Open Neurophysiology Environment
Project description
Open Neurophysiology Environment
The Open Neurophysiology Environment is a scheme for sharing neurophysiology data in a standardized manner. It is a Python API for searching and loading ONE-standardized data, stored either on a user’s local machine or on a remote server.
Please Click here for the main documentation page. For a quick primer on the file naming convention we use, click here.
NB: The API and backend database are still under active development, for the best experience please regularly update the package by running pip install -U ONE-api.
Requirements
ONE runs on Python 3.8 or later, and is tested on the latest Ubuntu and Windows (3.8 and 3.11 only).
Installing
Installing the package via pip typically takes a few seconds. To install, run
pip install ONE-api
Set up
For using ONE with a local cache directory:
from one.api import One
one = One(cache_dir='/home/user/downlaods/ONE/behavior_paper')
To use the default setup settings that connect you to the IBL public database:
from one.api import ONE
ONE.setup(silent=True) # Will use default information
one = ONE(password='international')
For setting up ONE for a given database e.g. internal IBL Alyx:
from one.api import ONE
one = ONE(base_url='https://alyx.internationalbrainlab.org')
Once you've setup the API for the first time, subsequent calls will use the same parameters:
from one.api import ONE
one = ONE()
To set up ONE for another database and make it the default:
from one.api import ONE
ONE.setup(base_url='https://test.alyx.internationalbrainlab.org', make_default=True)
one = ONE() # Connected to https://test.alyx.internationalbrainlab.org
Using ONE
To search for sessions:
from one.api import ONE
one = ONE()
print(one.search_terms()) # A list of search keyword arguments
# Search session with wheel timestamps from January 2021 onward
eids = one.search(date_range=['2021-01-01',], dataset='wheel.timestamps')
['d3372b15-f696-4279-9be5-98f15783b5bb']
# Search for project sessions with two probes
eids = one.search(data=['probe00', 'probe01'], project='brainwide')
To load data:
from one.api import ONE
one = ONE()
# Load an ALF object
eid = 'a7540211-2c60-40b7-88c6-b081b2213b21'
wheel = one.load_object(eid, 'wheel')
# Load a specific dataset
eid = 'a7540211-2c60-40b7-88c6-b081b2213b21'
ts = one.load_dataset(eid, 'wheel.timestamps', collection='alf')
# Download, but not load, a dataset
filename = one.load_dataset(eid, 'wheel.timestamps', download_only=True)
To share data:
from one.api import One
one = One.setup() # Enter the location of the ALF datasets when prompted
Further examples and tutorials can be found in the documentation.
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