pyautomagic 0.1.0

Description:

pyautomagic 0.1.0

pyautomagic







A Python3 version of the automagic EEG processing pipeline. Development in progress. This is all temporary.
References

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

Project Organization
├── 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:
Installation Guide
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.