Tweaks for passthrough devices and miniscope fixes

OpenEphys.Onix1/ConfigureNeuropixelsV1e.cs

@@ -141,8 +141,7 @@ public override IObservable<ContextTask> Process(IObservable<ContextTask> source
                 var serializer = new I2CRegisterContext(device, DS90UB9x.SER_ADDR);
 
                 // set I2C clock rate to ~400 kHz
-                serializer.WriteByte((uint)DS90UB9xSerializerI2CRegister.SCLHIGH, 20);
-                serializer.WriteByte((uint)DS90UB9xSerializerI2CRegister.SCLLOW, 20);
+                DS90UB9x.Set933I2CRate(device, 400e3);
 
                 // read probe metadata
                 var probeMetadata = new NeuropixelsV1eMetadata(serializer);
@@ -167,8 +166,8 @@ public override IObservable<ContextTask> Process(IObservable<ContextTask> source
                 var deviceInfo = new NeuropixelsV1eDeviceInfo(context, DeviceType, deviceAddress, probeControl);
                 var shutdown = Disposable.Create(() =>
                 {
-                    serializer.WriteByte((uint)DS90UB9xSerializerI2CRegister.GPIO10, NeuropixelsV1e.DefaultGPO10Config);
-                    serializer.WriteByte((uint)DS90UB9xSerializerI2CRegister.GPIO32, NeuropixelsV1e.DefaultGPO32Config);
+                    serializer.WriteByte((uint)DS90UB933SerializerI2CRegister.Gpio10, NeuropixelsV1e.DefaultGPO10Config);
+                    serializer.WriteByte((uint)DS90UB933SerializerI2CRegister.Gpio32, NeuropixelsV1e.DefaultGPO32Config);
                 });
                 return new CompositeDisposable(
                     DeviceManager.RegisterDevice(deviceName, deviceInfo),
@@ -194,10 +193,10 @@ static void ConfigureDeserializer(DeviceContext device)
             device.WriteRegister(DS90UB9x.DATALINES0, 0x3245106B); // Sync, psb[0], psb[1], psb[2], psb[3], psb[4], psb[5], psb[6],
             device.WriteRegister(DS90UB9x.DATALINES1, 0xFFFFFFFF);
 
+            DS90UB9x.Initialize933SerDesLink(device, DS90UB9xMode.Raw12BitHighFrequency);
+
             // configure deserializer I2C aliases
             var deserializer = new I2CRegisterContext(device, DS90UB9x.DES_ADDR);
-            uint coaxMode = 0x4 + (uint)DS90UB9xMode.Raw12BitHighFrequency; // 0x4 maintains coax mode
-            deserializer.WriteByte((uint)DS90UB9xDeserializerI2CRegister.PortMode, coaxMode);
 
             uint alias = NeuropixelsV1e.ProbeAddress << 1;
             deserializer.WriteByte((uint)DS90UB9xDeserializerI2CRegister.SlaveID1, alias);
@@ -211,16 +210,16 @@ static void ConfigureDeserializer(DeviceContext device)
         static void ResetProbe(I2CRegisterContext serializer, uint gpo10Config)
         {
             gpo10Config &= ~NeuropixelsV1e.Gpo10ResetMask;
-            serializer.WriteByte((uint)DS90UB9xSerializerI2CRegister.GPIO10, gpo10Config);
+            serializer.WriteByte((uint)DS90UB933SerializerI2CRegister.Gpio10, gpo10Config);
             Thread.Sleep(1);
             gpo10Config |= NeuropixelsV1e.Gpo10ResetMask;
-            serializer.WriteByte((uint)DS90UB9xSerializerI2CRegister.GPIO10, gpo10Config);
+            serializer.WriteByte((uint)DS90UB933SerializerI2CRegister.Gpio10, gpo10Config);
         }
 
         static uint TurnOnLed(I2CRegisterContext serializer, uint gpo23Config)
         {
             gpo23Config &= ~NeuropixelsV1e.Gpo32LedMask;
-            serializer.WriteByte((uint)DS90UB9xSerializerI2CRegister.GPIO32, gpo23Config);
+            serializer.WriteByte((uint)DS90UB933SerializerI2CRegister.Gpio32, gpo23Config);
 
             return gpo23Config;
         }

OpenEphys.Onix1/ConfigureNeuropixelsV2e.cs

@@ -137,9 +137,8 @@ public override IObservable<ContextTask> Process(IObservable<ContextTask> source
                 var gpo10Config = EnableProbeSupply(serializer);
 
                 // set I2C clock rate to ~400 kHz
-                serializer.WriteByte((uint)DS90UB9xSerializerI2CRegister.SCLHIGH, 20);
-                serializer.WriteByte((uint)DS90UB9xSerializerI2CRegister.SCLLOW, 20);
-
+                DS90UB9x.Set933I2CRate(device, 400e3);
+
                 // read probe metadata
                 var probeAMetadata = ReadProbeMetadata(serializer, NeuropixelsV2e.ProbeASelected);
                 var probeBMetadata = ReadProbeMetadata(serializer, NeuropixelsV2e.ProbeBSelected);
@@ -210,7 +209,7 @@ public override IObservable<ContextTask> Process(IObservable<ContextTask> source
                 var deviceInfo = new NeuropixelsV2eDeviceInfo(context, DeviceType, deviceAddress, gainCorrectionA, gainCorrectionB);
                 var shutdown = Disposable.Create(() =>
                 {
-                    serializer.WriteByte((uint)DS90UB9xSerializerI2CRegister.GPIO10, NeuropixelsV2e.DefaultGPO10Config);
+                    serializer.WriteByte((uint)DS90UB933SerializerI2CRegister.Gpio10, NeuropixelsV2e.DefaultGPO10Config);
                     SelectProbe(serializer, NeuropixelsV2e.NoProbeSelected);
                 });
                 return new CompositeDisposable(
@@ -237,10 +236,10 @@ static void ConfigureDeserializer(DeviceContext device)
             device.WriteRegister(DS90UB9x.DATALINES0, 0xFFFFF8A6); // NP A
             device.WriteRegister(DS90UB9x.DATALINES1, 0xFFFFF97B); // NP B
 
+            DS90UB9x.Initialize933SerDesLink(device, DS90UB9xMode.Raw12BitHighFrequency);
+
             // configure deserializer I2C aliases
             var deserializer = new I2CRegisterContext(device, DS90UB9x.DES_ADDR);
-            uint coaxMode = 0x4 + (uint)DS90UB9xMode.Raw12BitHighFrequency; // 0x4 maintains coax mode
-            deserializer.WriteByte((uint)DS90UB9xDeserializerI2CRegister.PortMode, coaxMode);
 
             uint alias = NeuropixelsV2e.ProbeAddress << 1;
             deserializer.WriteByte((uint)DS90UB9xDeserializerI2CRegister.SlaveID1, alias);
@@ -257,7 +256,7 @@ static uint EnableProbeSupply(I2CRegisterContext serializer)
             SelectProbe(serializer, NeuropixelsV2e.NoProbeSelected);
 
             // turn on analog supply and wait for boot
-            serializer.WriteByte((uint)DS90UB9xSerializerI2CRegister.GPIO10, gpo10Config);
+            serializer.WriteByte((uint)DS90UB933SerializerI2CRegister.Gpio10, gpo10Config);
             System.Threading.Thread.Sleep(20);
             return gpo10Config;
         }
@@ -269,16 +268,16 @@ static NeuropixelsV2eMetadata ReadProbeMetadata(I2CRegisterContext serializer, b
         }
         static void SelectProbe(I2CRegisterContext serializer, byte probeSelect)
         {
-            serializer.WriteByte((uint)DS90UB9xSerializerI2CRegister.GPIO32, probeSelect);
+            serializer.WriteByte((uint)DS90UB933SerializerI2CRegister.Gpio32, probeSelect);
             System.Threading.Thread.Sleep(20);
         }
 
         static void ResetProbes(I2CRegisterContext serializer, uint gpo10Config)
         {
             gpo10Config &= ~NeuropixelsV2e.GPO10ResetMask;
-            serializer.WriteByte((uint)DS90UB9xSerializerI2CRegister.GPIO10, gpo10Config);
+            serializer.WriteByte((uint)DS90UB933SerializerI2CRegister.Gpio10, gpo10Config);
             gpo10Config |= NeuropixelsV2e.GPO10ResetMask;
-            serializer.WriteByte((uint)DS90UB9xSerializerI2CRegister.GPIO10, gpo10Config);
+            serializer.WriteByte((uint)DS90UB933SerializerI2CRegister.Gpio10, gpo10Config);
         }
 
         static void ConfigureProbeStreaming(I2CRegisterContext i2cNP)

OpenEphys.Onix1/ConfigureNeuropixelsV2eBeta.cs

@@ -150,12 +150,11 @@ public override IObservable<ContextTask> Process(IObservable<ContextTask> source
                 var serializer = new I2CRegisterContext(device, DS90UB9x.SER_ADDR);
                 var gpo10Config = NeuropixelsV2eBeta.DefaultGPO10Config;
                 var gpo32Config = NeuropixelsV2eBeta.DefaultGPO32Config;
-                serializer.WriteByte((uint)DS90UB9xSerializerI2CRegister.GPIO10, gpo10Config);
-                serializer.WriteByte((uint)DS90UB9xSerializerI2CRegister.GPIO32, gpo32Config);
+                serializer.WriteByte((uint)DS90UB933SerializerI2CRegister.Gpio10, gpo10Config);
+                serializer.WriteByte((uint)DS90UB933SerializerI2CRegister.Gpio32, gpo32Config);
 
                 // set I2C clock rate to ~400 kHz
-                serializer.WriteByte((uint)DS90UB9xSerializerI2CRegister.SCLHIGH, 20);
-                serializer.WriteByte((uint)DS90UB9xSerializerI2CRegister.SCLLOW, 20);
+                DS90UB9x.Set933I2CRate(device, 400e3);
 
                 // read probe metadata
                 var probeAMetadata = ReadProbeMetadata(serializer, ref gpo32Config, NeuropixelsV2eBeta.SelectProbeA);
@@ -170,7 +169,7 @@ public override IObservable<ContextTask> Process(IObservable<ContextTask> source
                 // REC_NRESET and NRESET go high on both probes to take the ASIC out of reset
                 // TODO: not sure if REC_NRESET and NRESET are tied together on flex
                 gpo10Config |= NeuropixelsV2eBeta.GPO10ResetMask | NeuropixelsV2eBeta.GPO10NResetMask;
-                serializer.WriteByte((uint)DS90UB9xSerializerI2CRegister.GPIO10, gpo10Config);
+                serializer.WriteByte((uint)DS90UB933SerializerI2CRegister.Gpio10, gpo10Config);
                 System.Threading.Thread.Sleep(20);
 
                 // configure probe streaming
@@ -227,7 +226,7 @@ public override IObservable<ContextTask> Process(IObservable<ContextTask> source
 
                 // toggle probe LED
                 gpo32Config = (gpo32Config & ~NeuropixelsV2eBeta.GPO32LedMask) | (EnableLed ? 0 : NeuropixelsV2eBeta.GPO32LedMask);
-                serializer.WriteByte((uint)DS90UB9xSerializerI2CRegister.GPIO32, gpo32Config);
+                serializer.WriteByte((uint)DS90UB933SerializerI2CRegister.Gpio32, gpo32Config);
 
                 // Both probes are now streaming, hit them with a mux reset to (roughly) sync.
                 // NB: We have found that this gives PCLK-level synchronization MOST of the time.
@@ -238,8 +237,8 @@ public override IObservable<ContextTask> Process(IObservable<ContextTask> source
                 var deviceInfo = new NeuropixelsV2eDeviceInfo(context, DeviceType, deviceAddress, gainCorrectionA, gainCorrectionB);
                 var shutdown = Disposable.Create(() =>
                 {
-                    serializer.WriteByte((uint)DS90UB9xSerializerI2CRegister.GPIO10, NeuropixelsV2eBeta.DefaultGPO10Config);
-                    serializer.WriteByte((uint)DS90UB9xSerializerI2CRegister.GPIO32, NeuropixelsV2eBeta.DefaultGPO32Config);
+                    serializer.WriteByte((uint)DS90UB933SerializerI2CRegister.Gpio10, NeuropixelsV2eBeta.DefaultGPO10Config);
+                    serializer.WriteByte((uint)DS90UB933SerializerI2CRegister.Gpio32, NeuropixelsV2eBeta.DefaultGPO32Config);
                 });
                 return new CompositeDisposable(
                     DeviceManager.RegisterDevice(deviceName, deviceInfo),
@@ -265,10 +264,10 @@ static void ConfigureDeserializer(DeviceContext device)
             device.WriteRegister(DS90UB9x.DATALINES0, 0x00007654); // NP A
             device.WriteRegister(DS90UB9x.DATALINES1, 0x00000123); // NP B
 
+            DS90UB9x.Initialize933SerDesLink(device, DS90UB9xMode.Raw12BitHighFrequency);
+
             // configure deserializer I2C aliases
             var deserializer = new I2CRegisterContext(device, DS90UB9x.DES_ADDR);
-            uint coaxMode = 0x4 + (uint)DS90UB9xMode.Raw12BitHighFrequency; // 0x4 maintains coax mode
-            deserializer.WriteByte((uint)DS90UB9xDeserializerI2CRegister.PortMode, coaxMode);
 
             uint alias = NeuropixelsV2eBeta.ProbeAddress << 1;
             deserializer.WriteByte((uint)DS90UB9xDeserializerI2CRegister.SlaveID1, alias);
@@ -293,17 +292,17 @@ static void SelectProbe(I2CRegisterContext serializer, ref uint gpo32Config, byt
                 NeuropixelsV2eBeta.SelectProbeB => gpo32Config & ~NeuropixelsV2eBeta.ProbeSelectMask,
                 _ => gpo32Config
             };
-            serializer.WriteByte((uint)DS90UB9xSerializerI2CRegister.GPIO32, gpo32Config);
+            serializer.WriteByte((uint)DS90UB933SerializerI2CRegister.Gpio32, gpo32Config);
             System.Threading.Thread.Sleep(20);
         }
 
         static void SyncProbes(I2CRegisterContext serializer, uint gpo10Config)
         {
             gpo10Config &= ~NeuropixelsV2eBeta.GPO10NResetMask;
-            serializer.WriteByte((uint)DS90UB9xSerializerI2CRegister.GPIO10, gpo10Config);
+            serializer.WriteByte((uint)DS90UB933SerializerI2CRegister.Gpio10, gpo10Config);
 
             gpo10Config |= NeuropixelsV2eBeta.GPO10NResetMask;
-            serializer.WriteByte((uint)DS90UB9xSerializerI2CRegister.GPIO10, gpo10Config);
+            serializer.WriteByte((uint)DS90UB933SerializerI2CRegister.Gpio10, gpo10Config);
         }
 
         static void ConfigureProbeStreaming(I2CRegisterContext i2cNP)

OpenEphys.Onix1/ConfigureUclaMiniscopeV4.cs

@@ -158,13 +158,15 @@ override protected bool CheckLinkState(DeviceContext device)
                 const int FailureToWriteRegister = -6;
                 try
                 {
+                    ConfigureUclaMiniscopeV4Camera.ConfigureSerializer(ds90ub9x);
                     ConfigureUclaMiniscopeV4Camera.ConfigureCameraSystem(ds90ub9x, Camera.FrameRate, Camera.InterleaveLed);
                 }
                 catch (ONIException ex) when (ex.Number == FailureToWriteRegister)
                 {
                     return false;
                 }
 
+                Thread.Sleep(150);
                 var linkState = device.ReadRegister(PortController.LINKSTATE);
                 return (linkState & PortController.LINKSTATE_SL) != 0;
             }

OpenEphys.Onix1/ConfigureUclaMiniscopeV4Camera.cs

@@ -3,7 +3,6 @@
 using System.Drawing.Design;
 using System.Reactive.Disposables;
 using System.Reactive.Subjects;
-using System.Threading;
 using System.Xml.Serialization;
 using Bonsai;
 
@@ -190,15 +189,10 @@
             // acquisition. For this reason, the frame start needs to be marked.
             device.WriteRegister(DS90UB9x.MARK, (uint)DS90UB9xMarkMode.VsyncRising);
 
-            // set I2C clock rate to ~100 kHz
-            var deserializer = new I2CRegisterContext(device, DS90UB9x.DES_ADDR);
-            deserializer.WriteByte((uint)DS90UB9xSerializerI2CRegister.SCLHIGH, 0x7A);
-            deserializer.WriteByte((uint)DS90UB9xSerializerI2CRegister.SCLLOW, 0x7A);
-
-            // configure deserializer I2C aliases
-            uint coaxMode = 0x4 + (uint)DS90UB9xMode.Raw12BitLowFrequency; // 0x4 maintains coax mode
-            deserializer.WriteByte((uint)DS90UB9xDeserializerI2CRegister.PortMode, coaxMode);
+            DS90UB9x.Initialize933SerDesLink(device, DS90UB9xMode.Raw12BitLowFrequency);
 
+            var deserializer = new I2CRegisterContext(device, DS90UB9x.DES_ADDR);
+
             uint i2cAlias = UclaMiniscopeV4.AtMegaAddress << 1;
             deserializer.WriteByte((uint)DS90UB9xDeserializerI2CRegister.SlaveID1, i2cAlias);
             deserializer.WriteByte((uint)DS90UB9xDeserializerI2CRegister.SlaveAlias1, i2cAlias);
@@ -212,16 +206,21 @@
             deserializer.WriteByte((uint)DS90UB9xDeserializerI2CRegister.SlaveAlias3, i2cAlias);
         }
 
+        internal static void ConfigureSerializer(DeviceContext device)
+        {
+            DS90UB9x.Set933I2CRate(device, 80e3); //This is an arbitrary value that is proven to work, we need to test speed vs reliability vs bno sampling speed
+        }
+
         internal static void ConfigureCameraSystem(DeviceContext device, UclaMiniscopeV4FramesPerSecond frameRate, bool interleaveLed)
         {
             const int WaitUntilPllSettles = 200;
 
             // set up Python480
             var atMega = new I2CRegisterContext(device, UclaMiniscopeV4.AtMegaAddress);
             WriteCameraRegister(atMega, 16, 3); // Turn on PLL
-            Thread.Sleep(WaitUntilPllSettles);
+            //Thread.Sleep(WaitUntilPllSettles); //This sometimes has good effects, sometimes adverse, we just might want to redo this entire section (see issue #331 )
             WriteCameraRegister(atMega, 32, 0x7007); // Turn on clock management
-            Thread.Sleep(WaitUntilPllSettles);
+            //Thread.Sleep(WaitUntilPllSettles);
             WriteCameraRegister(atMega, 199, 666); // Defines granularity (unit = 1/PLL clock) of exposure and reset_length
             WriteCameraRegister(atMega, 200, 3300); // Set frame rate to 30 Hz
             WriteCameraRegister(atMega, 201, 3000); // Set Exposure

OpenEphys.Onix1/DS90UB9x.cs

@@ -1,4 +1,7 @@
-namespace OpenEphys.Onix1
+using System;
+using System.Threading;
+
+namespace OpenEphys.Onix1
 {
     static class DS90UB9x
     {
@@ -29,6 +32,28 @@ static class DS90UB9x
         // unmanaged default serializer / deserializer I2C addresses
         public const uint DES_ADDR = 0x30;
         public const uint SER_ADDR = 0x58;
+
+        internal static void Initialize933SerDesLink(DeviceContext device, DS90UB9xMode dataMode) //also valid for 913
+        {
+            Thread.Sleep(100); // Empirical. The gateware seems to need some milliseconds to get i2c initialized.
+
+            var deserializer = new I2CRegisterContext(device, DES_ADDR);
+            deserializer.WriteByte((uint)DS90UB9xDeserializerI2CRegister.PortSel, 0x01); // Enable port 0
+            deserializer.WriteByte((uint)DS90UB9xDeserializerI2CRegister.PortMode, 0x4 + (uint)dataMode); // 0x4 maintains coax mode
+            deserializer.WriteByte((uint)DS90UB9xDeserializerI2CRegister.I2CConfig, 0b01011000); // 7: i2c pass all (0), 6: i2c pass (1), 5: auto_ack (0), 4: BC enable (1), 3: BC crc en (1), 2: reserved (0) 1:0: bc freq (00) 2.5Mbps
+            deserializer.WriteByte((uint)DS90UB9xDeserializerI2CRegister.SerAlias, SER_ADDR << 1);
+            // Enable backchannel GPIO on deserializer. It is then the serializer task to decide if using them or use manual output
+            deserializer.WriteByte((uint)DS90UB9xDeserializerI2CRegister.GpioCtrl0, 0x10);
+            deserializer.WriteByte((uint)DS90UB9xDeserializerI2CRegister.GpioCtrl0, 0x32);
+        }
+
+        internal static void Set933I2CRate(DeviceContext device, double i2cRate)
+        {
+            var serializer = new I2CRegisterContext(device, SER_ADDR);
+            var sclTimes = (uint)Math.Round(1.0 / (100e-9 * i2cRate));
+            serializer.WriteByte((uint)DS90UB933SerializerI2CRegister.SclHigh, sclTimes);
+            serializer.WriteByte((uint)DS90UB933SerializerI2CRegister.SclLow, sclTimes);
+        }
     }
 
     enum DS90UB9xTriggerMode : uint
@@ -65,6 +90,12 @@ enum DS90UB9xMarkMode : uint
     enum DS90UB9xDeserializerI2CRegister
     {
         PortMode = 0x6D,
+        PortSel = 0x4C,
+        I2CConfig = 0x58,
+        GpioCtrl0 = 0x6E,
+        GpioCtrl1 = 0x6F,
+
+        SerAlias = 0x5C,
 
         SlaveID1 = 0x5E,
         SlaveID2 = 0x5F,
@@ -83,12 +114,20 @@ enum DS90UB9xDeserializerI2CRegister
         SlaveAlias7 = 0x6C,
     }
 
-    enum DS90UB9xSerializerI2CRegister
+    enum DS90UB933SerializerI2CRegister
     {
-        GPIO10 = 0x0D,
-        GPIO32 = 0x0E,
-        SCLHIGH = 0x0A,
-        SCLLOW = 0x0B
+        Gpio10 = 0x0D,
+        Gpio32 = 0x0E,
+        SclHigh = 0x11,
+        SclLow = 0x12
+    }
+
+    enum DS90UB953SerializerI2CRegister
+    {
+        GpioData = 0x0D,
+        GpioIOControl = 0x0E,
+        SclHigh = 0x0B,
+        SclLow = 0x0C
     }
 
     enum DS90UB9xMode
@@ -102,5 +141,5 @@ enum DS90UB9xDirection
     {
         Input = 0,
         Output = 1
-    }
+    }  
 }