msk-modelling-python 0.4.0

A Python package for musculoskeletal modelling (version 0.4.0)

msk_modelling_python v0.4.0

A Python package for musculoskeletal modelling.

Author: Basilio Goncalves, PhD, University of Vienna, 2024 https://ufind.univie.ac.at/de/person.html?id=1004543 https://github.com/basgoncalves

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Pre-requisites for Installation

1. Download a Code Interpreter
   I recommend Visual Studio Code, but use your preferred one.

2. Download and Install Python (>= 3.8)
   Make sure it is the correct bit version: Python 3.8

3. Download and Install OpenSim (suggest >=4.3)
   OpenSim Downloads

4. Install Rapid Env Editor (optional)
   Rapid Env Editor

5. MOKKA (optional / only Windows users) Open-source and cross-platform software to easily analyze biomechanical data

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Pip installation (works for python 3.8)

(for later versions try OpenSim using Conda) https://pypi.org/project/msk-modelling-python/0.4.0/

Activate your Virtual Environment**

you can use Python or Conda

cd <your project folder>
python -m venv msk

Note: replace 'msk' if you want a different name

.\msk\Scripts\activate

Install uv package manager

pip install uv

Install msk-modelling-python

uv pip install msk-modelling-python

Test usage

This launches the GUI.

python -m msk_modelling_python

To run in batch mode:

python -m msk_modelling_python -b msk_modelling_python/settings.py

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Work with the code

1. Activate your virtual enviroment (assume name 'msk')

   .\msk\Scripts\activate
   

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2. Clone this Module "msk_modelling_python" to your virtual environment

   cd .\msk\Lib\site-packages
   

   git clone https://github.com/basgoncalves/msk_modelling_python.git
   

   Note: Ensure the name of the package is exactly "msk_modelling_python"

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3. Run OpenSim Setup from Installation Folder
   See OpenSim Scripting in Python

   cd 'C:\OpenSim 4.5\sdk\Python'
   

   python setup_win_python38.py
   

   python -m pip install .
   

   Note: run commands from shell or terminal

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4. Add the Path to the OpenSim Libraries to Your Environment Variables
   Add the following paths to your PATH variable:

   C:\OpenSim 4.5\bin
   C:\OpenSim 4.5\lib
   

   Note: see for help https://answers.microsoft.com/en-us/windows/forum/all/change-system-variables-on-windows-11/f172c29e-fd9e-4f0b-949d-c4696bd656b8

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5. Verify the OpenSim Installation.

   python 
   

   import opensim as osim
   model = osim.Model()
   

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6. Install requirements (in the terminal)

   cd .\msk\Lib\site-packages\msk_modelling_python
   pip install -r requirements.txt
   

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7. Launch msk_modelling_python

   python -m msk_modelling_python
   

   Note: to configure batch processing, edit msk_modelling_python\settings.py (see BatchSettings and CEINMSSettings classes)

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8. Basic Usage

   GUI mode (default):

   python -m msk_modelling_python
   

   Batch mode — configure msk_modelling_python\settings.py first, then:

   python -m msk_modelling_python -b msk_modelling_python/settings.py
   

   Key settings to configure in settings.py:

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9. Use Example Scripts Use example scripts in the "ExampleScripts" directory to get started with common tasks and workflows.

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This package includes a combination of other packages and custom functions to manipulate and analyze biomechanical data. Originally inspired by the MATLAB version of BOPS (Batch OpenSim Processing Scripts) - BOPS

Tools to be Included:

• BTK
  BTK Documentation
• c3dServer
  c3dServer
• OpenSim
  OpenSim Scripting in Python
• 3D Slicer
  3D Slicer
• FEbioStudio
  FEbioStudio
• MeshLab 2023.12
  MeshLab
• Genesis
  Genesis

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Code Structure

1. msk_modelling_python — main package entry point; run with python -m msk_modelling_python

2. settings.py — central configuration file; edit BatchSettings, CEINMSSettings, UISettings, and RecordingSettings classes to control all pipeline behaviour

3. gui/ — PyQt-based graphical interface (launched by default); widgets for batch processing, C3D export, EMG, CEINMS calibration, and results viewing

4. utils/ — core processing functions: OpenSim (IK, ID, SO, MA), CEINMS, EMG normalisation, model scaling, C3D export, and XML helpers

5. core/ — session and analysis runner logic used by both GUI and batch modes

6. config/ — config manager for loading/saving settings

7. record/ — video recording and camera utilities for motion capture sessions

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Examples

Launch the GUI for interactive use:

python -m msk_modelling_python

For scripted/batch pipelines, configure msk_modelling_python\settings.py and run:

python -m msk_modelling_python -b msk_modelling_python/settings.py

The pipeline supports: C3D export → model scaling → IK → ID → SO → muscle analysis → CEINMS calibration → CEINMS execution.

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Contact

For any questions or inquiries, please contact:

• Name: Basilio Goncalves
• Email: [e-mail]
• ResearchGate: Basilio Goncalves

References

Thelen, D. G. -2003- J. Biomech. Eng. 125, 70–77

Lloyd, D. G. et al. -2003- J. Biomech. 36, 765–776

Delp, S. L. et al. -2007- IEEE Trans. Biomed. Eng. 54, 1940–1950

Pizzolato, C. et al. -2015- J. Biomech. 48, 3929–3936

Hicks, J. L. et al. -2015- J. Biomech. Eng. 137,

Rajagopal, A. et al. -2016- IEEE Trans. Biomed. Eng. 63, 2068–2079

Goncalves, B. A. M. et al. -2023- Gait Posture 106, S68

Goncalves, B. A. M. et al. -2024- Med. Sci. Sport. Exerc. 56, 402–410

Version updates 0.0.17

• Version bump with new images and path adjustments in classes

Version updates 0.0.20

• Attempted CEINMS2 integration via pip packaging

Version updates 0.3.6

• Updated utils
• Added CEINMS support with troubleshooting functions and executables for hybrid and synergy calibrations

Version updates 0.4.0

• Improved app and batch processing with new settings and GUI entry point
• Cleaned up stale files and moved CEINMS settings
• Added n8n-inspired workflow pipeline system with a complete OpenSim batch processing example and quick-start guide

Version: 0.4.0