Example Research Project

Analysis of vmp data. To run this yourself, follow the instructions below.

Requirements

Python users: Conda package manager
MATLAB users: MATLAB

Python setup

Open a terminal, navigate to this directory and install the environment and kernel using:

conda env create -f environment.yml
conda activate vmp-proj
python -m ipykernel install --user --name vmp-proj
conda deactivate

Check that you can activate it again using:

conda activate vmp-proj

With the environment active, download the data by navigating to the data/ and running:

python download_vmp_data.py

Download the MATLAB toolboxes by navigating to matlab_toolboxes/ and execute

python download_toolboxes.py

If you want to remove the environment and kernel later, see the instructions at the bottom.

Now you can proceed to the analysis.

MATLAB setup

Open MATLAB and navigate to data/. Run the script to download the data.

Then navigate to matlab_toolboxes/. Run the script to download the toolboxes.

Now you can proceed to the analysis.

Running the analysis

Within the analysis/ directory you can:

run python analyse_vmp_profile.py to execute the script (don't forget to conda activate vmp-proj!)
convert the python script to a notebook with jupytext --to=ipynb *.py then open with Jupyter Lab/Notebook
open up MATLAB and run analyse_vmp_profile.m.

Figures are saved to figures/.

Project Structure

example_research_project/
    ├── README.md          <- The top-level README for people using this project.
    ├── data/
    │   ├── external       <- Data pulled in from outside of this project.
    │   ├── internal       <- Data generated within this project.
    │   └── README.md      <- Information on data sources and retrieval. 
    │
    ├── analysis/          <- Jupyter notebooks, MATLAB code and anything else that constitutes analysis.
    │   ├── README.md      <- Any information about the analysis, such as execution order. 
    │   ├── *.py           <- Python files that can be converted to notebooks using jupytext.
    │   └── *.m            <- Analysis in MATLAB.
    │
    ├── figures/           <- Saved figures generated during analysis.
    │
    ├── environment.yml    <- Conda environment specification.
    │
    ├── matlab_toolboxes/  <- A place for 3rd party MATLAB toolboxes.
    │   ├── toolbox/
    │   ├── get_toolbox.m  <- Scripts to download toolboxes.
    │   └── get_toolbox.py
    │
    ├── setup_scripts/     <- Bash scripts for automatic setup.
    │   └── install.sh     <- Script to install something.

Automatic setup

Automatic setup is captured in the bash script setup_scripts/setup.sh, which can be run in a terminal assuming the above requirements are fulfilled (macOS/Linux systems only!):

cd setup_scripts
./setup.sh

Note that this will download the data and toolboxes, as well as install the kernel and environment.

To install/remove the environment separately from the downloads, use the following scripts:

./install_environment.sh

or:

./remove_environment.sh

If these don't execute, you might need to change the file permissions with chmod u+x *.sh.

If you run in to problems, see the instructions for manual setup above.

Removing the environment

To remove the kernel and environment manually use:

conda activate vmp-proj
jupyter kernelspec uninstall vmp-proj
conda deactivate
conda remove --name vmp-proj --all

jessecusack / example_research_project