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OpenCap Processing

This repository enables the post-processing of human movement kinematics collected using OpenCap. You can run kinematic analyses, download multiple sessions using scripting, and run muscle-driven simulations to estimate kinetics.

Publication

More information is available in our preprint:

Uhlrich SD*, Falisse A*, Kidzinski L*, 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. *contributed equally

Archived code base corresponding to publication: https://zenodo.org/record/7419973

Install requirements

General

  1. Install Anaconda
  2. Open Anaconda prompt
  3. Create environment (python 3.9 recommended): conda create -n opencap-processing python=3.9
  4. Activate environment: conda activate opencap-processing
  5. Install OpenSim: conda install -c opensim-org opensim=4.4=py39np120
    • Test that OpenSim was successfully installed:
      • Start python: python
      • Import OpenSim: import opensim
        • If you don't get any error message at this point, you should be good to go.
      • You can also double check which version you installed : opensim.GetVersion()
      • Exit python: quit()
    • Visit this webpage for more details about the OpenSim conda package.
  6. (Optional): Install an IDE such as Spyder: conda install spyder
  7. Clone the repository to your machine:
    • Navigate to the directory where you want to download the code: eg. cd Documents. Make sure there are no spaces in this path.
    • Clone the repository: git clone https://github.com/stanfordnmbl/opencap-processing.git
    • Navigate to the directory: cd opencap-processing
  8. Install required packages: python -m pip install -r requirements.txt
  9. Run python createAuthenticationEnvFile.py
    • An environment variable (.env file) will be saved after authenticating.

Muscle-driven simulations

  1. Windows only: Install Visual Studio
    • The Community variant is sufficient and is free for everyone.
    • During the installation, select the workload Desktop Development with C++.
    • The code was tested with the 2017, 2019, and 2022 Community editions.
  2. Linux only: Install OpenBLAS libraries
    • sudo apt-get install libopenblas-base

Examples

  • Run example.py for examples of how to run kinematic analyses
  • Run example_kinetics.py for examples of how to generate muscle-driven simulations
  • Moco

Download OpenCap data

Using Colab

  • Open batchDownload.ipynb in Colab and follow the instructions
    • You do not need to follow the install requirements above.

Locally

  • Follow the install requirements above
  • Open batchDownload.py and follow the instructions