Open Neurophysiology Environment
Project description
Open Neurophysiology Environment
NB: This package is currently in beta
Installing
For Python 3.8 or later, 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(client='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 examples/
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