Open Neurophysiology Environment

Project description

Open Neurophysiology Environment

CI workflow

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='http://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)  # 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='http://test.alyx.internationalbrainlab.org', make_default=True)
one = ONE()  # Connected to http://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/

Project details

Release history Release notifications | RSS feed

2.11.1

Nov 8, 2024

2.11.0

Nov 1, 2024

2.10.1

Oct 30, 2024

2.10.0

Oct 24, 2024

2.9.1

Sep 26, 2024

2.9.0

Sep 26, 2024

2.9rc0 pre-release

Aug 9, 2024

2.8.1

Jul 17, 2024

2.8.0

Jul 3, 2024

2.7.0

Mar 25, 2024

2.7rc2 pre-release

Mar 13, 2024

2.7rc1 pre-release

Mar 11, 2024

2.7rc0 pre-release

Mar 1, 2024

2.6.0

Jan 24, 2024

2.5.5

Jan 17, 2024

2.5.4

Jan 17, 2024

2.5.3

Jan 16, 2024

2.5.2

Jan 9, 2024

2.5.1

Dec 22, 2023

2.5.0

Nov 1, 2023

2.4.0

Oct 17, 2023

2.3.0

Sep 8, 2023

2.2.2

Aug 16, 2023

2.2.1

Aug 4, 2023

2.2.0

Aug 3, 2023

2.1.0

Jun 16, 2023

2.0.0

May 11, 2023

1.21.4

Apr 21, 2023

1.21.3

Mar 16, 2023

1.21.2

Mar 7, 2023

1.21.1

Mar 2, 2023

1.21.0

Feb 28, 2023

1.20.0

Feb 22, 2023

1.19.1

Jan 25, 2023

1.19.0

Jan 24, 2023

1.18.0

Jan 18, 2023

1.17.0

Jan 11, 2023

1.16.3

Dec 9, 2022

1.16.2

Oct 28, 2022

1.16.1

Oct 7, 2022

1.16.0

Sep 28, 2022

1.15.0

Sep 22, 2022

1.14.0

Aug 23, 2022

1.13.0

Jul 25, 2022

1.12.2

Jun 23, 2022

1.12.1

Jun 20, 2022

1.12.0

Jun 15, 2022

1.11.0

May 4, 2022

1.10.0

Apr 8, 2022

1.9.1

Mar 10, 2022

1.9.0

Feb 24, 2022

1.8.1

Feb 11, 2022

1.8.0

Feb 11, 2022

1.7.3

Feb 5, 2022

1.7.2

Jan 24, 2022

1.7.1

Jan 10, 2022

1.7.0

Dec 15, 2021

1.6.3

Dec 8, 2021

1.6.2

Oct 21, 2021

1.6.1

Oct 20, 2021

1.6.0

Oct 14, 2021

1.5.1

Oct 12, 2021

1.4.0

Sep 27, 2021

1.3.0

Sep 17, 2021

1.2.1

Sep 13, 2021

1.2.0

Sep 9, 2021

1.1.0

Sep 2, 2021

1.0.0

Aug 31, 2021

0.5.3

Aug 16, 2021

0.5.2

Aug 2, 2021

0.5.1

Jul 27, 2021

0.5.0

Jul 19, 2021

0.4.0

Jul 15, 2021

0.3.0

Jul 14, 2021

This version

0.2.3

Jul 7, 2021

0.2.2

Jul 7, 2021

0.2.1

Jul 7, 2021

0.2.0

Jul 6, 2021

0.1.6

Jun 28, 2021

0.1.5

Jun 21, 2021

0.1.4

Jun 17, 2021

0.1.3

Jun 11, 2021

0.1.1

Jun 9, 2021

0.1.0

Jun 9, 2021

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