Improvements

git-subtree-dir: NanoBrain
git-subtree-split: b3423b99a752cdabbc4e7c51565fb54425481feb

Editor/BrainPickerWindow.cs.meta

@@ -1,2 +1,11 @@
 fileFormatVersion: 2
-guid: 9197e2d322d23b5798ab4aef729815b0
+guid: 9197e2d322d23b5798ab4aef729815b0
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+  serializedVersion: 2
+  defaultReferences: []
+  executionOrder: 0
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Editor/Brain_Editor.cs.meta

@@ -1,2 +1,11 @@
 fileFormatVersion: 2
-guid: f05072314d39990639a2dbf99f322664
+guid: f05072314d39990639a2dbf99f322664
+MonoImporter:
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+  serializedVersion: 2
+  defaultReferences: []
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Editor/ClusterEditor.cs

@@ -64,22 +64,24 @@ namespace NanoBrain {
         public class GraphEditor : GraphView {
 
             protected ClusterPrefab prefab;
-            protected Nucleus currentPrefabNucleus;
+            //protected Nucleus currentPrefabNucleus;
 
             protected override Nucleus currentNucleus {
                 get => base.currentNucleus;
                 set {
                     base.currentNucleus = value;
-                    this.currentPrefabNucleus = value != null ? this.prefab.GetNucleus(value.name) : null;
+                    // this.currentPrefabNucleus = value != null ? this.prefab.GetNucleus(value.name) : null;
                 }
             }
 
-            public GraphEditor(ClusterPrefab prefab) : base(prefab.output.parent) {
+            public GraphEditor(ClusterPrefab prefab) : base(prefab.cluster.defaultOutput.parent) {
                 this.prefab = prefab;
 
                 // In a Prefab editor, no instance exists but we need it for the ClusterViewer.
                 // So we create a temporary instance
-                this.currentCluster = new(prefab);
+                //this.currentCluster = new(prefab);
+                this.currentCluster = prefab.cluster;
+                this.currentCluster.Refresh();
             }
 
             public void SetGraph(GameObject gameObject, VisualElement inspectorContainer) {
@@ -87,7 +89,7 @@ namespace NanoBrain {
 
                 if (Application.isPlaying == false)
                     this.serializedBrain = new SerializedObject(this.prefab);
-                this.selectedOutput = this.currentCluster.outputs[0];
+                this.selectedOutput = this.currentCluster.defaultOutput;
                 this.currentNucleus = this.selectedOutput;
                 //this.currentCluster = this.currentNucleus.parent;
                 Rebuild(inspectorContainer);
@@ -120,7 +122,7 @@ namespace NanoBrain {
                 // create a SerializedObject wrapper so Unity inspector controls work (and Undo)
                 SerializedObject so = new(prefabAsset);
 
-                foreach (Nucleus nucleus in this.prefab.nuclei) {
+                foreach (Nucleus nucleus in this.prefab.cluster.nuclei) {
                     nucleus.Initialize();
                 }
 
@@ -163,29 +165,10 @@ namespace NanoBrain {
                     GUILayout.Label(nucleusType, headerStyle);
 
                     // Nucleus name
-                    Cluster cluster = this.currentPrefabNucleus as Cluster;
-                    if (cluster != null) {
-                        EditorGUILayout.BeginHorizontal();
-                        if (GUILayout.Button(this.currentNucleus.parent.name))
-                            OnClusterClick(cluster);
-                        EditorGUI.BeginDisabledGroup(true);
-                        EditorGUILayout.TextField(this.currentNucleus.name, boldTextFieldStyle);
-                        EditorGUI.EndDisabledGroup();
-                        if (GUILayout.Button("Reimport"))
-                            ReimportCluster(cluster);
-                        EditorGUILayout.EndHorizontal();
-                    }
-                    else {
-                        string newName = EditorGUILayout.TextField(this.currentNucleus.name, boldTextFieldStyle);
-                        if (newName != this.currentNucleus.name) {
-                            Nucleus prefabNucleus = this.prefab.GetNucleus(this.currentNucleus.name);
-                            prefabNucleus.name = newName;
-                            // This changes it in the temporary cluster instance
-                            this.currentNucleus.name = newName;
-                            this.prefab.RefreshOutputs();
-                            // outputsPopup.choices = this.prefab.outputs.Select(output => output.name).ToList();
-                            anythingChanged = true;
-                        }
+                    string newName = EditorGUILayout.TextField(this.currentNucleus.name, boldTextFieldStyle);
+                    if (newName != this.currentNucleus.name) {
+                        this.currentNucleus.name = newName;
+                        anythingChanged = true;
                     }
 
                     // Current output value
@@ -204,7 +187,7 @@ namespace NanoBrain {
                     if (this.currentNucleus is MemoryCell memory)
                         MemoryCellInspector(memory, ref anythingChanged);
                     // Cluster
-                    else if (cluster != null)
+                    else if (this.currentNucleus is Cluster cluster)
                         ClusterInspector(cluster, ref anythingChanged);
                     // Other
                     else
@@ -230,10 +213,8 @@ namespace NanoBrain {
 
                 bool connecting = GUILayout.Button("Add Output Neuron");
                 if (connecting) {
-                    Nucleus newOutput = new Neuron(this.prefab, "New Output");
-                    // Regenerate the temporary clsuter instance
-                    // See also the constructor
-                    this.currentCluster = new(this.prefab);
+                    Nucleus newOutput = new Neuron(this.currentCluster, "New Output");
+                    this.currentCluster.Refresh();
                     this.currentNucleus = newOutput;
                     this.selectedOutput = this.currentNucleus;
                 }
@@ -281,9 +262,9 @@ namespace NanoBrain {
                 if (breakOnWake && this.currentNucleus is Neuron currentNeuron) {
                     if (currentNeuron.isSleeping == false)
                         Debug.Break();
+                    // trace = EditorGUILayout.Toggle("Trace", trace);
+                    // currentNeuron.trace = trace;
                 }
-                trace = EditorGUILayout.Toggle("Trace", trace);
-                this.currentNucleus.trace = trace;
             }
 
             protected void SynapsesInspector(ref bool anythingChanged) {
@@ -293,31 +274,30 @@ namespace NanoBrain {
                         Neuron.CombinatorType newCombinator = (Neuron.CombinatorType)EditorGUILayout.EnumPopup("Combinator", neuron2.combinator);
                         anythingChanged |= newCombinator != neuron2.combinator;
                         neuron2.combinator = newCombinator;
-                    }
 
-                    EditorGUIUtility.wideMode = true;
-                    float previousLabelWidth = EditorGUIUtility.labelWidth;
-                    EditorGUIUtility.labelWidth = 100;
+                        EditorGUIUtility.wideMode = true;
+                        float previousLabelWidth = EditorGUIUtility.labelWidth;
+                        EditorGUIUtility.labelWidth = 100;
 
-                    Vector3 newBias = EditorGUILayout.Vector3Field("Bias", this.currentNucleus.bias);
-                    if (newBias != this.currentPrefabNucleus.bias) {
-                        anythingChanged |= newBias != this.currentNucleus.bias;
-                        this.currentPrefabNucleus.bias = newBias;
-                        this.currentNucleus.bias = newBias;
+                        Vector3 newBias = EditorGUILayout.Vector3Field("Bias", neuron2.bias);
+                        if (newBias != neuron2.bias) {
+                            anythingChanged |= newBias != neuron2.bias;
+                            neuron2.bias = newBias;
+                        }
+                        EditorGUIUtility.labelWidth = previousLabelWidth;
                     }
-                    EditorGUIUtility.labelWidth = previousLabelWidth;
 
                     Nucleus[] array = null;
                     int elementIx = -1;
-                    if (this.currentPrefabNucleus.synapses.Count > 0) {
-                        Synapse[] synapses = this.currentPrefabNucleus.synapses.ToArray();
+                    if (this.currentNucleus is Neuron currentNeuron && currentNeuron.synapses.Count > 0) {
+                        Synapse[] synapses = currentNeuron.synapses.ToArray();
                         foreach (Synapse synapse in synapses) {
                             if (synapse.neuron == null)
                                 continue;
 
                             if (array != null) {
                                 if (synapse.neuron.parent is Cluster iCluster && elementIx > 0) {
-                                    int thisElementIx = Cluster.GetNucleusIndex(iCluster.clusterNuclei, synapse.neuron);
+                                    int thisElementIx = Cluster.GetNucleusIndex(iCluster.nuclei, synapse.neuron);
                                     if (thisElementIx == elementIx)
                                         continue;
                                     else
@@ -332,7 +312,7 @@ namespace NanoBrain {
                                 if (synapse.neuron.parent is Cluster iReceptor) {
                                     array = iReceptor.siblingClusters;
                                     if (iReceptor is Cluster iCluster)
-                                        elementIx = Cluster.GetNucleusIndex(iCluster.clusterNuclei, synapse.neuron);
+                                        elementIx = Cluster.GetNucleusIndex(iCluster.nuclei, synapse.neuron);
                                 }
                             }
 
@@ -348,21 +328,19 @@ namespace NanoBrain {
                             else {
                                 EditorGUILayout.BeginHorizontal();
 
-                                if (synapse.neuron.clusterPrefab != this.currentNucleus.clusterPrefab) {
+                                if (synapse.neuron.parent != this.currentNucleus.parent) {
                                     // If it is a different cluster
                                     GUIStyle labelStyle = new(GUI.skin.label);
                                     float labelWidth = 200;
-                                    if (synapse.neuron.clusterPrefab != null) {
-                                        labelWidth = labelStyle.CalcSize(new GUIContent($"{synapse.neuron.clusterPrefab.name}.")).x;
-                                        GUILayout.Label($"{synapse.neuron.clusterPrefab.name}", GUILayout.Width(labelWidth));
+                                    if (synapse.neuron.parent != null) {
+                                        labelWidth = labelStyle.CalcSize(new GUIContent($"{synapse.neuron.parent.name}.")).x;
+                                        GUILayout.Label($"{synapse.neuron.parent.name}", GUILayout.Width(labelWidth));
                                     }
-                                    string[] options = synapse.neuron.clusterPrefab.nuclei.Select(n => n.name).ToArray();
+                                    string[] options = synapse.neuron.parent.nuclei.Select(n => n.name).ToArray();
                                     int selectedIndex = System.Array.IndexOf(options, synapse.neuron.name);
                                     int newIndex = EditorGUILayout.Popup(selectedIndex, options);
                                     if (newIndex != selectedIndex) {
-                                        // Nucleus selectedNucleus = synapse.neuron.parent.clusterNuclei[newIndex];
-                                        // Neuron newNeuron = selectedNucleus as Neuron;
-                                        Neuron newNeuron = synapse.neuron.clusterPrefab.nuclei[newIndex] as Neuron;
+                                        Neuron newNeuron = synapse.neuron.parent.nuclei[newIndex] as Neuron;
                                         ChangeSynapse(synapse, newNeuron);
                                     }
                                 }
@@ -370,13 +348,12 @@ namespace NanoBrain {
                                     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();
+                                if (disconnecting) {
+                                    synapse.neuron.RemoveReceiver(this.currentNucleus);
+                                    this.currentCluster.Refresh();
                                     anythingChanged = true;
                                 }
                                 EditorGUILayout.EndHorizontal();
-
                             }
 
                             EditorGUI.indentLevel++;
@@ -443,13 +420,14 @@ namespace NanoBrain {
             }
 
             protected virtual void AddNeuronInput(Nucleus nucleus) {
-                Neuron newNeuroid = new(this.prefab, "New neuron");
-                newNeuroid.AddReceiver(nucleus);
-                this.currentNucleus = newNeuroid;
+                Neuron newNeuron = new(this.currentCluster, "New Neuron");
+                //Neuron newNeuroid = new(this.prefab.cluster, "New neuron");
+                newNeuron.AddReceiver(nucleus);
+                this.currentNucleus = newNeuron;
             }
 
             protected virtual void AddMemoryCellInput(Nucleus nucleus) {
-                MemoryCell newMemory = new(this.prefab, "New memory cell");
+                MemoryCell newMemory = new(this.prefab.cluster, "New memory cell");
                 newMemory.AddReceiver(nucleus);
                 this.currentNucleus = newMemory;
             }
@@ -458,7 +436,7 @@ namespace NanoBrain {
                 ClusterPickerWindow.ShowPicker(brain => OnClusterPicked(nucleus, brain), "Select Cluster");
             }
             private void OnClusterPicked(Nucleus nucleus, ClusterPrefab selectedPrefab) {
-                Cluster subclusterInstance = new(selectedPrefab, this.prefab);
+                Cluster subclusterInstance = new(selectedPrefab, this.currentCluster);
                 subclusterInstance.defaultOutput.AddReceiver(nucleus);
             }
 
@@ -493,11 +471,12 @@ namespace NanoBrain {
                 if (cluster == null)
                     return false;
 
-                IEnumerable<Nucleus> synapseNuclei = this.currentNucleus.synapses
+                Neuron currentNeuron = this.currentNucleus as Neuron;
+                IEnumerable<Nucleus> synapseNuclei = currentNeuron.synapses
                     .Where(synapse => synapse.neuron != null)
                     .Select(synapse => synapse.neuron);
 
-                IEnumerable<Nucleus> nuclei = cluster.nuclei
+                IEnumerable<Nucleus> nuclei = cluster.cluster.nuclei
                     .Except(synapseNuclei);
                 IEnumerable<string> nucleiNames = nuclei
                     .Select(n => {
@@ -513,10 +492,13 @@ namespace NanoBrain {
                 EditorGUILayout.EndHorizontal();
                 if (connecting) {
                     Nucleus nucleus = nuclei.ElementAt(selectedConnectNucleus);
-                    if (nucleus is Cluster subCluster)
+                    if (nucleus is Cluster subCluster) {
                         subCluster.AddArrayReceiver(this.currentNucleus);
-                    else if (nucleus is Neuron neuron)
+                    }
+                    else if (nucleus is Neuron neuron) {
                         neuron.AddReceiver(this.currentNucleus);
+                    }
+                    this.currentCluster.Refresh();
                 }
                 return connecting;
             }
@@ -537,10 +519,10 @@ namespace NanoBrain {
 
                 // this.prefab.nuclei.Remove(nucleus);
                 //  Neuron.Delete(nucleus);
-                this.prefab.RefreshOutputs();
+                this.prefab.cluster.RefreshOutputs();
 
 
-                this.currentNucleus = this.prefab.output;
+                this.currentNucleus = this.prefab.cluster.defaultOutput;
                 this.selectedOutput = this.currentNucleus;
             }
 
@@ -558,11 +540,6 @@ namespace NanoBrain {
                     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) {
@@ -596,8 +573,8 @@ namespace NanoBrain {
                     // }
                     // else {
                     // it is a neuron in a subcluster
-                    synapseNeuron.RemoveReceiver(this.currentPrefabNucleus);
-                    newNucleus.AddReceiver(this.currentPrefabNucleus);
+                    synapseNeuron.RemoveReceiver(this.currentNucleus);
+                    newNucleus.AddReceiver(this.currentNucleus);
                     // }
                 }
                 else {
@@ -606,19 +583,6 @@ namespace NanoBrain {
                 }
             }
 
-            protected virtual void DisconnectNucleus(Neuron nucleus) {
-                if (this.currentNucleus.clusterPrefab == null)
-                    return;
-                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.neuron as Neuron;
-                    synapseNeuron.RemoveReceiver(this.currentNucleus);
-                }
-            }
-
             #endregion Synapses 
 
             #endregion Inspector

Editor/ClusterEditor.cs.meta

@@ -1,2 +1,11 @@
 fileFormatVersion: 2
-guid: 1fc1fb7db9f7ad54a87d31313e7f457d
+guid: 1fc1fb7db9f7ad54a87d31313e7f457d
+MonoImporter:
+  externalObjects: {}
+  serializedVersion: 2
+  defaultReferences: []
+  executionOrder: 0
+  icon: {instanceID: 0}
+  userData: 
+  assetBundleName: 
+  assetBundleVariant: 

Editor/ClusterViewer.cs

@@ -106,6 +106,8 @@ namespace NanoBrain {
 
             public void SetGraph(GameObject gameObject) {
                 this.gameObject = gameObject;
+                if (this.currentCluster == null)
+                    return;
 
                 if (Application.isPlaying == false)
                     this.serializedBrain = new SerializedObject(this.currentCluster.prefab);
@@ -128,7 +130,7 @@ namespace NanoBrain {
             }
 
             public void OnIMGUI() {
-                if (Application.isPlaying == false)
+                if (Application.isPlaying == false && serializedBrain != null)
                     serializedBrain.Update();
 
                 Handles.BeginGUI();
@@ -211,7 +213,8 @@ namespace NanoBrain {
             }
 
             private void DescendGraph(Dag.Node receiver, ref int ix, Dag dag) {
-                foreach (Synapse synapse in receiver.nucleus.synapses) {
+                Neuron receiverNeuron = receiver.nucleus as Neuron;
+                foreach (Synapse synapse in receiverNeuron.synapses) {
                     Nucleus nucleus = synapse.neuron;
                     if (nucleus.parent != null && nucleus.parent != currentNucleus.parent) {
                         nucleus = nucleus.parent;
@@ -384,6 +387,9 @@ namespace NanoBrain {
             }
 
             protected void DrawSynapses(Nucleus nucleus, Vector3 parentPos, float size) {
+                if (nucleus is not Neuron neuron)
+                    return;
+
                 if (this.selectedSynapseNeuron != null) {
                     DrawClusterSynapses(this.selectedSynapseNeuron, parentPos, size);
                     return;
@@ -396,7 +402,7 @@ namespace NanoBrain {
                 float maxValue = 0;
                 int neuronCount = 0;
                 List<string> drawnNeuronNames = new();
-                foreach (Synapse synapse in nucleus.synapses) {
+                foreach (Synapse synapse in neuron.synapses) {
                     if (synapse.neuron == null)
                         continue;
 
@@ -423,7 +429,7 @@ namespace NanoBrain {
                 int row = 0;
                 //List<Neuron> drawnNeurons = new();
                 drawnNeuronNames = new();
-                foreach (Synapse synapse in nucleus.synapses) {
+                foreach (Synapse synapse in neuron.synapses) {
                     if (synapse.neuron is null)
                         continue;
 
@@ -482,14 +488,15 @@ namespace NanoBrain {
                             maxValue = 1;
                         float brightness = siblingNeuron.outputMagnitude / maxValue;
                         color = new Color(brightness, brightness, brightness, 1f);
-                    }                    DrawNucleus(siblingNeuron, position, size, color);
+                    }
+                    DrawNucleus(siblingNeuron, position, size, color);
                     GUIStyle style = new(EditorStyles.label) {
                         alignment = TextAnchor.UpperCenter,
                         normal = { textColor = Color.white },
                         fontStyle = FontStyle.Bold,
                     };
                     Vector3 labelPos = position - Vector3.down * (size + 5); // below neuron
-                    string name = $"{sibling.baseName}.{nucleus.name}";
+                    string name = $"{sibling.baseName}\n{nucleus.name}";
                     Handles.Label(labelPos, name, style);
                     row++;
                 }
@@ -497,6 +504,9 @@ namespace NanoBrain {
             }
 
             protected void DrawOutputs(Vector2 parentPos, float size) {
+                if (this.currentCluster == null)
+                    return;
+
                 // Determine the maximum value in this layer
                 // This is used to 'scale' the output value colors of the nuclei
                 float maxValue = 0;
@@ -603,18 +613,12 @@ namespace NanoBrain {
                     if (nucleus.parent != null && currentNucleus != null && nucleus.parent != currentNucleus.parent && nucleus.parent is Cluster parentCluster1) {
                         // This neuron is part of another cluster
                         parentCluster1.name ??= "";
-                        string baseName = "";
                         int colonPos = parentCluster1.name.IndexOf(":");
+                        string baseName;
                         if (colonPos > 0 && colonPos < parentCluster1.name.Length - 2)
-                            baseName = parentCluster1.name[..colonPos] + ".";
+                            baseName = parentCluster1.name[..colonPos] + "\n";
                         else
-                            baseName = parentCluster1.name + ".";
-                        // if (colonPos > 0 && colonPos < parentCluster1.name.Length - 2) {
-                        //     // if it is an array, we should not show the :0 of the first element
-                        //     //baseName = baseName[..colonPos];
-                        //     Handles.Label(labelPos, baseName + nucleus.name, style);
-                        // }
-                        // else
+                            baseName = parentCluster1.name + "\n";
                         Handles.Label(labelPos, baseName + nucleus.name, style);
                     }
                     else {
@@ -849,22 +853,34 @@ namespace NanoBrain {
 
             void OnSceneGUI(SceneView sceneView) {
                 if (this.gameObject != null) {
-                    // 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 {
-                    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);
+
+                    Handles.color = Color.yellow;
+                    if (this.selectedSynapseNeuron != null) {
+                        foreach (Cluster sibling in this.selectedSynapseNeuron.parent.siblingClusters) {
+                            Neuron siblingNeuron = sibling.GetNucleus(this.selectedSynapseNeuron.name) as Neuron;
+                            Vector3 worldVector = this.gameObject.transform.TransformVector(siblingNeuron.outputValue);
+                            Handles.DrawLine(this.gameObject.transform.position, this.gameObject.transform.position + worldVector);
+                        }
+                        // if (this.currentNucleus is Cluster cluster) {
+                        //     foreach (Cluster sibling in cluster.siblingClusters) {
+
+                        //     }
+                        // }
+                        // // 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 {
+                        if (this.currentNucleus is Neuron currentNeuron) {
+                            Vector3 worldVector = this.gameObject.transform.TransformVector(currentNeuron.outputValue);
+                            Handles.DrawLine(this.gameObject.transform.position, this.gameObject.transform.position + worldVector);
+                        }
                     }
-                    // }
                 }
             }
 

Editor/ClusterViewer.cs.meta

@@ -1,2 +1,11 @@
 fileFormatVersion: 2
-guid: 4fe58945c76d153edacc220597474ad2
+guid: 4fe58945c76d153edacc220597474ad2
+MonoImporter:
+  externalObjects: {}
+  serializedVersion: 2
+  defaultReferences: []
+  executionOrder: 0
+  icon: {instanceID: 0}
+  userData: 
+  assetBundleName: 
+  assetBundleVariant: 

Editor/ConfigurationChecker.cs.meta

@@ -1,2 +1,11 @@
 fileFormatVersion: 2
-guid: c7539a20f7894542ca347730cd8417b1
+guid: c7539a20f7894542ca347730cd8417b1
+MonoImporter:
+  externalObjects: {}
+  serializedVersion: 2
+  defaultReferences: []
+  executionOrder: 0
+  icon: {instanceID: 0}
+  userData: 
+  assetBundleName: 
+  assetBundleVariant: 

Editor/Neuron_Drawer.cs

@@ -0,0 +1,83 @@
+using UnityEngine;
+using UnityEditor;
+using Unity.Mathematics;
+using System;
+using System.Reflection;
+using System.Collections;
+
+namespace NanoBrain {
+    [CustomPropertyDrawer(typeof(Neuron))]
+    class Neuron_Drawer : PropertyDrawer {
+        public static void Insepctor(SerializedObject serializedObject, string propertyName ) {
+            EditorGUILayout.PropertyField(serializedObject.FindProperty(propertyName));
+        }
+
+        public override void OnGUI(Rect position, SerializedProperty property, GUIContent label) {
+            // Draw foldout + properties
+            label = EditorGUI.BeginProperty(position, label, property);
+
+            // Begin indent block
+            int indent = EditorGUI.indentLevel;
+            EditorGUI.indentLevel = 0;
+
+            object instance = GetTargetObjectOfProperty(property);
+
+            float lineHeight = EditorGUIUtility.singleLineHeight;
+            Rect r = new(position.x, position.y, position.width, lineHeight);
+            if (instance != null) {
+                FieldInfo field = typeof(Neuron).GetField("_outputValue", BindingFlags.NonPublic | BindingFlags.Instance);
+                if (field != null) {
+                    float3 val = (float3)field.GetValue(instance);
+                    EditorGUI.Vector3Field(r, $"Neuron: {label}", val);
+                }
+            }
+
+            EditorGUI.indentLevel = indent;
+            EditorGUI.EndProperty();
+        }
+
+        public override float GetPropertyHeight(SerializedProperty property, GUIContent label) {
+            // height for 1 line
+            return (EditorGUIUtility.singleLineHeight * 1) + (EditorGUIUtility.standardVerticalSpacing * 0);
+        }
+
+        public static object GetTargetObjectOfProperty(SerializedProperty prop) {
+            var path = prop.propertyPath.Replace(".Array.data[", "[");
+            object obj = prop.serializedObject.targetObject;
+            var elements = path.Split('.');
+            foreach (var element in elements) {
+                if (element.Contains("[")) {
+                    var elementName = element.Substring(0, element.IndexOf("["));
+                    var index = Convert.ToInt32(element.Substring(element.IndexOf("[")).Replace("[", "").Replace("]", ""));
+                    obj = GetValue_Imp(obj, elementName, index);
+                }
+                else {
+                    obj = GetValue_Imp(obj, element);
+                }
+            }
+            return obj;
+        }
+
+        static object GetValue_Imp(object source, string name) {
+            if (source == null)
+                return null;
+
+            Type t = source.GetType();
+            FieldInfo f = t.GetField(name, BindingFlags.NonPublic | BindingFlags.Public | BindingFlags.Instance);
+            if (f != null)
+                return f.GetValue(source);
+            PropertyInfo p = t.GetProperty(name, BindingFlags.NonPublic | BindingFlags.Public | BindingFlags.Instance);
+            return p?.GetValue(source, null);
+        }
+        static object GetValue_Imp(object source, string name, int index) {
+            if (GetValue_Imp(source, name) is not IEnumerable enumerable)
+                return null;
+            IEnumerator en = enumerable.GetEnumerator();
+            for (int i = 0; i <= index; i++) {
+                if (!en.MoveNext())
+                    return null;
+            }
+            return en.Current;
+        }
+    }
+}

Editor/Neuron_Drawer.cs.meta

@@ -0,0 +1,11 @@
+fileFormatVersion: 2
+guid: aa0e340763ca6299e93d514b271ae38d
+MonoImporter:
+  externalObjects: {}
+  serializedVersion: 2
+  defaultReferences: []
+  executionOrder: 0
+  icon: {instanceID: 0}
+  userData: 
+  assetBundleName: 
+  assetBundleVariant: 

LinearAlgebra.meta

@@ -1,8 +1,8 @@
-fileFormatVersion: 2
-guid: a4c7dfe43bdf504e29c5c97919d7a1c0
-folderAsset: yes
-DefaultImporter:
-  externalObjects: {}
-  userData: 
-  assetBundleName: 
-  assetBundleVariant: 
+fileFormatVersion: 2
+guid: a4c7dfe43bdf504e29c5c97919d7a1c0
+folderAsset: yes
+DefaultImporter:
+  externalObjects: {}
+  userData: 
+  assetBundleName: 
+  assetBundleVariant: 

LinearAlgebra/src.meta

@@ -1,8 +1,8 @@
-fileFormatVersion: 2
-guid: 6a602cec2c4009925b1d19ed36a98c6a
-folderAsset: yes
-DefaultImporter:
-  externalObjects: {}
-  userData: 
-  assetBundleName: 
-  assetBundleVariant: 
+fileFormatVersion: 2
+guid: 6a602cec2c4009925b1d19ed36a98c6a
+folderAsset: yes
+DefaultImporter:
+  externalObjects: {}
+  userData: 
+  assetBundleName: 
+  assetBundleVariant: 

LinearAlgebra/test.meta

@@ -1,8 +1,8 @@
-fileFormatVersion: 2
-guid: 9b84f664459d02b90894e460de42c219
-folderAsset: yes
-DefaultImporter:
-  externalObjects: {}
-  userData: 
-  assetBundleName: 
-  assetBundleVariant: 
+fileFormatVersion: 2
+guid: 9b84f664459d02b90894e460de42c219
+folderAsset: yes
+DefaultImporter:
+  externalObjects: {}
+  userData: 
+  assetBundleName: 
+  assetBundleVariant: 

Runtime/LinearAlgebra/test/SphericalTest.cs

@@ -1,4 +1,4 @@
-//#if !UNITY_5_6_OR_NEWER
+#if !UNITY_5_6_OR_NEWER
 using System;
 using System.Collections.Generic;
 using NUnit.Framework;
@@ -268,4 +268,4 @@ namespace LinearAlgebra.Test {
         
     }
 }
-//#endif
+#endif

Runtime/Scripts/Brain.cs

@@ -45,7 +45,7 @@ namespace NanoBrain {
         /// <param name="name">The name of the Neuron for which the weights are updated</param>
         /// <param name="weight">The new Synapse weight</param>
         public static void UpdateWeight(Cluster brain, string name, float weight) {
-            Nucleus root = brain.defaultOutput;
+            Neuron root = brain.defaultOutput;
             foreach (Synapse synapse in root.synapses) {
                 if (synapse.neuron.name == name) {
                     if (synapse.weight != weight) {

Runtime/Scripts/Brain.cs.meta

@@ -1,2 +1,11 @@
 fileFormatVersion: 2
-guid: 92f34a5e4027a1dc39efd8ce63cf6aba
+guid: 92f34a5e4027a1dc39efd8ce63cf6aba
+MonoImporter:
+  externalObjects: {}
+  serializedVersion: 2
+  defaultReferences: []
+  executionOrder: 0
+  icon: {instanceID: 0}
+  userData: 
+  assetBundleName: 
+  assetBundleVariant: 

Runtime/Scripts/Core/Cluster.cs

@@ -41,7 +41,7 @@ namespace NanoBrain {
         public Dictionary<int, Cluster> thingClusters = new();
 
         [SerializeReference]
-        public List<Nucleus> clusterNuclei = new();
+        public List<Nucleus> nuclei = new();
         // the nuclei sorted using topological sorting
         // to ensure that the cluster is computer in the right order
         public List<Nucleus> sortedNuclei;
@@ -58,10 +58,10 @@ namespace NanoBrain {
             this.name = prefab.name;
 
             this.parent = parent;
-            this.parent?.clusterNuclei.Add(this);
+            this.parent?.nuclei.Add(this);
             ClonePrefab();
             _ = this.inputs;
-            this.sortedNuclei = TopologicalSort(this.clusterNuclei);
+            this.sortedNuclei = TopologicalSort(this.nuclei);
         }
 
         /// <summary>
@@ -72,14 +72,15 @@ namespace NanoBrain {
         public Cluster(ClusterPrefab prefab, ClusterPrefab parent = null) {
             this.prefab = prefab;
             this.name = prefab.name;
-            this.clusterPrefab = parent;
+            if (parent != null)
+                this.parent = parent.cluster;
 
-            if (this.clusterPrefab != null)
-                this.clusterPrefab.nuclei.Add(this);
+            // if (this.parent.prefab != null)
+            //     this.parent.prefab.cluster.nuclei.Add(this);
 
             ClonePrefab();
             _ = this.inputs;
-            this.sortedNuclei = TopologicalSort(this.clusterNuclei);
+            this.sortedNuclei = TopologicalSort(this.nuclei);
         }
 
         /// <summary>
@@ -88,15 +89,13 @@ namespace NanoBrain {
         /// Strange that this does not take any parameters or return values.
         /// Where which the clone be found???
         private void ClonePrefab() {
-            Nucleus[] prefabNuclei = this.prefab.nuclei.ToArray();
+            Nucleus[] prefabNuclei = this.prefab.cluster.nuclei.ToArray();
 
             // first clone the nuclei without their connections
             foreach (Nucleus nucleus in prefabNuclei) {
                 nucleus.ShallowCloneTo(this);
             }
-            Nucleus[] clonedNuclei = this.clusterNuclei.ToArray();
-            // foreach (Nucleus n in clonedNuclei)
-            //     n.name += "(c)";            
+            Nucleus[] clonedNuclei = this.nuclei.ToArray();
 
             // Now clone the connections
             for (int nucleusIx = 0; nucleusIx < prefabNuclei.Length; nucleusIx++) {
@@ -110,10 +109,10 @@ namespace NanoBrain {
 
                 foreach (Synapse prefabSynapse in prefabNeuron.synapses) {
                     Neuron synapseNeuron = prefabSynapse.neuron;
-                    if (synapseNeuron.clusterPrefab != null && synapseNeuron.clusterPrefab != this.prefab) {
+                    if (synapseNeuron.parent.prefab != null && synapseNeuron.parent.prefab != this.prefab) {
                         // Neuron is in another cluster, find the cloned cluster first
-                        ClusterPrefab prefabCluster = synapseNeuron.clusterPrefab;
-                        Cluster clonedCluster = this.clusterNuclei.Find(n => n.name == prefabCluster.name) as Cluster;
+                        Cluster prefabCluster = synapseNeuron.parent;
+                        Cluster clonedCluster = this.nuclei.Find(n => n.name == prefabCluster.name) as Cluster;
                         if (clonedCluster == null)
                             continue;
 
@@ -122,7 +121,7 @@ namespace NanoBrain {
                         if (neuronIx < 0)
                             // Could not find the neuron in the prefab cluster
                             continue;
-                        if (clonedCluster.clusterNuclei[neuronIx] is not Neuron clonedSender)
+                        if (clonedCluster.nuclei[neuronIx] is not Neuron clonedSender)
                             // Could not find the neuron in the cloned cluster
                             continue;
 
@@ -141,28 +140,6 @@ namespace NanoBrain {
                         // Debug.Log($"Add synapse {clonedSender.name} -> {clonedNeuron.name}");
                     }
                 }
-
-                // // Copy the receivers, which will also create the synapses
-                // foreach (Nucleus receiver in prefabNeuron.receivers.ToArray()) {
-                //     int ix = GetNucleusIndex(prefabNuclei, receiver);
-                //     if (ix < 0)
-                //         continue;
-
-                //     if (clonedNuclei[ix] is not Nucleus clonedReceiver)
-                //         continue;
-
-                //     // Find the synapse for the weight
-                //     float weight = 1;
-                //     foreach (Synapse synapse in receiver.synapses) {
-                //         // Find the weight for this synapse
-                //         if (synapse.neuron == prefabNucleus) {
-                //             weight = synapse.weight;
-                //             break;
-                //         }
-                //     }
-
-                //     clonedNeuron.AddReceiver(clonedReceiver, weight);
-                // }
             }
 
             if (Application.isPlaying) {
@@ -179,7 +156,7 @@ namespace NanoBrain {
                         Debug.Log($"create {clonedCluster.prefab.name} sibling");
                         Cluster sibling = new(clonedCluster.prefab, this) {
                             name = $"{clonedCluster.baseName}: {instanceIx}",
-                            clusterPrefab = this.clusterPrefab,
+                            parent = this.parent,
                             instanceCount = this.instanceCount,
                         };
                         siblings.Add(sibling);
@@ -189,134 +166,47 @@ namespace NanoBrain {
                     foreach (Cluster sibling in siblings)
                         sibling.siblingClusters = siblingClusters;
                 }
-            }
-            /*
-                    for (int nucleusIx = 0; nucleusIx < clonedNuclei.Length; nucleusIx++) {
-                        Nucleus prefabNucleus = prefabNuclei[nucleusIx];
-                        if (prefabNucleus is not Cluster prefabCluster)
-                            continue;
 
-                        if (prefabCluster.instanceCount <= 1)
-                            continue;
-
-                        Cluster clonedNucleus = clonedNuclei[nucleusIx] as Cluster;
-                        if (prefabCluster == prefabCluster.siblingClusters[0]) {
-                            // We clone the array only for the first entry
-                            //NucleusArray clonedArray = new(prefabReceptor.nucleiArray.Length);
-                            Cluster[] clonedArray = new Cluster[prefabCluster.siblingClusters.Length];
-                            int arrayIx = 0;
-                            foreach (Cluster prefabArrayNucleus in prefabCluster.siblingClusters) {
-                                int arrayNucleusIx = GetNucleusIndex(prefabNuclei, prefabArrayNucleus);
-                                if (arrayNucleusIx >= 0) {
-                                    Cluster clonedArrayNucleus = clonedNuclei[arrayNucleusIx] as Cluster;
-                                    clonedArray[arrayIx] = clonedArrayNucleus;
-                                }
-                                else {
-                                    Debug.LogError($" Could not find prefab nucleus {prefabNucleus.name} in the clones");
-                                }
-                                arrayIx++;
-                            }
-                            clonedNucleus.siblingClusters = clonedArray;
-                        }
-                        else {
-                            // The others will refer to the array created for the first nucleus in the array
-                            int firstNucleusIx = GetNucleusIndex(prefabNuclei, prefabCluster.siblingClusters[0]);
-                            Cluster clonedFirstNucleus = clonedNuclei[firstNucleusIx] as Cluster;
-                            clonedNucleus.siblingClusters = clonedFirstNucleus.siblingClusters;
-                        }
-                    }
-        }
-
-        /*
-                    // Collect the subclusters
-                    List<Cluster> subClusters = new();
-                    foreach (Nucleus nucleus in prefabNuclei) {
-                        foreach (Synapse synapse in nucleus.synapses) {
-                            Nucleus synapseNucleus = synapse.neuron;
-                            Cluster subCluster = synapseNucleus.parent;
-                            if (subCluster is null ||
-                                synapseNucleus.clusterPrefab == this.clusterPrefab) {
-
-                                continue;
-                            }
-                            // if (synapseNucleus is not Cluster subCluster)
-                            //     continue;
-                            if (subClusters.Contains(subCluster))
-                                continue;
-                            subClusters.Add(subCluster);
-                        }
-                    }
-                    // Create the subcluster instances
-                    foreach (Cluster subCluster in subClusters) {
-                        for (int ix = 0; ix < subCluster.instanceCount; ix++) {
-                            // create the new instance
-                            Cluster clusterInstance = new(subCluster.prefab);
-                            // connect it
-                            foreach ((Neuron sender, Nucleus receiver) in subCluster.CollectConnections()) {
-                                int receiverIx = GetNucleusIndex(prefabNuclei, receiver);
-                                if (receiverIx < 0)
-                                    continue;
-
-                                if (clonedNuclei[receiverIx] is not Nucleus clonedReceiver)
-                                    continue;
-
-                                // Find the synapse for the weight
-                                float weight = 1;
-                                foreach (Synapse synapse in receiver.synapses) {
-                                    // Find the weight for this synapse
-                                    if (synapse.neuron == sender) {
-                                        weight = synapse.weight;
-                                        break;
-                                    }
-                                }
-
-                                if (clusterInstance.GetNucleus(sender.name) is not Neuron clonedSender)
-                                    continue;
-
-                                clonedSender.AddReceiver(clonedReceiver, weight);
-                            }
-                        }
-                    }
-        */
-
-            // foreach (Nucleus nucleus in this.clusterNuclei) {
-            //     if (nucleus is Cluster clonedSubCluster)
-            //         RestoreAllExternalReceivers(clonedSubCluster, this.prefab, this);
-            // }
-        }
-
-        private void CloneSynapses(Neuron prefabNeuron, Neuron clonedNeuron) {
-            foreach (Synapse prefabSynapse in prefabNeuron.synapses) {
-                Neuron synapseNeuron = prefabSynapse.neuron;
-                if (synapseNeuron.clusterPrefab != null && synapseNeuron.clusterPrefab != this.prefab) {
-                    // Neuron is in another cluster, find the cloned cluster first
-                    ClusterPrefab prefabCluster = synapseNeuron.clusterPrefab;
-                    Cluster clonedCluster = this.clusterNuclei.Find(n => n.name == prefabCluster.name) as Cluster;
-                    if (clonedCluster == null)
-                        continue;
-
-                    // Now find the neuron in that cloned cluster
-                    int neuronIx = GetNucleusIndex(prefabCluster.nuclei, prefabSynapse.neuron.name);
-                    if (neuronIx < 0)
-                        // Could not find the neuron in the prefab cluster
-                        continue;
-                    if (clonedCluster.clusterNuclei[neuronIx] is not Neuron clonedSender)
-                        // Could not find the neuron in the cloned cluster
-                        continue;
-
-                    clonedSender.AddReceiver(clonedNeuron, prefabSynapse.weight);
-                    //Debug.Log($"Add synapse {clonedCluster.name}.{clonedSender.name} -> {clonedNeuron.name} [{clonedSender.receivers.Count}]");
-                }
-                else {
-                    Neuron clonedSender = this.clusterNuclei.Find(n => n.name == prefabSynapse.neuron.name) as Neuron;
-                    // Copy the receivers which will also create the synapse
-                    clonedSender.AddReceiver(clonedNeuron, prefabSynapse.weight);
-                    // Debug.Log($"Add synapse {clonedSender.name} -> {clonedNeuron.name}");
+                // Ensure that all neurons are computed to initialize bias
+                foreach (Nucleus clonedNucleus in clonedNuclei) {
+                    if (clonedNucleus is not Cluster)
+                        clonedNucleus.UpdateStateIsolated();
                 }
             }
-
         }
 
+        // private void CloneSynapses(Neuron prefabNeuron, Neuron clonedNeuron) {
+        //     foreach (Synapse prefabSynapse in prefabNeuron.synapses) {
+        //         Neuron synapseNeuron = prefabSynapse.neuron;
+        //         if (synapseNeuron.parent.prefab != null && synapseNeuron.parent.prefab != this.prefab) {
+        //             // Neuron is in another cluster, find the cloned cluster first
+        //             ClusterPrefab prefabCluster = synapseNeuron.parent.prefab;
+        //             Cluster clonedCluster = this.nuclei.Find(n => n.name == prefabCluster.name) as Cluster;
+        //             if (clonedCluster == null)
+        //                 continue;
+
+        //             // Now find the neuron in that cloned cluster
+        //             int neuronIx = GetNucleusIndex(prefabCluster.cluster.nuclei, prefabSynapse.neuron.name);
+        //             if (neuronIx < 0)
+        //                 // Could not find the neuron in the prefab cluster
+        //                 continue;
+        //             if (clonedCluster.nuclei[neuronIx] is not Neuron clonedSender)
+        //                 // Could not find the neuron in the cloned cluster
+        //                 continue;
+
+        //             clonedSender.AddReceiver(clonedNeuron, prefabSynapse.weight);
+        //             //Debug.Log($"Add synapse {clonedCluster.name}.{clonedSender.name} -> {clonedNeuron.name} [{clonedSender.receivers.Count}]");
+        //         }
+        //         else {
+        //             Neuron clonedSender = this.nuclei.Find(n => n.name == prefabSynapse.neuron.name) as Neuron;
+        //             // Copy the receivers which will also create the synapse
+        //             clonedSender.AddReceiver(clonedNeuron, prefabSynapse.weight);
+        //             // Debug.Log($"Add synapse {clonedSender.name} -> {clonedNeuron.name}");
+        //         }
+        //     }
+
+        // }
+
         /// <summary>
         /// Sort the nuclei in a correct evaluation order
         /// </summary>
@@ -378,20 +268,20 @@ namespace NanoBrain {
         public override Nucleus Clone(ClusterPrefab parent) {
             Cluster clone = new(this.prefab, parent);
 
-            foreach (Synapse synapse in this.synapses) {
-                Synapse clonedSynapse = clone.AddSynapse(synapse.neuron);
-                clonedSynapse.weight = synapse.weight;
-            }
+            // foreach (Synapse synapse in this.synapses) {
+            //     Synapse clonedSynapse = clone.AddSynapse(synapse.neuron);
+            //     clonedSynapse.weight = synapse.weight;
+            // }
 
-            foreach (Nucleus nucleus in this.clusterNuclei) {
+            foreach (Nucleus nucleus in this.nuclei) {
                 if (nucleus is Neuron output) {
                     foreach (Nucleus receiver in output.receivers) {
-                        int ix = GetNucleusIndex(this.clusterNuclei, output);
+                        int ix = GetNucleusIndex(this.nuclei, output);
                         Debug.Log($"{output.name} -> {receiver.name}: {ix}");
                         if (ix < 0)
                             continue;
 
-                        if (clone.clusterNuclei[ix] is not Neuron clonedOutput)
+                        if (clone.nuclei[ix] is not Neuron clonedOutput)
                             continue;
 
                         clonedOutput.AddReceiver(receiver);
@@ -406,7 +296,7 @@ namespace NanoBrain {
             // Clusters should not be cloned, but instantiated from the prefab....
             Cluster clone = new(this.prefab, parent) {
                 name = this.name,
-                clusterPrefab = this.clusterPrefab,
+                parent = this.parent,
                 instanceCount = this.instanceCount,
             };
             // Somehow siblingClusters should be cloned too. Believe I do this in ClonePrefab right now.
@@ -416,23 +306,26 @@ namespace NanoBrain {
 
         private static void CopyAllExternalReceivers(Cluster sourceCluster, Cluster sibling, ClusterPrefab prefabParent, Cluster clonedParent) {
 
-            for (int nucleusIx = 0; nucleusIx < sourceCluster.clusterNuclei.Count; nucleusIx++) {
-                Nucleus sourceNucleus = sourceCluster.clusterNuclei[nucleusIx];
+            for (int nucleusIx = 0; nucleusIx < sourceCluster.nuclei.Count; nucleusIx++) {
+                Nucleus sourceNucleus = sourceCluster.nuclei[nucleusIx];
                 if (sourceNucleus is not Neuron sourceNeuron)
                     continue;
 
-                if (sibling.clusterNuclei[nucleusIx] is not Neuron clonedNeuron)
+                if (sibling.nuclei[nucleusIx] is not Neuron clonedNeuron)
                     continue;
 
                 // copy the receivers (and thus synapses) from the source to the sibling
                 foreach (Nucleus receiver in sourceNeuron.receivers) {
-                    int ix = GetNucleusIndex(clonedParent.clusterNuclei, receiver);
-                    if (ix < 0 || ix >= clonedParent.clusterNuclei.Count)
+                    if (receiver is not Neuron receiverNeuron)
+                        continue;
+
+                    int ix = GetNucleusIndex(clonedParent.nuclei, receiver);
+                    if (ix < 0 || ix >= clonedParent.nuclei.Count)
                         continue;
 
                     // Find the synapse for the weight
                     float weight = 1;
-                    foreach (Synapse synapse in receiver.synapses) {
+                    foreach (Synapse synapse in receiverNeuron.synapses) {
                         // Find the weight for this synapse
                         if (synapse.neuron == sourceNucleus) {
                             weight = synapse.weight;
@@ -530,42 +423,43 @@ namespace NanoBrain {
             }
         }
 
-        public virtual Cluster GetThingCluster() {
-            Cluster selectedCluster = SelectCluster();
-            return selectedCluster;
-        }
-        public virtual Cluster GetThingCluster(int thingId, string thingName = null) {
-            if (thingClusters.TryGetValue(thingId, out Cluster cluster))
-                return cluster;
+        // public virtual Cluster GetThingCluster() {
+        //     Cluster selectedCluster = SelectCluster();
+        //     return selectedCluster;
+        // }
+        // public virtual Cluster GetThingCluster(int thingId, string thingName = null) {
+        //     if (thingClusters.TryGetValue(thingId, out Cluster cluster))
+        //         return cluster;
 
-            Cluster selectedCluster = SelectCluster();
-            selectedCluster.name = baseName + ": " + thingName;
-            thingClusters[thingId] = selectedCluster;
-            return selectedCluster;
-        }
+        //     Cluster selectedCluster = SelectCluster();
+        //     selectedCluster.name = baseName + ": " + thingName;
+        //     thingClusters[thingId] = selectedCluster;
+        //     return selectedCluster;
+        // }
 
-        private Cluster SelectCluster() {
-            if (this.siblingClusters == null)
-                return this;
+        // private Cluster SelectCluster() {
+        //     if (this.siblingClusters == null)
+        //         return this;
 
-            // Find a sleeping cluster
-            foreach (Cluster cluster in this.siblingClusters) {
-                if (cluster.defaultOutput.isSleeping) {
-                    RemoveThingCluster(cluster);
-                    return cluster;
-                }
-            }
+        //     // Find a sleeping cluster
+        //     // foreach (Cluster cluster in this.siblingClusters) {
+        //     //     if (cluster.defaultOutput.isSleeping) {
+        //     //         RemoveThingCluster(cluster);
+        //     //         return cluster;
+        //     //     }
+        //     // }
 
-            // Otherwise find longest unused cluster
-            Cluster unusedCluster = this.siblingClusters[0];
-            for (int ix = 1; ix < this.siblingClusters.Length; ix++) {
-                if (this.siblingClusters[ix].defaultOutput.lastUpdate < unusedCluster.defaultOutput.lastUpdate)
-                    unusedCluster = this.siblingClusters[ix];
-            }
+        //     // Find longest unused cluster
+        //     // Note this uses the default output...
+        //     Cluster unusedCluster = this.siblingClusters[0];
+        //     for (int ix = 1; ix < this.siblingClusters.Length; ix++) {
+        //         if (this.siblingClusters[ix].defaultOutput.lastUpdate < unusedCluster.defaultOutput.lastUpdate)
+        //             unusedCluster = this.siblingClusters[ix];
+        //     }
 
-            RemoveThingCluster(unusedCluster);
-            return unusedCluster;
-        }
+        //     RemoveThingCluster(unusedCluster);
+        //     return unusedCluster;
+        // }
 
         private void RemoveThingCluster(Cluster cluster) {
             List<int> keysToRemove = new();
@@ -603,36 +497,34 @@ namespace NanoBrain {
             get {
                 if (this._inputs == null) {
                     this._inputs = new();
-                    foreach (Nucleus nucleus in this.clusterNuclei) {
+                    foreach (Nucleus nucleus in this.nuclei) {
+                        if (nucleus is not Neuron neuron)
+                            continue;
+
                         // inputs have no synapses
-                        if (nucleus.synapses.Count == 0)
+                        if (neuron.synapses.Count == 0)
                             this._inputs.Add(nucleus);
                     }
-                    ComputeOrders();
+                    RefreshComputeOrders();
                 }
                 return this._inputs;
             }
         }
 
-        public Dictionary<Nucleus, List<Nucleus>> computeOrders = new();
-        private void ComputeOrders() {
-            foreach (Nucleus nucleus in this.clusterNuclei) {
-                // if (nucleus is Cluster cluster) {
-                //     List<Synapse> synapses = this.CollectSynapsesTo(cluster);
-                //     foreach (Synapse synapse in synapses) {
-                //         computeOrders[synapse.neuron] = TopologicalSort2(synapse.neuron);
-                //         Debug.Log($"{this.baseName}: Order for {cluster.baseName}.{synapse.neuron.name}");
-                //     }
-                //     // List<Nucleus> receivers = cluster.CollectReceivers();
-                //     // foreach (Nucleus receiver in receivers)
-                //     //     computeOrders[receiver] = TopologicalSort2(receiver);
-                // }
-                // else {
-                    computeOrders[nucleus] = TopologicalSort2(nucleus);
-                    Debug.Log($"{this.baseName} Order for {nucleus.name}");
-                // }
+        private Dictionary<Nucleus, List<Nucleus>> _computeOrders;
+        public Dictionary<Nucleus, List<Nucleus>> computeOrders {
+            get {
+                if (_computeOrders == null || _computeOrders.Count == 0) {
+                    _computeOrders = new();
+                    foreach (Nucleus nucleus in this.nuclei)
+                        _computeOrders[nucleus] = TopologicalSort2(nucleus);
+                }
+                return _computeOrders;
             }
         }
+        public void RefreshComputeOrders() {
+            this._computeOrders = null;
+        }
 
         private List<Nucleus> TopologicalSort2(Nucleus startNode) {
             Dictionary<Nucleus, int> inDegree = new();
@@ -698,17 +590,17 @@ namespace NanoBrain {
 
         public virtual Neuron defaultOutput {//=> this.nuclei[0] as Nucleus;
             get {
-                if (this.clusterNuclei.Count > 0)
-                    return this.clusterNuclei[0] as Neuron;
+                if (this.nuclei.Count > 0)
+                    return this.nuclei[0] as Neuron;
                 return null;
             }
         }
         protected List<Neuron> _outputs = null;
         public List<Neuron> outputs {
             get {
-                if (this._outputs == null) {
+                if (this._outputs == null || this._outputs.Count == 0) {
                     this._outputs = new();
-                    foreach (Nucleus nucleus in this.clusterNuclei) {
+                    foreach (Nucleus nucleus in this.nuclei) {
                         if (nucleus is Neuron neuron && neuron.receivers.Count == 0)
                             this._outputs.Add(neuron);
                     }
@@ -721,7 +613,7 @@ namespace NanoBrain {
         }
 
         public bool TryGetNucleus(string nucleusName, out Nucleus foundNucleus) {
-            foreach (Nucleus receptor in this.clusterNuclei) {
+            foreach (Nucleus receptor in this.nuclei) {
                 if (receptor is Nucleus nucleus)
                     if (nucleus.name == nucleusName) {
                         foundNucleus = nucleus;
@@ -737,7 +629,7 @@ namespace NanoBrain {
             if (dotPosition >= 0) {
                 string clusterName = nucleusName[..dotPosition];
                 string clusterName0 = clusterName + ": 0";
-                foreach (Nucleus nucleus in this.clusterNuclei) {
+                foreach (Nucleus nucleus in this.nuclei) {
                     if (nucleus is Cluster cluster) {
                         if (cluster.name == clusterName || cluster.name == clusterName0) {
                             string subNucleusName = nucleusName[(dotPosition + 1)..];
@@ -749,9 +641,9 @@ namespace NanoBrain {
             }
             else {
                 string nucleusName0 = nucleusName + ": 0";
-                foreach (Nucleus nucleus in this.clusterNuclei) {
-                    if (nucleus is Cluster) { //IReceptor receptor) {
-                        if (nucleus.name == nucleusName | nucleus.name == nucleusName0)
+                foreach (Nucleus nucleus in this.nuclei) {
+                    if (nucleus is Cluster) {
+                        if (nucleus.name == nucleusName || nucleus.name == nucleusName0)
                             return nucleus;
                     }
                     else if (nucleus.name == nucleusName)
@@ -761,17 +653,70 @@ namespace NanoBrain {
             }
         }
 
+        public Neuron GetNeuron(string neuronName) {
+            foreach (Nucleus nucleus in this.nuclei) {
+                if (nucleus is Neuron neuron && neuron.name == neuronName)
+                    return neuron;
+            }
+            return null;
+        }
+
+        public Neuron GetNeuron(int thingId, string neuronName, string thingName = null) {
+            if (this.siblingClusters == null || this.siblingClusters.Length <= 1)
+                return this.GetNeuron(neuronName);
+
+            // See if we are already using a cluster for thingId
+            if (thingClusters.TryGetValue(thingId, out Cluster cluster))
+                return cluster.GetNeuron(neuronName);
+
+            // Find the cluster with the lowest value neuron
+            Neuron lowestNeuron = null;
+            foreach (Cluster sibling in this.siblingClusters) {
+                Neuron neuron = sibling.GetNeuron(neuronName);
+                if (lowestNeuron == null || neuron.outputMagnitude < lowestNeuron.outputMagnitude)
+                    lowestNeuron = neuron;
+            }
+            Cluster selectedCluster = lowestNeuron.parent;
+            RemoveThingCluster(selectedCluster);
+            selectedCluster.name = baseName + ": " + thingName;
+            thingClusters[thingId] = selectedCluster;
+            return lowestNeuron;
+            /*
+                        // Find a sleeping cluster
+                        // foreach (Cluster cluster in this.siblingClusters) {
+                        //     if (cluster.defaultOutput.isSleeping) {
+                        //         RemoveThingCluster(cluster);
+                        //         return cluster;
+                        //     }
+                        // }
+
+                        // Find longest unused cluster
+                        // Note this uses the default output...
+                        Cluster unusedCluster = this.siblingClusters[0];
+                        for (int ix = 1; ix < this.siblingClusters.Length; ix++) {
+                            if (this.siblingClusters[ix].defaultOutput.lastUpdate < unusedCluster.defaultOutput.lastUpdate)
+                                unusedCluster = this.siblingClusters[ix];
+                        }
+
+                        RemoveThingCluster(unusedCluster);
+                        //return unusedCluster;
+
+                        Cluster cluster = GetThingCluster(thingId, thingName);
+                        Neuron neuron = cluster?.GetNeuron(neuronName);
+                        return neuron;
+            */
+        }
         public bool DeleteNucleus(Nucleus nucleus) {
-            if (this.clusterNuclei.Contains(nucleus) == false) {
+            if (this.nuclei.Contains(nucleus) == false) {
                 // Try to find the nucleus by name
                 if (TryGetNucleus(nucleus.name, out nucleus) == false)
                     return false;
             }
 
             Neuron.Delete(nucleus);
-            int nucleusIx = this.clusterNuclei.IndexOf(nucleus);
-            this.clusterNuclei.Remove(nucleus);
-            this.prefab.nuclei.RemoveAt(nucleusIx);
+            //int nucleusIx = this.nuclei.IndexOf(nucleus);
+            this.nuclei.Remove(nucleus);
+            //this.prefab.cluster.nuclei.RemoveAt(nucleusIx);
             RefreshOutputs();
 
             return true;
@@ -781,7 +726,7 @@ namespace NanoBrain {
 
         public virtual List<Nucleus> CollectReceivers(bool removeDuplicates = false) {
             List<Nucleus> receivers = new();
-            foreach (Nucleus outputNucleus in this.clusterNuclei) {
+            foreach (Nucleus outputNucleus in this.nuclei) {
                 if (outputNucleus is not Neuron output)
                     continue;
 
@@ -789,7 +734,7 @@ namespace NanoBrain {
                 foreach (Nucleus receiver in output.receivers) {
                     // Debug.Log($"output    {receiver.name}");
                     // Only add receivers outside this cluster                    
-                    if (receiver.clusterPrefab != this.prefab) {
+                    if (receiver.parent.prefab != this.prefab) {
                         if (removeDuplicates == false || receivers.Contains(receiver) == false)
                             // Debug.Log($"   YES");
                             receivers.Add(receiver);
@@ -802,13 +747,13 @@ namespace NanoBrain {
         public List<(Neuron, Nucleus)> CollectConnections() {
             List<(Neuron, Nucleus)> connections = new();
 
-            foreach (Nucleus outputNucleus in this.clusterNuclei) {
+            foreach (Nucleus outputNucleus in this.nuclei) {
                 if (outputNucleus is not Neuron output)
                     continue;
 
                 foreach (Nucleus receiver in output.receivers) {
                     // Only add receivers outside this cluster
-                    if (receiver.clusterPrefab != this.prefab)
+                    if (receiver.parent.prefab != this.prefab)
                         connections.Add((output, receiver));
                 }
             }
@@ -817,10 +762,10 @@ namespace NanoBrain {
         public List<Synapse> CollectSynapsesTo(Cluster otherCluster) {
             List<Synapse> collectedSynapses = new();
 
-            foreach (Nucleus nucleus in this.clusterNuclei) {
+            foreach (Nucleus nucleus in this.nuclei) {
                 if (nucleus is not Neuron neuron)
                     continue;
-                foreach (Synapse synapse in nucleus.synapses) {
+                foreach (Synapse synapse in neuron.synapses) {
                     if (synapse.neuron.parent == otherCluster)
                         collectedSynapses.Add(synapse);
                 }
@@ -830,7 +775,7 @@ namespace NanoBrain {
 
         public void MoveReceivers(Cluster newCluster) {
             Debug.Log($"Move receivers for {this.name} to {newCluster.name}");
-            foreach (Nucleus outputNucleus in this.clusterNuclei) {
+            foreach (Nucleus outputNucleus in this.nuclei) {
                 if (outputNucleus is not Neuron output)
                     continue;
 
@@ -842,11 +787,13 @@ namespace NanoBrain {
                 Debug.Log($"Check {this.name}.{output.name} receivers");
                 Nucleus[] receivers = output.receivers.ToArray();
                 foreach (Nucleus receiver in receivers) {
-                    if (receiver.clusterPrefab != this.prefab) {
+                    if (receiver.parent.prefab != this.prefab) {
                         // Replace synapse with new synapse
                         // to the new cluster
                         Debug.Log($"move {receiver.name} from {this.name}.{output.name} to {newCluster.name}.{newOutput.name}");
-                        Synapse synapse = receiver.GetSynapse(output);
+                        if (receiver is not Neuron receiverNeuron)
+                            continue;
+                        Synapse synapse = receiverNeuron.GetSynapse(output);
                         newOutput.AddReceiver(receiver, synapse.weight);
                         output.RemoveReceiver(receiver);
                     }
@@ -867,41 +814,45 @@ namespace NanoBrain {
             }
 
             List<Nucleus> computeOrder = this.computeOrders[startNucleus];
-            //if (startNucleus.trace)
-            Debug.Log($"Update from {startNucleus.name}");
             foreach (Nucleus nucleus in computeOrder) {
                 if (nucleus is not Cluster) {
                     nucleus.UpdateStateIsolated();
-                    //if (startNucleus.trace && nucleus is Neuron neuron)
-                    Debug.Log($"   {nucleus.name}");
                     if (nucleus is Neuron neuron) {
                         foreach (Nucleus receiver in neuron.receivers) {
                             if (receiver.parent != this) {
-                                Debug.Log($"   External: {receiver.parent.name}.{receiver.name}");
+                                //Debug.Log($"   External: {receiver.parent.name}.{receiver.name}");
                                 receiver.parent.UpdateFromNucleus(receiver);
                             }
                         }
                     }
                 }
             }
-
-            // continue in parent
-            //this.parent?.UpdateFromNucleus(this);
-
-            UpdateNuclei();
+            //UpdateNuclei();
         }
 
         public override void UpdateStateIsolated() {
             throw new Exception("Cluster should not be updated!");
         }
 
-        public override void UpdateNuclei() {
-            foreach (Nucleus nucleus in this.clusterNuclei)
-                nucleus.UpdateNuclei();
-        }
+        // Don't think this does anything anymore...
+        // public override void UpdateNuclei() {
+        //     foreach (Nucleus nucleus in this.nuclei)
+        //         nucleus.UpdateNuclei();
+        // }
 
         #endregion Update
 
+        public void Refresh() {
+            // This should not be needed, but somehow somewhere the parent is changed...
+            foreach (Nucleus nucleus in this.nuclei) {
+                // if (nucleus is not Neuron neuron)
+                //     continue;
+                nucleus.parent = this;
+            }
+            RefreshOutputs();
+            RefreshComputeOrders();
+        }
+
     }
 
 }

Runtime/Scripts/Core/Cluster.cs.meta

@@ -1,2 +1,11 @@
 fileFormatVersion: 2
-guid: f13cdc4a175a9f379a00317ae68d8bea
+guid: f13cdc4a175a9f379a00317ae68d8bea
+MonoImporter:
+  externalObjects: {}
+  serializedVersion: 2
+  defaultReferences: []
+  executionOrder: 0
+  icon: {instanceID: 0}
+  userData: 
+  assetBundleName: 
+  assetBundleVariant: 

Runtime/Scripts/Core/MemoryCell.cs

@@ -12,7 +12,7 @@ namespace NanoBrain {
     [Serializable]
     public class MemoryCell : Neuron {
 
-        public MemoryCell(ClusterPrefab cluster, string name) : base(cluster, name) { }
+        // public MemoryCell(ClusterPrefab cluster, string name) : base(cluster, name) { }
         public MemoryCell(Cluster parent, string name) : base(parent, name) { }
 
         public bool staticMemory = false;

Runtime/Scripts/Core/MemoryCell.cs.meta

@@ -1,2 +1,11 @@
 fileFormatVersion: 2
-guid: 29633aa3fe5cd9dcc8d886051f45d4d8
+guid: 29633aa3fe5cd9dcc8d886051f45d4d8
+MonoImporter:
+  externalObjects: {}
+  serializedVersion: 2
+  defaultReferences: []
+  executionOrder: 0
+  icon: {instanceID: 0}
+  userData: 
+  assetBundleName: 
+  assetBundleVariant: 

Runtime/Scripts/Core/Neuron.cs

@@ -23,26 +23,91 @@ namespace NanoBrain {
         public Neuron(Cluster parent, string name) {
             this.parent = parent;
             this.name = name;
-            this.parent?.clusterNuclei.Add(this);
+            this.parent?.nuclei.Add(this);
         }
         /// <summary>
         /// Create a new Neuron in a Cluster Prefab
         /// </summary>
         /// <param name="prefab">The Cluster Preafb in which the new Neuron should be created</param>
         /// <param name="name">The name of the new Neuron</param>
-        public Neuron(ClusterPrefab prefab, string name) {
-            this.clusterPrefab = prefab;
-            this.name = name;
-            if (this.clusterPrefab != null) {
-                this.clusterPrefab.nuclei.Add(this);
-                this.clusterPrefab.RefreshOutputs();
-            }
-            else
-                Debug.LogError("No prefab when adding neuron to prefab");
-        }
+        // public Neuron(ClusterPrefab prefab, string name) {
+        //     this.clusterPrefab = prefab;
+        //     this.name = name;
+        //     if (this.clusterPrefab != null) {
+        //         this.clusterPrefab.cluster.nuclei.Add(this);
+        //         this.clusterPrefab.cluster.RefreshOutputs();
+        //     }
+        //     else
+        //         Debug.LogError("No prefab when adding neuron to prefab");
+        // }
 
         #region Serialization
 
+        /// <summary>
+        /// The bias
+        /// </summary>
+        /// The bias which a value which is always added to the combined value of the neuron
+        /// It does not have a synapse and therefore no weight of source nucleus
+        public Vector3 bias = Vector3.zero;
+
+        #region Synapses
+
+        [SerializeField]
+        private List<Synapse> _synapses = new();
+        /// <summary>
+        /// The synapses of the nucleus
+        /// </summary>
+        public List<Synapse> synapses => _synapses;
+
+        /// <summary>
+        /// Add a new synapse to this nuclues
+        /// </summary>
+        /// <param name="sendingNucleus">The nucleus from which the signals may originate</param>
+        /// <param name="weight">The weight applied to the input. Default value = 1</param>
+        /// <returns>The created Synapse</returns>
+        /// This will add a new input to this nucleus with the given weight.
+        public Synapse AddSynapse(Neuron sendingNucleus, float weight = 1) {
+            Synapse synapse = new(sendingNucleus, weight);
+            this.synapses.Add(synapse);
+            return synapse;
+        }
+
+        // public Synapse AddSynapse(ClusterPrefab clusterPrefab, string neuronName, float weight = 1) {
+
+        //     }
+
+        /// <summary>
+        /// Find a synapse
+        /// </summary>
+        /// <param name="sender">The sender of the input to the Synapse</param>
+        /// <returns>The found Synapse or null when the sender has no synapse to this nucleus.</returns>
+        public Synapse GetSynapse(Nucleus sender) {
+            foreach (Synapse synapse in this.synapses)
+                if (synapse.neuron == sender)
+                    return synapse;
+            return null;
+        }
+
+        /// <summary>
+        /// Remove a synapse from a Nucleus
+        /// </summary>
+        /// <param name="sendingNucleus">Remote the synapse connecting to this Nucleus</param>
+        public void RemoveSynapse(Nucleus sendingNucleus) {
+            this.synapses.RemoveAll(synapse => synapse.neuron == sendingNucleus);
+        }
+
+        #endregion Synapses
+
+        /// <summary>
+        /// Set the bias, recalculate the output and update all Nuclei receiving from this Nucleus
+        /// </summary>
+        /// <param name="inputValue"></param>
+        public virtual void SetBias(Vector3 inputValue) {
+            this.bias = inputValue;
+            this.lastUpdate = Time.time;
+            this.parent?.UpdateFromNucleus(this);
+        }
+
         /// <summary>
         /// The type of combinators
         /// </summary>
@@ -52,8 +117,6 @@ namespace NanoBrain {
             Sum,
             /// Multiply the weighted values
             Product,
-            /// Take the maximum of all the weighted values
-            Max,
         }
         /// <summary>
         /// The type of combinator used for this Neuron
@@ -211,16 +274,11 @@ namespace NanoBrain {
     public float outputSqrMagnitude => _outputValue.sqrMagnitude;
 
 #endif
-        public bool isFiring {
-            get {
-                SleepCheck();
-                return this.outputMagnitude > 0.5f;
-            }
-        }
+        public bool isFiring => this.outputMagnitude > 0.5f;
         public Action WhenFiring;
 
-
-        public virtual bool isSleeping => Time.time - this.lastUpdate > this.timeToSleep; //this.outputMagnitude == 0;
+        public bool persistOutput = false;
+        public virtual bool isSleeping => !persistOutput && (Time.time - this.lastUpdate > this.timeToSleep);
         public void SleepCheck() {
             if (this.isSleeping) {
 #if UNITY_MATHEMATICS
@@ -231,20 +289,27 @@ namespace NanoBrain {
             }
         }
 
-        [NonSerialized]
+        /// <summary>
+        /// Toggle for printing debugging trace data
+        /// </summary>
+        //public bool trace = false;
+
+        //[NonSerialized]
         public float lastUpdate = 0;
         public readonly float timeToSleep = 1f;
 
         /// \copydoc NanoBrain::Nucleus::ShallowCloneTo
         public override Nucleus ShallowCloneTo(Cluster newParent) {
-            Neuron clone = new(newParent, this.name);
+            Neuron clone = new(newParent, this.name) {
+                // prefabNucleus = this
+            };
             CloneFields(clone);
             return clone;
         }
 
         /// \copydoc NanoBrain::Nucleus::Clone
         public override Nucleus Clone(ClusterPrefab prefab) {
-            Neuron clone = new(prefab, this.name);
+            Neuron clone = new(prefab.cluster, this.name);
             CloneFields(clone);
             foreach (Synapse synapse in this.synapses) {
                 Synapse clonedSynapse = clone.AddSynapse(synapse.neuron);
@@ -257,8 +322,8 @@ namespace NanoBrain {
         }
 
         protected virtual void CloneFields(Neuron clone) {
-            clone.clusterPrefab = this.clusterPrefab;
             clone.bias = this.bias;
+            clone.persistOutput = this.persistOutput;
             clone.combinator = this.combinator;
             clone.curve = this.curve;
             clone.curvePreset = this.curvePreset;
@@ -268,8 +333,8 @@ namespace NanoBrain {
         public static void Delete(Nucleus nucleus) {
             if (nucleus == null)
                 return;
-            if (nucleus.synapses != null) {
-                foreach (Synapse synapse in nucleus.synapses) {
+            if (nucleus is Neuron neuron) {
+                foreach (Synapse synapse in neuron.synapses) {
                     if (synapse.neuron is Neuron synapse_nucleus) {
                         if (synapse_nucleus.receivers.Count > 1) {
                             // there is another nucleus feeding into this input nucleus
@@ -281,45 +346,43 @@ namespace NanoBrain {
                         }
                     }
                 }
-            }
-            if (nucleus is Neuron neuron) {
                 foreach (Nucleus receiver in neuron.receivers) {
-                    if (receiver != null && receiver.synapses != null)
-                        receiver.synapses.RemoveAll(s => s.neuron == nucleus);
+                    if (receiver is not Neuron receiverNeuron)
+                        continue;
+                    if (receiver != null && receiverNeuron.synapses != null)
+                        receiverNeuron.synapses.RemoveAll(s => s.neuron == nucleus);
                 }
             }
             else if (nucleus is Cluster cluster) {
                 // remove all receivers for this cluster
-                foreach (Nucleus clusterNucleus in cluster.clusterNuclei) {
+                foreach (Nucleus clusterNucleus in cluster.nuclei) {
                     if (clusterNucleus is Neuron output) {
                         foreach (Nucleus receiver in output.receivers) {
-                            receiver.synapses.RemoveAll(s => s.neuron == output);
+                            if (receiver is not Neuron receiverNeuron)
+                                continue;
+                            receiverNeuron.synapses.RemoveAll(s => s.neuron == output);
                         }
                     }
                 }
             }
 
 
-            if (nucleus.clusterPrefab != null) {
-                nucleus.clusterPrefab.nuclei.RemoveAll(n => n == nucleus);
-                nucleus.clusterPrefab.RefreshOutputs();
-                nucleus.clusterPrefab.GarbageCollection();
+            if (nucleus.parent.prefab != null) {
+                nucleus.parent.prefab.cluster.nuclei.RemoveAll(n => n == nucleus);
+                nucleus.parent.prefab.cluster.RefreshOutputs();
+                nucleus.parent.prefab.GarbageCollection();
             }
         }
 
         public override void UpdateStateIsolated() {
-            CheckSleepingSynapses();
             var result = Combinator();
-            this.outputValue = Activator(result);
+            this.outputValue = ApplyActivator(result);
             this.lastUpdate = Time.time;
         }
 
         protected void CheckSleepingSynapses() {
-            foreach (Synapse synapse in this.synapses) {
-                if (synapse.isSleeping) {
-                    synapse.neuron.outputValue = Vector3.zero;
-                }
-            }
+            foreach (Synapse synapse in this.synapses)
+                synapse.neuron.SleepCheck();
         }
 
         #region Combinator
@@ -329,42 +392,27 @@ namespace NanoBrain {
         protected Func<float3> Combinator => combinator switch {
             CombinatorType.Sum => CombinatorSum,
             CombinatorType.Product => CombinatorProduct,
-            CombinatorType.Max => CombinatorMax,
             _ => CombinatorSum
         };
 
         public float3 CombinatorSum() {
             float3 sum = this.bias;
-            foreach (Synapse synapse in this.synapses)
+            foreach (Synapse synapse in this.synapses) {
+                synapse.neuron.SleepCheck();
                 sum += synapse.weight * synapse.neuron.outputValue;
+            }
             return sum;
         }
 
         public float3 CombinatorProduct() {
             float3 product = this.bias;
             foreach (Synapse synapse in this.synapses) {
+                synapse.neuron.SleepCheck();
                 product *= synapse.weight * synapse.neuron.outputValue;
             }
             return product;
         }
 
-        public float3 CombinatorMax() {
-            float3 max = this.bias;
-            float maxLength = length(max);
-
-            //Applying the weight factors
-            foreach (Synapse synapse in this.synapses) {
-                float3 input = synapse.weight * synapse.neuron.outputValue;
-
-                float inputLength = length(input);
-                if (inputLength > maxLength) {
-                    max = input;
-                    maxLength = inputLength;
-                }
-            }
-            return max;
-        }
-
 #else
 
     protected Func<Vector3> Combinator => combinator switch {
@@ -413,6 +461,20 @@ namespace NanoBrain {
 
 #if UNITY_MATHEMATICS
 
+        // This does not allocate memory and seems faster than the solution below
+        float3 ApplyActivator(float3 x) {
+            switch (curvePreset) {
+                case ActivationType.Linear: return ActivatorLinear(x);
+                case ActivationType.Sqrt: return ActivatorSqrt(x);
+                case ActivationType.Power: return ActivatorPower(x);
+                case ActivationType.Reciprocal: return ActivatorReciprocal(x);
+                case ActivationType.Tanh: return ActivatorTanh(x);
+                case ActivationType.Binary: return ActivatorBinary(x);
+                case ActivationType.Normalized: return ActivatorNormalized(x);
+                default: return ActivatorCustom(x);
+            }
+        }
+
         public Func<float3, float3> Activator => this.curvePreset switch {
             ActivationType.Linear => ActivatorLinear,
             ActivationType.Sqrt => ActivatorSqrt,
@@ -524,25 +586,40 @@ namespace NanoBrain {
         }
 
         public virtual void AddReceiver(Nucleus receiverToAdd, float weight = 1) {
-            this._receivers.Add(receiverToAdd);
-            receiverToAdd.AddSynapse(this, weight);
+            if (receiverToAdd is not Neuron receiverNeuron)
+                return;
+            this._receivers.Add(receiverNeuron);
+            receiverNeuron.AddSynapse(this, weight);
             //Debug.Log($"Add synapse {this.clusterPrefab.name}.{this.name} -> {receiverToAdd.name} --- [{this.receivers.Count}]");
 
         }
 
         public virtual void RemoveReceiver(Nucleus receiverToRemove) {
-            this._receivers.RemoveAll(receiver => receiver == receiverToRemove);
-            receiverToRemove.synapses.RemoveAll(synapse => synapse.neuron == this);
+            if (receiverToRemove is not Neuron receiverNeuron)
+                return;
+            this._receivers.RemoveAll(receiver => receiver == receiverNeuron);
+            receiverNeuron.synapses.RemoveAll(synapse => synapse.neuron == this);
+
+            // Nucleus prefabReceiver = receiverToRemove.prefabNucleus;
+            // if (this.prefabNucleus is Neuron prefabNeuron && prefabReceiver != null) {
+            //     prefabNeuron.receivers.RemoveAll(receiver => receiver == prefabReceiver);
+            //     prefabReceiver.synapses.RemoveAll(synapse => synapse.neuron == prefabNeuron);
+            // }
         }
 
 
         #endregion Receivers
 
-        public override void ProcessStimulus(Vector3 inputValue) {
-            ;
+        /// <summary>
+        /// Process an external stimulus
+        /// </summary>
+        /// <param name="inputValue">The value of the stimulus</param>
+        /// <param name="thingId">The id of the thing causing the stimulus</param>
+        /// <param name="thingName">The name of the thing causing the stimulus</param>
+        public virtual void ProcessStimulus(Vector3 inputValue) {
             this.lastUpdate = Time.time;
             this.bias = inputValue;
-            this.parent.UpdateFromNucleus(this);
+            this.parent?.UpdateFromNucleus(this);
         }
     }
 

Runtime/Scripts/Core/Neuron.cs.meta

@@ -1,2 +1,11 @@
 fileFormatVersion: 2
-guid: 750748f3f0e7d472fbf88ab02987074c
+guid: 750748f3f0e7d472fbf88ab02987074c
+MonoImporter:
+  externalObjects: {}
+  serializedVersion: 2
+  defaultReferences: []
+  executionOrder: 0
+  icon: {instanceID: 0}
+  userData: 
+  assetBundleName: 
+  assetBundleVariant: 

Runtime/Scripts/Core/Nucleus.cs

@@ -17,11 +17,15 @@ public abstract class Nucleus {
     /// </summary>
     public string name;
 
+    // [NonSerialized]
+    // public Nucleus prefabNucleus;
+
     /// <summary>
     /// The cluster prefab in which the nucleus is located
     /// </summary>
-    [SerializeReference]
-    public ClusterPrefab clusterPrefab;
+    // [SerializeReference]
+    // public ClusterPrefab clusterPrefab;
+
     /// <summary>
     /// The cluster instance in which the nucleus is located
     /// </summary>
@@ -31,7 +35,7 @@ public abstract class Nucleus {
     /// <summary>
     /// Toggle for printing debugging trace data
     /// </summary>
-    public bool trace = false;
+    //public bool trace = false;
 
     /// <summary>
     /// Function to make a partial clone of this nucleus
@@ -61,60 +65,60 @@ public abstract class Nucleus {
 
     public virtual void Initialize() {}
 
-    #region Synapses
+    // #region Synapses
 
-    /// <summary>
-    /// The bias of the nucleus
-    /// </summary>
-    /// The bias which a value which is always added to the combined value of the nucleus
-    /// It does not have a synapse and therefore no weight of source nucleus
-    public Vector3 bias = Vector3.zero;
+    // /// <summary>
+    // /// The bias of the nucleus
+    // /// </summary>
+    // /// The bias which a value which is always added to the combined value of the nucleus
+    // /// It does not have a synapse and therefore no weight of source nucleus
+    // //public Vector3 bias = Vector3.zero;
 
-    [SerializeField]
-    private List<Synapse> _synapses = new();
-    /// <summary>
-    /// The synapses of the nucleus
-    /// </summary>
-    public List<Synapse> synapses => _synapses;
+    // [SerializeField]
+    // private List<Synapse> _synapses = new();
+    // /// <summary>
+    // /// The synapses of the nucleus
+    // /// </summary>
+    // public List<Synapse> synapses => _synapses;
 
-    /// <summary>
-    /// Add a new synapse to this nuclues
-    /// </summary>
-    /// <param name="sendingNucleus">The nucleus from which the signals may originate</param>
-    /// <param name="weight">The weight applied to the input. Default value = 1</param>
-    /// <returns>The created Synapse</returns>
-    /// This will add a new input to this nucleus with the given weight.
-    public Synapse AddSynapse(Neuron sendingNucleus, float weight = 1) {
-        Synapse synapse = new(sendingNucleus, weight);
-        this.synapses.Add(synapse);
-        return synapse;
-    }
+    // /// <summary>
+    // /// Add a new synapse to this nuclues
+    // /// </summary>
+    // /// <param name="sendingNucleus">The nucleus from which the signals may originate</param>
+    // /// <param name="weight">The weight applied to the input. Default value = 1</param>
+    // /// <returns>The created Synapse</returns>
+    // /// This will add a new input to this nucleus with the given weight.
+    // public Synapse AddSynapse(Neuron sendingNucleus, float weight = 1) {
+    //     Synapse synapse = new(sendingNucleus, weight);
+    //     this.synapses.Add(synapse);
+    //     return synapse;
+    // }
 
-    // public Synapse AddSynapse(ClusterPrefab clusterPrefab, string neuronName, float weight = 1) {
+    // // public Synapse AddSynapse(ClusterPrefab clusterPrefab, string neuronName, float weight = 1) {
             
-    //     }
+    // //     }
 
-    /// <summary>
-    /// Find a synapse
-    /// </summary>
-    /// <param name="sender">The sender of the input to the Synapse</param>
-    /// <returns>The found Synapse or null when the sender has no synapse to this nucleus.</returns>
-    public Synapse GetSynapse(Nucleus sender) {
-        foreach (Synapse synapse in this.synapses)
-            if (synapse.neuron == sender)
-                return synapse;
-        return null;
-    }
+    // /// <summary>
+    // /// Find a synapse
+    // /// </summary>
+    // /// <param name="sender">The sender of the input to the Synapse</param>
+    // /// <returns>The found Synapse or null when the sender has no synapse to this nucleus.</returns>
+    // public Synapse GetSynapse(Nucleus sender) {
+    //     foreach (Synapse synapse in this.synapses)
+    //         if (synapse.neuron == sender)
+    //             return synapse;
+    //     return null;
+    // }
 
-    /// <summary>
-    /// Remove a synapse from a Nucleus
-    /// </summary>
-    /// <param name="sendingNucleus">Remote the synapse connecting to this Nucleus</param>
-    public void RemoveSynapse(Nucleus sendingNucleus) {
-        this.synapses.RemoveAll(synapse => synapse.neuron == sendingNucleus);
-    }
+    // /// <summary>
+    // /// Remove a synapse from a Nucleus
+    // /// </summary>
+    // /// <param name="sendingNucleus">Remote the synapse connecting to this Nucleus</param>
+    // public void RemoveSynapse(Nucleus sendingNucleus) {
+    //     this.synapses.RemoveAll(synapse => synapse.neuron == sendingNucleus);
+    // }
 
-    #endregion Synapses
+    // #endregion Synapses
 
     #region Update
 
@@ -129,23 +133,14 @@ public abstract class Nucleus {
     public virtual void UpdateNuclei() {
     }
 
-    /// <summary>
-    /// Set the bias, recalculate the output and update all Nuclei receiving from this Nucleus
-    /// </summary>
-    /// <param name="inputValue"></param>
-    public virtual void SetBias(Vector3 inputValue) {
-        this.bias = inputValue;
-        this.parent.UpdateFromNucleus(this);
-    }
-
-    /// <summary>
-    /// Process an external stimulus
-    /// </summary>
-    /// <param name="inputValue">The value of the stimulus</param>
-    /// <param name="thingId">The id of the thing causing the stimulus</param>
-    /// <param name="thingName">The name of the thing causing the stimulus</param>
-    public virtual void ProcessStimulus(Vector3 inputValue) { //, int thingId = 0, string thingName = "") {
-    }
+    // /// <summary>
+    // /// Set the bias, recalculate the output and update all Nuclei receiving from this Nucleus
+    // /// </summary>
+    // /// <param name="inputValue"></param>
+    // public virtual void SetBias(Vector3 inputValue) {
+    //     this.bias = inputValue;
+    //     this.parent.UpdateFromNucleus(this);
+    // }
 
     #endregion Update
 

Runtime/Scripts/Core/Nucleus.cs.meta

@@ -1,2 +1,11 @@
 fileFormatVersion: 2
-guid: 4310eea6ab77628b085387a226c1c386
+guid: 4310eea6ab77628b085387a226c1c386
+MonoImporter:
+  externalObjects: {}
+  serializedVersion: 2
+  defaultReferences: []
+  executionOrder: 0
+  icon: {instanceID: 0}
+  userData: 
+  assetBundleName: 
+  assetBundleVariant: 

Runtime/Scripts/Core/Synapse.cs.meta

@@ -1,2 +1,11 @@
 fileFormatVersion: 2
-guid: 334a58eafccd60cbdb32f719e9e861c6
+guid: 334a58eafccd60cbdb32f719e9e861c6
+MonoImporter:
+  externalObjects: {}
+  serializedVersion: 2
+  defaultReferences: []
+  executionOrder: 0
+  icon: {instanceID: 0}
+  userData: 
+  assetBundleName: 
+  assetBundleVariant: 

Runtime/Scripts/ScriptableObjects/ClusterPrefab.cs

@@ -8,134 +8,146 @@ namespace NanoBrain {
     /// </summary>
     [CreateAssetMenu(menuName = "Passer/Cluster")]
     public class ClusterPrefab : ScriptableObject {
-        /// The nuclei in this cluster
-        [SerializeReference]
-        // This list should not include any clusters...
-        public List<Nucleus> nuclei = new();
 
-        /// <summary>
-        /// The output of this cluster
-        /// </summary>
-        /// <deprecated>This only returens the first(default) nucleus. Use outputs[0] instead</deprecated>
-        public virtual Nucleus output => this.nuclei[0] as Nucleus;
+        public Cluster cluster;
+        /*
+                /// The nuclei in this cluster
+                [SerializeReference]
+                // This list should not include any clusters...
+                public List<Nucleus> nuclei = new();
 
-        /// <summary>
-        /// The nuclei in this cluster which are meant for receiving signals from outside the cluster
-        /// </summary>
-        /// <remark>This is currently the nuclei which do not have any incoming synapse</remark>
-        public List<Nucleus> _inputs = null;
-        public virtual List<Nucleus> inputs {
-            get {
-                if (this._inputs == null) {
-                    this._inputs = new();
-                    foreach (Nucleus receptor in this.nuclei) {
-                        if (receptor is Nucleus nucleus) {
-                            // inputs have no incoming synapses yet.
-                            if (nucleus.synapses.Count == 0)
-                                this._inputs.Add(nucleus);
+                /// <summary>
+                /// The output of this cluster
+                /// </summary>
+                /// <deprecated>This only returens the first(default) nucleus. Use outputs[0] instead</deprecated>
+                public virtual Nucleus output => this.nuclei[0] as Nucleus;
+
+                /// <summary>
+                /// The nuclei in this cluster which are meant for receiving signals from outside the cluster
+                /// </summary>
+                /// <remark>This is currently the nuclei which do not have any incoming synapse</remark>
+                public List<Nucleus> _inputs = null;
+                public virtual List<Nucleus> inputs {
+                    get {
+                        if (this._inputs == null) {
+                            this._inputs = new();
+                            foreach (Nucleus receptor in this.nuclei) {
+                                if (receptor is Nucleus nucleus) {
+                                    // inputs have no incoming synapses yet.
+                                    if (nucleus.synapses.Count == 0)
+                                        this._inputs.Add(nucleus);
+                                }
+                            }
                         }
+                        return this._inputs;
                     }
                 }
-                return this._inputs;
-            }
-        }
-        /// <summary>
-        /// The nuclei in this cluster which are meant for sending signals onward
-        /// </summary>
-        private List<Nucleus> _outputs = null;
-        public List<Nucleus> outputs {
-            get {
-                if (this._outputs == null)
-                    RefreshOutputs();
-                return this._outputs;
-            }
-        }
-        /// <summary>
-        /// Redetermine the outpus in the cluster
-        /// </summary>
-        public void RefreshOutputs() {
-            this._outputs = new();
-            foreach (Nucleus nucleus in this.nuclei) {
-                if (nucleus is Neuron neuron && neuron.receivers.Count == 0)
-                    this._outputs.Add(nucleus);
-            }
-        }
-
+                /// <summary>
+                /// The nuclei in this cluster which are meant for sending signals onward
+                /// </summary>
+                private List<Nucleus> _outputs = null;
+                public List<Nucleus> outputs {
+                    get {
+                        if (this._outputs == null)
+                            RefreshOutputs();
+                        return this._outputs;
+                    }
+                }
+                /// <summary>
+                /// Redetermine the outpus in the cluster
+                /// </summary>
+                public void RefreshOutputs() {
+                    this._outputs = new();
+                    foreach (Nucleus nucleus in this.nuclei) {
+                        if (nucleus is Neuron neuron && neuron.receivers.Count == 0)
+                            this._outputs.Add(nucleus);
+                    }
+                }
+        */
         /// <summary>
         /// Retrieve a nucleus in this cluster
         /// </summary>
         /// <param name="nucleusName">The name of the nucleus</param>
         /// <returns>The Nucleus with the given name or null if no such Nucleus could be found</returns>
         public Nucleus GetNucleus(string nucleusName) {
-            foreach (Nucleus nucleus in this.nuclei) {
-                if (nucleus.name == nucleusName)
-                    return nucleus;
-            }
-            return null;
+            return cluster.GetNucleus(nucleusName);
+            // foreach (Nucleus nucleus in this.nuclei) {
+            //     if (nucleus.name == nucleusName)
+            //         return nucleus;
+            // }
+            // return null;
         }
 
         // Call this function to ensure that there is at least one nucleus
         // This is an invariant and should be ensured before the nucleus is used
         // because output requires it.
         public void EnsureInitialization() {
-            nuclei ??= new List<Nucleus>();
-            if (nuclei.Count == 0)
-                new Neuron(this, "Output"); // Every cluster should have at least 1 neuron
+            this.cluster.prefab = this;
+            this.cluster.name = this.name;
+            this.cluster.nuclei ??= new List<Nucleus>();
+            if (this.cluster.nuclei.Count <= 0)
+                new Neuron(this.cluster, "Output"); // Every cluster should have at least 1 neuron
+            this.cluster.instanceCount = 1;
+            // nuclei ??= new List<Nucleus>();
+            // if (nuclei.Count == 0)
+            //     new Neuron(this, "Output"); // Every cluster should have at least 1 neuron
         }
 
         public void GarbageCollection() {
-            HashSet<Nucleus> visitedNuclei = new();
-            foreach (Nucleus output in this.outputs)
-                MarkNuclei(visitedNuclei, output);
-            //Debug.Log($"Garbage collection found {visitedNuclei.Count} Nuclei");
-            this.nuclei.RemoveAll(nucleus => visitedNuclei.Contains(nucleus) == false);
+            // HashSet<Nucleus> visitedNuclei = new();
+            // foreach (Nucleus output in this.outputs)
+            //     MarkNuclei(visitedNuclei, output);
+            // //Debug.Log($"Garbage collection found {visitedNuclei.Count} Nuclei");
+            // this.nuclei.RemoveAll(nucleus => visitedNuclei.Contains(nucleus) == false);
         }
 
-        public void MarkNuclei(HashSet<Nucleus> visitedNuclei, Nucleus nucleus) {
-            if (nucleus is null)
-                return;
+        // public void MarkNuclei(HashSet<Nucleus> visitedNuclei, Nucleus nucleus) {
+        //     if (nucleus is null)
+        //         return;
 
-            if (nucleus.parent != null && nucleus.parent.prefab != this)
-                visitedNuclei.Add(nucleus.parent);
-            else
-                visitedNuclei.Add(nucleus);
-            if (nucleus.synapses != null) {
-                HashSet<Synapse> visitedSynapses = new();
-                foreach (Synapse synapse in nucleus.synapses) {
-                    if (synapse != null && synapse.neuron != null) {
-                        visitedSynapses.Add(synapse);
-                        if (synapse.neuron is Nucleus synapse_nucleus)
-                            MarkNuclei(visitedNuclei, synapse_nucleus);
-                    }
-                }
-                nucleus.synapses.RemoveAll(synapse => visitedSynapses.Contains(synapse) == false);
-            }
-            if (nucleus is Neuron neuron && neuron.receivers != null) {
-                HashSet<Nucleus> visitedReceivers = new();
-                foreach (Nucleus receiver in neuron.receivers) {
-                    if (receiver != null && receiver != null) {
-                        visitedReceivers.Add(receiver);
-                        visitedNuclei.Add(receiver);
-                    }
-                }
-                neuron.receivers.RemoveAll(receiver => visitedReceivers.Contains(receiver) == false);
-            }
-        }
+        //     if (nucleus.parent != null && nucleus.parent.prefab != this)
+        //         visitedNuclei.Add(nucleus.parent);
+        //     else
+        //         visitedNuclei.Add(nucleus);
+        //     if (nucleus is Neuron neuron) {
+        //         if (neuron.synapses != null) {
+        //             HashSet<Synapse> visitedSynapses = new();
+        //             foreach (Synapse synapse in neuron.synapses) {
+        //                 if (synapse != null && synapse.neuron != null) {
+        //                     visitedSynapses.Add(synapse);
+        //                     if (synapse.neuron is Nucleus synapse_nucleus)
+        //                         MarkNuclei(visitedNuclei, synapse_nucleus);
+        //                 }
+        //             }
+        //             neuron.synapses.RemoveAll(synapse => visitedSynapses.Contains(synapse) == false);
+        //         }
+        //         if (neuron.receivers != null) {
+        //             HashSet<Nucleus> visitedReceivers = new();
+        //             foreach (Nucleus receiver in neuron.receivers) {
+        //                 if (receiver != null && receiver != null) {
+        //                     visitedReceivers.Add(receiver);
+        //                     visitedNuclei.Add(receiver);
+        //                 }
+        //             }
+        //             neuron.receivers.RemoveAll(receiver => visitedReceivers.Contains(receiver) == false);
+        //         }
+        //     }
+        // }
 
-        public virtual void UpdateNuclei() {
-            foreach (Nucleus nucleus in this.nuclei)
-                nucleus.UpdateNuclei();
-        }
+        // public virtual void UpdateNuclei() {
+        //     foreach (Nucleus nucleus in this.nuclei)
+        //         nucleus.UpdateNuclei();
+        // }
 
-        public int GetNucleusIndex(Nucleus receiver) {
-            int ix = 0;
-            foreach (Nucleus nucleus in this.nuclei) {
-                if (receiver == nucleus)
-                    return ix;
-                ix++;
-            }
-            return -1;
-        }
+        // public int GetNucleusIndex(Nucleus receiver) {
+        //     int ix = 0;
+        //     foreach (Nucleus nucleus in this.nuclei) {
+        //         if (receiver == nucleus)
+        //             return ix;
+        //         ix++;
+        //     }
+        //     return -1;
+        // }
     }
 
 }