Software Engineering

In the previous post, we discussed preprocessing data with OpenSim. An important part of preprocessing is low-pass filtering of various pieces of data. In this post, we will explore many of the unanswered questions and ambiguities of low-pass filtering in OpenSim. Following stories and personal experience of strange and erroneous results coming from OpenSim filtering, I began to doubt the implementation in OpenSim. To verify the results, I set out to validate the filtering against 2 existing implementations in Python and Matlab. ...

In the previous post, we discussed setting up AddBiomeachanics for local data analysis. In this post, we’re going to from freshly collected laboratory data to motion reconstructions in OpenSim or AddBiomechanics. The Kuopio Gait dataset and Kuopio Full-Body (KFB) dataset were both collected in the HUMEA laboratory at the University of Eastern Finland. Using this data in downstream processing application, like OpenSim, requires preprocessing from the laboratory coordinate system and units to OpenSim’s coordinate system and units. ...

What is AddBiomechanics? In order to analyze motion capture data to create reconstructions of human motion, it is necessary to create scaled models, and calculate inverse kinematics (IK) and then inverse dynamics (ID). This process is tedious and often quite time-consuming. During the process, it is important to consider the marker residual error as well as the force residual error from force plates. This often necessitates manual tweaking to markers and model parameters to achieve a required error tolerance. ...

What is OpenSim Perhaps you have used OpenSim for muskuloskeletal modeling. Now you have found yourself here wondering how to build the project from source and what a python wheel is. To begin, building the project from source is no small feat and usually takes many hours of configuration and troubleshooting. If you succeed in this quest, you will emerge victoriously with a working python environment with the exact dependencies that you need. A Python wheel is simply a binary package which includes all the dynamic libraries a package needs to function on your platform so you don’t have to build everything from source. For more information on Python wheels check out this article. The point of this article though is to learn how to build the wheel, so we will of course be building everything from source. ...

Technical Debt Accumulation On a warm August day six months ago, I began a new journey as a doctoral researcher. As part of that journey, I have been diving into an open biomechanical modeling source software called OpenSim. Successfully compiling the code base for the first time was a non-trivial task and was a cause for major celebration. As a nearly 20 year old software project (the first public release was on August 20, 2007), it has expanded far beyond its initial purpose and accumulated significant technical debt along the way. ...