virtualbrainlab / ephys-link

A Python Socket.IO server that allows any Socket.IO-compliant application to communicate with manipulators used in electrophysiology experiments.

VirtualBrainLab

https://www.virtualbrainlab.org/

Preprocessing

For the IBL replay task data is preprocessed by these scripts: https://github.com/dbirman/iblreplay-preproc

Install instructions

[todo]

Assets/Resources folder: https://drive.google.com/drive/folders/1L1ICkdWjxzqmDzjKqNn6wgS_smnAgX4N?usp=sharing

ephys-link's Issues

Better code organization

• Separate functionality from server backend
• Document

Change to use event acknowledgements

• Register
• Read
• Goto

Do all of the GitHub things

Apply all of GitHub's recommendations for public repositories

• Everything under Community Standards
• Everything under Security
• Apply autoformatting and linting checks

Setup websocket

Debug flag

• CLI or something argument to turn off all printing
• Document

Drive to depth reads wrong position

If placed in queue, position is calculated way before

Make Linux and macOS compatible

Currently, using the DLL restricts the server to only run on windows environments. Linux should be compatible with the right tools and so is macOS (probably through some documentation).

• Works in Linux
• Works in macOS
• Document how to use/install

Documentation fixes

• Use an error reporting function or something to make it more streamlined
• Make sure error messages are correct in docs
• User NoReturn and check with mypy
• Make overridden functions public and put comments as appropriate

Use HTTPS

• https://stackoverflow.com/questions/51645324/how-to-setup-a-aiohttp-https-server-and-client

Automatically handle when devices are inside the brain

Automatically detect when a device is inside the brain and enable the appropriate movement restricting flags (like inside_brain). Extracted from #24

• Measure pressure to automatically detect if inside brain
• Set flags
• Document

Invalid method encountered when no system connected

Describe the bug
Non-crashing error called when no system is connected for an extended period of time (is repeatedly called)

Error handling request
Traceback (most recent call last):
  File "C:\Users\Kenneth\Documents\ephys-link\lib\site-packages\aiohttp\web_protocol.py", line 334, in data_received
    messages, upgraded, tail = self._request_parser.feed_data(data)
  File "aiohttp\_http_parser.pyx", line 551, in aiohttp._http_parser.HttpParser.feed_data
aiohttp.http_exceptions.BadStatusLine: 400, message="Bad status line 'Invalid method encountered'"

To Reproduce
Steps to reproduce the behavior:

1. Start server
2. Connect, then disconnect Pinpoint
3. Wait a very long time

Expected behavior
A clear and concise description of what you expected to happen.

Screenshots
If applicable, add screenshots to help explain your problem.

Explicitly enable write

• Send event to enable writing (otherwise only read operations allowed)
• Can be time bound (return back to read only after set time)
• Document set_inside_brain and set_can_write

Write position

Find better movement wait system

Currently using

while not movement.finished:
    await asyncio.sleep(0.1)

Because Sensapex API event is threading and server is using asyncio

Either:

• Convert server to use threading (may have performance hit)
• Convert Sensapex API to use asyncio

Sanity check before running

• Test all 4 axes before running
• Calibrate

Simultaneous movement

• Allow for multiple manipulators to move at once
• Update documentation about this
  • Add documentation for calibration functions

Write position infrastructure

• When given positional data, write that position to the manipulator
• Continuous position receive
• Multiple manipulators Sequential manipulator movement

Change stop button to be continuous

• When pressed, continue to send stop message
• Continuously calls stop (forces client to also recognize that the program is being stopped on start)

Emergency stop

Stop all movement and all queued movement

Document server

Put stuff about #5 , #6 , #7 into docs

• Call messages "events" instead
• Sensapex API installation instructions (for development; place in README and in doc website)
• Pip installation

Remove redundant data from callback

Since callback functions go directly back to the sender, manipulator ID is not needed

Callbacks are objects/dictionaries

• BestHTTP is expecting a dictionary object for callback arguments
• Document

Dependabot and CodeQL

Send position infrastructure

Read position and send the data over the server

Automatically build and push to PyPI

Documentation refactor (move to docs)

When you have a chance can you move everything in the README file to the virtualbrainlab.org documentation pages leaving only:

• a brief summary of the purpose
• minimal instructions to install & start the server
• link to the full documentation
• references
• citing section

See https://github.com/VirtualBrainLab/NPTrajectoryPlanner for an example

Unregister manipulator

• Do the opposite of register_manipulator
• Document

Static analysis

Apply DeepSource static analysis (if possible)

Fix documentation compatibility

Describe the bug

• Unable to import ephys_link.server
• Unable to import ephys_link.sensapex_handler
• Docstring may be in the wrong format

To Reproduce
Steps to reproduce the behavior:

1. make html in doc

Lock controller while performing movement

• Lock event (for Sensapex)
• Lock all axes except depth when inside brain
• Document this

Package into pip

Read data

Update unit tests

Unit tests do not use new dictionary return types

Transition to ephys-manip-link name

Return discoverable manipulators

• Event that returns discoverable/attachable manipulators (by ID)
• Document

Drawing demos

Figure out polling rate

• See if 60fps polling works

Restrict axis movement once inside brain

• Register when a probe is inside the brain
• All probes inside brain can only move along depth axis
• New (separate) function to only move probe along depth axis
• Document

Moved to #32

• Detect when probe is inside brain
• Detect pressure

Publish to Pypi

Launch server through a function

Set the light on moving manipulator

• Turn on the light on the manipulator that is moving.
• Set it back to whatever state it was before

Change package name to ephys-link

• Shorten name
• Update links

Allow CORS to Pinpoint

Add CORS options to allow for communication with Pinpoint

Document hardware setup for Ephys Link

Explain a ethernet connection is needed to the control unit

Change default options to be without emergency stop

Current defaults require emergency stop

Convert to use mm in output

Use mm instead of um in output to match what is expected in Pinpoint

Lock controller while moving remotely

• Lock/ignore controller input while doing a movement operation (to prevent experimenter from 🤬💩👆)
• Document

Use try-except-else-finally properly

• No scopes are created
• Use finally
• else branch

Might come up when doing #41

Continuous read script

For recording an experiment live

• Record/save positional data to a file
• Lock out all write movement
• Attach time stamp to all positional data
• Make sure they don't interfere with controller movement

Calibration with position watching

Fix calibration to watch for position instead of wait for 70 seconds