diff --git a/Directory.Build.props b/Directory.Build.props index 4c611c6a..20ad22c5 100644 --- a/Directory.Build.props +++ b/Directory.Build.props @@ -13,7 +13,7 @@ LICENSE true icon.png - 0.6.1 + 0.7.0 10.0 strict diff --git a/OpenEphys.Onix1/ConfigureNeuropixelsV1e.cs b/OpenEphys.Onix1/ConfigureNeuropixelsV1e.cs index 021a3e82..350ae4d9 100644 --- a/OpenEphys.Onix1/ConfigureNeuropixelsV1e.cs +++ b/OpenEphys.Onix1/ConfigureNeuropixelsV1e.cs @@ -183,7 +183,7 @@ public override IObservable Process(IObservable 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); diff --git a/OpenEphys.Onix1/Neuropixels.cs b/OpenEphys.Onix1/Neuropixels.cs new file mode 100644 index 00000000..2718db1e --- /dev/null +++ b/OpenEphys.Onix1/Neuropixels.cs @@ -0,0 +1,41 @@ +using System; +using System.Collections.Generic; +using System.Linq; + +namespace OpenEphys.Onix1 +{ + static class Neuropixels + { + internal static int[,] OrderChannelsByDepth(Electrode[] channelMap, int[,] frameIndex) + { + int rows = frameIndex.GetLength(0); + int cols = frameIndex.GetLength(1); + + var channelToPosition = new Dictionary(); + for (int row = 0; row < rows; row++) + { + for (int col = 0; col < cols; col++) + { + channelToPosition[frameIndex[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 (origRow, origCol) = channelToPosition[e.Channel]; + + spatialRawToChannel[origRow, origCol] = index++; + } + + return spatialRawToChannel; + } + } +} diff --git a/OpenEphys.Onix1/NeuropixelsV1eData.cs b/OpenEphys.Onix1/NeuropixelsV1eData.cs index c42de3fd..0908c24f 100644 --- a/OpenEphys.Onix1/NeuropixelsV1eData.cs +++ b/OpenEphys.Onix1/NeuropixelsV1eData.cs @@ -44,6 +44,18 @@ public int BufferSize set => bufferSize = (int)(Math.Ceiling((double)value / NeuropixelsV1.FramesPerRoundRobin) * NeuropixelsV1.FramesPerRoundRobin); } + /// + /// Gets or sets a boolean value that controls if the channels are ordered by depth. + /// + /// + /// If is false, then channels are ordered from 0 to 383. + /// If is true, then channels are ordered based on the depth + /// of the electrodes + /// + [Description("Determines if the channels are returned ordered by depth.")] + [Category(DeviceFactory.ConfigurationCategory)] + public bool OrderByDepth { get; set; } = false; + /// /// Generates a sequence of objects. /// @@ -52,6 +64,7 @@ public unsafe override IObservable Generate() { var spikeBufferSize = BufferSize; var lfpBufferSize = spikeBufferSize / NeuropixelsV1.FramesPerRoundRobin; + var orderByDepth = OrderByDepth; return DeviceManager.GetDevice(DeviceName).SelectMany(deviceInfo => { @@ -59,6 +72,7 @@ public unsafe override IObservable Generate() var device = info.GetDeviceContext(typeof(NeuropixelsV1e)); var passthrough = device.GetPassthroughDeviceContext(typeof(DS90UB9x)); var probeData = device.Context.GetDeviceFrames(passthrough.Address); + int[,] channelOrder = orderByDepth ? Neuropixels.OrderChannelsByDepth(info.ProbeConfiguration.ChannelMap, RawToChannel) : RawToChannel; return Observable.Create(observer => { @@ -73,7 +87,7 @@ public unsafe override IObservable 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) @@ -93,5 +107,43 @@ public unsafe override IObservable Generate() }); }); } + + // ADC to channel + // First dimension: ADC index + // Second dimension: frame index within super frame + // Output: channel number + static readonly int[,] RawToChannel = { + {0, 2, 4, 6, 8, 10, 12, 14, 16, 18, 20, 22 }, + {1, 3, 5, 7, 9, 11, 13, 15, 17, 19, 21, 23 }, + {24, 26, 28, 30, 32, 34, 36, 38, 40, 42, 44, 46 }, + {25, 27, 29, 31, 33, 35, 37, 39, 41, 43, 45, 47 }, + {48, 50, 52, 54, 56, 58, 60, 62, 64, 66, 68, 70 }, + {49, 51, 53, 55, 57, 59, 61, 63, 65, 67, 69, 71 }, + {72, 74, 76, 78, 80, 82, 84, 86, 88, 90, 92, 94 }, + {73, 75, 77, 79, 81, 83, 85, 87, 89, 91, 93, 95 }, + {96, 98, 100, 102, 104, 106, 108, 110, 112, 114, 116, 118 }, + {97, 99, 101, 103, 105, 107, 109, 111, 113, 115, 117, 119 }, + {120, 122, 124, 126, 128, 130, 132, 134, 136, 138, 140, 142 }, + {121, 123, 125, 127, 129, 131, 133, 135, 137, 139, 141, 143 }, + {144, 146, 148, 150, 152, 154, 156, 158, 160, 162, 164, 166 }, + {145, 147, 149, 151, 153, 155, 157, 159, 161, 163, 165, 167 }, + {168, 170, 172, 174, 176, 178, 180, 182, 184, 186, 188, 190 }, + {169, 171, 173, 175, 177, 179, 181, 183, 185, 187, 189, 191 }, + {192, 194, 196, 198, 200, 202, 204, 206, 208, 210, 212, 214 }, + {193, 195, 197, 199, 201, 203, 205, 207, 209, 211, 213, 215 }, + {216, 218, 220, 222, 224, 226, 228, 230, 232, 234, 236, 238 }, + {217, 219, 221, 223, 225, 227, 229, 231, 233, 235, 237, 239 }, + {240, 242, 244, 246, 248, 250, 252, 254, 256, 258, 260, 262 }, + {241, 243, 245, 247, 249, 251, 253, 255, 257, 259, 261, 263 }, + {264, 266, 268, 270, 272, 274, 276, 278, 280, 282, 284, 286 }, + {265, 267, 269, 271, 273, 275, 277, 279, 281, 283, 285, 287 }, + {288, 290, 292, 294, 296, 298, 300, 302, 304, 306, 308, 310 }, + {289, 291, 293, 295, 297, 299, 301, 303, 305, 307, 309, 311 }, + {312, 314, 316, 318, 320, 322, 324, 326, 328, 330, 332, 334 }, + {313, 315, 317, 319, 321, 323, 325, 327, 329, 331, 333, 335 }, + {336, 338, 340, 342, 344, 346, 348, 350, 352, 354, 356, 358 }, + {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 } }; } } diff --git a/OpenEphys.Onix1/NeuropixelsV1eDataFrame.cs b/OpenEphys.Onix1/NeuropixelsV1eDataFrame.cs index 82b71024..2adcbf77 100644 --- a/OpenEphys.Onix1/NeuropixelsV1eDataFrame.cs +++ b/OpenEphys.Onix1/NeuropixelsV1eDataFrame.cs @@ -4,7 +4,7 @@ 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) { var frameCountStartIndex = index * NeuropixelsV1.FramesPerSuperFrame; frameCountBuffer[frameCountStartIndex] = (amplifierData[31] << 10) | (amplifierData[39] << 0); @@ -23,7 +23,7 @@ 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 +35,7 @@ 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 +46,7 @@ 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 +58,7 @@ 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); @@ -76,44 +76,6 @@ internal static unsafe void CopyAmplifierBuffer(ushort* amplifierData, int[] fra 5, 13, 21, 29, 37, 6, 14, 22, 30, 38, 7, 15 }; - - // ADC to channel - // First dimension: ADC index - // Second dimension: frame index within super frame - // Output: channel number - static readonly int[,] RawToChannel = { - {0, 2, 4, 6, 8, 10, 12, 14, 16, 18, 20, 22 }, - {1, 3, 5, 7, 9, 11, 13, 15, 17, 19, 21, 23 }, - {24, 26, 28, 30, 32, 34, 36, 38, 40, 42, 44, 46 }, - {25, 27, 29, 31, 33, 35, 37, 39, 41, 43, 45, 47 }, - {48, 50, 52, 54, 56, 58, 60, 62, 64, 66, 68, 70 }, - {49, 51, 53, 55, 57, 59, 61, 63, 65, 67, 69, 71 }, - {72, 74, 76, 78, 80, 82, 84, 86, 88, 90, 92, 94 }, - {73, 75, 77, 79, 81, 83, 85, 87, 89, 91, 93, 95 }, - {96, 98, 100, 102, 104, 106, 108, 110, 112, 114, 116, 118 }, - {97, 99, 101, 103, 105, 107, 109, 111, 113, 115, 117, 119 }, - {120, 122, 124, 126, 128, 130, 132, 134, 136, 138, 140, 142 }, - {121, 123, 125, 127, 129, 131, 133, 135, 137, 139, 141, 143 }, - {144, 146, 148, 150, 152, 154, 156, 158, 160, 162, 164, 166 }, - {145, 147, 149, 151, 153, 155, 157, 159, 161, 163, 165, 167 }, - {168, 170, 172, 174, 176, 178, 180, 182, 184, 186, 188, 190 }, - {169, 171, 173, 175, 177, 179, 181, 183, 185, 187, 189, 191 }, - {192, 194, 196, 198, 200, 202, 204, 206, 208, 210, 212, 214 }, - {193, 195, 197, 199, 201, 203, 205, 207, 209, 211, 213, 215 }, - {216, 218, 220, 222, 224, 226, 228, 230, 232, 234, 236, 238 }, - {217, 219, 221, 223, 225, 227, 229, 231, 233, 235, 237, 239 }, - {240, 242, 244, 246, 248, 250, 252, 254, 256, 258, 260, 262 }, - {241, 243, 245, 247, 249, 251, 253, 255, 257, 259, 261, 263 }, - {264, 266, 268, 270, 272, 274, 276, 278, 280, 282, 284, 286 }, - {265, 267, 269, 271, 273, 275, 277, 279, 281, 283, 285, 287 }, - {288, 290, 292, 294, 296, 298, 300, 302, 304, 306, 308, 310 }, - {289, 291, 293, 295, 297, 299, 301, 303, 305, 307, 309, 311 }, - {312, 314, 316, 318, 320, 322, 324, 326, 328, 330, 332, 334 }, - {313, 315, 317, 319, 321, 323, 325, 327, 329, 331, 333, 335 }, - {336, 338, 340, 342, 344, 346, 348, 350, 352, 354, 356, 358 }, - {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 } }; } [StructLayout(LayoutKind.Sequential, Pack = 1)] diff --git a/OpenEphys.Onix1/NeuropixelsV1eDeviceInfo.cs b/OpenEphys.Onix1/NeuropixelsV1eDeviceInfo.cs index 50a54f5e..30eb5685 100644 --- a/OpenEphys.Onix1/NeuropixelsV1eDeviceInfo.cs +++ b/OpenEphys.Onix1/NeuropixelsV1eDeviceInfo.cs @@ -4,7 +4,7 @@ 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; @@ -12,6 +12,7 @@ public NeuropixelsV1eDeviceInfo(ContextTask context, Type deviceType, uint devic AdcThresholds = probeControl.AdcThresholds; AdcOffsets = probeControl.AdcOffsets; InvertPolarity = invertPolarity; + ProbeConfiguration = probeConfiguration; } public double ApGainCorrection { get; } @@ -19,5 +20,6 @@ public NeuropixelsV1eDeviceInfo(ContextTask context, Type deviceType, uint devic public ushort[] AdcThresholds { get; } public ushort[] AdcOffsets { get; } public bool InvertPolarity { get; } + public NeuropixelsV1ProbeConfiguration ProbeConfiguration { get; } } }