Join members of the OpenSim Team on Wednesday July 26th for an introduction to OpenSim and new tools for rapidly developing musculoskeletal simulations.

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1. Create an OpenCap account: https://www.app.opencap.ai/.

2. Demo #1: Colab

The first demo of the OpenCap portion of the workshop will be completed with Colab. In order to execute code, a Google account sign-in is required. Create an account if you don't have one already and if you would like to run code yourself.

Here is the link to the notebook we will use during the workshop.

3. Demo #2: Install requirements

The second demo of the OpenCap portion of the workshop may be completed in Windows, Mac, or Linux. It will require cloning/downloading the opencap-processing Github repository and setting up a Python environment using Anaconda. Follow the install instructions here or perform the following steps:

1. Open the Anaconda Prompt.

2. Create environment (python 3.9 10 recommended)

   Code Block
   (base) C:\Users\me> conda create -n opencap-processing python=3.910

   
   

3. Activate environment

   Code Block
   (base) C:\Users\me> conda activate opencap-processing

   
   

4. Install OpenSim within environment

   Code Block
   (opencap-processing) C:\Users\me> conda install -c opensim-org opensim=4.4.1=py39np120py310np121

   
   

5. (Optional): Install an IDE such as Spyder (you can use any IDE or run code from the terminal)

   Code Block
   (opencap-processing) C:\Users\me> conda install spyder

   
   

6. Clone/download the repository to your machine
   1. Using Git

      1. Navigate to the directory where you want to download the code. For example:

         Code Block
         (opencap-processing) C:\Users\me> cd Documents

         
         

      2. Clone the repository

         Code Block
         (opencap-processing) C:\Users\me\Documents> git clone https://github.com/stanfordnmbl/opencap-processing.git

         
         

   2. Without using Git
      
      1. Download the repository by visiting https://github.com/stanfordnmbl/opencap-processing/archive/refs/heads/main.zip
      2. Unzip the folder
         • We will assume your PATH looks like C:\Users\me\Documents\opencap-processing and that the path to the README file is C:\Users\me\Documents\opencap-processing\README.md
7. Install required Python packages

   1. Navigate to the repository (make sure you are in Documents)

      Code Block
      (opencap-processing) C:\Users\me\Documents> cd opencap-processing

      
      

   2. Install packages

      Code Block
      (opencap-processing) C:\Users\me\Documents\opencap-processing> python -m pip install -r requirements.txt

      
      

8. Create environment variable for authentication, you will be prompted to provide your OpenCap credentials. An environment variable (.env file) will be saved after authenticating.

   Code Block
   (opencap-processing) C:\Users\me\Documents\opencap-processing> python createAuthenticationEnvFile.py

   
   

9. Run example.py to verify that everything was correctly installed so far. If you get some plots popping out, then you can proceed to step 10.

   Code Block
   (opencap-processing) C:\Users\me\Documents\opencap-processing> python createAuthenticationEnvFileexample.py

   
   

10. If you're a Mac user, you can stop here. If you're on Windows or Linux, you'll need this extra step. This part of the workshop will involve running dynamic simulations of walking using OpenSimAD, which is a custom version of OpenSim with support for Automatic Differentiation (AD). OpenSimAD requires a compiler, which is not installed by default on Windows, and the OpenBLAS libraries, which you need to manually install on Linux.

    1. (Windows only): Install Visual Studio

       1. The Community variant is sufficient and is free for everyone.

       2. During the installation, select the workload Desktop Development with C++.

       3. The code was tested with the 2017, 2019, and 2022 Community editions.

    2. (Linux only): Install OpenBLAS libraries

       Code Block
       sudo apt-get install libopenblas-base

       
       

11. Run Examples/example_walking_opensimAD.py to verify that everything was correctly installed so far. If you see some IPOPT iterations, then you're all set. We'll go through the example during the workshop.

    Code Block
    (opencap-processing) C:\Users\me\Documents\opencap-processing> cd Examples (opencap-processing) C:\Users\me\Documents\opencap-processing\Examples> example_walking_opensimAD.py

    
    

12. (Optional): Download the processed example data from Demo #2 as reference. The folder name (4d5c3eb1-1a59-4ea1-9178-d3634610561c) is the identifier of the session. If you follow all the steps of the workshop, files will be downloaded/generated under opencap-processing/Data/4d5c3eb1-1a59-4ea1-9178-d3634610561c. If you run into issues during the workshop (eg, when compiling files), you can download the processed example data and copy them under ./opencap-processing/Data/4d5c3eb1-1a59-4ea1-9178-d3634610561c (make sure the path to the metadata file looks like: opencap-processing/Data/4d5c3eb1-1a59-4ea1-9178-d3634610561c/sessionMetadata.yaml). This should allow you to complete the workshop.

Part 2: AddBiomechanics

1. Create account

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OpenSim with Python (Windows only)

1. Open the Anaconda Prompt (or, Powershell on Windows, Terminal on Mac, etc).

2. If not using the Anaconda Prompt, you may need to initialize conda for shell interaction by running

   Code Block
   > conda init <shell-name>

   where <shell-name> is one of the following: cmd.exe (Windows default), bash (macOS default), powershell, fish, zsh, tcsh, xonsh.

3. Create a new conda environment for Python 3.10.

   Code Block
   (base) C:\Users\me> conda create -n addbio-processing python=3.10 matplotlib

   
   

4. Activate the conda environment.

   Code Block
   (base) C:\Users\me> conda activate tgcs2023addbio-processing

   
   

5. If paths to previous OpenSim versions exist on your PYTHONPATH environment variable, remove them and restart the shell.

6. Install the OpenSim conda package. This installs a version of OpenSim including Moco that is compatible with Python 3.10 and includes NumPy 1.21. 

   Code Block
   (addbio-processing) C:\Users\me> conda install -c opensim-org opensim-moco=4.4.1=py310np121

   
   

7. Launch a Python interpreter from your conda environment.

   Code Block
   (addbio-processing) C:\Users\me> python

   
   

8. Test the OpenSim configuration by checking the timestamp from running 

   Code Block
   >>> import opensim >>> opensim.GetVersionAndDate()

   in the Python interpreter; the date should be in June July 2023.

OpenSim with Matlab

1. Download Go to the  OpenSim 4.4.1 softwarerelease page here.
2. In the dropdown window under "Assets", select the distribution for your platform.
   
   1. Windows users: download opensim-core-4.4.1-win.zip. 
   2. Mac users: download opensim-core-4.4.1-mac.zip. 
3. Install OpenSim to a location of your choice; perhaps C:\opensim-core-4.4.1 (on Windows).If you use Windows
4. The next step is platform dependent:
   1. For Windows users, edit your PATH environment variable to include OpenSim’s bin directory (e.g.,
    
   1. C:\opensim-core-4.4.1\bin). See here for instructions. Make sure to remove any previous OpenSim installations from your PATH.

   2. For Mac users, authorize the OpenSim distribution by running the following command in the Terminal

      Code Block
      $ xattr -r -d com.apple.quarantine <opensim_install_directory>

      where <opensim_install_directory> is the directory where you unzipped the installation (e.g., /Applications/opensim-core-4.4.1/).

5. Configure OpenSim with Matlab by starting Matlab and starting Matlab and running configureOpenSim.m, located at C:\opensim-core-4.4.1\Resources\Code\Matlab.

6. After the script completes, restart Matlab and test the configuration by checking the timestamp from running 

   Code Block
   >> org.opensim.modeling.opensimCommon.GetVersionAndDate()

    in the Matlab command window; the date should be in July 2023.

7. Test that the visualizer is working by running the following:

   Code Block
   >> cd 'C:\opensim-core-4.4.1\Resources\Code\Matlab\Moco' >> exampleSlidingMass

   You should see a visualizer window appear with a sliding mass animation. Hit ESC twice to close the window.

8. Note for OpenSim 3.3 users: You cannot concurrently use OpenSim 3.3 and 4.4 in Matlab; to switch versions you must re-run configureOpenSim.m and edit your PATH environment variable.

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Download the example data here: ExampleData.zip AddBiomechanicsExampleFiles.zip.

The top level directory contained in the zip folder is /AddBiomechanics, and contains two subdirectories: /AddBiomechanics/Data and /AddBiomechanics/Results. The Data folder contains the model file, marker trajectories, and ground reaction forces needed to complete the workshop. The text editor you choose should support XML formatting since modifying the OpenSim model file will be necessary. The Results folder contains result files already processed by AddBiomechanics, which will be necessary in the latter half of the tutorial, but may be also useful if technical difficulties occur. The Scripts folder contains copies of the additional Moco scripts from the hands-on portion of the tutorial.

The completed example can be found on the web here: TGCS2023_ExampleSubject. Participants may use this link to view the settings used for the example or to visualize and plot the processed data.

Documentation

OpenSim API docs

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Visit the Moco website here.

Slides

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View file
name TGCS2023OpenSimWorkshop.pdf height 250

Publications

Uhlrich SD, Falisse A, Kidzinski L, Muccini J, Ko M, Chaudhari AS, Hicks JL, Delp SL (2022) OpenCap: 3D human movement dynamics from smartphone videos. bioRxiv. https://doi.org/10.1101/2022.07.07.499061

Werling K, Bianco NA, Raitor M, Stingel J, Hicks JL, Collins SH, Delp SL, Liu CK (2023) AddBiomechanics: Automating model scaling, inverse kinematics, and inverse dynamics from human motion data through sequential optimization. bioRxiv. https://doi.org/10.1101/2023.06.15.545116

Dembia CL, Bianco NA, Falisse A, Hicks JL, Delp SL (2020) OpenSim Moco: Musculoskeletal optimal control. PLoS Comput Biol 16(12): e1008493. https://doi.org/10.1371/journal.pcbi.1008493

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