alyx-connector 2.1.44

Alyx Connector, based on the Open Neurophysiology Environment

Python Connector to Alyx-Local instance(s)

Install

Install with

pip install alyx-connector

or

pip install git+https://github.com/JostTim/alyx-local-connector.git@docker-compatible

First use

You need to create a connector object to the alyx_instance that you are using. The easyest way to create one at the beginning, or for any other new connection with a different username or to a different instance, you can use the Connector.setup() class function :

from alyx_connector import Connector

connector = Connector.setup()

You will be prompted to enter informations for setting the new connection.

First, the address of the server :

Second, the username to use :

Optionally, decide wether to make this the default address and username combo, when you call Connector() without arguments, at later times :

Lastly, the password to use with that address / username combo : (if successfull, the server will provide a token that will be saved by the connector for that adress/username combo, so that you don't need to retype the password again, but the pasword itself is not saved for security reasons)

If the connection succeeds, you will get a connector object :

Subsequent uses

After setting up at least a first connection, you can use the connector at later times (even after restarting python) using several ways :

Using the default server / username :

from alyx_connector import Connector
connector = Connector()

Using a specific server, but the default username for that server :

from alyx_connector import Connector
connector = Connector(url="127.0.0.1")

Using a specific server and username :

from alyx_connector import Connector
connector = Connector(url="127.0.0.1", username="myname")

At any time, you can check the server and username used by the connect, by typing connector.url or connector.username

Accessing experimental data using the connector

Searching for a session

The main use of the connector is usually to search experimental sessions data, based on some filter.

To get a table of session when the animal used is for example named ea04, you can type :

sessions = connector.search(subject = "ea04")

you will get a pandas.DataFrame where each row is corresponding to a session, and each column to some information relative to that session, as available on the alyx-local website.

Example :

You can get the session infos narrative for example, for the third session that you obtained here, by doing :

session = sessions.iloc[3] # get the third session in the table, by index order
print(session.narrative) # print the narrative

You can also access the json based fields : session.json and session.extended_qc, which are standard python dictionnaries. (containing potentially nested data that you entered)

session.json

The json field is meant as a way to store additionnal metadata that you cannot enter inside the regular session table fields. (as different experiments may need different fields)

The extended_qc field is meant as a way to store detailed Quality Check information, that you can use to get only the sessions that passed particular criterias after checking the data. (non exhaustive examples : a noise level in the electrophy recordings, etc...)