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sovabids
Visit the documentation <https://sovabids.readthedocs.io/>_
.. after-init-label
-
sovabids is a python package for automating eeg2bids conversion.
-
sovabids can be used through (click to see the examples): a.
its python API <https://sovabids.readthedocs.io/en/latest/auto_examples/lemon_example.html#using-the-python-api>_ b.its CLI entry points <https://sovabids.readthedocs.io/en/latest/auto_examples/lemon_example.html#using-the-cli-tool>_ c.its JSON-RPC entry points (needs a server running the backend) <https://sovabids.readthedocs.io/en/latest/auto_examples/rpc_example.html>_ d.its minimal web-app GUI <https://sovabids.readthedocs.io/en/latest/auto_examples/gui_example.html>_
.. note::
The advantage of the JSON-RPC way is that it can be used from other programming languages.
Limitation:
Do notice that at the moment the files have to be on the same computer that runs the server.
.. warning::
Currently meg2bids conversion is not supported, but this is a targeted feature.
.. tip::
By default sovabids will skip files already converted. If you want to overwrite previous conversions currently you need to delete the output folder (by yourself) and start sovabids over again.
Architecture
The main elements of sovabids are:
- A source path with the original dataset.
- A bids path that will be the output path of the conversion.
- A rules file that configures how the conversion is done from the general perspective.
- A mapping file that encodes how the conversion is performed to each individual file of the dataset.
Internally sovabids uses MNE-Python <https://github.com/mne-tools/mne-python> and MNE-BIDS <https://github.com/mne-tools/mne-bids> to perform the conversion. In a sense is a wrapper that allows to do conversions from the command line.
Installation
.. code-block:: bash
git clone https://github.com/yjmantilla/sovabids.git cd sovabids pip install -r requirements-user.txt
Installation for GUI usage
This will install sovabids for usage with an experimental web gui, and as an experimental plugin for bidscoin.
.. code-block:: bash
git clone https://github.com/yjmantilla/sovabids.git cd sovabids pip install -r requirements-gui.txt
Installation for developers
Fork this repo and run:
.. code-block:: bash
git clone https://github.com/
Notice that the requirements-dev.txt file already has the sovabids installation using editable mode.
Basic Usage
The easiest way is to use sovabids through its CLI entry-points as follows:
sovapply ^^^^^^^^
Use the sovapply entry-point to produce a mapping file from a source path, an output bids root path and a rules filepath.
.. code-block:: bash
sovapply source_path bids_path rules_path
By default the mapping file made will have the following filepath:
.. code-block:: text
bids_path/code/sovabids/mappings.yml
sovaconvert ^^^^^^^^^^^
Use the sovaconvert entry-point to convert the dataset given its mapping file.
.. code-block:: bash
sovaconvert mapping_file
Funding
.. raw:: html
Acknowledgments
sovabids is developed with the help of the following entities:
.. raw:: html
Academic Works
-
Poster for the Big Data Neuroscience Workshop 2022 (Austin, Texas) <https://www.canva.com/design/DAFMDNgVuGU/UTEbbAYk0JG0d-JpdjQOQg/view?utm_content=DAFMDNgVuGU&utm_campaign=designshare&utm_medium=link2&utm_source=sharebutton>_ -
Poster for OHBM 2022 Anual Meeting <https://www.canva.com/design/DAFBHD1bCs4/FNZLtwC78ip_5jt7bcAajw/view?utm_content=DAFBHD1bCs4&utm_campaign=designshare&utm_medium=link2&utm_source=sharebutton>_ -
Video for OHBM 2022 Anual Meeting <https://youtu.be/7M7JLrl6KAk>_ -
Poster for the eResearch Australasia Conference 2021 <https://www.canva.com/design/DAErO4bo4uk/gnHqwkVFs2qP7U1FhlViVQ/view?utm_content=DAErO4bo4uk&utm_campaign=designshare&utm_medium=link&utm_source=publishsharelink>_
What does sova means?
sova is a contraction of 'eso va' which mean 'that goes' in spanish.
Nevertheless the real usage by the original developers is just to convey the idea of :
we will make it happen, we dont know how, but we will