Metadata-Version: 2.1
Name: msk-modelling-python
Version: 0.0.11
Summary: A Python package for musculoskeletal modelling (version 0.0.11)
Home-page: https://github.com/your_username/msk_modelling_python
Author: Bas
Author-email: basilio.goncalves7@gmail.com
License: UNKNOWN
Description: # msk_modelling_python (pre-release)
        
        A Python package for musculoskeletal modelling.
        
        **Author:** Basilio Goncalves, PhD, University of Vienna, 2024
        
        ---
        
        ## Pre-requisites for Installation
        
        1. **Download a Code Interpreter**  
            I recommend [Visual Studio Code](https://code.visualstudio.com/download), but use your preferred one.
        
        2. **Download and Install Python (>= 3.8)**  
            Make sure it is the correct bit version: [Python 3.8](https://www.python.org/downloads/release/python-380/)
        
        3. **Download and Install OpenSim (suggest >=4.3)**  
            [OpenSim Downloads](https://simtk.org/frs/?group_id=91)
        
        4. **Install Rapid Env Editor (optional)**  
            [Rapid Env Editor](https://www.rapidee.com/en/about)
        
        5. **MOKKA (optional / only Windows users)**
            [Open-source and cross-platform software to easily analyze biomechanical data](https://biomechanical-toolkit.github.io/mokka/)
        ---
        
        ## Pip installation (testing...)
        
        ```bash
        pip install msk_modelling_python
        
        ```
        
        ## Test usage
        ``` python
        import msk_modelling_python as msk
        
        msk.bops.greet()
        ```
        
        ## Work with the code 
        
        1. **Create a Virtual Environment**
             ```sh
             python -m venv msk
             ```
             Note: replace 'msk' if you want a different name
        ---
        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"*
        ---
        
        3. **Run OpenSim Setup from Installation Folder**  
            See [OpenSim Scripting in Python](https://simtk-confluence.stanford.edu:8443/display/OpenSim/Scripting+in+Python)
             ```sh
             .\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    
        ---
        
        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
        ---
        5. **Verify the OpenSim Installation (in python)**
             ```python
             import opensim as osim
             model = osim.Model()
             print("OpenSim model created successfully!")
             ```
        ---
        6. **Install requirements (in the terminal)**
             ```powershell
             cd .\<myenv>\Lib\site-packages\msk_modelling_python
             pip install -r requirements.txt
             ```
        ---
        7. **Testing msk_modelling_python (in python)**
             ```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
        ---
        8. **Basic Usage**
             ```python
             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
             ```
        ---
        9. **Use Example Scripts**
             Use example scripts in the "ExampleScripts" directory to get started with common tasks and workflows.
        
        ---
        
        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](https://simtk.org/projects/bops/)
        
        ## Tools to be Included:
        - **BTK**  
          [BTK Documentation](https://biomechanical-toolkit.github.io/docs/Wrapping/Python/_getting_started.html)
        - **c3dServer**  
          [c3dServer](https://www.c3dserver.com/)
        - **OpenSim**  
          [OpenSim Scripting in Python](https://simtk-confluence.stanford.edu:8443/display/OpenSim/Scripting+in+Python)
        - **3D Slicer**  
          [3D Slicer](https://www.slicer.org/)
        - **FEbioStudio**  
          [FEbioStudio](https://febio.org/)
        - **MeshLab 2023.12**  
          [MeshLab](https://www.meshlab.net/)
        
        ---
        
        ## 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. **ui**
             Functions to create user interface.
        
        4. **osim commands**
        ---
        
        ## Examples
        
        Find examples under ".\example_data\example_modules".
        
        ---
        
        ## Contact
        
        For any questions or inquiries, please contact:
        
        - **Name:** Basilio Goncalves
        - **Email:** basilio.goncalves@univie.ac.at
        - **ResearchGate:** [Basilio Goncalves](https://www.researchgate.net/profile/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 0.3.0
        
        - fix import bops
        - testing the inclusion of opensim (v.4.5)
        - classes should be working
        
        
        
        Version: 0.0.11
Platform: UNKNOWN
Classifier: Programming Language :: Python :: 3
Classifier: License :: OSI Approved :: MIT License
Classifier: Operating System :: OS Independent
Requires-Python: >=3.8
Description-Content-Type: text/markdown
