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.
Release history Release notifications | RSS feed
Download files
Download the file for your platform. If you're not sure which to choose, learn more about installing packages.
Source Distribution
Built Distribution
File details
Details for the file ONE-api-2.5.4.tar.gz.
File metadata
- Download URL: ONE-api-2.5.4.tar.gz
- Upload date:
- Size: 970.2 kB
- Tags: Source
- Uploaded using Trusted Publishing? No
- Uploaded via: twine/4.0.2 CPython/3.11.5
File hashes
| Algorithm | Hash digest | |
|---|---|---|
| SHA256 | 5f2675686ef23eb251c5195306fe441307d0bc13fd36feedfb823e516698c6d5 |
|
| MD5 | 8044840c50a1b24a0aa34d04a2cefd60 |
|
| BLAKE2b-256 | 6840338fa9f07512da314041803aa143994b2554ac5e43ce1211c2487693a2f9 |
File details
Details for the file ONE_api-2.5.4-py3-none-any.whl.
File metadata
- Download URL: ONE_api-2.5.4-py3-none-any.whl
- Upload date:
- Size: 113.2 kB
- Tags: Python 3
- Uploaded using Trusted Publishing? No
- Uploaded via: twine/4.0.2 CPython/3.11.5
File hashes
| Algorithm | Hash digest | |
|---|---|---|
| SHA256 | 02186babe153505c4a18c7a830fd500949edde5ed8e84818640b3f6a35d3c2c0 |
|
| MD5 | dae4534ddb7602c393f100e7a65a12d1 |
|
| BLAKE2b-256 | e7da2a7748eb62830cd93a7cc60371f67b38e41cbaf0a3cd4810ab4b63590256 |
