Open Neurophysiology Environment
Project description
Open Neurophysiology Environment
Click here for the main documentation page.
Requirements
ONE runs on Python 3.7 or later, and is tested on the latest Ubuntu and Windows (3.7 and 3.8 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')
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')
To use the default setup settings that connect you to the IBL public database:
from one.api import ONE
one = ONE(silent=True, password='international') # Will use default information
Once you've setup the server, 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 OneAlyx, ONE
OneAlyx.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)
Further examples and tutorials can be found in the documentation.
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