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https://github.com/hoechenberger/openneuro-py
A client for accessing OpenNeuro datasets, written in Python.
https://github.com/hoechenberger/openneuro-py
Last synced: about 23 hours ago
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A client for accessing OpenNeuro datasets, written in Python.
- Host: GitHub
- URL: https://github.com/hoechenberger/openneuro-py
- Owner: hoechenberger
- License: gpl-3.0
- Created: 2020-12-12T22:33:42.000Z (about 4 years ago)
- Default Branch: main
- Last Pushed: 2024-12-23T17:01:42.000Z (13 days ago)
- Last Synced: 2024-12-28T05:14:38.243Z (8 days ago)
- Language: Python
- Homepage:
- Size: 681 KB
- Stars: 61
- Watchers: 5
- Forks: 12
- Open Issues: 8
-
Metadata Files:
- Readme: README.md
- License: LICENSE
Awesome Lists containing this project
README
# openneuro-py
A Python client for accessing [OpenNeuro](https://openneuro.org)
datasets.
## Installation
```shell
# 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`:
```shell
# via conda:
conda install -c conda-forge ipywidgets
# or via pip:
pip install ipywidgets
```
## Basic usage – command line interface
### Getting help
```shell
openneuro-py --help
openneuro-py download --help
openneuro-py login --help
```
### Download an entire dataset
```shell
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.
```shell
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
```shell
openneuro-py download --dataset=ds000246 \
--exclude=sub-emptyroom
```
### Download only a single file
```shell
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:
```shell
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:
```shell
openneuro-py login
```
Paste the API key and press return.
## Basic usage – Python interface
```python
import openneuro as on
on.download(dataset='ds000246', target-dir='data/bids')
```