+    }
+
+    public void AddArrayReceiver(Nucleus receiverToAdd, float weight = 1) {
+        IReceptorHelpers.AddArrayReceiver(this, receiverToAdd, weight);
     }
 
     public override void UpdateStateIsolated() {
-        float3 sum = this.bias;
-
-        foreach (Nucleus nucleus in this.sortedNuclei)
-            nucleus.UpdateStateIsolated();
-
-        this.outputValue = this.defaultOutput.outputValue;
-        this.stale = 0;
-
-        UpdateNuclei();
+        // Clusters don't do anything,
+        // The nuclei in them do the work
+        // and should be called directly, not from the cluster
     }
 
     public override void UpdateNuclei() {
-        this.stale++;
-        if (this.stale > staleValueForSleep && lengthsq(this.bias) > 0) {
-            this.bias = new float3(0, 0, 0);
-            this.parent.UpdateFromNucleus(this);
-        }
-
         foreach (Nucleus nucleus in this.clusterNuclei)
             nucleus.UpdateNuclei();
     }
 
-    public virtual void ProcessStimulus(Vector3 inputValue, int thingId = 0, string thingName = null) {
-        this.array ??= new NucleusArray(this.parent);
-        this.array.ProcessStimulus(thingId, inputValue, thingName);
+    public override void ProcessStimulus(Vector3 inputValue, int thingId = 0, string thingName = null) {
+        Debug.LogError("Process Stimulus was called on clusterreceptor without a neuron specified");
+    }
+
+    private readonly Dictionary<int, ClusterReceptor> thingReceivers = new();
+
+    public virtual void ProcessStimulus(Neuron input, Vector3 inputValue, int thingId = 0, string thingName = null) {
+        CleanupReceivers();
+
+        if (!thingReceivers.TryGetValue(thingId, out ClusterReceptor selectedReceiver))
+            selectedReceiver = FindReceiver2(thingId, inputValue, input);
+        if (selectedReceiver == null)
+            return;
+
+        if (thingName != null) {
+            string baseName = selectedReceiver.name;
+            int colonPos = selectedReceiver.name.IndexOf(":");
+            if (colonPos > 0)
+                baseName = selectedReceiver.name[..colonPos];
+            selectedReceiver.name = baseName + ": " + thingName;
+        }
+
+        int inputIx = GetNucleusIndex(this.clusterNuclei, input);
+        if (inputIx < 0)
+            return;
+
+        if (selectedReceiver.clusterNuclei[inputIx] is Neuron selectedNeuron)
+            selectedNeuron.ProcessStimulusDirect(inputValue);
+    }
+
+    private ClusterReceptor FindReceiver2(int thingId, float3 inputValue, Neuron input) {
+        // No existing nucleus for this thing
+        ClusterReceptor selectedReceiver = null;
+        float selectedMagnitude = 0;
+        foreach (ClusterReceptor receiver in this.nucleiArray.Cast<ClusterReceptor>()) {
+            if (thingReceivers.ContainsValue(receiver) == false) {
+                // We found an unusued receiver
+                thingReceivers.Add(thingId, receiver);
+                return receiver;
+            }
+            else if (receiver.defaultOutput.isSleeping) {
+                // A sleeping receiver is not active and can therefore always be used
+                thingReceivers.Add(thingId, receiver);
+                receiver.bias = float3(0, 0, 0);
+                return receiver;
+            }
+            else if (selectedReceiver == null) {
+                // If we haven't found a receiver yet, just start by taking the first
+                selectedReceiver = receiver;
+                selectedMagnitude = length(selectedReceiver.defaultOutput.outputValue);
+            }
+            // Look for the receiver with the lowest output magnitude
+            else {
+                float magnitude = length(receiver.defaultOutput.outputValue);
+
+                if (length(receiver.defaultOutput.outputValue) < selectedMagnitude) {
+                    selectedReceiver = receiver;
+                    selectedMagnitude = length(selectedReceiver.defaultOutput.outputValue);
+                }
+            }
+        }
+        if (selectedReceiver != null) {
+            // To re-initialize the cluster (esp. memory cells)
+            // we update the cluster neuron twice.
+            // Bit of a hack.....
+            int inputIx = GetNucleusIndex(this.clusterNuclei, input);
+            if (inputIx >= 0) {
+                if (selectedReceiver.clusterNuclei[inputIx] is Neuron selectedNeuron)
+                    selectedNeuron.ProcessStimulusDirect(inputValue);
+            }
+
+            // Replace the receiver
+            // Find the thingId current associated with the receiver
+            int keyToRemove = thingReceivers.FirstOrDefault(r => r.Value.Equals(selectedReceiver)).Key;
+            if (keyToRemove != 0 || thingReceivers.ContainsKey(keyToRemove))
+                thingReceivers.Remove(keyToRemove);
+            // And add the new association
+            thingReceivers.Add(thingId, selectedReceiver);
+        }
+        return selectedReceiver;
+    }
+
+
+    private void CleanupReceivers() {
+        // Remove a thing-receiver connection when the nucleus is inactive
+        List<int> receiversToRemove = new();
+        foreach (KeyValuePair<int, ClusterReceptor> item in thingReceivers) {
+            if (item.Value != null && item.Value.defaultOutput.isSleeping)
+                receiversToRemove.Add(item.Key);
+        }
+        foreach (int thingId in receiversToRemove) {
+            Nucleus selectedReceiver = thingReceivers[thingId];
+
+            thingReceivers.Remove(thingId);
+
+            int colonPos = selectedReceiver.name.IndexOf(":");
+            if (colonPos > 0)
+                selectedReceiver.name = selectedReceiver.name[..colonPos];
+
+        }
     }
 }

Editor/ClusterInspector.cs

@@ -19,12 +19,6 @@ public class ClusterInspector : Editor {
     public override VisualElement CreateInspectorGUI() {
         ClusterPrefab prefab = target as ClusterPrefab;
 
-        // string path = AssetDatabase.GetAssetPath(prefab); // or known path
-        // Debug.Log($"{path}");
-        // ClusterPrefab currentWrapper = AssetDatabase.LoadAssetAtPath<ClusterPrefab>(path);
-        // if (currentWrapper == null)
-        //     Debug.LogError("CreateInspectorGUI: Cluster Prefab is not found on disk");
-
         if (prefab != null)
             prefab.EnsureInitialization();
 
@@ -182,7 +176,7 @@ public class ClusterInspector : Editor {
             if (this.prefabAsset == null) {
                 // create in memory save if it doesn't exist
                 this.prefabAsset = CreateInstance<ClusterPrefab>();
-                Debug.LogError("Cluster Prefab is not found on disk");
+                //Debug.LogError("Cluster Prefab is not found on disk");
             }
             DrawInspector(inspectorContainer);
         }
@@ -221,7 +215,7 @@ public class ClusterInspector : Editor {
 
             if (selectedNucleus.synapses != null) {
                 foreach (Synapse synapse in selectedNucleus.synapses) {
-                    Nucleus input = synapse.nucleus;
+                    Nucleus input = synapse.neuron;
                     AddToLayer(currentLayer, input);
                     // Debug.Log($"layer {layerIx} nucleus {input.name}");
                 }
@@ -265,45 +259,14 @@ public class ClusterInspector : Editor {
 
             // Draw selected Nucleus
             if (expandArray) {
-                // if (this.currentNucleus is ReceptorArray receptor) {
-                //     float maxValue = 0;
-                //     foreach (Nucleus nucleus in receptor.instances) {
-                //         float value = length(nucleus.outputValue);
-                //         if (value > maxValue)
-                //             maxValue = value;
-                //     }
-
-                //     float spacing = 400f / receptor.instances.Count();
-                //     float margin = 10 + spacing / 2;
-                //     float xMin = 150 - size;
-                //     float xMax = 150 + size;
-                //     float yMin = 10 + margin - size / 2;
-                //     float yMax = 400 - margin + size;
-                //     Vector3[] verts = new Vector3[4] {
-                //     new(xMin, yMin, 0),
-                //     new(xMax, yMin, 0),
-                //     new(xMax, yMax, 0),
-                //     new(xMin, yMax, 0)
-                // };
-                //     Handles.color = Color.black;
-                //     Handles.DrawAAConvexPolygon(verts);
-                //     int row = 0;
-                //     foreach (Nucleus nucleus in receptor.instances) {
-                //         Vector3 pos = new(150, margin + row * spacing, 0.0f);
-                //         Handles.color = Color.white;
-                //         // The selected nucleus highlight ring
-                //         Handles.DrawSolidDisc(pos, Vector3.forward, size + 2);
-                //         DrawNucleus(nucleus, pos, maxValue, size);
-                //         row++;
-                //     }
-                // }
-                //            else
                 if (this.currentNucleus is IReceptor receptor1) {
                     float maxValue = 0;
                     foreach (Nucleus nucleus in receptor1.nucleiArray) {
-                        float value = length(nucleus.outputValue);
-                        if (value > maxValue)
-                            maxValue = value;
+                        if (nucleus is Neuron neuron) {
+                            float value = length(neuron.outputValue);
+                            if (value > maxValue)
+                                maxValue = value;
+                        }
                     }
 
                     float spacing = 400f / receptor1.nucleiArray.Count();
@@ -348,7 +311,13 @@ public class ClusterInspector : Editor {
                     Handles.color = Color.white;
                     // The selected nucleus highlight ring
                     Handles.DrawSolidDisc(position, Vector3.forward, size + 2);
-                    DrawNucleus(this.currentNucleus, position, length(this.currentNucleus.outputValue), 20);
+                    float maxValue = 1;
+                    if (this.currentNucleus is Neuron neuron)
+                        maxValue = length(neuron.outputValue);
+                    else if (this.currentNucleus is Cluster cluster)
+                        maxValue = length(cluster.defaultOutput.outputValue);
+
+                    DrawNucleus(this.currentNucleus, position, maxValue, 20);
 
                 }
             }
@@ -356,12 +325,17 @@ public class ClusterInspector : Editor {
                 Handles.color = Color.white;
                 // The selected nucleus highlight ring
                 Handles.DrawSolidDisc(position, Vector3.forward, size + 2);
-                DrawNucleus(this.currentNucleus, position, length(this.currentNucleus.outputValue), 20);
+                float maxValue = 1;
+                if (this.currentNucleus is Neuron neuron)
+                    maxValue = length(neuron.outputValue);
+                else if (this.currentNucleus is Cluster cluster)
+                    maxValue = length(cluster.defaultOutput.outputValue);
+                DrawNucleus(this.currentNucleus, position, maxValue, 20);
             }
         }
 
         private void DrawReceivers(Nucleus nucleus, Vector3 parentPos, float size) {
-            List<Nucleus> receivers = null;
+            List<Nucleus> receivers;
             if (nucleus is Neuron neuron)
                 receivers = neuron.receivers;
             else if (nucleus is Cluster cluster)
@@ -417,20 +391,25 @@ public class ClusterInspector : Editor {
             int neuronCount = 0;
             List<Nucleus[]> drawnArrays = new();
             foreach (Synapse synapse in nucleus.synapses) {
-                if (synapse.nucleus is Receptor receptor) {
+                if (synapse.neuron == null)
+                    continue;
+
+                if (synapse.neuron is Receptor receptor) {
                     if (drawnArrays.Contains(receptor.nucleiArray))
                         continue;
                     drawnArrays.Add(receptor.nucleiArray);
                 }
-                else if (synapse.nucleus.parent is ClusterReceptor clusterReceptor) {
+                else if (synapse.neuron.parent is ClusterReceptor clusterReceptor) {
                     if (drawnArrays.Contains(clusterReceptor.nucleiArray))
                         continue;
                     drawnArrays.Add(clusterReceptor.nucleiArray);
                 }
-                float value = length(synapse.nucleus.outputValue) * synapse.weight;
-                // Debug.Log($"{synapse.nucleus.name}: {value}  {length(synapse.nucleus.outputValue)} {synapse.weight}");
-                if (value > maxValue)
-                    maxValue = value;
+                if (synapse.neuron is Neuron synapseNeuron) {
+                    float value = length(synapseNeuron.outputValue) * synapse.weight;
+                    // Debug.Log($"{synapse.nucleus.name}: {value}  {length(synapse.nucleus.outputValue)} {synapse.weight}");
+                    if (value > maxValue)
+                        maxValue = value;
+                }
                 neuronCount++;
             }
 
@@ -441,12 +420,15 @@ public class ClusterInspector : Editor {
             int row = 0;
             drawnArrays = new();
             foreach (Synapse synapse in nucleus.synapses) {
-                if (synapse.nucleus is Receptor neuron) {
+                if (synapse.neuron is null)
+                    continue;
+                    
+                if (synapse.neuron is Receptor neuron) {
                     if (drawnArrays.Contains(neuron.nucleiArray))
                         continue;
                     drawnArrays.Add(neuron.nucleiArray);
                 }
-                else if (synapse.nucleus.parent is ClusterReceptor clusterReceptor) {
+                else if (synapse.neuron.parent is ClusterReceptor clusterReceptor) {
                     if (drawnArrays.Contains(clusterReceptor.nucleiArray))
                         continue;
                     drawnArrays.Add(clusterReceptor.nucleiArray);
@@ -458,18 +440,20 @@ public class ClusterInspector : Editor {
                 if (Application.isPlaying) {
                     if (maxValue == 0 || !float.IsFinite(maxValue))
                         maxValue = 1;
-                    float brightness = length(synapse.nucleus.outputValue * synapse.weight) / maxValue;
+                    float brightness = 0;
+                    if (synapse.neuron is Neuron synapseNeuron)
+                        brightness = length(synapseNeuron.outputValue * synapse.weight) / maxValue;
                     color = new Color(brightness, brightness, brightness, 1f);
                 }
-                if (synapse.nucleus.parent != null && synapse.nucleus.parent != this.currentNucleus.parent) {
+                if (synapse.neuron.parent != null && synapse.neuron.parent != this.currentNucleus.parent) {
                     // the synapse nucleus is part of a subcluster
-                    DrawNucleus(synapse.nucleus.parent, pos, maxValue, size, color);
+                    DrawNucleus(synapse.neuron.parent, pos, maxValue, size, color);
                 }
                 // else if (synapse.nucleus.cluster != null && synapse.nucleus.cluster != this.currentNucleus.cluster) {
                 //     DrawNucleus(synapse.nucleus.parent, pos, maxValue, size, color);
                 // }
                 else {
-                    DrawNucleus(synapse.nucleus, pos, maxValue, size, color);
+                    DrawNucleus(synapse.neuron, pos, maxValue, size, color);
                 }
                 row++;
             }
@@ -478,7 +462,9 @@ public class ClusterInspector : Editor {
         private void DrawNucleus(Nucleus nucleus, Vector3 position, float maxValue, float size) {
             Color color;
             if (Application.isPlaying) {
-                float brightness = length(nucleus.outputValue) / maxValue;
+                float brightness = 0;
+                if (nucleus is Neuron neuron)
+                    brightness = length(neuron.outputValue) / maxValue;
                 color = new Color(brightness, brightness, brightness, 1f);
             }
             else
@@ -505,11 +491,11 @@ public class ClusterInspector : Editor {
                 fontStyle = FontStyle.Bold,
             };
 
-            if (nucleus is Receptor receptor1) {
-                // draw the array size label
-                if (expandArray) { //} && receptor1.array.nuclei.First() == this.currentNucleus) {
+            if (nucleus is IReceptor receptor1) {
+                if (expandArray) {
+                    // Put array indices above elements
                     style.alignment = TextAnchor.LowerCenter;
-                    Vector3 labelPos1 = position + Vector3.down * (size + 5); // below disc along up axis
+                    Vector3 labelPos1 = position + Vector3.down * (size + 5); // below disc 
                     int colonPos1 = nucleus.name.IndexOf(":");
                     if (colonPos1 > 0) {
                         string extName = nucleus.name[(colonPos1 + 2)..];
@@ -517,6 +503,7 @@ public class ClusterInspector : Editor {
                     }
                 }
                 else {
+                    // draw the array size label
                     if (color.grayscale > 0.5f)
                         style.normal.textColor = Color.black;
                     else
@@ -525,59 +512,27 @@ public class ClusterInspector : Editor {
                     style.normal.textColor = Color.white;
                 }
             }
-            // if (nucleus is ReceptorArray receptor) {
-            //     if (color.grayscale > 0.5f)
-            //         style.normal.textColor = Color.black;
-            //     else
-            //         style.normal.textColor = Color.white;
-            //     Handles.Label(labelPosition, receptor.instances.Count().ToString(), style);
-            // }
 
-            if (nucleus is ClusterReceptor clusterReceptor) {
-                // draw the array size label
-                if (expandArray && clusterReceptor.array.nuclei.First() == this.currentNucleus) {
-                    style.alignment = TextAnchor.LowerCenter;
-                    Vector3 labelPos2 = position + Vector3.down * (size + 5); // below disc along up axis
-                    int colonPos2 = nucleus.name.IndexOf(":");
-                    if (colonPos2 > 0) {
-                        string extName = nucleus.name[(colonPos2 + 2)..];
-                        Handles.Label(labelPos2, extName, style);
-                    }
-                }
-                else {
-                    if (color.grayscale > 0.5f)
-                        style.normal.textColor = Color.black;
-                    else
-                        style.normal.textColor = Color.white;
-                    Handles.Label(labelPosition, clusterReceptor.array.nuclei.Length.ToString(), style);
-                    style.normal.textColor = Color.white;
+            if (expandArray == false || nucleus is not IReceptor) {
+                // put name below nucleus
+                Vector3 labelPos = position - Vector3.down * (size + 5); // below neuron
+                style.alignment = TextAnchor.UpperCenter;
+
+                int colonPos = nucleus.name.IndexOf(":");
+                if (colonPos > 0 && colonPos < nucleus.name.Length - 2) {
+                    // if it is an array, we should not show the :0 of the first element
+                    string baseName = nucleus.name[..colonPos];
+                    Handles.Label(labelPos, baseName, style);
                 }
+                else
+                    Handles.Label(labelPos, nucleus.name, style);
+
             }
 
-            // if (expandArray && nucleus is Receptor receptor2 && receptor2.array.nuclei.First() == this.currentNucleus) {
-            //     style.alignment = TextAnchor.LowerCenter;
-            //     Vector3 labelPos = position + Vector3.down * (size + 5); // below disc along up axis
-            //     int colonPos = nucleus.name.IndexOf(":");
-            //     if (colonPos > 0) {
-            //         string extName = nucleus.name[(colonPos + 2)..];
-            //         Handles.Label(labelPos, extName, style);
-            //     }
-            // }
-            // else {
-            style.alignment = TextAnchor.UpperCenter;
-            Vector3 labelPos = position - Vector3.down * (size + 5); // below disc along up axis
-            int colonPos = nucleus.name.IndexOf(":");
-            if (expandArray && nucleus is Receptor) { //} || (colonPos > 0 && colonPos < nucleus.name.Length - 2)) {
-                // string baseName = nucleus.name[..colonPos];
-                // Handles.Label(labelPos, baseName, style);
-            }
-            else
-                Handles.Label(labelPos, nucleus.name, style);
-            // }
-
+            // Draw Cluster ring
             if (nucleus is Cluster) {
                 Handles.color = Color.white;
-                Handles.DrawWireDisc(position, Vector3.forward, size + 10);
+                Handles.DrawWireDisc(position, Vector3.forward, size + 5);
             }
 
             // Tooltip
@@ -599,9 +554,13 @@ public class ClusterInspector : Editor {
 
         private void HandleMouseHover(Nucleus nucleus, Rect rect) {
             GUIContent tooltip;
-            tooltip = new(
-                $"{nucleus.name}" +
-                $"\nValue: {length(nucleus.outputValue)}");
+            if (nucleus is Neuron neuron) {
+                tooltip = new(
+                    $"{nucleus.name}" +
+                    $"\nValue: {length(neuron.outputValue)}");
+            }
+            else
+                tooltip = new($"{nucleus.name}");
 
             Vector2 mousePosition = Event.current.mousePosition;
 
@@ -619,11 +578,11 @@ public class ClusterInspector : Editor {
                 else
                     expandArray = false;
             }
-            else if (nucleus is ReceptorInstance receptor) {
-                this.currentNucleus = receptor.receptor;
-                expandArray = false;
-                BuildLayers();
-            }
+            // else if (nucleus is ReceptorInstance receptor) {
+            //     this.currentNucleus = receptor.receptor;
+            //     expandArray = false;
+            //     BuildLayers();
+            // }
             else {
                 this.currentNucleus = nucleus;
                 expandArray = false;
@@ -631,6 +590,7 @@ public class ClusterInspector : Editor {
             }
         }
 
+        private VisualElement inspectorIMGUIContainer;
         private bool showSynapses = true;
         private bool showActivation = true;
         protected bool breakOnWake = false;
@@ -645,9 +605,9 @@ public class ClusterInspector : Editor {
 
             // create a SerializedObject wrapper so Unity inspector controls work (and Undo)
             SerializedObject so = new(prefabAsset);
-            IMGUIContainer container = new(() => InspectorHandler(so));
+            this.inspectorIMGUIContainer = new IMGUIContainer(() => InspectorHandler(so));
 
-            inspectorContainer.Add(container);
+            inspectorContainer.Add(inspectorIMGUIContainer);
         }
 
         void InspectorHandler(SerializedObject serializedObject) {
@@ -675,11 +635,16 @@ public class ClusterInspector : Editor {
                 this.currentNucleus.name = newName;
                 this.prefab.RefreshOutputs();
                 outputsField.choices = this.prefab.outputs.Select(output => output.name).ToList();
+                anythingChanged = true;
             }
 
             if (Application.isPlaying) {
-                GUIContent nameLabel = new("Output", this.currentNucleus.outputValue.ToString());
-                EditorGUILayout.FloatField(nameLabel, length(this.currentNucleus.outputValue));
+                if (currentNucleus is Neuron currentNeuron1) {
+                    GUIContent nameLabel = new("Output", currentNeuron1.outputValue.ToString());
+                    EditorGUILayout.FloatField(nameLabel, length(currentNeuron1.outputValue));
+                }
+                else
+                    EditorGUILayout.LabelField(" ");
             }
             else
                 EditorGUILayout.LabelField(" ");
@@ -687,162 +652,164 @@ public class ClusterInspector : Editor {
             if (this.currentNucleus is MemoryCell memory) {
                 memory.staticMemory = EditorGUILayout.Toggle("Static Memory", memory.staticMemory);
             }
-            if (this.currentNucleus is ReceptorArray receptor) {
-                EditorGUILayout.BeginHorizontal();
-                EditorGUILayout.IntField("Receptor size", receptor.instances.Count());
-                if (GUILayout.Button("Add")) {
-                    Undo.RecordObject(prefabAsset, "Receptor add " + prefabAsset.name);
-                    receptor.AddReceptor(this.prefab);
-                    anythingChanged = true;
-                }
-                if (GUILayout.Button("Del")) {
-                    Undo.RecordObject(prefabAsset, "Receptor delete " + prefabAsset.name);
-                    receptor.RemoveReceptor();
-                    anythingChanged = true;
-                }
-                EditorGUILayout.EndHorizontal();
-            }
-            if (this.currentNucleus is Receptor receptor1) {
+
+            if (this.currentNucleus is IReceptor receptor1) {
                 EditorGUILayout.BeginHorizontal();
                 EditorGUILayout.IntField("Array size", receptor1.nucleiArray.Count());
                 if (GUILayout.Button("Add")) {
                     Undo.RecordObject(prefabAsset, "Array add " + prefabAsset.name);
-                    //receptor1.array.AddNucleus(this.prefab);
                     receptor1.AddReceptorElement(this.prefab);
                     anythingChanged = true;
                 }
                 if (GUILayout.Button("Del")) {
                     Undo.RecordObject(prefabAsset, "Array delete " + prefabAsset.name);
-                    //receptor1.array.RemoveNucleus();
                     receptor1.RemoveReceptorElement();
                     anythingChanged = true;
                 }
                 EditorGUILayout.EndHorizontal();
             }
-            else if (this.currentNucleus is ClusterReceptor receptor2) {
-                EditorGUILayout.BeginHorizontal();
-                EditorGUILayout.IntField("Array size", receptor2.array.nuclei.Count());
-                if (GUILayout.Button("Add")) {
-                    Undo.RecordObject(prefabAsset, "Array add " + prefabAsset.name);
-                    receptor2.array.AddNucleus(this.prefab);
-                    anythingChanged = true;
-                }
-                if (GUILayout.Button("Del")) {
-                    Undo.RecordObject(prefabAsset, "Array delete " + prefabAsset.name);
-                    receptor2.array.RemoveNucleus();
-                    anythingChanged = true;
-                }
-                EditorGUILayout.EndHorizontal();
-            }
-
 
             // Synapses
 
             if (this.currentNucleus is not Receptor && this.currentNucleus is not ClusterReceptor) {
                 showSynapses = EditorGUILayout.BeginFoldoutHeaderGroup(showSynapses, "Synapses");
                 if (showSynapses) {
-
-                    anythingChanged = ConnectNucleus(this.prefab, this.currentNucleus);
-                    anythingChanged = AddSynapse(this.prefab, this.currentNucleus);
-                    EditorGUILayout.Space();
-
                     if (this.currentNucleus is Neuron neuron2) {
                         Neuron.CombinatorType newCombinator = (Neuron.CombinatorType)EditorGUILayout.EnumPopup("Combinator", neuron2.combinator);
                         anythingChanged |= newCombinator != neuron2.combinator;
                         neuron2.combinator = newCombinator;
                     }
 
+                    EditorGUIUtility.wideMode = true;
+                    EditorGUIUtility.labelWidth = 100;
                     Vector3 newBias = EditorGUILayout.Vector3Field("Bias", this.currentNucleus.bias);
                     anythingChanged |= newBias != this.currentNucleus.bias;
                     this.currentNucleus.bias = newBias;
 
                     Nucleus[] array = null;
+                    int elementIx = -1;
                     if (this.currentNucleus.synapses.Count > 0) {
                         Synapse[] synapses = this.currentNucleus.synapses.ToArray();
                         foreach (Synapse synapse in synapses) {
-                            if (synapse.nucleus == null)
+                            if (synapse.neuron == null)
                                 continue;
 
                             if (array != null) {
-                                if (array.Contains(synapse.nucleus))
-                                    continue;
-                                if (array.Contains(synapse.nucleus.parent))
+                                if (synapse.neuron.parent is Cluster iCluster && elementIx > 0) {
+                                    int thisElementIx = Cluster.GetNucleusIndex(iCluster.clusterNuclei, synapse.neuron);
+                                    if (thisElementIx == elementIx)
+                                        continue;
+                                    else
+                                        elementIx = thisElementIx;
+                                }
+                                // if (array.Contains(synapse.nucleus))
+                                //     continue;
+                                else if (array.Contains(synapse.neuron.parent))
                                     continue;
                             }
                             else {
-                                if (synapse.nucleus.parent is ClusterReceptor clusterReceptor)
-                                    array = clusterReceptor.nucleiArray;
-                                else if (synapse.nucleus is Receptor receptor2) // && receptor2.array != null && receptor2.array.nuclei.Length > 1)
-                                    array = receptor2.nucleiArray;
+                                if (synapse.neuron.parent is IReceptor iReceptor) {
+                                    array = iReceptor.nucleiArray;
+                                    if (iReceptor is Cluster iCluster)
+                                        elementIx = Cluster.GetNucleusIndex(iCluster.clusterNuclei, synapse.neuron);
+                                }
+                                // else if (synapse.nucleus is Receptor receptor2) // && receptor2.array != null && receptor2.array.nuclei.Length > 1)
+                                //     array = receptor2.nucleiArray;
                             }
 
                             EditorGUILayout.Space();
 
                             if (Application.isPlaying) {
-                                Vector3 value = synapse.nucleus.outputValue * synapse.weight;
-                                GUIContent synapseValueLabel = new(synapse.nucleus.name, synapse.nucleus.outputValue.ToString());
-                                EditorGUILayout.FloatField(synapseValueLabel, length(synapse.nucleus.outputValue));
+                                if (synapse.neuron is Neuron synapseNeuron) {
+                                    Vector3 value = synapseNeuron.outputValue * synapse.weight;
+                                    GUIContent synapseValueLabel = new(synapse.neuron.name, synapseNeuron.outputValue.ToString());
+                                    EditorGUILayout.FloatField(synapseValueLabel, length(synapseNeuron.outputValue));
+                                }
                             }
                             else {
                                 EditorGUILayout.BeginHorizontal();
 
-                                if (synapse.nucleus.parent != null && synapse.nucleus.parent != this.currentNucleus) {
+                                if (synapse.neuron.parent != null && synapse.neuron.parent != this.currentNucleus) {
+                                    // If it is a cluster
                                     GUIStyle labelStyle = new(GUI.skin.label);
-                                    float labelWidth = labelStyle.CalcSize(new GUIContent($"{synapse.nucleus.clusterPrefab.name}.")).x;
-                                    EditorGUILayout.LabelField($"{synapse.nucleus.clusterPrefab.name}", GUILayout.Width(labelWidth));
-                                    string[] options = synapse.nucleus.parent.clusterNuclei.Select(n => n.name).ToArray();
-                                    int selectedIndex = System.Array.IndexOf(options, synapse.nucleus.name);
+                                    float labelWidth = 200;
+                                    if (synapse.neuron.clusterPrefab != null) {
+                                        labelWidth = labelStyle.CalcSize(new GUIContent($"{synapse.neuron.parent.baseName}.")).x;
+                                        GUILayout.Label($"{synapse.neuron.parent.baseName}", GUILayout.Width(labelWidth));
+                                    }
+                                    string[] options = synapse.neuron.parent.clusterNuclei.Select(n => n.name).ToArray();
+                                    int selectedIndex = System.Array.IndexOf(options, synapse.neuron.name);
                                     int newIndex = EditorGUILayout.Popup(selectedIndex, options);
-                                    if (newIndex != selectedIndex && synapse.nucleus.parent.clusterNuclei[newIndex] is Neuron newNeuron)
+                                    if (newIndex != selectedIndex && synapse.neuron.parent.clusterNuclei[newIndex] is Neuron newNeuron)
                                         ChangeSynapse(synapse, newNeuron);
                                 }
                                 else
-                                    EditorGUILayout.LabelField(synapse.nucleus.name);
-                                if (GUILayout.Button("Disconnect") && synapse.nucleus is Neuron synapseNeuron) {
+                                    GUILayout.Label(synapse.neuron.name);
+
+                                bool disconnecting = GUILayout.Button("Disconnect", GUILayout.Width(80));
+                                if (disconnecting && synapse.neuron is Neuron synapseNeuron) {
                                     synapseNeuron.RemoveReceiver(this.currentNucleus);
                                     this.prefab.GarbageCollection();
                                     anythingChanged = true;
                                 }
                                 EditorGUILayout.EndHorizontal();
+
                             }
 
                             EditorGUI.indentLevel++;
-                            synapse.weight = EditorGUILayout.FloatField("Weight", synapse.weight);
+                            float newWeight = EditorGUILayout.FloatField("Weight", synapse.weight);
+                            if (newWeight != synapse.weight) {
+                                if (synapse.neuron.parent is IReceptor receptor) {
+                                    Nucleus[] receptorArray = receptor.nucleiArray;
+                                    foreach (Synapse s in this.currentNucleus.synapses) {
+                                        if (s.neuron.parent is IReceptor r && r.nucleiArray == receptorArray)
+                                            s.weight = newWeight;
+                                    }
+                                }
+                                else
+                                    synapse.weight = newWeight;
+                                anythingChanged = true;
+                            }
                             EditorGUI.indentLevel--;
                         }
                     }
+
+                    EditorGUILayout.Space();
+                    anythingChanged |= ConnectNucleus(this.prefab, this.currentNucleus);
+                    anythingChanged |= AddSynapse(this.prefab, this.currentNucleus);
                 }
                 EditorGUILayout.EndFoldoutHeaderGroup();
             }
 
             // Activation
 
-            EditorGUILayout.Space();
-            showActivation = EditorGUILayout.BeginFoldoutHeaderGroup(showActivation, "Activation");
-            if (showActivation) {
-                if (this.currentNucleus is Neuron neuron) {
-                    if (this.currentNucleus is not MemoryCell) {
-                        EditorGUILayout.BeginHorizontal();
-                        EditorGUILayout.LabelField("Activation Curve", GUILayout.Width(150));
-                        if (neuron.curveMax > 0)
-                            EditorGUILayout.CurveField(neuron.curve, Color.cyan, new Rect(0, 0, 1, neuron.curveMax));
-                        else
-                            EditorGUILayout.CurveField(neuron.curve, Color.cyan, new Rect(0, neuron.curveMax, 1, -neuron.curveMax));
-                        Neuron.CurvePresets newPreset = (Neuron.CurvePresets)EditorGUILayout.EnumPopup(neuron.curvePreset, GUILayout.Width(100));
-                        anythingChanged |= newPreset != neuron.curvePreset;
-                        neuron.curvePreset = newPreset;
-                        EditorGUILayout.EndHorizontal();
-                    }
-                    if (neuron is Receptor receptor2) {
-                        if (receptor2.nucleiArray == null || receptor2.nucleiArray.Count() == 0)
-                            receptor2.array = new NucleusArray(neuron);
-                    }
-                }
-
+            if (this.currentNucleus is not Cluster) {
                 EditorGUILayout.Space();
-            }
-            EditorGUILayout.EndFoldoutHeaderGroup();
+                showActivation = EditorGUILayout.BeginFoldoutHeaderGroup(showActivation, "Activation");
+                if (showActivation) {
+                    if (this.currentNucleus is Neuron neuron) {
+                        if (this.currentNucleus is not MemoryCell) {
+                            EditorGUILayout.BeginHorizontal();
+                            EditorGUILayout.LabelField("Activation Curve", GUILayout.Width(150));
+                            if (neuron.curveMax > 0)
+                                EditorGUILayout.CurveField(neuron.curve, Color.cyan, new Rect(0, 0, 1, neuron.curveMax));
+                            else
+                                EditorGUILayout.CurveField(neuron.curve, Color.cyan, new Rect(0, neuron.curveMax, 1, -neuron.curveMax));
+                            Neuron.CurvePresets newPreset = (Neuron.CurvePresets)EditorGUILayout.EnumPopup(neuron.curvePreset, GUILayout.Width(100));
+                            anythingChanged |= newPreset != neuron.curvePreset;
+                            neuron.curvePreset = newPreset;
+                            EditorGUILayout.EndHorizontal();
+                        }
+                        if (neuron is Receptor receptor2) {
+                            if (receptor2.nucleiArray == null || receptor2.nucleiArray.Count() == 0)
+                                receptor2.array = new NucleusArray(neuron);
+                        }
+                    }
 
+                    EditorGUILayout.Space();
+                }
+                EditorGUILayout.EndFoldoutHeaderGroup();
+            }
 
             if (GUILayout.Button("Delete this neuron"))
                 DeleteNucleus(this.currentNucleus);
@@ -854,8 +821,8 @@ public class ClusterInspector : Editor {
 
             EditorGUILayout.Space();
             breakOnWake = EditorGUILayout.Toggle("Break on wake", breakOnWake);
-            if (breakOnWake) {
-                if (this.currentNucleus.isSleeping == false)
+            if (breakOnWake && this.currentNucleus is Neuron currentNeuron) {
+                if (currentNeuron.isSleeping == false)
                     Debug.Break();
             }
             trace = EditorGUILayout.Toggle("Trace", trace);
@@ -870,26 +837,20 @@ public class ClusterInspector : Editor {
 
         void OnSceneGUI(SceneView sceneView) {
             if (this.gameObject != null) {
-                if (this.currentNucleus is ReceptorArray receptor && expandArray) {
-                    foreach (Nucleus nucleus in receptor.instances) {
-                        Vector3 worldVector = this.gameObject.transform.TransformVector(nucleus.outputValue);
-                        Handles.color = Color.yellow;
-                        Handles.DrawLine(this.gameObject.transform.position, this.gameObject.transform.position + worldVector);
-                    }
-                }
-                else {
-                    if (this.currentNucleus is Receptor receptor1) {
-                        foreach (Nucleus nucleus in receptor1.nucleiArray) {
-                            Vector3 worldVector = this.gameObject.transform.TransformVector(nucleus.outputValue);
+                if (this.currentNucleus is IReceptor receptor) {
+                    foreach (Nucleus nucleus in receptor.nucleiArray) {
+                        if (nucleus is Neuron neuron) {
+                            Vector3 worldVector = this.gameObject.transform.TransformVector(neuron.outputValue);
                             Handles.color = Color.yellow;
                             Handles.DrawLine(this.gameObject.transform.position, this.gameObject.transform.position + worldVector);
                         }
                     }
-                    else {
-                        Vector3 worldVector = this.gameObject.transform.TransformVector(this.currentNucleus.outputValue);
+                }
+                else {
+                    if (this.currentNucleus is Neuron currentNeuron) {
+                        Vector3 worldVector = this.gameObject.transform.TransformVector(currentNeuron.outputValue);
                         Handles.color = Color.yellow;
                         Handles.DrawLine(this.gameObject.transform.position, this.gameObject.transform.position + worldVector);
-
                     }
                 }
             }
@@ -905,21 +866,21 @@ public class ClusterInspector : Editor {
                 case Nucleus.Type.MemoryCell:
                     AddMemoryCellInput(nucleus);
                     break;
-                case Nucleus.Type.Selector:
-                    AddSelectorInput(nucleus);
-                    break;
+                // case Nucleus.Type.Selector:
+                //     AddSelectorInput(nucleus);
+                //     break;
                 case Nucleus.Type.Cluster:
                     AddClusterInput(nucleus);
                     break;
-                case Nucleus.Type.Pulsar:
-                    AddPulsarInput(nucleus);
-                    break;
+                // case Nucleus.Type.Pulsar:
+                //     AddPulsarInput(nucleus);
+                //     break;
                 case Nucleus.Type.Receptor:
                     AddReceptorInput(nucleus);
                     break;
-                case Nucleus.Type.ReceptorArray:
-                    AddReceptorArrayInput(nucleus);
-                    break;
+                // case Nucleus.Type.ReceptorArray:
+                //     AddReceptorArrayInput(nucleus);
+                //     break;
                 case Nucleus.Type.ClusterReceptor:
                     AddClusterReceptorInput(nucleus);
                     break;
@@ -935,19 +896,19 @@ public class ClusterInspector : Editor {
             BuildLayers();
         }
 
-        protected void AddSelectorInput(Nucleus nucleus) {
-            Selector newSelector = new(this.prefab, "New Selector");
-            newSelector.AddReceiver(nucleus);
-            this.currentNucleus = newSelector;
-            BuildLayers();
-        }
+        // protected void AddSelectorInput(Nucleus nucleus) {
+        //     Selector newSelector = new(this.prefab, "New Selector");
+        //     newSelector.AddReceiver(nucleus);
+        //     this.currentNucleus = newSelector;
+        //     BuildLayers();
+        // }
 
-        protected void AddPulsarInput(Nucleus nucleus) {
-            Pulsar newPulsar = new(this.prefab, "New Pulsar");
-            newPulsar.AddReceiver(nucleus);
-            this.currentNucleus = newPulsar;
-            BuildLayers();
-        }
+        // protected void AddPulsarInput(Nucleus nucleus) {
+        //     Pulsar newPulsar = new(this.prefab, "New Pulsar");
+        //     newPulsar.AddReceiver(nucleus);
+        //     this.currentNucleus = newPulsar;
+        //     BuildLayers();
+        // }
 
         protected virtual void AddMemoryCellInput(Nucleus nucleus) {
             MemoryCell newMemory = new(this.prefab, "New memory cell");
@@ -959,6 +920,10 @@ public class ClusterInspector : Editor {
         protected virtual void AddClusterInput(Nucleus nucleus) {
             ClusterPickerWindow.ShowPicker(brain => OnClusterPicked(nucleus, brain), "Select Cluster");
         }
+        private void OnClusterPicked(Nucleus nucleus, ClusterPrefab prefab) {
+            Cluster subclusterInstance = new(prefab, this.prefab);
+            subclusterInstance.defaultOutput.AddReceiver(nucleus);
+        }
 
         protected virtual void AddReceptorInput(Nucleus nucleus) {
             Receptor newReceptor = new(this.prefab, "New Receptor");
@@ -967,25 +932,14 @@ public class ClusterInspector : Editor {
             BuildLayers();
         }
 
-        protected virtual void AddReceptorArrayInput(Nucleus nucleus) {
-            // ReceptorArray newReceptor = new(this.prefab, "New Receptor");
-            // newReceptor.AddReceiver(nucleus);
-            // this.currentNucleus = newReceptor;
-            // BuildLayers();
-        }
-
         protected virtual void AddClusterReceptorInput(Nucleus nucleus) {
             ClusterPickerWindow.ShowPicker(prefab => OnClusterReceptorPicked(nucleus, prefab), "Select Cluster");
         }
-
-        private void OnClusterPicked(Nucleus nucleus, ClusterPrefab prefab) {
-            Cluster subclusterInstance = new(prefab, this.prefab);
-            subclusterInstance.defaultOutput.AddReceiver(nucleus);
-        }
-
         private void OnClusterReceptorPicked(Nucleus nucleus, ClusterPrefab selectedPrefab) {
             ClusterReceptor clusterInstance = new(selectedPrefab, this.prefab, "New " + selectedPrefab.name);
             clusterInstance.defaultOutput.AddReceiver(nucleus);
+            this.currentNucleus = clusterInstance;
+            BuildLayers();
         }
 
         private void EditCluster(Cluster subCluster) {
@@ -995,32 +949,41 @@ public class ClusterInspector : Editor {
             var editor = Editor.CreateEditor(subCluster.prefab);
         }
 
+        int selectedConnectNucleus = -1;
         // Connect to another nucleus in the same cluster
         protected virtual bool ConnectNucleus(ClusterPrefab cluster, Nucleus nucleusToConnect) {
             if (cluster == null)
                 return false;
 
             IEnumerable<Nucleus> synapseNuclei = this.currentNucleus.synapses
-                .Where(synapse => synapse.nucleus != null)
-                .Select(synapse => synapse.nucleus);
+                .Where(synapse => synapse.neuron != null)
+                .Select(synapse => synapse.neuron);
 
             IEnumerable<Nucleus> nuclei = cluster.nuclei
                 .Except(synapseNuclei);
-            IEnumerable<string> nucleiNames = nuclei.Select(n => n.name);
+            IEnumerable<string> nucleiNames = nuclei
+                .Select(n => {
+                    int idx = n.name.IndexOf(':');
+                    return idx < 0 ? n.name : n.name[..idx];
+                })
+                .Distinct();
 
             string[] names = nucleiNames.ToArray();
-            int selectedIndex = -1;
-            selectedIndex = EditorGUILayout.Popup("Connect", selectedIndex, names);
-            if (selectedIndex < 0)
-                return false;
+            EditorGUILayout.BeginHorizontal();
+            selectedConnectNucleus = EditorGUILayout.Popup(selectedConnectNucleus, names);
+            bool connecting = GUILayout.Button("Connect", GUILayout.Width(80));
+            EditorGUILayout.EndHorizontal();
+            if (connecting) {
+                Nucleus nucleus = nuclei.ElementAt(selectedConnectNucleus);
+                if (nucleus is IReceptor receptor)
+                    receptor.AddArrayReceiver(this.currentNucleus);
+                else if (nucleus is Neuron neuron)
+                    neuron.AddReceiver(this.currentNucleus);
+                else if (nucleus is Cluster subCluster)
+                    subCluster.defaultOutput.AddReceiver(this.currentNucleus);
 
-            Nucleus nucleus = nuclei.ElementAt(selectedIndex);
-            if (nucleus is Neuron neuron)
-                neuron.AddReceiver(this.currentNucleus);
-            else if (nucleus is Cluster subCluster)
-                subCluster.defaultOutput.AddReceiver(this.currentNucleus);
-
-            return true;
+            }
+            return connecting;
         }
 
         protected virtual void DeleteNucleus(Nucleus nucleus) {
@@ -1049,24 +1012,61 @@ public class ClusterInspector : Editor {
             BuildLayers();
         }
 
+        Nucleus.Type selectedType = Nucleus.Type.None;
         protected virtual bool AddSynapse(ClusterPrefab cluster, Nucleus nucleus) {
             if (cluster == null)
                 return false;
 
-            Nucleus.Type selectedType = (Nucleus.Type)EditorGUILayout.EnumPopup("Add", Nucleus.Type.None);
-            if (selectedType == Nucleus.Type.None)
-                return false;
+            EditorGUILayout.BeginHorizontal();
+            selectedType = (Nucleus.Type)EditorGUILayout.EnumPopup(selectedType);
+            bool connecting = GUILayout.Button("Add", GUILayout.Width(80));
+            EditorGUILayout.EndHorizontal();
 
-            AddInput(selectedType, this.currentNucleus);
-            return true;
+            if (connecting) {
+                AddInput(selectedType, this.currentNucleus);
+            }
+            return connecting;
+            // if (selectedType == Nucleus.Type.None)
+            //     return false;
+
+            // AddInput(selectedType, this.currentNucleus);
+            // return true;
         }
 
         protected virtual void ChangeSynapse(Synapse synapse, Neuron newNucleus) {
-            Neuron synapseNeuron = synapse.nucleus as Neuron;
-            if (synapse.nucleus.parent is Cluster subCluster && subCluster.prefab != this.prefab) {
-                // it is a neuron in a subcluster
-                synapseNeuron.RemoveReceiver(this.currentNucleus);
-                newNucleus.AddReceiver(this.currentNucleus);
+            Neuron synapseNeuron = synapse.neuron as Neuron;
+            if (synapse.neuron.parent is Cluster subCluster && subCluster.prefab != this.prefab) {
+                if (synapse.neuron.parent is ClusterReceptor receptor) {
+                    // the new nucleus is part of a (cluster) receptor,
+                    // so we have to change all synapses to this nucleus array elements
+                    int oldNucleusIx = Cluster.GetNucleusIndex(subCluster.clusterNuclei, synapse.neuron);
+                    int newNucleusIx = Cluster.GetNucleusIndex(subCluster.clusterNuclei, newNucleus);
+                    foreach (Nucleus element in receptor.nucleiArray) {
+                        if (element is not ClusterReceptor clusterReceptor)
+                            continue;
+                        // Get the same neuron as the synapse.nucleus in a different element
+                        // of the ClusterReceptor array
+                        Nucleus oldElementNucleus = clusterReceptor.clusterNuclei[oldNucleusIx];
+                        if (oldElementNucleus is not Neuron oldElementNeuron)
+                            continue;
+                        // Get the same neuron as newNucleus in a different element
+                        // of the ClusterReceptor array
+                        Nucleus newElementNucleus = clusterReceptor.clusterNuclei[newNucleusIx];
+                        if (newElementNucleus is not Neuron newElementNeuron)
+                            continue;
+
+                        oldElementNeuron.RemoveReceiver(this.currentNucleus);
+                        newElementNeuron.AddReceiver(this.currentNucleus);
+                        // Now find the synapse which pointed to the old Neuron
+                        // Synapse synapseForUpdate = this.currentNucleus.GetSynapse(oldElementNeuron);
+                        // synapseForUpdate.nucleus = newElementNeuron;
+                    }
+                }
+                else {
+                    // it is a neuron in a subcluster
+                    synapseNeuron.RemoveReceiver(this.currentNucleus);
+                    newNucleus.AddReceiver(this.currentNucleus);
+                }
             }
             else {
                 synapseNeuron.RemoveReceiver(this.currentNucleus);
@@ -1077,12 +1077,12 @@ public class ClusterInspector : Editor {
         protected virtual void DisconnectNucleus(Neuron nucleus) {
             if (this.currentNucleus.clusterPrefab == null)
                 return;
-            string[] names = this.currentNucleus.synapses.Select(synapse => synapse.nucleus.name).ToArray();
+            string[] names = this.currentNucleus.synapses.Select(synapse => synapse.neuron.name).ToArray();
             int selectedIndex = -1;
             selectedIndex = EditorGUILayout.Popup("Disconnect from", selectedIndex, names);
             if (selectedIndex >= 0 && selectedIndex < this.currentNucleus.clusterPrefab.nuclei.Count) {
                 Synapse synapse = this.currentNucleus.synapses[selectedIndex];
-                Neuron synapseNeuron = synapse.nucleus as Neuron;
+                Neuron synapseNeuron = synapse.neuron as Neuron;
                 synapseNeuron.RemoveReceiver(this.currentNucleus);
             }
         }

Editor/NanoBrain_Editor.cs

@@ -17,8 +17,10 @@ public class NanoBrainComponent_Editor : Editor {
     public void OnEnable() {
         component = target as NanoBrain;
 
-        if (Application.isPlaying == false)
-            brainProp = serializedObject.FindProperty(nameof(NanoBrain.defaultBrain));
+        if (Application.isPlaying == false && serializedObject != null) {
+            string propertyName = nameof(NanoBrain.defaultBrain);
+            brainProp = serializedObject.FindProperty(propertyName);
+        }
     }
 
     public override VisualElement CreateInspectorGUI() {

IReceptor.cs

@@ -3,49 +3,71 @@ using UnityEngine;
 public interface IReceptor {
     public string GetName();
 
-    // public NucleusArray array {
-    //     get; set;
-    // }
     public Nucleus[] nucleiArray { get; set; }
 
     public void AddReceptorElement(ClusterPrefab prefab);
     public void RemoveReceptorElement();
 
+    public void AddArrayReceiver(Nucleus receiverToAdd, float weight = 1);
+
     public void ProcessStimulus(Vector3 inputValue, int thingId = 0, string thingName = null);
 }
 
 public static class IReceptorHelpers {
-    public static Nucleus[] AddReceptorElement(Nucleus[] nucleiArray, ClusterPrefab prefab) {
-        if (nucleiArray.Length == 0) {
+
+    public static void AddReceptorElement(IReceptor receptor, ClusterPrefab prefab) {
+        if (receptor.nucleiArray.Length == 0) {
             Debug.LogError("Empty perceptoid array, cannot add");
-            return null;
         }
-        int newLength = nucleiArray.Length + 1;
+        int newLength = receptor.nucleiArray.Length + 1;
         Nucleus[] newArray = new Nucleus[newLength];
 
-        for (int i = 0; i < nucleiArray.Length; i++)
-            newArray[i] = nucleiArray[i];
-        if (nucleiArray[0] is Nucleus nucleus) {
+        string baseName = receptor.GetName();
+        int colonPos = baseName.IndexOf(":");
+        if (colonPos > 0)
+            baseName = baseName[..colonPos];
+
+        for (int i = 0; i < receptor.nucleiArray.Length; i++)
+            newArray[i] = receptor.nucleiArray[i];
+        if (receptor.nucleiArray[0] is Nucleus nucleus) {
             newArray[newLength - 1] = nucleus.Clone(prefab);
-            newArray[newLength - 1].name += $": {newLength - 1}";
+            newArray[newLength - 1].name = $"{baseName}: {newLength - 1}";
         }
 
-        return newArray;
+        foreach (Nucleus element in receptor.nucleiArray) {
+            if (element is IReceptor receptorElement) {
+                receptorElement.nucleiArray = newArray;
+            }
+        }
     }
 
-    public static Nucleus[] RemoveReceptorElement(Nucleus[] nucleiArray) {
-        int newLength = nucleiArray.Length - 1;
+    public static void RemoveReceptorElement(IReceptor receptor) {
+        int newLength = receptor.nucleiArray.Length - 1;
         if (newLength == 0) {
             Debug.LogWarning("Perceptoid array cannot be empty");
-            return null;
         }
-        Nucleus[] newPerceptei = new Nucleus[newLength];
+        Nucleus[] newArray = new Nucleus[newLength];
         for (int i = 0; i < newLength; i++)
-            newPerceptei[i] = nucleiArray[i];
+            newArray[i] = receptor.nucleiArray[i];
         // Delete the last perception
-        if (nucleiArray[newLength] is Nucleus nucleus)
-            Neuron.Delete(nucleus); //this._nuclei[newLength]);
+        if (receptor.nucleiArray[newLength] is Nucleus nucleus)
+            Neuron.Delete(nucleus);
+            
+        foreach (Nucleus element in receptor.nucleiArray) {
+            if (element is IReceptor receptorElement) {
+                receptorElement.nucleiArray = newArray;
+            }
+        }
+
+    }
+
+    public static void AddArrayReceiver(IReceptor receptor, Nucleus receiverToAdd, float weight = 1) {
+        foreach (Nucleus element in receptor.nucleiArray) {
+            if (element is Cluster cluster)
+                cluster.defaultOutput.AddReceiver(receiverToAdd, weight);
+            if (element is Neuron neuron)
+                neuron.AddReceiver(receiverToAdd, weight);
+        }
 
-        return newPerceptei;
     }
 }

Icons.meta

@@ -0,0 +1,8 @@
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Icons/NeuraalNetwerkIcoonSchets1.png.meta

@@ -0,0 +1,117 @@
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Identity.asset

@@ -11,20 +11,25 @@ MonoBehaviour:
   m_EditorHideFlags: 0
   m_Script: {fileID: 11500000, guid: 60a957541c24c57e78018c202ebb1d9b, type: 3}
   m_Name: Identity
-  m_EditorClassIdentifier: Assembly-CSharp::Cluster
+  m_EditorClassIdentifier: Assembly-CSharp::ClusterPrefab
   nuclei:
-  - rid: 2243601383627161705
+  - rid: 2262690531574022216
   references:
     version: 2
     RefIds:
-    - rid: 2243601383627161705
+    - rid: -2
+      type: {class: , ns: , asm: }
+    - rid: 2262690531574022216
       type: {class: Neuron, ns: , asm: Assembly-CSharp}
       data:
-        _name: Output
+        name: Output
+        clusterPrefab: {fileID: 11400000}
+        parent:
+          rid: -2
+        trace: 0
+        bias: {x: 0, y: 0, z: 0}
         _synapses: []
-        _receivers: []
-        _array:
-          rid: 2243601383627161706
+        combinator: 0
         _curvePreset: 0
         curve:
           serializedVersion: 2
@@ -51,10 +56,4 @@ MonoBehaviour:
           m_PostInfinity: 2
           m_RotationOrder: 4
         curveMax: 1
-        average: 0
-    - rid: 2243601383627161706
-      type: {class: NucleusArray, ns: , asm: Assembly-CSharp}
-      data:
-        _nuclei:
-        - rid: 2243601383627161705
-        name: Output
+        _receivers: []

MemoryCell.cs

@@ -1,7 +1,5 @@
 using System;
-using UnityEngine;
 using Unity.Mathematics;
-using static Unity.Mathematics.math;
 
 [Serializable]
 public class MemoryCell : Neuron {

NanoBrain.cs

@@ -20,7 +20,7 @@ public class NanoBrain : MonoBehaviour {
     public static void UpdateWeight(Cluster brain, string name, float weight) {
         Nucleus root = brain.defaultOutput;
         foreach (Synapse synapse in root.synapses) {
-            if (synapse.nucleus.name == name) {
+            if (synapse.neuron.name == name) {
                 if (synapse.weight != weight) {
                     synapse.weight = weight;
                     // Debug.Log($"Updated weight for {name}");

Neuroid.cs

@@ -1,82 +0,0 @@
-/*
-using UnityEngine;
-using Unity.Mathematics;
-using static Unity.Mathematics.math;
-
-[System.Serializable]
-public class Neuroid : Neuron {
-
-    public bool average = false;
-
-    public Neuroid(Cluster brain, string name) : base(name) {
-        this.cluster = brain;
-        if (this.cluster != null) {
-            this.cluster.nuclei.Add(this);
-        }
-        else
-            Debug.LogError("No neuroid network");
-    }
-
-    public Neuroid(string name) : base(name) { }
-
-    public override INucleus Clone() {
-        Neuroid clone = new(this.name) {
-            cluster = this.cluster,
-            array = this.array,
-            curve = this.curve,
-            curvePreset = this.curvePreset,
-            curveMax = this.curveMax,
-            average = this.average
-        };
-        if (clone.cluster != null)
-            clone.cluster.nuclei.Add(clone);
-
-        foreach (Synapse synapse in this.synapses) {
-            Synapse clonedSynapse = clone.AddSynapse(synapse.nucleus);
-            clonedSynapse.weight = synapse.weight;
-        }
-        foreach (INucleus receiver in this.receivers) {
-            clone.AddReceiver(receiver);
-        }
-        return clone;
-    }
-
-    public override void UpdateState() {
-        float3 sum = new(0, 0, 0);
-        int n = 0;
-
-        //Applying the weight factgors
-        foreach (Synapse synapse in this.synapses) {
-            sum = sum + (synapse.weight * synapse.nucleus.outputValue);
-            if (lengthsq(synapse.nucleus.outputValue) != 0)
-                n++;
-        }
-        if (average)
-            sum /= n;
-
-        // Activation function
-        Vector3 result;
-        switch (this.curvePreset) {
-            case CurvePresets.Linear:
-                result = sum;
-                break;
-            case CurvePresets.Sqrt:
-                result = normalize(sum) * System.MathF.Sqrt(length(sum));
-                break;
-            case CurvePresets.Power:
-                result = normalize(sum) * System.MathF.Pow(length(sum), 2);
-                break;
-            case CurvePresets.Reciprocal:
-                result = normalize(sum) * (1 / length(sum));
-                break;
-            default:
-                float activatedValue = this.curve.Evaluate(length(sum));
-                result = normalize(sum) * activatedValue;
-                break;
-        }
-        UpdateResult(result);
-    }
-
-}
-
-*/

Neuroid.cs.meta

@@ -1,2 +0,0 @@
-fileFormatVersion: 2
-guid: 771f64aec709af240a39b1d918bbc829

Neuron.cs

@@ -1,6 +1,5 @@
 using System;
 using System.Collections.Generic;
-using System.Linq;
 using UnityEngine;
 using UnityEditor;
 using Unity.Mathematics;
@@ -117,6 +116,23 @@ public class Neuron : Nucleus {
 
     #endregion Serialization
 
+    protected float3 _outputValue;
+    public virtual float3 outputValue {
+        get { return _outputValue; }
+        set {
+            _outputValue = value;
+            if (this.isFiring)
+                WhenFiring?.Invoke();
+        }
+    }
+    public bool isFiring => length(_outputValue) > 0.5f;
+    public Action WhenFiring;
+
+    public virtual bool isSleeping => lengthsq(this.outputValue) == 0;
+    [NonSerialized]
+    public int stale = 1000;
+    public readonly int staleValueForSleep = 20;
+
     // this clone the nucleus without the synapses and receivers
     public override Nucleus ShallowCloneTo(Cluster newParent) {
         Neuron clone = new(newParent, this.name);
@@ -128,7 +144,7 @@ public class Neuron : Nucleus {
         Neuron clone = new(prefab, this.name);
         CloneFields(clone);
         foreach (Synapse synapse in this.synapses) {
-            Synapse clonedSynapse = clone.AddSynapse(synapse.nucleus);
+            Synapse clonedSynapse = clone.AddSynapse(synapse.neuron);
             clonedSynapse.weight = synapse.weight;
         }
         foreach (Nucleus receiver in this.receivers) {
@@ -148,7 +164,7 @@ public class Neuron : Nucleus {
 
     public static void Delete(Nucleus nucleus) {
         foreach (Synapse synapse in nucleus.synapses) {
-            if (synapse.nucleus is Neuron synapse_nucleus) {
+            if (synapse.neuron is Neuron synapse_nucleus) {
                 if (synapse_nucleus.receivers.Count > 1) {
                     // there is another nucleus feeding into this input nucleus
                     synapse_nucleus.receivers.RemoveAll(r => r == nucleus);
@@ -162,13 +178,14 @@ public class Neuron : Nucleus {
         if (nucleus is Neuron neuron) {
             foreach (Nucleus receiver in neuron.receivers) {
                 if (receiver != null && receiver.synapses != null)
-                    receiver.synapses.RemoveAll(s => s.nucleus == nucleus);
+                    receiver.synapses.RemoveAll(s => s.neuron == nucleus);
             }
-        } else if (nucleus is Cluster cluster) {
+        }
+        else if (nucleus is Cluster cluster) {
             // remove all receivers for this cluster
             foreach (Neuron output in cluster.outputs) {
                 foreach (Nucleus receiver in output.receivers) {
-                    receiver.synapses.RemoveAll(s => s.nucleus == output);
+                    receiver.synapses.RemoveAll(s => s.neuron == output);
                 }
             }
         }
@@ -198,29 +215,30 @@ public class Neuron : Nucleus {
     public float3 CombinatorSum() {
         float3 sum = this.bias;
         foreach (Synapse synapse in this.synapses)
-            sum += synapse.weight * synapse.nucleus.outputValue;
+            sum += synapse.weight * synapse.neuron.outputValue;
         return sum;
     }
 
     public float3 CombinatorProduct() {
         float3 product = this.bias;
-        foreach (Synapse synapse in this.synapses)
-            product *= synapse.weight * synapse.nucleus.outputValue;
+        foreach (Synapse synapse in this.synapses) {
+            product *= synapse.weight * synapse.neuron.outputValue;
+        }
         return product;
     }
 
     public float3 CombinatorMax() {
         float3 max = this.bias;
-        float maxSqrLength = lengthsq(max);
+        float maxLength = length(max);
 
         //Applying the weight factors
         foreach (Synapse synapse in this.synapses) {
-            float3 input = synapse.weight * synapse.nucleus.outputValue;
+            float3 input = synapse.weight * synapse.neuron.outputValue;
 
-            float inputSqrlength = lengthsq(input);
-            if (inputSqrlength > maxSqrLength) {
+            float inputLength = length(input);
+            if (inputLength > maxLength) {
                 max = input;
-                maxSqrLength = inputSqrlength;
+                maxLength = inputLength;
             }
         }
         return max;
@@ -230,7 +248,7 @@ public class Neuron : Nucleus {
 
     #region Activator
 
-    protected Func<float3, float3> Activator => this.curvePreset switch {
+    public Func<float3, float3> Activator => this.curvePreset switch {
         CurvePresets.Linear => ActivatorLinear,
         CurvePresets.Sqrt => ActivatorSqrt,
         CurvePresets.Power => ActivatorPower,
@@ -278,19 +296,9 @@ public class Neuron : Nucleus {
         set { _receivers = value; }
     }
 
-    public virtual void AddReceiver(Nucleus receiverToAdd, float weight = 1) {        
-        // if (this is IReceptor receptor) {
-        //     foreach (Nucleus element in receptor.array.nuclei) {
-        //         if (element is Neuron neuron) {
-        //             neuron._receivers.Add(receiverToAdd);
-        //             receiverToAdd.AddSynapse(element, weight);
-        //         }
-        //     }
-        // }
-        // else {
-            this._receivers.Add(receiverToAdd);
-            receiverToAdd.AddSynapse(this, weight);
-        // }
+    public virtual void AddReceiver(Nucleus receiverToAdd, float weight = 1) {
+        this._receivers.Add(receiverToAdd);
+        receiverToAdd.AddSynapse(this, weight);
     }
 
     public virtual void RemoveReceiver(Nucleus receiverToRemove) {
@@ -298,23 +306,29 @@ public class Neuron : Nucleus {
             foreach (Nucleus element in receptor.nucleiArray) {
                 if (element is Neuron neuron) {
                     neuron._receivers.RemoveAll(receiver => receiver == receiverToRemove);
-                    receiverToRemove.synapses.RemoveAll(synapse => synapse.nucleus == neuron);
+                    receiverToRemove.synapses.RemoveAll(synapse => synapse.neuron == neuron);
                 }
             }
         }
         else {
             this._receivers.RemoveAll(receiver => receiver == receiverToRemove);
-            receiverToRemove.synapses.RemoveAll(synapse => synapse.nucleus == this);
+            receiverToRemove.synapses.RemoveAll(synapse => synapse.neuron == this);
         }
     }
 
 
     #endregion Receivers
 
-    public virtual void ProcessStimulus(Vector3 inputValue, string thingName = null) {
+    public override void ProcessStimulus(Vector3 inputValue, int thingId = 0, string thingName = null) {
+        if (this.parent is ClusterReceptor clusterReceptor)
+            clusterReceptor.ProcessStimulus(this, inputValue, thingId, thingName);
+        else
+            ProcessStimulusDirect(inputValue, thingId, thingName);
+    }
+
+    public void ProcessStimulusDirect(Vector3 inputValue, int thingId = 0, string thingName = null) {
         this.stale = 0;
         this.bias = inputValue;
         this.parent.UpdateFromNucleus(this);
     }
-
 }

NewVelocity.asset.meta

@@ -0,0 +1,8 @@
+fileFormatVersion: 2
+guid: 61eea9f818639ec20b7a7bf4e86fff66
+NativeFormatImporter:
+  externalObjects: {}
+  mainObjectFileID: 11400000
+  userData: 
+  assetBundleName: 
+  assetBundleVariant: 

Nucleus.cs

@@ -1,8 +1,6 @@
 using System;
 using System.Collections.Generic;
 using UnityEngine;
-using Unity.Mathematics;
-using static Unity.Mathematics.math;
 
 [Serializable]
 public abstract class Nucleus {
@@ -13,22 +11,6 @@ public abstract class Nucleus {
     [SerializeReference]
     public Cluster parent;
 
-    protected float3 _outputValue;
-    public virtual float3 outputValue {
-        get { return _outputValue; }
-        set {
-            _outputValue = value;
-            if (this.isFiring)
-                WhenFiring?.Invoke();
-        }
-    }
-    public bool isFiring => length(_outputValue) > 0.5f;
-    public Action WhenFiring;
-
-    public virtual bool isSleeping => lengthsq(this.outputValue) == 0;
-    [NonSerialized]
-    public int stale = 1000;
-    public readonly int staleValueForSleep = 20;
     public bool trace = false;
 
     public abstract Nucleus ShallowCloneTo(Cluster parent);
@@ -38,11 +20,8 @@ public abstract class Nucleus {
         None,
         Neuron,
         MemoryCell,
-        Selector,
         Cluster,
-        Pulsar,
         Receptor,
-        ReceptorArray,
         ClusterReceptor,
     }
 
@@ -54,7 +33,7 @@ public abstract class Nucleus {
     private List<Synapse> _synapses = new();
     public List<Synapse> synapses => _synapses;
 
-    public Synapse AddSynapse(Nucleus sendingNucleus, float weight = 1.0f) {
+    public Synapse AddSynapse(Neuron sendingNucleus, float weight = 1.0f) {
         Synapse synapse = new(sendingNucleus, weight);
         this.synapses.Add(synapse);
         return synapse;
@@ -62,19 +41,17 @@ public abstract class Nucleus {
 
     public Synapse GetSynapse(Nucleus sender) {
         foreach (Synapse synapse in this.synapses)
-            if (synapse.nucleus == sender)
+            if (synapse.neuron == sender)
                 return synapse;
         return null;
     }
 
     public void RemoveSynapse(Nucleus sendingNucleus) {
-        this.synapses.RemoveAll(synapse => synapse.nucleus == sendingNucleus);
+        this.synapses.RemoveAll(synapse => synapse.neuron == sendingNucleus);
     }
 
     #endregion Synapses
 
-
-
     #region Update
 
     public abstract void UpdateStateIsolated();
@@ -83,11 +60,13 @@ public abstract class Nucleus {
     }
 
     public virtual void SetBias(Vector3 inputValue) {
-        this.stale = 0;
         this.bias = inputValue;
         this.parent.UpdateFromNucleus(this);
     }
 
+    public virtual void ProcessStimulus(Vector3 inputValue, int thingId = 0, string thingName = "") {
+    }
+
     #endregion Update
 
 }

NucleusArray.cs

@@ -69,9 +69,11 @@ public class NucleusArray {
     private Nucleus FindReceiver(int thingId, float3 inputValue) {
         // No existing nucleus for this thing
         float inputMagnitude = length(inputValue);
-        Nucleus selectedReceiver = null;
+        Neuron selectedReceiver = null;
         float selectedMagnitude = 0;
-        foreach (Nucleus receiver in this._nuclei) {
+        foreach (Nucleus nucleusReceiver in this._nuclei) {
+            if (nucleusReceiver is not Neuron receiver)
+                continue;
             if (thingReceivers.ContainsValue(receiver) == false) {
                 // We found an unusued receiver
                 thingReceivers.Add(thingId, receiver);
@@ -111,6 +113,10 @@ public class NucleusArray {
 
     public virtual void ProcessStimulus(int thingId, Vector3 inputValue, string thingName = null) {
         CleanupReceivers();
+
+        if (this._nuclei[0] is Neuron neuron)
+            inputValue = neuron.Activator(inputValue);
+
         if (!thingReceivers.TryGetValue(thingId, out Nucleus selectedReceiver)) {
             // No existing nucleus for this thing
             selectedReceiver = FindReceiver(thingId, inputValue);
@@ -127,15 +133,14 @@ public class NucleusArray {
         }
 
         if (selectedReceiver is Neuron selectedNucleus)
-            selectedNucleus.ProcessStimulus(inputValue);
-        //selectedReceiver.parent.UpdateFromNucleus(selectedReceiver);
+            selectedNucleus.ProcessStimulusDirect(inputValue);
     }
 
     private void CleanupReceivers() {
         // Remove a thing-receiver connection when the nucleus is inactive
         List<int> receiversToRemove = new();
         foreach (KeyValuePair<int, Nucleus> item in thingReceivers) {
-            if (item.Value != null && item.Value.isSleeping)
+            if (item.Value != null && item.Value is Neuron neuron && neuron.isSleeping)
                 receiversToRemove.Add(item.Key);            
         }
         foreach (int thingId in receiversToRemove) {

Perceptoid.cs

@@ -1,105 +0,0 @@
-/*
-using UnityEngine;
-
-[System.Serializable]
-public class Perceptoid : Neuroid {
-    // A neuroid which has no neurons as input
-    // But receives value from a receptor
-
-    public NanoBrain brain;
-    public Receptor receptor;
-    public string baseName;
-
-    public int thingId;
-
-    //[SerializeField]
-    // Needs serialization!!!!
-    [SerializeReference]
-    public PercepteiArray array;
-
-    #region Serialization
-
-    [SerializeField]
-    public int thingType;
-
-    public override void Rebuild(NanoBrain brain) {
-        base.Rebuild(brain);
-        this.receptor = Receptor.GetReceptor(brain, thingType);
-        this.receptor.perceptei.Add(this);
-        if (string.IsNullOrEmpty(this.baseName))
-            this.baseName = this.name;
-    }
-
-    public override void Deserialize(Nucleus nucleus) {
-        base.Deserialize(nucleus);
-
-        if (nucleus is Perceptoid perceptoid)
-            this.receptor.thingType = perceptoid.thingType;
-
-        // Point all receivers to this perceptoid instead of the default nucleus
-        foreach (INucleus receiver in nucleus.receivers) {
-            foreach (Synapse synapse in receiver.synapses) {
-                if (synapse.nucleus == nucleus)
-                    synapse.nucleus = this;
-            }
-        }
-        // Point all synapses to this perceptoid instead of the default nucleus
-        // foreach (Synapse synapse in nucleus.synapses) {
-        //     foreach (INucleus r in synapse.nucleus.receivers) {
-        //         if (r == nucleus)
-        //             this.receiver = this;
-        //     }
-        // }
-        // Copying disabled for now        
-        // // Copy all the synapses
-        // this.synapses = nucleus.synapses;
-        // // Copy all receivers
-        // this.receivers = nucleus.receivers;
-    }
-
-    #endregion Serialization
-
-    public Perceptoid(NanoBrain brain, int thingType, string name = "sensor") : base(name) {
-        this.brain = brain;
-        this.cluster = brain.cluster;
-        if (this.cluster != null) {
-            brain.perceptei.Add(this);
-        }
-        else
-            Debug.LogError("No neuroid network");
-
-        this.nucleusType = nameof(Perceptoid);
-        this.name = name;
-        this.baseName = name;
-        this.thingType = thingType;
-        this.receptor = Receptor.GetReceptor(brain, thingType);
-        this.receptor.perceptei.Add(this);
-        this.array = new PercepteiArray(this);
-    }
-
-    public Perceptoid(PercepteiArray array) : base(array.name) {
-        this.array = array;
-        Perceptoid source = array.perceptei[0];
-        this.brain = source.brain;
-        this.cluster = source.cluster;
-        if (this.brain != null) {
-            this.brain.perceptei.Add(this);
-        }
-        else
-            Debug.LogError("No neuroid network");
-
-        this.nucleusType = nameof(Perceptoid);
-        this.name = source.baseName;
-        this.baseName = source.baseName;
-        this.thingType = source.thingType;
-        this.receptor = Receptor.GetReceptor(this.brain, this.thingType);
-        this.receptor.perceptei.Add(this);
-    }
-
-    public override void UpdateState() {
-        Vector3 result = this.receptor.localPosition;
-        UpdateResult(result);
-    }
-
-}
-*/

Perceptoid.cs.meta

@@ -1,2 +0,0 @@
-fileFormatVersion: 2
-guid: 702f634001a21a9d7ae1057c8ce356e9

Pulsar.cs

@@ -1,54 +0,0 @@
-using System;
-using Unity.Mathematics;
-
-/// <summary>
-/// The Pulsar represents a type of neuron that operates based on
-/// the product of its weighted inputs rather than the traditional summation. 
-/// Drawing inspiration from the concept of pulsars in astrophysics
-/// —highly magnetized rotating neutron stars that emit beams of radiation—
-/// the Pulsar could symbolize dynamic, focused output based on the interaction of multiple factors.
-/// </summary>
-/// Multiplicative Functionality:
-/// Instead of summing inputs, the Pulsar takes the weighted product of its inputs. 
-/// This means that all inputs must be active (non-zero) for the neuron to "pulse" or activate.
-/// Output Behavior:
-/// The output could amplify or diminish depending on the magnitude of the inputs.
-/// The product would be sensitive to small values,
-/// which means that even a small input could significantly lower the overall output if multiplied.
-/// Activation Mechanism:
-/// The activation function can further refine the output from the product result.
-/// For instance, a certain threshold could be used to determine if a pulse occurs.
-/// Modeling Complex Interactions: 
-/// The Pulsar could be particularly beneficial for modeling situations where interactions multiply rather than add.
-/// This is useful in fields such as economics (e.g., compound growth models),
-/// biology (e.g., interaction of hormones), and machine learning where multiplicative relationships exist.
-[Serializable]
-public class Pulsar : Neuron {
-    public Pulsar(Cluster parent, string name) : base(parent, name) {
-        // To prevent mistakes, bias one (instead of zero for standard neurons)
-        this.bias = new float3(1, 1, 1);
-    }
-    public Pulsar(ClusterPrefab parent, string name) : base(parent, name) {
-        // To prevent mistakes, bias one (instead of zero for standard neurons)
-        this.bias = new float3(1, 1, 1);
-    }
-
-    public override Nucleus ShallowCloneTo(Cluster newParent) {
-        Pulsar clone = new(newParent, this.name);
-        CloneFields(clone);
-        return clone;
-    }
-
-    public override void UpdateStateIsolated() {
-        float3 product = this.bias;
-
-        //Applying the weight factors
-        foreach (Synapse synapse in this.synapses) {
-            float3 input = synapse.weight * synapse.nucleus.outputValue;
-            product *= input;
-        }
-
-        // Activation function
-        this.outputValue = Activator(product);
-    }
-}

Pulsar.cs.meta

@@ -1,2 +0,0 @@
-fileFormatVersion: 2
-guid: 46bd155173053a01585411c3e07f85d4

Receptor.cs

@@ -48,24 +48,19 @@ public class Receptor : Neuron, IReceptor {
     }
 
     public void AddReceptorElement(ClusterPrefab prefab) {
-        this.nucleiArray = IReceptorHelpers.AddReceptorElement(this.nucleiArray, prefab);
+        IReceptorHelpers.AddReceptorElement(this, prefab);
     }
 
     public void RemoveReceptorElement() {
-        this.nucleiArray = IReceptorHelpers.RemoveReceptorElement(this.nucleiArray);
+        IReceptorHelpers.RemoveReceptorElement(this);
     }
 
     public virtual void AddArrayReceiver(Nucleus receiverToAdd, float weight = 1) {
-        foreach (Nucleus element in this._array.nuclei) {
-            if (element is Neuron neuron) {
-                neuron.AddReceiver(receiverToAdd, weight);
-            }
-        }
+        IReceptorHelpers.AddArrayReceiver(this, receiverToAdd, weight);
     }
 
     public override void UpdateStateIsolated() {
         this.outputValue = this.bias;
-        //Debug.Log($"Receptor {this.name} outputvalue = {this.outputValue}");
     }
 
     public override void UpdateNuclei() {
@@ -76,7 +71,7 @@ public class Receptor : Neuron, IReceptor {
         }
     }
 
-    public virtual void ProcessStimulus(Vector3 inputValue, int thingId = 0, string thingName = null) {
+    public override void ProcessStimulus(Vector3 inputValue, int thingId = 0, string thingName = null) {
         this._array ??= new NucleusArray(this.parent);
         this._array.ProcessStimulus(thingId, inputValue, thingName);
     }

ReceptorArray.cs

@@ -1,261 +0,0 @@
-using System;
-using System.Collections.Generic;
-using System.Linq;
-using UnityEngine;
-using Unity.Mathematics;
-using static Unity.Mathematics.math;
-
-[Serializable]
-public class ReceptorInstance : Nucleus {
-    public ReceptorInstance(Cluster parent, string name) {
-        this.parent = parent;
-        this.name = name;
-        // We explicitly do not add this to the parent, as it is serialized in the ReceptorArray
-    }
-    public ReceptorInstance(ClusterPrefab prefab, string name) {
-        this.clusterPrefab = prefab;
-        this.name = name;
-        // We explicitly do not add this to the prefab, as it is serialized in the ReceptorArray
-    }
-    public override Nucleus ShallowCloneTo(Cluster parent) {
-        ReceptorInstance clone = new(parent, name + " +1") {
-            receptor = this.receptor
-        };
-        return clone;
-    }
-    public override Nucleus Clone(ClusterPrefab prefab) {
-        ReceptorInstance clone = new(prefab, name) {
-            receptor = this.receptor
-        };
-        return clone;
-    }
-
-    [SerializeReference]
-    public ReceptorArray receptor;
-
-    public override void UpdateStateIsolated() {
-    }
-}
-
-[Serializable]
-public class ReceptorArray : Nucleus {
-    public ReceptorArray(Cluster parent, string name) {
-        this.parent = parent;
-        this.name = name;
-        this._instances = new ReceptorInstance[1];
-        this._instances[0] = new ReceptorInstance(parent, this.name + "[0]") {
-            receptor = this
-        };
-        this.parent?.clusterNuclei.Add(this);
-    }
-    public ReceptorArray(ClusterPrefab prefab, string name) {
-        this.clusterPrefab = prefab;
-        this.name = name;
-        this._instances = new ReceptorInstance[1];
-        this._instances[0] = new ReceptorInstance(prefab, this.name + "[0]") {
-            receptor = this
-        };
-        if (this.clusterPrefab != null)
-            this.clusterPrefab.nuclei.Add(this);
-        else
-            Debug.LogError("No prefab when adding receptor to prefab");
-
-    }
-
-    public override Nucleus ShallowCloneTo(Cluster parent) {
-        ReceptorArray clone = new(parent, name) {
-            _instances = new ReceptorInstance[this.instances.Length]
-        };
-        for (int ix = 0; ix < this.instances.Length; ix++) {
-            clone._instances[ix] = new ReceptorInstance(parent, $"{this.name} [{ix}]") {
-              receptor = clone
-            };
-        }
-
-        return clone;
-    }
-
-    public override Nucleus Clone(ClusterPrefab prefab) {
-        ReceptorArray clone = new(prefab, this.name) {
-            _instances = new ReceptorInstance[this.instances.Length]
-        };
-        for (int ix = 0; ix < this.instances.Length; ix++) {
-            clone._instances[ix] = new ReceptorInstance(prefab, this.name) {
-                receptor = this
-            };
-        }
-
-        foreach (Synapse synapse in this.synapses) {
-            Synapse clonedSynapse = clone.AddSynapse(synapse.nucleus);
-            clonedSynapse.weight = synapse.weight;
-        }
-        // foreach (Nucleus receiver in this.receivers) {
-        //     clone.AddReceiver(receiver);
-        // }
-        return clone;
-    }
-
-    [SerializeReference]
-    private ReceptorInstance[] _instances = new ReceptorInstance[0];
-    public ReceptorInstance[] instances {
-        get {
-            return _instances;
-        }
-    }
-
-    public void AddReceptor(ClusterPrefab prefab) {
-        if (this._instances.Length == 0) {
-            Debug.LogError("Empty receptor array, cannot add");
-            return;
-        }
-        int newLength = this._instances.Length + 1;
-        ReceptorInstance[] newArray = new ReceptorInstance[newLength];
-
-        for (int i = 0; i < this._instances.Length; i++)
-            newArray[i] = this._instances[i];
-        ReceptorInstance newReceptor = (ReceptorInstance)this._instances[0].Clone(prefab);
-        newReceptor.name = $"{this.name} [{this._instances.Length}]";
-        newArray[newLength - 1] = newReceptor;
-
-        this._instances = newArray;
-    }
-
-    public void RemoveReceptor() {
-        int newLength = this._instances.Length - 1;
-        if (newLength == 0) {
-            Debug.LogWarning("Receptor array cannot be empty");
-            return;
-        }
-        ReceptorInstance[] newPerceptei = new ReceptorInstance[newLength];
-        for (int i = 0; i < newLength; i++)
-            newPerceptei[i] = this._instances[i];
-        // Delete the last perception
-        if (this._instances[newLength] is Nucleus nucleus)
-            Neuron.Delete(nucleus); //this._nuclei[newLength]);
-
-        this._instances = newPerceptei;
-    }
-
-    private Dictionary<int, Nucleus> thingReceivers = new();
-
-    // public override void ProcessStimulus(int thingId, Vector3 inputValue, string thingName = null) {
-    //     ProcessStimulus(inputValue, thingId, thingName);
-    // }
-    public virtual void ProcessStimulus(Vector3 inputValue, int thingId = 0, string thingName = null) {
-        CleanupReceivers();
-        if (!thingReceivers.TryGetValue(thingId, out Nucleus selectedReceiver)) {
-            //Debug.Log($" no receiver found for {thingId}");
-            // No existing nucleus for this thing
-            selectedReceiver = SelectReceptor(thingId, inputValue);
-        }
-        if (selectedReceiver == null)
-            return;
-
-        if (thingName != null) {
-            string baseName = selectedReceiver.name;
-            int colonPos = selectedReceiver.name.IndexOf(":");
-            if (colonPos > 0)
-                baseName = selectedReceiver.name[..colonPos];
-            selectedReceiver.name = baseName + ": " + thingName;
-        }
-
-        //if (selectedReceiver is Neuron selectedNucleus) {
-        selectedReceiver.stale = 0;
-        selectedReceiver.outputValue = inputValue;
-        this.parent.UpdateFromNucleus(this);
-        //selectedNucleus.ProcessStimulus(inputValue);
-        //}
-    }
-
-    private void CleanupReceivers() {
-        // Remove a thing-receiver connection when the nucleus is inactive
-        List<int> receiversToRemove = new();
-        thingReceivers ??= new();
-
-        foreach (KeyValuePair<int, Nucleus> item in thingReceivers) {
-            if (item.Value.isSleeping)
-                receiversToRemove.Add(item.Key);
-        }
-        foreach (int thingId in receiversToRemove) {
-            Nucleus selectedReceiver = thingReceivers[thingId];
-
-            // Debug.Log($" removed receiver for {thingId}");
-            thingReceivers.Remove(thingId);
-
-            int colonPos = selectedReceiver.name.IndexOf(":");
-            if (colonPos > 0)
-                selectedReceiver.name = selectedReceiver.name[..colonPos];
-        } 
-
-    }
-
-    private Nucleus SelectReceptor(int thingId, float3 inputValue) {
-        // No existing nucleus for this thing
-        float inputMagnitude = length(inputValue);
-        Nucleus selectedReceiver = null;
-        float selectedMagnitude = 0;
-        this._instances ??= new ReceptorInstance[0];
-        foreach (Nucleus receiver in this._instances) {
-            if (thingReceivers.ContainsValue(receiver) == false) {
-                // We found an unusued receiver
-                // Debug.Log($"{thingId} -> [{receiver.name}]");
-                thingReceivers.Add(thingId, receiver);
-                return receiver;
-            }
-            else if (receiver.isSleeping) {
-                // A sleeping receiver is not active and can therefore always be used
-                thingReceivers.Add(thingId, receiver);
-                Debug.Log($"{thingId} -> [{selectedReceiver.name}]");
-                return receiver;
-            }
-            else if (selectedReceiver == null) {
-                // If we haven't found a receiver yet, just start by taking the first
-                selectedReceiver = receiver;
-                selectedMagnitude = length(selectedReceiver.outputValue);
-            }
-            // Look for the receiver with the lowest magnitude
-            else {
-                float magnitude = length(receiver.outputValue);
-
-                if (magnitude < inputMagnitude && length(receiver.outputValue) < selectedMagnitude) {
-                    selectedReceiver = receiver;
-                    selectedMagnitude = length(selectedReceiver.outputValue);
-                }
-            }
-        }
-        if (selectedReceiver != null) {
-            // Replace the receiver
-            // Find the thingId current associated with the receiver
-            int keyToRemove = thingReceivers.FirstOrDefault(r => r.Value.Equals(selectedReceiver)).Key;
-            if (keyToRemove != 0 || thingReceivers.ContainsKey(keyToRemove))
-                thingReceivers.Remove(keyToRemove);
-            // And add the new association
-            thingReceivers.Add(thingId, selectedReceiver);
-        }
-        return selectedReceiver;
-    }
-
-    public override void UpdateStateIsolated() {
-        float3 sum = this.bias;
-
-        // Receptors do not have inputs, so we ignore the synapses
-        foreach (Nucleus nucleus in this._instances)
-            sum += nucleus.outputValue;
-
-        this.outputValue = sum / _instances.Length;
-        this.stale = 0;
-
-        UpdateNuclei();
-    }
-
-    public override void UpdateNuclei() {
-        foreach (Nucleus nucleus in this.instances) {
-            nucleus.stale++;
-            if (nucleus.stale > staleValueForSleep && lengthsq(nucleus.outputValue) > 0) {
-                nucleus.outputValue = Vector3.zero;
-                //this.UpdateStateIsolated();
-                this.parent.UpdateFromNucleus(this);
-            }
-        }
-    }
-}

ReceptorArray.cs.meta

@@ -1,2 +0,0 @@
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Selector.cs

@@ -1,62 +0,0 @@
-using System;
-using Unity.Mathematics;
-using static Unity.Mathematics.math;
-
-[Serializable]
-public class Selector : Neuron {
-    public Selector(Cluster parent, string name) : base(parent, name) { }
-    public Selector(ClusterPrefab parent, string name) : base(parent, name) {}
-
-    public override Nucleus ShallowCloneTo(Cluster newParent) {
-        Selector clone = new(newParent, this.name) {
-            // array = this.array,
-            curve = this.curve,
-            curvePreset = this.curvePreset,
-            curveMax = this.curveMax,
-        };
-        return clone;
-    }
-
-    public override void UpdateStateIsolated() { //float3 bias) {
-        float3 max = this.bias;
-        float maxSqrLength = lengthsq(max);
-
-        //Applying the weight factors
-        foreach (Synapse synapse in this.synapses) {
-            float3 input = synapse.weight * synapse.nucleus.outputValue;
-
-            float inputSqrlength = lengthsq(input);
-            if (inputSqrlength > maxSqrLength) {
-                max = input;
-                maxSqrLength = inputSqrlength;
-            }
-        }
-
-        // Activation function
-        float3 result;
-        switch (this.curvePreset) {
-            case CurvePresets.Linear:
-                result = max;
-                break;
-            case CurvePresets.Sqrt:
-                result = normalize(max) * System.MathF.Sqrt(length(max));
-                break;
-            case CurvePresets.Power:
-                result = normalize(max) * System.MathF.Pow(length(max), 2);
-                break;
-            case CurvePresets.Reciprocal: {
-                    float magnitude = length(max);
-                    if (magnitude > 0)
-                        result = normalize(max) * (1 / magnitude);
-                    else
-                        result = float3(0, 0, 0);
-                    break;
-                }
-            default:
-                float activatedValue = this.curve.Evaluate(length(max));
-                result = normalize(max) * activatedValue;
-                break;
-        }
-        this.outputValue = result;
-    }
-}

Selector.cs.meta

@@ -1,2 +0,0 @@
-fileFormatVersion: 2
-guid: 4218c2f3f15af944db0eadd6e1500d17

Synapse.cs

@@ -4,12 +4,12 @@ using UnityEngine;
 [Serializable]
 public class Synapse {
     [SerializeReference]
-    public Nucleus nucleus;
+    public Neuron neuron;
 
     public float weight;
 
-    public Synapse(Nucleus nucleus, float weight = 1.0f) {
-        this.nucleus = nucleus;
+    public Synapse(Neuron nucleus, float weight = 1.0f) {
+        this.neuron = nucleus;
         this.weight = weight;
     }
 }

Velocity.asset

@@ -13,18 +13,31 @@ MonoBehaviour:
   m_Name: Velocity
   m_EditorClassIdentifier: Assembly-CSharp::ClusterPrefab
   nuclei:
-  - rid: 2243601425629446539
+  - rid: 2262690551513219315
+  - rid: 2262690551513219316
+  - rid: 2262690551513219317
   references:
     version: 2
     RefIds:
-    - rid: 2243601425629446539
+    - rid: -2
+      type: {class: , ns: , asm: }
+    - rid: 2262690551513219315
       type: {class: Neuron, ns: , asm: Assembly-CSharp}
       data:
-        _name: Output
-        _synapses: []
-        _receivers: []
-        _array:
-          rid: 2243601425629446540
+        name: Velocity
+        clusterPrefab: {fileID: 11400000}
+        parent:
+          rid: -2
+        trace: 0
+        bias: {x: 0, y: 0, z: 0}
+        _synapses:
+        - nucleus:
+            rid: 2262690551513219316
+          weight: 1
+        - nucleus:
+            rid: 2262690551513219317
+          weight: 1
+        combinator: 0
         _curvePreset: 0
         curve:
           serializedVersion: 2
@@ -51,10 +64,65 @@ MonoBehaviour:
           m_PostInfinity: 2
           m_RotationOrder: 4
         curveMax: 1
-        average: 0
-    - rid: 2243601425629446540
-      type: {class: NucleusArray, ns: , asm: Assembly-CSharp}
+        _receivers: []
+    - rid: 2262690551513219316
+      type: {class: Neuron, ns: , asm: Assembly-CSharp}
       data:
-        _nuclei:
-        - rid: 2243601425629446539
-        name: Output
+        name: Position
+        clusterPrefab: {fileID: 11400000}
+        parent:
+          rid: -2
+        trace: 0
+        bias: {x: 0, y: 0, z: 0}
+        _synapses: []
+        combinator: 0
+        _curvePreset: 0
+        curve:
+          serializedVersion: 2
+          m_Curve:
+          - serializedVersion: 3
+            time: 0
+            value: 0
+            inSlope: 0
+            outSlope: 1
+            tangentMode: 0
+            weightedMode: 0
+            inWeight: 0
+            outWeight: 0
+          - serializedVersion: 3
+            time: 1000
+            value: 1000
+            inSlope: 1
+            outSlope: 0
+            tangentMode: 0
+            weightedMode: 0
+            inWeight: 0
+            outWeight: 0
+          m_PreInfinity: 2
+          m_PostInfinity: 2
+          m_RotationOrder: 4
+        curveMax: 1
+        _receivers:
+        - rid: 2262690551513219315
+    - rid: 2262690551513219317
+      type: {class: MemoryCell, ns: , asm: Assembly-CSharp}
+      data:
+        name: New memory cell
+        clusterPrefab: {fileID: 11400000}
+        parent:
+          rid: -2
+        trace: 0
+        bias: {x: 0, y: 0, z: 0}
+        _synapses: []
+        combinator: 0
+        _curvePreset: 0
+        curve:
+          serializedVersion: 2
+          m_Curve: []
+          m_PreInfinity: 2
+          m_PostInfinity: 2
+          m_RotationOrder: 4
+        curveMax: 1
+        _receivers:
+        - rid: 2262690551513219315
+        staticMemory: 0