A repository for running virtual cortical stimulation on linear time-varying network based models. Paper is here:

Maintained(ish) by: Adam Li (adam2392 at gmail dot com)

1. conda and conda-env

   conda create -n cortstim source activate cortstim conda env create -f environment.yaml python=3.6 conda install --file requirements_conda.txt

or

conda create -n cortstim scipy numpy pandas scikit-learn matplotlib seaborn pyqt=5 ipykernel pytest
conda install mayavi   
conda install -c conda-forge mne
conda install -c anaconda natsort pylint flake8 tqdm
conda install -c bioconda snakemake
conda install -c numba numba
conda install xlrd

Here, we describe the main modules to run the entire software package.

1. Epilepsy Data Platform (EDP) The main i/o software for dealing with data that are used in this software. We generally support edf, fif, and any related MNE-python supported data format. We provide a preformatter pipeline to convert some raw data into our desired .fif/.json format.

2. Epilepsy Data Models (EDM) The main compute package that supports running on a single core, multiple core, or SLURM HPC environment. It will run the complete algorithm from data input read in with the IO module.

autopep8 --in-place --recursive --max-line-length=80 ./cortstim/
autopep8 --in-place --recursive --max-line-length=80 ./tests/
pylint ./cortstim/
pylint ./tests/
pytest --cov-config=.coveragerc --cov=./cortstim/ tests/
coverage-badge -f -o coverage.svg

If you rerun documentation and want to generate it into sphinx-docs.

sphinx-quickstart

Some useful commands for housekeeping on conda.

conda clean --all
conda update --all
conda update conda
conda env export > environment.yaml

Adding a kernel to jupyter from your conda environment

conda create -n cortstim scipy numpy pandas scikit-learn matplotlib seaborn pyqt=5 ipykernel pytest
conda install mayavi   
conda install -c conda-forge mne
conda install -c anaconda natsort pylint flake8 tqdm
conda install -c bioconda snakemake
conda install -c numba numba
conda install xlrd
python -m ipykernel install --name cortstim --user 
jupyter kernelspec uninstall yourKernel
jupyter kernelspec list

All data analysis assumes a structure:

• higher level (e.g. center, organized batch of datasets)
  • patient_id
    • seeg
      • edf
      • fif
    • scalp
      • edf
      • fif

1. https://ieeexplore.ieee.org/document/7963378
2. https://ieeexplore.ieee.org/document/8037439