Fix multiple pheromone placement

Cluster.cs

@@ -18,6 +18,7 @@ public class Cluster : Nucleus {
         this.parent?.nuclei.Add(this);
 
         ClonePrefab();
+        _ = this.inputs;
         this.sortedNuclei = TopologicalSort(this.nuclei);
         // Does not work because we have nuclei with the same names in an nucleusArray
         // 'Pheromone steering'
@@ -33,6 +34,7 @@ public class Cluster : Nucleus {
             this.cluster.nuclei.Add(this);
 
         ClonePrefab();
+        _ = this.inputs;
         this.sortedNuclei = TopologicalSort(this.nuclei);
         //this.nucleiDict = nuclei.ToDictionary(nucleus => nucleus.name);
     }
@@ -127,6 +129,7 @@ public class Cluster : Nucleus {
             if (inDegree[node] == 0) // Nodes with no dependencies            
                 queue.Enqueue(node);
         }
+        // The queue basically stores all input nuclei?
 
         List<Nucleus> sortedOrder = new();
         while (queue.Count > 0) {
@@ -200,11 +203,107 @@ public class Cluster : Nucleus {
                     if (nucleus.synapses.Count == 0)
                         this._inputs.Add(nucleus);
                 }
+                ComputeOrders();
             }
             return this._inputs;
         }
     }
 
+    public Dictionary<Nucleus, List<Nucleus>> computeOrders = new();
+    private void ComputeOrders() {
+        foreach (Nucleus input in this._inputs) {
+            computeOrders[input] = TopologicalSort2(input);
+        }
+    }
+
+    private List<Nucleus> TopologicalSort2(Nucleus startNode) {
+        Dictionary<Nucleus, int> inDegree = new Dictionary<Nucleus, int>();
+        HashSet<Nucleus> visited = new HashSet<Nucleus>();
+
+        // Initialize in-degrees and mark all nodes as unvisited
+        foreach (Nucleus node in this.nuclei) {
+            inDegree[node] = 0;
+        }
+
+        // Calculate in-degrees for all nodes reachable from the start node
+        Queue<Nucleus> queue = new Queue<Nucleus>();
+        queue.Enqueue(startNode);
+        visited.Add(startNode);
+
+        while (queue.Count > 0) {
+            Nucleus current = queue.Dequeue();
+            foreach (Nucleus receiver in current.receivers) {
+                if (!visited.Contains(receiver)) {
+                    visited.Add(receiver);
+                    queue.Enqueue(receiver);
+                }
+                inDegree[receiver]++;
+            }
+        }
+
+        // Perform topological sort on all reachable nodes
+        queue.Clear();
+        foreach (var node in visited) {
+            if (inDegree[node] == 0) {
+                queue.Enqueue(node);
+            }
+        }
+
+        List<Nucleus> sortedOrder = new List<Nucleus>();
+        while (queue.Count > 0) {
+            Nucleus current = queue.Dequeue();
+            sortedOrder.Add(current); // Process the node
+
+            foreach (Nucleus receiver in current.receivers) {
+                if (visited.Contains(receiver)) {
+                    inDegree[receiver]--;
+                    if (inDegree[receiver] == 0) // If all dependencies resolved
+                        queue.Enqueue(receiver);
+                }
+            }
+        }
+
+        // Check for cycles in the graph
+        if (sortedOrder.Count != visited.Count)
+            throw new InvalidOperationException("Graph is not a DAG; a cycle exists.");
+
+        return sortedOrder;
+    }
+
+    private List<Nucleus> TopologicalSort3(Nucleus startNode) {
+        Dictionary<Nucleus, int> inDegree = new();
+        foreach (Nucleus node in this.nuclei)
+            inDegree[node] = 0; // Initialize in-degree to zero
+
+        // Calculate in-degrees
+        foreach (Nucleus node in this.nuclei) {
+            foreach (Nucleus receiver in node.receivers)
+                inDegree[receiver]++;
+        }
+
+        Queue<Nucleus> queue = new();
+        queue.Enqueue(startNode);
+
+        List<Nucleus> sortedOrder = new();
+        while (queue.Count > 0) {
+            Nucleus current = queue.Dequeue();
+            sortedOrder.Add(current); // Process the node
+
+            foreach (Nucleus receiver in current.receivers) {
+                inDegree[receiver]--;
+                if (inDegree[receiver] == 0) // If all dependencies resolved
+                    queue.Enqueue(receiver);
+            }
+        }
+
+        Debug.Log($"Compute order for {startNode.name} length = {sortedOrder.Count}");
+        // Check for cycles in the graph
+        // if (sortedOrder.Count != this.nuclei.Count)
+        //     throw new InvalidOperationException("Graph is not a DAG; a cycle exists.");
+
+        return sortedOrder;
+    }
+
     public virtual Nucleus output {//=> this.nuclei[0] as Nucleus;
         get {
             if (this.nuclei.Count > 0)
@@ -250,6 +349,24 @@ public class Cluster : Nucleus {
 
     #region Update
 
+    public void UpdateFromNucleus(Nucleus startNucleus) {
+        // no bias+synapse input state calculation for now...
+
+        List<Nucleus> computeOrder = this.computeOrders[startNucleus];
+        if (startNucleus.trace)
+            Debug.Log($"Update from {startNucleus.name}");
+        foreach (Nucleus nucleus in computeOrder) {
+            nucleus.UpdateStateIsolated();
+            if (startNucleus.trace)
+                Debug.Log($"   {nucleus.name} = {nucleus.outputValue}");
+        }
+
+        this.outputValue = this.output.outputValue;
+        this.stale = 0;
+
+        UpdateNuclei();
+    }
+
     public override void UpdateStateIsolated() {
         Vector3 sum = this.bias;
 
@@ -263,7 +380,7 @@ public class Cluster : Nucleus {
 
         foreach (Nucleus nucleus in this.sortedNuclei)
             nucleus.UpdateStateIsolated();
-        
+
         this.outputValue = this.output.outputValue;
         this.stale = 0;
 
@@ -271,9 +388,9 @@ public class Cluster : Nucleus {
     }
 
     public override void UpdateNuclei() {
-        this.stale++;
-        if (this.stale > staleValueForSleep)
-            _outputValue = Vector3.zero;
+        // this.stale++;
+        // if (this.stale > staleValueForSleep)
+        //     _outputValue = Vector3.zero;
 
         foreach (Nucleus nucleus in this.nuclei)
             nucleus.UpdateNuclei();

Editor/ClusterInspector.cs

@@ -500,6 +500,7 @@ public class ClusterInspector : Editor {
         private bool showSynapses = true;
         private bool showActivation = true;
         protected bool breakOnWake = false;
+        protected bool trace = false;
         void DrawInspector(VisualElement inspectorContainer) {
             if (inspectorContainer == null)
                 return;
@@ -638,6 +639,9 @@ public class ClusterInspector : Editor {
                     if (this.currentNucleus.isSleeping == false)
                         Debug.Break();
                 }
+                trace = EditorGUILayout.Toggle("Trace", trace);
+                this.currentNucleus.trace = trace;
+
             });
 
             inspectorContainer.Add(container);

Nucleus.cs

@@ -31,6 +31,7 @@ public abstract class Nucleus {
     [NonSerialized]
     public int stale = 1000;
     public readonly int staleValueForSleep = 20;
+    public bool trace = false;
 
     public abstract Nucleus ShallowCloneTo(Cluster parent);
     public abstract Nucleus Clone(ClusterPrefab prefab);
@@ -101,6 +102,9 @@ public abstract class Nucleus {
     public abstract void UpdateStateIsolated();
 
     public virtual void UpdateNuclei() {
+        if (this.array == null || this.array.nuclei == null || this.array.nuclei.Length <= 1)
+            return;
+
         this.stale++;
         if (this.stale > staleValueForSleep) {
             //Debug.Log($"{this.name} goes to sleep, stale = {this.stale}");

NucleusArray.cs

@@ -127,7 +127,8 @@ public class NucleusArray {
 
         if (selectedReceiver is Neuron selectedNucleus)
             selectedNucleus.ProcessStimulus(inputValue);
-        selectedReceiver.parent.UpdateStateIsolated();
+        //selectedReceiver.parent.UpdateStateIsolated();
+        selectedReceiver.parent.UpdateFromNucleus(selectedReceiver);
     }
 
     private void CleanupReceivers() {