This repository contains code for reproducing results in the associated manuscript: "Kinematic coupling of the glenohumeral and scapulothoracic joints generates humeral axial rotation".

This repository relies on Anaconda for installing dependencies. All commands below should be run from the Anaconda Prompt. After installing Anaconda and cloning the repository, make sure you are in the same directory as environment.yml and run:

conda env create --file environment.yml

All code within the repository relies on two configuration files (logging.ini and parameters.json) to locate the associated data repository, configure analysis parameters, and instantiate logging. The location of the config directory is specified as a command line parameter (so it is feasible for this folder to reside anywhere in the filesystem). Analysis and figure generation tasks must be executed as module scripts:

python -m st_generated_axial_rot.figures.axial_rot_corr config

Template logging - template.ini and parameters - template.json files are located in the config directory and should be copied and renamed to logging.ini and parameters.json. Parameters.md explains each parameter within parameters.json. Each analysis and figure generation task contains Python documentation describing its utility and the parameters that it expects from parameters.json.

The associated data repository containing biplane fluoroscopy derived humerus and scapula kinematics can be found on Zenodo: . The biplane_vicon_db_dir parameter should point to the database folder of this repository. This analysis also relies on 2 additional supporting data files which reside in the data directory.

The config directory contains configuration files.

The data directory contains two data files indicating the start and end frames that should be utilized when analyzing external rotation at 90° of abduction and external rotation in adduction trials.

The euler_angles_angular_velocity.mlx file is a MATLAB Live Script that was utilized to generate Appendix 2 of the manuscript. It explains why Euler angles are ill-suited for quantifying physiologic joint motion and why angular velocity (once properly projected) is best suited for this task.

The st_generated_axial_rot directory contains code for reproducing the analysis of the associated manuscript. Within st_generated_axial_rot the following packages exist:

• analysis - contains code for various analyses that were undertaken to analyze the contributions of the scapulothoracic and glenohumeral joints to humerothoracic axial rotation, elevation, and plane of elevation.
• figures - contains code for reproducing the figures in the associated manuscript.
• common - contains common code utilized by both analysis and figures.

This code is licensed according to the most restrictive license (GPLv3) of the packages that it utilizes: spm1d.