Cleanup

Cluster.cs

@@ -7,14 +7,6 @@ using static Unity.Mathematics.math;
 
 [Serializable]
 public class Cluster : Nucleus {
-    // The ScriptableObject asset from which the runtime object has been created
-
-    // [SerializeField]
-    // protected string _name;
-    // public virtual string name {
-    //     get => _name;
-    //     set => _name = value;
-    // }
 
     #region Init
 
@@ -181,8 +173,6 @@ public class Cluster : Nucleus {
 
     public ClusterPrefab prefab;
 
-    // public ClusterPrefab cluster { get; set; }
-    // public Cluster parent { get; set; }
 
     [SerializeReference]
     public List<Nucleus> nuclei = new();
@@ -215,14 +205,6 @@ public class Cluster : Nucleus {
         }
     }
 
-    // Not sure if this belongs here...
-    // [SerializeReference]
-    // private NucleusArray _array;
-    // public NucleusArray array {
-    //     get { return _array; }
-    //     set { _array = value; }
-    // }
-
     public bool TryGetNucleus(string nucleusName, out Nucleus foundNucleus) {
         foreach (Nucleus receptor in this.nuclei) {
             if (receptor is Nucleus nucleus)
@@ -244,92 +226,14 @@ public class Cluster : Nucleus {
         return null;
     }
 
-    #region Synapses
-
-    // [SerializeField]
-    // private List<Synapse> _synapses = new();
-    // public List<Synapse> synapses => _synapses;
-
-    // public Synapse AddSynapse(Nucleus sendingNucleus, float weight = 1.0f) {
-    //     Synapse synapse = new(sendingNucleus, weight);
-    //     this._synapses.Add(synapse);
-    //     return synapse;
-    // }
-
-    // Does this even exist already?
-    public void RemoveSynapse() {
-
-    }
-
-    #endregion Synapses
-
-    #region Receivers
-
-    // [SerializeReference]
-    // private List<Nucleus> _receivers = new();
-    // public List<Nucleus> receivers {
-    //     get { return _receivers; }
-    //     set { _receivers = value; }
-    // }
-
-    // public virtual void AddReceiver(Nucleus receivingNucleus, float weight = 1) {
-    //     this._receivers.Add(receivingNucleus);
-    //     receivingNucleus.AddSynapse(this, weight);
-    // }
-
-    // public void RemoveReceiver(Nucleus receiverNucleus) {
-    //     this._receivers.RemoveAll(receiver => receiver == receiverNucleus);
-    //     receiverNucleus.synapses.RemoveAll(synapse => synapse.nucleus == this);
-    // }
-
-    #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;
-    //     }
-    // }
-
     #region Update
 
-    // public virtual void UpdateState() {
-    //     UpdateState(new float3(0, 0, 0));
-    // }
-
-    // public void UpdateState(float3 bias) {
-    //     float3 sum = bias; // new(0, 0, 0);
-
-    //     //Applying the weight factors
-    //     foreach (Synapse synapse in this.synapses) {
-    //         sum += synapse.weight * synapse.nucleus.outputValue;
-    //     }
-
-    //     //this.inputs[0].UpdateState(sum);
-    //     this.inputs[0].UpdateStateIsolated(sum);
-    //     foreach (IReceptor receptor in this.sortedNuclei) {
-    //         if (receptor is Nucleus nucleus && nucleus != this.inputs[0])
-    //             nucleus.UpdateStateIsolated();
-    //     }
-
-    //     UpdateResult(this.output.outputValue);
-    // }
-
     public override void UpdateStateIsolated() {
         float3 bias = new(0, 0, 0);
         UpdateStateIsolated(bias);
     }
     public override void UpdateStateIsolated(float3 bias) {
-        float3 sum = bias; // new(0, 0, 0);
+        float3 sum = bias;
 
         //Applying the weight factors
         foreach (Synapse synapse in this.synapses) {
@@ -339,42 +243,25 @@ public class Cluster : Nucleus {
             }
         }
 
-        //this.inputs[0].UpdateState(sum);
         this.inputs[0].UpdateStateIsolated(sum);
         foreach (Nucleus receptor in this.sortedNuclei) {
-            if (receptor is Nucleus nucleus && nucleus != this.inputs[0]) {
+            if (receptor is Nucleus nucleus && nucleus != this.inputs[0])
-                //if (nucleus.isSleeping == false)
                 nucleus.UpdateStateIsolated();
         }
-        }
         this.outputValue = this.output.outputValue;
 
         UpdateNuclei();
     }
 
-    // public virtual void UpdateResult(Vector3 result) {
-    //     // float d = Vector3.Distance(result, this.outputValue);
-    //     // if (d < 0.5f) {
-    //     //     //Debug.Log($"insignificant update: {d}");
-    //     //     return;
-    //     // }
-
-    //     this.outputValue = result;
-    //     foreach (Nucleus receiver in this.receivers)
-    //         receiver.UpdateState();
-    // }
-
     public override void UpdateNuclei() {
         this.stale++;
         if (this.stale > 5)
             _outputValue = Vector3.zero;
 
-        //foreach (IReceptor nucleus in this.prefab.nuclei)
         foreach (Nucleus nucleus in this.nuclei)
             nucleus.UpdateNuclei();
     }
 
     #endregion Update
 
-    #endregion Runtime    
 }

Editor/NanoBrain_Editor.cs

@@ -87,30 +87,6 @@ public class NanoBrainComponent_Editor : Editor {
         return root;
     }
 
-    // void OnSceneGUI() {
-    //     if (Application.isPlaying && board != null)
-    //     board.OnIMGUI();
-    // }
-
-    // void OnSceneGui(SceneView sv) {
-    //     if (Application.isPlaying == false)
-    //         return;
-    //     // May need some throttling here...
-    //     if (board != null) {
-    //         Debug.Log(".");
-    //         board.OnIMGUI();
-    //     }
-
-    //     // EditorApplication.delayCall = UpdateInspectorUI;
-    // }
-
-    // void UpdateInspectorUI() {
-    //     if (board != null) {
-    //         Debug.Log(".");
-    //         board.OnIMGUI();
-    //     }
-    // }
-
     private void UpdateLayout(float containerWidth) {
         // if (containerWidth > 800f) {
             mainContainer.style.flexDirection = FlexDirection.Row;

INucleus.cs

@@ -1,59 +0,0 @@
-/*
-using System.Collections.Generic;
-using Unity.Mathematics;
-
-public interface INucleus {
-
-    #region static struct
-
-    // Cluster
-    public ClusterPrefab cluster { get; }
-    public Cluster parent { get; }
-
-    // Senders
-    public List<Synapse> synapses { get; }
-    public Synapse AddSynapse(Nucleus sender, float weight = 1.0f);
-
-    public NucleusArray array { get; set; }
-
-    #endregion static struct
-
-    #region dynamic state
-
-    // public void UpdateState();
-    // public void UpdateState(float3 inputValue);
-    // public void UpdateStateIsolated();
-    // public void UpdateStateIsolated(float3 inputValue);
-
-    #endregion dynamic state
-
-    #region static
-
-    public string name { get; set; }
-
-    // Receivers
-    // public List<Nucleus> receivers { get; set; }
-
-    // public void AddReceiver(Nucleus receiver, float weight = 1);
-    // public void RemoveReceiver(Nucleus receiverNucleus);
-
-    #endregion static
-
-    #region dynamic
-
-    // float3 to prepare for SIMD
-    public float3 outputValue { get; }
-
-    public void UpdateNuclei();
-    public bool isSleeping { get; }
-
-    #endregion dynamic
-
-    // public INucleus ShallowCloneTo(Cluster parent);
-    // public INucleus Clone();
-}
-
-// public interface IReceptor {
-// }
-
-*/

INucleus.cs.meta

@@ -1,2 +0,0 @@
-fileFormatVersion: 2
-guid: 6a8a0e8965cea660abff254cab8a4723

MemoryCell.cs

@@ -8,10 +8,6 @@ public class MemoryCell : Neuron {
 
     public MemoryCell(ClusterPrefab cluster, string name) : base(cluster, name) { }
     public MemoryCell(Cluster parent, string name) : base(parent, name) { }
-    //     this.parent = parent;
-    //     this.name = name;
-    //     this.parent?.nuclei.Add(this);
-    // }
 
     public override Nucleus ShallowCloneTo(Cluster newParent) {
         MemoryCell clone = new(newParent, this.name) {
@@ -29,24 +25,6 @@ public class MemoryCell : Neuron {
     private float3 _memorizedValue;
     private float _memorizedTime;
 
-    // public override void UpdateState(float3 bias) {
-    //     // A memorycell does not have an activation function
-    //     float3 result = bias;
-    //     int n = 0;
-
-    //     //Applying the weight factgors
-    //     foreach (Synapse synapse in this.synapses) {
-    //         result += synapse.weight * synapse.nucleus.outputValue;
-    //         if (lengthsq(synapse.nucleus.outputValue) != 0)
-    //             n++;
-    //     }
-
-    //     if (this.average)
-    //         result /= n;
-
-    //     UpdateResult(result);
-    // }
-
     public override void UpdateStateIsolated() {
         float3 bias = new(0, 0, 0);
         UpdateStateIsolated(bias);
@@ -73,22 +51,5 @@ public class MemoryCell : Neuron {
         this._memorizedTime = Time.time;
     }
 
-    // public override void UpdateResult(Vector3 result) {
-    //     // output value is the previous value
-    //     // if (this.deltaValue) {
-    //     //     float deltaTime = Time.time - this._memorizedTime;
-    //     //     this._outputValue = this._memorizedValue * deltaTime;
-    //     // }
-    //     //else
-    //     this.outputValue = this._memorizedValue;
-
-    //     // Store the result for the next time
-    //     this._memorizedValue = result;
-    //     this._memorizedTime = Time.time;
-
-    //     foreach (INucleus receiver in this.receivers)
-    //         receiver.UpdateState();
-    // }
-
     #endregion State
 }

NanoBrain.cs

@@ -13,22 +13,10 @@ public class NanoBrain : MonoBehaviour {
                     name = defaultBrain.name + " (Instance)"
                 };
             }
-            // SwarmControl sc = FindFirstObjectByType<SwarmControl>();
-            // if (sc != null) {
-            //     UpdateWeight(brainInstance, "Containment", sc.containmentForce);
-            //     UpdateWeight(brainInstance, "Cohesion", sc.cohesionForce);
-            //     UpdateWeight(brainInstance, "Separation", sc.separationForce);
-            //     UpdateWeight(brainInstance, "Alignment", sc.alignmentForce);
-            // }
             return brainInstance;
         }
     }
 
-    //     public void Awake() {
-    //     brainInstance = new Cluster(defaultBrain);
-    // }
-
-
     public static void UpdateWeight(Cluster brain, string name, float weight) {
         Nucleus root = brain.output;
         foreach (Synapse synapse in root.synapses) {

Neuron.cs

@@ -24,31 +24,6 @@ public class Neuron : Nucleus {
         //     Debug.LogError("No neuroid network");
     }
 
-    // [SerializeField]
-    // protected string _name;
-    // public virtual string name {
-    //     get => _name;
-    //     set => _name = value;
-    // }
-
-    // [SerializeField]
-    // private List<Synapse> _synapses = new();
-    // public List<Synapse> synapses => _synapses;
-
-    // [SerializeReference]
-    // private List<INucleus> _receivers = new();
-    // public List<INucleus> receivers {
-    //     get { return _receivers; }
-    //     set { _receivers = value; }
-    // }
-
-    // [SerializeReference]
-    // private NucleusArray _array;
-    // public NucleusArray array {
-    //     get { return _array; }
-    //     set { _array = value; }
-    // }
-
     #region Serialization
 
     public enum CurvePresets {
@@ -102,9 +77,6 @@ public class Neuron : Nucleus {
 
     #region Runtime state (not serialized)
 
-    // public ClusterPrefab cluster { get; set; }
-    // public Cluster parent { get; set; }
-
     #region Activation
 
     public static class Presets {
@@ -153,31 +125,6 @@ public class Neuron : Nucleus {
 
     #endregion Activation
 
-    // protected float3 _outputValue;
-    // public virtual float3 outputValue {
-    //     get { return _outputValue; }
-    //     set {
-    //         this.stale = 0;
-    //         // this._isSleeping = false;
-    //         _outputValue = value;
-    //     }
-    // }
-
-    // [NonSerialized]
-    // private int stale = 1000;
-
-    // private bool _isSleeping = false;
-    // public bool isSleeping => _isSleeping;
-    // public bool isSleeping => lengthsq(this.outputValue) == 0;
-
-    // public void UpdateNuclei() {
-    //     this.stale++;
-    //     // this._isSleeping = this.stale > 2;
-    //     // if (isSleeping)
-    //     if (this.stale > 2)
-    //         _outputValue = Vector3.zero;
-    // }
-
     #endregion Runtime state
 
     // this clone the nucleus without the synapses and receivers
@@ -214,16 +161,6 @@ public class Neuron : Nucleus {
         return clone;
     }
 
-    // public virtual void AddReceiver(INucleus receivingNucleus, float weight = 1) {
-    //     this._receivers.Add(receivingNucleus);
-    //     receivingNucleus.AddSynapse(this, weight);
-    // }
-
-    // public void RemoveReceiver(INucleus receiverNucleus) {
-    //     this._receivers.RemoveAll(receiver => receiver == receiverNucleus);
-    //     receiverNucleus.synapses.RemoveAll(synapse => synapse.nucleus == this);
-    // }
-
     public static void Delete(Nucleus nucleus) {
         foreach (Synapse synapse in nucleus.synapses) {
             if (synapse.nucleus is Neuron synapse_nucleus) {
@@ -248,59 +185,6 @@ public class Neuron : Nucleus {
         }
     }
 
-    // public Synapse AddSynapse(IReceptor sendingNucleus, float weight = 1.0f) {
-    //     Synapse synapse = new(sendingNucleus, weight);
-    //     this.synapses.Add(synapse);
-    //     return synapse;
-    // }
-
-    // public virtual void UpdateState() {
-    //     //UpdateState(new float3(0, 0, 0));
-    //     this.parent?.UpdateState();
-    // }
-
-    // public virtual void UpdateState(float3 inputValue) {
-    //     float3 sum = inputValue;
-    //     int n = 0;
-
-    //     //Applying the weight factgors
-    //     foreach (Synapse synapse in this.synapses) {
-    //         sum += synapse.weight * synapse.nucleus.outputValue;
-
-    //         // Perhaps synapses should be removed when the output value goes to 0....
-    //         if (lengthsq(synapse.nucleus.outputValue) != 0)
-    //             n++;
-    //     }
-    //     if (this.average && n > 0)
-    //         sum /= n;
-
-    //     // Activation function
-    //     Vector3 result;
-    //     switch (this.curvePreset) {
-    //         case CurvePresets.Linear:
-    //             result = sum;
-    //             break;
-    //         case CurvePresets.Sqrt:
-    //             result = normalize(sum) * System.MathF.Sqrt(length(sum));
-    //             break;
-    //         case CurvePresets.Power:
-    //             result = normalize(sum) * System.MathF.Pow(length(sum), 2);
-    //             break;
-    //         case CurvePresets.Reciprocal:
-    //             result = normalize(sum) * (1 / length(sum));
-    //             break;
-    //         default:
-    //             float activatedValue = this.curve.Evaluate(length(sum));
-    //             result = normalize(sum) * activatedValue;
-    //             break;
-    //     }
-    //     UpdateResult(result);
-    // }
-
-    // public virtual void UpdateStateIsolated() {
-    //     UpdateStateIsolated(new float3(0, 0, 0));
-    // }
-
     public float3 bias = float3(0, 0, 0);
     public override void UpdateStateIsolated(float3 bias_unused) {
         float3 sum = this.bias;
@@ -354,21 +238,4 @@ public class Neuron : Nucleus {
         //Debug.Log($"{this.name} processed stimulus");
         this.bias = inputValue;
     }
-
-    // public virtual void UpdateResult(Vector3 result) {
-    //     // float d = Vector3.Distance(result, this.outputValue);
-    //     // if (d < 0.5f) {
-    //     //     //Debug.Log($"insignificant update: {d}");
-    //     //     return;
-    //     // }
-
-    //     this.outputValue = result;
-    //     if (lengthsq(outputValue) != 0) {
-    //         Debug.Log($"{this.parent.name}.{this.name}: {this.outputValue}");
-    //     }
-
-    //     foreach (INucleus receiver in this.receivers)
-    //         receiver.UpdateState();
-
-    // }
 }