Synaptic delay entered in the junction definition overrides the gener…

…ic synaptic delay value.

SiliFish.UI/Controls/Model Edit/InterPoolControl.cs

@@ -264,8 +264,8 @@ public void SetInterPoolTemplate(List<CellPoolTemplate> pools, InterPoolTemplate
                 numMaxOutgoing.SetValue(interPoolTemplate.CellReach.MaxOutgoing);
 
                 numConductance.SetValue(interPoolTemplate.Weight);
-                numDelay.SetValue(interPoolTemplate.Delay_ms);
                 eFixedDuration.Text = interPoolTemplate.FixedDuration_ms?.ToString() ?? "";
+                eSynDelay.Text = interPoolTemplate.Delay_ms?.ToString() ?? "";
                 if (interPoolTemplate.SynapseParameters != null)
                 {
                     synapseControl.SetSynapseParameters(interPoolTemplate.SynapseParameters);
@@ -286,6 +286,9 @@ public InterPoolTemplate GetInterPoolTemplate()
             double? fixedDuration = null;
             if (!string.IsNullOrEmpty(eFixedDuration.Text) && double.TryParse(eFixedDuration.Text, out double fd))
                 fixedDuration = fd;
+            double? synDelay = null;
+            if (!string.IsNullOrEmpty(eSynDelay.Text) && double.TryParse(eSynDelay.Text, out double sd))
+                synDelay = sd;
             interPoolTemplate.CellReach = new CellReach
             {
                 Ascending = cbAscending.Checked,
@@ -303,8 +306,8 @@ public InterPoolTemplate GetInterPoolTemplate()
             interPoolTemplate.ConnectionType = ddConnectionType.SelectedItem != null ? (ConnectionType)ddConnectionType.SelectedItem : ConnectionType.NotSet;
             interPoolTemplate.DistanceMode = (DistanceMode)Enum.Parse(typeof(DistanceMode), ddDistanceMode.Text);
             interPoolTemplate.Weight = (double)numConductance.Value;
-            interPoolTemplate.Delay_ms = (double)numDelay.Value;
             interPoolTemplate.FixedDuration_ms = fixedDuration;
+            interPoolTemplate.Delay_ms = synDelay;
             interPoolTemplate.Name = eName.Text;
             interPoolTemplate.Description = eDescription.Text;
             interPoolTemplate.Probability = (double)numProbability.Value;

SiliFish.UI/Controls/Model Edit/JunctionControl.cs

@@ -153,8 +153,8 @@ public void SetJunction(JunctionBase junction, bool newJunc)
                 sourceCell = gapJunction.Cell1;
                 targetCell = gapJunction.Cell2;
                 numConductance.SetValue(gapJunction.Weight);
-                numDelay.SetValue(gapJunction.Delay_ms);
                 eFixedDuration.Text = gapJunction.FixedDuration_ms.ToString();
+                eSynDelay.Text = gapJunction.Delay_ms.ToString();
                 ddConnectionType.SelectedItem = ConnectionType.Gap;
             }
             else if (junction is ChemicalSynapse syn)
@@ -164,8 +164,8 @@ public void SetJunction(JunctionBase junction, bool newJunc)
                 ddConnectionType.SelectedItem = targetCell is MuscleCell ? ConnectionType.NMJ : ConnectionType.Synapse;
                 synapseControl.SetSynapseParameters(syn.SynapseParameters);
                 numConductance.SetValue(syn.Weight);
-                numDelay.SetValue(syn.Delay_ms);
                 eFixedDuration.Text = syn.FixedDuration_ms.ToString();
+                eSynDelay.Text = syn.Delay_ms.ToString();
             }
             if (this.junction != null)
             {
@@ -270,7 +270,9 @@ public List<JunctionBase> GetJunctions()
             double? fixedDuration = null;
             if (!string.IsNullOrEmpty(eFixedDuration.Text) && double.TryParse(eFixedDuration.Text, out double fd))
                 fixedDuration = fd;
-            double delay = (double)numDelay.Value;
+            double? delay = null;
+            if (!string.IsNullOrEmpty(eSynDelay.Text) && double.TryParse(eSynDelay.Text, out double sd))
+                delay = sd;
             double conductance = (double)numConductance.Value;
             DistanceMode distanceMode = (DistanceMode)Enum.Parse(typeof(DistanceMode), ddDistanceMode.Text);
             List<JunctionBase> junctions = new();

SiliFish.UI/SiliFish.UI.csproj

@@ -6,7 +6,7 @@
     <UseWindowsForms>true</UseWindowsForms>
     <ImplicitUsings>enable</ImplicitUsings>
 	<IncludeAllContentForSelfExtract>true</IncludeAllContentForSelfExtract>
-	<Version>2.5.1</Version>
+	<Version>2.5.2</Version>
 	<PackageIcon>fishbone2BlueBG.png</PackageIcon>
 	<ApplicationIcon>Resources\fishbone2BlueBG.ico</ApplicationIcon>
 	<SupportedOSPlatformVersion>7.0</SupportedOSPlatformVersion>

SiliFish/Definitions/GlobalSettings.cs

@@ -35,9 +35,7 @@ public class GlobalSettings
 
         public static bool SameYAxis = true;
         public static bool ShowZeroValues = true;
-
         public static int DefaultPlotWidth = 800;
-
         public static int DefaultPlotHeight = 200;
 
         public static int MaxNumberOfUnits = 100;

SiliFish/ModelUnits/Architecture/ModelSettings.cs

@@ -27,12 +27,16 @@ public class ModelSettings
         [Description("Default conduction velocity of currents between cells."),
             DisplayName("Conduction Velocity"),
             Category("Default Values")]
-        public double cv { get; set; } = 0.2; 
+        public double cv { get; set; } = 0.2;
 
         [Description("Default delay in chemical synapses."),
             DisplayName("Synaptic Delay"),
             Category("Default Values")]
-        public double syanptic_delay { get; set; } = 0.5; 
+        public double synaptic_delay { get; set; } = 0.5;
+        [Description("Default delay in electrical junctions."),
+            DisplayName("Gap Junction Delay"),
+            Category("Default Values")]
+        public double gap_delay { get; set; } = 0;
 
         [Description("Default reversal potential of glutamate."),
             Category("Default Values")]

SiliFish/ModelUnits/Cells/CellPool.cs

@@ -419,7 +419,7 @@ public void ReachToCellPoolViaGapJunction(CellPool target,
             double weight,
             double probability, 
             DistanceMode distanceMode,
-            double delay_ms,
+            double? delay_ms,
             double? fixedduration_ms)
         {
             int maxIncoming = reach.MaxIncoming;
@@ -476,7 +476,7 @@ public void ReachToCellPoolViaChemSynapse(CellPool target,
             double weight,
             double probability, 
             DistanceMode distanceMode, 
-            double delay_ms,
+            double? delay_ms,
             double? fixedduration_ms)
         {
             int maxIncoming = reach.MaxIncoming;

SiliFish/ModelUnits/Junction/ChemicalSynapse.cs

@@ -89,7 +89,8 @@ public override void ImportValues(List<string> values)
                 Core.Conductance = Weight;
                 if (double.TryParse(values[iter++], out double d))
                     FixedDuration_ms = d;
-                Delay_ms = double.Parse(values[iter++]);
+                if (double.TryParse(values[iter++], out double dd))
+                    Delay_ms = dd;
                 Active = bool.Parse(values[iter++]);
                 if (iter < values.Count)
                     TimeLine_ms.ImportValues(new[] { values[iter++] }.ToList());
@@ -186,8 +187,8 @@ public override void InitForSimulation(int nmax, bool trackCurrent)
             else
             {
                 double distance = Util.Distance(PreNeuron.Coordinate, PostCell.Coordinate, DistanceMode);
-                int delay = (int)((Delay_ms + model.Settings.syanptic_delay) / model.RunParam.DeltaT);
-                duration = Math.Max((int)(distance / (PreNeuron.ConductionVelocity * model.RunParam.DeltaT)), 1);
+                int delay = (int)((Delay_ms ?? model.Settings.synaptic_delay) / model.RunParam.DeltaT);
+                duration = Math.Max((int)Math.Round(distance / (PreNeuron.ConductionVelocity * model.RunParam.DeltaT)), 1);
                 duration += delay;
             }
         }
@@ -196,7 +197,7 @@ public void SetFixedDuration(double dur)
         {
             FixedDuration_ms = dur;
         }
-        public void SetDelay(double delay)
+        public void SetDelay(double? delay)
         {
             Delay_ms = delay;
         }