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 paper:

Uhlrich SD*, Falisse A*, Kidzinski L*, Ko M, Chaudhari AS, Hicks JL, Delp SL, 2022. OpenCap: Human movement dynamics from smartphone videos. PLoS Comput Biol 19(10): e1011462. https://doi.org/10.1371/journal.pcbi.1011462. *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 3.11 recommended): conda create -n opencap-processing python=3.11
4. Activate environment: conda activate opencap-processing
5. Install OpenSim: conda install -c opensim-org opensim=4.5=py311np123
   • 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
3. MacOs: As of now this workflow is supported only on x86_64 architecture. If you intend to use this workflow use x86_64 conda environment even on apple silicon (arm64 is not supported yet).

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
  • The Moco folder contains examples for generating muscle-driven simulations using OpenSim 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