Scripting with Matlab

Sept 06, 2021

1 Setting up your Matlab Scripting Environment
- 1.1 Test that OpenSim is properly configured with MATLAB
2 Loading OpenSim Libraries
- 2.1 To Load the OpenSim Libraries in Matlab
3 Finding the Methods Available for a Class in the OpenSim Libraries
- 3.1 View all methods in an OpenSim class
- 3.2 View all method signatures in an OpenSim class
4 Utilities
5 Example Scripts
6 Reading in and Writing Data to File
7 Adding Geometry Paths to Matlab
8 Using a model's "Lists" through iterators
9 Using PropertyHelper to set Property values for plugin classes
10 Show OpenSim's log messages in the Matlab Command Window
11 Additional information
12 Troubleshooting

Setting up your Matlab Scripting Environment

These instructions assume that you've already installed OpenSim version 4.0 or later (see Installation Guide for more info). As noted above, OpenSim 4.0 requires 64-bit Matlab.

Launch MATLAB. If you're using Windows and you have OpenSim 3.x configured with Matlab, make sure to "Run as administrator" (available by right-clicking the MATLAB application in the start menu, etc.).
Change your Current Folder to the OpenSim Matlab Scripts directory. On Windows, by default, this is C:/Users/<username>/Documents/OpenSim/4.0/Code/Matlab.
Run the configureOpenSim.m file from the current folder. The script will prompt you to choose your OpenSim installation directory (we will refer to this as OPENSIM_INSTALL_DIR). On Windows, by default, this is C:/OpenSim 4.0.
When the script finishes, you should see a dialog box notifying you if the script succeeded. If the script did not succeed, read the output in the command window for more information.
Windows users: ensure that the OPENSIM_INSTALL_DIR/bin directory (e.g., C:/OpenSim 4.0/bin) appears in your system PATH environment variable, and that it appears before any other OpenSim installations you may have on your PATH. The steps to set your path are shown in the animated image below. Double click the image to zoom in. Or see here for additional help on setting your PATH environment variable.
Restart MATLAB; the OpenSim libraries will not be recognized until doing so.
Test that everything is configured correctly: In the command window, run the following:

Test that OpenSim is properly configured with MATLAB

>>> org.opensim.modeling.opensimCommon.GetVersion()	% This should print the version of OpenSim that you've configured with MATLAB

The configureOpenSim.m file will detect any installations of OpenSim that were previously configured with MATLAB, and will "remove" them from MATLAB (the other OpenSim installations are not deleted, they are simply no longer configured with MATLAB). The configureOpenSim.m file also backs up any changes it makes to MATLAB configuration files.

These manual setup are tailored for Windows and MATLAB 2012b and later, with side notes for macOS and MATLAB 2012a and earlier.

Find the location where you installed OpenSim (e.g., C:\OpenSim 4.0). We will refer to this directory as OPENSIM_INSTALL_DIR. Substitute your specific directory in the instructions below. In the images, we use C:\OpenSim 4.0.

Launch MATLAB

Tell MATLAB about OpenSim's Java library (.jar)

Tell Matlab about OpenSim's C++ libraries, which the Java library depends on

Add the OpenSim Utilities directory to MATLAB's PATH variable

Please report any issues you have with the configureOpenSim.m file so that other users need not perform these manual steps in the future.

Loading OpenSim Libraries

Once you have set up the OpenSim-Matlab environment you must import the OpenSim libraries to be able to have access to the OpenSim classes. Since imported libraries are not Global variables, you must import the libraries at the beginning of all scripts or functions that use OpenSim classes. This included nested functions or classes.

To Load the OpenSim Libraries in Matlab

>> import org.opensim.modeling.* % Import OpenSim Libraries

Finding the Methods Available for a Class in the OpenSim Libraries

Often, it is difficult to know exactly what methods are available for an OpenSim class (e.g., Model, Muscle) and so using the API Documentation regularly will be useful. However, you can very quickly get a list of the available methods and the interfaces to those methods by using the built-in Matlab functions methods and methodsview().

methods() will output a list of all the methods available for a given OpenSim class to the MATLAB command window. Below is an example of methods you can call on the Model class. A list of methods is printed to the command window (cut off here since the list is very long).

View all methods in an OpenSim class

>> methods(Model)
Methods for class Model:

LoadOpenSimLibrary                            getDefaultSubsystem                           notifyAll                                     
Model                                         getDescription                                overrideAllActuators                          
PrintPropertyInfo                             getDiscreteVariableValue                      postScale                                     
RegisterType                                  getDisplayHints                               preScale                                      
RenameType                                    getDocumentFileName                           print                                         
SafeCopy                                      getDocumentFileVersion                        printBasicInfo                                
addAnalysis                                   getFilePath                                   printComponentsMatching                       
addBody                                       getForceSet                                   printControlStorage                           
addComponent                                  getForceSubsystem                             printDetailedInfo                             
addConstraint                                 getForceUnits                                 printInputInfo                                
addContactGeometry                            getFrameList                                  printOutputInfo                               
addController                                 getFunctionClassNames                         printSocketInfo                               
addForce                                      getGravity                                    printSubcomponentInfo                         
addJoint                                      getGravityForce                               readObjectFromXMLNodeOrFile 
...											  ...											...

methodsview() is useful to get a list of the methods and the method signatures (arguments, return type) for an OpenSim class. When calling methodsview(), a Matlab pop-up window will be generated that shows the method names, the arguments you can input, and the return type.

View all method signatures in an OpenSim class

>> myModel = Model()
>> methodsview(myModel)

Tab-completion can be used to get quick access to a method name and is most useful when you know the method name (or the first few letters of the method name). In the GIF below, the tab key is pressed after "myModel." is typed to open the tab-completion window.

Utilities

OpenSim provides utility functions for some common tasks. If you have installed OpenSim, these scripts are located in the resources directory (e.g., C:/Users/<username>/Documents/OpenSim/4.0/Code/Matlab/Utilities).

File Name(s)	Description

File Name(s)	Description
osimC3D.m	Import data from a C3D file to OpenSim Tables. See the c3dExport.m example below for a use case.
osimTableFromStruct.m osimTableToStruct.m	Convert between an OpenSim Table and Matlab Struct. These utilities convert between OpenSim TimeSeriesTables (a new storage format from OpenSIm 4.0 for time series data, details below) and Matlab Structs. Be aware that any metadata in your Table will be lost when you convert to a Matlab Struct.
osimVec3FromArray.m osimVec3ToArray.m	Convert between an OpenSim Vec3 and a Matlab Array.
osimList2MatlabCell.m	Get a Matlab cell array populated with an OpenSim's Model's list (e.g., Body). See the section "Using a model's "Lists" through iterators" below for more details and usage.

Example Scripts

If you have installed OpenSim, these scripts are located in the resources directory (e.g., C:/Users/<username>/Documents/OpenSim/4.0/Code/Matlab).

File Name(s)	Description

File Name(s)	Description
c3dExport.m	Load a C3D file into OpenSim Tables and write out the marker and force data to corresponding .trc and .mot files.
OpenSimCreateTugOfWarModel.m TugOfWar_CompleteRunVisualize.m	Generate a simple tug of war model, run a simulation, and visualize the results.
prescribeMotionInModel.m	Create an OpenSim model with coordinates prescribed according to an input motion file. It uses a helper function defined in the script createPrescribedMotionModel.
setupAndRunAnalyzeBatchExample.m	Generate OpenSim Setup Files for the Analyze>MuscleAnalysis tool and runs the Analyze tool. You must run setupAndRunIKBatchExample first to generate the motion files used in this example.
setupAndRunIKBatchExample.m	Run multiple inverse kinematics trials for the model Subject01 located in the subfolder "testData/subject01". User must specify the results directory (e.g. "IKResults"), the .osim model (e.g. "subject01_gait2392_scaled.osim"), and the .trc files (e.g. in folder "MarkerData"). To see the results, load the model and IK output in the GUI.
simpleOptimizerExample.m simpleOptimizerObjectiveFunction.m	Run a simple optimization to find the elbow flexion angle where the moment arm of the biceps femoris short head is maximized.
strengthScaler.m	Functionthat loads a model and itsmuscles,then creates a new model where all muscles are scaled by a common scale factor. Takes 3 inputs: 1) the path and name of an existing OpenSim model, 2) the path and name of the new model to be outputted, and 3) the scale factor. If no input model names are given, the user is prompted to choose a model to scale and all muscle strengths are doubled.
wiringInputsAndOutputsWithTableReporter.m	Create a Reporter and wire the Inputs and Outputs necessary to report the system's center of mass.