Skip to content
Permalink
Branch: master
Find file Copy path
Find file Copy path
289 lines (265 sloc) 21.9 KB

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.

v4.1

  • 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).

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

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.

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
You can’t perform that action at this time.