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Packages and libraries are collections of classes and methods (see Introduction to the OpenSim API for background) that have a well-defined interface and can be imported into your programming environment to utilize. These can be packages to browse files, read and write files, do mathematics operations, and run  run simulations. The commands below are common packages or libraries you will find useful.

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ActionGUI CommandMatlab/Python Command
Loads the specified model in the GUIloadModel(modelFileName) 
Creates a handle to the current model in the GUImyModel = getCurrentModel() 
Load a model from file (Create Model Object)myModel = modeling.Model(modelFileName)myModel = Model('gait2354.osim')
Creates a copy of myModel.myModelCopy = modeling.Model(myModel)myModelCopy = Model(myModel)
Initialize the model and get the default statemyState = myModel.initSystem()myState = myModel.initSystem()

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ActionClass InformationGetting a Handle to a SetReference an Object by indexGet object from a nameAlternative 'long path'
Body Set
New window link
BodyOpenSim::BodySet
Linkhttps://simtk.org/api_docs/opensim/api_docs/classOpenSim_1_1BodySet.html
bodySet= myModel.getBodySet()rightFemur = bodySet().get(1)rightFemur = bodySet().get("femur_r")rightFemur =myModel.getBodySet().get("femur_r")
Joint Set
New window link
BodyOpenSim::JointSet
Linkhttps://simtk.org/api_docs/opensim/api_docs/classOpenSim_1_1JointSet.html
jointSet = myModel.getJointSet()rightHip = jointSet ().get(7)rightHip = jointSet().get("hip_r")rightHip = myModel.getJointSet().get("hip_r")
Coordinate Set
New window link
BodyOpenSim::CoordinateSet
Linkhttps://simtk.org/api_docs/opensim/api_docs/classOpenSim_1_1CoordinateSet.html
cordSet= myModel.getCoordinateSet()hip_coord = cordSet().get(4)hip_coord = cordSet().get("hip_flexion_r")hip_coord = cordSet().get("hip_flexion_r")
Muscle Set
New window link
BodyMuscles
Linkhttps://simtk.org/api_docs/opensim/api_docs/classOpenSim_1_1Muscle.html
muscleSet= myModel.getMuscles()recFemR = muscleSet().get(3)rec_fem_r = recFemRt().get("'recFem_r")rec_fem_r= myModel.getMuscles().get("'recFem_r")
Path Point of a Muscle
New window link
BodyOpenSim; PathPoint
Linkhttps://simtk.org/api_docs/opensim/api_docs/classOpenSim_1_1PathPoint.html
pathPoints = myModel.getMuscles().get("'recFem_r").getGeometryPath().getPathPointSet()recFemPathPoint1 = pathPoints.get(0)recFemPathPoint1 = pathPoints.get("rect_fem_r-P1")recFemPathPoint1 = myModel.getMuscles().get("'recFem_r").getGeometryPath().getPathPointSet()

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Code Block
languagepython
titleChange the ECRB muscle properties in the GUI
>>> ECRB = myModel.getMuscles().get("ECRB")               # Get a handle to the ECRB
>>> backupTendonSlackLength = ECRB.getTendonSlackLength() # Back up the original tendon slack length (just in case)
>>> ECRB.setTendonSlackLength(0.2105)                     # Prescribe a new Tendon slack length
>>> myModel.initSystem()                                  # Re-initialize the model

 


You may need to downcast an object from an abstract class (e.g., Muscle)  to a derived class (e.g., Thelen2003Muscle) in order to gain access to its properties and methods. Here is an example:

Code Block
languagenone
>> import org.opensim.modeling.*
>> myModel = Model('arm26.osim');
>> mcl_TRIlong = Thelen2003Muscle.safeDownCast( myModel.getMuscles().get('TRIlong') );
>> mcl_TRIlong.setFmaxTendonStrain( 0.5*mcl_TRIlong.getFmaxTendonStrain() );

Outputs

OpenSim 4.0 uses component outputs and reporters to collect variables of interest and print them to file. To display the output names for a component, use the method getOutputNames();

Code Block
>>> muscle.getOutputNames();

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Tools contain a number of grouped Methods that allow you to run a study. For example, to scale a Model to match experimental data the ScaleTool groups GenericModelMaker(), ModelScaler() and MarkerPlacer() together. The AnalyzeTool() can group StaticOptimization() and MuscleAnalysis() together to output muscle states of a Static Optimization.  

 

Command or ClassPlatformAction
getScriptsDir()GUIReturns the path of your scripts directory
java.io.FileGUIA representation of file and directory pathnames that allows you to easily create files and directories, get all the files in a given directory, and more. Read more here: http://docs.oracle.com/javase/1.4.2/docs/api/java/io/File.html
getInstallDir()GUIReturns the path of your OpenSim Install directory
getResourcesDir()GUIReturns the path of your resources directory containg models and code examples (e.g., 'C/Users/<username>/Documents/OpenSim/4.0').
os.chdir(NewWorkingDirectoryName)GUI, PythonChanges the working directory of the scripting shell (default is your OpenSim installation directory) to the directory specified by NewWorkingDirectoryName. You  need to import the python os package before using it (i.e. import os).
execfile("ScriptFileName")GUI, PythonExecutes a script. Can be used in shell or as part of script. File name can be absolute path to file or relative to the current directory.

 

Working with Vectors, Matrices, and Other SimTK Classes

We've exposed the most commonly used SimTK classes. In particular:

CommandPlatformDescription

modeling.Vec3()

modeling.Vec3(double e)

modeling.Vec3(double e0, double e1, double e2)

AllCreates a Simtk Vec3 object (a vector of length 3). If passed only one argument (double e) all elements will be set to e.
modeling.Vector(int length, double e)AllCreates a Simtk Vector with specified length. All elements are set to e.

modeling.Mat33(double e)

modeling.Mat33(double e0, ... , double e8)

AllCreates a Simtk Mat33 object (a 3x3 matrix). If passed only one argument (double e), the diagonal elements will be set to e and other elements set to zero.

modeling.Inertia()

See doxygen link at right for additional constructors

AllCreates a Simtk Inertia object. All constructors are available except symmetric matrix constructors.
modeling.State()AllCreates a Simtk State object. See the doxygen link for more information.

modeling.Stage()

modeling.Stage(int level)

All

Creates a Simtk Stage object, optionally realized to level l. See the doxygen link for more information.

Helpful tips:

  • For Simbody doxygen links above Vec3P corresponds to a modeling.Vec3 object and RealP corresponds to a double value.
  • To see the available methods for these objects, use methodsview() or tab completion (Matlab only).
  • You can find more information in the SimTK Basics section of the User's Guide. Note that only the SimTK classes listed above are available through scripting.
  • You can also find more information in the section below on Handling C++ Templates.

ArrayDouble

In many cases the function you're trying to call takes an argument type different from the object you have already. This is true even moving data between Matlab and Java objects, and between objects in the SimTK namespace and those in the OpenSim namespace. In particular, many OpenSim methods return an ArrayDouble (Array<double) and you would prefer to convert the array to a different type. The following set of convenience methods are "Adaptors" intended to help you pass data around between OpenSim objects and low level SimTK objects.

For Matlab, leave off "modeling". For Python, change "modeling" to "opensim".

CommandPlatformDescription
modeling.ArrayDouble.createVec3([0.0,0.05,0.35])AllCreates a SimTK::Vec3

modeling.ArrayDouble.getAsVec3()

Allreturns SimTK::Vec3 populated from ArrayDouble of size 3.
modeling.ArrayDouble.getAsVector()Allreturn SimTK::Vector populated from ArrayDouble
modeling.ArrayDouble.populateFromVector(SimTK::Vector aVector)Allpopulate an ArrayDouble from the passed in SimTK Vector
modeling.ArrayDouble.getValuesFromVec3(SimTK::Vec3 vec3) Allreturns an ArrayDouble populated from the passed in SimTK Vec3
Info

When referring to indexed elements remember that Matlab begins indexing at 1 while OpenSim data structures begin at 0.

Advanced Multibody Calculations with Simbody

In 4.0, you can perform advanced multibody calculations in scripting via the SimbodyMatterSubsystem inside the OpenSim Model (model.getMatterSubsystem()). The SimbodyMatterSubsystem class allows you to compute the mass matrix, Jacobians, inverse dynamics moments, etc.

Code Block
titleUse the Simbody Inverse Dynamics Operator in Matlab
model = Model('arm26.osim');
s = model.initSystem();
% For the given inputs, we will use the inverse dynamics operator
% (calcResidualForce()) to compute the first column
% of the mass matrix. We accomplish this by setting all inputs to 0
% except for the acceleration of the first coordinate.
%   f_residual = M udot + f_inertial + f_applied 
%              = M ~[1, 0, ...] + 0 + 0
model.realizeVelocity(s);
appliedMobilityForces = Vector();
appliedBodyForces = VectorOfSpatialVec();
knownUdot = Vector(s.getNU(), 0.0);
knownUdot.set(0, 1.0);
knownLambda = Vector();
residualMobilityForces = Vector();
smss = model.getMatterSubsystem();
smss.calcResidualForce(s, appliedMobilityForces, appliedBodyForces, ...
                       knownUdot, knownLambda, residualMobilityForces);

Class Templates (Vec3(), Array<double>, Vector() )

A summary of Templatized Class use in scripting can be found on the Scripting Versions of OpenSim C++ API Calls page. 

Templates are advanced C++ constructs that are used extensively throughout the OpenSim API and Simbody API. If you see notation like Array<double> in the doxygen or C++ code that you are trying to replicate, this means you're working with a templatized class and, to use that class in scripting, will need to find its appropriate mapping in the scripting environment. For more information, and a easy to use ummary of the C++ to scripting mappings, see the Scripting Versions of OpenSim C++ API Calls page. 

Obtaining Position and Velocity Information

For more information regarding multibody system states, refer to the SimTK Simulation Concepts documentation in the Developer's Guide.

In order to obtain simulation position or velocity state information you must have a State object in hand. 

Code Block
languagepython
titleUsing State Objects
>>> state = myModel.initSystem();
>>> myModel.equilibrateMuscles(state);

Now you can use methods on Body objects (actually, from the Frame class) to obtain the location or velocity of a point in the ground frame.

Code Block
languagepy
>>> body = myModel.getBodySet().get('r_ulna_radius_hand')
>>> massCenter = body.getMassCenter(massCenter)
>>> body.getStationVelocityInGround(state, massCenter)
>>> dir(body) # List other methods available on Body.

Using the Simbody Visualizer

You can use the visualizer from Simbody in Matlab and Python. To do so call the "setUseVisualizer" method and pass in the parameter "true", and when you run the simulation the Simbody Visualizer GUI will pop up. The example of usage is described in "TugOfWar_CompleteRunVisualizer.m"

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Parent and Concrete Classes

If you are calling a method or function (e.g., getting or setting properties) that you are pretty sure should work, but you are getting an error that the method doesn't exist, this may mean that you need to downcast. In the C++ programming language, programmers use a concept called "inheritance" to build up complexity without re-writing the same code multiple times. For example, in OpenSim Thelen2003Muscle and MillardMuscle both rely on code in the common parent Muscle class that they "inherit" from.

If you have a handle to a base class object (e.g. Muscle)  you may need to downcast the object to one of its derived (or concrete) classes, like the Thelen2003Muscle, in order to gain access to properties and methods specific to the concrete class. In the below example, we get a reference to a muscle in the model and return the class name and concrete class name;

Code Block
>>> model = Model(path2model)
>>> muscle = model.getMuscles().get(0);
>>> muscle.getClassName()
muscle
>>> muscle.getConcreteClassName()
Thelen2003Muscle


Then to get a reference to the concrete class you use the safeDownCast() method. 

Code Block
>>> muscle = model.getMuscles().get(0);    # The object you get here is of base class Muscle
>>> thelenMuscle = Thelen2003Muscle.safeDownCast(muscle)  # To use a method specific to Thelen2003Muscle you need to safeDownCast
>>> timeConstant = thelenMuscle.getActivationTimeConstant() # Get property that is present is specific to Thelen2003Muscle 


Outputs

OpenSim 4.0 uses component outputs and reporters to collect variables of interest and print them to file. To display the output names for a component, use the method getOutputNames();

Code Block
>>> muscle.getOutputNames();

Reading Data from TRC Files into TimeSeriesTable

To read marker trajectories from a trc file into a TimeSeriesTableVec3, construct a table by passing the filename into the TimeSeriesTableVec3 constructor. Afterwards, you can query the TimeSeriesTable for the data as shown in the code snippet below.

Code Block
>>> markerData  = TimeSeriesTableVec3('markerdata.trc');
>>> numDataRows = markerData.getNumRows();
>>> numMarkersInTable = markerData.getNumColumns();


Using the Tools

Tools contain a number of grouped Methods that allow you to run a study. For example, to scale a Model to match experimental data the ScaleTool groups GenericModelMaker(), ModelScaler() and MarkerPlacer() together. The AnalyzeTool() can group StaticOptimization() and MuscleAnalysis() together to output muscle states of a Static Optimization. Tools can be initialized from a setup file (.xml) that has stored settings. They also have methods that methods can be called to change the input models, data files, and some settings. Use the API documentation or methodsview() in Matlab (described above) to explore the methods that are available for the Tool you are using. 

Command or ClassPlatformAction
scale = ScaleTool('Scale_Setup_file.xml')MatlabReturns a Scaletool object with properties defined in the Scale_Setup_File.xml 

ik = InverseKinematicsTool()

ik.run()

Matlab

Returns an InverseKinematicsTool object with default properties. You must set the properties of the tool. 

Begin the Inverse Kinematics simulation by calling the run() method.

rra = RRATool'RRA_Setup.xml')

rra.setAdjustCOMToReduceResiduals(1)

rra.run()

Matlab

Returns an RRATool object with properties defined in the RRA.

Allow RRA to alter the trunk COM by using the setAdjustCOMToReduceResiduals() method.

Begin the RRA simulation by calling the run() method.

so = AnalyzeTool('SO_Setup.xml')MatlabReturns an AnalzeTool that has a Static Optimization analysis included. 


Working with Vectors, Matrices, and Other SimTK Classes

We've exposed the most commonly used SimTK classes. In particular:

CommandPlatformDescription

modeling.Vec3()

modeling.Vec3(double e)

modeling.Vec3(double e0, double e1, double e2)

AllCreates a Simtk Vec3 object (a vector of length 3). If passed only one argument (double e) all elements will be set to e.
modeling.Vector(int length, double e)AllCreates a Simtk Vector with specified length. All elements are set to e.

modeling.Mat33(double e)

modeling.Mat33(double e0, ... , double e8)

AllCreates a Simtk Mat33 object (a 3x3 matrix). If passed only one argument (double e), the diagonal elements will be set to e and other elements set to zero.

modeling.Inertia()

See doxygen link at right for additional constructors

AllCreates a Simtk Inertia object. All constructors are available except symmetric matrix constructors.
modeling.State()AllCreates a Simtk State object. See the doxygen link for more information.

modeling.Stage()

modeling.Stage(int level)

All

Creates a Simtk Stage object, optionally realized to level l. See the doxygen link for more information.

Helpful tips:

  • For Simbody doxygen links above Vec3P corresponds to a modeling.Vec3 object and RealP corresponds to a double value.
  • To see the available methods for these objects, use methodsview() or tab completion (Matlab only).
  • You can find more information in the SimTK Basics section of the User's Guide. Note that only the SimTK classes listed above are available through scripting.
  • You can also find more information in the section below on Handling C++ Templates.

ArrayDouble

In many cases the function you're trying to call takes an argument type different from the object you have already. This is true even moving data between Matlab and Java objects, and between objects in the SimTK namespace and those in the OpenSim namespace. In particular, many OpenSim methods return an ArrayDouble (Array<double) and you would prefer to convert the array to a different type. The following set of convenience methods are "Adaptors" intended to help you pass data around between OpenSim objects and low level SimTK objects.

For Matlab, leave off "modeling". For Python, change "modeling" to "opensim".

CommandPlatformDescription
modeling.ArrayDouble.createVec3([0.0,0.05,0.35])AllCreates a SimTK::Vec3

modeling.ArrayDouble.getAsVec3()

Allreturns SimTK::Vec3 populated from ArrayDouble of size 3.
modeling.ArrayDouble.getAsVector()Allreturn SimTK::Vector populated from ArrayDouble
modeling.ArrayDouble.populateFromVector(SimTK::Vector aVector)Allpopulate an ArrayDouble from the passed in SimTK Vector
modeling.ArrayDouble.getValuesFromVec3(SimTK::Vec3 vec3) Allreturns an ArrayDouble populated from the passed in SimTK Vec3


Info

When referring to indexed elements remember that Matlab begins indexing at 1 while OpenSim data structures begin at 0.

Advanced Multibody Calculations with Simbody

In 4.0, you can perform advanced multibody calculations in scripting via the SimbodyMatterSubsystem inside the OpenSim Model (model.getMatterSubsystem()). The SimbodyMatterSubsystem class allows you to compute the mass matrix, Jacobians, inverse dynamics moments, etc.

Code Block
titleUse the Simbody Inverse Dynamics Operator in Matlab
model = Model('arm26.osim');
s = model.initSystem();
% For the given inputs, we will use the inverse dynamics operator
% (calcResidualForce()) to compute the first column
% of the mass matrix. We accomplish this by setting all inputs to 0
% except for the acceleration of the first coordinate.
%   f_residual = M udot + f_inertial + f_applied 
%              = M ~[1, 0, ...] + 0 + 0
model.realizeVelocity(s);
appliedMobilityForces = Vector();
appliedBodyForces = VectorOfSpatialVec();
knownUdot = Vector(s.getNU(), 0.0);
knownUdot.set(0, 1.0);
knownLambda = Vector();
residualMobilityForces = Vector();
smss = model.getMatterSubsystem();
smss.calcResidualForce(s, appliedMobilityForces, appliedBodyForces, ...
                       knownUdot, knownLambda, residualMobilityForces);

Class Templates (Vec3(), Array<double>, Vector() )

A summary of Templatized Class use in scripting can be found on the Scripting Versions of OpenSim C++ API Calls page. 

Templates are advanced C++ constructs that are used extensively throughout the OpenSim API and Simbody API. If you see notation like Array<double> in the doxygen or C++ code that you are trying to replicate, this means you're working with a templatized class and, to use that class in scripting, will need to find its appropriate mapping in the scripting environment. For more information, and a easy to use ummary of the C++ to scripting mappings, see the Scripting Versions of OpenSim C++ API Calls page. 

Obtaining Position and Velocity Information

For more information regarding multibody system states, refer to the SimTK Simulation Concepts documentation in the Developer's Guide.

In order to obtain simulation position or velocity state information you must have a State object in hand. 

Code Block
languagepython
titleUsing State Objects
>>> state = myModel.initSystem();
>>> myModel.equilibrateMuscles(state);

Now you can use methods on Body objects (actually, from the Frame class) to obtain the location or velocity of a point in the ground frame.

Code Block
languagepy
>>> body = myModel.getBodySet().get('r_ulna_radius_hand')
>>> massCenter = body.getMassCenter(massCenter)
>>> body.getStationVelocityInGround(state, massCenter)
>>> dir(body) # List other methods available on Body.

Using the Simbody Visualizer

You can use the visualizer from Simbody in Matlab and Python. To do so call the "setUseVisualizer" method and pass in the parameter "true", and when you run the simulation the Simbody Visualizer GUI will pop up. The example of usage is described in "TugOfWar_CompleteRunVisualizer.m"

Code Block
osimModel = Model('tug_of_war_muscles_controller.osim');
osimModel.setUseVisualizer(true);

Set verbosity or logging level

Info

Applies to OpenSim 4.2 (unreleased) and above.

You can control how much detail is printed to the console using the following:

Code Block
Logger.setLevel("Off");
Logger.setLevel("Critical");
Logger.setLevel("Error");
Logger.setLevel("Warn");
Logger.setLevel("Info"); % default
Logger.setLevel("Debug");
Logger.setLevel("Trace");

When performing batch processing or optimization you can turn off logging completely by calling Logger.setLevel("Off").

You can always add a new file during runtime to start logging into (in addition to whatever the current logging behavior is). This can be done by calling

Code Block
languagecpp
Logger.addFileSink('logs_folder/full_path.log');

Make sure you have permission to write to the logs_folder.

Batch Processing

There are several examples in the Matlab scripts and GUI scripts that show how to perform batch processing by calling the OpenSim API (e.g. Analyze, IK). We encourage you to use this approach rather than using Matlab's xml parsing tools. To read more about why this is the case, please see the scripting FAQ:

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