fix a bug when testing the tool

1. when getting constant reference from OpenSim make sure to specify (e.g.,
const auto& something = opensim.getSomething())
2. fix bug in print_muscle_attachments setting

Author: Dimitar Stanev

CPP/MuscleForceDirection/MuscleForceDirection.cpp

@@ -75,7 +75,7 @@ MuscleForceDirection::MuscleForceDirection(
 // CLONE CONSTRUCTOR
 Object* MuscleForceDirection::copy() const {
     MuscleForceDirection* object = new MuscleForceDirection(*this);
-    return (object);
+    return object;
 }
 
 //============  OPERATORS  ============
@@ -93,7 +93,7 @@ MuscleForceDirection& MuscleForceDirection::operator=(
     _bodyNames = aMuscleForceDirection._bodyNames;
     _effectInsertion = aMuscleForceDirection._effectInsertion;
 
-    return (*this);
+    return *this;
 }
 
 // setNull()
@@ -130,7 +130,7 @@ void MuscleForceDirection::setupProperties() {
             "directions are desired at the effective muscle attachments.");
     _propertySet.append(&_boolEffectiveInsertionsProp);
 
-    _boolPrintAttachPointProp.setName("print_attachments");
+    _boolPrintAttachPointProp.setName("print_muscle_attachments");
     _boolPrintAttachPointProp.setComment(
             "Flag (true or false)specifying whether a storage file with the "
             "position of the muscle attachments will be printed.");
@@ -197,7 +197,7 @@ void MuscleForceDirection::constructDescriptionAttachments() {
 // constructColumnLabels() for the output results
 void MuscleForceDirection::constructColumnLabels() {
     if (_model == NULL) return;
-    const Set<Muscle> muscleSet = _model->getMuscles();
+    const auto& muscleSet = _model->getMuscles();
 
     // Get the indexes of the muscles attached to the specified bodies.
     _muscleIndices = getMusclesIndexForBody(_model, _bodyNames);
@@ -210,7 +210,7 @@ void MuscleForceDirection::constructColumnLabels() {
     if (!_expressInLocalFrame) {
         // get ground body name
         auto groundbody = _model->getGround();
-        std::string GroundName = groundbody.getName();
+        auto GroundName = groundbody.getName();
 
         // creates labels for muscles in global reference frame
         for (int i = 0; i < _muscleIndices.getSize(); i++) {
@@ -229,7 +229,7 @@ void MuscleForceDirection::constructColumnLabels() {
         for (int i = 0; i < _muscleIndices.getSize(); i++) {
             j = _muscleIndices[i];
 
-            const PathPointSet& pathpointSet =
+            const auto& pathpointSet =
                     muscleSet[j].getGeometryPath().getPathPointSet();
             int SetLast = pathpointSet.getSize() - 1;
 
@@ -300,14 +300,14 @@ void MuscleForceDirection::setModel(Model& aModel) {
 // RECORD: THE CORE OF THE ANALYSIS
 int MuscleForceDirection::record(const SimTK::State& s) {
     // Muscles
-    const BodySet& bodySet = _model->getBodySet();
-    const Set<Muscle>& muscleSet = _model->getMuscles();
+    const auto& bodySet = _model->getBodySet();
+    const auto& muscleSet = _model->getMuscles();
 
     // the analysis to be performed is defined within the for loop.
     for (int i = 0; i < _muscleIndices.getSize(); i++) {
         // Extract the path of selected muscle
-        Muscle& muscle = muscleSet.get(_muscleIndices[i]);
-        const GeometryPath& path = muscle.getGeometryPath();
+        const auto& muscle = muscleSet.get(_muscleIndices[i]);
+        const auto& path = muscle.getGeometryPath();
 
         /* ----------NOTE-------------------------------------------
         GetCurrentPath doesn't work as well as PointForceDirection.
@@ -420,7 +420,7 @@ int MuscleForceDirection::record(const SimTK::State& s) {
         for (int k = 0; k < PFDs.getSize(); k++) { delete PFDs[k]; }
     }
 
-    return (0);
+    return 0;
 }
 
 // BEGIN
@@ -437,7 +437,7 @@ int MuscleForceDirection::begin(SimTK::State& s) {
     int status = 0;
     if (_storeDir.getSize() <= 0) { status = record(s); }
 
-    return (status);
+    return status;
 }
 // STEP
 
@@ -446,7 +446,7 @@ int MuscleForceDirection::step(const SimTK::State& s, int stepNumber) {
 
     record(s);
 
-    return (0);
+    return 0;
 }
 
 // END
@@ -455,7 +455,7 @@ int MuscleForceDirection::end(SimTK::State& s) {
 
     record(s);
 
-    return (0);
+    return 0;
 }
 
 // Print results.
@@ -485,7 +485,7 @@ int MuscleForceDirection::printResults(const string& aBaseName,
                              aDT, aExtension);
     }
 
-    return (0);
+    return 0;
 }
 
 // UTILITIES Utilities implemented by Luca Modenese (check on 15th March 2012).
@@ -495,8 +495,8 @@ int MuscleForceDirection::printResults(const string& aBaseName,
 bool MuscleForceDirection::isMuscleAttachedToBody(const Muscle& aMuscle,
                                                   const string& aBodyName) {
     bool Attached = false;
-    OpenSim::GeometryPath aGeometryPath = aMuscle.getGeometryPath();
-    OpenSim::PathPointSet aPointSet = aGeometryPath.getPathPointSet();
+    const auto& aGeometryPath = aMuscle.getGeometryPath();
+    const auto& aPointSet = aGeometryPath.getPathPointSet();
     int FinalPointIndex = aPointSet.getSize() - 1;
 
     /* ---------NOTE--------------------------------------------
@@ -517,7 +517,7 @@ bool MuscleForceDirection::isMuscleAttachedToBody(const Muscle& aMuscle,
 Array<int> MuscleForceDirection::getMusclesIndexForBody(
         Model* model, const Array<std::string>& bodyNames) {
     // Entire muscleset
-    const Set<Muscle> muscles = model->getMuscles();
+    const auto& muscles = model->getMuscles();
     Array<int> musclesIndexForBody;
 
     // CASE 1: the 'all' flag is considered: all muscles will be analyzed.
@@ -532,10 +532,10 @@ Array<int> MuscleForceDirection::getMusclesIndexForBody(
     else {
         int k = 0, n = 0;
 
-        OpenSim::Array<int> MusclesIndexForBody_temp;
-        // OpenSim::Set<OpenSim::Muscle>  muscles = _model->getMuscles();
+        Array<int> MusclesIndexForBody_temp;
+        // Set<Muscle>  muscles = _model->getMuscles();
         for (int n_body = 0; n_body < bodyNames.getSize(); ++n_body) {
-            std::string aBodyName = bodyNames.get(n_body);
+            auto aBodyName = bodyNames.get(n_body);
 
             /*----------------NOTE----------------------------------------------
             Here an array of indexes MusclesIndexForBody_temp is created
@@ -599,7 +599,7 @@ void MuscleForceDirection::getEffectiveAttachments(
     --------------------------------------------*/
 
     const auto& InitialBody = aPFDs[0]->frame();
-    std::string InitialBodyName = InitialBody.getName();
+    auto InitialBodyName = InitialBody.getName();
     // int effecInsertProx;
     for (int n = 0; n < N_points; n++) {
         const auto& FollowBody = aPFDs[n]->frame();
@@ -615,7 +615,7 @@ void MuscleForceDirection::getEffectiveAttachments(
     is found. The previous point is the effective insertion.
     --------------------------------------------*/
     const auto& FinalBody = aPFDs[N_points - 1]->frame();
-    std::string FinalBodyName = FinalBody.getName();
+    auto FinalBodyName = FinalBody.getName();
     for (int n = N_points - 1; n >= 0; n--) {
         const auto& PreviousBody = aPFDs[n]->frame();
         if (FinalBodyName != PreviousBody.getName()) {
@@ -626,8 +626,8 @@ void MuscleForceDirection::getEffectiveAttachments(
 }
 
 // NormalizeVec3 is an inline function to calculate the norm of a vector Vec3.
-inline void MuscleForceDirection::NormalizeVec3(SimTK::Vec3& v1,
-                                                SimTK::Vec3& rNormv1) {
+void MuscleForceDirection::NormalizeVec3(SimTK::Vec3& v1,
+                                         SimTK::Vec3& rNormv1) {
     double Magnitude =
             sqrt(pow(v1[0], 2.0) + pow(v1[1], 2.0) + pow(v1[2], 2.0));
     rNormv1 = v1 / Magnitude;

CPP/MuscleForceDirection/MuscleForceDirection.h

@@ -19,9 +19,7 @@ namespace OpenSim {
 
 class Model;
 
-class OSIMPLUGIN_API MuscleForceDirection : public Analysis
-
-{
+class OSIMPLUGIN_API MuscleForceDirection : public Analysis {
     OpenSim_DECLARE_CONCRETE_OBJECT(MuscleForceDirection, Analysis);
 
  protected:
@@ -75,9 +73,9 @@ class OSIMPLUGIN_API MuscleForceDirection : public Analysis
     // COPY CONSTRUCTOR
     MuscleForceDirection(const MuscleForceDirection& aObject);
     // DESTRUCTOR
-    virtual ~MuscleForceDirection();
+    ~MuscleForceDirection();
     // CLONE
-    virtual Object* copy() const;
+    Object* copy() const;
 
  private:
     // ZERO DATA AND NULL POINTERS
@@ -94,15 +92,15 @@ class OSIMPLUGIN_API MuscleForceDirection : public Analysis
 #endif
 
     //========================== Required Methods =============================
-    virtual void setModel(Model& aModel);
+    void setModel(Model& aModel) override;
     // INTEGRATION
-    virtual int begin(SimTK::State& s);
-    virtual int step(const SimTK::State& s, int stepNumber);
-    virtual int end(SimTK::State& s);
+    int begin(SimTK::State& s);
+    int step(const SimTK::State& s, int stepNumber) override;
+    int end(SimTK::State& s);
     // IO
-    virtual int printResults(const std::string& aBaseName,
-                             const std::string& aDir = "", double aDT = -1.0,
-                             const std::string& aExtension = ".sto");
+    int printResults(const std::string& aBaseName, const std::string& aDir = "",
+                     double aDT = -1.0,
+                     const std::string& aExtension = ".sto") override;
 
  protected:
     //========================== Internal Methods =============================
@@ -121,8 +119,7 @@ class OSIMPLUGIN_API MuscleForceDirection : public Analysis
     static void
     getEffectiveAttachments(const Array<PointForceDirection*>& aPFDs,
                             int& effecInsertProx, int& effecInsertDist);
-    inline void NormalizeVec3(SimTK::Vec3& v1, SimTK::Vec3& rNormv1);
-
+    void NormalizeVec3(SimTK::Vec3& v1, SimTK::Vec3& rNormv1);
 }; // END of class MuscleForceDirection
 
 };     // namespace OpenSim

CPP/legacy_code/README.md

@@ -1,3 +1,5 @@
 # Overview
-Code originally exported from svn repository set up at https://simtk.org/projects/force_direction.
-It was rearranged for this repository, which is the one currently supported.
+
+Code originally exported from svn repository set up at
+https://simtk.org/projects/force_direction.  It was rearranged for
+this repository, which is the one currently supported.

tests/Arm26/MySetupFile.xml

@@ -1,29 +1,28 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <OpenSimDocument Version="20302">
-	<AnalyzeTool name="ArmFlexion">
-		<model_file> arm26.osim </model_file>
-		<results_directory> . </results_directory>
-		<output_precision> 12 </output_precision>
-		<initial_time>       0.00000000 </initial_time>
-		<final_time>       1.00000000 </final_time>
-		<AnalysisSet name="Analyses">
-			<objects>
-				<MuscleForceDirection name="MuscleForceDirection">
-					<on> true </on>
-					<start_time>     0.00000000 </start_time>
-					<end_time>       1.00000000 </end_time>
-					<step_interval> 1 </step_interval>
-					<in_degrees> true </in_degrees>
-					<local_ref_system> true </local_ref_system>
-					<effec_attachments> false </effec_attachments>
-					<print_muscle_attachments> false </print_muscle_attachments>
-					<body_names> all </body_names>
-				</MuscleForceDirection>
-			</objects>
-			<groups/>
-		</AnalysisSet>
-		<coordinates_file> elbow_flexion.mot </coordinates_file>
-		<lowpass_cutoff_frequency_for_coordinates>     6.0 </lowpass_cutoff_frequency_for_coordinates>
-	</AnalyzeTool>
+  <AnalyzeTool name="ArmFlexion">
+    <model_file> arm26.osim </model_file>
+    <results_directory> . </results_directory>
+    <output_precision> 12 </output_precision>
+    <initial_time>       0.00000000 </initial_time>
+    <final_time>       1.00000000 </final_time>
+    <AnalysisSet name="Analyses">
+      <objects>
+        <MuscleForceDirection name="MuscleForceDirection">
+          <on> true </on>
+          <start_time>     0.00000000 </start_time>
+          <end_time>       1.00000000 </end_time>
+          <step_interval> 1 </step_interval>
+          <in_degrees> true </in_degrees>
+          <local_ref_system> true </local_ref_system>
+          <effec_attachments> false </effec_attachments>
+          <print_muscle_attachments> false </print_muscle_attachments>
+          <body_names> all </body_names>
+        </MuscleForceDirection>
+      </objects>
+      <groups/>
+    </AnalysisSet>
+    <coordinates_file> elbow_flexion.mot </coordinates_file>
+    <lowpass_cutoff_frequency_for_coordinates>     6.0 </lowpass_cutoff_frequency_for_coordinates>
+  </AnalyzeTool>
 </OpenSimDocument>
-