feat: Ammr test upd (#42)

* 2par iteration 2

* add neutral angles

* refactor positions matrices to be pointers and allow users to open in tree.
add warning when npos does not match nstep

* add abduction pos

* refactor studies to avoid lower leg calibration errors

* expand RoM studies for new cal method

* fix wrong conditional logic

* start new test subfolders

* move deltoid test

* move gui template tests

* move thoracic tests

* move abdominal test

* refactor passive flexible test

* refactor kinematic test

* fix missing libdef files

* mock new data structure in TLEM leg model

* lower hip flexion RoM to avoid RecFem penetration

* add main folder to empty test files

* lower hip flexion to avoid recfem penetration in old cal routine

* use local density as other segs

* fix failing loads

* fix path in moved tests

* add strength test

* fix missing file

* fix double include

* update leg cal interface to range of motion data

* add range of motion def to trunk

* add arm range of motion def

* fix conditional logic

* fic conditonals around calibration

* add trunk cal test

* upd existing cal study to run w. felx thorac

* implement 3e mus mdls for spline defined trunk muscles

* add known failures

* change to ignore instead of known-failure

* remove 3e models from ribcage muscles

* adjust test files failing on warnings

* convert pelvis-sacrum and ribcage muscles to simple muscle models

* exclude pelvic floor muscles from calibration

* change to Pm test in each RoM study

* only ignore lower_body tests

* fix missing quotes in .ini file

* fix ignore path relative to test folder

Body/AAUHuman/Arm/ArmData1.1/ArmModelMuscleParameters.any

@@ -63,7 +63,7 @@
  #define _TENDON_LENGTH_DESIGNVAR(x) (x)
  #define _FIBER_LENGTH_DESIGNVAR(x) DesignVar(x)
 #endif
-#if BM_CALIBRATION_TYPE == _CALIBRATION_TYPE_2PAR_
+#if (BM_CALIBRATION_TYPE == _CALIBRATION_TYPE_2PAR_) | (BM_CALIBRATION_TYPE == _EXPERIMENTAL_CALIBRATION_TYPE_2PAR_)
  #define _TENDON_LENGTH_DESIGNVAR(x) (x)
  #define _FIBER_LENGTH_DESIGNVAR(x) (x)
 #endif

Body/AAUHuman/Arm/ShoulderArmModel.root.any

@@ -156,16 +156,24 @@ AnyDoc ArmDoc ={
   #path BM_ARM_DATASET_PATH "../ARM/"+BM_ARM_DATASET
 #endif
 
+AnyFolder Data = {
+  AnyFolder unscaled = {
+    AnyFolder &ModelParameters = ..ModelParameters;
+    AnyFolder STL = {#include "<BM_ARM_DATASET_PATH>/STL/STL.any"};
+    AnyFolder StandardParameters = {
+      #include "..\BodyModels\Include\BodyParameters.any"
+      #include "StandardParameters.any"
+    };
+  };
+  #include "rangeOfMotion.any"
+};
 
 AnyFolder ModelParameters = {
   #include "<BM_ARM_DATASET_PATH>/ArmModelParameters.any"
   #include "<BM_ARM_DATASET_PATH>/ArmModelMuscleParameters.any"
 };
 
-AnyFolder STL = {
-  #include "<BM_ARM_DATASET_PATH>/STL/STL.any"    
-};
-
+AnyFolder &STL = Data.unscaled.STL;
 
 #include "ScapulaContactElipsoid.any"
 AnyFolder MuscleModels = {};

Body/AAUHuman/Arm/rangeOfMotion.any

@@ -0,0 +1,30 @@
+/* Range of Motion definition for the Arm */
+
+AnyFolder RangeOfMotion = {
+  AnyFolder Shoulder = {
+    AnyVar MaxGlenohumeralFlexionAngle = 160;
+    AnyVar MaxGlenohumeralExtensionAngle = -70;
+    AnyVar MaxGlenohumeralAbductionAngle = 178;
+    AnyVar MaxGlenohumeralAdductionAngle = -44;
+    AnyVar MaxGlenohumeralExternalRotationAngle = 89;
+    AnyVar MaxGlenohumeralInternalRotationAngle = 89;
+    AnyVar MaxScapulaClaviculaElevationAngle = 40;
+    AnyVar MaxScapulaClaviculaDepressionAngle = -5;
+    AnyVar MaxScapulaClaviculaProtractionAngle = 15;
+    AnyVar MaxScapulaClaviculaRetractionAngle = -36;
+  };
+
+  AnyFolder Elbow = {
+    AnyVar MaxFlexionAngle = 150;
+    AnyVar MaxExtensionAngle = 0;
+    AnyVar MaxPronationAngle = 90;
+    AnyVar MaxSupinationAngle = -90;
+  };
+
+  AnyFolder Wrist = {
+    AnyVar MaxFlexionAngle = 85;
+    AnyVar MaxExtensionAngle = -70;
+    AnyVar MaxAbductionAngle = 20;
+    AnyVar MaxAdductionAngle = -35;
+  };
+};

Body/AAUHuman/BodyModels/GenericBodyModel/BodyModel.BodyPartsSetup.any

@@ -88,7 +88,7 @@
 //
 // Muscle Calibration related logic
 //
-#if BM_CALIBRATION_TYPE == _CALIBRATION_TYPE_2PAR_ & BM_TRUNK_CERVICAL_RHYTHM == OFF
+#if ((BM_CALIBRATION_TYPE == _CALIBRATION_TYPE_2PAR_) | (BM_CALIBRATION_TYPE == _EXPERIMENTAL_CALIBRATION_TYPE_2PAR_)) & BM_TRUNK_CERVICAL_RHYTHM == OFF
 
   AnyInt bm_cervical_rhythm_notice1= notice(0, strformat("\n"+
       "------------------------------------------------------------------------------------------------------\n"+

Body/AAUHuman/BodyModels/GenericBodyModel/BodyModel.ClassTemplates.any

@@ -0,0 +1,33 @@
+/**
+  Class Template for providing the folder structure of the body model
+*/
+#class_template BodyModelFolderStructure() {
+  AnyFolder Trunk = {
+  };
+  AnyFolder Right = {
+    AnyFolder ShoulderArm = {
+      AnyFolder Shoulder = {};
+      AnyFolder Elbow = {};
+      AnyFolder Wrist = {};
+    };
+    AnyFolder Leg = {
+      AnyFolder Hip = {};
+      AnyFolder Knee = {};
+      AnyFolder Ankle = {};
+      AnyFolder SubTalar = {};
+    };
+  };
+  AnyFolder Left = {
+    AnyFolder ShoulderArm = {
+      AnyFolder Shoulder = {};
+      AnyFolder Elbow = {};
+      AnyFolder Wrist = {};
+    };
+    AnyFolder Leg = {
+      AnyFolder Hip = {};
+      AnyFolder Knee = {};
+      AnyFolder Ankle = {};
+      AnyFolder SubTalar = {};
+    };
+  };
+};

Body/AAUHuman/BodyModels/GenericBodyModel/BodyModel.constants.any

@@ -120,6 +120,8 @@
 
 #define _CALIBRATION_TYPE_2PAR_ 2
 
+#define _EXPERIMENTAL_CALIBRATION_TYPE_2PAR_ 3
+
 #define _CALIBRATION_TYPE_CUSTOM_ 0
 
 #define CONST_MUSCLES_NONE 0

Body/AAUHuman/BodyModels/GenericBodyModel/BodyModel.defaults.preprocess.any

@@ -229,6 +229,22 @@
       "------------------------------------------------------------------------------------------------------------------------ "));
 #endif
 
+
+#ifdef BM_CALIBRATION_TYPE
+#if BM_CALIBRATION_TYPE == _EXPERIMENTAL_CALIBRATION_TYPE_2PAR_
+#ifdef BM_LEG_MODEL
+#if BM_LEG_MODEL == _LEG_MODEL_TLEM1_ 
+   AnyInt not_implemented_calibration_for_TLEM1 = warn(0, strformat("\n"+
+      "------------------------------------------------------------------------------------------------------\n"+
+      "    The Experimental 2-parameter calibration routine (BM_CALIBRATION_TYPE == _EXPERIMENTAL_CALIBRATION_TYPE_2PAR_ \n"+
+      "    is not compatible with The Twente Lower Extremity Model v.1 (TLEM1). \n"+
+      "    Please use the TLEM 2 (which is default or set: #define BM_LEG_MODEL _LEG_MODEL_TLEM2_) \n"+
+      "-------------------------------------------------------------------------------------------------------"));
+#endif
+#endif
+#endif
+#endif
+
 #ifndef ANYBODY_PYTHON_SUPPRESS_NOTICE
 #if ANYBODY_PYTHON_AVAILABLE == 0
   AnyMessage PythonMissing = 

Body/AAUHuman/BodyModels/GenericBodyModel/Calibration/CalibrationStudy.ClassTemplates.any

@@ -0,0 +1,119 @@
+/** 
+  Class template for creating a model that can be used to calibrate the legs 
+*/
+#class_template LegCalibrationModel(Side, BodyModelRef) {
+  AnyComponentDefinition CDef = {};
+
+  #var AnyObjectPtr HipPositions;
+  #var AnyObjectPtr KneePositions;
+  #var AnyObjectPtr AnklePositions;
+  #var AnyObjectPtr SubTalarPositions;
+
+  AnyFolder &Pelvis = BodyModelRef.Trunk.Segments.PelvisSeg;
+  AnyFolder &Sacrum = BodyModelRef.Trunk.Segments.SacrumSeg;
+  AnyFolder &Thorax = BodyModelRef.Trunk.Segments.ThoraxSeg;
+
+  AnySeg &L1 = BodyModelRef.Trunk.Segments.L1Seg;
+  AnySeg &L2 = BodyModelRef.Trunk.Segments.L2Seg;
+  AnySeg &L3 = BodyModelRef.Trunk.Segments.L3Seg;
+  AnySeg &L4 = BodyModelRef.Trunk.Segments.L4Seg;
+  AnySeg &L5 = BodyModelRef.Trunk.Segments.L5Seg;
+
+  AnyFolder &LumbarJoints = BodyModelRef.Trunk.Joints.Lumbar;
+
+  AnyFolder &LegSegments = BodyModelRef.Side.Leg.Seg;
+  AnyFolder &LegJoints = BodyModelRef.Side.Leg.Jnt;
+
+  AnyFolder &Muscles = BodyModelRef.Side.Leg.Mus;
+
+  // Constraints
+  AnyFixedRefFrame ground = {
+    AnyRefNode node = {
+      ARel = ..Pelvis.Axes0;
+      sRel = ..Pelvis.r0;
+    };
+  };
+
+  AnyKinEq ThoraxFix = {
+    AnyKinMeasure& PelvisThoraxExtension = BodyModelRef.Interface.Trunk.PelvisThoraxExtension;
+    AnyKinMeasure& PelvisThoraxLateralBending = BodyModelRef.Interface.Trunk.PelvisThoraxLateralBending;
+    AnyKinMeasure& PelvisThoraxRotation = BodyModelRef.Interface.Trunk.PelvisThoraxRotation;
+  };
+
+  AnyKinEq PelvisFix = {
+    AnyKinLinear Lin = {
+      AnyRefFrame &ground = ..ground.node;
+      AnyRefFrame &Pelvis = ..Pelvis;
+    };
+    AnyKinRotational Rot = {
+      Type = RotAxesAngles;
+      AnyRefFrame &ground = ..ground.node;
+      AnyRefFrame &Pelvis = ..Pelvis;
+    };
+  };
+
+  AnyKinEqInterPolDriver Hip = {
+    AnyKinRotational &Spherical = .BodyModelRef.Interface.Side.HipFlexion.HipMeasure;
+    Type = PiecewiseLinear;
+    T = linspace(0,1,SizesOf(Data)[1]);
+    Data = Obj2Num(.HipPositions)' * pi/180;
+    Reaction.Type = {Off, Off, Off};
+    AnyInt expect_nPos_to_match_nStep = warn(eqfun(NumElemOf(T), ..nStep), strformat("The number of calibration positions (Data) in the: " + NameOf(ObjGetParent(0)) + " driver does not match the number of positions (nStep) in the study."));
+
+  };
+
+  AnyKinEqInterPolDriver Knee = {
+    AnyKinMeasure& Hinge = .BodyModelRef.Interface.Side.KneeFlexion;
+    Type = PiecewiseLinear;
+    T = linspace(0,1,SizesOf(Data)[1]);
+    Data = {Obj2Num(.KneePositions)} * pi/180;
+    Reaction.Type = {Off};
+    AnyInt expect_nPos_to_match_nStep = warn(eqfun(NumElemOf(T), ..nStep), strformat("The number of calibration positions (Data) in the: " + NameOf(ObjGetParent(0)) + " driver does not match the number of positions (nStep) in the study."));
+
+  };
+
+  AnyKinEqInterPolDriver Ankle = {
+    AnyKinMeasure& Hinge = .BodyModelRef.Interface.Side.AnklePlantarFlexion;
+    Type = PiecewiseLinear;
+    T = linspace(0,1,SizesOf(Data)[1]);
+    Data = {Obj2Num(.AnklePositions)} * pi/180;
+    Reaction.Type = {Off};
+    AnyInt expect_nPos_to_match_nStep = warn(eqfun(NumElemOf(T), ..nStep), strformat("The number of calibration positions (Data) in the: " + NameOf(ObjGetParent(0)) + " driver does not match the number of positions (nStep) in the study."));
+
+  };
+
+  AnyKinEqInterPolDriver SubTalar = {
+    AnyKinMeasure& Hinge = .BodyModelRef.Interface.Side.SubTalarEversion;
+    Type = PiecewiseLinear;
+    T = linspace(0,1,SizesOf(Data)[1]);
+    Data = {Obj2Num(.SubTalarPositions)} * pi/180;
+    Reaction.Type = {Off};
+    AnyInt expect_nPos_to_match_nStep = warn(eqfun(NumElemOf(T), ..nStep), strformat("The number of calibration positions (Data) in the: " + NameOf(ObjGetParent(0)) + " driver does not match the number of positions (nStep) in the study."));
+
+  };
+};
+
+
+/**
+  Class template for creating calibrationstudies with same settings
+ */
+#class_template LegCalibrationStudy(
+  __CLASS__ = AnyBodyCalibrationStudy,
+  BodyModelRef,
+  Side,
+) {
+  // Study settings
+  FiberAndTendonLengthAdjustment.CalibrateTendonAtMaxForceOnOff = Off;
+  Kinematics.SmallStepAssumptionOnOff = Off;
+  InitialConditions.SmallStepAssumptionOnOff = Off;
+  Kinematics.PosAnalysisOnlyOnOff = On;
+  InitialConditions.PosAnalysisOnlyOnOff = On;
+
+  LegCalibrationModel ModelRef(Side=Side, BodyModelRef=BodyModelRef) = {
+    HipPositions = .HipPositions;
+    KneePositions = .KneePositions;
+    AnklePositions = .AnklePositions;
+    SubTalarPositions = .SubTalarPositions;
+  };
+};
+

Body/AAUHuman/BodyModels/GenericBodyModel/Calibration/RValues.any

@@ -0,0 +1,12 @@
+/** 
+  Folder containing different R values (ratios of muscle fiber length to optimal fiber
+  length) for different purposes.
+*/
+AnyFolder RValues = { 
+  AnyFloat RMinNoMuscleForce = 0.5;
+  AnyFloat RMinDefault = 0.6;
+
+  AnyFloat RMaxDefault = 1.2; 
+  AnyFloat RMaxActiveStretching = 1.3; 
+  AnyFloat RMaxPassiveForceEqualToFMax = 1.5;
+};