c3d-parser

C3D-parser

Installing the Python package:

It is recommended that you create a new virtual environment before installing this package, to avoid any potential dependency conflicts with the packages already installed in your Python environment.

If you intend to use this package directly from your Python environment you will also need to install the OpenSim Python distribution yourself. This can be installed using Conda, or by building the Python bindings from source. Development and testing have been done using Python 3.11 and OpenSim 4.5, so we recommend installing those releases if possible. Though most recent Python and OpenSim versions should work as well.

After activating your Python environment and installing OpenSim you can run pip install c3d-parser to install the application. It can then be started by running the command c3d_parser.

Installing the Windows executable:

The latest release of the C3D-Parser also provides a Windows installer for setting up an executable version of the application. Simply download and run C3D-Parser-{release-version}.exe for any release in the GitHub repository Releases.

Usage:

To process and analyse a session of gait data, first select your lab's marker-set using the "Lab" drop-down (if your lab is not shown, or you require a marker set other than the one we provide please see the section on custom marker sets). Next, select the local gait session directory using the "Input" line-edit or associated directory chooser, and select a directory to output the results. Each trial in the session will be automatically classified as "Static" or "Dynamic", but you can override these classifications by right-clicking on the item in question. You can exclude specific trials from the analysis by using the check-boxes provided.

Finally, the application also requires a collection of subject information for the processing step, including height, weight, knee-widths and leg-lengths. This information will be automatically filled using the metadata contained in your static C3D file, but you should check these values to make sure they are accurate. Once you are ready, click "Process Data" to begin.

The application will create an OpenSim model using the input data and will run IK and ID. The results from IK and ID will be displayed in the "Kinematic" and "Kinetic" tabs respectively. You can select specific gait cycles and can choose to exclude them from the combined, normalised results that are created at the end of the harmonisation process.

Once the "Harmonise Data" button is pressed, the user exclusions will be considered and the final output files will be produced. All outputs are written to the user-defined output directory.

Options

A number of user settings are available under "View" -> "Options". The "Line Width" option refers to the width of the lines displayed on the graphs in the visualisation tabs. Both "Data Directories" define the starting directories used when choosing the "Input" and "Output" paths in the main window. These settings are retained after you close the application.

Custom marker sets

The application pre-defines a number of lab-specific marker sets. If the marker sets we provide do not fit your needs you can adjust one of the existing marker sets or create a new one from scratch using the custom marker set dialog under "Marker" -> "Custom Marker Set".

You can import an initial mapping from one of the existing marker sets using the "Import" button.

We recommend that you specify your input session directory (using the "Input" line-edit in the main window) before opening the custom marker set dialog, this way the drop-down menu associated with each required marker will be populated with the list of markers defined in your static trial. Otherwise, you will have to type in the marker names manually, which is time-consuming and prone to errors. The dialog will also attempt to match any commonly named markers that it identifies in your static trial.

Your custom marker set must define: "ASI", "KNE", "ANK", "MED", "HEE", either "PSI" or "SACR", either "KNEM" or "KAX".

Valid input data:

To be able to create an OpenSim model from your static C3D file, it must contain either: medial knee markers; or KAD markers as well as knee-width values in the C3D metadata PROCESSING section (so that we can calculate virtual positions for the medial markers based on the lateral knee marker positions).

It is recommended that your static C3D file defines the subject's height and weight in the metadata PROCESSING section, otherwise you will be prompted for this information.

Additionally, to be able to cover a wide range of inputs whilst keep the UI as minimal as possible, we have had to adopt a fairly strict policy on what is considered a 'valid' gait event. If a foot strike occurs over multiple force plates, we will be unable to use the GRF data associated with that stance phase. This will also affect which gait cycles are considered valid when normalising the results from ID.