Merge pull request #458 from open-ephys/issue-321

bparks13 · web-flow · commit f6d20d49bb0a · 2025-06-17T13:10:36.000-04:00
Rename channel configuration to probe group for clarity
diff --git a/Directory.Build.props b/Directory.Build.props
@@ -13,7 +13,7 @@
     <PackageLicenseFile>LICENSE</PackageLicenseFile>
     <UseArtifactsOutput>true</UseArtifactsOutput>
     <PackageIcon>icon.png</PackageIcon>
-    <VersionPrefix>0.5.0</VersionPrefix>
+    <VersionPrefix>0.5.1</VersionPrefix>
     <VersionSuffix></VersionSuffix>
     <LangVersion>10.0</LangVersion>
     <Features>strict</Features>
diff --git a/OpenEphys.Onix1.Design/NeuropixelsV1ChannelConfigurationDialog.cs b/OpenEphys.Onix1.Design/NeuropixelsV1ChannelConfigurationDialog.cs
@@ -29,7 +29,7 @@ public partial class NeuropixelsV1ChannelConfigurationDialog : ChannelConfigurat
         /// </summary>
         /// <param name="probeConfiguration">A <see cref="NeuropixelsV1ProbeConfiguration"/> object holding the current configuration settings.</param>
         public NeuropixelsV1ChannelConfigurationDialog(NeuropixelsV1ProbeConfiguration probeConfiguration)
-            : base(probeConfiguration.ChannelConfiguration)
+            : base(probeConfiguration.ProbeGroup)
         {
             zedGraphChannels.ZoomButtons = MouseButtons.None;
             zedGraphChannels.ZoomButtons2 = MouseButtons.None;
@@ -57,7 +57,7 @@ internal override ProbeGroup DefaultChannelLayout()
         internal override void LoadDefaultChannelLayout()
         {
             ProbeConfiguration = new(ProbeConfiguration.SpikeAmplifierGain, ProbeConfiguration.LfpAmplifierGain, ProbeConfiguration.Reference, ProbeConfiguration.SpikeFilter);
-            ProbeGroup = ProbeConfiguration.ChannelConfiguration;
+            ProbeGroup = ProbeConfiguration.ProbeGroup;
 
             OnFileOpenHandler();
         }
@@ -67,7 +67,7 @@ internal override bool OpenFile<T>()
             if (base.OpenFile<NeuropixelsV1eProbeGroup>())
             {
                 ProbeConfiguration = new((NeuropixelsV1eProbeGroup)ProbeGroup, ProbeConfiguration.SpikeAmplifierGain, ProbeConfiguration.LfpAmplifierGain, ProbeConfiguration.Reference, ProbeConfiguration.SpikeFilter);
-                ProbeGroup = ProbeConfiguration.ChannelConfiguration;
+                ProbeGroup = ProbeConfiguration.ProbeGroup;
 
                 OnFileOpenHandler();
 
@@ -114,7 +114,7 @@ internal override void DrawScale()
             const int MinorTickIncrement = 10;
             const int MinorTickLength = 5;
 
-            if (ProbeConfiguration.ChannelConfiguration.Probes.ElementAt(0).SiUnits != ProbeSiUnits.um)
+            if (ProbeConfiguration.ProbeGroup.Probes.ElementAt(0).SiUnits != ProbeSiUnits.um)
             {
                 MessageBox.Show("Warning: Expected ProbeGroup units to be in microns, but it is in millimeters. Scale might not be accurate.");
             }
@@ -216,7 +216,7 @@ internal override void HighlightEnabledContacts()
 
         internal override void UpdateContactLabels()
         {
-            if (ProbeConfiguration.ChannelConfiguration == null)
+            if (ProbeConfiguration.ProbeGroup == null)
                 return;
 
             var textObjs = zedGraphChannels.GraphPane.GraphObjList.OfType<TextObj>()
diff --git a/OpenEphys.Onix1.Design/NeuropixelsV1ProbeConfigurationDialog.cs b/OpenEphys.Onix1.Design/NeuropixelsV1ProbeConfigurationDialog.cs
@@ -170,7 +170,7 @@ private void SpikeFilterIndexChanged(object sender, EventArgs e)
         private void SetChannelPreset(ChannelPreset preset)
         {
             var probeConfiguration = ChannelConfiguration.ProbeConfiguration;
-            var electrodes = NeuropixelsV1eProbeGroup.ToElectrodes(ChannelConfiguration.ProbeConfiguration.ChannelConfiguration);
+            var electrodes = NeuropixelsV1eProbeGroup.ToElectrodes(ChannelConfiguration.ProbeConfiguration.ProbeGroup);
 
             switch (preset)
             {
@@ -432,7 +432,7 @@ private void ViewAdcs_Click(object sender, EventArgs e)
 
         private void EnableSelectedContacts()
         {
-            var electrodes = NeuropixelsV1eProbeGroup.ToElectrodes(ChannelConfiguration.ProbeConfiguration.ChannelConfiguration);
+            var electrodes = NeuropixelsV1eProbeGroup.ToElectrodes(ChannelConfiguration.ProbeConfiguration.ProbeGroup);
 
             var selectedElectrodes = electrodes.Where((e, ind) => ChannelConfiguration.SelectedContacts[ind])
                                                .ToArray();
diff --git a/OpenEphys.Onix1.Design/NeuropixelsV2eChannelConfigurationDialog.cs b/OpenEphys.Onix1.Design/NeuropixelsV2eChannelConfigurationDialog.cs
@@ -27,7 +27,7 @@ public partial class NeuropixelsV2eChannelConfigurationDialog : ChannelConfigura
         /// </summary>
         /// <param name="probeConfiguration">A <see cref="NeuropixelsV2QuadShankProbeConfiguration"/> object holding the current configuration settings.</param>
         public NeuropixelsV2eChannelConfigurationDialog(NeuropixelsV2QuadShankProbeConfiguration probeConfiguration)
-            : base(probeConfiguration.ChannelConfiguration)
+            : base(probeConfiguration.ProbeGroup)
         {
             zedGraphChannels.ZoomButtons = MouseButtons.None;
             zedGraphChannels.ZoomButtons2 = MouseButtons.None;
@@ -52,7 +52,7 @@ internal override ProbeGroup DefaultChannelLayout()
         internal override void LoadDefaultChannelLayout()
         {
             ProbeConfiguration = new(ProbeConfiguration.Probe, ProbeConfiguration.Reference);
-            ProbeGroup = ProbeConfiguration.ChannelConfiguration;
+            ProbeGroup = ProbeConfiguration.ProbeGroup;
 
             OnFileOpenHandler();
         }
@@ -108,7 +108,7 @@ internal override void DrawScale()
             const int MinorTickIncrement = 10;
             const int MinorTickLength = 5;
 
-            if (ProbeConfiguration.ChannelConfiguration.Probes.ElementAt(0).SiUnits != ProbeSiUnits.um)
+            if (ProbeConfiguration.ProbeGroup.Probes.ElementAt(0).SiUnits != ProbeSiUnits.um)
             {
                 MessageBox.Show("Warning: Expected ProbeGroup units to be in microns, but it is in millimeters. Scale might not be accurate.");
             }
@@ -211,7 +211,7 @@ internal override void HighlightEnabledContacts()
 
         internal override void UpdateContactLabels()
         {
-            if (ProbeConfiguration.ChannelConfiguration == null)
+            if (ProbeConfiguration.ProbeGroup == null)
                 return;
 
             var textObjs = zedGraphChannels.GraphPane.GraphObjList.OfType<TextObj>()
diff --git a/OpenEphys.Onix1.Design/NeuropixelsV2eDialog.cs b/OpenEphys.Onix1.Design/NeuropixelsV2eDialog.cs
@@ -76,7 +76,6 @@ private void InvertPolarityChanged(object sender, EventArgs e)
                 if (channelConfiguration.Tag != sendingDialog.Tag)
                 {
                     channelConfiguration.SetInvertPolarity(sendingDialog.InvertPolarity);
-                    //channelConfiguration.Refresh();
                 }
             }
         }
diff --git a/OpenEphys.Onix1.Design/NeuropixelsV2eProbeConfigurationDialog.cs b/OpenEphys.Onix1.Design/NeuropixelsV2eProbeConfigurationDialog.cs
@@ -168,7 +168,7 @@ private void SelectedChannelPresetChanged(object sender, EventArgs e)
         private void SetChannelPreset(ChannelPreset preset)
         {
             var probeConfiguration = ChannelConfiguration.ProbeConfiguration;
-            var electrodes = NeuropixelsV2eProbeGroup.ToElectrodes(ChannelConfiguration.ProbeConfiguration.ChannelConfiguration);
+            var electrodes = NeuropixelsV2eProbeGroup.ToElectrodes(ChannelConfiguration.ProbeConfiguration.ProbeGroup);
 
             switch (preset)
             {
@@ -622,7 +622,7 @@ internal void EnableContacts_Click(object sender, EventArgs e)
 
         private void EnableSelectedContacts()
         {
-            var selected = NeuropixelsV2eProbeGroup.ToElectrodes(ChannelConfiguration.ProbeConfiguration.ChannelConfiguration)
+            var selected = NeuropixelsV2eProbeGroup.ToElectrodes(ChannelConfiguration.ProbeConfiguration.ProbeGroup)
                                                    .Where((e, ind) => ChannelConfiguration.SelectedContacts[ind])
                                                    .ToArray();
 
diff --git a/OpenEphys.Onix1/NeuropixelsV1ProbeConfiguration.cs b/OpenEphys.Onix1/NeuropixelsV1ProbeConfiguration.cs
@@ -43,7 +43,7 @@ public class NeuropixelsV1ProbeConfiguration
         /// </summary>
         public NeuropixelsV1ProbeConfiguration()
         {
-            ChannelMap = NeuropixelsV1eProbeGroup.ToChannelMap(ChannelConfiguration);
+            ChannelMap = NeuropixelsV1eProbeGroup.ToChannelMap(ProbeGroup);
         }
 
         /// <summary>
@@ -60,28 +60,28 @@ public NeuropixelsV1ProbeConfiguration(NeuropixelsV1Gain spikeAmplifierGain, Neu
             LfpAmplifierGain = lfpAmplifierGain;
             Reference = reference;
             SpikeFilter = spikeFilter;
-            ChannelConfiguration = new();
-            ChannelMap = NeuropixelsV1eProbeGroup.ToChannelMap(ChannelConfiguration);
+            ProbeGroup = new();
+            ChannelMap = NeuropixelsV1eProbeGroup.ToChannelMap(ProbeGroup);
         }
 
         /// <summary>
         /// Copy constructor initializes a new instance of <see cref="NeuropixelsV1ProbeConfiguration"/> using the given <see cref="NeuropixelsV1eProbeGroup"/>
         /// values and the given gain / reference / filter settings.
         /// </summary>
-        /// <param name="channelConfiguration">Desired or current <see cref="NeuropixelsV1eProbeGroup"/> variable.</param>
+        /// <param name="probeGroup">Desired or current <see cref="NeuropixelsV1eProbeGroup"/> variable.</param>
         /// <param name="spikeAmplifierGain">Desired or current <see cref="NeuropixelsV1Gain"/> for the spike-band.</param>
         /// <param name="lfpAmplifierGain">Desired or current <see cref="NeuropixelsV1Gain"/> for the LFP-band.</param>
         /// <param name="reference">Desired or current <see cref="NeuropixelsV1ReferenceSource"/>.</param>
         /// <param name="spikeFilter">Desired or current option to filer the spike-band.</param>
-        public NeuropixelsV1ProbeConfiguration(NeuropixelsV1eProbeGroup channelConfiguration, NeuropixelsV1Gain spikeAmplifierGain, NeuropixelsV1Gain lfpAmplifierGain, NeuropixelsV1ReferenceSource reference, bool spikeFilter)
+        public NeuropixelsV1ProbeConfiguration(NeuropixelsV1eProbeGroup probeGroup, NeuropixelsV1Gain spikeAmplifierGain, NeuropixelsV1Gain lfpAmplifierGain, NeuropixelsV1ReferenceSource reference, bool spikeFilter)
         {
             SpikeAmplifierGain = spikeAmplifierGain;
             LfpAmplifierGain = lfpAmplifierGain;
             Reference = reference;
             SpikeFilter = spikeFilter;
-            ChannelMap = NeuropixelsV1eProbeGroup.ToChannelMap(channelConfiguration);
-            ChannelConfiguration = new();
-            ChannelConfiguration.UpdateDeviceChannelIndices(ChannelMap);
+            ChannelMap = NeuropixelsV1eProbeGroup.ToChannelMap(probeGroup);
+            ProbeGroup = new();
+            ProbeGroup.UpdateDeviceChannelIndices(ChannelMap);
         }
 
         /// <summary>
@@ -95,9 +95,9 @@ public NeuropixelsV1ProbeConfiguration(NeuropixelsV1ProbeConfiguration probeConf
             LfpAmplifierGain = probeConfiguration.LfpAmplifierGain;
             Reference = probeConfiguration.Reference;
             SpikeFilter = probeConfiguration.SpikeFilter;
-            ChannelConfiguration = new();
-            ChannelConfiguration.UpdateDeviceChannelIndices(probeConfiguration.ChannelMap);
-            ChannelMap = NeuropixelsV1eProbeGroup.ToChannelMap(ChannelConfiguration);
+            ProbeGroup = new();
+            ProbeGroup.UpdateDeviceChannelIndices(probeConfiguration.ChannelMap);
+            ChannelMap = NeuropixelsV1eProbeGroup.ToChannelMap(ProbeGroup);
         }
 
         /// <summary>
@@ -172,37 +172,37 @@ public void SelectElectrodes(NeuropixelsV1Electrode[] electrodes)
                 }
             }
 
-            ChannelConfiguration.UpdateDeviceChannelIndices(ChannelMap);
+            ProbeGroup.UpdateDeviceChannelIndices(ChannelMap);
         }
 
         /// <summary>
         /// Gets or sets the <see cref="NeuropixelsV1eProbeGroup"/> channel configuration for this probe.
         /// </summary>
         [XmlIgnore]
         [Category("Configuration")]
-        [Description("Defines the shape of the probe, and which contacts are currently selected for streaming")]
-        public NeuropixelsV1eProbeGroup ChannelConfiguration { get; set; } = new();
+        [Description("Defines all aspects of the probe group, including probe contours, electrode size and location, enabled channels, etc.")]
+        public NeuropixelsV1eProbeGroup ProbeGroup { get; set; } = new();
 
         /// <summary>
-        /// Gets or sets a string defining the <see cref="ChannelConfiguration"/> in Base64.
+        /// Gets or sets a string defining the <see cref="ProbeGroup"/> in Base64.
         /// This variable is needed to properly save a workflow in Bonsai, but it is not
         /// directly accessible in the Bonsai editor.
         /// </summary>
         [Browsable(false)]
         [Externalizable(false)]
-        [XmlElement(nameof(ChannelConfiguration))]
-        public string ChannelConfigurationString
+        [XmlElement(nameof(ProbeGroup))]
+        public string ProbeGroupString
         {
             get
             {
-                var jsonString = JsonConvert.SerializeObject(ChannelConfiguration);
+                var jsonString = JsonConvert.SerializeObject(ProbeGroup);
                 return Convert.ToBase64String(Encoding.UTF8.GetBytes(jsonString));
             }
             set
             {
                 var jsonString = Encoding.UTF8.GetString(Convert.FromBase64String(value));
-                ChannelConfiguration = JsonConvert.DeserializeObject<NeuropixelsV1eProbeGroup>(jsonString);
-                SelectElectrodes(NeuropixelsV1eProbeGroup.ToChannelMap(ChannelConfiguration));
+                ProbeGroup = JsonConvert.DeserializeObject<NeuropixelsV1eProbeGroup>(jsonString);
+                SelectElectrodes(NeuropixelsV1eProbeGroup.ToChannelMap(ProbeGroup));
             }
         }
     }
diff --git a/OpenEphys.Onix1/NeuropixelsV1eProbeGroup.cs b/OpenEphys.Onix1/NeuropixelsV1eProbeGroup.cs
@@ -191,11 +191,11 @@ internal void UpdateDeviceChannelIndices(NeuropixelsV1Electrode[] channelMap)
         /// <summary>
         /// Convert a <see cref="NeuropixelsV1eProbeGroup"/> object to a list of electrodes, which only includes currently enabled electrodes
         /// </summary>
-        /// <param name="channelConfiguration">A <see cref="NeuropixelsV1eProbeGroup"/> object</param>
+        /// <param name="probeGroup">A <see cref="NeuropixelsV1eProbeGroup"/> object</param>
         /// <returns>List of <see cref="NeuropixelsV1Electrode"/>'s that are enabled</returns>
-        public static NeuropixelsV1Electrode[] ToChannelMap(NeuropixelsV1eProbeGroup channelConfiguration)
+        public static NeuropixelsV1Electrode[] ToChannelMap(NeuropixelsV1eProbeGroup probeGroup)
         {
-            var enabledContacts = channelConfiguration.GetContacts().Where(c => c.DeviceId != -1);
+            var enabledContacts = probeGroup.GetContacts().Where(c => c.DeviceId != -1);
 
             if (enabledContacts.Count() != NeuropixelsV1.ChannelCount)
             {
@@ -212,13 +212,13 @@ public static NeuropixelsV1Electrode[] ToChannelMap(NeuropixelsV1eProbeGroup cha
         /// <summary>
         /// Convert a ProbeInterface object to a list of electrodes, which includes all possible electrodes.
         /// </summary>
-        /// <param name="channelConfiguration">A <see cref="NeuropixelsV1eProbeGroup"/> object.</param>
+        /// <param name="probeGroup">A <see cref="NeuropixelsV1eProbeGroup"/> object.</param>
         /// <returns>List of <see cref="NeuropixelsV1Electrode"/> electrodes.</returns>
-        public static List<NeuropixelsV1Electrode> ToElectrodes(NeuropixelsV1eProbeGroup channelConfiguration)
+        public static List<NeuropixelsV1Electrode> ToElectrodes(NeuropixelsV1eProbeGroup probeGroup)
         {
             List<NeuropixelsV1Electrode> electrodes = new();
 
-            foreach (var c in channelConfiguration.GetContacts())
+            foreach (var c in probeGroup.GetContacts())
             {
                 electrodes.Add(new NeuropixelsV1Electrode(c.Index));
             }
diff --git a/OpenEphys.Onix1/NeuropixelsV2QuadShankProbeConfiguration.cs b/OpenEphys.Onix1/NeuropixelsV2QuadShankProbeConfiguration.cs
@@ -115,25 +115,25 @@ public NeuropixelsV2QuadShankProbeConfiguration(NeuropixelsV2Probe probe, Neurop
         public NeuropixelsV2QuadShankProbeConfiguration(NeuropixelsV2QuadShankProbeConfiguration probeConfiguration)
         {
             Reference = probeConfiguration.Reference;
-            var probes = probeConfiguration.ChannelConfiguration.Probes.ToList().Select(probe => new Probe(probe));
-            ChannelConfiguration = new(probeConfiguration.ChannelConfiguration.Specification, probeConfiguration.ChannelConfiguration.Version, probes.ToArray());
-            ChannelMap = NeuropixelsV2eProbeGroup.ToChannelMap(ChannelConfiguration);
+            var probes = probeConfiguration.ProbeGroup.Probes.ToList().Select(probe => new Probe(probe));
+            ProbeGroup = new(probeConfiguration.ProbeGroup.Specification, probeConfiguration.ProbeGroup.Version, probes.ToArray());
+            ChannelMap = NeuropixelsV2eProbeGroup.ToChannelMap(ProbeGroup);
             Probe = probeConfiguration.Probe;
         }
 
         /// <summary>
         /// Initializes a new instance of the <see cref="NeuropixelsV2QuadShankProbeConfiguration"/> class with the given
         /// <see cref="NeuropixelsV2eProbeGroup"/> channel configuration. The <see cref="ChannelMap"/> is automatically 
-        /// generated from the <see cref="ChannelConfiguration"/>. 
+        /// generated from the <see cref="ProbeGroup"/>. 
         /// </summary>
-        /// <param name="channelConfiguration">The existing <see cref="NeuropixelsV2eProbeGroup"/> instance to use.</param>
+        /// <param name="probeGroup">The existing <see cref="NeuropixelsV2eProbeGroup"/> instance to use.</param>
         /// <param name="reference">The <see cref="NeuropixelsV2QuadShankReference"/> reference value.</param>
         /// <param name="probe">The <see cref="NeuropixelsV2Probe"/> for this probe.</param>
         [JsonConstructor]
-        public NeuropixelsV2QuadShankProbeConfiguration(NeuropixelsV2eProbeGroup channelConfiguration, NeuropixelsV2QuadShankReference reference, NeuropixelsV2Probe probe)
+        public NeuropixelsV2QuadShankProbeConfiguration(NeuropixelsV2eProbeGroup probeGroup, NeuropixelsV2QuadShankReference reference, NeuropixelsV2Probe probe)
         {
-            ChannelMap = NeuropixelsV2eProbeGroup.ToChannelMap(channelConfiguration);
-            ChannelConfiguration = channelConfiguration;
+            ChannelMap = NeuropixelsV2eProbeGroup.ToChannelMap(probeGroup);
+            ProbeGroup = probeGroup;
             Reference = reference;
             Probe = probe;
         }
@@ -193,7 +193,7 @@ public void SelectElectrodes(NeuropixelsV2QuadShankElectrode[] electrodes)
                 }
             }
 
-            ChannelConfiguration.UpdateDeviceChannelIndices(ChannelMap);
+            ProbeGroup.UpdateDeviceChannelIndices(ChannelMap);
         }
 
         /// <summary>
@@ -202,28 +202,28 @@ public void SelectElectrodes(NeuropixelsV2QuadShankElectrode[] electrodes)
         [XmlIgnore]
         [Category("Configuration")]
         [Description("Defines the shape of the probe, and which contacts are currently selected for streaming")]
-        public NeuropixelsV2eProbeGroup ChannelConfiguration { get; private set; } = new();
+        public NeuropixelsV2eProbeGroup ProbeGroup { get; private set; } = new();
 
         /// <summary>
-        /// Gets or sets a string defining the <see cref="ChannelConfiguration"/> in Base64.
+        /// Gets or sets a string defining the <see cref="ProbeGroup"/> in Base64.
         /// This variable is needed to properly save a workflow in Bonsai, but it is not
         /// directly accessible in the Bonsai editor.
         /// </summary>
         [Browsable(false)]
         [Externalizable(false)]
-        [XmlElement(nameof(ChannelConfiguration))]
-        public string ChannelConfigurationString
+        [XmlElement(nameof(ProbeGroup))]
+        public string ProbeGroupString
         {
             get
             {
-                var jsonString = JsonConvert.SerializeObject(ChannelConfiguration);
+                var jsonString = JsonConvert.SerializeObject(ProbeGroup);
                 return Convert.ToBase64String(Encoding.UTF8.GetBytes(jsonString));
             }
             set
             {
                 var jsonString = Encoding.UTF8.GetString(Convert.FromBase64String(value));
-                ChannelConfiguration = JsonConvert.DeserializeObject<NeuropixelsV2eProbeGroup>(jsonString);
-                SelectElectrodes(NeuropixelsV2eProbeGroup.ToChannelMap(ChannelConfiguration));
+                ProbeGroup = JsonConvert.DeserializeObject<NeuropixelsV2eProbeGroup>(jsonString);
+                SelectElectrodes(NeuropixelsV2eProbeGroup.ToChannelMap(ProbeGroup));
             }
         }
     }
diff --git a/OpenEphys.Onix1/NeuropixelsV2eProbeGroup.cs b/OpenEphys.Onix1/NeuropixelsV2eProbeGroup.cs

Original file line number	Diff line number	Diff line change
`@@ -29,7 +29,7 @@ public partial class NeuropixelsV1ChannelConfigurationDialog : ChannelConfigurat`
`29`	`29`	`/// </summary>`
`30`	`30`	`/// <param name="probeConfiguration">A <see cref="NeuropixelsV1ProbeConfiguration"/> object holding the current configuration settings.</param>`
`31`	`31`	`public NeuropixelsV1ChannelConfigurationDialog(NeuropixelsV1ProbeConfiguration probeConfiguration)`
`32`		`- : base(probeConfiguration.ChannelConfiguration)`
	`32`	`+ : base(probeConfiguration.ProbeGroup)`
`33`	`33`	`{`
`34`	`34`	`zedGraphChannels.ZoomButtons = MouseButtons.None;`
`35`	`35`	`zedGraphChannels.ZoomButtons2 = MouseButtons.None;`
`@@ -57,7 +57,7 @@ internal override ProbeGroup DefaultChannelLayout()`
`57`	`57`	`internal override void LoadDefaultChannelLayout()`
`58`	`58`	`{`
`59`	`59`	`ProbeConfiguration = new(ProbeConfiguration.SpikeAmplifierGain, ProbeConfiguration.LfpAmplifierGain, ProbeConfiguration.Reference, ProbeConfiguration.SpikeFilter);`
`60`		`- ProbeGroup = ProbeConfiguration.ChannelConfiguration;`
	`60`	`+ ProbeGroup = ProbeConfiguration.ProbeGroup;`
`61`	`61`
`62`	`62`	`OnFileOpenHandler();`
`63`	`63`	`}`
`@@ -67,7 +67,7 @@ internal override bool OpenFile<T>()`
`67`	`67`	`if (base.OpenFile<NeuropixelsV1eProbeGroup>())`
`68`	`68`	`{`
`69`	`69`	`ProbeConfiguration = new((NeuropixelsV1eProbeGroup)ProbeGroup, ProbeConfiguration.SpikeAmplifierGain, ProbeConfiguration.LfpAmplifierGain, ProbeConfiguration.Reference, ProbeConfiguration.SpikeFilter);`
`70`		`- ProbeGroup = ProbeConfiguration.ChannelConfiguration;`
	`70`	`+ ProbeGroup = ProbeConfiguration.ProbeGroup;`
`71`	`71`
`72`	`72`	`OnFileOpenHandler();`
`73`	`73`
`@@ -114,7 +114,7 @@ internal override void DrawScale()`
`114`	`114`	`const int MinorTickIncrement = 10;`
`115`	`115`	`const int MinorTickLength = 5;`
`116`	`116`
`117`		`- if (ProbeConfiguration.ChannelConfiguration.Probes.ElementAt(0).SiUnits != ProbeSiUnits.um)`
	`117`	`+ if (ProbeConfiguration.ProbeGroup.Probes.ElementAt(0).SiUnits != ProbeSiUnits.um)`
`118`	`118`	`{`
`119`	`119`	`MessageBox.Show("Warning: Expected ProbeGroup units to be in microns, but it is in millimeters. Scale might not be accurate.");`
`120`	`120`	`}`
`@@ -216,7 +216,7 @@ internal override void HighlightEnabledContacts()`
`216`	`216`
`217`	`217`	`internal override void UpdateContactLabels()`
`218`	`218`	`{`
`219`		`- if (ProbeConfiguration.ChannelConfiguration == null)`
	`219`	`+ if (ProbeConfiguration.ProbeGroup == null)`
`220`	`220`	`return;`
`221`	`221`
`222`	`222`	`var textObjs = zedGraphChannels.GraphPane.GraphObjList.OfType<TextObj>()`
Original file line number	Diff line number	Diff line change
`@@ -170,7 +170,7 @@ private void SpikeFilterIndexChanged(object sender, EventArgs e)`
`170`	`170`	`private void SetChannelPreset(ChannelPreset preset)`
`171`	`171`	`{`
`172`	`172`	`var probeConfiguration = ChannelConfiguration.ProbeConfiguration;`
`173`		`- var electrodes = NeuropixelsV1eProbeGroup.ToElectrodes(ChannelConfiguration.ProbeConfiguration.ChannelConfiguration);`
	`173`	`+ var electrodes = NeuropixelsV1eProbeGroup.ToElectrodes(ChannelConfiguration.ProbeConfiguration.ProbeGroup);`
`174`	`174`
`175`	`175`	`switch (preset)`
`176`	`176`	`{`
`@@ -432,7 +432,7 @@ private void ViewAdcs_Click(object sender, EventArgs e)`
`432`	`432`
`433`	`433`	`private void EnableSelectedContacts()`
`434`	`434`	`{`
`435`		`- var electrodes = NeuropixelsV1eProbeGroup.ToElectrodes(ChannelConfiguration.ProbeConfiguration.ChannelConfiguration);`
	`435`	`+ var electrodes = NeuropixelsV1eProbeGroup.ToElectrodes(ChannelConfiguration.ProbeConfiguration.ProbeGroup);`
`436`	`436`
`437`	`437`	`var selectedElectrodes = electrodes.Where((e, ind) => ChannelConfiguration.SelectedContacts[ind])`
`438`	`438`	`.ToArray();`
Original file line number	Diff line number	Diff line change
`@@ -27,7 +27,7 @@ public partial class NeuropixelsV2eChannelConfigurationDialog : ChannelConfigura`
`27`	`27`	`/// </summary>`
`28`	`28`	`/// <param name="probeConfiguration">A <see cref="NeuropixelsV2QuadShankProbeConfiguration"/> object holding the current configuration settings.</param>`
`29`	`29`	`public NeuropixelsV2eChannelConfigurationDialog(NeuropixelsV2QuadShankProbeConfiguration probeConfiguration)`
`30`		`- : base(probeConfiguration.ChannelConfiguration)`
	`30`	`+ : base(probeConfiguration.ProbeGroup)`
`31`	`31`	`{`
`32`	`32`	`zedGraphChannels.ZoomButtons = MouseButtons.None;`
`33`	`33`	`zedGraphChannels.ZoomButtons2 = MouseButtons.None;`
`@@ -52,7 +52,7 @@ internal override ProbeGroup DefaultChannelLayout()`
`52`	`52`	`internal override void LoadDefaultChannelLayout()`
`53`	`53`	`{`
`54`	`54`	`ProbeConfiguration = new(ProbeConfiguration.Probe, ProbeConfiguration.Reference);`
`55`		`- ProbeGroup = ProbeConfiguration.ChannelConfiguration;`
	`55`	`+ ProbeGroup = ProbeConfiguration.ProbeGroup;`
`56`	`56`
`57`	`57`	`OnFileOpenHandler();`
`58`	`58`	`}`
`@@ -108,7 +108,7 @@ internal override void DrawScale()`
`108`	`108`	`const int MinorTickIncrement = 10;`
`109`	`109`	`const int MinorTickLength = 5;`
`110`	`110`
`111`		`- if (ProbeConfiguration.ChannelConfiguration.Probes.ElementAt(0).SiUnits != ProbeSiUnits.um)`
	`111`	`+ if (ProbeConfiguration.ProbeGroup.Probes.ElementAt(0).SiUnits != ProbeSiUnits.um)`
`112`	`112`	`{`
`113`	`113`	`MessageBox.Show("Warning: Expected ProbeGroup units to be in microns, but it is in millimeters. Scale might not be accurate.");`
`114`	`114`	`}`
`@@ -211,7 +211,7 @@ internal override void HighlightEnabledContacts()`
`211`	`211`
`212`	`212`	`internal override void UpdateContactLabels()`
`213`	`213`	`{`
`214`		`- if (ProbeConfiguration.ChannelConfiguration == null)`
	`214`	`+ if (ProbeConfiguration.ProbeGroup == null)`
`215`	`215`	`return;`
`216`	`216`
`217`	`217`	`var textObjs = zedGraphChannels.GraphPane.GraphObjList.OfType<TextObj>()`
Original file line number	Diff line number	Diff line change
`@@ -76,7 +76,6 @@ private void InvertPolarityChanged(object sender, EventArgs e)`
`76`	`76`	`if (channelConfiguration.Tag != sendingDialog.Tag)`
`77`	`77`	`{`
`78`	`78`	`channelConfiguration.SetInvertPolarity(sendingDialog.InvertPolarity);`
`79`		`- //channelConfiguration.Refresh();`
`80`	`79`	`}`
`81`	`80`	`}`
`82`	`81`	`}`
Original file line number	Diff line number	Diff line change
`@@ -168,7 +168,7 @@ private void SelectedChannelPresetChanged(object sender, EventArgs e)`
`168`	`168`	`private void SetChannelPreset(ChannelPreset preset)`
`169`	`169`	`{`
`170`	`170`	`var probeConfiguration = ChannelConfiguration.ProbeConfiguration;`
`171`		`- var electrodes = NeuropixelsV2eProbeGroup.ToElectrodes(ChannelConfiguration.ProbeConfiguration.ChannelConfiguration);`
	`171`	`+ var electrodes = NeuropixelsV2eProbeGroup.ToElectrodes(ChannelConfiguration.ProbeConfiguration.ProbeGroup);`
`172`	`172`
`173`	`173`	`switch (preset)`
`174`	`174`	`{`
`@@ -622,7 +622,7 @@ internal void EnableContacts_Click(object sender, EventArgs e)`
`622`	`622`
`623`	`623`	`private void EnableSelectedContacts()`
`624`	`624`	`{`
`625`		`- var selected = NeuropixelsV2eProbeGroup.ToElectrodes(ChannelConfiguration.ProbeConfiguration.ChannelConfiguration)`
	`625`	`+ var selected = NeuropixelsV2eProbeGroup.ToElectrodes(ChannelConfiguration.ProbeConfiguration.ProbeGroup)`
`626`	`626`	`.Where((e, ind) => ChannelConfiguration.SelectedContacts[ind])`
`627`	`627`	`.ToArray();`
`628`	`628`
Original file line number	Diff line number	Diff line change
`@@ -191,11 +191,11 @@ internal void UpdateDeviceChannelIndices(NeuropixelsV1Electrode[] channelMap)`
`191`	`191`	`/// <summary>`
`192`	`192`	`/// Convert a <see cref="NeuropixelsV1eProbeGroup"/> object to a list of electrodes, which only includes currently enabled electrodes`
`193`	`193`	`/// </summary>`
`194`		`- /// <param name="channelConfiguration">A <see cref="NeuropixelsV1eProbeGroup"/> object</param>`
	`194`	`+ /// <param name="probeGroup">A <see cref="NeuropixelsV1eProbeGroup"/> object</param>`
`195`	`195`	`/// <returns>List of <see cref="NeuropixelsV1Electrode"/>'s that are enabled</returns>`
`196`		`- public static NeuropixelsV1Electrode[] ToChannelMap(NeuropixelsV1eProbeGroup channelConfiguration)`
	`196`	`+ public static NeuropixelsV1Electrode[] ToChannelMap(NeuropixelsV1eProbeGroup probeGroup)`
`197`	`197`	`{`
`198`		`- var enabledContacts = channelConfiguration.GetContacts().Where(c => c.DeviceId != -1);`
	`198`	`+ var enabledContacts = probeGroup.GetContacts().Where(c => c.DeviceId != -1);`
`199`	`199`
`200`	`200`	`if (enabledContacts.Count() != NeuropixelsV1.ChannelCount)`
`201`	`201`	`{`
`@@ -212,13 +212,13 @@ public static NeuropixelsV1Electrode[] ToChannelMap(NeuropixelsV1eProbeGroup cha`
`212`	`212`	`/// <summary>`
`213`	`213`	`/// Convert a ProbeInterface object to a list of electrodes, which includes all possible electrodes.`
`214`	`214`	`/// </summary>`
`215`		`- /// <param name="channelConfiguration">A <see cref="NeuropixelsV1eProbeGroup"/> object.</param>`
	`215`	`+ /// <param name="probeGroup">A <see cref="NeuropixelsV1eProbeGroup"/> object.</param>`
`216`	`216`	`/// <returns>List of <see cref="NeuropixelsV1Electrode"/> electrodes.</returns>`
`217`		`- public static List<NeuropixelsV1Electrode> ToElectrodes(NeuropixelsV1eProbeGroup channelConfiguration)`
	`217`	`+ public static List<NeuropixelsV1Electrode> ToElectrodes(NeuropixelsV1eProbeGroup probeGroup)`
`218`	`218`	`{`
`219`	`219`	`List<NeuropixelsV1Electrode> electrodes = new();`
`220`	`220`
`221`		`- foreach (var c in channelConfiguration.GetContacts())`
	`221`	`+ foreach (var c in probeGroup.GetContacts())`
`222`	`222`	`{`
`223`	`223`	`electrodes.Add(new NeuropixelsV1Electrode(c.Index));`
`224`	`224`	`}`
Original file line number	Diff line number	Diff line change
`@@ -115,25 +115,25 @@ public NeuropixelsV2QuadShankProbeConfiguration(NeuropixelsV2Probe probe, Neurop`
`115`	`115`	`public NeuropixelsV2QuadShankProbeConfiguration(NeuropixelsV2QuadShankProbeConfiguration probeConfiguration)`
`116`	`116`	`{`
`117`	`117`	`Reference = probeConfiguration.Reference;`
`118`		`- var probes = probeConfiguration.ChannelConfiguration.Probes.ToList().Select(probe => new Probe(probe));`
`119`		`- ChannelConfiguration = new(probeConfiguration.ChannelConfiguration.Specification, probeConfiguration.ChannelConfiguration.Version, probes.ToArray());`
`120`		`- ChannelMap = NeuropixelsV2eProbeGroup.ToChannelMap(ChannelConfiguration);`
	`118`	`+ var probes = probeConfiguration.ProbeGroup.Probes.ToList().Select(probe => new Probe(probe));`
	`119`	`+ ProbeGroup = new(probeConfiguration.ProbeGroup.Specification, probeConfiguration.ProbeGroup.Version, probes.ToArray());`
	`120`	`+ ChannelMap = NeuropixelsV2eProbeGroup.ToChannelMap(ProbeGroup);`
`121`	`121`	`Probe = probeConfiguration.Probe;`
`122`	`122`	`}`
`123`	`123`
`124`	`124`	`/// <summary>`
`125`	`125`	`/// Initializes a new instance of the <see cref="NeuropixelsV2QuadShankProbeConfiguration"/> class with the given`
`126`	`126`	`/// <see cref="NeuropixelsV2eProbeGroup"/> channel configuration. The <see cref="ChannelMap"/> is automatically`
`127`		`- /// generated from the <see cref="ChannelConfiguration"/>.`
	`127`	`+ /// generated from the <see cref="ProbeGroup"/>.`
`128`	`128`	`/// </summary>`
`129`		`- /// <param name="channelConfiguration">The existing <see cref="NeuropixelsV2eProbeGroup"/> instance to use.</param>`
	`129`	`+ /// <param name="probeGroup">The existing <see cref="NeuropixelsV2eProbeGroup"/> instance to use.</param>`
`130`	`130`	`/// <param name="reference">The <see cref="NeuropixelsV2QuadShankReference"/> reference value.</param>`
`131`	`131`	`/// <param name="probe">The <see cref="NeuropixelsV2Probe"/> for this probe.</param>`
`132`	`132`	`[JsonConstructor]`
`133`		`- public NeuropixelsV2QuadShankProbeConfiguration(NeuropixelsV2eProbeGroup channelConfiguration, NeuropixelsV2QuadShankReference reference, NeuropixelsV2Probe probe)`
	`133`	`+ public NeuropixelsV2QuadShankProbeConfiguration(NeuropixelsV2eProbeGroup probeGroup, NeuropixelsV2QuadShankReference reference, NeuropixelsV2Probe probe)`
`134`	`134`	`{`
`135`		`- ChannelMap = NeuropixelsV2eProbeGroup.ToChannelMap(channelConfiguration);`
`136`		`- ChannelConfiguration = channelConfiguration;`
	`135`	`+ ChannelMap = NeuropixelsV2eProbeGroup.ToChannelMap(probeGroup);`
	`136`	`+ ProbeGroup = probeGroup;`
`137`	`137`	`Reference = reference;`
`138`	`138`	`Probe = probe;`
`139`	`139`	`}`
`@@ -193,7 +193,7 @@ public void SelectElectrodes(NeuropixelsV2QuadShankElectrode[] electrodes)`
`193`	`193`	`}`
`194`	`194`	`}`
`195`	`195`
`196`		`- ChannelConfiguration.UpdateDeviceChannelIndices(ChannelMap);`
	`196`	`+ ProbeGroup.UpdateDeviceChannelIndices(ChannelMap);`
`197`	`197`	`}`
`198`	`198`
`199`	`199`	`/// <summary>`
`@@ -202,28 +202,28 @@ public void SelectElectrodes(NeuropixelsV2QuadShankElectrode[] electrodes)`
`202`	`202`	`[XmlIgnore]`
`203`	`203`	`[Category("Configuration")]`
`204`	`204`	`[Description("Defines the shape of the probe, and which contacts are currently selected for streaming")]`
`205`		`- public NeuropixelsV2eProbeGroup ChannelConfiguration { get; private set; } = new();`
	`205`	`+ public NeuropixelsV2eProbeGroup ProbeGroup { get; private set; } = new();`
`206`	`206`
`207`	`207`	`/// <summary>`
`208`		`- /// Gets or sets a string defining the <see cref="ChannelConfiguration"/> in Base64.`
	`208`	`+ /// Gets or sets a string defining the <see cref="ProbeGroup"/> in Base64.`
`209`	`209`	`/// This variable is needed to properly save a workflow in Bonsai, but it is not`
`210`	`210`	`/// directly accessible in the Bonsai editor.`
`211`	`211`	`/// </summary>`
`212`	`212`	`[Browsable(false)]`
`213`	`213`	`[Externalizable(false)]`
`214`		`- [XmlElement(nameof(ChannelConfiguration))]`
`215`		`- public string ChannelConfigurationString`
	`214`	`+ [XmlElement(nameof(ProbeGroup))]`
	`215`	`+ public string ProbeGroupString`
`216`	`216`	`{`
`217`	`217`	`get`
`218`	`218`	`{`
`219`		`- var jsonString = JsonConvert.SerializeObject(ChannelConfiguration);`
	`219`	`+ var jsonString = JsonConvert.SerializeObject(ProbeGroup);`
`220`	`220`	`return Convert.ToBase64String(Encoding.UTF8.GetBytes(jsonString));`
`221`	`221`	`}`
`222`	`222`	`set`
`223`	`223`	`{`
`224`	`224`	`var jsonString = Encoding.UTF8.GetString(Convert.FromBase64String(value));`
`225`		`- ChannelConfiguration = JsonConvert.DeserializeObject<NeuropixelsV2eProbeGroup>(jsonString);`
`226`		`- SelectElectrodes(NeuropixelsV2eProbeGroup.ToChannelMap(ChannelConfiguration));`
	`225`	`+ ProbeGroup = JsonConvert.DeserializeObject<NeuropixelsV2eProbeGroup>(jsonString);`
	`226`	`+ SelectElectrodes(NeuropixelsV2eProbeGroup.ToChannelMap(ProbeGroup));`
`227`	`227`	`}`
`228`	`228`	`}`
`229`	`229`	`}`