Clean up submodule and add remarks

- Add remarks for ProbeConfiguration variables - Add Category attributes to Neuropixels properties - Remove submodule and reference OpenEphys.ProbeInterface directly from NuGet - Remove AnyCPU options
open-ephys · Aug 14, 2024 · 35b02e4 · 35b02e4
1 parent a5aff1b
commit 35b02e4
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Showing 11 changed files with 36 additions and 43 deletions.
diff --git a/.gitmodules b/.gitmodules
@@ -1,3 +0,0 @@
-[submodule "OpenEphys.ProbeInterface"]
-	path = OpenEphys.ProbeInterface
-	url = https://github.com/open-ephys/OpenEphys.ProbeInterface

diff --git a/OpenEphys.Onix1.Design/ChannelConfigurationDialog.cs b/OpenEphys.Onix1.Design/ChannelConfigurationDialog.cs
@@ -4,7 +4,7 @@
 using System.Windows.Forms;
 using ZedGraph;
 using System;
-using OpenEphys.ProbeInterface;
+using OpenEphys.ProbeInterface.NET;
 using System.Collections.Generic;
 
 namespace OpenEphys.Onix1.Design
@@ -19,7 +19,7 @@ public abstract partial class ChannelConfigurationDialog : Form
         /// <summary>
         /// Local variable that holds the channel configuration in memory until the user presses Okay
         /// </summary>
-        ProbeGroup ChannelConfiguration;
+        internal ProbeGroup ChannelConfiguration;
 
         internal readonly List<int> ReferenceContacts = new();
 

diff --git a/OpenEphys.Onix1.Design/NeuropixelsV2eChannelConfigurationDialog.cs b/OpenEphys.Onix1.Design/NeuropixelsV2eChannelConfigurationDialog.cs
@@ -3,7 +3,7 @@
 using System.Drawing;
 using System.Linq;
 using System.Windows.Forms;
-using OpenEphys.ProbeInterface;
+using OpenEphys.ProbeInterface.NET;
 using ZedGraph;
 
 namespace OpenEphys.Onix1.Design
@@ -57,6 +57,10 @@ internal override ProbeGroup DefaultChannelLayout()
         internal override void LoadDefaultChannelLayout()
         {
             ProbeConfiguration = new(ProbeConfiguration.Probe, ProbeConfiguration.Reference);
+            ChannelConfiguration = ProbeConfiguration.ChannelConfiguration;
+
+            DrawProbeGroup();
+            RefreshZedGraph();
 
             OnFileOpenHandler();
         }

diff --git a/OpenEphys.Onix1.Design/OpenEphys.Onix1.Design.csproj b/OpenEphys.Onix1.Design/OpenEphys.Onix1.Design.csproj
@@ -11,14 +11,14 @@
   </PropertyGroup>
 
   <ItemGroup>
-    <PackageReference Include="Bonsai.Design" Version="2.8.1" />
+    <PackageReference Include="Bonsai.Design" Version="2.8.5" />
     <PackageReference Include="Newtonsoft.Json" Version="13.0.3" />
+    <PackageReference Include="OpenEphys.ProbeInterface.NET" Version="0.1.0" />
     <PackageReference Include="ZedGraph" Version="5.1.7" />
   </ItemGroup>
 
   <ItemGroup>
     <ProjectReference Include="..\OpenEphys.Onix1\OpenEphys.Onix1.csproj" />
-    <ProjectReference Include="..\OpenEphys.ProbeInterface\OpenEphys.ProbeInterface\OpenEphys.ProbeInterface.csproj" />
   </ItemGroup>
 
   <ItemGroup>

diff --git a/OpenEphys.Onix1.sln b/OpenEphys.Onix1.sln
@@ -12,40 +12,20 @@ Project("{2150E333-8FDC-42A3-9474-1A3956D46DE8}") = "Solution Items", "Solution
 		Directory.Build.props = Directory.Build.props
 	EndProjectSection
 EndProject
-Project("{9A19103F-16F7-4668-BE54-9A1E7A4F7556}") = "OpenEphys.ProbeInterface", "OpenEphys.ProbeInterface\OpenEphys.ProbeInterface\OpenEphys.ProbeInterface.csproj", "{CDC8058A-48DD-49FE-BFC8-9F12F353D29D}"
-EndProject
 Global
 	GlobalSection(SolutionConfigurationPlatforms) = preSolution
-		Debug|Any CPU = Debug|Any CPU
 		Debug|x64 = Debug|x64
-		Release|Any CPU = Release|Any CPU
 		Release|x64 = Release|x64
 	EndGlobalSection
 	GlobalSection(ProjectConfigurationPlatforms) = postSolution
-		{353B1EBC-F8EB-4D99-8331-9FF15EC17F38}.Debug|Any CPU.ActiveCfg = Debug|x64
-		{353B1EBC-F8EB-4D99-8331-9FF15EC17F38}.Debug|Any CPU.Build.0 = Debug|x64
 		{353B1EBC-F8EB-4D99-8331-9FF15EC17F38}.Debug|x64.ActiveCfg = Debug|x64
 		{353B1EBC-F8EB-4D99-8331-9FF15EC17F38}.Debug|x64.Build.0 = Debug|x64
-		{353B1EBC-F8EB-4D99-8331-9FF15EC17F38}.Release|Any CPU.ActiveCfg = Release|x64
-		{353B1EBC-F8EB-4D99-8331-9FF15EC17F38}.Release|Any CPU.Build.0 = Release|x64
 		{353B1EBC-F8EB-4D99-8331-9FF15EC17F38}.Release|x64.ActiveCfg = Release|x64
 		{353B1EBC-F8EB-4D99-8331-9FF15EC17F38}.Release|x64.Build.0 = Release|x64
-		{149E86EC-B865-463D-81A8-8290CA7F8871}.Debug|Any CPU.ActiveCfg = Debug|x64
-		{149E86EC-B865-463D-81A8-8290CA7F8871}.Debug|Any CPU.Build.0 = Debug|x64
 		{149E86EC-B865-463D-81A8-8290CA7F8871}.Debug|x64.ActiveCfg = Debug|x64
 		{149E86EC-B865-463D-81A8-8290CA7F8871}.Debug|x64.Build.0 = Debug|x64
-		{149E86EC-B865-463D-81A8-8290CA7F8871}.Release|Any CPU.ActiveCfg = Release|x64
-		{149E86EC-B865-463D-81A8-8290CA7F8871}.Release|Any CPU.Build.0 = Release|x64
 		{149E86EC-B865-463D-81A8-8290CA7F8871}.Release|x64.ActiveCfg = Release|x64
 		{149E86EC-B865-463D-81A8-8290CA7F8871}.Release|x64.Build.0 = Release|x64
-		{CDC8058A-48DD-49FE-BFC8-9F12F353D29D}.Debug|Any CPU.ActiveCfg = Debug|Any CPU
-		{CDC8058A-48DD-49FE-BFC8-9F12F353D29D}.Debug|Any CPU.Build.0 = Debug|Any CPU
-		{CDC8058A-48DD-49FE-BFC8-9F12F353D29D}.Debug|x64.ActiveCfg = Debug|Any CPU
-		{CDC8058A-48DD-49FE-BFC8-9F12F353D29D}.Debug|x64.Build.0 = Debug|Any CPU
-		{CDC8058A-48DD-49FE-BFC8-9F12F353D29D}.Release|Any CPU.ActiveCfg = Release|Any CPU
-		{CDC8058A-48DD-49FE-BFC8-9F12F353D29D}.Release|Any CPU.Build.0 = Release|Any CPU
-		{CDC8058A-48DD-49FE-BFC8-9F12F353D29D}.Release|x64.ActiveCfg = Release|Any CPU
-		{CDC8058A-48DD-49FE-BFC8-9F12F353D29D}.Release|x64.Build.0 = Release|Any CPU
 	EndGlobalSection
 	GlobalSection(SolutionProperties) = preSolution
 		HideSolutionNode = FALSE

diff --git a/OpenEphys.Onix1/ConfigureNeuropixelsV2e.cs b/OpenEphys.Onix1/ConfigureNeuropixelsV2e.cs
@@ -51,6 +51,12 @@ public ConfigureNeuropixelsV2e(ConfigureNeuropixelsV2e configureNode)
         /// <summary>
         /// Gets or sets the electrode configuration for Probe A.
         /// </summary>
+        /// <remarks>
+        /// Configuration is accomplished using a GUI to aid in channel selection and relevant configuration properties.
+        /// To open a probe configuration GUI, select the ellipses next the <see cref="ProbeConfigurationA"/> variable
+        /// in the property pane, or double-click <see cref="ConfigureNeuropixelsV2eHeadstage"/> to configure both
+        /// probes and the <see cref="ConfigureNeuropixelsV2eBno055"/> simultaneously.
+        /// </remarks>
         [Category(ConfigurationCategory)]
         [Description("Probe A electrode configuration.")]
         [Editor("OpenEphys.Onix1.Design.NeuropixelsV2eProbeConfigurationEditor, OpenEphys.Onix1.Design", typeof(UITypeEditor))]
@@ -63,6 +69,7 @@ public ConfigureNeuropixelsV2e(ConfigureNeuropixelsV2e configureNode)
         /// Each probe must be provided with a gain calibration file that contains calibration data
         /// specific to each probe. This file is mandatory for accurate recordings.
         /// </remarks>
+        [Category(ConfigurationCategory)]
         [FileNameFilter("Gain calibration files (*_gainCalValues.csv)|*_gainCalValues.csv")]
         [Description("Path to the gain calibration file for probe A.")]
         [Editor("Bonsai.Design.OpenFileNameEditor, Bonsai.Design", DesignTypes.UITypeEditor)]
@@ -71,6 +78,12 @@ public ConfigureNeuropixelsV2e(ConfigureNeuropixelsV2e configureNode)
         /// <summary>
         /// Gets or sets the electrode configuration for Probe B.
         /// </summary>
+        /// <remarks>
+        /// Configuration is accomplished using a GUI to aid in channel selection and relevant configuration properties.
+        /// To open a probe configuration GUI, select the ellipses next the <see cref="ProbeConfigurationB"/> variable
+        /// in the property pane, or double-click <see cref="ConfigureNeuropixelsV2eHeadstage"/> to configure both
+        /// probes and the <see cref="ConfigureNeuropixelsV2eBno055"/> simultaneously.
+        /// </remarks>
         [Category(ConfigurationCategory)]
         [Description("Probe B electrode configuration.")]
         [Editor("OpenEphys.Onix1.Design.NeuropixelsV2eProbeConfigurationEditor, OpenEphys.Onix1.Design", typeof(UITypeEditor))]
@@ -83,6 +96,7 @@ public ConfigureNeuropixelsV2e(ConfigureNeuropixelsV2e configureNode)
         /// Each probe must be provided with a gain calibration file that contains calibration data
         /// specific to each probe. This file is mandatory for accurate recordings.
         /// </remarks>
+        [Category(ConfigurationCategory)]
         [FileNameFilter("Gain calibration files (*_gainCalValues.csv)|*_gainCalValues.csv")]
         [Description("Path to the gain calibration file for probe B.")]
         [Editor("Bonsai.Design.OpenFileNameEditor, Bonsai.Design", DesignTypes.UITypeEditor)]

diff --git a/OpenEphys.Onix1/ConfigureNeuropixelsV2eBeta.cs b/OpenEphys.Onix1/ConfigureNeuropixelsV2eBeta.cs
@@ -54,6 +54,7 @@ public ConfigureNeuropixelsV2eBeta()
         /// Each probe must be provided with a gain calibration file that contains calibration data
         /// specific to each probe. This file is mandatory for accurate recordings.
         /// </remarks>
+        [Category(ConfigurationCategory)]
         [FileNameFilter("Gain calibration files (*_gainCalValues.csv)|*_gainCalValues.csv")]
         [Description("Path to the gain calibration file for probe A.")]
         [Editor("Bonsai.Design.OpenFileNameEditor, Bonsai.Design", DesignTypes.UITypeEditor)]
@@ -73,6 +74,7 @@ public ConfigureNeuropixelsV2eBeta()
         /// Each probe must be provided with a gain calibration file that contains calibration data
         /// specific to each probe. This file is mandatory for accurate recordings.
         /// </remarks>
+        [Category(ConfigurationCategory)]
         [FileNameFilter("Gain calibration files (*_gainCalValues.csv)|*_gainCalValues.csv")]
         [Description("Path to the gain calibration file for probe B.")]
         [Editor("Bonsai.Design.OpenFileNameEditor, Bonsai.Design", DesignTypes.UITypeEditor)]

diff --git a/OpenEphys.Onix1/NeuropixelsV2.cs b/OpenEphys.Onix1/NeuropixelsV2.cs
@@ -39,10 +39,10 @@ internal static BitArray[] GenerateShankBits(NeuropixelsV2QuadShankProbeConfigur
         {
             BitArray[] shankBits =
             {
-                new(NeuropixelsV2.RegistersPerShank, false),
-                new(NeuropixelsV2.RegistersPerShank, false),
-                new(NeuropixelsV2.RegistersPerShank, false),
-                new(NeuropixelsV2.RegistersPerShank, false)
+                new(RegistersPerShank, false),
+                new(RegistersPerShank, false),
+                new(RegistersPerShank, false),
+                new(RegistersPerShank, false)
             };
 
 
@@ -69,7 +69,7 @@ internal static BitArray[] GenerateShankBits(NeuropixelsV2QuadShankProbeConfigur
                 shankBits[3][1285] = true;
             }
 
-            const int PixelOffset = (NeuropixelsV2.ElectrodePerShank - 1) / 2;
+            const int PixelOffset = (ElectrodePerShank - 1) / 2;
             const int ReferencePixelOffset = 3;
             foreach (var c in probe.ChannelMap)
             {
@@ -89,8 +89,8 @@ internal static BitArray[] GenerateBaseBits(NeuropixelsV2QuadShankProbeConfigura
         {
             BitArray[] baseBits =
             {
-                new(NeuropixelsV2.ChannelCount * NeuropixelsV2.BaseBitsPerChannel / 2, false),
-                new(NeuropixelsV2.ChannelCount * NeuropixelsV2.BaseBitsPerChannel / 2, false)
+                new(ChannelCount * BaseBitsPerChannel / 2, false),
+                new(ChannelCount * BaseBitsPerChannel / 2, false)
             };
 
             var referenceBit = probe.Reference switch
@@ -103,10 +103,10 @@ internal static BitArray[] GenerateBaseBits(NeuropixelsV2QuadShankProbeConfigura
                 _ => throw new InvalidOperationException("Invalid reference selection."),
             };
 
-            for (int i = 0; i < NeuropixelsV2.ChannelCount; i++)
+            for (int i = 0; i < ChannelCount; i++)
             {
                 var configIndex = i % 2;
-                var bitOffset = (382 - i + configIndex) / 2 * NeuropixelsV2.BaseBitsPerChannel;
+                var bitOffset = (382 - i + configIndex) / 2 * BaseBitsPerChannel;
                 baseBits[configIndex][bitOffset + 0] = false; // standby bit
                 baseBits[configIndex][bitOffset + referenceBit] = true;
             }

diff --git a/OpenEphys.Onix1/NeuropixelsV2eProbeGroup.cs b/OpenEphys.Onix1/NeuropixelsV2eProbeGroup.cs
@@ -2,7 +2,7 @@
 using System.Collections.Generic;
 using System.Linq;
 using Newtonsoft.Json;
-using OpenEphys.ProbeInterface;
+using OpenEphys.ProbeInterface.NET;
 
 namespace OpenEphys.Onix1
 {

diff --git a/OpenEphys.Onix1/OpenEphys.Onix1.csproj b/OpenEphys.Onix1/OpenEphys.Onix1.csproj
@@ -13,10 +13,7 @@
     <PackageReference Include="Bonsai.Core" Version="2.8.5" />
     <PackageReference Include="clroni" Version="6.1.2" />
     <PackageReference Include="OpenCV.Net" Version="3.4.2" />
-  </ItemGroup>
-
-  <ItemGroup>
-    <ProjectReference Include="..\OpenEphys.ProbeInterface\OpenEphys.ProbeInterface\OpenEphys.ProbeInterface.csproj" />
+    <PackageReference Include="OpenEphys.ProbeInterface.NET" Version="0.1.0" />
   </ItemGroup>
 
 </Project>
diff --git a/OpenEphys.ProbeInterface b/OpenEphys.ProbeInterface