spinal-population-dynamics-paper

Code to reproduce the figures from Wimalasena et al. 2025

🛠️ Environment Setup

To ensure reproducibility, this repository includes an environment.yml file specifying the required Python packages and versions.

🔧 Create the Conda Environment

Make sure you have conda or mamba installed.

Then run:

conda env create -f environment.yml

This will create a new conda environment (named spinal-pop-dyn-figs or as specified in the YAML file).

▶️ Activate the Environment

Once created, activate the environment:

conda activate spinal-pop-dyn-figs

You are now ready to run the figure generation scripts.

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🧪 Generating Figures

🚀 Suggested Method (VSCode Interactive Window)

The recommended way to run the figure scripts is to open them in Visual Studio Code and use the Interactive Python window (e.g., Jupyter-style cells). This allows step-by-step execution and interactive debugging.

Each script is designed to generate one figure directly from the source data in data/SourceData.xlsx.

⚠️ Make sure the data file is present before running scripts. See data/README.md for setup instructions.

👥 Switching Between Subjects

Some figure scripts support switching between subjects via a C_ID variable defined near the top of the file.

To generate figures for a specific subject:

C_ID = "1"  # or "2"