mirgee / thesis_project

This is the source code of my diploma thesis project.

Thesis project

This is the source code of my diploma thesis project.

Setup

Add absolute path to thesis_project/src/ folder to your PYTHONPATH env variable.

export PYTHONPATH=$PYTHONPATH:{full_path_to_repo}/thesis_project/src/

You may also want to add this to your .bashrc, so that the variable stays set after user logout:

echo "PYTHONPATH=$PYTHONPATH:{full_path_to_repo}/thesis_project/src/" >> ~/.bashrc

Install dependencies into a conda environment:

conda env update -f thesis.yml
conda activate thesis
pip3 install -r requirements.txt

I use git-lfs for the datafiles. You may need to run

git lfs install
git lfs update
git lfs fetch

All the sensitive data in the repository is encoded using git-crypt. If you want access, please, send me an email and I will send you a keyfile. After installing git-crypt, simply run

git-crypt unlock /path/to/keyfile

How to run a specific file

Each file run must have information about the parent module, which means that to run just, e.g. plot_eeg_from_file.main(), you have to pass -m flag to the interpreter, and give the absolute module name:

python -m src.visualization.interactive_plot_eeg_from_file raw/1a.tdt

Alternatively, after adding the source code root to PYTHONPATH and activating conda environment with all the dependencies installed, you can just run:

python src/visualization/interactive_plot_eeg_from_file raw/1a.tdt