Opensim Python
Brittany Bhadd
Python is a widely used general purpose programming language. Python is free and open source, with a large user community that encourages sharing and user contributions. The Python language is very flexible, supporting object-oriented and procedural styles of computing. The Python design philosophy also emphasizes code readability which makes sharing and using code easier than with some other languages.
The fastest way to get started with OpenSim scripting with Python is to install one of our pre-built Conda packages. We highly recommend trying this option first before a manual installation, especially if you have not used Python before.
For information about how to install Conda and create a Python environment, please consult the Conda user guide. Once you have Conda installed and activated in your terminal (or Anaconda prompt), use the following commands to create and activate a new Conda environment.
The following instructions will refer to a directory , where you installed some version of OpenSim. On Windows this might look like C:\OpenSim 4.X, and on MacOS it might look like /Applications/OpenSim 4.X. The installation directory can be identified by the subfolders "bin" and "sdk". If you built from source on Mac or Linux, where the installation directory might use a Unix-like folder structure with subfolders "lib", "libexec", and "share".
To install, first navigate to the location of the OpenSim Python package within the OpenSim installation. If you are using OpenSim's GUI distribution, this location is /sdk/Python. If you built OpenSim from source on Mac or Linux, this location is likely /lib/python3.x/site-packages.
To install the OpenSim Python bindings on all platforms, run the following command. Note that if you have a Conda environment activated, this command with install OpenSim as a package into your Conda environment.
While we strongly recommend upgrading to a recent version of OpenSim and using the install instructions above, for legacy purposes, you may expand the following section to install older versions of OpenSim and Python.
Scripts can are located wherever you installed the resources that come packaged OpenSim distribution (i.e., the folder you choose after opening the GUI the first time after installation). For example, on Windows the might be C:\Users\username\Documents\OpenSim\4.X.
You can find a series of OpenSim scripting tutorials written using Jupyter notebooks here. These notebooks leverage Google Colab, a service for hosting interactive Jupyter notebooks in the cloud, and condacolab, a package that enables creating Conda environments in Google Colab.
OpenSim is supported by the Mobilize Center , an NIH Biomedical Technology Resource Center (grant P41 EB027060); the Restore Center , an NIH-funded Medical Rehabilitation Research Resource Network Center (grant P2C HD101913); and the Wu Tsai Human Performance Alliance through the Joe and Clara Tsai Foundation. See the People page for a list of the many people who have contributed to the OpenSim project over the years. 2010-2024 OpenSim. All rights reserved.
Download Moco for Windows or Mac from -moco. The Moco distribution contains a MATLAB/Java package, a Python package, a C++ library, and a command-line tool. Currently, Moco does not have a graphical user interface.
If you want to edit Moco's C++ code or use Moco on a platform for which we do not distribute binaries (e.g., Linux), then you must build Moco from source. Developing your own cost module does not require building Moco from source.
To use the Python package that comes with the Moco distribution, you must use the same Python distribution with which Moco was built. For Windows, this is the Python 3 distribution from python.org. For Mac, this is the Python 3 package from Homebrew.
Unfortunately, Moco does not yet provide any examples of XML files for use with the command-line interface. However, the MATLAB/Python examples can generate XML files that you can then use through the command-line interface.
My first try of creating a package.
SimTK's OpenSim (not the VR OpenSimulator) has a build script for Ubuntu and Debian that I was able to edit until it compiled, I expected it to be harder actually.
This process pulls a bunch of dependencies into a build subfolder and uses them during the process. I thought, I could create a package with the Arch way of
- install dependencies in the system (this I managed) and
- use them when installing something else
*The patches are
- fixing the ezc3d path, because the aur package has slightly different structure
- changing set_target_properties to set_property
the latter might not fix that dependency, but the compilation error doesn't seem to be connected
So, things like cmake and autoconf are likely makedepends, not depends. You should only place runtime dependencies in depends=(), and leave everything that opensim-core-git needs to build in makedepends=(). And don't use pastebin.com for pastes, use GitHub gists, or paste.rs, ix.io, or any of the other pastebins recommended on the IRC channels. pastebin.com has been known to push malware, and is generally not considered safe to use. So I'm not looking at your output until you put it somewhere else.
Instead of using sed to modify CMakeLists.txt, why not modify the file the way you want, and generate a patch with diff -u, and supply the patch along with your PKGBUILD, and use the patch command to apply the patch?
The first one likely fails because of the errors on line 921 and 91 of CMakeLists.txt, you have to scroll up to see them. I see the one on line 91 is the set_target_properties error, you likely need to fix it for set_target_properties as set_property (singular) is likely causing problems during the compilation. For the error on line 921, I would avoid relative paths if possible, so a /path/like/this/deep/subdirectory/../../other/path would essentially expand to /path/like/this/other/path. Using the relative parent directory .. like that is prone to error, and rather brittle should the directory structure change at all.
Have you installed OpenSIM using your GitHub link manually? You'll likely run into the same or similar issues if you do it outside of the PKGBUILD/makepkg process. I wouldn't try drafting the PKGBUILD until you can get it compiled and working manually. Basically, keep track of all the packages you have to install just to build it manually, and determine which ones are necessary only for building it (many of them are already part of the base-devel package). Also keep track of which files you need to modify (like CMakeLists.txt), and build patches for them once you get everything working. Follow Creating packages once you're ready to make the PKGBUILD.
If you can't get it built outside of makepkg/PKGBUILD, work with upstream support until you get it compiled and running. Once you get it compiled and running, you can run ldd against the main OpenSIM executable to determine which runtime libraries it uses, and ensure you populate the depends=() with the packages that provide those libraries.
Copyright: 2018 Seth et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Data Availability: Executables for the OpenSim application are freely available for download from Open-source code for OpenSim is available on GitHub at -org/opensim-core (for core libraries and command-line applications) and -org/opensim-gui (for building the graphical user interface and OpenSim distribution).
(A) Locations of visitors to the OpenSim documentation (sessions per country in the 1-year period ending April 21, 2018). Since its launch in 2012, the OpenSim documentation wiki has been visited by over 25,000 users from around the world per year [30]. (B) Publications citing OpenSim by research category (Web of Science). Note that journals, and thus citations of OpenSim, may belong to more than one research category. According to Google Scholar, OpenSim [27] has been cited 1947 times as of June 13, 2018; based on analysis of the subset of these papers published in 2016, we estimate that 3/4 of these publications make use of the software. (C) Cumulative downloads of OpenSim since its release in August 2007. 35,915 users have downloaded the software as of June 13, 2018 [31]. World map in (A) created using tools at
This paper describes the design and capabilities of OpenSim and provides a sampling of the types of research questions that can be answered using OpenSim. The software was first released in August 2007 as a research tool for generating simulations of movement. Early versions of the software were used primarily for studying human gait and exploring the effects of pathologies and treatments [27, 32]. We have introduced many additional capabilities in recent years, among which are enhancements in four key areas. First, new accurate models for modeling muscle contraction dynamics, muscle metabolic power, joint kinematics, and assistive devices have been introduced. These models enable users to closely replicate human and animal movements, and to explore metabolic cost under natural and engineered conditions. An extensive test suite ensures these models are correctly implemented, robust, and efficient. Second, users are now able to explore beyond predefined workflows and create custom studies that combine existing computational tools in new ways. For example, users can now access muscle-related variables like moment arms [33], fiber lengths, and passive fiber forces directly from a model, without running a complicated analysis in the OpenSim application. This functionality is available through the C++ API as well as MATLAB and Python scripting interfaces, ensuring the tools are accessible to researchers with differing computational backgrounds. Third, OpenSim now includes functionality for controlling data flow, such as converting data from motion capture file formats and managing data within a simulation. Without the help of third-party tools, users can read in experimental data from files in standard motion capture file formats to plot the data in OpenSim and use it to generate simulations. Fourth, the OpenSim desktop application incorporates a modern cross-platform visualizer with tools for creating animations of movement (Fig 3), which provides users with more control over the visualization and allows use on both Windows and Mac operating systems. These capabilities enable groundbreaking work in the academic, clinical, and industrial arenas.
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