A Python3 package for eeg (pre)processing from Automagic.
A Python3 version of the automagic EEG processing pipeline. Development in progress. This is all temporary.
- Paper: https://www.biorxiv.org/content/10.1101/460469v1
- Paper: https://www.ncbi.nlm.nih.gov/pubmed/31233907
- Matlab github repo: https://github.com/methlabUZH/automagic
├── LICENSE ├── Makefile <- Makefile with commands like `make data` or `make train` ├── README.md <- The top-level README for developers using this project. ├── data │ ├── external <- Data from third party sources. │ ├── interim <- Intermediate data that has been transformed. │ ├── processed <- The final, canonical data sets for modeling. │ └── raw <- The original, immutable data dump. │ ├── docs <- A default Sphinx project; see sphinx-doc.org for details │ ├── notebooks <- Jupyter notebooks. Naming convention is a number (for ordering), │ the creator's initials, and a short `-` delimited description, e.g. │ `1.0-jqp-initial-data-exploration`. │ ├── references <- Data dictionaries, manuals, and all other explanatory materials. │ ├── reports <- Generated analysis as HTML, PDF, LaTeX, etc. │ └── figures <- Generated graphics and figures to be used in reporting │ ├── requirements.txt <- The requirements file for reproducing the analysis environment, e.g. │ generated with `pip freeze > requirements.txt` │ ├── setup.py <- makes project pip installable (pip install -e .) so src can be imported ├── pyautomagic | ├── src <- Src/ from automagic (matlab) │ ├── __init__.py <- Makes src a Python module │ │ │ ├── base <- Scripts that are configuration files, or other code used by the entire pyautomagic repo. │ │ │ ├── gui <- Scripts for the gui │ │ │ ├── preprocessing <- Scripts for running EEG preprocessing │ │ │ └── visualization <- Scripts to visualize results, etc. │ └── tox.ini <- tox file with settings for running tox; see tox.testrun.org
Intended Users / Usage
Researchers dealing with EEG data. The main (default) workflow is summarized in:
For installation instructions, see installation guide.
Setup Jupyter Kernel To Test
You need to install ipykernel to expose your conda environment to jupyter notebooks.
conda install ipykernel python -m ipykernel install --name pyautomagic --user # now you can run jupyter lab and select a kernel jupyter lab
Testing and Documentation
For contributing, please see contribution guide.
For running tests, please see testing guide.
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