NeuropixelsV2eDataFrame.cs

using System.Runtime.InteropServices;
using OpenCV.Net;

namespace OpenEphys.Onix1
{
    /// <summary>
    /// Buffered data from a NeuropixelsV2e device.
    /// </summary>
    public class NeuropixelsV2eDataFrame : BufferedDataFrame
    {
        /// <summary>
        /// Initializes a new instance of the <see cref="NeuropixelsV2eDataFrame"/> class.
        /// </summary>
        /// <param name="clock">An array of <see cref="DataFrame.Clock"/> values.</param>
        /// <param name="hubClock">An array of hub clock counter values.</param>
        /// <param name="amplifierData">An array of multi-channel amplifier data.</param>
        public NeuropixelsV2eDataFrame(ulong[] clock, ulong[] hubClock, Mat amplifierData)
            : base(clock, hubClock)
        {
            AmplifierData = amplifierData;
        }

        /// <summary>
        /// Gets the amplifier data array.
        /// </summary>
        /// <remarks>
        /// Wide band (0.5 Hz - 10 kHz) electrophysiology data array. Each element is an amplified sample from
        /// 384 electrodes (rows) acquired at 30 kHz (columns). Each sample is a 12-bit, offset binary value
        /// encoded as a <see cref="ushort"/>. To convert to microvolts, the following equation can be used:
        /// <code>
        /// V_electrode (µV) = 3.05176 µV/bit × (ADC result – 2048) bits
        /// </code>
        /// </remarks>
        public Mat AmplifierData { get; }

        internal static unsafe ushort GetProbeIndex(oni.Frame frame)
        {
            var data = (NeuropixelsV2Payload*)frame.Data.ToPointer();
            return data->ProbeIndex;
        }

        internal static unsafe void CopyAmplifierBuffer(ushort* amplifierData, ushort[,] amplifierBuffer, int index, double gainCorrection)
        {
            // Loop over 16 "frames" within each "super-frame"
            for (int i = 0; i < NeuropixelsV2e.FramesPerSuperFrame; i++)
            {
                // The period of ADC data within data array is 36 words
                var adcDataOffset = i * NeuropixelsV2e.FrameWords;

                for (int k = 0; k < NeuropixelsV2e.AdcsPerProbe; k++)
                {
                    amplifierBuffer[RawToChannel[k, i], index] = (ushort)(gainCorrection * amplifierData[AdcIndicies[k] + adcDataOffset]);
                }
            }
        }

        // ADC & frame-index to channel mapping
        // First dimension: data index
        // Second dimension: frame index within super frame

        static readonly int[] AdcIndicies = {
            0, 1, 2,
            4, 5, 6,
            8, 9, 10,
            12, 13, 14,
            16, 17, 18,
            20, 21, 22,
            24, 25, 26,
            28, 29, 30
        };

        static readonly int[,] RawToChannel = {
            { 0, 2, 4, 6, 8, 10, 12, 14, 16, 18, 20, 22, 24, 26, 28, 30 },                          // Data Index 9, ADC 0
            { 128, 130, 132, 134, 136, 138, 140, 142, 144, 146, 148, 150, 152, 154, 156, 158 },     // Data Index 10, ADC 8
            { 256, 258, 260, 262, 264, 266, 268, 270, 272, 274, 276, 278, 280, 282, 284, 286 },     // Data Index 11, ADC 16

            { 1, 3, 5, 7, 9, 11, 13, 15, 17, 19, 21, 23, 25, 27, 29, 31 },                          // Data Index 13, ADC 1
            { 129, 131, 133, 135, 137, 139, 141, 143, 145, 147, 149, 151, 153, 155, 157, 159 },     // Data Index 14, ADC 9
            { 257, 259, 261, 263, 265, 267, 269, 271, 273, 275, 277, 279, 281, 283, 285, 287 },     // Data Index 15, ADC 17

            { 32, 34, 36, 38, 40, 42, 44, 46, 48, 50, 52, 54, 56, 58, 60, 62 },                     // Data Index 17, ADC 2
            { 160, 162, 164, 166, 168, 170, 172, 174, 176, 178, 180, 182, 184, 186, 188, 190 },     // Data Index 18, ADC 10
            { 288, 290, 292, 294, 296, 298, 300, 302, 304, 306, 308, 310, 312, 314, 316, 318 },     // Data Index 19, ADC 18

            { 33, 35, 37, 39, 41, 43, 45, 47, 49, 51, 53, 55, 57, 59, 61, 63 },                     // Data Index 21, ADC 3
            { 161, 163, 165, 167, 169, 171, 173, 175, 177, 179, 181, 183, 185, 187, 189, 191 },     // Data Index 22, ADC 11
            { 289, 291, 293, 295, 297, 299, 301, 303, 305, 307, 309, 311, 313, 315, 317, 319 },     // Data Index 23, ADC 19

            { 64, 66, 68, 70, 72, 74, 76, 78, 80, 82, 84, 86, 88, 90, 92, 94 },                     // Data Index 25, ADC 4
            { 192, 194, 196, 198, 200, 202, 204, 206, 208, 210, 212, 214, 216, 218, 220, 222 },     // Data Index 26, ADC 12
            { 320, 322, 324, 326, 328, 330, 332, 334, 336, 338, 340, 342, 344, 346, 348, 350 },     // Data Index 27, ADC 20

            { 65, 67, 69, 71, 73, 75, 77, 79, 81, 83, 85, 87, 89, 91, 93, 95 },                     // Data Index 29, ADC 5
            { 193, 195, 197, 199, 201, 203, 205, 207, 209, 211, 213, 215, 217, 219, 221, 223 },     // Data Index 30, ADC 13
            { 321, 323, 325, 327, 329, 331, 333, 335, 337, 339, 341, 343, 345, 347, 349, 351 },     // Data Index 31, ADC 21

            { 96, 98, 100, 102, 104, 106, 108, 110, 112, 114, 116, 118, 120, 122, 124, 126 },       // Data Index 33, ADC 6
            { 224, 226, 228, 230, 232, 234, 236, 238, 240, 242, 244, 246, 248, 250, 252, 254 },     // Data Index 34, ADC 14
            { 352, 354, 356, 358, 360, 362, 364, 366, 368, 370, 372, 374, 376, 378, 380, 382 },     // Data Index 35, ADC 22

            { 97, 99, 101, 103, 105, 107, 109, 111, 113, 115, 117, 119, 121, 123, 125, 127 },       // Data Index 37, ADC 7
            { 225, 227, 229, 231, 233, 235, 237, 239, 241, 243, 245, 247, 249, 251, 253, 255 },     // Data Index 38, ADC 15
            { 353, 355, 357, 359, 361, 363, 365, 367, 369, 371, 373, 375, 377, 379, 381, 383 },     // Data Index 39, ADC 23

        };
    }

    [StructLayout(LayoutKind.Sequential, Pack = 1)]
    unsafe struct NeuropixelsV2Payload
    {
        public ulong HubClock;
        public ushort ProbeIndex;
        public ulong Reserved;
        public fixed ushort AmplifierData[NeuropixelsV2e.ChannelCount];
    }
}