Add option to order Neuropixels channels by depth

OpenEphys.Onix1/ChannelHelper.cs

@@ -0,0 +1,48 @@
+using System;
+using System.Collections.Generic;
+using System.Linq;
+
+namespace OpenEphys.Onix1
+{
+    class ChannelHelper
+    {
+        internal static int[,] OrderChannelsByDepth(Electrode[] channelMap, int[,] originalOrder)
+        {
+            int rows = originalOrder.GetLength(0);
+            int cols = originalOrder.GetLength(1);
+
+            var channelToPosition = new Dictionary<int, (int row, int col)>();
+            for (int row = 0; row < rows; row++)
+            {
+                for (int col = 0; col < cols; col++)
+                {
+                    channelToPosition[originalOrder[row, col]] = (row, col);
+                }
+            }
+
+            var spatiallyOrdered = channelMap
+                .OrderBy(x => x.Position.Y)
+                .ThenBy(x => x.Position.X)
+                .ToArray();
+
+            var spatialRawToChannel = new int[rows, cols];
+            int index = 0;
+
+            foreach (var e in spatiallyOrdered)
+            {
+                var (newRow, newCol) = channelToPosition[index++];
+                var (origRow, origCol) = channelToPosition[e.Channel];
+
+                spatialRawToChannel[origRow, origCol] = originalOrder[newRow, newCol];
+            }
+
+            if (spatialRawToChannel.Cast<int>().Distinct().Count() != originalOrder.Length)
+            {
+                throw new InvalidOperationException($"An error occurred reordering the channels by depth. Expected {originalOrder.Length} channels," +
+                    $" but only found {spatialRawToChannel.Cast<int>().Distinct().Count()} unique channels.");
+            }
+
+            return spatialRawToChannel;
+        }
+    }
+}

OpenEphys.Onix1/ConfigureNeuropixelsV1e.cs

@@ -183,7 +183,7 @@ public override IObservable<ContextTask> Process(IObservable<ContextTask> source
                     TurnOnLed(serializer, NeuropixelsV1e.DefaultGPO32Config);
                 }
 
-                var deviceInfo = new NeuropixelsV1eDeviceInfo(context, DeviceType, deviceAddress, probeControl, invertPolarity);
+                var deviceInfo = new NeuropixelsV1eDeviceInfo(context, DeviceType, deviceAddress, probeControl, invertPolarity, ProbeConfiguration);
                 var shutdown = Disposable.Create(() =>
                 {
                     serializer.WriteByte((uint)DS90UB933SerializerI2CRegister.Gpio10, NeuropixelsV1e.DefaultGPO10Config);

OpenEphys.Onix1/NeuropixelsV1eData.cs

@@ -44,6 +44,18 @@ public int BufferSize
             set => bufferSize = (int)(Math.Ceiling((double)value / NeuropixelsV1.FramesPerRoundRobin) * NeuropixelsV1.FramesPerRoundRobin);
         }
 
+        /// <summary>
+        /// Gets or sets a boolean value that controls if the channels are ordered by depth.
+        /// </summary>
+        /// <remarks>
+        /// If <see cref="OrderByDepth"/> is false, then channels are ordered from 0 to 383. 
+        /// If <see cref="OrderByDepth"/> is true, then channels are ordered based on the depth
+        /// of the electrodes
+        /// </remarks>
+        [Description("Determines if the channels are returned ordered by depth.")]
+        [Category(DeviceFactory.ConfigurationCategory)]
+        public bool OrderByDepth { get; set; } = false;
+
         /// <summary>
         /// Generates a sequence of <see cref="NeuropixelsV1DataFrame"/> objects.
         /// </summary>
@@ -52,13 +64,15 @@ public unsafe override IObservable<NeuropixelsV1DataFrame> Generate()
         {
             var spikeBufferSize = BufferSize;
             var lfpBufferSize = spikeBufferSize / NeuropixelsV1.FramesPerRoundRobin;
+            var orderByDepth = OrderByDepth;
 
             return DeviceManager.GetDevice(DeviceName).SelectMany(deviceInfo =>
             {
                 var info = (NeuropixelsV1eDeviceInfo)deviceInfo;
                 var device = info.GetDeviceContext(typeof(NeuropixelsV1e));
                 var passthrough = device.GetPassthroughDeviceContext(typeof(DS90UB9x));
                 var probeData = device.Context.GetDeviceFrames(passthrough.Address);
+                int[,] channelOrder = orderByDepth ? NeuropixelsV1eDataFrame.OrderChannelsByDepth(info.ProbeConfiguration.ChannelMap) : null;
 
                 return Observable.Create<NeuropixelsV1DataFrame>(observer =>
                 {
@@ -73,7 +87,7 @@ public unsafe override IObservable<NeuropixelsV1DataFrame> Generate()
                         frame =>
                         {
                             var payload = (NeuropixelsV1ePayload*)frame.Data.ToPointer();
-                            NeuropixelsV1eDataFrame.CopyAmplifierBuffer(payload->AmplifierData, frameCountBuffer, spikeBuffer, lfpBuffer, sampleIndex, info.ApGainCorrection, info.LfpGainCorrection, info.AdcThresholds, info.AdcOffsets, info.InvertPolarity);
+                            NeuropixelsV1eDataFrame.CopyAmplifierBuffer(payload->AmplifierData, frameCountBuffer, spikeBuffer, lfpBuffer, sampleIndex, info.ApGainCorrection, info.LfpGainCorrection, info.AdcThresholds, info.AdcOffsets, info.InvertPolarity, channelOrder);
                             hubClockBuffer[sampleIndex] = payload->HubClock;
                             clockBuffer[sampleIndex] = frame.Clock;
                             if (++sampleIndex >= spikeBufferSize)

OpenEphys.Onix1/NeuropixelsV1eDataFrame.cs

@@ -4,8 +4,10 @@ namespace OpenEphys.Onix1
 {
     class NeuropixelsV1eDataFrame
     {
-        internal static unsafe void CopyAmplifierBuffer(ushort* amplifierData, int[] frameCountBuffer, ushort[,] spikeBuffer, ushort[,] lfpBuffer, int index, double apGainCorrection, double lfpGainCorrection, ushort[] thresholds, ushort[] offsets, bool invertPolarity)
+        internal static unsafe void CopyAmplifierBuffer(ushort* amplifierData, int[] frameCountBuffer, ushort[,] spikeBuffer, ushort[,] lfpBuffer, int index, double apGainCorrection, double lfpGainCorrection, ushort[] thresholds, ushort[] offsets, bool invertPolarity, int[,] channelOrder = null)
         {
+            channelOrder ??= RawToChannel;
+
             var frameCountStartIndex = index * NeuropixelsV1.FramesPerSuperFrame;
             frameCountBuffer[frameCountStartIndex] = (amplifierData[31] << 10) | (amplifierData[39] << 0);
 
@@ -23,7 +25,7 @@ internal static unsafe void CopyAmplifierBuffer(ushort* amplifierData, int[] fra
                 for (int k = 0; k < NeuropixelsV1.AdcCount; k++)
                 {
                     var a = amplifierData[adcToFrameIndex[k]];
-                    lfpBuffer[RawToChannel[k, lfpFrameIndex], lfpBufferIndex] = (ushort)(lfpInversionOffset - lfpGainCorrection * (a > thresholds[k] ? a - offsets[k] : a));
+                    lfpBuffer[channelOrder[k, lfpFrameIndex], lfpBufferIndex] = (ushort)(lfpInversionOffset - lfpGainCorrection * (a > thresholds[k] ? a - offsets[k] : a));
                 }
 
                 // Loop over 12 AP frames within each "super-frame"
@@ -35,7 +37,7 @@ internal static unsafe void CopyAmplifierBuffer(ushort* amplifierData, int[] fra
                     for (int k = 0; k < NeuropixelsV1.AdcCount; k++)
                     {
                         var a = amplifierData[adcToFrameIndex[k] + adcDataOffset];
-                        spikeBuffer[RawToChannel[k, i], index] = (ushort)(apInversionOffset - apGainCorrection * (a > thresholds[k] ? a - offsets[k] : a));
+                        spikeBuffer[channelOrder[k, i], index] = (ushort)(apInversionOffset - apGainCorrection * (a > thresholds[k] ? a - offsets[k] : a));
                     }
 
                     frameCountBuffer[frameCountStartIndex + i + 1] = (amplifierData[adcDataOffset + 31] << 10) | (amplifierData[adcDataOffset + 39] << 0);
@@ -46,7 +48,7 @@ internal static unsafe void CopyAmplifierBuffer(ushort* amplifierData, int[] fra
                 for (int k = 0; k < NeuropixelsV1.AdcCount; k++)
                 {
                     var a = amplifierData[adcToFrameIndex[k]];
-                    lfpBuffer[RawToChannel[k, lfpFrameIndex], lfpBufferIndex] = (ushort)(lfpGainCorrection * (a > thresholds[k] ? a - offsets[k] : a));
+                    lfpBuffer[channelOrder[k, lfpFrameIndex], lfpBufferIndex] = (ushort)(lfpGainCorrection * (a > thresholds[k] ? a - offsets[k] : a));
                 }
 
                 // Loop over 12 AP frames within each "super-frame"
@@ -58,7 +60,7 @@ internal static unsafe void CopyAmplifierBuffer(ushort* amplifierData, int[] fra
                     for (int k = 0; k < NeuropixelsV1.AdcCount; k++)
                     {
                         var a = amplifierData[adcToFrameIndex[k] + adcDataOffset];
-                        spikeBuffer[RawToChannel[k, i], index] = (ushort)(apGainCorrection * (a > thresholds[k] ? a - offsets[k] : a));
+                        spikeBuffer[channelOrder[k, i], index] = (ushort)(apGainCorrection * (a > thresholds[k] ? a - offsets[k] : a));
                     }
 
                     frameCountBuffer[frameCountStartIndex + i + 1] = (amplifierData[adcDataOffset + 31] << 10) | (amplifierData[adcDataOffset + 39] << 0);
@@ -114,6 +116,11 @@ internal static unsafe void CopyAmplifierBuffer(ushort* amplifierData, int[] fra
             {337, 339, 341, 343, 345, 347, 349, 351, 353, 355, 357, 359 },
             {360, 362, 364, 366, 368, 370, 372, 374, 376, 378, 380, 382 },
             {361, 363, 365, 367, 369, 371, 373, 375, 377, 379, 381, 383 } };
+
+        internal static int[,] OrderChannelsByDepth(Electrode[] channelMap)
+        {
+            return ChannelHelper.OrderChannelsByDepth(channelMap, RawToChannel);
+        }
     }
 
     [StructLayout(LayoutKind.Sequential, Pack = 1)]

OpenEphys.Onix1/NeuropixelsV1eDeviceInfo.cs

@@ -4,20 +4,22 @@ namespace OpenEphys.Onix1
 {
     class NeuropixelsV1eDeviceInfo : DeviceInfo
     {
-        public NeuropixelsV1eDeviceInfo(ContextTask context, Type deviceType, uint deviceAddress, NeuropixelsV1eRegisterContext probeControl, bool invertPolarity)
+        public NeuropixelsV1eDeviceInfo(ContextTask context, Type deviceType, uint deviceAddress, NeuropixelsV1eRegisterContext probeControl, bool invertPolarity, NeuropixelsV1ProbeConfiguration probeConfiguration)
             : base(context, deviceType, deviceAddress)
         {
             ApGainCorrection = probeControl.ApGainCorrection;
             LfpGainCorrection = probeControl.LfpGainCorrection;
             AdcThresholds = probeControl.AdcThresholds;
             AdcOffsets = probeControl.AdcOffsets;
             InvertPolarity = invertPolarity;
+            ProbeConfiguration = probeConfiguration;
         }
 
         public double ApGainCorrection { get; }
         public double LfpGainCorrection { get; }
         public ushort[] AdcThresholds { get; }
         public ushort[] AdcOffsets { get; }
         public bool InvertPolarity { get; }
+        public NeuropixelsV1ProbeConfiguration ProbeConfiguration { get; }
     }
 }