test(reference): Leg Improvements reference branch

.gitignore

@@ -14,9 +14,7 @@ Application/MocapExamples/Rehazenter-adult-walking-model/Output/*
 *_[0-9][0-9][0-9][0-9].png
 *.mp4
 *_Preview.png
-*).anymcr
-*).txt
-
 ffmpeg2pass-*.log
 # pixi environments
 .pixi
+

Application/MocapExamples/Plug-in-gait_Simple/Setup/MarkerProtocol.any

@@ -257,7 +257,7 @@ OptX=OFF , OptY=OFF , OptZ=OFF,
 WeightX=1.0,WeightY=1.0,WeightZ=1.0,
 UseC3DWeightResiduals=ON
 ) = {
-  sRelOpt = {0.0135, 0.02, 0.00};
+  sRelOpt = {0.014, 0.02, 0.00};
 };
 #endif
 
@@ -270,7 +270,7 @@ OptX=OFF, OptY=OFF , OptZ=OFF,
 WeightX=1.0,WeightY=1.0,WeightZ=1.0,
 UseC3DWeightResiduals=ON
 ) = {
-  sRelOpt =  {-0.015, 0.01, 0.0};
+  sRelOpt =  {-0.025, 0.01, -0.0};
 };
 #endif
 
@@ -344,7 +344,7 @@ PlaceMarkerAt = MetatarsalJoint1Node,
 OptX=OFF,OptY=OFF ,OptZ=OFF,
 UseC3DWeightResiduals=ON
 ) = {
-  sRelOpt = {0.0135, 0.02, 0.00};
+  sRelOpt = {0.014, 0.02, 0.00};
 };
 #endif
 
@@ -357,7 +357,7 @@ OptX=OFF, OptY=OFF, OptZ=OFF,
 WeightX=1.0,WeightY=1.0,WeightZ=1.0,
 UseC3DWeightResiduals=ON
 ) = {
-  sRelOpt =  {-0.015, 0.01, 0.0};
+  sRelOpt =  {-0.025, 0.01, 0.0};
 };
 #endif
 

Application/Validation/WilkeSpinalDiscPressure/SpinePressureLyingOnBack/SpinePressureLyingOnBack.main.any

@@ -28,7 +28,7 @@ Main = {
     AnyVar BackRestHeadResRotZPos = 0;    ///< Rotation of the head rest wrt the back rest
     AnyVar GlobalLegRestRotZPos = 90;     ///< Inclination of the leg rest
     AnyVar GlobalBackRestRotZPos = 90;    ///< Back rest inclination
-    AnyVar LegRestFootRestLinYPos = 0.1675; //< Position of the footrest along the leg rest
+    AnyVar LegRestFootRestLinYPos = 0.164; //< Position of the footrest along the leg rest
   }; // DrvPos
 
   /// Driver Velocities - angles are in degrees per second

Body/AAUHuman/LegTLEM/Jnt.any

@@ -6,7 +6,7 @@
 //
 
 #if BM_FOOT_MODEL == _FOOT_MODEL_DEFAULT_
-#if (TLEM_JOINT_TYPE_ANKLE != _JOINT_TYPE_USERDEFINED_)
+#if (BM_JOINT_TYPE_ANKLE_RIGHT != _JOINT_TYPE_USERDEFINED_ & _LEFT_RIGHT_ == "Right") | (BM_JOINT_TYPE_ANKLE_LEFT != _JOINT_TYPE_USERDEFINED_ & _LEFT_RIGHT_ == "Left")
 AnyRevoluteJoint Ankle = {
   Axis = z; //flexion extension
   //Axis2  =  x; //abduction adduction
@@ -20,7 +20,7 @@ AnyRevoluteJoint Ankle = {
 };
 #endif
 
-#if (TLEM_JOINT_TYPE_SUBTALAR != _JOINT_TYPE_USERDEFINED_)
+#if (BM_JOINT_TYPE_SUBTALAR_RIGHT != _JOINT_TYPE_USERDEFINED_ & _LEFT_RIGHT_ == "Right") | (BM_JOINT_TYPE_SUBTALAR_LEFT != _JOINT_TYPE_USERDEFINED_ & _LEFT_RIGHT_ == "Left")
 AnyRevoluteJoint SubTalar = {
   //Axis1 = z; //flexion extension
   Axis =  z; //inversion eversion 
@@ -35,9 +35,7 @@ AnyRevoluteJoint SubTalar = {
 #endif
 #endif
 
-#if (TLEM_JOINT_TYPE_KNEE != _JOINT_TYPE_USERDEFINED_)
-
-
+#if (BM_JOINT_TYPE_KNEE_RIGHT != _JOINT_TYPE_USERDEFINED_ & _LEFT_RIGHT_ == "Right") | (BM_JOINT_TYPE_KNEE_LEFT != _JOINT_TYPE_USERDEFINED_ & _LEFT_RIGHT_ == "Left")
 AnyRevoluteJoint Knee = {
   Axis = z;
   AnyRefNode &ThighNode = ..Seg.Thigh.KneeJoint;
@@ -50,7 +48,7 @@ AnyRevoluteJoint Knee = {
 
 #endif
 
-#if (TLEM_JOINT_TYPE_PATELLOFEMORAL != _JOINT_TYPE_USERDEFINED_)
+#if (BM_JOINT_TYPE_PATELLOFEMORAL_RIGHT != _JOINT_TYPE_USERDEFINED_ & _LEFT_RIGHT_ == "Right") | (BM_JOINT_TYPE_PATELLOFEMORAL_LEFT != _JOINT_TYPE_USERDEFINED_ & _LEFT_RIGHT_ == "Left")
 AnyRevoluteJoint PatellaFemur = {
   Axis = z;
   AnyRefNode &ThighNode = ..Seg.Thigh.PatellaFemurJoint;
@@ -70,7 +68,7 @@ AnyRevoluteJoint PatellaFemur = {
 
 
 
-#if (TLEM_JOINT_TYPE_PATELLATENDON != _JOINT_TYPE_USERDEFINED_)
+#if (BM_JOINT_TYPE_PATELLATENDON_RIGHT != _JOINT_TYPE_USERDEFINED_ & _LEFT_RIGHT_ == "Right") | (BM_JOINT_TYPE_PATELLATENDON_LEFT != _JOINT_TYPE_USERDEFINED_ & _LEFT_RIGHT_ == "Left")
 AnyFolder KinematicMeasures = {
   AnyKinPLine Patella = {
     // These are the nodes that the measure refers to. The connection is regarded
@@ -187,7 +185,7 @@ AnyKinEqSimpleDriver PatellaMovement = {
 //
 #endif
 
-#if (TLEM_JOINT_TYPE_HIP != _JOINT_TYPE_USERDEFINED_)
+#if (BM_JOINT_TYPE_HIP_RIGHT != _JOINT_TYPE_USERDEFINED_ & _LEFT_RIGHT_ == "Right") | (BM_JOINT_TYPE_HIP_LEFT != _JOINT_TYPE_USERDEFINED_ & _LEFT_RIGHT_ == "Left")
 // Defined with the femoral node first so reactions are reported in femur based reference frame.
 AnySphericalJoint Hip = {
   AnyRefNode &ThighNode = ..Seg.Thigh.HipJoint;

Body/AAUHuman/LegTLEM/Leg.root.any

@@ -29,13 +29,11 @@ Please find a description of the model in the seg.any file.
     AnyRevoluteJoint &SubTalar = .Jnt.SubTalar;
     #endif
     #if BM_JOINT_TYPE_KNEE_RIGHT != _JOINT_TYPE_USERDEFINED_
-    AnyKinMeasure &Knee = .Jnt.Knee;
+    AnyRevoluteJoint &Knee = .Jnt.Knee;
     #endif
     AnySphericalJoint &Hip = .Jnt.Hip;
 
   }; 
-
-  #include "JointTypeDefinitions.any"
 
   // Definition of the leg segments
   AnyFolder Seg = {

Body/AAUHuman/LegTLEM/Mus.any

@@ -18,131 +18,89 @@
 
 #if BM_FOOT_MODEL == _FOOT_MODEL_DEFAULT_
 
-
-
-
-
-AnyMuscleShortestPath SoleusMedialis1 = {
+AnyMuscleViaPoint SoleusMedialis1 = {
   AnyMuscleModel &MusMdl = ..MuscleModels.SoleusMedialis1Par;
   AnyRefNode &Org = ..Seg.Shank.SoleusMedialis1Node;
-  AnyRefNode &Via1 = ..Seg.Foot.SoleusMedialis1SuperiorNode;
   AnyRefNode &Ins = ..Seg.Foot.SoleusMedialis1Node;
-  AnySurface &srf1 = ..Seg.Shank.AchillesWrapping1.Cyl; 
-  AnySurface &srf2 = ..Seg.Shank.AchillesWrapping2.Cyl; 
-  SPLine = {
-    StringMesh = 30;
-    AnyMatrix InitWrapPos = {
-      transf3D({1.005*.srf1.Radius, 0, 0.5*.srf1.Length }, &.srf1 ) ,
-      transf3D({-1.005*.srf2.Radius, 0, 0.5*.srf2.Length }, &.srf2 )
-    };
-    InitWrapPosVecArr = {&InitWrapPos, None};
-  };
-  viewMuscle = {#include "../drawSettings/MusDrawSettings.any"};
+  viewMuscle = {#include "../DrawSettings/MusDrawSettings.any"};
 };
 
-AnyMuscleShortestPath SoleusMedialis2 = {
+AnyMuscleViaPoint SoleusMedialis2 = {
   AnyMuscleModel &MusMdl = ..MuscleModels.SoleusMedialis2Par;
   AnyRefNode &Org = ..Seg.Shank.SoleusMedialis2Node;
-  AnyRefNode &Via1 = ..Seg.Foot.SoleusMedialis2SuperiorNode;
   AnyRefNode &Ins = ..Seg.Foot.SoleusMedialis2Node;
-  AnySurface &srf1 = ..Seg.Shank.AchillesWrapping1.Cyl; 
-  AnySurface &srf2 = ..Seg.Shank.AchillesWrapping2.Cyl; 
-  SPLine.StringMesh = 30;
-  SPLine.InitWrapPosVecArr = .SoleusMedialis1.SPLine.InitWrapPosVecArr;
-  viewMuscle = {#include "../drawSettings/MusDrawSettings.any"};
+  viewMuscle = {#include "../DrawSettings/MusDrawSettings.any"};
 };
 
-AnyMuscleShortestPath SoleusMedialis3 = {
+AnyMuscleViaPoint SoleusMedialis3 = {
   AnyMuscleModel &MusMdl = ..MuscleModels.SoleusMedialis3Par;
   AnyRefNode &Org = ..Seg.Shank.SoleusMedialis3Node;
-  AnyRefNode &Via1 = ..Seg.Foot.SoleusMedialis3SuperiorNode;
   AnyRefNode &Ins = ..Seg.Foot.SoleusMedialis3Node;
-  AnySurface &srf1 = ..Seg.Shank.AchillesWrapping1.Cyl; 
-  AnySurface &srf2 = ..Seg.Shank.AchillesWrapping2.Cyl; 
-  SPLine.StringMesh = 30;
-  SPLine.InitWrapPosVecArr = .SoleusMedialis1.SPLine.InitWrapPosVecArr;
-  viewMuscle = {#include "../drawSettings/MusDrawSettings.any"};
+  viewMuscle = {#include "../DrawSettings/MusDrawSettings.any"};
 };
 
-AnyMuscleShortestPath SoleusLateralis1 = {
+AnyMuscleViaPoint SoleusLateralis1 = {
   AnyMuscleModel &MusMdl = ..MuscleModels.SoleusLateralis1Par;
   AnyRefNode &Org = ..Seg.Shank.SoleusLateralis1Node;
-  AnyRefNode &Via1 = ..Seg.Foot.SoleusLateralis1SuperiorNode;
   AnyRefNode &Ins = ..Seg.Foot.SoleusLateralis1Node;
-  AnySurface &srf1 = ..Seg.Shank.AchillesWrapping1.Cyl; 
-  AnySurface &srf2 = ..Seg.Shank.AchillesWrapping2.Cyl; 
-  SPLine.StringMesh = 30;
-  SPLine.InitWrapPosVecArr = .SoleusMedialis1.SPLine.InitWrapPosVecArr;
-  viewMuscle = {#include "../drawSettings/MusDrawSettings.any"};
+  viewMuscle = {#include "../DrawSettings/MusDrawSettings.any"};
 };
 
-AnyMuscleShortestPath SoleusLateralis2 = {
+AnyMuscleViaPoint SoleusLateralis2 = {
   AnyMuscleModel &MusMdl = ..MuscleModels.SoleusLateralis2Par;
   AnyRefNode &Org = ..Seg.Shank.SoleusLateralis2Node;
-  AnyRefNode &Via1 = ..Seg.Foot.SoleusLateralis2SuperiorNode;
   AnyRefNode &Ins = ..Seg.Foot.SoleusLateralis2Node;
-  AnySurface &srf1 = ..Seg.Shank.AchillesWrapping1.Cyl; 
-  AnySurface &srf2 = ..Seg.Shank.AchillesWrapping2.Cyl; 
-  SPLine.StringMesh = 30;
-  SPLine.InitWrapPosVecArr = .SoleusMedialis1.SPLine.InitWrapPosVecArr;
-  viewMuscle = {#include "../drawSettings/MusDrawSettings.any"};
+  viewMuscle = {#include "../DrawSettings/MusDrawSettings.any"};
 };
 
-AnyMuscleShortestPath SoleusLateralis3 = {
+AnyMuscleViaPoint SoleusLateralis3 = {
   AnyMuscleModel &MusMdl = ..MuscleModels.SoleusLateralis3Par;
   AnyRefNode &Org = ..Seg.Shank.SoleusLateralis3Node;
-  AnyRefNode &Via1 = ..Seg.Foot.SoleusLateralis3SuperiorNode;  
   AnyRefNode &Ins = ..Seg.Foot.SoleusLateralis3Node;
-  AnySurface &srf1 = ..Seg.Shank.AchillesWrapping1.Cyl; 
-  AnySurface &srf2 = ..Seg.Shank.AchillesWrapping2.Cyl; 
-  SPLine.StringMesh = 30;
-  SPLine.InitWrapPosVecArr = .SoleusMedialis1.SPLine.InitWrapPosVecArr;
-  viewMuscle = {#include "../drawSettings/MusDrawSettings.any"};
+  viewMuscle = {#include "../DrawSettings/MusDrawSettings.any"};
 };
 
 
-
 AnyMuscleShortestPath GastrocnemiusLateralis1 = {
   AnyMuscleModel &MusMdl = ..MuscleModels.GastrocnemiusLateralis1Par;
   AnyRefNode &Org = ..Seg.Thigh.GastrocnemiusLateralis1Node;
   AnySurface &srf = ..Seg.Thigh.GastroWrapSurf.cyl; 
-  AnySurface &srf1 = ..Seg.Shank.AchillesWrapping1.Cyl; 
-  AnySurface &srf2 = ..Seg.Shank.AchillesWrapping2.Cyl; 
+  //  AnyRefNode &Via1 = ..Seg.Thigh.GastrocnemiusLateralis1ViaNode;
+  //  AnyRefNode &Via2 = ..Seg.Thigh.GastrocnemiusLateralis2ViaNode;
+  //  AnyRefNode &Via3 = ..Seg.Thigh.GastrocnemiusLateralis3ViaNode;
+  //  AnyRefNode &Via4 = ..Seg.Thigh.GastrocnemiusLateralis4ViaNode;
+  //  AnyRefNode &Via5 = ..Seg.Thigh.GastrocnemiusLateralis5ViaNode;
+  //  AnyRefNode &Via6 = ..Seg.Thigh.GastrocnemiusLateralis6ViaNode;
   AnyRefNode &Via7 = ..Seg.Shank.GastrocnemiusLateralis7ViaNode;
   AnyRefNode &Via8 = ..Seg.Shank.GastrocnemiusLateralis8ViaNode;
   AnyRefNode &Via9 = ..Seg.Shank.GastrocnemiusLateralis9ViaNode;
-  AnyRefNode &Via10 =..Seg.Foot.GastrocnemiusLateralis1SuperiorNode;
+  AnyRefNode &Via10 = ..Seg.Shank.GastrocnemiusLateralis10ViaNode;
   AnyRefNode &Ins = ..Seg.Foot.GastrocnemiusLateralis1Node;
   SPLine = {
     StringMesh = 30;
     AnyMatrix InitWrapPos1 = {
       transf3D({1.1*.srf.Radius, ...Sign*1.1*.srf.Radius, 0.5*.srf.Length }, &.srf ) ,
     };
-    AnyMatrix InitWrapPos2 = {
-      transf3D({1.005*.srf1.Radius, 0, 0.5*.srf1.Length }, &.srf1 ) ,
-      transf3D({-1.005*.srf2.Radius, 0, 0.5*.srf2.Length }, &.srf2 )
-    };
-
-    InitWrapPosVecArr = {&InitWrapPos1,None,None,&InitWrapPos2, None};
+    InitWrapPosVecArr = {&InitWrapPos1,None,None, None, None};
   };
-  viewMuscle = {#include "../DrawSettings/MusDrawSettings.any"};
 };
 
 AnyMuscleShortestPath GastrocnemiusMedialis1 = {
   AnyMuscleModel &MusMdl = ..MuscleModels.GastrocnemiusMedialis1Par;
   AnyRefNode &Org = ..Seg.Thigh.GastrocnemiusMedialis1Node;
   AnyRefNode &Via1 = ..Seg.Thigh.GastrocnemiusMedialis1ViaNode;
   AnySurface &srf = ..Seg.Thigh.GastroWrapSurf.cyl; 
-  AnySurface &srf1 = ..Seg.Shank.AchillesWrapping1.Cyl; 
-  AnySurface &srf2 = ..Seg.Shank.AchillesWrapping2.Cyl; 
+  //  AnyRefNode &Via2 = ..Seg.Thigh.GastrocnemiusMedialis2ViaNode;
+  //  AnyRefNode &Via3 = ..Seg.Thigh.GastrocnemiusMedialis3ViaNode;
   AnyRefNode &Via4 = ..Seg.Shank.GastrocnemiusMedialis4ViaNode;
   AnyRefNode &Via5 = ..Seg.Shank.GastrocnemiusMedialis5ViaNode;
   AnyRefNode &Via6 = ..Seg.Shank.GastrocnemiusMedialis6ViaNode;
   AnyRefNode &Via7 = ..Seg.Shank.GastrocnemiusMedialis7ViaNode;
-  AnyRefNode &Via8 =..Seg.Foot.GastrocnemiusMedialis1SuperiorNode;
+  AnyRefNode &Via8 = ..Seg.Shank.GastrocnemiusMedialis8ViaNode;
+  AnyRefNode &Via9 = ..Seg.Shank.GastrocnemiusMedialis9ViaNode;
   AnyRefNode &Ins = ..Seg.Foot.GastrocnemiusMedialis1Node;
   SPLine.StringMesh = 30;
-  SPLine.InitWrapPosVecArr = {None, &.GastrocnemiusLateralis1.SPLine.InitWrapPos1,None, None, None, &.GastrocnemiusLateralis1.SPLine.InitWrapPos2, None};
+  SPLine.InitWrapPosVecArr = {None, &.GastrocnemiusLateralis1.SPLine.InitWrapPos1,None, None, None, None, None, None};
   viewMuscle = {#include "../DrawSettings/MusDrawSettings.any"};
 };  
 
@@ -1840,20 +1798,15 @@ AnyMuscleShortestPath Plantaris1 = {
   AnyMuscleModel &MusMdl = ..MuscleModels.Plantaris1Par;
   AnyRefNode &Org = ..Seg.Thigh.Plantaris1Node;
   AnySurface &srf = ..Seg.Thigh.GastroWrapSurf.cyl; 
-  AnySurface &srf1 = ..Seg.Shank.AchillesWrapping1.Cyl; 
-  AnySurface &srf2 = ..Seg.Shank.AchillesWrapping2.Cyl;   
-  AnyRefNode &Via1 =..Seg.Foot.Plantaris1SuperiorNode;
-  AnyRefNode &Ins = ..Seg.Foot.Plantaris1Node;
-  SPLine = {
-    StringMesh = 30;
+  SPLine = {  
     AnyMatrix InitWrapPos = {
       transf3D({1.1*.srf.Radius, ...Sign*1.1*.srf.Radius, 0.5*.srf.Length }, &.srf ) ,
-      transf3D({1.005*.srf1.Radius, 0, 0.5*.srf1.Length }, &.srf1 ) ,
-      transf3D({-1.005*.srf2.Radius, 0, 0.5*.srf2.Length }, &.srf2 )
     };
-    InitWrapPosVecArr = {&InitWrapPos, None};
+    StringMesh = 90;
+    InitWrapPosVecArr = {&InitWrapPos};
   };
-  viewMuscle = {#include "../drawSettings/MusDrawSettings.any"};
+  AnyRefNode &Ins = ..Seg.Foot.Plantaris1Node;
+  AnyDrawMuscle DrwMus = {#include "../DrawSettings/MusDrawSettings.any"};
 };
 #endif