feat: New 2par calibration interface

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/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 +1,27 @@
+/**
+  Class Template for providing the folder structure of the body model
+*/
+#class_template BodyModelFolderStructure() {
+  AnyFolder Trunk = {
+    AnyFolder Right = {};
+    AnyFolder Left = {};
+  };
+  AnyFolder Right = {
+    AnyFolder ShoulderArm = {};
+    AnyFolder Leg = {
+      AnyFolder Hip = {};
+      AnyFolder Knee = {};
+      AnyFolder Ankle = {};
+      AnyFolder SubTalar = {};
+    };
+  };
+  AnyFolder Left = {
+    AnyFolder ShoulderArm = {};
+    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;
+};

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

@@ -0,0 +1,90 @@
+/** 
+  Folder containing the range of motion for the joints in the body model. The folder
+  also contains Predefined Positions for each joint. Can be used by calibration
+  studies. Hip positions are {Flexion/Extension, Abduction/Adduction,
+  Internal/External Rotation} angles Knee positions are {Flexion/Extension} angles
+  Ankle positions are {Plantar/Dorsi flexion, Inversion/Eversion} angles
+*/
+BodyModelFolderStructure RangeOfMotion() = {
+  Right.Leg.Hip = {
+    // TODO: bke - TBC DO we want more levels for the degree of freedom?
+    // Hip.ExternalRotation = {AnyFloat Min, AnyFloat Max}; ??
+    AnyVar MaxExternalRotationAngle ??= 30;
+    AnyVar MaxInternalRotationAngle ??= -30;
+    AnyVar MaxAdductionAngle ??= -15;
+    AnyVar MaxAdductionInExtensionAngle ??= -10;
+    AnyVar MaxAbductionAngle ??= 40;
+    AnyVar MaxFlexionAngle ??= 120;
+    AnyVar MaxExtensionAngle ??= -20;
+    AnyVar MaxExtensionInAdductionAngle ??= -10;
+    AnyVar MaxFlexionInAbductionAngle ??= 90;
+    AnyVar MinFlexionInAdduction ??= 5;  
+
+    // Hip positions
+    AnyFloat Neutral ??= { 0, 0, 0 }; 
+    AnyFloat InternallyRotated ??= { 0, 0, MaxInternalRotationAngle };
+    AnyFloat ExternallyRotated ??= { 0, 0, MaxExternalRotationAngle };
+    AnyFloat Adduction ??= { MinFlexionInAdduction,  MaxAdductionAngle, 0};
+    AnyFloat Abduction ??= { 0,  MaxAbductionAngle, 0};
+    AnyFloat Flexed ??= { MaxFlexionAngle,  0, 0};
+    AnyFloat FlexedAndAdducted ??= { MaxFlexionAngle,  MaxAdductionAngle, 0};
+    AnyFloat FlexedAndAbducted ??= { MaxFlexionInAbductionAngle,  MaxAbductionAngle, 0};
+    AnyFloat Extended ??= { MaxExtensionAngle,  0, 0};
+    AnyFloat ExtendedAndAdducted ??= { MaxExtensionInAdductionAngle,  MaxAdductionInExtensionAngle, 0};
+    AnyFloat AbductedAndExternallyRotated ??= {0,  MaxAbductionAngle,  MaxExternalRotationAngle};
+  };
+
+  Right.Leg.Knee = {
+    AnyVar Neutral ??= 0;
+    AnyVar MaxFlexionAngle ??= 130;
+    AnyVar MaxExtensionAngle ??= -3;
+  };
+
+  Right.Leg.Ankle = {
+    AnyVar Neutral ??= 0;
+    AnyVar MaxPlantarFlexionAngle ??= 45;
+    AnyVar MaxDorsiFlexionAngle ??= -20;
+    AnyVar MaxInversionAngle ??= 15;
+    AnyVar MaxEversionAngle ??= -20;
+  };
+
+  // Left side is by default a mirror of the right side
+  Left.Leg.Hip = {
+    AnyVar MaxExternalRotationAngle ??= ...Right.Leg.Hip.MaxExternalRotationAngle;
+    AnyVar MaxInternalRotationAngle ??= ...Right.Leg.Hip.MaxInternalRotationAngle;
+    AnyVar MaxAdductionAngle ??= ...Right.Leg.Hip.MaxAdductionAngle;
+    AnyVar MaxAdductionInExtensionAngle ??= ...Right.Leg.Hip.MaxAdductionInExtensionAngle;
+    AnyVar MaxAbductionAngle ??= ...Right.Leg.Hip.MaxAbductionAngle;
+    AnyVar MaxFlexionAngle ??= ...Right.Leg.Hip.MaxFlexionAngle;
+    AnyVar MaxExtensionAngle ??= ...Right.Leg.Hip.MaxExtensionAngle;
+    AnyVar MaxExtensionInAdductionAngle ??= ...Right.Leg.Hip.MaxExtensionInAdductionAngle;
+    AnyVar MaxFlexionInAbductionAngle ??= ...Right.Leg.Hip.MaxFlexionInAbductionAngle;
+    AnyVar MinFlexionInAdduction ??= ...Right.Leg.Hip.MinFlexionInAdduction;
+
+    // Hip positions
+    AnyFloat Neutral ??= ...Right.Leg.Hip.Neutral;
+    AnyFloat InternallyRotated ??= ...Right.Leg.Hip.InternallyRotated;
+    AnyFloat ExternallyRotated ??= ...Right.Leg.Hip.ExternallyRotated;
+    AnyFloat Adduction ??= ...Right.Leg.Hip.Adduction;
+    AnyFloat Flexed ??= ...Right.Leg.Hip.Flexed;
+    AnyFloat FlexedAndAdducted ??= ...Right.Leg.Hip.FlexedAndAdducted;
+    AnyFloat FlexedAndAbducted ??= ...Right.Leg.Hip.FlexedAndAbducted;
+    AnyFloat Extended ??= ...Right.Leg.Hip.Extended;
+    AnyFloat ExtendedAndAdducted ??= ...Right.Leg.Hip.ExtendedAndAdducted;
+    AnyFloat AbductedAndExternallyRotated ??= ...Right.Leg.Hip.AbductedAndExternallyRotated;
+};
+
+  Left.Leg.Knee = {
+    AnyVar Neutral ??= ...Right.Leg.Knee.Neutral;
+    AnyVar MaxFlexionAngle ??= ...Right.Leg.Knee.MaxFlexionAngle;
+    AnyVar MaxExtensionAngle ??= ...Right.Leg.Knee.MaxExtensionAngle;
+  };
+
+  Left.Leg.Ankle = {
+    AnyVar Neutral ??= ...Right.Leg.Ankle.Neutral;
+    AnyVar MaxPlantarFlexionAngle ??= ...Right.Leg.Ankle.MaxPlantarFlexionAngle;
+    AnyVar MaxDorsiFlexionAngle ??= ...Right.Leg.Ankle.MaxDorsiFlexionAngle;
+    AnyVar MaxInversionAngle ??= ...Right.Leg.Ankle.MaxInversionAngle;
+    AnyVar MaxEversionAngle ??= ...Right.Leg.Ankle.MaxEversionAngle;
+  };
+};

Body/AAUHuman/BodyModels/GenericBodyModel/CalibrationSequence.any

@@ -1,10 +1,22 @@
 
-//This file controls which calibrations to be made on the model 
+//This file controls which calibrations to be made on the model
+#include "Calibration/CalibrationStudy.ClassTemplates.any"
+#include "BodyModel.ClassTemplates.any"
+
 AnyFolder Calibration={  
   AnyComponentDefinition obj = {};
   #if BM_CALIBRATION_TYPE == _CALIBRATION_TYPE_2PAR_
-  AnyFloat RMin = DesignVar(0.5); ///< Muscle fiber length's ratio to the optimal fiber length at the lower extreme for the given range of motion.
-  AnyFloat RMax = DesignVar(1.0); ///< Muscle fiber length's ratio to the optimal fiber length at the upper extreme for the given range of motion. 
+    AnyFloat RMin = DesignVar(0.5); ///< Muscle fiber length's ratio to the optimal fiber length at the lower extreme for the given range of motion.
+    AnyFloat RMax = DesignVar(1.0); ///< Muscle fiber length's ratio to the optimal fiber length at the upper extreme for the given range of motion. 
+  #endif
+
+  #if BM_CALIBRATION_TYPE ==_EXPERIMENTAL_CALIBRATION_TYPE_2PAR_
+
+
+    #include "Calibration/RValues.any"
+    #include "Calibration/RangeOfMotionDefinition.any"
+
+
   #endif
 
   #if BM_LEG_RIGHT & BM_LEG_MODEL_IS_TLEM & (BM_LEG_MUSCLES_RIGHT == _MUSCLES_3E_HILL_)
@@ -18,6 +30,9 @@ AnyFolder Calibration={
       };
       #include "<BM_LEG_TLEM_PATH>/Calibration/CalibrationSequenceRight2Par.any"
     #endif
+    #if (BM_CALIBRATION_TYPE == _EXPERIMENTAL_CALIBRATION_TYPE_2PAR_) & (BM_LEG_MODEL != _LEG_MODEL_TLEM1_)
+       #include "<BM_LEG_TLEM_PATH>/Calibration/2ParRightCalStudies.any"
+    #endif
     #if BM_CALIBRATION_TYPE == _CALIBRATION_TYPE_CUSTOM_
       // Allow user to implement their own calibration
     #endif
@@ -34,6 +49,9 @@ AnyFolder Calibration={
       };
       #include "<BM_LEG_TLEM_PATH>/Calibration/CalibrationSequenceLeft2Par.any"  
     #endif
+    #if (BM_CALIBRATION_TYPE == _EXPERIMENTAL_CALIBRATION_TYPE_2PAR_) & (BM_LEG_MODEL != _LEG_MODEL_TLEM1_)
+      #include "<BM_LEG_TLEM_PATH>/Calibration/2ParLeftCalStudies.any"
+    #endif
     #if BM_CALIBRATION_TYPE == _CALIBRATION_TYPE_CUSTOM_
       // Allow user to implement their own calibration
     #endif
@@ -65,6 +83,10 @@ AnyFolder Calibration={
     // 2Par PEFactor will be set here
     #include "../../Arm/Calibration/CalibrationSequenceRight2Par.any"
   #endif
+  #if BM_CALIBRATION_TYPE == _EXPERIMENTAL_CALIBRATION_TYPE_2PAR_
+    // 2Par PEFactor will be set here
+    #include "../../Arm/Calibration/CalibrationSequenceRight2Par.any"
+  #endif
   #if BM_CALIBRATION_TYPE == _CALIBRATION_TYPE_CUSTOM_
     // Allow user to implement their own calibration
   #endif
@@ -78,6 +100,10 @@ AnyFolder Calibration={
     // 2Par PEFactor will be set here
     #include "../../Arm/Calibration/CalibrationSequenceLeft2Par.any"
   #endif
+  #if BM_CALIBRATION_TYPE == _EXPERIMENTAL_CALIBRATION_TYPE_2PAR_
+    // 2Par PEFactor will be set here
+    #include "../../Arm/Calibration/CalibrationSequenceLeft2Par.any"
+  #endif
   #if BM_CALIBRATION_TYPE == _CALIBRATION_TYPE_CUSTOM_
     // Allow user to implement their own calibration
   #endif
@@ -91,6 +117,10 @@ AnyFolder Calibration={
     // 2Par PEFactor will be set here
     #include "../../Trunk/Calibration/MuscleCalibrationSequence2Par.any"
   #endif
+  #if BM_CALIBRATION_TYPE == _EXPERIMENTAL_CALIBRATION_TYPE_2PAR_
+    // 2Par PEFactor will be set here
+    #include "../../Trunk/Calibration/MuscleCalibrationSequence2Par.any"
+  #endif
   #if BM_CALIBRATION_TYPE == _CALIBRATION_TYPE_CUSTOM_
     // Allow user to implement their own calibration
   #endif
@@ -104,10 +134,7 @@ AnyFolder Calibration={
   #endif
   #endif
 
-
   AnyOperationSequence CalibrationSequence ={
      AnyOperationDummy PlaceHolderOpr = {};
   };
-
-
 };