Read a Specific Line From a File Matlab
Setting upwards your Matlab Scripting Environment
These instructions assume that you've already installed OpenSim version iv.0 or later (meet Installation Guide for more info). As noted to a higher place, OpenSim iv.0 requires 64-bit Matlab.
- Launch MATLAB. If you're using Windows and you lot have OpenSim 3.10 configured with Matlab, make sure to "Run as administrator" (available past correct-clicking the MATLAB application in the start card, etc.).
- Change your Current Folder to the OpenSim Matlab Scripts directory. On Windows, past default, this isC:/Users/<username>/Documents/OpenSim/iv.0/Code/Matlab.
- Run theconfigureOpenSim.m file from the electric current folder. The script volition prompt you to choose your OpenSim installation directory (we will refer to this as OPENSIM_INSTALL_DIR). On Windows, past default, this isC:/OpenSim four.0.
- When the script finishes, you should see a dialog box notifying yous if the script succeeded. If the script did not succeed, read the output in the control window for more information.
- Windows users: ensure that theOPENSIM_INSTALL_DIR/bin directory (eastward.g., C:/OpenSim 4.0/bin) appears in your system PATH surround variable, and that it appears before any other OpenSim installations y'all may take on your PATH. The steps to set your path are shown in the animated epitome 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 exist recognized until doing so.
- Test that everything is configured correctly: In the control window, run the following:
>>> 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 volition "remove" them from MATLAB (the other OpenSim installations arenot deleted, they are simply no longer configured with MATLAB). The configureOpenSim.g file too backs upwardly whatsoever 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 asOPENSIM_INSTALL_DIR. Substitute your specific directory in the instructions below. In the images, we use C:\OpenSim 4.0.
Launch MATLAB
- If you lot have MATLAB 2012b or later on, you can launch MATLAB regularly.
- If you have MATLAB 2012a or before, you lot must run MATLAB as an administrator: right-click MATLAB in your First menu, and select Run every bit ambassador.
Tell MATLAB virtually OpenSim's Java library (.jar)
- In the MATLAB Command Window, type edit(fullfile(prefdir, 'javaclasspath.txt')).
- For MATLAB 2012a or earlier, type edit classpath.txt instead.
- Add OPENSIM_INSTALL_DIR\sdk\Java\org-opensim-modeling.jar to the terminate of the file.
- On macOS, utilise forward slashes (/) instead of dorsum slashes (\).
- Remove any entries for previous versions of OpenSim (in either fullfile(prefdir, 'javaclasspath.txt')or classpath.txt, even if you have MATLAB 2012b or later).
Tell Matlab about OpenSim'southward C++ libraries, which the Java library depends on
- In the MATLAB Command Window, type edit(fullfile(prefdir, 'javalibrarypath.txt')).
- For MATLAB 2012a or earlier, type edit librarypath.txt instead.
- Add OPENSIM_INSTALL_DIR\bin\ to the cease of the file.
- On macOS, apply forward slashes (/) instead of back slashes (\).
- Remove any entries for previous versions of OpenSim (in either fullfile(prefdir, 'javalibrarypath.txt')or librarypath.txt, even if you have MATLAB 2012b or later).
Add the OpenSim Utilities directory to MATLAB's PATH variable
- In the MATLAB Control Window, type pathtool (or editpath in older versions of MATLAB).
- Click Add Folder... and select C:\Users\<username>\Documents\OpenSim\4.0\Code\Matlab\Utilities folder (by default).
- Remove any entries for previous versions of OpenSim.
- On macOS, yous will run across forward slashes (/) instead of back slashes (\).
Please report any issues you have with the configureOpenSim.m file so that other users need not perform these manual steps in the futurity.
Loading OpenSim Libraries
Once yous have set upward the OpenSim-Matlab environs you lot must import the OpenSim libraries to be able to have access to the OpenSim classes. Since imported libraries are not Global variables, you lot must import the libraries at the offset of all scripts or functions that apply OpenSim classes. This included nested functions or classes.
>> import org.opensim.modeling.* % Import OpenSim Libraries
Finding the Methods Available for a Class in the OpenSim Libraries
Ofttimes, it is difficult to know exactly what methods are available for an OpenSim class (e.k., Model, Musculus) so using the API Documentation regularly will be useful. Nonetheless, you tin can very rapidly get a list of the bachelor methods and the interfaces to those methods past using the built-in Matlab functions methods and methodsview().
methods() will output a list of all the methods available for a given OpenSim grade to the MATLAB control window. Below is an instance of methods you can call on the Model class. A list of methods is printed to the control window (cut off hither since the list is very long).
>> methods(Model) Methods for class Model: LoadOpenSimLibrary getDefaultSubsystem notifyAll Model getDescription overrideAllActuators PrintPropertyInfo getDiscreteVariableValue postScale RegisterType getDisplayHints preScale RenameType getDocumentFileName impress 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.
>> 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 proper 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 yous 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(due south) | Description |
|---|---|
| osimC3D.m | Import data from a C3D file to OpenSim Tables. Encounter the c3dExport.m example below for a utilize case. |
| osimTableFromStruct.thousand | Catechumen between an OpenSim Table and Matlab Struct. These utilities convert between OpenSim TimeSeriesTables (a new storage format from OpenSIm 4.0 for fourth dimension serial information, details below) and Matlab Structs. Exist aware that any metadata in your Tabular array will be lost when yous catechumen to a Matlab Struct. |
| osimVec3FromArray.g osimVec3ToArray.m | Convert betwixt an OpenSim Vec3 and a Matlab Array. |
| osimList2MatlabCell.m | Get a Matlab jail cell array populated with an OpenSim's Model'southward list (e.grand., Body). Run into the section "Using a model'due south "Lists" through iterators" below for more details and usage. |
Case Scripts
If you accept installed OpenSim, these scripts are located in the resources directory (e.chiliad., C:/Users/<username>/Documents/OpenSim/4.0/Lawmaking/Matlab).
| File Proper name(s) | Description |
|---|---|
| c3dExport.m | Load a C3D file into OpenSim Tables and write out the marker and strength data to respective .trc and .mot files. |
| OpenSimCreateTugOfWarModel.m TugOfWar_CompleteRunVisualize.g | Generate a uncomplicated tug of war model, run a simulation, and visualize the results. |
| prescribeMotionInModel.m | Create an OpenSim model with coordinates prescribed co-ordinate to an input motion file. Information technology 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. Y'all must run setupAndRunIKBatchExample starting time to generate the motion files used in this case. |
| setupAndRunIKBatchExample.m | Run multiple inverse kinematics trials for the model Subject01 located in the subfolder "testData/subject01". User must specify the results directory (east.thou. "IKResults"), the .osim model (east.g. "subject01_gait2392_scaled.osim"), and the .trc files (east.chiliad. in folder "MarkerData"). To run into the results, load the model and IK output in the GUI. |
| simpleOptimizerExample.one thousand | Run a unproblematic optimization to find the elbow flexion angle where the moment arm of the biceps femoris short head is maximized. |
| strengthScaler.1000 | Functionthat loads a model and itsmuscles,then creates a new model where all muscles are scaled past a common scale cistron. Takes 3 inputs: ane) the path and proper name of an existing OpenSim model, 2) the path and name of the new model to exist outputted, and three) the calibration 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 organization's heart of mass. |
Reading in and Writing Information to File
Reading from and writing to files has been improved with the introduction of tables and file adapters (available as of OpenSim 4.0). The code blocks below demonstrate how to read and write vector and scalar (double) data from and to a file.
| Reading Data from file | Writing Data to File |
|---|---|
| Vec3 (Vector) Data % Define the path to the file filepath = 'subject01_walk1.trc'; % Utilize the Vec3 TimeSeriesTable to read the Vec3 type data file. opensimTable = TimeSeriesTableVec3(filepath); % Apply the OpenSim Utility part, osimTable2Struct to % convert the OpenSim tabular array into a Matlab Struct for ease of employ. matlabStruct_markerData = osimTableToStruct(opensimTable); | % Ascertain output file name/path filepath = 'myMarkerTrial_01.trc'; % Write the TimeSeriesTableVec3 to file TRCFileAdapter().write(opensimTable,filepath) |
| Double (Scalar) Information % Define the path to the file filepath = 'subject01_walk1_grf.mot'; % Use the standard TimeSeriesTable to read the information file. opensimTable = TimeSeriesTable(filepath); % Use the OpenSim Utility office, osimTable2Struct to % convert the OpenSim table into a Matlab Struct for ease of apply. matlabStruct_grfData = osimTableToStruct(opensimTable); | % Define output file name/path filepath = 'myMarkerTrial_01_grf.mot'; % Write the TimeSeriesTable to file STOFileAdapter().write(opensimTable,filepath) |
Adding Geometry Paths to Matlab
OpenSim verifies that Model's Geometry mesh files exists when you load a model and whenever you lot subsequently operate on it. If you lot have a Geometry file divers in your model, and the Geometry path is non set, you will become a warning for each piece of Geometry that can't exist establish, as shown in the image beneath.
These warning tin get cumbersome, especially if you are doing batch processing or iterative analysis. To stop the warnings, yous have to set the Geometry folder path of OpenSim:ModelVisualizer() in Matlab. Copy and paste the below code and update the path to your local OpenSim Geometry directory.
>>> path='/Users/username/Applications/OpenSim 4.0/OpenSim 4.0.app/Contents/Resources/OpenSim/Geometry'; >>> ModelVisualizer.addDirToGeometrySearchPaths(path);
Alternatively, a 'workaround' that if you are non visualizing the model is to remove the geometry from the model. This should simply be used if you are doing many model instantiations or initSystem() calls and don't need to visualize the model.
Using a model's "Lists" through iterators
Lists, such equally BodyList and MuscleList, are useful ways to go access to all components of that blazon in the model. Admission is available through an iterator. Iterators are a different way of getting references to objects in the model and Matlab users may be unfamiliar with them. For a discussion of iterators, encounter this StackOverflow word.
Iterate over all bodies in a model (fifty-fifty bodies not in the model'southward BodySet)
model = Model("my_model.osim") bodyList = model.getBodyList(); # Get the Model's BodyList iter = bodyList.begin(); # Start the iterator at the outset of the list while ~iter.equals(bodyList.end()) # Stay in the loop until the iterator reaches the cease of the list iter.getName() # Print name to console iter.next() # Move the iterator to the next body in the list end Getting a unmarried reference from a list
We have included a Matlab part— osimList2MatlabCell() — that converts an OpenSim List to a Matlab cell array. Then, you tin can use simple Matlab methods to go references to objects.
model = Model("my_model.osim") references = osimList2MatlabCell(model,'Torso') % Get a cell array of references to all the bodies in a model Pelvis = references{i} % Get the first body in the list. Using PropertyHelper to set Property values for plugin classes
Classes defined in plugins are not bachelor for direct access in Matlab, nonetheless classes that are subclasses of OpenSim "Object" contain backdrop that can be accessed and modified using the PropertyHelper class. The exact syntax depends on the basic data type of the property, for case
prop = obj.getPropertyByName("propertyName") currentValue = PropertyHelper.getValueDouble(prop) PropertyHelper.setValueDouble(newValue, prop) Prove OpenSim'southward log messages in the Matlab Control Window
Applies to OpenSim 4.ii and above.
Some versions of Matlab practice not show OpenSim'southward log messages by default. To see these messages in the Matlab Command Window, run the following command:
myMatlabLog = JavaLogSink() Logger.addSink(myMatlabLog)
Boosted data
Troubleshooting
- OpenSim 4.0 requires 64-bit Matlab.
- When referring to indexed elements remember that Matlab begins indexing at 1 while OpenSim data structures begin at 0.
- Errors related to osimJavaJNI not existence on the path or "coffee.lang.NoClassDefFoundError" occur considering the OPENSIM_INSTALL_DIR/bin directory is non on the system (Windows) path. Be sure the OPENSIM_INSTALL_DIR/bin directory has been added to the system PATH environment variable. (Note that the system PATH surround variable is singled-out from MATLAB'south path variable.)
- If y'all're seeing errors maxim failed dependencies with osimJavaJNI.dll, you would need to accept Visual Studio redistribution bundle installed (which would come up with any Visual Studio installation). You can just install the bundle files without Visual Studio on the Microsoft download site (For example 32-flake VS 2010 package is located hither).
Source: https://simtk-confluence.stanford.edu:8443/display/OpenSim/Scripting+with+Matlab
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