Support RHS2116 streaming and stimulation #67

glopesdev · 2024-03-31T21:21:56Z

This PR adds basic support for RHS2116 configuration, amplifier data streaming and stimulation functionality.

Support acquisition from RHS2116, writing filter settings, etc.
Add stimulus sequence definition to RHS2116 configuration
Will require GUI support for configuring the stimulus waveform.
Tested with hardcoded stimulus parameters and it works great.

Fixes #26

jonnew

Overall, I think this is move in the right direction. However, base virtual functions return void and are therefore ripe for redundancy and abuse. It makes me wonder if we should really just virtualize the entire headstage finding procedure and tell the headstage to figure it out and let us know if it finds anything or not.

OpenEphys.Onix/OpenEphys.Onix/ConfigureHeadstageRhs2116.cs

- Support acquisition from RHS2116, writing filter settings, etc. - Does not have the ability to configure or trigger stimulus sequences and does not yet include a Rhs2116TriggerDevice in ConfigureHeadstageRhs2116. GUI support will be critical for this.

- Add stimulus trigger device to headstage - Add stimulus sequence definition to RHS2116 configuration - This will require GUI support for configuring the stimulus waveform. - Tested with hardcoded stimulus parameters and it works great.

- Stimulus trigger device accepts a delay in microsends to the applicatin of a stimulus - Mark CheckLinkStatus as virtual so headstage can be reset between power cycles (see #120) - Rebase main and take advantage of latest improvments with respect to port voltage override

- The voltage drop is what it is. Im getting reliable locking with this the algorithm that is implemented in ConfigureHeadstageRhs2116LinkController

glopesdev · 2024-07-02T14:23:28Z

OpenEphys.Onix/OpenEphys.Onix/ConfigureHeadstageRhs2116.cs

+                    if (base.CheckLinkState(device))
                    {
                        SetPortVoltage(device, voltage + VoltageOffset);
-                        if (CheckLinkState(device))
-                        {
-                            // TODO: The RHS2116 headstage needs an additional reset after power on
-                            // to provide its device table.
-                            Thread.Sleep(500);
-                            device.Context.Reset();
-                            return true;
-                        }
-                        else break;
+                        return CheckLinkState(device);


Just noticed this now, and was really confused. If we just need to reset before the last check, why not simply add device.Context.Reset() before the return call?

My suspicion is that perhaps this is related to the case where we want to just set a port voltage override and therefore the code does not go through this path?

In that case, maybe the best would be to mark ConfigurePortVoltageOverride itself as virtual and override that?

I think this was addressed in #124 which does what you suggest.

glopesdev · 2024-07-02T14:24:59Z

Bonsai/Bonsai.config

    <AssemblyLocation assemblyName="Microsoft.Web.WebView2.Core" processorArchitecture="MSIL" location="Packages\Microsoft.Web.WebView2.1.0.1823.32\lib\net45\Microsoft.Web.WebView2.Core.dll" />
    <AssemblyLocation assemblyName="Microsoft.Web.WebView2.WinForms" processorArchitecture="MSIL" location="Packages\Microsoft.Web.WebView2.1.0.1823.32\lib\net45\Microsoft.Web.WebView2.WinForms.dll" />
    <AssemblyLocation assemblyName="Microsoft.Web.WebView2.Wpf" processorArchitecture="MSIL" location="Packages\Microsoft.Web.WebView2.1.0.1823.32\lib\net45\Microsoft.Web.WebView2.Wpf.dll" />
    <AssemblyLocation assemblyName="OpenCV.Net" processorArchitecture="MSIL" location="Packages\OpenCV.Net.3.4.2\lib\net462\OpenCV.Net.dll" />
+    <AssemblyLocation assemblyName="OpenEphys.PhaseDetector" processorArchitecture="MSIL" location="Packages\OpenEphys.PhaseDetector.0.6.0\lib\net472\OpenEphys.PhaseDetector.dll" />


Is the phase detector package used in the implementation, or just for examples?

Oops. Should not be there. Also don't know why I committed this file.

- First shot at using XML documentaiton to generate coherent and user-friendly documentation

- Improve ConfigureAnalogIO.Process documentation - Use standard enum documentation practices

- Clarification and typo fixes

Minor updates to documentation

- Neuropixels 2.0 has a completely different register map compared to 2.0-beta. This is reflected in the changes in this commit. - Common static helper functions for 1.0, 2.0, and 2.0-beta were moved to BitHelper.cs and NeuropixelV2.cs

- There was lingering discussion after merge into main occured, this attempts to address that

- It was left connected to the last probe configured which caused a huge amount of cross talk if i2c bus was used during acquisition

- Gain corrections were not used in NeuropixelsV1 - Gain corrections for NeuropixelsV2 were changed form fixed point multiplication to floating point since we are no longer doing this on an FPGA

Fix register mapping for Neuropixels 2.0 public probes

- Emphasize Device Manager is singleton - Remove information on oni Hubs from MutliDeviceFactory since this has nothing to do with ONI even though it kinda feels like it does

Resolve issues in discussion of #189

Publish packages to github on release

Update bootstrapper version

- Support acquisition from RHS2116, writing filter settings, etc. - Does not have the ability to configure or trigger stimulus sequences and does not yet include a Rhs2116TriggerDevice in ConfigureHeadstageRhs2116. GUI support will be critical for this.

- Add stimulus trigger device to headstage - Add stimulus sequence definition to RHS2116 configuration - This will require GUI support for configuring the stimulus waveform. - Tested with hardcoded stimulus parameters and it works great.

- Stimulus trigger device accepts a delay in microsends to the applicatin of a stimulus - Mark CheckLinkStatus as virtual so headstage can be reset between power cycles (see #120) - Rebase main and take advantage of latest improvments with respect to port voltage override

- The voltage drop is what it is. Im getting reliable locking with this the algorithm that is implemented in ConfigureHeadstageRhs2116LinkController

- Up to date with frame distribution, DeviceType, etc.

…to issue-26

- Deleted bracket by accident - Incorrectly removed virtual keywork from CheckLinkStatus function declaration

bparks13 · 2024-08-08T20:03:14Z

OpenEphys.Onix/OpenEphys.Onix/ConfigureHeadstageRhs2116.cs

This file (along with a few others in the same OpenEphys.Onix/OpenEphys.Onix folder path) are leftovers from the old folder pattern. These should be removed.

bparks13 · 2024-08-08T20:04:13Z

OpenEphys.Onix1/ConfigureRhs2116.cs

+
+                return new CompositeDisposable(
+                    DeviceManager.RegisterDevice(deviceName, device, DeviceType),
+                    analogLowCutoff.Subscribe(newValue =>


All calls should be using the SubscribeSafe method instead of Subscribe.

glopesdev added the feature New planned feature label Mar 31, 2024

glopesdev added this to the 0.1.0 milestone Mar 31, 2024

glopesdev requested review from jonnew and aacuevas March 31, 2024 21:21

glopesdev mentioned this pull request Mar 31, 2024

Changes to port voltage tuning algorithm based on testing #46

Closed

jonnew reviewed Apr 1, 2024

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jonnew mentioned this pull request Apr 1, 2024

Add HS64 electrical stim and trigger nodes #66

Merged

glopesdev force-pushed the issue-26 branch from eb0a4b8 to 317cbc7 Compare April 3, 2024 23:13

glopesdev self-assigned this May 21, 2024

glopesdev modified the milestones: 0.1.0, 0.2.0 Jun 4, 2024

jonnew force-pushed the issue-26 branch from 317cbc7 to 203054b Compare June 28, 2024 16:07

jonnew and others added 6 commits June 28, 2024 12:09

Finish headstage RHS2116 support

5a136d6

- Add stimulus trigger device to headstage - Add stimulus sequence definition to RHS2116 configuration - This will require GUI support for configuring the stimulus waveform. - Tested with hardcoded stimulus parameters and it works great.

Move register class to top-level for consistency

fcf921a

Fix indentation for consistency

50e29db

Remove un-resolvable TODO comment

ea49ff5

- The voltage drop is what it is. Im getting reliable locking with this the algorithm that is implemented in ConfigureHeadstageRhs2116LinkController

jonnew force-pushed the issue-26 branch from 203054b to ea49ff5 Compare June 28, 2024 18:04

glopesdev commented Jul 2, 2024

View reviewed changes

glopesdev and others added 10 commits July 4, 2024 13:15

Ensure any BNO polling exceptions are routed

cbb9f70

Ensure exception is thrown on configuration error

39ee5bc

Ensure dynamic configuration exceptions are routed

5818b57

Remove unused fields and properties

e60f898

Refactor context task to allow async dispose

35d1862

Avoid rethrowing exception if routed to observer

191bedb

Terminate frame distribution if read frame throws

6eb907a

Document analog IO

75c12ef

- First shot at using XML documentaiton to generate coherent and user-friendly documentation

NeuropixelsV1e documentation

7a7bd95

Address comments in #142

4eb85eb

- Improve ConfigureAnalogIO.Process documentation - Use standard enum documentation practices

jonnew and others added 24 commits August 2, 2024 11:12

Minor updates to documentation

9215835

- Clarification and typo fixes

Publish packages to github on release

7e2c852

Ensure build suffix is declared at job level

0b071bf

Change spelling

7a3a6c2

Merge pull request #189 from open-ephys/20240802-docs-update

7cb45a2

Minor updates to documentation

Resolve issues in discussion of #189

de8af86

- There was lingering discussion after merge into main occured, this attempts to address that

Disconnect i2c bus from probes before streaming

beb4610

- It was left connected to the last probe configured which caused a huge amount of cross talk if i2c bus was used during acquisition

Fix neuropixels gain corrections

b86733c

- Gain corrections were not used in NeuropixelsV1 - Gain corrections for NeuropixelsV2 were changed form fixed point multiplication to floating point since we are no longer doing this on an FPGA

Merge pull request #190 from open-ephys/issue-186

62aa90b

Fix register mapping for Neuropixels 2.0 public probes

Address review in #194

e2b7f72

- Emphasize Device Manager is singleton - Remove information on oni Hubs from MutliDeviceFactory since this has nothing to do with ONI even though it kinda feels like it does

Minor wording review

ee8a775

Merge pull request #194 from open-ephys/20240804-docs-update

cf48a92

Resolve issues in discussion of #189

Merge pull request #196 from open-ephys/release-automation

3cbf6ca

Publish packages to github on release

Update bootstrapper version

13fb905

Merge pull request #197 from open-ephys/bootstrapper-update

7ac700f

Update bootstrapper version

Finish headstage RHS2116 support

4209da7

- Add stimulus trigger device to headstage - Add stimulus sequence definition to RHS2116 configuration - This will require GUI support for configuring the stimulus waveform. - Tested with hardcoded stimulus parameters and it works great.

Fix indentation for consistency

84ec7ed

Remove un-resolvable TODO comment

6e8133e

- The voltage drop is what it is. Im getting reliable locking with this the algorithm that is implemented in ConfigureHeadstageRhs2116LinkController

Bring rhs2116 classes up to date with latest API

208d631

- Up to date with frame distribution, DeviceType, etc.

Merge branch 'issue-26' of github.com:open-ephys/onix-bonsai-onix1 in…

068c681

…to issue-26

Fix sytax errors introduced during conflict resolution

07871b4

- Deleted bracket by accident - Incorrectly removed virtual keywork from CheckLinkStatus function declaration

bparks13 reviewed Aug 8, 2024

View reviewed changes

jonnew modified the milestones: 0.2.0, 0.3.0 Aug 13, 2024

jonnew modified the milestones: 0.3.0, 0.4.0 Aug 26, 2024

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Support RHS2116 streaming and stimulation #67

Support RHS2116 streaming and stimulation #67

glopesdev commented Mar 31, 2024

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jonnew Jul 22, 2024

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bparks13 Aug 8, 2024

Support RHS2116 streaming and stimulation #67

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Support RHS2116 streaming and stimulation #67

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