A Python client for OpenNeuro.
Project description
openneuro-py
A Python client for accessing OpenNeuro datasets.
Installation
# via conda:
conda install -c conda-forge openneuro-py
# or via pip:
pip install openneuro-py
Jupyter and IPython support
To get basic support for Jupyter Lab, Jupyter Notebook, IPython interactive
sessions, and VS Code's interactive Jupyter interface, you will also need to
install ipywidgets:
# via conda:
conda install -c conda-forge ipywidgets
# or via pip:
pip install ipywidgets
Basic usage – command line interface
Getting help
openneuro-py --help
openneuro-py download --help
openneuro-py login --help
Download an entire dataset
openneuro-py download --dataset=ds000246
Specify a target directory
To store the downloaded files in a specific directory, use the
--target_dir switch. The directory will be created if it doesn't exist
already.
openneuro-py download --dataset=ds000246 \
--target_dir=data/bids
Continue an interrupted download
Interrupted downloads will resume where they left off when you run the command again.
Advanced usage – command line interface
Exclude a directory from the download
openneuro-py download --dataset=ds000246 \
--exclude=sub-emptyroom
Download only a single file
openneuro-py download --dataset=ds000246 \
--include=sub-0001/meg/sub-0001_coordsystem.json
Note that a few essential BIDS files are always downloaded in addition.
Download or exclude multiple files
--include and --exclude can be passed multiple times:
openneuro-py download --dataset=ds000246 \
--include=sub-0001/meg/sub-0001_coordsystem.json \
--include=sub-0001/meg/sub-0001_acq-LPA_photo.jpg
Use an API token to log in
To download private datasets, you will need an API key that grants you access permissions. Go to OpenNeuro.org, My Account → Obtain an API Key. Copy the key, and run:
openneuro-py login
Paste the API key and press return.
Basic usage – Python interface
import openneuro as on
on.download(dataset='ds000246', target_dir='data/bids')
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