Bring rhs2116 up to date with main and gateware 0.3

- Stimulus trigger device accepts a delay in microsends to the applicatin of a stimulus - Mark CheckLinkStatus as virtual so headstage can be reset between power cycles (see #120) - Rebase main and take advantage of latest improvments with respect to port voltage override
open-ephys · Jun 28, 2024 · 203054b · 203054b
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diff --git a/Bonsai/Bonsai.config b/Bonsai/Bonsai.config
@@ -1,23 +1,26 @@
 <?xml version="1.0" encoding="utf-8"?>
 <PackageConfiguration xmlns:xsd="http://www.w3.org/2001/XMLSchema" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
   <Packages>
-    <Package id="Bonsai" version="2.8.1" />
-    <Package id="Bonsai.Core" version="2.8.1" />
-    <Package id="Bonsai.Design" version="2.8.0" />
+    <Package id="Bonsai" version="2.8.3" />
+    <Package id="Bonsai.Core" version="2.8.2" />
+    <Package id="Bonsai.Design" version="2.8.1" />
     <Package id="Bonsai.Design.Visualizers" version="2.8.0" />
     <Package id="Bonsai.Dsp" version="2.8.0" />
     <Package id="Bonsai.Dsp.Design" version="2.8.0" />
-    <Package id="Bonsai.Editor" version="2.8.0" />
+    <Package id="Bonsai.Editor" version="2.8.2" />
     <Package id="Bonsai.Scripting.Expressions" version="2.8.0" />
     <Package id="Bonsai.Scripting.Expressions.Design" version="2.8.0" />
     <Package id="Bonsai.System" version="2.8.0" />
     <Package id="Bonsai.System.Design" version="2.8.0" />
     <Package id="Bonsai.Vision" version="2.8.0" />
     <Package id="Bonsai.Vision.Design" version="2.8.0" />
+    <Package id="Bonsai.Windows.Input" version="2.7.0" />
     <Package id="jacobslusser.ScintillaNET" version="3.6.3" />
     <Package id="Markdig" version="0.18.1" />
+    <Package id="MathNet.Numerics" version="5.0.0" />
     <Package id="Microsoft.Web.WebView2" version="1.0.1823.32" />
     <Package id="OpenCV.Net" version="3.4.2" />
+    <Package id="OpenEphys.PhaseDetector" version="0.6.0" />
     <Package id="OpenTK" version="3.1.0" />
     <Package id="OpenTK.GLControl" version="3.1.0" />
     <Package id="Rx-Core" version="2.2.5" />
@@ -43,26 +46,31 @@
     <AssemblyReference assemblyName="Bonsai.System.Design" />
     <AssemblyReference assemblyName="Bonsai.Vision" />
     <AssemblyReference assemblyName="Bonsai.Vision.Design" />
+    <AssemblyReference assemblyName="Bonsai.Windows.Input" />
+    <AssemblyReference assemblyName="OpenEphys.PhaseDetector" />
   </AssemblyReferences>
   <AssemblyLocations>
-    <AssemblyLocation assemblyName="Bonsai" processorArchitecture="MSIL" location="Packages\Bonsai.2.8.1\lib\net48\Bonsai.exe" />
-    <AssemblyLocation assemblyName="Bonsai.Core" processorArchitecture="MSIL" location="Packages\Bonsai.Core.2.8.1\lib\net462\Bonsai.Core.dll" />
-    <AssemblyLocation assemblyName="Bonsai.Design" processorArchitecture="MSIL" location="Packages\Bonsai.Design.2.8.0\lib\net462\Bonsai.Design.dll" />
+    <AssemblyLocation assemblyName="Bonsai" processorArchitecture="MSIL" location="Packages\Bonsai.2.8.3\lib\net48\Bonsai.exe" />
+    <AssemblyLocation assemblyName="Bonsai.Core" processorArchitecture="MSIL" location="Packages\Bonsai.Core.2.8.2\lib\net462\Bonsai.Core.dll" />
+    <AssemblyLocation assemblyName="Bonsai.Design" processorArchitecture="MSIL" location="Packages\Bonsai.Design.2.8.1\lib\net462\Bonsai.Design.dll" />
     <AssemblyLocation assemblyName="Bonsai.Design.Visualizers" processorArchitecture="MSIL" location="Packages\Bonsai.Design.Visualizers.2.8.0\lib\net462\Bonsai.Design.Visualizers.dll" />
     <AssemblyLocation assemblyName="Bonsai.Dsp" processorArchitecture="MSIL" location="Packages\Bonsai.Dsp.2.8.0\lib\net462\Bonsai.Dsp.dll" />
     <AssemblyLocation assemblyName="Bonsai.Dsp.Design" processorArchitecture="MSIL" location="Packages\Bonsai.Dsp.Design.2.8.0\lib\net462\Bonsai.Dsp.Design.dll" />
-    <AssemblyLocation assemblyName="Bonsai.Editor" processorArchitecture="MSIL" location="Packages\Bonsai.Editor.2.8.0\lib\net472\Bonsai.Editor.dll" />
+    <AssemblyLocation assemblyName="Bonsai.Editor" processorArchitecture="MSIL" location="Packages\Bonsai.Editor.2.8.2\lib\net472\Bonsai.Editor.dll" />
     <AssemblyLocation assemblyName="Bonsai.Scripting.Expressions" processorArchitecture="MSIL" location="Packages\Bonsai.Scripting.Expressions.2.8.0\lib\net462\Bonsai.Scripting.Expressions.dll" />
     <AssemblyLocation assemblyName="Bonsai.Scripting.Expressions.Design" processorArchitecture="MSIL" location="Packages\Bonsai.Scripting.Expressions.Design.2.8.0\lib\net462\Bonsai.Scripting.Expressions.Design.dll" />
     <AssemblyLocation assemblyName="Bonsai.System" processorArchitecture="MSIL" location="Packages\Bonsai.System.2.8.0\lib\net462\Bonsai.System.dll" />
     <AssemblyLocation assemblyName="Bonsai.System.Design" processorArchitecture="MSIL" location="Packages\Bonsai.System.Design.2.8.0\lib\net462\Bonsai.System.Design.dll" />
     <AssemblyLocation assemblyName="Bonsai.Vision" processorArchitecture="MSIL" location="Packages\Bonsai.Vision.2.8.0\lib\net462\Bonsai.Vision.dll" />
     <AssemblyLocation assemblyName="Bonsai.Vision.Design" processorArchitecture="MSIL" location="Packages\Bonsai.Vision.Design.2.8.0\lib\net462\Bonsai.Vision.Design.dll" />
+    <AssemblyLocation assemblyName="Bonsai.Windows.Input" processorArchitecture="MSIL" location="Packages\Bonsai.Windows.Input.2.7.0\lib\net462\Bonsai.Windows.Input.dll" />
     <AssemblyLocation assemblyName="Markdig" processorArchitecture="MSIL" location="Packages\Markdig.0.18.1\lib\net40\Markdig.dll" />
+    <AssemblyLocation assemblyName="MathNet.Numerics" processorArchitecture="MSIL" location="Packages\MathNet.Numerics.5.0.0\lib\net48\MathNet.Numerics.dll" />
     <AssemblyLocation assemblyName="Microsoft.Web.WebView2.Core" processorArchitecture="MSIL" location="Packages\Microsoft.Web.WebView2.1.0.1823.32\lib\net45\Microsoft.Web.WebView2.Core.dll" />
     <AssemblyLocation assemblyName="Microsoft.Web.WebView2.WinForms" processorArchitecture="MSIL" location="Packages\Microsoft.Web.WebView2.1.0.1823.32\lib\net45\Microsoft.Web.WebView2.WinForms.dll" />
     <AssemblyLocation assemblyName="Microsoft.Web.WebView2.Wpf" processorArchitecture="MSIL" location="Packages\Microsoft.Web.WebView2.1.0.1823.32\lib\net45\Microsoft.Web.WebView2.Wpf.dll" />
     <AssemblyLocation assemblyName="OpenCV.Net" processorArchitecture="MSIL" location="Packages\OpenCV.Net.3.4.2\lib\net462\OpenCV.Net.dll" />
+    <AssemblyLocation assemblyName="OpenEphys.PhaseDetector" processorArchitecture="MSIL" location="Packages\OpenEphys.PhaseDetector.0.6.0\lib\net472\OpenEphys.PhaseDetector.dll" />
     <AssemblyLocation assemblyName="OpenTK" processorArchitecture="MSIL" location="Packages\OpenTK.3.1.0\lib\net20\OpenTK.dll" />
     <AssemblyLocation assemblyName="OpenTK.GLControl" processorArchitecture="MSIL" location="Packages\OpenTK.GLControl.3.1.0\lib\net20\OpenTK.GLControl.dll" />
     <AssemblyLocation assemblyName="ScintillaNET" processorArchitecture="MSIL" location="Packages\jacobslusser.ScintillaNET.3.6.3\lib\net40\ScintillaNET.dll" />

diff --git a/OpenEphys.Onix/OpenEphys.Onix.Design/OpenEphys.Onix.Design.csproj b/OpenEphys.Onix/OpenEphys.Onix.Design/OpenEphys.Onix.Design.csproj
@@ -10,7 +10,7 @@
   </PropertyGroup>
 
   <ItemGroup>
-    <PackageReference Include="Bonsai.Core" Version="2.8.0" />
+    <PackageReference Include="Bonsai.Core" Version="2.8.2" />
   </ItemGroup>
 
   <ItemGroup>

diff --git a/OpenEphys.Onix/OpenEphys.Onix/ConfigureFmcLinkController.cs b/OpenEphys.Onix/OpenEphys.Onix/ConfigureFmcLinkController.cs
@@ -21,7 +21,7 @@ public ConfigureFmcLinkController()
                      "Consult the device datasheet and documentation for allowable voltage ranges.")]
         public double? PortVoltage { get; set; } = null;
 
-        protected bool CheckLinkState(DeviceContext device)
+        protected virtual bool CheckLinkState(DeviceContext device)
         {
             var linkState = device.ReadRegister(FmcLinkController.LINKSTATE);
             return (linkState & FmcLinkController.LINKSTATE_SL) != 0;

diff --git a/OpenEphys.Onix/OpenEphys.Onix/ConfigureHeadstageRhs2116.cs b/OpenEphys.Onix/OpenEphys.Onix/ConfigureHeadstageRhs2116.cs
@@ -31,12 +31,12 @@ public ConfigureHeadstageRhs2116()
         [TypeConverter(typeof(HubDeviceConverter))]
         public ConfigureRhs2116Trigger StimulusTrigger { get; set; } = new();
 
-        internal override void UpdateDeviceNames(string hubName)
+        internal override void UpdateDeviceNames()
         {
-            LinkController.DeviceName = $"{hubName}/{nameof(LinkController)}";
-            Rhs2116A.DeviceName = $"{hubName}/{nameof(Rhs2116A)}";
-            Rhs2116B.DeviceName = $"{hubName}/{nameof(Rhs2116B)}";
-            StimulusTrigger.DeviceName = $"{hubName}/{nameof(StimulusTrigger)}";
+            LinkController.DeviceName = GetFullDeviceName(nameof(LinkController));
+            Rhs2116A.DeviceName = GetFullDeviceName(nameof(Rhs2116A));
+            Rhs2116B.DeviceName = GetFullDeviceName(nameof(Rhs2116B));
+            StimulusTrigger.DeviceName = GetFullDeviceName(nameof(StimulusTrigger));
         }
 
         public PortName Port
@@ -53,6 +53,16 @@ public PortName Port
             }
         }
 
+
+        [Description("If defined, it will override automated voltage discovery and apply the specified voltage" +
+                     "to the headstage. Warning: this device requires 3.4V to 4.4V for proper operation." +
+                     "Supplying higher voltages may result in damage to the headstage.")]
+        public double? PortVoltage
+        {
+            get => LinkController.PortVoltage;
+            set => LinkController.PortVoltage = value;
+        }
+
         internal override IEnumerable<IDeviceConfiguration> GetDevices()
         {
             yield return LinkController;
@@ -65,40 +75,38 @@ class ConfigureHeadstageRhs2116LinkController : ConfigureFmcLinkController
         {
             protected override bool ConfigurePortVoltage(DeviceContext device)
             {
-                const uint MinVoltage = 33;
-                const uint MaxVoltage = 50;
-                const uint VoltageOffset = 25;
-                const uint VoltageIncrement = 02;
+                const double MinVoltage = 3.3;
+                const double MaxVoltage = 4.4;
+                const double VoltageOffset = 2.0;
+                const double VoltageIncrement = 0.2;
 
-                for (uint voltage = MinVoltage; voltage <= MaxVoltage; voltage += VoltageIncrement)
+                for (var voltage = MinVoltage; voltage <= MaxVoltage; voltage += VoltageIncrement)
                 {
                     SetPortVoltage(device, voltage);
-                    if (CheckLinkState(device))
+                    if (base.CheckLinkState(device))
                     {
                         SetPortVoltage(device, voltage + VoltageOffset);
-                        if (CheckLinkState(device))
-                        {
-                            // TODO: The RHS2116 headstage needs an additional reset after power on
-                            // to provide its device table.
-                            Thread.Sleep(500);
-                            device.Context.Reset();
-                            return true;
-                        }
-                        else break;
+                        return CheckLinkState(device);
                     }
                 }
 
                 return false;
             }
 
-            private void SetPortVoltage(DeviceContext device, uint voltage)
+            private void SetPortVoltage(DeviceContext device, double voltage)
             {
-                const int WaitUntilVoltageOffSettles = 500;
-                const int WaitUntilVoltageOnSettles = 500;
                 device.WriteRegister(FmcLinkController.PORTVOLTAGE, 0);
-                Thread.Sleep(WaitUntilVoltageOffSettles);
-                device.WriteRegister(FmcLinkController.PORTVOLTAGE, voltage);
-                Thread.Sleep(WaitUntilVoltageOnSettles);
+                Thread.Sleep(500);
+                device.WriteRegister(FmcLinkController.PORTVOLTAGE, (uint)(10 * voltage));
+                Thread.Sleep(500);
+            }
+
+            protected override bool CheckLinkState(DeviceContext device)
+            {
+                // NB: The RHS2116 headstage needs an additional reset after power on to provide its device table.
+                device.Context.Reset();
+                var linkState = device.ReadRegister(FmcLinkController.LINKSTATE);
+                return (linkState & FmcLinkController.LINKSTATE_SL) != 0;
             }
         }
     }

diff --git a/OpenEphys.Onix/OpenEphys.Onix/ConfigureRhs2116.cs b/OpenEphys.Onix/OpenEphys.Onix/ConfigureRhs2116.cs
@@ -172,6 +172,7 @@ static class Rhs2116
         // constants
         public const int AmplifierChannelCount = 16;
         public const int StimMemorySlotsAvailable = 1024;
+        public const double SampleFrequencyHz = 30.1932367151e3;
 
         // managed registers
         public const uint ENABLE = 0x8000; // Enable or disable the data output stream (32767)

diff --git a/OpenEphys.Onix/OpenEphys.Onix/OpenEphys.Onix.csproj b/OpenEphys.Onix/OpenEphys.Onix/OpenEphys.Onix.csproj
@@ -11,7 +11,7 @@
   </PropertyGroup>
 
   <ItemGroup>
-    <PackageReference Include="Bonsai.Core" Version="2.8.0" />
+    <PackageReference Include="Bonsai.Core" Version="2.8.2" />
     <PackageReference Include="clroni" Version="6.1.0" />
     <PackageReference Include="OpenCV.Net" Version="3.4.2" />
   </ItemGroup>

diff --git a/OpenEphys.Onix/OpenEphys.Onix/Rhs2116Data.cs b/OpenEphys.Onix/OpenEphys.Onix/Rhs2116Data.cs
@@ -41,8 +41,8 @@ public unsafe override IObservable<Rhs2116DataFrame> Generate()
                                 clockBuffer[sampleIndex] = frame.Clock;
                                 if (++sampleIndex >= bufferSize)
                                 {
-                                    var amplifierData = BufferHelper.CopyBuffer(amplifierBuffer, bufferSize, Rhs2116.AmplifierChannelCount, Depth.U16);
-                                    var dcData = BufferHelper.CopyBuffer(dcBuffer, bufferSize, Rhs2116.AmplifierChannelCount, Depth.U16);
+                                    var amplifierData = BufferHelper.CopyTranspose(amplifierBuffer, bufferSize, Rhs2116.AmplifierChannelCount, Depth.U16);
+                                    var dcData = BufferHelper.CopyTranspose(dcBuffer, bufferSize, Rhs2116.AmplifierChannelCount, Depth.U16);
                                     observer.OnNext(new Rhs2116DataFrame(clockBuffer, hubClockBuffer, amplifierData, dcData));
                                     hubClockBuffer = new ulong[bufferSize];
                                     clockBuffer = new ulong[bufferSize];

diff --git a/OpenEphys.Onix/OpenEphys.Onix/Rhs2116StimulusTrigger.cs b/OpenEphys.Onix/OpenEphys.Onix/Rhs2116StimulusTrigger.cs
@@ -6,19 +6,25 @@
 
 namespace OpenEphys.Onix
 {
-    public class Rhs2116StimulusTrigger : Sink<bool>
+    public class Rhs2116StimulusTrigger : Sink<double>
     {
         [TypeConverter(typeof(Rhs2116Trigger.NameConverter))]
         public string DeviceName { get; set; }
 
-        public override IObservable<bool> Process(IObservable<bool> source)
+        public override IObservable<double> Process(IObservable<double> source)
         {
             return Observable.Using(
                 () => DeviceManager.ReserveDevice(DeviceName),
                 disposable => disposable.Subject.SelectMany(deviceInfo =>
                 {
-                    var device = deviceInfo.GetDeviceContext(typeof(Rhs2116Trigger));
-                    return source.Do(t => device.WriteRegister(Rhs2116Trigger.TRIGGER, t ? 1u : 0u));
+                var device = deviceInfo.GetDeviceContext(typeof(Rhs2116Trigger));
+                    return source.Do(t =>
+                    {
+                        const double SampleFrequencyMegaHz = Rhs2116.SampleFrequencyHz / 1e6;
+                        var delaySamples = (int)(t * SampleFrequencyMegaHz);
+                        device.WriteRegister(Rhs2116Trigger.TRIGGER, (uint)(delaySamples << 12 | 0x1));
+                    });
+
                 }));
         }
     }