msk-modelling-python 0.2.1

A Python package for musculoskeletal modelling (version 0.2.1)

msk_modelling_python (pre-release)

A Python package for musculoskeletal modelling.

Author: Basilio Goncalves, PhD, University of Vienna, 2024

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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

Create a Virtual Environment**

python -m venv msk

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

Install uv package manager

pip install uv

Install msk-modelling-python

uv pip install msk-modelling-python

Test usage

import msk_modelling_python as msk
msk.bops.greet()

Install opensim

import msk_modelling_python as msk
msk.install_opensim.run()

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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

   .\msk\Scripts\activate
   

   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. Testing msk_modelling_python (in python)

   import msk_modelling_python as msk
   msk.run_bops()
   

   Note: to change the performance of msk.run_bops() edit the settings file in .\msk_modelling_python\src\bops\settings.json

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8. Basic Usage

   import msk_modelling_python as msk
   
   # test msk
   msk.bops.Platypus().happy()
   
   # export c3d
   c3d_file_path = r'path\to\your\file.c3d'
   msk.bops.export_c3d(c3d_file_path)
   
   # run IK
   trial = msk.Project
   

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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. 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 This is the main package including all the modules needed for msk modelling, stats, data_processing, etc. This package contains subpackages that can be used independently.

2. bops Batch Opensim Processing Software
   Package with functions and classes to use Opensim, CEINMS, stats, and others for easier processing.

3. workflow ⭐ NEW! Workflow Pipeline System inspired by n8n
   Create and execute automated processing pipelines with a simple, intuitive API.

   from msk_modelling_python.workflow import Pipeline, WorkflowNode
   
   # Create a pipeline
   pipeline = Pipeline("OpenSim Analysis", "IK -> ID -> SO -> JRA")
   
   # Add nodes
   ik_node = WorkflowNode("IK", run_ik_function, {"model": "path/to/model.osim"})
   id_node = WorkflowNode("ID", run_id_function)
   
   pipeline.add_node(ik_node, is_start=True)
   pipeline.add_node(id_node)
   pipeline.connect("IK", "ID")
   
   # Execute
   results = pipeline.execute()
   

   See WORKFLOW_README.md for detailed documentation.

4. ui Functions to create user interface.

5. osim commands

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Examples

Find examples under ".\example_data\example_modules".

Workflow Examples: See example_data/workflow_example.py for complete pipeline examples including:

• OpenSim analysis pipelines (IK -> ID -> SO -> JRA)
• Batch processing workflows
• Data processing pipelines

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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 0.1.0

• include openSim.py with functions to improve opensim management

Version: 0.2.1