Merge branch 'opensim-org:main' into main

Bindings/Java/tests/TestTables.java

@@ -265,6 +265,36 @@ public static void test_DataTable() {
         assert tableFlat.getNumRows()             == 3;
         assert tableFlat.getNumColumns()          == 12;
         System.out.println(tableFlat);
+        table = new DataTable();
+        labels = new StdVectorString();
+        labels.add("col0.0"); labels.add("col0.1"); labels.add("col0.2");
+        labels.add("col0.3"); labels.add("col0.4"); labels.add("col0.5");
+        labels.add("col0.6"); labels.add("col0.7"); labels.add("col0.8");
+        labels.add("col1.0"); labels.add("col1.1"); labels.add("col1.2");
+        labels.add("col1.3"); labels.add("col1.4"); labels.add("col1.5");
+        labels.add("col1.6"); labels.add("col1.7"); labels.add("col1.8");
+        table.setColumnLabels(labels);
+        row = new RowVector(18, 1);
+        table.appendRow(1, row);
+        row = new RowVector(18, 2);
+        table.appendRow(2, row);
+        row = new RowVector(18, 3);
+        table.appendRow(3, row);
+        assert table.getColumnLabels().size() == 18;
+        assert table.getNumRows()             == 3;
+        assert table.getNumColumns()          == 18;
+        DataTableRotation tableRot = table.packRotation();
+        assert tableRot.getColumnLabel(0).equals("col0");
+        assert tableRot.getNumRows()    == 3;
+        assert tableRot.getNumColumns() == 2;
+        System.out.println(tableRot);
+        tableFlat = tableRot.flatten();
+        assert tableFlat.getColumnLabels().size() == 18;
+        assert tableFlat.getColumnLabel( 0).equals("col0_1");
+        assert tableFlat.getColumnLabel(15).equals("col1_7");
+        assert tableFlat.getNumRows()             == 3;
+        assert tableFlat.getNumColumns()          == 18;
+        System.out.println(tableFlat);
     }
 
     public static void test_DataTableVec3() {

Bindings/OpenSimHeaders_simulation.h

@@ -148,6 +148,7 @@
 #include <OpenSim/Simulation/OpenSense/IMU.h>
 #include <OpenSim/Simulation/OpenSense/OpenSenseUtilities.h>
 
+#include <OpenSim/Simulation/StatesDocument.h>
 #include <OpenSim/Simulation/StatesTrajectory.h>
 #include <OpenSim/Simulation/StatesTrajectoryReporter.h>
 

Bindings/Python/tests/test_DataTable.py

@@ -130,7 +130,7 @@ def test_DataTable(self):
                 row[1] == 200 and
                 row[2] == 300 and
                 row[3] == 400)
-        row0 = table.getRowAtIndex(0)
+        row0 = table.updRowAtIndex(0)
         row0[0] = 10
         row0[1] = 10
         row0[2] = 10
@@ -140,7 +140,7 @@ def test_DataTable(self):
                 row0[1] == 10 and
                 row0[2] == 10 and
                 row0[3] == 10)
-        row2 = table.getRow(0.3)
+        row2 = table.updRow(0.3)
         row2[0] = 20
         row2[1] = 20
         row2[2] = 20
@@ -152,15 +152,15 @@ def test_DataTable(self):
                 row2[3] == 20)
         print(table)
         # Edit columns of the table.
-        col1 = table.getDependentColumnAtIndex(1)
+        col1 = table.updDependentColumnAtIndex(1)
         col1[0] = 30
         col1[1] = 30
         col1[2] = 30
         col1 = table.getDependentColumnAtIndex(1)
         assert (col1[0] == 30 and
                 col1[1] == 30 and
                 col1[2] == 30)
-        col3 = table.getDependentColumn('3')
+        col3 = table.updDependentColumn('3')
         col3[0] = 40
         col3[1] = 40
         col3[2] = 40
@@ -299,6 +299,40 @@ def test_DataTable(self):
         assert tableFlat.getNumRows()           == 3
         assert tableFlat.getNumColumns()        == 12
         print(tableFlat)
+        table = osim.DataTable()
+        table.setColumnLabels(('col0_x', 'col0_y', 'col0_z',
+                               'col1_x', 'col1_y', 'col1_z',
+                               'col2_x', 'col2_y', 'col2_z',
+                               'col3_x', 'col3_y', 'col3_z',
+                               'col4_x', 'col4_y', 'col4_z',
+                               'col5_x', 'col5_y', 'col5_z'))
+        row = osim.RowVector([1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1])
+        table.appendRow(1, row)
+        row = osim.RowVector([2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2])
+        table.appendRow(2, row)
+        row = osim.RowVector([3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3])
+        table.appendRow(3, row)
+        assert len(table.getColumnLabels()) == 18
+        assert table.getNumRows()           == 3
+        assert table.getNumColumns()        == 18
+        table.setColumnLabels(('col0_0', 'col0_1', 'col0_2',
+                               'col0_3', 'col0_4', 'col0_5',
+                               'col0_6', 'col0_7', 'col0_8',
+                               'col1_0', 'col1_1', 'col1_2',
+                               'col1_3', 'col1_4', 'col1_5',
+                               'col1_6', 'col1_7', 'col1_8'))
+        tableRot = table.packRotation()
+        tableRot.getColumnLabels() == ('col0', 'col1')
+        tableRot.getNumRows()    == 3
+        tableRot.getNumColumns() == 2
+        print(tableRot)
+        tableFlat = tableRot.flatten()
+        assert len(tableFlat.getColumnLabels()) == 18
+        assert tableFlat.getColumnLabel( 0) == 'col0_1'
+        assert tableFlat.getColumnLabel(15) == 'col1_7'
+        assert tableFlat.getNumRows()           == 3
+        assert tableFlat.getNumColumns()        == 18
+        print(tableFlat)
 
     def test_TimeSeriesTable(self):
         print()
@@ -475,15 +509,15 @@ def test_DataTableVec3(self):
         print(tableDouble)
 
         # Edit rows of the table.
-        row0 = table.getRowAtIndex(0)
+        row0 = table.updRowAtIndex(0)
         row0[0] = osim.Vec3(10, 10, 10)
         row0[1] = osim.Vec3(10, 10, 10)
         row0[2] = osim.Vec3(10, 10, 10)
         row0 = table.getRowAtIndex(0)
         assert (str(row0[0]) == str(osim.Vec3(10, 10, 10)) and
                 str(row0[1]) == str(osim.Vec3(10, 10, 10)) and
                 str(row0[2]) == str(osim.Vec3(10, 10, 10)))
-        row2 = table.getRow(0.3)
+        row2 = table.updRow(0.3)
         row2[0] = osim.Vec3(20, 20, 20)
         row2[1] = osim.Vec3(20, 20, 20)
         row2[2] = osim.Vec3(20, 20, 20)
@@ -493,15 +527,15 @@ def test_DataTableVec3(self):
                 str(row2[2]) == str(osim.Vec3(20, 20, 20)))
         print(table)
         # Edit columns of the table.
-        col1 = table.getDependentColumnAtIndex(1)
+        col1 = table.updDependentColumnAtIndex(1)
         col1[0] = osim.Vec3(30, 30, 30)
         col1[1] = osim.Vec3(30, 30, 30)
         col1[2] = osim.Vec3(30, 30, 30)
         col1 = table.getDependentColumnAtIndex(1)
         assert (str(col1[0]) == str(osim.Vec3(30, 30, 30)) and
                 str(col1[1]) == str(osim.Vec3(30, 30, 30)) and
                 str(col1[2]) == str(osim.Vec3(30, 30, 30)))
-        col2 = table.getDependentColumn('2')
+        col2 = table.updDependentColumn('2')
         col2[0] = osim.Vec3(40, 40, 40)
         col2[1] = osim.Vec3(40, 40, 40)
         col2[2] = osim.Vec3(40, 40, 40)

Bindings/common.i

@@ -253,6 +253,14 @@ DATATABLE_CLONE(double, SimTK::Rotation_<double>)
     packSpatialVec(std::vector<std::string> suffixes) {
         return $self->pack<SimTK::SpatialVec>();
     }
+    DataTable_<double, SimTK::Rotation_<double>>
+    packRotation() {
+        return $self->pack<SimTK::Rotation_<double>>();
+    }
+    DataTable_<double, SimTK::Rotation_<double>>
+    packRotation(std::vector<std::string> suffixes) {
+        return $self->pack<SimTK::Rotation_<double>>();
+    }
 }
 
 %ignore OpenSim::TimeSeriesTable_::TimeSeriesTable_(TimeSeriesTable_ &&);
@@ -294,6 +302,14 @@ DATATABLE_CLONE(double, SimTK::Rotation_<double>)
     packSpatialVec(std::vector<std::string> suffixes) {
         return $self->pack<SimTK::SpatialVec>();
     }
+    TimeSeriesTable_<SimTK::Rotation_<double>>
+    packRotation() {
+        return $self->pack<SimTK::Rotation_<double>>();
+    }
+    TimeSeriesTable_<SimTK::Rotation_<double>>
+    packRotation(std::vector<std::string> suffixes) {
+        return $self->pack<SimTK::Rotation_<double>>();
+    }
 }
 %extend OpenSim::TimeSeriesTable_<SimTK::Vec3> {
     TimeSeriesTable_<double> flatten() {
@@ -335,6 +351,14 @@ DATATABLE_CLONE(double, SimTK::Rotation_<double>)
         return $self->flatten(suffixes);
     }
 }
+%extend OpenSim::TimeSeriesTable_<SimTK::Rotation_<double>> {
+    TimeSeriesTable_<double> flatten() {
+        return $self->flatten();
+    }
+    TimeSeriesTable_<double> flatten(std::vector<std::string> suffixes) {
+        return $self->flatten(suffixes);
+    }
+}
 
 %include <OpenSim/Common/AbstractDataTable.h>
 %include <OpenSim/Common/DataTable.h>
@@ -371,7 +395,7 @@ DATATABLE_CLONE(double, SimTK::Rotation_<double>)
 %shared_ptr(OpenSim::IMUDataReader)
 %shared_ptr(OpenSim::XsensDataReader)
 %shared_ptr(OpenSim::APDMDataReader)
-%shared_ptr(OpenSim::STOFileAdapter_<duoble>)
+%shared_ptr(OpenSim::STOFileAdapter_<double>)
 %shared_ptr(OpenSim::STOFileAdapter_<SimTK::Vec3>)
 %shared_ptr(OpenSim::STOFileAdapter_<SimTK::UnitVec3>)
 %shared_ptr(OpenSim::STOFileAdapter_<SimTK::Quaternion>)

Bindings/moco.i

@@ -138,6 +138,10 @@ namespace OpenSim {
 %include <OpenSim/Moco/MocoTropterSolver.h>
 %include <OpenSim/Moco/MocoCasADiSolver/MocoCasADiSolver.h>
 %include <OpenSim/Moco/MocoStudy.h>
+%template(analyzeVec3) OpenSim::MocoStudy::analyze<SimTK::Vec3>;
+%template(analyzeSpatialVec) OpenSim::MocoStudy::analyze<SimTK::SpatialVec>;
+%template(analyzeRotation) OpenSim::MocoStudy::analyze<SimTK::Rotation_<double>>;
+
 %include <OpenSim/Moco/MocoStudyFactory.h>
 
 %include <OpenSim/Moco/MocoTool.h>
@@ -148,5 +152,6 @@ namespace OpenSim {
 %template(analyzeMocoTrajectory) OpenSim::analyzeMocoTrajectory<double>;
 %template(analyzeMocoTrajectoryVec3) OpenSim::analyzeMocoTrajectory<SimTK::Vec3>;
 %template(analyzeMocoTrajectorySpatialVec) OpenSim::analyzeMocoTrajectory<SimTK::SpatialVec>;
+%template(analyzeMocoTrajectoryRotation) OpenSim::analyzeMocoTrajectory<SimTK::Rotation_<double>>;
 
 %include <OpenSim/Moco/ModelOperatorsDGF.h>

Bindings/simulation.i

@@ -253,6 +253,7 @@ OpenSim::ModelComponentSet<OpenSim::Controller>;
 
 %template(StdVectorIMUs) std::vector< OpenSim::IMU* >;
 
+%include <OpenSim/Simulation/StatesDocument.h>
 %include <OpenSim/Simulation/StatesTrajectory.h>
 // This enables iterating using the getBetween() method.
 %template(IteratorRangeStatesTrajectoryIterator)
@@ -263,6 +264,7 @@ OpenSim::ModelComponentSet<OpenSim::Controller>;
 %template(analyze) OpenSim::analyze<double>;
 %template(analyzeVec3) OpenSim::analyze<SimTK::Vec3>;
 %template(analyzeSpatialVec) OpenSim::analyze<SimTK::SpatialVec>;
+%template(analyzeRotation) OpenSim::analyze<SimTK::Rotation_<double>>;
 
 %include <OpenSim/Simulation/VisualizerUtilities.h>
 

CHANGELOG.md

@@ -12,8 +12,8 @@ v4.6
   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 
+- 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 `Output`s to `ExpressionBasedCoordinateForce`, `ExpressionBasedPointToPointForce`, and `ExpressionBasedBushingForce` for accessing force values. (#3872)
 - `PointForceDirection` no longer has a virtual destructor, is `final`, and its `scale` functionality
@@ -23,12 +23,24 @@ v4.6
   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 
+- 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) 
+- 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)
 
 v4.5.1
 ======
@@ -93,6 +105,8 @@ pointer to avoid crashes in scripting due to invalid pointer ownership (#3781).
 - 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).
+- 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)
 
 v4.5
 ====

OpenSim/Common/Test/testComponentInterface.cpp

@@ -390,7 +390,7 @@ class Bar : public Component {
         // and to access a dv that is not type double.
         // The following calls put the mo and dv into the maps used to contain
         // all mo's and dv's exposed in OpenSim. When Stage::Topology is
-        // realized, they will allocated in class Bar's override of
+        // realized, they will be allocated in class Bar's override of
         // extendRealizeTopology(). See below.
         bool allocate = false;
         int maxFlagValue = 1;
@@ -401,6 +401,8 @@ class Bar : public Component {
     // Manually allocate and update the index and subsystem for
     // a discrete variable and a modeling option as though they were
     // natively allocated in Simbody and brought into OpenSim.
+    // Note, as of May 2024, this is also what one would need to do in order
+    // to add a discrete variable that is a type other than double.
     void extendRealizeTopology(SimTK::State& state) const override {
         Super::extendRealizeTopology(state);
 
@@ -2057,7 +2059,7 @@ TEST_CASE("Component Interface State Trajectories")
     }
 
     // Create a new state trajectory (as though deserializing)
-    // newTraj must be must the expected size before any set calls.
+    // newTraj must be the expected size before any set calls.
     SimTK::Array_<SimTK::State> newTraj;
     for (int i = 0; i < nsteps; ++i) newTraj.emplace_back(s);
     // state variables