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This document lists the changes to opensim-core that are introduced with each new version, starting with version 4.0. When possible, we provide the GitHub issues or pull requests that are related to the items below. If there is no issue or pull request related to the change, then we may provide the commit.

This is not a comprehensive list of changes but rather a hand-curated collection of the more notable ones. For a comprehensive history, see the OpenSim Core GitHub repo.

v4.6

  • The performance of getStateVariableValue, getStateVariableDerivativeValue, and getModelingOption was improved in the case where provided string is just the name of the value, rather than a path to it (#3782)
  • Fixed bugs in MocoStepTimeAsymmetryGoal::printDescriptionImpl() where there were missing or incorrect values printed. (#3842)
  • Added ModOpPrescribeCoordinateValues which can prescribe motion of joints in a model given a table of data. (#3862)
  • Fixed bugs in convertToMocoTrajectory() and MocoTrajectory::resampleWithFrequency() by updating interpolate() to allow extrapolation using the extrapolate flag. Combined with the ignoreNaNs flag, this prevents NaNs from occurring in the output. (#3867)
  • Added Outputs to ExpressionBasedCoordinateForce, ExpressionBasedPointToPointForce, and ExpressionBasedBushingForce for accessing force values. (#3872)
  • PointForceDirection no longer has a virtual destructor, is final, and its scale functionality has been marked as [[deprecated]] (#3890)
  • Added ExpressionBasedFunction for creating Functions based on user-defined mathematical expressions. (#3892)
  • Added ForceProducer, ForceConsumer, and ForceApplier, which are fundamental APIs for force-producing components. The ForceProducer API was also rolled out to a variety of existing Force components, which means that API users can now now ask many Force components what forces they produce (see #3891 for a comprehensive overview).
  • Made improvements to MocoUtilities::createExternalLoadsTableForGait(): center of pressure values are now set to zero, rather than NaN, when vertical force is zero, and the vertical torque is returned in the torque columns (rather than the sum of the sphere torques) to be consistent with the center of pressure GRF representation.
  • Fixed an issue where a copy of an OpenSim::Model containing a OpenSim::ExternalLoads could not be finalized (#3926)
  • Updated all code examples to use c++14 (#3929)
  • Added class OpenSim::StateDocument as a systematic means of serializing and deserializing a complete trajectory (i.e., time history) of all states in the SimTK::State to and from a single .ostates file. Prior to StatesDocument, only the trajectories of continuous states (e.g., joint angles, joint speeds, muscle forces, and the like) could be systematically written to file, either in the form of a Storage file or as a TimeSeriesTable file, leaving discrete states (e.g., muscle excitations and contact model anchor points) and modeling options (e.g., joint clamps) unserialized. StatesDocument, on the other hand, serializes all continuous states, discrete states, and modeling options registered with OpenSim::Component. Whereas neither Storage files nor TimeSeriesTable files are currently able to handle mixed variable types, StatesDocument is able to accommodate variables of type bool, int, double, Vec2, Vec3, Vec4, Vec5, and Vec6 all in the same .ostates file. .ostate files are written in XML format and internally carry the name of the OpenSim model to which the states belong, a date/time stamp of when the file was written, and a user-specified note. .ostate files also support a configurable output precision. At the highest ouput precsion (~20 significant figures), serialization/deserialization is a lossless process. (#3902)
  • Improved OpenSim::IO::stod string-to-decimal parsing function by making it not-locale-dependant (#3943, #3924; thanks @alexbeattie42)
  • Improved the performance of ComponentPath traversal (e.g. as used by Component::getComponent, Component::getStateVariableValue)
  • Added Python and Java (Matlab) scripting support for TimeSeriesTable_<SimTK::Rotation>. (#3940)
  • Added the templatized MocoStudy::analyze<T>() and equivalent scripting counterparts: analyzeVec3, analyzeSpatialVec, analyzeRotation. (#3940)
  • Added ConstantCurvatureJoint to the SWIG bindings; it is now available in Matlab and Python (#3957).
  • Added methods and Outputs for calculating the angular momentum of a Body. (#3962)
  • Updated TabOpLowPassFilter so that by default the processed table is trimmed to the original time range after padding and filtering. The original behavior (no trimming) can be enabled via the new property trim_to_original_time_range. (#3969)

v4.5.1

  • Added support for list Sockets via the macro OpenSim_DECLARE_LIST_SOCKET. The macro-generated method appendSocketConnectee_* can be used to connect Objects to a list Socket. In addition, Component and Socket have new getConnectee overloads that take an index to a desired object in the list Socket (#3652).
  • Added ComponentPath::root(), which returns a ComponentPath equivalent to "/"
  • Added ComponentPath::separator(), which returns the separator that's placed between elements of the path (i.e. '/')
  • ComponentPath is now less-than (<) comparable, making it usable in (e.g.) std::map
  • ComponentPath now has a std::hash<T> implementation, making it usable in (e.g.) std::unordered_map
  • Added .clear() and .empty() to ComponentPath for more parity with std::string's semantics
  • Added tryGetSocket and tryUpdSocket to the Component interface, which provides a non-throwing way of querying a component's sockets by name (#3673)
  • Added tryGetOutput and tryUpdOutput to the Component interface, which provides a non-throwing way of querying a component's outputs by name (#3673)
  • The XMLDocument that is held within OpenSim::Object is now reference-counted, to help ensure it is freed (e.g. when an exception is thrown)
  • Calling getConnectee no longer strongly requires that finalizeConnection has been called on the socket. The implementation will now fall back to the (slower) method of following the socket's connectee path property. This is useful if (e.g.) following sockets during a call to Component::finalizeConnections
  • Controller now manages the list of controlled actuators using a list Socket instead of a Set<Actuators> (#3683). The actuator_list property has been removed from Controller in lieu of the list Socket, which appears as socket_actuators in the XML. This change also necessitated the addition of an added initSystem() call in AbstractTool::updateModelForces() so that connected actuators have the same root component as the Model at the time of Socket connection. Finally, PrescribedController::prescribeControlForActuator(int, Function*) is now deprecated in favor of PrescribedController::prescribeControlForActuator(const std::string&, Function*).
  • Bumped the version of ezc3d to 1.5.8, which can now deal properly with Type-3 force platforms and c3d from Shadow
  • Added StationDefinedFrame component, which is a Frame component that automatically computes its position and orientation from Stations in the model
  • Models with PrescribedControllers are now supported by Moco (#3701). Controls for actuators controlled by PrescribedControllers are now excluded from the optimization problem.
  • Fixed documentation error in Umberger2010MuscleMetabolicsProbe where muscle mass was incorrectly omitted for the activation maintenance rate.
  • Methods are now available in OpenSim::Component for generating a list of all ModelingOptions and DiscreteVariables in an OpenSim::Model or other Component. (#3745)
  • OpenSim::Component accessor methods for ModelingOptions and DiscreteVariabless now accept both absolute and relative component paths. (#3745)
  • DiscreteVariables in OpenSim can now be a range of numerical types, including bool, int, double, Vec2, Vec3, ..., Vec6, and Quaternion. (#3745)
  • DiscreteVariables and ModelingOptions allocated natively in Simbody can now be added to an OpenSim::Component and accessed via its Component API. To support this capability, getDiscreteVariableIndex() has been replaced by getDiscreteVariableIndexes() which returns both the index of the discrete variable and the index of the SimTK::Subsystem to which the descrete variable belongs. (#3745)
  • Computationally efficient methods are now available for extracting the time histories of individual state variables, discrete states, and modeling options from a state trajectory (i.e., a SimTK::Array_<SimTK::State>). Collectively, these methods form the basis for performing a comprehensive serialzation of a state trajectory to file. (#3745)
  • Computationally efficient methods are now available for building a state trajectory (i.e., a SimTK::Array_<SimTK::State>) from the time histories of individual state variables, discrete states, and modeling options. Collectively, these methods form the basis for performing a comprehenvise deserialization of a states trajectory from file. (#3745)
  • Added Model::calcForceContributionsSum(), a wrapper method for GeneralForceSubsystem for efficiently calculating a subset of a model's body and mobility forces. (#3755)
  • Added Force::getForceIndex() to allow accessing the SimTK::ForceIndex for force elements. (#3755)
  • Improved performance in MultivariatePolynomialFunction and added convenience methods for automatically generating function derivatives (#3767).
  • Added options to PolynomialPathFitter for including moment arm and lengthening speed functions in generated FunctionBasedPaths (#3767).
  • The signature for PrescribedController::prescribeControlForActuator() was changed to take a Function via a const reference rather than a pointer to avoid crashes in scripting due to invalid pointer ownership (#3781).
  • Added option to PolynomialPathFitter to use stepwise regression for fitting a minimal set of polynomial coefficients for a FunctionBasedPath (#3779).
  • Fixed a bug in SimulationUtilities::analyze that would provide an incorrectly sized control vector to the model if controls were missing from the input controls table. (#3769)
  • Added InputController, an intermediate abstract class of Controller that provides supports for controllers that map scalar control values from a list Input (connected to Outputs from one or more ModelComponents) to model actuator controls. (#3769)
  • Updated Moco stack to use Casadi 3.6.5, IPOPT 3.14.16, and compatible MUMPS and Metis. (#3693, #3807)
  • Upgrade Python and NumPy versions to 3.10 and 1.25, repectively, in ci workflow (#3794).
  • Fixed bug in report.py preventing plotting multiple MocoParameter values. (#3808)
  • Added SynergyController, a controller that computes controls for a model based on a linear combination of a set of Input control signals and a set of synergy vectors. (#3796)
  • Fixed bug in OpenSim::PiecewiseLinearFunction that prevented proper initialization of the coefficient array when the number of function points is equal to 1. (#3817)
  • Updated PolynomialPathFitter to use all available hardware threads during parallelization. (#3818)
  • Exposed TimeSeriesTable::trimToIndices to public API. (#3824)
  • Fixed bug in Logger::cout, now it works at any logger level. (#3826)
  • Fixed bugs in MocoCasOCProblem and CasOC::Problem with incorrect string formatting. (#3828)
  • Fixed MocoOrientationTrackingGoal::initializeOnModelImpl to check for missing kinematic states, but allow other missing columns. (#3830)
  • Improved exception handling for internal errors in MocoCasADiSolver. Problems will now abort and print a descriptive error message (rather than fail due to an empty trajectory). (#3834)
  • Upgraded the Ipopt dependency Metis to version 5.1.0 on Unix and macOS to enable building on osx-arm64 (#3874).

v4.5

  • Added AbstractGeometryPath which is a base class for GeometryPath and other path types (#3388). All path-based forces now own the property path of type AbstractGeometryPath instead of the GeometryPath unnamed property. Getters and setters have been added to these forces to provide access to concrete path types (e.g., updPath<T>). In Ligament and Blankevoort1991Ligament, usages of get_GeometryPath, upd_GeometryPath, etc., need to be updated to getGeometryPath, updGeometryPath, etc., or a suitable alternative.
  • Fixed a minor memory leak when calling OpenSim::CoordinateCouplerConstraint::setFunction (#3541)
  • Increase the number of input dimensions supported by MultivariatePolynomialFunction to 6 (#3386)
  • Added Assertion.h and associated OPENSIM_ASSERT* macros (#3531)
  • Replaced uses of assert with OPENSIM_ASSERT, so that assertion may be configured via cmake in the future, and so that OpenSim (esp. debug builds) throw instead of terminating the process (#3531)
  • Fixed mis-indexing into an OpenSim::ObjectProperty now throws an exception rather than segfaulting (#3347)
  • PointToPointSpring now throws an exception on finalizing connections if both sides of the spring are connected to the same base frame (#3485)
  • Clarified that OpenSim::Controller's actuator_list takes a list of actuator names, rather than paths (#3484)
  • Deleting elements from an OpenSim::Coordinate range now throws an exception during finalizeFromProperties (previously: it would let you do it, and throw later when Coordinate::getMinRange() or Coordinate::getMaxRange() were called, #3532)
  • Added FunctionBasedPath, a class for representing paths in Forces based on Function objects (#3389)
  • Introduced the method Model::getCoordinateNamesInMultibodyTreeOrder for convenient access to internal coordinate ordering for scripting users (#3569)
  • Fixed a bug where constructing a ModelProcessor from a Model object led to an invalid Model
  • Added LatinHypercubeDesign, a class for generating Latin hypercube designs using random and algorithm methods (#3570)
  • Refactor c3dExport.m file as a Matlab function (#3501), also expose method to allow some operations on tableColumns (multiplyAssign) to speed up data processing.
  • Fixed xml-related memory leaks that were occuring when deserializing OpenSim models. (Issue #3537, PR #3594)
  • Fixed a minor bug when the locally installed package (via pip) couldn't find the dependencies (PR #3593). Added data_files argument to the setup.py to copy all the dependencies into the opensim package folder in the Python environment.
  • Added PolynomialPathFitter, A utility class for fitting a set of FunctionBasedPaths to existing geometry-path in an OpenSim model using MultivariatePolynomialFunctions (#3390)
  • Added examplePolynomialPathFitter.py, a scripting example that demonstrates how to use PolynomialPathFitter (#3607)
  • Fixed a bug where using to_numpy() to convert RowVectorViews to Python arrays returned incorrect data (#3613)
  • Bumped the version of ezc3d which can now Read Kistler files
  • Updated scripting method addTableMetaDataString to support overwriting metadata value for an existing key (#3589)
  • Exposed simbody methods to obtain GravityForces, MobilityForces and BodyForces (#3490)
  • Simbody was updated such that the headers it transitively exposes to downstream projects are compatible with C++20 (#3619)
  • Moved speed computation from computeForce in children of ScalarActuator to dedicated getSpeed function.
  • Fix type problem with BufferedOrientationReference (Issue #3415, PR #3644)
  • Fixed setting the color of a PathSpring's GeometryPath should now update the color of the PathSpring geometry

v4.4.1

  • IMU::calcGyroscopeSignal() now reports angular velocities in the IMU frame.
  • Update report.py to set specific colors for plotted trajectories
  • Made Component::getSocketNames a const member method (previously: non-const)
  • Added ModOpReplaceMusclesWithPathActuators to the list of available model operators in ModelOperators.h
  • Modifed the swig interface files to make OpenSim::PathPointSet adopt new PathPoints inserted into it. (Issue #3276)
  • Remove references to obsoleted dependency BTK, use ezc3d exclusively.
  • Fixed an issue with IPOPT libraries when building OpenSim with OPENSIM_WITH_CASADI = ON but OPENSIM_WITH_TROPTER = OFF (Issue #3267).
  • Removed all references to deprecated environment variable OPENSIM_HOME.
  • Fix issue where templatized Property classes are not available to Objects defined in plugins.
  • Minimum supported version for Java is now 1.8 in the cmake files (Issue #3215).
  • Fix CSV file adapter hanging on csv files that are missing end-header (issue #2432).
  • Improve documentation for MotionType to serve scripting users (Issue #3324).
  • Drop support for 32-bit Matlab in build system since Matlab stopped providing 32-bit distributions (issue #3373).
  • Hotfixed body inertia not being updated after changing the 'inertia' property of a body (Issue #3395).
  • Fixed segfault that can occur when working with OpenSim::Models that are initialized from invalid XML (osim) data (#3409)
  • Deduplicated SmoothSegmentedFunction data when constructing the muscle curves (#3442).
  • Added OpenSim::AbstractSocket::canConnectTo(Object const&) const, for faster socket connectivity checks (#3451)
  • Fixed the CoordinateCouplerConstraint bug preventing functions with multiple independent coordinates (#3435)
  • Removed memory leak tests from testInitState and testComponents, because external analyzers (e.g. libASAN) are better-suited to this (#3459)
  • Fixed CMC_TaskSet memory leak whenever it is copied (#3457)
  • Added SIMBODY_EXTRA_CMAKE_ARGS to dependencies/CMakeLists.txt, which lets integrators customize Simbody via the OpenSim superbuild (#3455)
  • Fixed out-of-bounds memory access in testAssemblySolver (#3460)
  • The property, input, output, and socket macros (e.g. OpenSim_DECLARE_PROPERTY) can now be used outside of the OpenSim namespace and no longer require a using namespace OpenSim; declaration in order to work (#3468)
  • Fixed runtime segfault that can occur when trying to use a WrapObject that is not a child of a PhysicalFrame (#3465)
  • Fixed issues #3083 #2575 where analog data is not pulled out from c3d files, a a new function getAnalogDataTable() has been added to the C3DFileAdapter
  • Fixed segfault that can occur when building models with unusual joint topologies (it now throws an OpenSim::Exception instead, #3299)
  • Add calcMomentum, calcAngularMomentum, calcLinearMomentum, and associated Outputs to Model (#3474)
  • Fix issue where a different init.py is used by conda package and dev environment, the fix allows developers to install local builds into conda. (#3502)
  • Changed control points in SegmentedQuinticBezierToolkit to be of SimTK::Vec6 type instead of SimTK::Vector (#3481).
  • Added a cylinder wrapping test: testWrapCylinder.cpp (#3498)

v4.4

  • Updated ezc3d to version 1.5.0 which better manages the events defined in a c3d file.
  • Fixed an issue that could happen sometimes with ScaleTool where loading the model file or marker set file could fail if the file was given as an absolute path (Issue #3109, PR #3110)
  • Fixed an issue with SWIG with OpenSim::Body::getRotationInGround() where it would return an object without the correct SimTK::Rotation methods.
  • Fixed OpenSim::Arrow start_point property being ignored
  • Fixed objects being set as not up to date with their properties by finalizeFromProperties
  • Throw exception if body masses are either NaN or -ve (Issue #3130)
  • Fixed issue #3176 where McKibbenActuator is not registered and can't be serialized to XML files
  • Fixed issue #3191 where CustomJoint coordinates ordering in model files affects coordinate definitions.
  • Fixed issue #3220 Memory leak running InverseKinematicsTool repeatedly and using Kinematics analysis.

v4.3

  • Introduced IMU component that models a typical Inertial Measurement Unit (IMU) with corresponding outputs for orientation, accelerometer, and gyroscope signals.
  • Introduced IMUDataReporter (analysis) to record signals from IMU components placed on models.
  • Fixed a bug with Actuation analysis that would lead to extra columns in the output when an actuator is disabled (Issue #2977).
  • Fix issue where including path in output file name caused output to not be written without warning, now warning is given and file is written (Issue #3042).
  • Fix copy-paste bug in reporting orientation errors (Issue #2893, fixed by Henrik-Norgren).
  • Upgrade bindings to use SWIG version 4.0 (allowing doxygen comments to carry over to Java/Python files).
  • Added createSyntheticIMUAccelerationSignals() to SimulationUtilities to generate "synthetic" IMU accelerations based on passed in state trajectory.
  • Fixed incorrect header information in BodyKinematics file output
  • Fixed bug applying non-uniform scaling to inertia matrix of a Body due to using local vaiable of type SysMat33 (Issue #2871).
  • Default build to python 3.8 and numpy 1.20 (special instructions for using python 3.8+ on windows at https://simtk-confluence.stanford.edu/display/OpenSim/Scripting+in+Python)

v4.2

  • Fixed a bug with InverseDynamicsTool/InverseDynamicsSolver to account for cases where a model has extra slots in its State's "q" (PR #2971)
  • Added Bhargava2004SmoothedMuscleMetabolics, a smoothed version of the Bhargava metabolics model designed for gradient-based optimization (i.e., Moco).
  • Fixed a bug in Millard2012EquilibriumMuscle::extendFinalizeFromProperties(): the end point slopes on the inverse force velocity curves are constrained to yield a valid curve. A warning is noted in the log if the slopes are small enough that numerical integration might be slow.
  • Added logging to Millard2012EquilibriumMuscle::extendFinalizeFromProperties(): whenever an internal setting is changed automatically these changes are noted in the log. To avoid seeing these messages, update the corresponding properties in the .osim file to the values noted in the log message.
  • Introduced new logging system based on spdlog https://github.com/gabime/spdlog.git. The transition should be transparent to end users with default settings except that the name of the log file is now opensim.log. Main features are:
    • The ability to customize error level for reporting (in increasing level of verbosity): Off, Critical, Error, Warn, Info, Debug, Trace
    • The ability to start logging to a specified file on the fly.
    • Log file messages are time stamped and the format can be changed by users
    • More details and additional functionality is described in the Developer's Guide, and Doxygen pages of OpenSim::Logger class.
  • Add the ActivationCoordinateActuator component, which is a CoordinateActuator with simple activation dynamics (PR #2699).
  • Easily convert Matlab matrices and Python NumPy arrays to and from OpenSim Vectors and Matrices. See Matlab example matrixConversions.m and Python example numpy_conversions.py.
  • Users have more control over which messages are logged. Messages are now logged to opensim.log instead of out.log and err.log. Users can control logging levels via Logger::setLevel().
  • Fix a segfault that occurs when using OpenSim's Python Package with Anaconda's Python on a Mac.
  • Expose PropertyHelper class to python bindings to allow editing of objects using the properties interface (useful for editing objects defined in plugins) in python (consistent with Java/Matlab).
  • Whitespace is trimmed when reading table metadata for STO, MOT, and CSV files.
  • Introduce utilities for creating SimTK::Vectors, linear interpolation, updating table column labels from v3.3 to v4.0 syntax, solving for a function's root using bisection (OpenSim/Common/CommonUtilities.h) (PR #2808).
  • Introduce utilities for querying, filtering, and resampling TimeSeriesTables (OpenSim/Common/TableUtilities.h) (PR #2808).
  • StatesTrajectories can now be created from a TimeSeriesTable of states.
  • Minor performance improvements (5-10 %) for controller-heavy models (PR #2806)
  • Controller::isEnabled will now only return whether the particular controller is enabled
    • Previously, it would return false if its parent Model's Model::getAllControllersEnabled returned false
    • The previous behavior would mean that Controller::setEnabled(true); return Controller::isEnabled(); could return false
  • When building from source, CMake now outputs more detailed information about dependencies.
  • The new Matlab examplePointMass.m shows how to build and simulate a point-mass model.
  • Fix OpenSense calibration algorithm to handle models facing an arbitrary direction. The calibration algorithm now aligns one axis of the provided Orientation Sensor data with the x-axis of the base segment (e.g. pelvis) of the model in default pose.
  • For PrescribedController, the controls_file column labels can now be absolute paths to actuators (previously, the column labels were required to be actuator names).
  • Fixed a critical bug in Induced Accelerations Analysis which prevents analysis to run when external forces are present (PR #2847).
  • For PrescribedController, the controls_file column labels can now be absolute paths to actuators (previously, the column labels were required to be actuator names).
  • CMCTool now supports the setSolveForEquilibrium() method inherited by AbstractTool, which allows users to disable a call to Model::equilibrateMuscles() when running CMC. This setting is true by default, so the default behavior remains the same.
  • The Matlab utility osimTableToStruct() now handles column labels that start with a non-letter character by prepending 'a_' instead of 'unlabeled'.
  • Removed Path abstract base class (PR #2844)
    • Unused by OpenSim and related projects
  • Improved the performance of ComponentPath (PR #2844)
    • This improves the performance of component-heavy models by ~5-10 %
    • The behavior and interface of ComponentPath should remain the same
  • The new Matlab CustomStaticOptimization.m guides the user to build their own custom static optimization code.
  • Dropped support for separate Kinematics for application of External Loads. ([PR #2770] (#2770)).
  • Refactored InverseKinematicsSolver to allow for adding (live) Orientation data to track, introduced BufferedOrientationsReference to queue data (PR #2855)
  • opensim.log will only be created/opened when the first message is logged to it (PR #2880):
    • Previously, opensim.log would always be created, even if nothing was logged
  • Added a CMake option, OPENSIM_DISABLE_LOG_FILE (PR #2880):
    • When set, disables opensim.log from being used by the logger by default when the first message is written to the log
    • Log messages are still written to the standard output/error streams
    • Previously, opensim.log would always be created - even if nothing was written to it (fixed above)
    • Setting OPENSIM_DISABLE_LOG_FILE only disables the automatic creation of opensim.log. File logging can still be manually be enabled by calling Logger::addFileSink()
    • This flag is OFF by default. So standard builds will still observe the existing behavior (opensim.log is created).
  • Fix bug in visualization of EllipsoidJoint that was not attaching to the correct frame ([PR #2887] (#2887))
  • Fix bug in error reporting of sensor tracking (PR #2893)
  • Throw an exception rather than log an error message when an unrecognized type is encountered in xml/osim files (PR #2914)
  • Added ScapulothoracicJoint as a builtin Joint type instead of a plugin (PRs #2877 and #2932)

v4.1

  • Added OrientationsReference as the frame orientation analog to the location of experimental markers. Enables experimentally measured orientations from wearable sensors (e.g. from IMUs) to be tracked by reference frames in the model. A correspondence between the experimental (IMU frame) orientation column label and that of the virtual frame on the Model is expected. The InverseKinematicsSolver was extended to simultaneously track the OrientationsReference if provided. (PR #2412)
  • Removed the undocumented bool dumpName argument from Object::dump() and made the method const so it can be safely called on const objects. (PR #2412)
  • MarkersReference convenience constructors were updated to take a const reference to a MarkerWeightSet as its second argument. If a Set is not empty, then only the markers listed are used as reference signals. That means InverseKinematicsTool no longer tracks all experimental markers even those not in the MarkerWeightSet. One can quickly track all experimental markers (that have a corresponding model marker) by simply providing an empty Set, in which case all markers are assigned the default weight (typically 1.0).
  • Model files from very old versions (pre 1.8.1) are not supported, an exception is thrown rather than fail quietly (issue #2395).
  • Initializing a Component from an existing Component with correct socket connectees yields invalid paths (issue #2418).
  • Reading DataTables from files has been simplified. Reading one table from a file typically uses the Table constructor except when the data-source/file contains multiple tables. (In these cases e.g. C3D files, use C3DFileAdapter.read method, then use functions in C3DFileAdapter to get the individual TimeSeriesTable(s)). Writing tables to files has not changed.
  • Exposed convertMillimeters2Meters() in osimC3D.m. This function converts COP and moment data from mm to m and now must be invoked prior to writing force data to file. Previously, this was automatically performed during writing forces to file.
  • Methods that operate on SimTK::Vec are now available through Java/Matlab and python bindings to add/subtract/divide/multiply vec contents with a scalar (PR #2558)
  • The new Stopwatch class allows C++ API users to easily measure the runtime of their code.
  • If finalizeConnections() method was not called on a model after making changes and before printing, an exception is thrown to avoid creating corrupt model files quietly (PR #2529)
  • Updated the docopt.cpp dependency so that OpenSim can be compiled with Visual C++ from Visual Studio 2019.
  • Added Blankevoort1991Ligament force component which represents ligament fibers as non-linear path springs. The force-strain curve has a quadratic toe region at low strains and a linear stiffness region at high strains. (PR #2632)
  • Updated Simbody to 3.7 to fix an issue with the simbody-visualizer on macOS 10.15 Catalina.
  • On Mac and Linux, we include a shell script opensim-install-command-line.sh to make OpenSim's command-line tools easily accessible.
  • Added the compliant SmoothSphereHalfSpaceForce component, for use with direct collocation and Moco.

Converting from v4.0 to v4.1

  • The OpenSim::Array constructor is now marked explicit, which prevents accidental implicit conversion to Array. If you relied on this implicit conversion, you will need to update your code to use the constructor explicitly.

Bug Fixes

  • Fixed bug in osimTable2Struct.m for renaming unlabelled markers (PR #2491)
  • Fixed bug that resulted in an exception when reading C3D files without forces. Now, if the C3D doesn't contain markers or forces, an empty table will be returned (PR #2421)
  • Fix bug that resulted in activations and forces reported for Actuators that are disabled during StaticOptimization (issue #2438) Disabled actuators are now ignored in StaticOptimization.
  • OpenSim no longer supports model file formats predating version 1.8.1 (PR #2498)
  • FunctionBasedBushingForce now applies damping if specified (it was incorrectly ignored in 4.0) issue #2512
  • TRCFileAdapter.write() uses the number of columns and rows in the supplied dataTable to set the "NumMarkers" and "NumRows" Metadata in the output file. Users won't have to set this metadata string manually. #2510

Documentation

Other Changes

  • Performance of reading large data files has been significantly improved. A 50MB .sto file would take 10-11 min to read now takes 2-3 seconds. (PR #2399)
  • Added Matlab example script of plotting the Force-length properties of muscles in a models; creating an Actuator file from a model; building and simulating a simple arm model; using OutputReporters to record and write marker location and coordinate values to file.
  • Added Python example that demonstrates how to run an optimization using the cma package and how to avoid an expensive call to initSystem() within the objective function. (PR #2604)
  • OpenSim 4.1 ships with Python3 bindings as default. It is still possible to create bindings for Python2 if desired by setting CMake variable OPENSIM_PYTHON_VERSION to 2
  • For CMake, the option OPENSIM_COPY_DEPENDENCIES option is now an advanced option, and a warning is provided if this option is off but wrapping is turned on.

v4.0

Converting from v3.x to v4.0

  • A significant difference between v3.3 and 4.0 is the naming of dependencies. Unique names were not enforced in 3.3, which led to undefined behavior. In 4.0, Component pathnames must be unique. That is a Component must be unique with respect to its peers. A Model named model cannot have multiple subcomponents with the name toes either as bodies or joints, because the pathname /model/toes will not uniquely identify the Component. However, multiple toes bodies can be used as long as they are not subcomponents of the same Component. For example, a device Component with a toes Body will have no issues since this toes Body has a unique pathname, /model/device/toes, which is unambiguous. One could also create a multi-legged model, where each leg is identical, with hip and knee joints and upper and lower bodies, but each being unique because each Leg Component that contains the leg subcomponents, is uniquely named like /model/leg1 and /model/leg4/ and thus all of their subcomponents are unique, e.g.: /model/leg1/knee vs. /model/leg4/knee.

  • Component naming is more strictly enforced and names with spaces are no longer accepted. Spaces are only allowable as separators for Output or Channel names that satisfy a list Input. (PR #1955)

  • The Actuator class has been renamed to ScalarActuator (and Actuator_ has been renamed to Actuator) (PR #126). If you have subclassed from Actuator, you must now subclass from ScalarActuator.

  • Methods like Actuator::getForce are renamed to use "Actuator" instead (e.g., Actuator::getActuator) (PR #209).

  • Markers are now ModelComponents (PR #188). Code is included for conversion on serialization/de-serialization.

  • MarkerSet::addMarker() was removed (PR #1898). Please use Model::addMarker() to add markers to your model.

  • Body::getMassCenter now returns a Vec3 instead of taking a Vec3 reference as an argument (commit cb0697d98).

  • The following virtual methods in ModelComponent have been moved:

    • connectToModel -> extendConnectToModel
    • addToSystem -> extendAddToSystem
    • initStateFromProperties -> extendInitStateFromProperties
    • setPropertiesFromState -> extendSetPropertiesFromState

    The original methods (without extend) still exist, but they are now non-virtual. To invoke connectToModel on an entire Model, you still call Model::connectToModel. This change has been made to make a distinction between the user interface and the Component developer (extension) interface. IMPORTANT The calls to Super::addToSystem, etc. in the implementation of these methods must now also use the extend variants. Otherwise, you will enter into an infinite recursion.

  • OpenSim now makes substantial use of C++11 features; if you compile OpenSim, your compiler must support C++11. Also, any C++ project in which you use OpenSim must also be compiled with C++11.

  • The following components have been upgraded to use Sockets to connect to other components they depend on (instead of string properties):

    • ContactGeometry (ContactSphere, ContactHalfSpace, ContactMesh)

  • Many of the methods in ScaleTool have now been marked const.

  • We created a new unified command line interface that will replace the single-tool command line executables (scale, ik, id, rra, cmc, etc.).

    • scale -S setup.xml -> opensim run-tool setup.xml.
    • scale -PS -> opensim print-xml scale
    • scale -PropertyInfo ... -> opensim info ...
    • versionUpdate ... -> opensim update-file ...

  • The CoordinateSet property in Joint has been replaced with a coordinates list property and enumerations have been added for accessing the Coordinates owned by a Joint. Code like myPlanarJoint.getCoordinateSet()[0] now becomes myPlanarJoint.getCoordinate(PlanarJoint::Coord::RotationZ) (PRs #1116, #1210, and #1222).

  • The reverse property in Joint can no longer be set by the user; Model uses SimTK::MultibodyGraphMaker to determine whether joints should be reversed when building the multibody system. The joint's transform and coordinates maintain a parent->child sense even if the joint has been reversed. For backwards compatibility, a joint's parent and child PhysicalFrames are swapped when opening a Model if the reverse element is set to true.

  • The MotionType of a Coordinate is now fully determined by the Joint. The user cannot set the MotionType for a Coordinate. There are instances such as in the leg6dof9musc and Rajagopal2015 models, where a Coordinate was assigned an incorrect type (e.g. when a coordinate of a CustomJoint is not a measure of a Cartesian angle). In 4.0, the coordinate is correctly marked as Coupled since a function couples the coordinate value to the angular displacement of the patella in Cartesian space. NOTE, this causes issues (e.g. opensim-org/opensim-gui#617, #2088) when using kinematics files generated in 3.3 (or earlier) where Rotational coordinates have been converted to degrees. Because OpenSim 4.0 does not recognize the coordinate's MotionType to be Rotational it will not convert it back to radians internally. For motion files generated prior to 4.0 where the file has inDegrees=yes, please use the following conversion utility: updatePre40KinematicsFilesFor40MotionType(). When loading a pre-4.0 model, OpenSim will warn users of any changes in MotionType when updating an existing model to OpenSim 4.0.

  • Manager::integrate(SimTK::State&) has been removed and replaced by Manager::integrate(double). You must also now call Manager::initialize(SimTK::State&) before integrating or pass the initialization state into a convenience constructor. Here is a before-after example (see the documentation in the Manager class for more details):

    • Before:
      • Manager manager(model);
      • manager.setInitialTime(0.0);
      • manager.setFinalTime(1.0);
      • manager.integrate(state);
    • After:
      • Manager manager(model);
      • state.setTime(0.0);
      • manager.initialize(state);
      • manager.integrate(1.0);
    • After (using a convenience constructor):
      • state.setTime(0.0);
      • Manager manager(model, state);
      • manager.integrate(1.0);

  • Manager::setIntegrator(SimTK::Integrator) has been removed and replaced by Manager::setIntegratorMethod(IntegratorMethod) which uses an enum and can be used by the MATLAB/Python interface. See the method's documentation for examples. Integrator settings are now handled by the Manager through the following new functions:

    • setIntegratorAccuracy(double)
    • setIntegratorMinimumStepSize(double)
    • setIntegratorMaximumStepSize(double)
    • setIntegratorInternalStepLimit(int)

  • Muscle::equilibrate(SimTK::State&) has been removed from the Muscle interface in order to reduce the number and variety of muscle equilibrium methods. Actuator::computeEquilibrium(SimTK::State&) is overridden by Muscle and invokes pure virtual Muscle::computeInitialFiberEquilibrium(SimTK::State&).

  • Millard2012EquilibriumMuscle::computeFiberEquilibriumAtZeroVelocity(SimTK::State&) and computeInitialFiberEquilibrium(SimTK::State&) were combined into a single method: Millard2012EquilibriumMuscle::computeFiberEquilibrium(SimTK::State&, bool useZeroVelocity) where fiber-velocity can be estimated from the state or assumed to be zero if the flag is true.

  • Millard2012EquilibriumMuscle::computeInitialFiberEquilibrium(SimTK::State&) invokes computeFiberEquilibrium() with useZeroVelocity = true to maintain its previous behavior.

  • Model::replaceMarkerSet() was removed. (PR #1938) Please use Model::updMarkerSet() to edit the model's MarkerSet instead.

  • The argument list for Model::scale() was changed: the finalMass and preserveMassDist arguments were swapped and the preserveMassDist argument is no longer optional. The default argument for preserveMassDist in OpenSim 3.3 was false. (PR #1994)

  • A GeometryPath without PathPoints is considered invalid, since it does not represent a physical system. You must specify PathPoints to define a valid GeometryPath for a Muscle, Ligament, PathSpring, etc... that is added to a Model. (PR #1948)

    • Before (no longer valid): 
      Model model;
Thelen2003Muscle* muscle = new Thelen2003Muscle("muscle", ...);
// GeometryPath throws: "A valid path requires at least two PathPoints."
model.addForce(muscle);
    • After (now required): 
      Model model;
Thelen2003Muscle* muscle = new Thelen2003Muscle("muscle", ...);
// require at least two path points to have a valid muscle GeometryPath
muscle->addNewPathPoint("p1", ...);
muscle->addNewPathPoint("p2", ...);
model.addForce(muscle);

  • The JointReaction analysis interface has changed in a few ways:

    • "express_in_frame" now takes a Frame name. "child" and "parent" keywords are also still accepted, provided that no Frame is named "child" or "parent"
    • If the number of elements in "apply_on_bodies" or "express_in_frame" is neither of length 1 or the same length as indicated by "joint_names", an exception is thrown. This was previously a warning.

  • Updated wrapping properties

Composing a Component from other components

Component now maintains a list property of components which it owns. You add a (sub) Component to a parent Component by calling addComponent and passing a heap allocated (new Component) to the parent which you want to take ownership of the new subcomponent. Ownership determines how the subcomponent is serialized (appears within the parent) and the order in which of Component interface methods (above) are propagated to the subcomponent. Access to contained components is provided through getComponent<C>(path) or getComponentList<C> where C is any Component type (default is Component to get all subcomponents). These methods always traverse down into a Component's list of components. All subcomponents that are properties of (and thus owned by) a parent Component are accessible this way. The Model's typed %Sets and add####() methods are no longer necessary to compose a Model, since any Component can now be composed of components. Model still supports addd####() methods and de/serialization of Sets, but components added via addComponent are NOT included in the Sets but contained in the Component's components property list. Details in PR#1014. Note, it is now strictly required that immediate subcomponents have unique names. For example, a Model cannot contain two bodies in its BodySet named tibia or a Body and a Joint named toes, since it is ambiguous as to which tibia Body or toes Component is being referenced.

Bug Fixes

  • Fixed a typo in one of the method names for AbstractTool verifyUniqueComulnLabels -> verifyUniqueColumnLabels (PR #130)
  • Fixed bug where Body VisibleObject was not serialized when writing a model to XML (PR #139)
  • Fixed memory leaks in AssemblySolver and using Simtk::XML (PR #176)
  • Fixed model mass scaling. When 'preserve mass distribution' is unchecked (GUI) the input mass was previously not respected and the resulting scaled model mass does not equal the input mass. The modelscaler() now alters the body masses and inertias to match the input mass. (PR #230)
  • Fixed a bug in the equilibrium solution of Millard and Thelen muscles, where the initial activation and fiber-length values (for solving for equilibrium) were always coming from the default values. This was unnecessary, because unless specified otherwise, the state automatically contains the default values. This fixes an issue where initial states activations from a file were not respected by the Forward Tool and instead, the initial activations would revert to the model defaults. (PR #272)
  • Fixed a bug where MuscleAnalysis was producing empty moment arm files. We now avoid creating empty Moment and MomentArm storage files when _computeMoments is False. (PR #324)
  • Fixed bug causing the muscle equilibrium solve routine in both Thelen2003Muscle and Millard2012EquilibriumMuscle to fail to converge and erroneously return the minimum fiber length. The fix added a proper reduction in step-size when errors increase and limiting the fiber-length to its minimum. (PR #1728)
  • Fixed a bug where Models with Bodies and Joints (and other component types) with the same name were loaded without error. Duplicately named Bodies were simply being ignored and only the first Body of that name in the BodySet was being used, for example, to connect a Body to its parent via its Joint, or to affix path points to its respective Body. Now, duplicate names are flagged and renamed so they are uniquely identified. (PR #1887)
  • Fixed bug and speed issue with model.setStateVariableValues() caused by enforcing constraints after each coordinate value was being set (PR #1911). Removing the automatic enforcement of constraints makes setting all state values much faster, but also requires calling model.assemble() afterwards. Enforcing constraints after setting each coordinate value individually was also incorrect, since it neglected the effect of other coordinate changes have on the current coordinate. All coordinate values must be set before enforcing constraints.
  • Fixed a bug that resulted in incorrect Ligament resting lengths after scaling. (PR #1994)

New Classes

  • Added a BodyActuator component, which applies a spatial force on a specified Point of a Body (PR #126)

  • Created Frame, PhysicalFrame, OffsetFrame, PhysicalOffsetFrame, Station and Marker ModelComponents (PR #188, PR #325, PR #339). Marker did not previously comply with the Model Component interface.

  • A Body is a PhysicalFrame

  • Connections to Bodies upgraded to PhysicalFrames and locations on these frames are now represented by PhysicalOffsetFrame (PR #370)

  • Joints were refactored so that the base Joint manages the parent and child frame connections, including the definition of local PhysicalOffsetFrames to handle offsets defined as separate location and orientation properties. (PR #589)

  • The WeldConstraint and BushingForces (BushingForce, CoupledBushingForce, FunctionBasedBushingForce, and ExpressionBasedBushingForce) were similarly unified (like Joints) to handle the two Frames that these classes require to operate. A LinkTwoFrames intermediate class was introduced to house the common operations. Convenience constructors for WeldConstraint and BushingFrames were affected and now require the name of the Component as the first argument. (PR #649)

  • The new StatesTrajectory class allows users to load an exact representation of previously-computed states from a file. (PR #730)

  • Added Point as a new base class for all points, which include: Station, Marker, and PathPoints

  • Added OutputReporter as an Analysis so that users can use the existing AnalyzeTool and ForwardTool to extract Output values of interest, without modifications to the GUI. (PR #1991)

Removed Classes

The following classes are no longer supported in OpenSim and are removed in OpenSim 4.0.

  • Muscle class ContDerivMuscle_Depredated.

MATLAB and Python interfaces

  • The SimbodyMatterSubsystem class--which provides operators related to the mass matrix, Jacobians, inverse dynamics, etc.--is now accessible in MATLAB and Python (PR #930).
  • Changed wrapping of SimTK::Array_<OpenSim::CoordinateReference> from ArrayCoordinateReference to SimTKArrayCoordinateReference for consistency with other classes. (PR #1842)

MATLAB interface

  • The configureOpenSim.m function should no longer require administrator privileges for most users, and gives more verbose output to assist with troubleshooting.
  • New MATLAB examples were added: Hopper-Device and Knee-Reflex.

Python interface

  • Improved error handling. Now, OpenSim's error messages show up as exceptions in Python.
  • The Python bindings can now be built for Python 3 (as well as Python 2).

Other Changes

  • Support for compiling the source code with Microsoft Visual Studio 2017.
  • There is now a formal CMake mechanism for using OpenSim in your own C++ project. See cmake/SampleCMakeLists.txt. (PR #187)
  • Substantial cleanup of the internal CMake scripts.
  • Lepton was upgraded to the latest version (PR #349)
  • Made Object::print a const member function (PR #191)
  • Improved the testOptimization/OptimizationExample to reduce the runtime (PR #416)
  • InverseKinematics tool outputs marker error .sto file if report error flag is true.
  • Marker location file output name in IK changed to reflect trial name for batch processing.
  • Created a method ScaleTool::run(), making it easier to run the Scale Tool programmatically in MATLAB or python.
  • Thelen2003Muscle, Millard2012EquilibriumMuscle, and Millard2012AccelerationMuscle now throw an exception if the force equilibrium calculation fails to converge (PR #1201).
  • Thelen2003Muscle and Millard2012EquilibriumMuscle no longer clamp excitations (i.e. controls) internally. If controls are out of bounds an Exception is thrown. Also, the min_control property now defaults to the minimum_activation. It is the responsibility of the controller (or solver) to provide controls that are within the valid ranges defined by the Actuators and that includes the specific bounds of Muscle models. (PR #1548)
  • The buildinfo.txt file, which contains the name of the compiler used to compile OpenSim and related information, is now named OpenSim_buildinfo.txt and may be installed in a different location.
  • macOS and Linux users should no longer need to set LD_LIBRARY_PATH or DYLD_LIBRARY_PATH to use OpenSim libraries.
  • The scale() method was removed from the SimbodyEngine class (the contents were moved into Model::scale()). (PR #1994)
  • Any class derived from ModelComponent can now add its own implementation of extendPreScale(), extendScale(), and/or extendPostScale() to control how its properties are updated during scaling. (PR #1994)
  • The source code for the "From the Ground Up: Building a Passive Dynamic Walker Example" was added to this repository.
  • OpenSim no longer looks for the simbody-visualizer using the environment variable OPENSIM_HOME. OpenSim uses PATH instead.
  • The Thelen2003Muscle now depend on separate components for modeling pennation, and activation dynamics.

Documentation

  • Improved Doxygen layout and fixed several bugs and warnings (various)
  • All mentions of SimTK/Simbody classes in OpenSim's Doxygen now provide links directly to SimTK/Simbody's doxygen.
  • Added a detailed README.md wtith build instructions, as well as guides to contributing and developing (CONTRIBUTING.md).
  • Included GIFs in Doxygen for several commonly used Joint types