Merge branch 'main' into feature_abspath-in-component-exceptions

opensim-org · Jan 21, 2025 · f30869c · f30869c
2 parents 068f242 + b4ba7ca
commit f30869c
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diff --git a/Applications/Analyze/test/CMakeLists.txt b/Applications/Analyze/test/CMakeLists.txt
@@ -1,11 +1,13 @@
+find_package(Catch2 REQUIRED
+        HINTS "${OPENSIM_DEPENDENCIES_DIR}/catch2")
 
 file(GLOB TEST_PROGS "test*.cpp")
 file(GLOB TEST_FILES *.osim *.xml *.sto *.mot)
 
 OpenSimAddTests(
     TESTPROGRAMS ${TEST_PROGS}
     DATAFILES ${TEST_FILES}
-    LINKLIBS osimTools
+    LINKLIBS osimTools Catch2::Catch2WithMain
     )
 
 if(BUILD_TESTING)

diff --git a/Applications/Analyze/test/testPointKinematics.cpp b/Applications/Analyze/test/testPointKinematics.cpp
@@ -0,0 +1,165 @@
+/* -------------------------------------------------------------------------- *
+ *                       OpenSim:  testPointKinematics.cpp                    *
+ * -------------------------------------------------------------------------- *
+ * The OpenSim API is a toolkit for musculoskeletal modeling and simulation.  *
+ * See http://opensim.stanford.edu and the NOTICE file for more information.  *
+ * OpenSim is developed at Stanford University and supported by the US        *
+ * National Institutes of Health (U54 GM072970, R24 HD065690) and by DARPA    *
+ * through the Warrior Web program.                                           *
+ *                                                                            *
+ * Copyright (c) 2005-2024 Stanford University and the Authors                *
+ * Author(s): Alexander Beattie                                               *
+ *                                                                            *
+ * Licensed under the Apache License, Version 2.0 (the "License"); you may    *
+ * not use this file except in compliance with the License. You may obtain a  *
+ * copy of the License at http://www.apache.org/licenses/LICENSE-2.0.         *
+ *                                                                            *
+ * Unless required by applicable law or agreed to in writing, software        *
+ * distributed under the License is distributed on an "AS IS" BASIS,          *
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.   *
+ * See the License for the specific language governing permissions and        *
+ * limitations under the License.                                             *
+ * -------------------------------------------------------------------------- */
+
+// INCLUDE
+#include <limits>
+#include <iterator> // std::next
+
+#include <OpenSim/Analyses/PointKinematics.h>
+#include <OpenSim/Simulation/Model/Model.h>
+#include <OpenSim/Tools/AnalyzeTool.h>
+
+#include <catch2/catch_all.hpp>
+
+using namespace OpenSim;
+
+constexpr double tol = std::numeric_limits<double>::epsilon() * 10;
+
+TEST_CASE("PointKinematics Construction with Blank Model", "[PointKinematics]") {
+    Model model;
+    PointKinematics pk(&model);
+
+    REQUIRE(pk.getBody() == nullptr);
+    REQUIRE(pk.getRelativeToBody() == nullptr);
+    REQUIRE(pk.getPointName() == "NONAME");
+}
+
+TEST_CASE("PointKinematics Construction with No Model", "[PointKinematics]") {
+    PointKinematics pk;
+
+    REQUIRE(pk.getBody() == nullptr);
+    REQUIRE(pk.getRelativeToBody() == nullptr);
+    REQUIRE(pk.getPointName() == "NONAME");
+}
+
+TEST_CASE("PointKinematics Set and Get Body", "[PointKinematics]") {
+    Model model("SinglePin.osim");
+    const auto &bodies = model.getComponentList<Body>();
+    const auto bodyIt = bodies.begin();
+    const auto body = *bodyIt;
+
+    PointKinematics pk(&model);
+    pk.setBody(&body);
+
+    REQUIRE(pk.getBody() == &body);
+    REQUIRE(pk.getBody()->getName() == body.getName());
+}
+
+TEST_CASE("PointKinematics Set and Get RelativeToBody", "[PointKinematics]") {
+    Model model("subject01.osim");
+    const auto &bodies = model.getComponentList<Body>();
+    // Gets the 2nd body (which is at index 1)
+    const auto bodyIt = std::next(bodies.begin(),1);
+    const auto body = *bodyIt;
+
+    PointKinematics pk(&model);
+    pk.setRelativeToBody(&body);
+
+    REQUIRE(pk.getRelativeToBody() == &body);
+    REQUIRE(pk.getRelativeToBody()->getName() == body.getName());
+}
+
+TEST_CASE("PointKinematics Set and Get Point", "[PointKinematics]") {
+    Model model;
+    PointKinematics pk(&model);
+    SimTK::Vec3 point(1.0, 2.0, 3.0);
+
+    pk.setPoint(point);
+    SimTK::Vec3 retrievedPoint;
+    pk.getPoint(retrievedPoint);
+
+    REQUIRE_THAT(retrievedPoint[0], Catch::Matchers::WithinAbs(1.0,tol));
+    REQUIRE_THAT(retrievedPoint[1], Catch::Matchers::WithinAbs(2.0,tol));
+    REQUIRE_THAT(retrievedPoint[2], Catch::Matchers::WithinAbs(3.0,tol));
+}
+
+TEST_CASE("PointKinematics Record Kinematics Single Body", "[PointKinematics]") {
+    std::string model_name = "subject01.osim";
+    std::string coordinates_file_name = "subject01_walk1_ik.mot";
+
+    Model model(model_name);
+    model.initSystem();
+
+    AnalyzeTool analyzeTool;
+    analyzeTool.setName("test_analysis");
+    analyzeTool.setModel(model);
+    analyzeTool.setModelFilename(model_name);
+    analyzeTool.setCoordinatesFileName(coordinates_file_name);
+    analyzeTool.setLowpassCutoffFrequency(-1);
+    analyzeTool.setResultsDir("results");
+
+    const auto &bodies = model.getComponentList<Body>();
+    const auto bodyIt = bodies.begin();
+    const auto body1 = *bodyIt;
+    // Gets the 2nd body (which is at index 1)
+    const auto bodyIt2 = std::next(bodies.begin(),1);
+    const auto body2 = *bodyIt2;
+
+    PointKinematics pk(&model);
+    pk.setBody(&body1);
+    pk.setRelativeToBody(&body2);
+    pk.setPoint(SimTK::Vec3(1.0, 2.0, 3.0));
+    analyzeTool.updAnalysisSet().cloneAndAppend(pk);
+
+    std::string output_file_name = "test_analysis_point_kinematics_1.xml";
+    analyzeTool.print(output_file_name);
+    AnalyzeTool roundTrip(output_file_name);
+    roundTrip.run();
+}
+
+TEST_CASE("PointKinematics Record Kinematics Whole Body", "[PointKinematics]") {
+    std::string model_name = "subject01.osim";
+    std::string coordinates_file_name = "subject01_walk1_ik.mot";
+
+    Model model(model_name);
+    model.initSystem();
+
+    AnalyzeTool analyzeTool;
+    analyzeTool.setName("test_analysis");
+    analyzeTool.setModel(model);
+    analyzeTool.setModelFilename(model_name);
+    analyzeTool.setCoordinatesFileName(coordinates_file_name);
+    analyzeTool.setLowpassCutoffFrequency(-1);
+    analyzeTool.setResultsDir("results");
+
+    const auto &bodies = model.getComponentList<Body>();
+    for (auto& root : bodies) {
+        const std::string& root_name = root.getName();
+        for (auto& sub_component: bodies) {
+            const std::string& sub_component_name = sub_component.getName();
+            // Create point kinematics reporter
+            PointKinematics pointKin;
+            pointKin.setPointName(root_name + "-" + sub_component_name);
+            pointKin.setPoint(SimTK::Vec3(1.0, 2.0, 3.0));
+            pointKin.setBody(&root);
+            pointKin.setRelativeToBody(&sub_component);
+            analyzeTool.updAnalysisSet().cloneAndAppend(pointKin);
+        }
+    }
+
+    std::string output_file_name = "test_analysis_point_kinematics_2.xml";
+    analyzeTool.print(output_file_name);
+    AnalyzeTool roundTrip(output_file_name);
+    roundTrip.run();
+}
+
diff --git a/Bindings/CMakeLists.txt b/Bindings/CMakeLists.txt
@@ -1,5 +1,5 @@
 if(BUILD_PYTHON_WRAPPING OR BUILD_JAVA_WRAPPING)
-    find_package(SWIG 4.1.1 EXACT REQUIRED)
+    find_package(SWIG 4.1.1 REQUIRED)
 endif()
 
 # Flags are both Python and Java bindings will use.

diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -53,6 +53,7 @@ v4.6
   in the intersection of names in the model and names in the provided referece/data. Remove methods that are index based from public interface.(#3951) 
 - Replace usages of `OpenSim::make_unique` with `std::make_unique` and remove wrapper function now that C++14 is used in OpenSim (#3979). 
 - Add utility method `createVectorLinspaceInterval` for the `std::vector` type and add unit tests. Utilize the new utility method to fix a bug (#3976) in creating the uniformly sampled time interval from the experimental data sampling frequency in `APDMDataReader` and `XsensDataReader` (#3977).
+- Fix Point Kinematics Reporter variable and initialization error and add unit tests (#3966)
 - The message associated with `OpenSim::PropertyException` now includes the full absolute path to the component that threw the exception (#3987).
 
 

diff --git a/OpenSim/Analyses/PointKinematics.cpp b/OpenSim/Analyses/PointKinematics.cpp
@@ -368,15 +368,15 @@ void PointKinematics::setRelativeToBody(const PhysicalFrame* aBody)
     // CHECK
     if (aBody==NULL) {
         log_warn("PointKinematics.setRelativeToBody: null body pointer.");
-        _body = NULL;
+        _relativeToBody = NULL;
         return;
     }
 
     // SET
     _relativeToBody = aBody;
     _relativeToBodyName = aBody->getName();
     log_info("PointKinematics.setRelativeToBody: set relative-to body to {}.",
-            _bodyName);
+            _relativeToBodyName);
 }
 
 //_____________________________________________________________________________

diff --git a/OpenSim/Common/DelimFileAdapter.h b/OpenSim/Common/DelimFileAdapter.h
@@ -307,6 +307,7 @@ DelimFileAdapter<T>::clone() const {
 template<typename T>
 typename DelimFileAdapter<T>::OutputTables
 DelimFileAdapter<T>::extendRead(const std::string& fileName) const {
+#ifndef SWIG
     OPENSIM_THROW_IF(fileName.empty(),
                      EmptyFileName);
 
@@ -468,6 +469,7 @@ DelimFileAdapter<T>::extendRead(const std::string& fileName) const {
     output_tables.emplace(tableString(), table);
 
     return output_tables;
+#endif
 }
 
 template<typename T>

diff --git a/OpenSim/Moco/MocoUtilities.h b/OpenSim/Moco/MocoUtilities.h
@@ -117,7 +117,7 @@ OSIMMOCO_API void prescribeControlsToModel(const MocoTrajectory& trajectory,
 OSIMMOCO_API MocoTrajectory simulateTrajectoryWithTimeStepping(
         const MocoTrajectory& trajectory, Model model,
         double integratorAccuracy = SimTK::NaN);
-
+#ifndef SWIG
 /// Convert a trajectory covering half the period of a symmetric motion into a
 /// trajectory over the full period. This is useful for simulations of half a
 /// gait cycle.
@@ -171,12 +171,23 @@ OSIMMOCO_API MocoTrajectory createPeriodicTrajectory(
                                             ".*lumbar_bending(?!/value).*",
                                             ".*lumbar_rotation.*"},
         std::vector<std::string> negateAndShiftPatterns = {
-                                                   ".*pelvis_list/value",
-                                                   ".*pelvis_tz/value",
-                                                   ".*lumbar_bending/value"},
+                                            ".*pelvis_list/value",
+                                            ".*pelvis_tz/value",
+                                            ".*lumbar_bending/value"},
         std::vector<std::pair<std::string, std::string>> symmetryPatterns =
                 {{R"(_r(\/|_|$))", "_l$1"}, {R"(_l(\/|_|$))", "_r$1"}});
-
+#else 
+// Variant that doesn't take symmetryPatterns which are unusable from scripting
+OSIMMOCO_API MocoTrajectory createPeriodicTrajectory(
+        const MocoTrajectory& halfPeriodTrajectory,
+        std::vector<std::string> addPatterns = {".*pelvis_tx/value"},
+        std::vector<std::string> negatePatterns = {".*pelvis_list(?!/value).*",
+                ".*pelvis_rotation.*", ".*pelvis_tz(?!/value).*",
+                ".*lumbar_bending(?!/value).*", ".*lumbar_rotation.*"},
+        std::vector<std::string> negateAndShiftPatterns = {
+                ".*pelvis_list/value", ".*pelvis_tz/value",
+                ".*lumbar_bending/value"});
+#endif
 /// This obtains the value of the OPENSIM_MOCO_PARALLEL environment variable.
 /// The value has the following meanings:
 /// - 0: run in series (not parallel).