Ephys Link
Code Organization
Ephys Link is a modular application structured in 3 layers to enable future extensibility:
The Server
Manipulator Platforms
Manipulator Instances
1. The Server
At its core, Ephys Link is a Python-based Socket.IO server that is used to communicate between client applications and manipulator platforms. The server declares a standardized set of Socket.IO events that clients can call to enact platform specific manipulator API calls. All events, their inputs, and return values are error checked on the server.
In code, the server is an asynchronous HTTP server with events declared
with the @sio.event annotation. It is also responsible for handling CLI
arguments, starting the serial connection to the emergency stop button, and
launching the GUI.
2. Manipulator Platforms
Each manipulator platform implements the set of events declared by the Socket.IO server. Manipulator platforms are responsible for managing connected manipulator instances and API calls that affect all instances simultaneously (such as calibration and emergency stops).
Manipulator platforms are also responsible for taking inputs in “Unified Space” and converting them into each platform’s particular coordinate system. Unified Space is defined as the right-hand coordinate system rotated 180° around the Y-axis. This means +X is to the left, +Y is forward, +Z is downward, and +Depth is also downward.
In code, a platform is represented as a class that inherits the abstract
class PlatformHandler. The PlatformHandler class defines the implementation
of events and pre-implements standard error checking for input and output.
Platform classes typically start with some call to initialize the platform’s
specific API and manage the available/visible manipulators.
3. Manipulator Instances
To help with manipulator management, each in vivo manipulator can be instantiated as a manipulator class specific to the platform. This class encapsulates details and implementations specific to an instance of a manipulator such as its ID, position, and movement queue. Certain API’s such as the Sensapex uMp API return a manipulator object which can be stored in the manipulator instance class.
Developing and Adding Manipulator Platforms to Ephys Link
Ephys Link primarily support Sensapex uMp Micromanipulators and New Scale manipulators. However, with the modular design defined in the Code Organization section, it is very easy to add custom platforms to Ephys Link.
Installing Ephys Link for development
Clone the repo
cd ephys-linkpip install .[dev]to install the package and its development dependenciesephys-linklaunches the serverUnit tests are available to run under the
tests/directory
Adding a new platform
Before beginning to write a platform handler, ensure the target platform has some windows-compatible API and (ideally) some python library to interface with. Once an API connection can be established, the platform handler can be implemented in the following steps:
Create a new module in
src/ephys_link/platforms/with the name of the platform (e.g.my_platform.py).Create a new class that inherits from
PlatformHandlerand implement the abstract methods.Follow
src/ephys_link/platforms/sensapex_handler.pyas an example. Error checking is handled within thePlatformHandlerclass so only implement the necessary API calls to the platform.
Optionally, add a platform manipulator class that inherits
PlatformManipulatorinsrc/ephys_link/platforms. As described in the code organization section, a platform manipulator class definition can be used to help abstract code specific to instances of manipulators away from general platform management code.Follow
src/ephys_link/platforms/sensapex_manipulator.pyas an example.
Add the new platform to the launch command in
src/ephys_link/server.pyAdd a new case for the platform in the match statement in the
launch_serverfunction. The case pattern will be the input string used in the CLI to select this platform with the-t/--typeargument.Set the
platformvariable to the imported platform. Useimportlibto do so (use thesensapexandnew_scalecases as examples).
General code practices
Type hinting is implemented where possible.
All functions and classes must have a Sphinx/reStructuredText formatted docstring.
Only one client can be connected to the server at a time.
Leave unimplemented functions as
raise NotImplementedErrorinstead ofpass.For safety, ensure the
stopfunction is implemented for all manipulators and that it is called when the server is stopped.
Deployment
Ephys Link is published to the Python Package Index (PyPI). To publish a new version:
Be a collaborator to the Ephys Link PyPI project
Update the
versionnumber inpyproject.tomlInstall development dependencies:
pip install .[dev]Build the package:
python -m buildCheck the build integrity:
twine check dist/*Test upload to the test PyPI server:
twine upload --repository testpypi dist/*Upload to the PyPI server:
twine upload dist/*
Developing a client application
Ephys Link can be interfaced with any Socket.IO client or used directly as a python library. The following is information that can be helpful for developers looking to build client applications that utilize Ephys Link.
Importing Ephys Link as a Python library
For Python applications, Ephys Link can be imported as a library. To do so:
Follow the installation instructions
Use
from ephys_link import serverand callserver.launch_server("sensapex", 8081, 8080)to start the serverThe first argument is the platform type (e.g.
"sensapex"or"new_scale").The second argument is the port to listen for Socket.IO connections on.
The third argument is the port to listen for Pathfinder HTTP connections on.
Socket.IO application
As a Socket.IO server, Ephys Link defines a standardized set of Socket.IO events that can be used to interact with manipulator platforms. The following section describes the available events and how to use them.
Socket.IO Events and API
This is a list of available Socket.IO events. The code shown is pseudo-Socket.IO code that can be used to interact with the server. The exact implementation will depend on the platform and Socket.IO interface used.
In general:
Each event will take in an input and call a callback function with a response dictionary/object as the argument
Before a manipulator can be used, it must be registered and calibrated
Before a manipulator can be moved (including being calibrated), it must have its movement enabled
A manipulator’s position can be read before its movement is enabled, though
The server will log unknown events, but will not return callback arguments or emit any messages
Table of Contents
Getting the server’s version number
It may be useful for the client to know the version number of the server. This can be used to make a quick compatibility check for features and platform availability.
Event: get_version
Expected Arguments: None
Callback Responses Format: version: string (e.g. 'x.y.z')
Example
# Get server version number
sio.emit('get_version', callback=my_callback_func)
Getting available manipulators
Many implementations may want to first find out what manipulators are available. This can be done by simply sending this event which takes no arguments. A callback will return a list of the available manipulators.
Event: get_manipulators
Expected Arguments: None
Callback Responses Format: (manipulators: list[str], error: string)
Error message ( |
Description |
|---|---|
|
No errors, the list of all discoverable/available manipulators is returned |
|
An unknown error has occurred getting discoverable/available manipulators |
manipulatorswill be an empty list on error, however, it is possible that there truly are no discoverable/available/compatible manipulators
Example
# Get available manipulators
sio.emit('get_manipulators', callback=my_callback_func)
Registering a manipulator
Some platforms require manipulators to be “registered” before use. Sensapex is one such platform.
Event: register_manipulator
Expected Arguments:
Manipulator ID:
str
Callback Responses Format: string
Error message ( |
Description |
|---|---|
|
No errors, registered manipulator with ID |
|
Manipulator is already registered, no action taken |
|
The manipulator is not discoverable by the API and may be disconnected or offline |
|
An unknown error has occurred while registering |
Example
# Register manipulator with ID "1"
sio.emit('register_manipulator', "1", callback=my_callback_func)
Unregistering a manipulator
Any registered manipulator can be easily disconnected from control by simply unregistering it.
Event: unregister_manipulator
Expected Arguments:
Manipulator ID:
str
Callback Responses Format: string
Error message ( |
Description |
|---|---|
|
No errors, unregistered manipulator with ID |
|
The manipulator is not registered and therefore cannot be unregistered |
|
An unknown error has occurred while unregistering |
Example
# Unregister manipulator with ID "1"
sio.emit('unregister_manipulator', "1", callback=my_callback_func)
Calibrating a manipulator
To ensure all manipulators are working properly before applying autonomous
control, all manipulators must have their movement checked and calibrated. This
is done by invoking the calibrate API call on the manipulator. If the platform
does not support a calibration call, use
the bypass calibration event.
Event: calibrate
Expected Arguments:
Manipulator ID:
str
Callback Responses Format: string
Error message ( |
Description |
|---|---|
|
No errors, calibrated manipulator with ID |
|
Manipulator is not registered yet |
|
An unknown error has occurred while calibrating |
|
The manipulator does not have write/movement privileges or it needs to be enabled |
Example
# Calibrate manipulator "1"
sio.emit('calibrate', "1", callback=my_callback_func)
Bypassing calibration
The calibration requirement may be bypassed by sending this event.
Event: bypass_calibration
Expected Arguments:
Manipulator ID:
str
Callback Responses Format: string:
Error message ( |
Description |
|---|---|
|
No errors, bypassed calibration for manipulator with ID |
|
Manipulator is not registered yet |
|
An unknown error has occurred while bypassing calibration |
Example
# Bypass calibration for manipulator "1"
sio.emit('bypass_calibration', "1", callback=my_callback_func)
Enable movement
To prevent accidental movement commands, a manipulator must have its movement feature enabled. A manipulator may have its movement enabled for a set period or enabled indefinitely. Relevant information is passed through the event. Once a write lease has expired, an event is emitted back to the server with the ID of the manipulator which can no longer write as the payload.
Event: set_can_write
Expected Arguments (dictionary/object with the following format):
manipulator_id:strcan_write:boolhours:float
Callback Responses Format: (state: bool, error: string)
Error message ( |
Description |
|---|---|
|
No errors, set state is returned |
|
Invalid/unexpected argument format |
|
An unknown error occurred while starting this function |
|
Manipulator is not registered yet |
|
An unknown error has occurred enabling movement |
state: Will beFalseif one was not provided properly in the request or if an error occurred
Response Event: write_disabled (sent when the write lease has expired)
Payload: manipulator_id: str
Example
# Enable movement for manipulator 1 indefinitely (0 = indefinite hours)
sio.emit('set_can_write', {
'manipulator_id': "1",
'can_write': True,
'hours': 0
})
Get a manipulator’s position
Receive the position of a specified manipulator as X, Y, Z, W (depth) in mm from the origin.
Event: get_pos
Expected Arguments:
Manipulator ID:
str
Callback Responses Format: (position: array, error: string)
Error message ( |
Description |
|---|---|
|
No errors, position is returned |
|
Manipulator is not registered yet |
|
Manipulator is not calibrated yet |
|
An unknown error has occurred while getting position |
position: Will be an empty array if one was not provided properly in the request or if an error occurred
# Get the position of manipulator "1"
sio.emit('get_pos', "1", callback=my_callback_func)
Get a manipulator’s angles
Receive the angles of a specified manipulator as Yaw, Pitch, Roll in degrees.
Yaw is 0° at the posterior and increases clockwise. Pitch is 0° when the probe is vertical (pointed straight down) and increases as the probe is tilted backward (towards posterior when Yaw is also 0°). The probe faces anterior when all 3 values are 0°. Roll increases clockwise.
Event: get_angles
Expected Arguments:
Manipulator ID:
str
Callback Responses Format: (angles: array, error: string)
Error message ( |
Description |
|---|---|
|
No errors, position is returned |
|
Manipulator is not registered yet |
|
Manipulator is not calibrated yet |
|
An unknown error has occurred while getting position |
angles: Will be an empty array if one was not provided properly in the request or if an error occurred
# Gets the angles of manipulator "1"
sio.emit('get_angles', "1", callback=my_callback_func)
Set the position of a manipulator
Instructs a manipulator to go to a position relative to the origin in mm.
Manipulators move asynchronously from each other. This means large batches of movement events can be sent to the server for several manipulators and each manipulator will move through the events assigned to them independently.
When a manipulator is set to be “inside” the brain, it will have all axes except
the depth axis locked. This is to prevent accidental lateral movement while
inside brain tissue. This state is set by set_inside_brain
. One may also explicitly specify movement in only the depth axis
using drive_to_depth
Event: goto_pos
Expected Arguments (dictionary/object with the following format):
manipulator_id:strpos:float[4](in x, y, z, w as mm from the origin)speed:int(in mm/s)
Callback Responses Format: (position: array, error: string)
Error message ( |
Description |
|---|---|
|
No errors, position is returned |
|
Invalid/unexpected argument format |
|
An unknown error occurred while starting this function |
|
Emergency stop was used and manipulator movements have been canceled |
|
Manipulator is not registered yet |
|
Manipulator is not calibrated yet |
|
An unknown error has occurred while moving to position |
position: Will be an empty array if one was not provided properly in the request or if an error occurred
# Set manipulator "1" to position 0, 0, 0, 0 at 2000 µm/s
sio.emit('goto_pos', {
'manipulator_id': "1",
'pos': [0, 0, 0, 0],
'speed': 2
})
Drive to depth
Instructs a manipulator to go to a specific depth in mm. This is equivalent to setting the position of the manipulator to the same position but with a different depth. This function helps to explicitly make sure no other axis except the depth axis is moving during a movement call.
Event: drive_to_depth
Expected Arguments (dictionary/object with the following format):
manipulator_id:strdepth:float(in mm from the origin)speed:int(in mm/s)
Callback Responses (depth: float, error: string)
Error message ( |
Description |
|---|---|
|
No errors, position is returned |
|
Invalid/unexpected argument format |
|
An unknown error occurred while starting this function |
|
Emergency stop was used and manipulator movements have been canceled |
|
Manipulator is not registered yet |
|
Manipulator is not calibrated yet |
|
An unknown error has occurred while driving to depth |
Example
# Drive manipulator "1" to a depth of 1000 µm at 2000 µm/s
sio.emit('drive_to_depth', {
'manipulator_id': "1",
'depth': 1,
'speed': 2
})
Set “inside brain” state
Sets the “inside brain” state of a manipulator. When a manipulator is inside the brain, it will have all axes except the depth axis locked. This is to prevent accidental lateral movement while inside brain tissue. For Sensapex manipulators, the rotary controller will also be locked to prevent accidental movement.
Event: set_inside_brain
Expected Arguments (dictionary/object with the following format):
manipulator_id:strinside:bool
Callback Responses (state: bool, error: string)
Error message ( |
Description |
|---|---|
|
No errors, position is returned |
|
Invalid/unexpected argument format |
|
An unknown error occurred while starting this function |
|
Manipulator is not registered yet |
|
Manipulator is not calibrated yet |
|
An unknown error has occurred while setting inside brain |
Example
# Set manipulator "1" to be inside the brain
sio.emit('inside_brain', {
'manipulator_id': "1",
'inside': True
})
Emergency Stop
There are two ways an emergency stop can be triggered: through this event or the
hardware/serial attached button. The server will connect to the first serial
device it finds which names itself “USB Serial Device” (which is what an Arduino
would appear as) and listen for any serial input from this source (at a baud
rate of 9600). The system will poll the serial port every 50 ms to check. The
Arduino is running this sketch
which will continuously send 1 (followed by a new line symbol) through serial
whenever the stop button is pressed.
Both the Socket.IO event and the serial method will stop all movement, remove all movement in the queue, and set all manipulators to be non-writable. Therefore, one must re-enable movement on the manipulators again before continuing.
Event: stop
Expected Arguments (dictionary/object with the following format):
None
Callback Responses Format: bool
true: No errors, all movement stoppedfalse: An unknown error has occurred while stopping all movement
Example
# Stop all movement
sio.emit('stop')