Carlos Ion Panel

Assets/Scripts/C2M2/CellData.cs

@@ -21,6 +21,10 @@ public class CellData
         public int refinementLevel;
         public double timeStep;
         public double endTime;
+        // Gating variable data
+        public GatingVariableData[] gates;
+        // Ion‐channel data
+        public ChannelData[] channels;
 
         // Clamp data
         [System.Serializable]
@@ -35,14 +39,22 @@ public struct ClampData
 
         // Simulation state
         public double[] U;
-        public double[] M;
-        public double[] N;
-        public double[] H;
-
         public double[] Upre;
-        public double[] Mpre;
-        public double[] Npre;
-        public double[] Hpre;
+
+        // Gating Variables
+        [System.Serializable]
+        public class GatingVariableData {
+            public string name;
+            public double[] current;
+            public double[] previous;
+        }
+
+        // Ion Channels
+        [System.Serializable]
+        public class ChannelData {
+            public string name;
+            public bool isActive;
+        }
 
         // Graph data
         [System.Serializable]

Assets/Scripts/C2M2/GameManager.cs

@@ -24,14 +24,10 @@ public class GameManager : MonoBehaviour
 
         // vectors used in SparseSolve; for loading
         public double[] U;
-        public double[] M;
-        public double[] N;
-        public double[] H;
-
         public double[] Upre;
-        public double[] Mpre;
-        public double[] Npre;
-        public double[] Hpre;
+        public Dictionary<string, double[]> currentStates;
+        public Dictionary<string, double[]> previousStates;
+
 
         // for loading a file
         private bool loading = false;

Assets/Scripts/C2M2/Menu.cs

@@ -2,6 +2,7 @@
 using System.Collections;
 using System.Collections.Generic;
 using System.IO;
+using System.Linq;
 using UnityEngine;
 using TMPro;
 
@@ -139,14 +140,34 @@ public void Save()
                     data = new CellData();
 
                     data.U = sim.Get1DValues(); // voltage at every node
-                    data.M = sim.getM(); // M vector
-                    data.N = sim.getN(); // N vector
-                    data.H = sim.getH(); // H vector
-
                     data.Upre = sim.getUpre(); // Upre vector
-                    data.Mpre = sim.getMpre(); // Mpre vector
-                    data.Npre = sim.getNpre(); // Npre vector
-                    data.Hpre = sim.getHpre(); // Hpre vector
+
+                    // Gating Variable Vectors
+                    var curr = sim.getCurrentStates();
+                    var prev = sim.getPreviousStates();
+
+                    var gatingVariableList = new List<CellData.GatingVariableData>();
+                    foreach (var kvp in curr)
+                    {
+                        gatingVariableList.Add(new CellData.GatingVariableData {
+                            name     = kvp.Key,
+                            current  = kvp.Value,
+                            previous = prev[kvp.Key],    // lookup by the same key
+                        });
+                    }
+
+                    data.gates = gatingVariableList.ToArray();
+
+                    // Save active ion channels
+                    var channelList = new List<CellData.ChannelData>();
+                    foreach (var channel in sim.ionChannels) {
+                        bool active = sim.activeIonChannels.Contains(channel);
+                        channelList.Add(new CellData.ChannelData{ 
+                            name = channel.Name,
+                            isActive = active
+                        });
+                    }
+                    data.channels = channelList.ToArray();
 
                     data.simID = sim.simID;
                     data.pos = sim.transform.position;
@@ -230,7 +251,7 @@ IEnumerator ShowSaveButton()
                 SaveButtonVisible(true);
         }
 
-        /// <summary>
+/// <summary>
         /// Load a file. Return true if successful.
         /// </summary>
         public bool Load(String f)
@@ -277,6 +298,7 @@ public bool Load(String f)
 
                 int ID = 0; // this will be the current ID when placing a new cell after loading
 
+
                 for (; i <= limit; i++)
                 {
                     // retrieve saved data
@@ -288,16 +310,23 @@ public bool Load(String f)
 
                     // restore vectors
                     gm.U = data.U;
-                    gm.M = data.M;
-                    gm.N = data.N;
-                    gm.H = data.H;
-
                     gm.Upre = data.Upre;
-                    gm.Mpre = data.Mpre;
-                    gm.Npre = data.Npre;
-                    gm.Hpre = data.Hpre;
+
+                    // Build Gating Variables and Ion Channels
+
+                    var currStates  = new Dictionary<string,double[]>();
+                    var prevStates = new Dictionary<string,double[]>();
+
+                    foreach(var g in data.gates) {
+                        currStates[g.name] = g.current;
+                        prevStates[g.name] = g.previous;
+                    }
+
+                    gm.currentStates = currStates;
+                    gm.previousStates = prevStates;
 
                     GameObject go;
+
                     try
                     {
                         go = loader.Load(new RaycastHit()); // load the cell
@@ -313,9 +342,20 @@ public bool Load(String f)
                         finishedLoading = true;
                         return false;
                     }
-
+                    
                     SparseSolverTestv1 sim = go.GetComponent<SparseSolverTestv1>();
 
+                    // 1) initialize ion channels (so sim.ionChannels is populated)
+                    sim.InitializeIonChannel();  
+                    // 2) clear active channels then enable/disable each one according to what was saved
+                    sim.activeIonChannels.Clear();
+                    // Load Ion Channels 
+                    foreach (var cd in data.channels) {
+                        // find the matching IonChannel object
+                        var match = sim.ionChannels.FirstOrDefault(ch => ch.Name == cd.name);
+                        if (match != null && cd.isActive) sim.activeIonChannels.Add(match);
+                    }
+
                     // restore cell ID
                     sim.simID = data.simID;
                     ID = sim.simID;
@@ -352,12 +392,16 @@ public bool Load(String f)
                         for (int j = 0; j < data.graphs.Length; j++)
                         {
                             var graphObj = Instantiate(graphPrefab);
+
                             NDLineGraph g = graphObj.GetComponent<NDLineGraph>();
                             g.ndgraph.FocusVert = data.graphs[j].vertex;
                             g.ndgraph.simulation = sim;
                             graphM.graphs.Add(g.ndgraph);
                             foreach (Vector3 v in data.graphs[j].positions)
+                            {
                                 g.positions.Add(v);
+
+                            }
                         }
                     }
 
@@ -385,7 +429,7 @@ public bool Load(String f)
                     }
                     syn = Instantiate(GameManager.instance.synapseManagerPrefab.GetComponent<SynapseManager>().synapsePrefab, ndsim.transform).GetComponentInChildren<Synapse>();
                     syn.AttachToSimulation(ndsim, synD.syns[j].synVert);
-                    syn.SwitchModel(synD.syns[j].model);
+                    // syn.SwitchModel(synD.syns[j].model);
                 }
 
                 finishedLoading = true; // this is for ChangeGradient

Assets/Scripts/C2M2/NeuronalDynamics/IonChannels/IonChannel.cs

@@ -0,0 +1,58 @@
+using System;
+using System.Collections.Generic;
+using Vector = MathNet.Numerics.LinearAlgebra.Vector<double>;
+namespace C2M2.NeuronalDynamics.Simulation
+{
+    public class GatingVariable
+    {
+        // Name of the gating variable (i.e: n, m, h)
+        public string Name { get; }
+
+        // Alpha and Beta functions for the gating variable
+        public Func<Vector, Vector> Alpha { get; }
+        public Func<Vector, Vector> Beta { get; }
+
+        public double Exponent { get; }
+
+        // Probability is the initial state probability for the gating variable
+        public double Probability { get; set; }
+
+        // New flag: if true, this gating variable is computed instantaneously. Default: set to false.
+        public bool IsInstant { get; set; }
+
+        public GatingVariable(string name, Func<Vector, Vector> alpha, Func<Vector, Vector> beta, double exponent, double probability, int nodeCount, bool isInstant = false)
+        {
+            Name = name;
+            Alpha = alpha;
+            Beta = beta;
+            Exponent = exponent;
+            Probability = probability;
+            IsInstant = isInstant;
+        }
+    }
+
+    public class IonChannel
+    {
+        public string Name { get; set; }                  // Name of the ion channel (e.g., K+ channel)
+        public double Conductance { get; set; }           // g (conductance)
+        public double ReversalPotential { get; set; }     // E (reversal potential)
+        public List<GatingVariable> GatingVariables { get; set; } // List of gating variables (can be dynamic)
+
+        public IonChannel(string name, double conductance, double reversalPotential)
+        {
+            Name = name;
+            Conductance = conductance;
+            ReversalPotential = reversalPotential;
+            GatingVariables = new List<GatingVariable>();
+        }
+        public void AddGatingVariable(GatingVariable gatingVariable)
+        {
+            GatingVariables.Add(gatingVariable);
+        }
+
+        public void RemoveGatingVariable(GatingVariable gatingVariable)
+        {
+            GatingVariables.Remove(gatingVariable);
+        }
+    }
+}