Merge pull request #433 from open-ephys/issue-422

Map Rhd2164 ephys channels into Intan order

Author: jonnew

OpenEphys.Onix1/BufferHelper.cs

@@ -1,4 +1,5 @@
-using OpenCV.Net;
+using System;
+using OpenCV.Net;
 
 namespace OpenEphys.Onix1
 {
@@ -47,5 +48,35 @@ public static Mat CopyTranspose<TBuffer>(
             CV.Mul(transposeBuffer, scale, data);
             return data;
         }
+
+        public static Mat CopyTranspose<TBuffer>(
+        TBuffer[] buffer,
+        int sampleCount,
+        int channelCount,
+        Depth depth,
+        int[] channelMap)
+        where TBuffer : unmanaged
+        {
+            if (channelMap == null || channelMap.Length != channelCount)
+            {
+                return CopyTranspose(buffer, sampleCount, channelCount, depth);
+            }
+
+            using var bufferHeader = Mat.CreateMatHeader(
+                buffer,
+                sampleCount,
+                channelCount,
+                depth,
+                channels: 1);
+            var data = new Mat(bufferHeader.Rows, bufferHeader.Cols, depth, 1);
+
+            for (int i = 0; i < bufferHeader.Cols; i++)
+                CV.Copy(bufferHeader.GetCol(channelMap[i]), data.GetCol(i));
+
+            var transposeData = new Mat(bufferHeader.Cols, bufferHeader.Rows, depth, 1);
+
+            CV.Transpose(data, transposeData);
+            return transposeData;
+        }
     }
 }

OpenEphys.Onix1/Rhd2164Data.cs

@@ -20,6 +20,15 @@ namespace OpenEphys.Onix1
     [Description("Produces a sequence of Rhd2164DataFrame objects with data from an Intan Rhd2164 bioacquisition chip.")]
     public class Rhd2164Data : Source<Rhd2164DataFrame>
     {
+        private readonly static int[] EphysChannelMap = new[] {0 ,  2,  4,  6,  8, 10, 12, 14,
+                                                               16, 18, 20, 22, 24, 26, 28, 30,
+                                                               32, 34, 36, 38, 40, 42, 44, 46,
+                                                               48, 50, 52, 54, 56, 58, 60, 62,
+                                                               1 , 3 , 5 , 7 , 9 , 11, 13, 15,
+                                                               17, 19, 21, 23, 25, 27, 29, 31,
+                                                               33, 35, 37, 39, 41, 43, 45, 47,
+                                                               49, 51, 53, 55, 57, 59, 61, 63};
+
         /// <inheritdoc cref = "SingleDeviceFactory.DeviceName"/>
         [TypeConverter(typeof(Rhd2164.NameConverter))]
         [Description(SingleDeviceFactory.DeviceNameDescription)]
@@ -66,7 +75,7 @@ public unsafe override IObservable<Rhd2164DataFrame> Generate()
                             clockBuffer[sampleIndex] = frame.Clock;
                             if (++sampleIndex >= bufferSize)
                             {
-                                var amplifierData = BufferHelper.CopyTranspose(amplifierBuffer, bufferSize, Rhd2164.AmplifierChannelCount, Depth.U16);
+                                var amplifierData = BufferHelper.CopyTranspose(amplifierBuffer, bufferSize, Rhd2164.AmplifierChannelCount, Depth.U16, EphysChannelMap);
                                 var auxData = BufferHelper.CopyTranspose(auxBuffer, bufferSize, Rhd2164.AuxChannelCount, Depth.U16);
                                 observer.OnNext(new Rhd2164DataFrame(clockBuffer, hubClockBuffer, amplifierData, auxData));
                                 hubClockBuffer = new ulong[bufferSize];

OpenEphys.Onix1/Rhd2164DataFrame.cs

@@ -27,11 +27,12 @@ public Rhd2164DataFrame(ulong[] clock, ulong[] hubClock, Mat amplifierData, Mat
         /// </summary>
         /// <remarks>
         /// Electrophysiology samples are organized in 64xN matrix with rows representing electrophysiology
-        /// channel number and N columns representing sample index. Each column is a 64-channel vector of ADC
-        /// samples whose acquisition time is indicated by the corresponding elements in <see
-        /// cref="DataFrame.Clock"/> and <see cref="DataFrame.HubClock"/>. Each ADC sample is a 16-bit,
-        /// offset binary value encoded as a <see cref="ushort"/>. The following equation can be used to
-        /// convert a sample to microvolts:
+        /// channel number and N columns representing sample index. Channels are ordered in accordance with
+        /// the Rhd2164 input number specified on its datasheet (channel 0 corresponds to input 0, channel 1
+        /// corresponds to input 1, and so on). Each column is a 64-channel vector of ADC samples whose
+        /// acquisition time is indicated by the corresponding elements in <see cref="DataFrame.Clock"/> and
+        /// <see cref="DataFrame.HubClock"/>. Each ADC sample is a 16-bit, offset binary value encoded as a
+        /// <see cref="ushort"/>. The following equation can be used to convert a sample to microvolts:
         /// <code>
         /// Electrode Voltage (µV) = 0.195 × (ADC Sample – 32768)
         /// </code>
@@ -42,11 +43,13 @@ public Rhd2164DataFrame(ulong[] clock, ulong[] hubClock, Mat amplifierData, Mat
         /// Gets the buffered auxiliary data array. 
         /// </summary>
         /// <remarks>
-        /// Auxiliary samples are organized in 3xN matrix with rows representing electrophysiology channel
-        /// number and N columns representing sample index. Each column is a 3-channel vector of ADC samples
-        /// whose acquisition time is indicated by the corresponding elements in <see cref="DataFrame.Clock"/>
-        /// and <see cref="DataFrame.HubClock"/>. Each ADC sample is a 16-bit <see cref="ushort"/>. The
-        /// following equation can be used to convert a sample to volts:
+        /// Auxiliary samples are organized in 3xN matrix with rows representing auxiliary channel number and N
+        /// columns representing sample index. Channels are ordered in accordance with the Rhd2164 input
+        /// number specified on its datasheet (channel 0 corresponds to auxiliary input 0, channel 1
+        /// corresponds to auxiliary input 1, and channel 2 corresponds to auxiliary input 2). Each column is
+        /// a 3-channel vector of ADC samples whose acquisition time is indicated by the corresponding
+        /// elements in <see cref="DataFrame.Clock"/> and <see cref="DataFrame.HubClock"/>. Each ADC sample is
+        /// a 16-bit <see cref="ushort"/>. The following equation can be used to convert a sample to volts:
         /// <code>
         /// Auxiliary Voltage (V) = 0.0000374 × ADC Sample
         /// </code>