Make use of NeuropixelsV1Helper in Nric1384 configuration

- Remove some redundancy when parsing calibration files
- Fix error in NeuropixelsV1eAdcCalibration that is preventing any valid
  file from being parsed

OpenEphys.Onix1.Design/NeuropixelsV1eDialog.cs

@@ -269,7 +269,8 @@ private void CheckStatus()
             {
                 gainCorrection = NeuropixelsV1Helper.TryParseGainCalibrationFile(ConfigureNode.GainCalibrationFile, 
                                                                                  ConfigureNode.ProbeConfiguration.SpikeAmplifierGain,
-                                                                                 ConfigureNode.ProbeConfiguration.LfpAmplifierGain);
+                                                                                 ConfigureNode.ProbeConfiguration.LfpAmplifierGain,
+                                                                                 960);
             }
             catch (IOException ex)
             {

OpenEphys.Onix1/ConfigureNric1384.cs

@@ -5,7 +5,7 @@
 namespace OpenEphys.Onix1
 {
     /// <summary>
-    /// Configures a Nric184 bioacquisition device.
+    /// Configures a Nric184 bioacquisition chip.
     /// </summary>
     public class ConfigureNric1384 : SingleDeviceFactory
     {
@@ -141,6 +141,8 @@ static class Nric1384
         public const int ID = 33;
 
         public const int I2cAddress = 0x70;
+        public const int ChannelCount = 384;
+        public const int ElectrodeCount = 384;
 
         // managed registers
         public const uint ENABLE = 0x8000; // Enable or disable the data output stream

OpenEphys.Onix1/NeuropixelsV1Helper.cs

@@ -63,7 +63,7 @@ public static class NeuropixelsV1Helper
                                                    .Where(l => l.Ok)
                                                    .Select(l => l.Param);
 
-                           return calibrationValues.Count() == NumberOfAdcParameters
+                           return calibrationValues.Count() != NumberOfAdcParameters
                            ? null
                            : new NeuropixelsV1eAdc {
                                CompP = calibrationValues.ElementAt(0),
@@ -99,13 +99,13 @@ public static class NeuropixelsV1Helper
         /// <param name="apGain">Current <see cref="NeuropixelsV1Gain"/> for the AP data.</param>
         /// <param name="lfpGain">Current <see cref="NeuropixelsV1Gain"/> for the LFP data.</param>
         /// <returns><see cref="NeuropixelsV1eGainCorrection"/> object that contains the AP and LFP gain correction values. This object is null if the file was not successfully parsed.</returns>
-        public static NeuropixelsV1eGainCorrection? TryParseGainCalibrationFile(string gainCalibrationFile, NeuropixelsV1Gain apGain, NeuropixelsV1Gain lfpGain)
+        public static NeuropixelsV1eGainCorrection? TryParseGainCalibrationFile(string gainCalibrationFile, NeuropixelsV1Gain apGain, NeuropixelsV1Gain lfpGain, int electrodeCount)
         {
             if (!File.Exists(gainCalibrationFile)) return null;
 
             var lines = File.ReadLines(gainCalibrationFile);
 
-            if (lines.Count() != NeuropixelsV1e.ElectrodeCount + 1) return null;
+            if (lines.Count() != electrodeCount + 1) return null;
             if (!ulong.TryParse(lines.ElementAt(0), out var serialNumber)) return null;
 
             if (!lines
@@ -117,7 +117,7 @@ public static class NeuropixelsV1Helper
                 })
                 .Where(l => l.Ok)
                 .Select(l => l.Channel)
-                .SequenceEqual(Enumerable.Range(0, NeuropixelsV1e.ElectrodeCount))) return null;
+                .SequenceEqual(Enumerable.Range(0, electrodeCount))) return null;
 
             var apIndex = Array.IndexOf(Enum.GetValues(typeof(NeuropixelsV1Gain)), apGain);
             var apGainCorrections = lines

OpenEphys.Onix1/NeuropixelsV1eRegisterContext.cs

@@ -51,7 +51,8 @@ public NeuropixelsV1eRegisterContext(DeviceContext deviceContext, uint i2cAddres
                     $"match the ADC calibration file serial number: {adcCalibration.Value.SerialNumber}.");
             }
 
-            var gainCorrection = NeuropixelsV1Helper.TryParseGainCalibrationFile(gainCalibrationFile, probeConfiguration.SpikeAmplifierGain, probeConfiguration.LfpAmplifierGain);
+            var gainCorrection = NeuropixelsV1Helper.TryParseGainCalibrationFile(gainCalibrationFile, 
+                probeConfiguration.SpikeAmplifierGain, probeConfiguration.LfpAmplifierGain, NeuropixelsV1e.ElectrodeCount);
 
             if (!gainCorrection.HasValue)
             {

OpenEphys.Onix1/Nric1384RegisterContext.cs

@@ -1,6 +1,6 @@
 using System;
 using System.Collections;
-using System.Linq;
+using System.IO;
 
 namespace OpenEphys.Onix1
 {
@@ -13,7 +13,6 @@ class Nric1384RegisterContext : I2CRegisterContext
         const byte ReferenceSource = 0b001; // All, hardcoded
         const int BaseConfigurationBitCount = 2448;
         const int BaseConfigurationConfigOffset = 576;
-        const int NumberOfGains = 8;
         const uint ShiftRegisterSuccess = 1 << 7;
 
         readonly DeviceContext device;
@@ -24,51 +23,42 @@ class Nric1384RegisterContext : I2CRegisterContext
         public Nric1384RegisterContext(DeviceContext deviceContext, NeuropixelsV1Gain apGain, NeuropixelsV1Gain lfpGain, bool apFilter, string gainCalibrationFile, string adcCalibrationFile)
             : base(deviceContext, Nric1384.I2cAddress)
         {
+
             device = deviceContext;
 
-            if (gainCalibrationFile == null || adcCalibrationFile == null)
+            if (!File.Exists(gainCalibrationFile))
             {
-                throw new ArgumentException("Calibration files must be specified.");
+                throw new ArgumentException("A gain calibration file must be specified for the Nric1384 chip.");
             }
 
-            System.IO.StreamReader gainFile = new(gainCalibrationFile);
-            var sn = UInt64.Parse(gainFile.ReadLine());
-
-            System.IO.StreamReader adcFile = new(adcCalibrationFile);
-            if (sn != UInt64.Parse(adcFile.ReadLine()))
-                throw new ArgumentException("Calibration file serial numbers do not match.");
+            if (!File.Exists(adcCalibrationFile))
+            {
+                throw new ArgumentException("An ADC calibration file must be specified for the Nric1384 chip.");
+            }
 
-            // parse gain correction file
-            var gainCorrections = gainFile.ReadLine().Split(',').Skip(1);
+            var adcCalibration = NeuropixelsV1Helper.TryParseAdcCalibrationFile(adcCalibrationFile);
 
-            if (gainCorrections.Count() != 2 * NumberOfGains)
-                throw new ArgumentException("Incorrectly formatted gain correction calibration file.");
+            if (!adcCalibration.HasValue)
+            {
+                throw new ArgumentException($"The calibration file \"{adcCalibrationFile}\" is invalid.");
+            }
 
-            ApGainCorrection = double.Parse(gainCorrections.ElementAt(Array.IndexOf(Enum.GetValues(typeof(NeuropixelsV1Gain)), apGain)));
-            LfpGainCorrection = double.Parse(gainCorrections.ElementAt(Array.IndexOf(Enum.GetValues(typeof(NeuropixelsV1Gain)), lfpGain) + 8));
+            var gainCorrection = NeuropixelsV1Helper.TryParseGainCalibrationFile(gainCalibrationFile,apGain, lfpGain, Nric1384.ElectrodeCount);
 
-            // parse ADC calibration file
-            for (var i = 0; i < NeuropixelsV1e.AdcCount; i++)
+            if (!gainCorrection.HasValue)
             {
-                var adcCal = adcFile.ReadLine().Split(',').Skip(1);
-                if (adcCal.Count() != NumberOfGains)
-                {
-                    throw new ArgumentException("Incorrectly formatted ADC calibration file.");
-                }
+                throw new ArgumentException($"The calibration file \"{gainCalibrationFile}\" is invalid.");
+            }
 
-                Adcs[i] = new NeuropixelsV1eAdc
-                {
-                    CompP = int.Parse(adcCal.ElementAt(0)),
-                    CompN = int.Parse(adcCal.ElementAt(1)),
-                    Slope = int.Parse(adcCal.ElementAt(2)),
-                    Coarse = int.Parse(adcCal.ElementAt(3)),
-                    Fine = int.Parse(adcCal.ElementAt(4)),
-                    Cfix = int.Parse(adcCal.ElementAt(5)),
-                    Offset = int.Parse(adcCal.ElementAt(6)),
-                    Threshold = int.Parse(adcCal.ElementAt(7))
-                };
+            if (adcCalibration.Value.SerialNumber != gainCorrection.Value.SerialNumber)
+            {
+                throw new ArgumentException($"The ADC calibration file's serial number ({adcCalibration.Value.SerialNumber}) " +
+                    $"does not match the gain calibration file's serial number ({gainCorrection.Value.SerialNumber}).");
             }
 
+            ApGainCorrection = gainCorrection.Value.ApGainCorrectionFactor;
+            LfpGainCorrection = gainCorrection.Value.LfpGainCorrectionFactor;
+
             // create shift-register bit arrays
             for (int i = 0; i < NeuropixelsV1e.ChannelCount; i++)
             {
@@ -100,6 +90,8 @@ public Nric1384RegisterContext(DeviceContext deviceContext, NeuropixelsV1Gain ap
 
             }
 
+            Adcs = adcCalibration.Value.Adcs;
+
             int k = 0;
             foreach (var adc in Adcs)
             {
@@ -172,7 +164,6 @@ public Nric1384RegisterContext(DeviceContext deviceContext, NeuropixelsV1Gain ap
                 BaseConfigs[configIdx][slopeOffset + 8] = cfix[1];
                 BaseConfigs[configIdx][slopeOffset + 9] = cfix[2];
                 BaseConfigs[configIdx][slopeOffset + 10] = cfix[3];
-
             }
         }
 
@@ -201,7 +192,7 @@ public void WriteShiftRegisters()
 
                 for (int j = 0; j < 2; j++)
                 {
-                    var baseBytes = BitArrayToBytes(BaseConfigs[i]);
+                    var baseBytes = BitHelper.ToBitReversedBytes(BaseConfigs[i]);
 
                     WriteByte(Nric1384.SR_LENGTH1, (uint)baseBytes.Length % 0x100);
                     WriteByte(Nric1384.SR_LENGTH2, (uint)baseBytes.Length / 0x100);
@@ -218,30 +209,17 @@ public void WriteShiftRegisters()
                 }
             }
 
-            // gain corrections
-            device.WriteRegister(Nric1384.LFP_GAIN, (uint)(LfpGainCorrection * (1 << 14)));
-            device.WriteRegister(Nric1384.AP_GAIN, (uint)(ApGainCorrection * (1 << 14)));
-        }
-
-        // Bits go into the shift registers MSB first
-        // This creates a *bit-reversed* byte array from a bit array
-        private static byte[] BitArrayToBytes(BitArray bits)
-        {
-            if (bits.Length == 0)
+            // write adc thresholds and offsets
+            for (uint i = 0; i < Adcs.Length; i++)
             {
-                throw new ArgumentException("Shift register data is empty", nameof(bits));
+                var thresh = (uint)Adcs[i].Threshold;
+                var offset = (uint)Adcs[i].Offset;    
+                device.WriteRegister(Nric1384.ADC00_OFF_THRESH + i, offset << 10 | thresh);
             }
 
-            var bytes = new byte[(bits.Length - 1) / 8 + 1];
-            bits.CopyTo(bytes, 0);
-
-            for (int i = 0; i < bytes.Length; i++)
-            {
-                // NB: http://graphics.stanford.edu/~seander/bithacks.html
-                bytes[i] = (byte)((bytes[i] * 0x0202020202ul & 0x010884422010ul) % 1023);
-            }
-
-            return bytes;
+            // gain corrections
+            device.WriteRegister(Nric1384.LFP_GAIN, (uint)(LfpGainCorrection * (1 << 14)));
+            device.WriteRegister(Nric1384.AP_GAIN, (uint)(ApGainCorrection * (1 << 14)));
         }
     }
 }