Move to ClusterPfab

Assembly-CSharp.csproj

@@ -73,7 +73,6 @@
     <Compile Include="Assets/NanoBrain/LinearAlgebra/src/Vector2Int.cs" />
     <Compile Include="Assets/Scenes/Boids/Scripts/SwarmControl.cs" />
     <Compile Include="Assets/NanoBrain/INucleus.cs" />
-    <Compile Include="Assets/NanoBrain/ClusterInstance.cs" />
     <Compile Include="Assets/NanoBrain/LinearAlgebra/src/Spherical.cs" />
     <Compile Include="Assets/NanoBrain/LinearAlgebra/test/Vector3FloatTest.cs" />
     <Compile Include="Assets/NanoBrain/MemoryCell.cs" />
@@ -81,6 +80,7 @@
     <Compile Include="Assets/Scenes/Boids/Scripts/Boid.cs" />
     <Compile Include="Assets/NanoBrain/LinearAlgebra/src/SwingTwist.cs" />
     <Compile Include="Assets/NanoBrain/LinearAlgebra/test/SphericalTest.cs" />
+    <Compile Include="Assets/NanoBrain/ClusterPrefab.cs" />
     <Compile Include="Assets/NanoBrain/Cluster.cs" />
     <Compile Include="Assets/NanoBrain/Synapse.cs" />
     <Compile Include="Assets/NanoBrain/LinearAlgebra/test/Vector3IntTest.cs" />

Assets/NanoBrain/Cluster.cs

@@ -1,84 +1,259 @@
+using System;
 using System.Collections.Generic;
 using UnityEngine;
+using Unity.Mathematics;
+using static Unity.Mathematics.math;
 
-[CreateAssetMenu(menuName = "Passer/Cluster")]
+[System.Serializable]
-public class Cluster : ScriptableObject {
+public class Cluster : INucleus {
-
-    public Cluster cluster => this;
-
     // The ScriptableObject asset from which the runtime object has been created
-    public Cluster asset;
+    public readonly ClusterPrefab prefab;
+
+    public ClusterPrefab cluster { get; set; }
+
+    [SerializeField]
+    protected string _name;
+    public virtual string name {
+        get => _name;
+        set => _name = value;
+    }
+
+    // Hmm, a cluster instance can never be part of a scriptable object...(Cluster)
+    public Cluster(ClusterPrefab parent, ClusterPrefab prefab) {
+        this.prefab = prefab;
+        this.cluster = parent;
+        if (this.cluster != null)
+            this.cluster.nuclei.Add(this);
+
+        // foreach (IReceptor nucleus in this.prefab.nuclei) {
+        //     IReceptor clone = nucleus.CloneTo(null);
+        //     this.dynamicNuclei.Add(clone);
+        // }
+    }
+
+    public virtual IReceptor Clone() {
+        Neuron clone = new(this.cluster, this.name) {
+            array = this.array,
+        };
+
+        foreach (Synapse synapse in this.synapses) {
+            Synapse clonedSynapse = clone.AddSynapse(synapse.nucleus);
+            clonedSynapse.weight = synapse.weight;
+        }
+        foreach (INucleus receiver in this.receivers) {
+            clone.AddReceiver(receiver);
+        }
+        return clone;
+    }
+
+    // Not sure if this belongs here...
+    [SerializeReference]
+    private NucleusArray _array;
+    public NucleusArray array {
+        get { return _array; }
+        set { _array = value; }
+    }
+
+    #region Synapses
+
+    // class ClusterSynapse : Synapse {
+    //     public IReceptor receptor;
+    //     public ClusterSynapse(IReceptor nucleus, INucleus receptor, float weight = 1.0f) : base(nucleus, weight) {
+    //         this.receptor = receptor;
+    //     }
+    // }
+    [SerializeField]
+    private List<Synapse> _synapses = new();
+    public List<Synapse> synapses => _synapses;
+
+    public Synapse AddSynapse(IReceptor sendingNucleus) {
+        Synapse synapse = new(sendingNucleus); //, this.prefab.inputs[0]);
+        this._synapses.Add(synapse);
+        return synapse;
+        // else {
+        //     INucleus receptor = (INucleus)this.prefab.nuclei.Find(nucleus => nucleus is INucleus n && nucleus.name == nucleusName);
+        //     ClusterSynapse synapse = new(sendingNucleus, receptor);
+        //     receptor.AddSynapse(sendingNucleus);
+        // }
+        // // Add synapse to which neuron?
+        // return null;
+    }
+
+    // Does this even exist already?
+    public void RemoveSynapse() {
+
+    }
+
+    #endregion Synapses
+
+    #region Receivers
 
     [SerializeReference]
-    public List<IReceptor> nuclei = new();
+    private List<INucleus> _receivers = new();
-
+    public List<INucleus> receivers {
-    // public List<Cluster> subClusters = new();
+        get { return _receivers; }
-    public void AddSubCluster(ClusterInstance subCluster) {
+        set { _receivers = value; }
-        this.nuclei.Add(subCluster);
     }
 
-    public INucleus output => this.nuclei[0] as INucleus;
+    public virtual void AddReceiver(INucleus receivingNucleus) {
+        this._receivers.Add(receivingNucleus);
+        receivingNucleus.AddSynapse(this);
+    }
 
-    public List<INucleus> _inputs = null;
+    public void RemoveReceiver(INucleus receiverNucleus) {
-    public List<INucleus> inputs {
+        this._receivers.RemoveAll(receiver => receiver == receiverNucleus);
-        get {
+        receiverNucleus.synapses.RemoveAll(synapse => synapse.nucleus == this);
-            if (this._inputs == null) {
+    }
-                this._inputs = new();
+
-                foreach (IReceptor receptor in this.nuclei) {
+    // public void AddReceiver(INucleus receivingNucleus) {
-                    if (receptor is INucleus nucleus)
+    //     int newLength = this._receivers.Count + 1;
-                        this._inputs.Add(nucleus);
+    //     INucleus[] newReceivers = new INucleus[newLength];
-                }
+
-            }
+    //     // Copy the existing receivers
-            return this._inputs;
+    //     for (int ix = 0; ix < this._receivers.Count; ix++)
+    //         newReceivers[ix] = this._receivers[ix];
+    //     // Add the new receivers
+    //     newReceivers[this._receivers.Count] = receivingNucleus;
+    //     // Replace the receivers with the new receivers
+    //     this._receivers = new(newReceivers);
+
+    //     receivingNucleus.AddSynapse(this);
+    // }
+
+    // public void RemoveReceiver(INucleus receivingNucleus) {
+    //     Debug.Log("Clusterinstance. remote receiver");
+    //     int newLength = this._receivers.Count - 1;
+    //     if (newLength < 0)
+    //         //  Array was empty, so we cannot remove anything
+    //         return;
+
+    //     INucleus[] newReceivers = new INucleus[newLength];
+
+    //     int newIx = 0;
+    //     // Copy all receivers except receivingNucleus
+    //     for (int ix = 0; ix < this._receivers.Count; ix++) {
+    //         if (this._receivers[ix] == receivingNucleus)
+    //             // skip the receiver we want to remote
+    //             continue;
+
+    //         if (newIx >= newLength)
+    //             // We want to copy more elements than expected
+    //             // the receivingNucleus is not found
+    //             // and the original array is returned
+    //             return;
+    //         newReceivers[newIx] = this._receivers[ix];
+    //         newIx++;
+    //     }
+    //     this._receivers = new(newReceivers);
+    // }
+
+    #endregion Receivers
+
+    #region Runtime
+
+    [NonSerialized]
+    private int stale = 1000;
+    public bool isSleeping => lengthsq(this.outputValue) == 0;
+
+    [NonSerialized]
+    protected float3 _outputValue;
+    public virtual float3 outputValue {
+        get { return _outputValue; }
+        set {
+            this.stale = 0;
+            _outputValue = value;
         }
     }
 
-    // Call this function to ensure that there is at least one nucleus
+    #region Update
-    // This is an invariant and should be ensured before the nucleus is used
+
-    // because output requires it.
+    public virtual void UpdateState() {
-    public void EnsureInitialization() {
+        UpdateState(new float3(0, 0, 0));
-        nuclei ??= new List<IReceptor>();
-        if (nuclei.Count == 0)
-            new Neuron(this, "Output"); // Every cluster should have at least 1 neuron
     }
 
-    public void GarbageCollection() {
+    public void UpdateState(float3 inputValue) {
-        HashSet<INucleus> visitedNuclei = new();
+        float3 sum = inputValue; // new(0, 0, 0);
-        MarkNuclei(visitedNuclei, this.output);
-        //Debug.Log($"Garbage collection found {visitedNuclei.Count} Nuclei");
-        this.nuclei.RemoveAll(nucleus => nucleus is INucleus n && visitedNuclei.Contains(n) == false);
-    }
 
-    public void MarkNuclei(HashSet<INucleus> visitedNuclei, INucleus nucleus) {
+        //Applying the weight factgors
-        if (nucleus is null)
+        foreach (Synapse synapse in this.synapses) {
-            return;
+            sum += synapse.weight * synapse.nucleus.outputValue;
-
-        visitedNuclei.Add(nucleus);
-        if (nucleus.synapses != null) {
-            HashSet<Synapse> visitedSynapses = new();
-            foreach (Synapse synapse in nucleus.synapses) {
-                if (synapse != null && synapse.nucleus != null) {
-                    visitedSynapses.Add(synapse);
-                    if (synapse.nucleus is INucleus synapse_nucleus)
-                        MarkNuclei(visitedNuclei, synapse_nucleus);
-                }
-            }
-            nucleus.synapses.RemoveAll(synapse => visitedSynapses.Contains(synapse) == false);
-        }
-        if (nucleus.receivers != null) {
-            HashSet<INucleus> visitedReceivers = new();
-            foreach (INucleus receiver in nucleus.receivers) {
-                if (receiver != null && receiver != null) {
-                    visitedReceivers.Add(receiver);
-                    visitedNuclei.Add(receiver);
-                }
-            }
-            nucleus.receivers.RemoveAll(receiver => visitedReceivers.Contains(receiver) == false);
         }
+        
+        // This does not work because the prefab nucleus does not have a state
+        this.prefab.inputs[0].UpdateState(sum);
     }
 
     public void UpdateNuclei() {
-        foreach (IReceptor nucleus in this.nuclei)
+        this.stale++;
+        if (this.stale >  2)
+            _outputValue = Vector3.zero;
+
+        foreach (IReceptor nucleus in this.prefab.nuclei)
             nucleus.UpdateNuclei();
     }
-}
+
+    #endregion Update
+
+    #endregion Runtime    
+
+    /*
+        [SerializeField]
+        private List<IReceptor> _dynamicNuclei;
+        public List<IReceptor> dynamicNuclei {// = new();
+            get {
+                if (_dynamicNuclei == null) {
+                    this._dynamicNuclei = new();
+                    foreach (IReceptor nucleus in this.prefab.nuclei) {
+                        IReceptor clone = nucleus.CloneTo(null);
+                        this._dynamicNuclei.Add(clone);
+                    }
+                }
+                return this._dynamicNuclei;
+            }
+        }
+
+        public List<INucleus> _inputs = null;
+        public List<INucleus> inputs {
+            get {
+                this._inputs = new();
+                if (this.dynamicNuclei != null) {
+                    foreach (IReceptor receptor in this.dynamicNuclei) {
+                        if (receptor is INucleus nucleus)
+                            this._inputs.Add(nucleus);
+                    }
+                }
+                return this._inputs;
+            }
+        }
+
+        public INucleus output => this.dynamicNuclei[0] as INucleus;
+
+        public float3 outputValue => this.output.outputValue;
+
+
+        public IReceptor CloneTo(ClusterPrefab parent) {
+            Cluster clone = new(parent, this.prefab);
+            return clone;
+        }
+        public IReceptor Clone() {
+            Cluster clone = new(this.cluster, this.prefab);
+            return clone;
+        }
+
+        #region Properties
+
+        public string name {
+            get { return prefab.name; }
+            set { prefab.name = value; }
+        }
+
+        public bool isSleeping => lengthsq(this.outputValue) == 0;
+
+        public NucleusArray array { get; set; }
+
+        #endregion Properties
+
+
+    */
+
+}

Assets/NanoBrain/Cluster.cs.meta

@@ -1,2 +1,2 @@
 fileFormatVersion: 2
-guid: 60a957541c24c57e78018c202ebb1d9b
+guid: f13cdc4a175a9f379a00317ae68d8bea

Assets/NanoBrain/ClusterInstance.cs

@@ -1,138 +0,0 @@
-using System.Collections.Generic;
-using UnityEngine;
-using Unity.Mathematics;
-using static Unity.Mathematics.math;
-
-[System.Serializable]
-public class ClusterInstance : INucleus {
-    // The ScriptableObject asset from which the runtime object has been created
-    public Cluster asset;
-
-    public Cluster cluster => this.asset;
-
-    public List<IReceptor> dynamicNuclei = new();
-
-    public INucleus output => this.asset.nuclei[0] as INucleus;
-    public float3 outputValue => this.output.outputValue;
-
-    public ClusterInstance(Cluster asset) {
-        this.asset = asset;
-        foreach (IReceptor nucleus in this.asset.nuclei)
-            dynamicNuclei.Add(nucleus.Clone());
-    }
-
-    public IReceptor Clone() {
-        ClusterInstance clone = new(this.asset);
-        return clone;
-    }
-
-    #region Properties
-
-    public string name {
-        get { return asset.name; }
-        set { asset.name = value; }
-    }
-
-    public bool isSleeping => lengthsq(this.outputValue) == 0;
-
-    public NucleusArray array { get; set; }
-
-    #endregion Properties
-
-    #region Synapses
-
-    [SerializeReference]
-    private List<Synapse> _synapses = new();
-    public List<Synapse> synapses => new(_synapses);
-
-    public Synapse AddSynapse(IReceptor sendingNucleus, string nucleusName = null) {
-        if (nucleusName == null) {
-            Synapse synapse = new(sendingNucleus);
-            this._synapses.Add(synapse);
-            // Nice, but this is not yet connected to the nucleusName
-        } else {
-            INucleus receptor = (INucleus)this.asset.nuclei.Find(nucleus => nucleus is INucleus n && nucleus.name == nucleusName);
-            receptor.AddSynapse(sendingNucleus);
-        }
-        // Add synapse to which neuron?
-        return null;
-    }
-
-    // Does this even exist already?
-    public void RemoveSynapse() {
-
-    }
-
-    #endregion Synapses
-
-    #region Receivers
-
-    [SerializeReference]
-    private List<INucleus> _receivers = new();
-    public List<INucleus> receivers {
-        get { return _receivers; }
-        set { _receivers = value; }
-    }
-
-    public void AddReceiver(INucleus receivingNucleus) {
-        int newLength = this._receivers.Count + 1;
-        INucleus[] newReceivers = new INucleus[newLength];
-
-        // Copy the existing receivers
-        for (int ix = 0; ix < this._receivers.Count; ix++)
-            newReceivers[ix] = this._receivers[ix];
-        // Add the new receivers
-        newReceivers[this._receivers.Count] = receivingNucleus;
-        // Replace the receivers with the new receivers
-        this._receivers = new(newReceivers);
-
-        receivingNucleus.AddSynapse(this);
-    }
-
-    public void RemoveReceiver(INucleus receivingNucleus) {
-        int newLength = this._receivers.Count - 1;
-        if (newLength < 0)
-            //  Array was empty, so we cannot remove anything
-            return;
-
-        INucleus[] newReceivers = new INucleus[newLength];
-
-        int newIx = 0;
-        // Copy all receivers except receivingNucleus
-        for (int ix = 0; ix < this._receivers.Count; ix++) {
-            if (this._receivers[ix] == receivingNucleus)
-                // skip the receiver we want to remote
-                continue;
-
-            if (newIx >= newLength)
-                // We want to copy more elements than expected
-                // the receivingNucleus is not found
-                // and the original array is returned
-                return;
-            newReceivers[newIx] = this._receivers[ix];
-            newIx++;
-        }
-        this._receivers = new(newReceivers);
-    }
-
-    #endregion Receivers
-
-    #region Update
-
-    public void UpdateState() {
-        float3 sum = new(0, 0, 0);
-
-        //Applying the weight factgors
-        foreach (Synapse synapse in this.synapses) {
-            sum += synapse.weight * synapse.nucleus.outputValue;
-        }
-        this.asset.inputs[0].UpdateState();        
-    }
-
-    public void UpdateNuclei() {
-        foreach (IReceptor nucleus in this.asset.nuclei)
-            nucleus.UpdateNuclei();
-    }
-
-    #endregion Update
-}

Assets/NanoBrain/ClusterInstance.cs.meta

@@ -1,2 +0,0 @@
-fileFormatVersion: 2
-guid: f13cdc4a175a9f379a00317ae68d8bea

Assets/NanoBrain/ClusterPrefab.cs

@@ -0,0 +1,84 @@
+using System.Collections.Generic;
+using UnityEngine;
+
+[CreateAssetMenu(menuName = "Passer/Cluster")]
+public class ClusterPrefab : ScriptableObject {
+
+    //public virtual Cluster cluster {get;set;}
+
+    // The ScriptableObject asset from which the runtime object has been created
+    //public Cluster asset;
+
+    [SerializeReference]
+    public List<IReceptor> nuclei = new();
+
+    // public List<Cluster> subClusters = new();
+    // public void AddSubCluster(ClusterInstance subCluster) {
+    //     this.nuclei.Add(subCluster);
+    // }
+
+    public virtual INucleus output => this.nuclei[0] as INucleus;
+
+    public List<INucleus> _inputs = null;
+    public virtual List<INucleus> inputs {
+        get {
+            if (this._inputs == null) {
+                this._inputs = new();
+                foreach (IReceptor receptor in this.nuclei) {
+                    if (receptor is INucleus nucleus)
+                        this._inputs.Add(nucleus);
+                }
+            }
+            return this._inputs;
+        }
+    }
+
+    // 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<IReceptor>();
+        if (nuclei.Count == 0)
+            new Neuron(this, "Output"); // Every cluster should have at least 1 neuron
+    }
+
+    public void GarbageCollection() {
+        HashSet<INucleus> visitedNuclei = new();
+        MarkNuclei(visitedNuclei, this.output);
+        //Debug.Log($"Garbage collection found {visitedNuclei.Count} Nuclei");
+        this.nuclei.RemoveAll(nucleus => nucleus is INucleus n && visitedNuclei.Contains(n) == false);
+    }
+
+    public void MarkNuclei(HashSet<INucleus> visitedNuclei, INucleus nucleus) {
+        if (nucleus is null)
+            return;
+
+        visitedNuclei.Add(nucleus);
+        if (nucleus.synapses != null) {
+            HashSet<Synapse> visitedSynapses = new();
+            foreach (Synapse synapse in nucleus.synapses) {
+                if (synapse != null && synapse.nucleus != null) {
+                    visitedSynapses.Add(synapse);
+                    if (synapse.nucleus is INucleus synapse_nucleus)
+                        MarkNuclei(visitedNuclei, synapse_nucleus);
+                }
+            }
+            nucleus.synapses.RemoveAll(synapse => visitedSynapses.Contains(synapse) == false);
+        }
+        if (nucleus.receivers != null) {
+            HashSet<INucleus> visitedReceivers = new();
+            foreach (INucleus receiver in nucleus.receivers) {
+                if (receiver != null && receiver != null) {
+                    visitedReceivers.Add(receiver);
+                    visitedNuclei.Add(receiver);
+                }
+            }
+            nucleus.receivers.RemoveAll(receiver => visitedReceivers.Contains(receiver) == false);
+        }
+    }
+
+    public virtual void UpdateNuclei() {
+        foreach (IReceptor nucleus in this.nuclei)
+            nucleus.UpdateNuclei();
+    }
+}

Assets/NanoBrain/ClusterPrefab.cs.meta

@@ -0,0 +1,2 @@
+fileFormatVersion: 2
+guid: 60a957541c24c57e78018c202ebb1d9b

Assets/NanoBrain/INucleus.cs

@@ -6,11 +6,11 @@ public interface INucleus : IReceptor {
     #region static struct
 
     // Cluster
-    public Cluster cluster { get; }
+    public ClusterPrefab cluster { get; }
 
     // Senders
     public List<Synapse> synapses { get; }
-    public Synapse AddSynapse(IReceptor sender, string nucleusName = null);
+    public Synapse AddSynapse(IReceptor sender);
 
     public NucleusArray array { get; set; }
 
@@ -19,6 +19,7 @@ public interface INucleus : IReceptor {
     #region dynamic state
 
     public void UpdateState();
+    public void UpdateState(float3 inputValue);
 
 
     #endregion dynamic state
@@ -47,6 +48,7 @@ public interface IReceptor {
 
     #endregion dynamic
 
+    //public IReceptor CloneTo(ClusterPrefab parent);
     public IReceptor Clone();
 }
 

Assets/NanoBrain/Identity.asset

@@ -12,123 +12,19 @@ MonoBehaviour:
   m_Script: {fileID: 11500000, guid: 60a957541c24c57e78018c202ebb1d9b, type: 3}
   m_Name: Identity
   m_EditorClassIdentifier: Assembly-CSharp::Cluster
-  asset: {fileID: 0}
   nuclei:
-  - rid: 2243601242842202241
+  - rid: 2243601383627161705
   references:
     version: 2
     RefIds:
-    - rid: -2
+    - rid: 2243601383627161705
-      type: {class: , ns: , asm: }
-    - rid: 2243601242842202241
       type: {class: Neuron, ns: , asm: Assembly-CSharp}
       data:
         _name: Output
-        _synapses:
-        - basicNucleus:
-            rid: 2243601249170358348
-          cluster:
-            rid: -2
-          weight: 1
-          curveMax: 1
-        _receivers: []
-        _array:
-          rid: 2243601242842202242
-        _curvePreset: 0
-        curve:
-          serializedVersion: 2
-          m_Curve:
-          - serializedVersion: 3
-            time: 0
-            value: 0
-            inSlope: 0
-            outSlope: 1
-            tangentMode: 0
-            weightedMode: 0
-            inWeight: 0
-            outWeight: 0
-          - serializedVersion: 3
-            time: 1000
-            value: 1000
-            inSlope: 1
-            outSlope: 0
-            tangentMode: 0
-            weightedMode: 0
-            inWeight: 0
-            outWeight: 0
-          m_PreInfinity: 2
-          m_PostInfinity: 2
-          m_RotationOrder: 4
-        curveMax: 1
-        average: 0
-    - rid: 2243601242842202242
-      type: {class: NucleusArray, ns: , asm: Assembly-CSharp}
-      data:
-        _nuclei:
-        - rid: 2243601242842202241
-        name: Output
-    - rid: 2243601249170358348
-      type: {class: Neuron, ns: , asm: Assembly-CSharp}
-      data:
-        _name: New neuron
         _synapses: []
-        _receivers:
-        - rid: 2243601249170358349
-        _array:
-          rid: 2243601249170358350
-        _curvePreset: 0
-        curve:
-          serializedVersion: 2
-          m_Curve:
-          - serializedVersion: 3
-            time: 0
-            value: 0
-            inSlope: 0
-            outSlope: 1
-            tangentMode: 0
-            weightedMode: 0
-            inWeight: 0
-            outWeight: 0
-          - serializedVersion: 3
-            time: 1000
-            value: 1000
-            inSlope: 1
-            outSlope: 0
-            tangentMode: 0
-            weightedMode: 0
-            inWeight: 0
-            outWeight: 0
-          m_PreInfinity: 2
-          m_PostInfinity: 2
-          m_RotationOrder: 4
-        curveMax: 1
-        average: 0
-    - rid: 2243601249170358349
-      type: {class: ClusterInstance, ns: , asm: Assembly-CSharp}
-      data:
-        asset: {fileID: 11400000}
-        _receivers:
-        - rid: 2243601249170358351
-    - rid: 2243601249170358350
-      type: {class: NucleusArray, ns: , asm: Assembly-CSharp}
-      data:
-        _nuclei:
-        - rid: 2243601249170358348
-        name: New neuron
-    - rid: 2243601249170358351
-      type: {class: Neuron, ns: , asm: Assembly-CSharp}
-      data:
-        _name: Output
-        _synapses:
-        - basicNucleus:
-            rid: 2243601249170358349
-          cluster:
-            rid: -2
-          weight: 1
-          curveMax: 1
         _receivers: []
         _array:
-          rid: 2243601249170358352
+          rid: 2243601383627161706
         _curvePreset: 0
         curve:
           serializedVersion: 2
@@ -156,9 +52,9 @@ MonoBehaviour:
           m_RotationOrder: 4
         curveMax: 1
         average: 0
-    - rid: 2243601249170358352
+    - rid: 2243601383627161706
       type: {class: NucleusArray, ns: , asm: Assembly-CSharp}
       data:
         _nuclei:
-        - rid: 2243601249170358351
+        - rid: 2243601383627161705
         name: Output

Assets/NanoBrain/MemoryCell.cs

@@ -6,7 +6,7 @@ using static Unity.Mathematics.math;
 [Serializable]
 public class MemoryCell : Neuron {
 
-    public MemoryCell(Cluster cluster, string name) : base(cluster, name) {}
+    public MemoryCell(ClusterPrefab cluster, string name) : base(cluster, name) {}
 
     #region Parameters
 

Assets/NanoBrain/Neuron.cs

@@ -87,7 +87,7 @@ public class Neuron : INucleus {
 
     #region Runtime state (not serialized)
 
-    public Cluster cluster { get; set; }
+    public ClusterPrefab cluster { get; set; }
 
     #region Activation
 
@@ -165,20 +165,40 @@ public class Neuron : INucleus {
 
     #endregion Runtime state
 
-    public Neuron(Cluster brain, string name) {
+    public Neuron(ClusterPrefab parent, string name) {
-        this.cluster = brain;
+        this.cluster = parent;
         this.name = name;
         if (this.cluster != null) {
             this.cluster.nuclei.Add(this);
         }
-        else
+        // else
-            Debug.LogError("No neuroid network");
+        //     Debug.LogError("No neuroid network");
     }
 
     // public Neuron(string name) {
     //     this._name = name;
     // }
 
+    public virtual IReceptor CloneTo(ClusterPrefab parent) {
+        Neuron clone = new(parent, this.name) {
+            array = this.array,
+            curve = this.curve,
+            curvePreset = this.curvePreset,
+            curveMax = this.curveMax,
+            average = this.average
+        };
+        // if (clone.cluster != null)
+        //     clone.cluster.nuclei.Add(clone);
+
+        foreach (Synapse synapse in this.synapses) {
+            Synapse clonedSynapse = clone.AddSynapse(synapse.nucleus);
+            clonedSynapse.weight = synapse.weight;
+        }
+        foreach (INucleus receiver in this.receivers) {
+            clone.AddReceiver(receiver);
+        }
+        return clone;
+    }
     public virtual IReceptor Clone() {
         Neuron clone = new(this.cluster, this.name) {
             array = this.array,
@@ -187,8 +207,8 @@ public class Neuron : INucleus {
             curveMax = this.curveMax,
             average = this.average
         };
-        if (clone.cluster != null)
+        // if (clone.cluster != null)
-            clone.cluster.nuclei.Add(clone);
+        //     clone.cluster.nuclei.Add(clone);
 
         foreach (Synapse synapse in this.synapses) {
             Synapse clonedSynapse = clone.AddSynapse(synapse.nucleus);
@@ -234,14 +254,18 @@ public class Neuron : INucleus {
         }
     }
 
-    public Synapse AddSynapse(IReceptor sendingNucleus, string nucleusName = null) {
+    public Synapse AddSynapse(IReceptor sendingNucleus) {
         Synapse synapse = new(sendingNucleus);
         this.synapses.Add(synapse);
         return synapse;
     }
 
     public virtual void UpdateState() {
-        float3 sum = new(0, 0, 0);
+        UpdateState(new float3(0, 0, 0));
+    }
+
+    public virtual void UpdateState(float3 inputValue) {
+        float3 sum = inputValue;//new(0, 0, 0);
         int n = 0;
 
         //Applying the weight factgors
@@ -255,7 +279,7 @@ public class Neuron : INucleus {
             if (lengthsq(synapse.nucleus.outputValue) != 0)
                 n++;
         }
-        if (this.average)
+        if (this.average && n > 0)
             sum /= n;
 
         // Activation function

Assets/NanoBrain/NucleusArray.cs

@@ -6,7 +6,7 @@ using UnityEngine;
 public class NucleusArray {
     [SerializeReference]
     private INucleus[] _nuclei;
-    private Cluster[] _clusters;
+    private ClusterPrefab[] _clusters;
     public IEnumerable<INucleus> nuclei {
         get {
             // if (_nuclei == null)
@@ -23,12 +23,12 @@ public class NucleusArray {
         this.name = nucleus.name;
         this._nuclei = new INucleus[1];
         this._nuclei[0] = nucleus;
-        this._clusters = new Cluster[0];
+        this._clusters = new ClusterPrefab[0];
     }
-    public NucleusArray(Cluster cluster) {
+    public NucleusArray(ClusterPrefab cluster) {
         this.name = cluster.name;
         this._nuclei = new INucleus[0];
-        this._clusters = new Cluster[1];
+        this._clusters = new ClusterPrefab[1];
         this._clusters[0] = cluster;
     }
 

Assets/NanoBrain/Receptor.cs

@@ -5,7 +5,7 @@ using static Unity.Mathematics.math;
 
 public class Receptor : IReceptor {
 
-    private Cluster cluster;
+    private ClusterPrefab cluster;
 
     [SerializeField]
     protected string _name;
@@ -14,20 +14,20 @@ public class Receptor : IReceptor {
         set => _name = value;
     }
 
-    public Receptor(Cluster cluster) {
+    public Receptor(ClusterPrefab cluster) {
         this.cluster = cluster;
         if (cluster != null)
             cluster.nuclei.Add(this);
     }
 
-    public Receptor(Cluster cluster, INucleus nucleus) {
+    public Receptor(ClusterPrefab cluster, INucleus nucleus) {
         this.cluster = cluster;
         if (cluster != null)
             cluster.nuclei.Add(this);
         this.AddReceiver(nucleus);
     }
 
-    public static Receptor CreateReceptor(Cluster cluster, string nucleusName) {
+    public static Receptor CreateReceptor(ClusterPrefab cluster, string nucleusName) {
         if (cluster == null)
             return null;
 
@@ -45,6 +45,15 @@ public class Receptor : IReceptor {
             return receptor;
     }
 
+    public virtual IReceptor CloneTo(ClusterPrefab parent) {
+        Receptor clone = new(parent);
+
+        foreach (INucleus receiver in this.receivers) {
+            clone.AddReceiver(receiver);
+        }
+
+        return clone;
+    }
     public virtual IReceptor Clone() {
         Receptor clone = new(this.cluster);
 

Assets/NanoBrain/Synapse.cs

@@ -4,18 +4,19 @@ using UnityEngine;
 [Serializable]
 public class Synapse {
     // Support access to cluster of basic nucleus
-    public IReceptor nucleus => basicNucleus;
+    //public IReceptor nucleus => basicNucleus;
+
+
+    //[SerializeReference]
+    //public Cluster cluster;
 
     [SerializeReference]
-    private IReceptor basicNucleus;
+    public IReceptor nucleus;
-
-    [SerializeReference]
-    public ClusterInstance cluster;
 
     public float weight;
 
     public Synapse(IReceptor nucleus, float weight = 1.0f) {
-        this.basicNucleus = nucleus;
+        this.nucleus = nucleus;
         this.weight = weight;
     }
 }

Assets/NanoBrain/Velocity.asset

@@ -12,50 +12,7 @@ MonoBehaviour:
   m_Script: {fileID: 11500000, guid: 60a957541c24c57e78018c202ebb1d9b, type: 3}
   m_Name: Velocity
   m_EditorClassIdentifier: Assembly-CSharp::Cluster
-  asset: {fileID: 0}
+  nuclei: []
-  nuclei:
-  - rid: 2243601362379866169
   references:
     version: 2
-    RefIds:
+    RefIds: []
-    - rid: 2243601362379866169
-      type: {class: Neuron, ns: , asm: Assembly-CSharp}
-      data:
-        _name: Output
-        _synapses: []
-        _receivers: []
-        _array:
-          rid: 2243601362379866170
-        _curvePreset: 0
-        curve:
-          serializedVersion: 2
-          m_Curve:
-          - serializedVersion: 3
-            time: 0
-            value: 0
-            inSlope: 0
-            outSlope: 1
-            tangentMode: 0
-            weightedMode: 0
-            inWeight: 0
-            outWeight: 0
-          - serializedVersion: 3
-            time: 1000
-            value: 1000
-            inSlope: 1
-            outSlope: 0
-            tangentMode: 0
-            weightedMode: 0
-            inWeight: 0
-            outWeight: 0
-          m_PreInfinity: 2
-          m_PostInfinity: 2
-          m_RotationOrder: 4
-        curveMax: 1
-        average: 0
-    - rid: 2243601362379866170
-      type: {class: NucleusArray, ns: , asm: Assembly-CSharp}
-      data:
-        _nuclei:
-        - rid: 2243601362379866169
-        name: Output

Assets/NanoBrain/VisualEditor/Editor/BrainPickerWindow.cs

@@ -5,11 +5,11 @@ using System.Linq;
 
 public class BrainPickerWindow : EditorWindow {
     private Vector2 scroll;
-    private Cluster[] items = new Cluster[0];
+    private ClusterPrefab[] items = new ClusterPrefab[0];
-    private Action<Cluster> onPicked;
+    private Action<ClusterPrefab> onPicked;
     private string search = "";
 
-    public static void ShowPicker(Action<Cluster> onPicked, string title = "Select Cluster") {
+    public static void ShowPicker(Action<ClusterPrefab> onPicked, string title = "Select Cluster") {
         var w = CreateInstance<BrainPickerWindow>();
         w.titleContent = new GUIContent(title);
         w.minSize = new Vector2(360, 320);
@@ -23,7 +23,7 @@ public class BrainPickerWindow : EditorWindow {
     private void RefreshList() {
         var guids = AssetDatabase.FindAssets("t:Cluster");
         items = guids
-            .Select(g => AssetDatabase.LoadAssetAtPath<Cluster>(AssetDatabase.GUIDToAssetPath(g)))
+            .Select(g => AssetDatabase.LoadAssetAtPath<ClusterPrefab>(AssetDatabase.GUIDToAssetPath(g)))
             .Where(b => b != null)
             .OrderBy(b => b.name)
             .ToArray();
@@ -47,7 +47,7 @@ public class BrainPickerWindow : EditorWindow {
                 continue;
 
             EditorGUILayout.BeginHorizontal();
-            EditorGUILayout.LabelField(EditorGUIUtility.ObjectContent(it, typeof(Cluster)), GUILayout.Height(20));
+            EditorGUILayout.LabelField(EditorGUIUtility.ObjectContent(it, typeof(ClusterPrefab)), GUILayout.Height(20));
             if (GUILayout.Button("Select", GUILayout.Width(70))) {
                 onPicked?.Invoke(it);
                 Close();

Assets/NanoBrain/VisualEditor/Editor/ClusterInspector.cs

@@ -7,7 +7,7 @@ using UnityEngine.UIElements;
 using Unity.Mathematics;
 using static Unity.Mathematics.math;
 
-[CustomEditor(typeof(Cluster))]
+[CustomEditor(typeof(ClusterPrefab))]
 public class ClusterInspector : Editor {
     protected static VisualElement mainContainer;
     protected static VisualElement inspectorContainer;
@@ -17,7 +17,7 @@ public class ClusterInspector : Editor {
     #region Start
 
     public override VisualElement CreateInspectorGUI() {
-        Cluster cluster = target as Cluster;
+        ClusterPrefab cluster = target as ClusterPrefab;
 
         serializedObject.Update();
 
@@ -72,7 +72,7 @@ public class ClusterInspector : Editor {
     }
 
     public class GraphView : VisualElement {
-        Cluster cluster;
+        ClusterPrefab cluster;
         SerializedObject serializedBrain;
         INucleus currentNucleus;
         GameObject gameObject;
@@ -123,7 +123,7 @@ public class ClusterInspector : Editor {
             subscribed = false;
         }
 
-        public void SetGraph(GameObject gameObject, Cluster brain, INucleus nucleus, VisualElement inspectorContainer) {
+        public void SetGraph(GameObject gameObject, ClusterPrefab brain, INucleus nucleus, VisualElement inspectorContainer) {
             this.gameObject = gameObject;
             this.cluster = brain;
             if (Application.isPlaying == false)
@@ -410,7 +410,7 @@ public class ClusterInspector : Editor {
                     Handles.Label(labelPos, nucleus.name, style);
                 }
 
-                if (nucleus is ClusterInstance cluster) {
+                if (nucleus is Cluster cluster) {
                     Handles.color = Color.white;
                     Handles.DrawWireDisc(position, Vector3.forward, size + 10);
                 }
@@ -529,7 +529,7 @@ public class ClusterInspector : Editor {
                         if (synapse.nucleus != null) {
                             EditorGUILayout.Space();
 
-                            EditorGUI.BeginDisabledGroup(synapse.nucleus.isSleeping);
+                            //EditorGUI.BeginDisabledGroup(synapse.nucleus.isSleeping);
                             if (Application.isPlaying)
                                 EditorGUILayout.FloatField(synapse.nucleus.name, length(synapse.nucleus.outputValue) * synapse.weight);
                             else {
@@ -543,7 +543,7 @@ public class ClusterInspector : Editor {
                             EditorGUI.indentLevel++;
                             synapse.weight = EditorGUILayout.FloatField("Weight", synapse.weight);
                             EditorGUI.indentLevel--;
-                            EditorGUI.EndDisabledGroup();
+                            //EditorGUI.EndDisabledGroup();
                         }
                     }
                 }
@@ -563,7 +563,7 @@ public class ClusterInspector : Editor {
                 if (GUILayout.Button("Delete this neuron"))
                     DeleteNeuron(this.currentNucleus);
 
-                if (this.currentNucleus is ClusterInstance subCluster) {
+                if (this.currentNucleus is Cluster subCluster) {
                     if (GUILayout.Button("Edit Cluster"))
                         EditCluster(subCluster);
                 }
@@ -588,7 +588,7 @@ public class ClusterInspector : Editor {
         }
 
         protected virtual void AddInputNeuron(INucleus nucleus) {
-            Neuron newNeuroid = new(this.cluster.cluster, "New neuron");
+            Neuron newNeuroid = new(this.cluster, "New neuron");
             newNeuroid.AddReceiver(nucleus);
             this.currentNucleus = newNeuroid;
             BuildLayers();
@@ -610,7 +610,7 @@ public class ClusterInspector : Editor {
         }
 
         protected virtual void AddInputMemoryCell(INucleus nucleus) {
-            MemoryCell newMemory = new(this.cluster.cluster, "New memory cell");
+            MemoryCell newMemory = new(this.cluster, "New memory cell");
             newMemory.AddReceiver(nucleus);
             this.currentNucleus = newMemory;
             BuildLayers();
@@ -620,22 +620,23 @@ public class ClusterInspector : Editor {
             BrainPickerWindow.ShowPicker(brain => OnClusterPicked(nucleus, brain), "Select Cluster");
         }
 
-        private void OnClusterPicked(INucleus nucleus, Cluster subCluster) {
+        private void OnClusterPicked(INucleus nucleus, ClusterPrefab subCluster) {
-            ClusterInstance clusterInstance = new(subCluster);
+            Cluster subclusterInstance = new(this.cluster, subCluster);
-            this.cluster.AddSubCluster(clusterInstance);
+            //this.cluster.AddSubCluster(subclusterInstance);
-            clusterInstance.AddReceiver(nucleus);
+            //this.cluster.nuclei.Add(subclusterInstance);
+            subclusterInstance.AddReceiver(nucleus);
         }
 
-        private void EditCluster(ClusterInstance subCluster) {
+        private void EditCluster(Cluster subCluster) {
             //var currentActiveObject = Selection.activeObject;
-            Selection.activeObject = subCluster.asset;
+            Selection.activeObject = subCluster.prefab;
-            EditorGUIUtility.PingObject(subCluster.asset);
+            EditorGUIUtility.PingObject(subCluster.prefab);
-            var editor = Editor.CreateEditor(subCluster.asset);
+            var editor = Editor.CreateEditor(subCluster.prefab);
             //Selection.activeObject = currentActiveObject;
         }
 
         // Connect to another nucleus in the same cluster
-        protected virtual void ConnectNucleus(Cluster cluster, INucleus nucleus) {
+        protected virtual void ConnectNucleus(ClusterPrefab cluster, INucleus nucleus) {
             if (cluster == null)
                 return;
 
@@ -705,9 +706,9 @@ public class ClusterWrapper : ScriptableObject {
     //public string title;
     public Vector2 position;
     INucleus node;
-    Cluster graph; // needed to write back and mark dirty
+    ClusterPrefab graph; // needed to write back and mark dirty
 
-    public ClusterWrapper Init(INucleus node, Cluster graphAsset) {
+    public ClusterWrapper Init(INucleus node, ClusterPrefab graphAsset) {
         this.node = node;
         this.graph = graphAsset;
         //this.title = " A " + node.name;

Assets/NanoBrain/VisualEditor/Editor/NanoBrainComponent_Editor.cs

@@ -23,7 +23,7 @@ public class NanoBrainComponent_Editor : Editor {
 
     public override VisualElement CreateInspectorGUI() {
         //NanoBrainComponent component = target as NanoBrainComponent;
-        Cluster brain = Application.isPlaying ? component.brain : component.defaultBrain;
+        ClusterPrefab brain = Application.isPlaying ? component.brain : component.defaultBrain;
 
         if (Application.isPlaying == false)
             serializedObject.Update();

Assets/NanoBrain/VisualEditor/NanoBrainComponent.cs

@@ -1,11 +1,11 @@
 using UnityEngine;
 
 public class NanoBrainComponent : MonoBehaviour {
-    public Cluster defaultBrain;
+    public ClusterPrefab defaultBrain;
-    private Cluster brainInstance;
+    private ClusterPrefab brainInstance;
 
     public INucleus root => brainInstance.output;
-    public Cluster brain {
+    public ClusterPrefab brain {
         get {
             if (brainInstance == null && defaultBrain != null) {
                 brainInstance = Instantiate(defaultBrain);
@@ -23,7 +23,7 @@ public class NanoBrainComponent : MonoBehaviour {
         }
     }
 
-    public static void UpdateWeight(Cluster brain, string name, float weight) {
+    public static void UpdateWeight(ClusterPrefab brain, string name, float weight) {
         INucleus root = brain.output;
         foreach (Synapse synapse in root.synapses) {
             if (synapse.nucleus.name == name) {

Assets/Scenes/Boids/New Cluster.asset

@@ -12,50 +12,7 @@ MonoBehaviour:
   m_Script: {fileID: 11500000, guid: 60a957541c24c57e78018c202ebb1d9b, type: 3}
   m_Name: New Cluster
   m_EditorClassIdentifier: Assembly-CSharp::Cluster
-  asset: {fileID: 0}
+  nuclei: []
-  nuclei:
-  - rid: 2243601249170358341
   references:
     version: 2
-    RefIds:
+    RefIds: []
-    - rid: 2243601249170358341
-      type: {class: Neuron, ns: , asm: Assembly-CSharp}
-      data:
-        _name: Output
-        _synapses: []
-        _receivers: []
-        _array:
-          rid: 2243601249170358342
-        _curvePreset: 0
-        curve:
-          serializedVersion: 2
-          m_Curve:
-          - serializedVersion: 3
-            time: 0
-            value: 0
-            inSlope: 0
-            outSlope: 1
-            tangentMode: 0
-            weightedMode: 0
-            inWeight: 0
-            outWeight: 0
-          - serializedVersion: 3
-            time: 1000
-            value: 1000
-            inSlope: 1
-            outSlope: 0
-            tangentMode: 0
-            weightedMode: 0
-            inWeight: 0
-            outWeight: 0
-          m_PreInfinity: 2
-          m_PostInfinity: 2
-          m_RotationOrder: 4
-        curveMax: 1
-        average: 0
-    - rid: 2243601249170358342
-      type: {class: NucleusArray, ns: , asm: Assembly-CSharp}
-      data:
-        _nuclei:
-        - rid: 2243601249170358341
-        name: Output

Assets/Scenes/Boids/Scripts/Editor/SwarmControl_Editor.cs

@@ -10,9 +10,9 @@ public class SwarmControl_Editor : Editor {
 
         if (EditorGUI.EndChangeCheck()) {
             SwarmControl swarmControl = (SwarmControl)target;
-            Cluster[] nanoBrains = FindObjectsByType<Cluster>(FindObjectsSortMode.None);
+            ClusterPrefab[] nanoBrains = FindObjectsByType<ClusterPrefab>(FindObjectsSortMode.None);
 
-            foreach (Cluster brain in nanoBrains) {
+            foreach (ClusterPrefab brain in nanoBrains) {
                 NanoBrainComponent.UpdateWeight(brain, "Avoidance", swarmControl.avoidanceForce);
                 NanoBrainComponent.UpdateWeight(brain, "Cohesion", swarmControl.cohesionForce);
                 NanoBrainComponent.UpdateWeight(brain, "Separation", swarmControl.separationForce);