feat: Added system for setting inverse initialial conditions from marker tracking.

Application/MocapExamples/Plug-in-gait_Simple/FullBody.main.any

@@ -8,6 +8,7 @@
 
 // Enter and edit Lab-Specific Data in this file:
 #path MOCAP_LAB_SPECIFIC_DATA "Setup/LabSpecificData.any"
+#define MOCAP_MANNEQUIN_OUTPUT ON
 
 // Include the AnyMoCap Framwork
 #include "<ANYMOCAP_MODEL>"

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

@@ -67,48 +67,48 @@ Main.ModelSetup.TrialSpecificData =
 
 
 
-    PelvisThoraxExtension = -10;
-    PelvisThoraxLateralBending = 0;
-    PelvisThoraxRotation = 0;
+    PelvisThoraxExtension = DesignVar(0);
+    PelvisThoraxLateralBending = DesignVar(0);
+    PelvisThoraxRotation = DesignVar(0);
 
-    NeckExtension = 0;
-    NeckLateralBending = 0;
-    NeckRotation = 0;
+    NeckExtension = DesignVar(0);
+    NeckLateralBending = DesignVar(0);
+    NeckRotation = DesignVar(0);
 
     Right = {
 
-      HipFlexion = 20;
-      HipAbduction = 4;
-      HipExternalRotation = -19;
-      KneeFlexion = 8;
-      AnklePlantarFlexion = -10;
-      SubTalarEversion = 0;
+      HipFlexion = DesignVar(0);
+      HipAbduction = DesignVar(0);
+      HipExternalRotation = DesignVar(0);
+      KneeFlexion = DesignVar(0);
+      AnklePlantarFlexion = DesignVar(0);
+      SubTalarEversion = DesignVar(0);
 
-      GlenohumeralFlexion = -18;
-      GlenohumeralAbduction = 0;
-      GlenohumeralExternalRotation = 0;
-      ElbowFlexion = 20;
-      ElbowPronation = 0;
-      WristFlexion = 0;
-      WristAbduction = 0;
+      GlenohumeralFlexion = DesignVar(0);
+      GlenohumeralAbduction = DesignVar(1);
+      GlenohumeralExternalRotation = DesignVar(0);
+      ElbowFlexion = DesignVar(0);
+      ElbowPronation = DesignVar(0);
+      WristFlexion = DesignVar(0);
+      WristAbduction = DesignVar(0);
 
   };
     Left = {
 
-      HipFlexion = -23;
-      HipAbduction = 0;
-      HipExternalRotation = 0;
-      KneeFlexion = 14;
-      AnklePlantarFlexion = -15;
-      SubTalarEversion = 0;
+      HipFlexion = DesignVar(0);
+      HipAbduction = DesignVar(0);
+      HipExternalRotation = DesignVar(0);
+      KneeFlexion = DesignVar(0);
+      AnklePlantarFlexion = DesignVar(0);
+      SubTalarEversion = DesignVar(0);
 
-      GlenohumeralFlexion = 28;
-      GlenohumeralAbduction = 8;
-      GlenohumeralExternalRotation = 0;
-      ElbowFlexion = 24;
-      ElbowPronation = 0;
-      WristFlexion = 0;
-      WristAbduction = 0;
+      GlenohumeralFlexion = DesignVar(0);
+      GlenohumeralAbduction = DesignVar(1);
+      GlenohumeralExternalRotation = DesignVar(0);
+      ElbowFlexion = DesignVar(0);
+      ElbowPronation = DesignVar(0);
+      WristFlexion = DesignVar(0);
+      WristAbduction = DesignVar(0);
 
   };
 

Body/AAUHuman/Trunk/MannequinValuesFromModel.any

@@ -14,4 +14,4 @@
     AnyVar AnyVar_PelvisThoraxLateralBending=.InterfaceFolder.PelvisThoraxLateralBending.Pos[0]*180/pi; 
     AnyVar AnyVar_PelvisThoraxRotation=.InterfaceFolder.PelvisThoraxRotation.Pos[0]*180/pi;        
 
-    AnyVar AnyVar_NeckExtension=0; 
+    AnyVar AnyVar_NeckExtension=-1*.InterfaceFolder.SkullThoraxFlexion.Pos[0]*180/pi; 

Tools/AnyMocap/CheckAnyMocapConfiguration.any

@@ -14,6 +14,10 @@
 #endif
 #endif
 
+// Switch for saving the MannequinValuesFromModel structure when running marker tracking
+#ifndef MOCAP_MANNEQUIN_OUTPUT
+#define MOCAP_MANNEQUIN_OUTPUT OFF
+#endif
 
 // Prefix which can be used by the application to distinques trials
 #ifndef MOCAP_OUTPUT_FILENAME_PREFIX 

Tools/AnyMocap/JointAngleOutputs.any

@@ -232,7 +232,115 @@ AnyFolder JointAngleOutputs = {
   #endif
 
 #endif
-
+
+
+#if MOCAP_MANNEQUIN_OUTPUT == ON
+
+AnyOutputFile OutputFile_MannequinValuesFromModel_Trunk ={
+   SepSign = ",";
+   SepSpaceAutoOnOff = Off;
+   Header.TitleSectionOnOff = Off;
+   Header.ConstSectionOnOff = Off;
+   Header.ConstSectionSaveOptionsOnOff = Off;
+   Header.VarSectionOnOff = Off;
+   FileName = TEMP_PATH+"/"+ MOCAP_TEST_FILENAME_PREFIX + MOCAP_OUTPUT_FILENAME_PREFIX + Main.ModelSetup.TrialSpecificData.TrialFileName + "-MannequinValuesFromModel-Trunk.txt";
+   Values = {
+      &..BodyModel.MannequinValuesFromModel.AnyFolder_Posture.AnyVar_PelvisPosX,
+      &..BodyModel.MannequinValuesFromModel.AnyFolder_Posture.AnyVar_PelvisPosY,
+      &..BodyModel.MannequinValuesFromModel.AnyFolder_Posture.AnyVar_PelvisPosZ,
+      &..BodyModel.MannequinValuesFromModel.AnyFolder_Posture.AnyVar_PelvisRotX,
+      &..BodyModel.MannequinValuesFromModel.AnyFolder_Posture.AnyVar_PelvisRotY,
+      &..BodyModel.MannequinValuesFromModel.AnyFolder_Posture.AnyVar_PelvisRotZ,
+      &..BodyModel.MannequinValuesFromModel.AnyFolder_Posture.AnyVar_PelvisThoraxExtension,
+      &..BodyModel.MannequinValuesFromModel.AnyFolder_Posture.AnyVar_PelvisThoraxLateralBending,
+      &..BodyModel.MannequinValuesFromModel.AnyFolder_Posture.AnyVar_PelvisThoraxRotation,
+      &..BodyModel.MannequinValuesFromModel.AnyFolder_Posture.AnyVar_NeckExtension,   
+   };
+};
+
+#if BM_LEG_RIGHT & BM_LEG_MODEL_IS_TLEM
+AnyOutputFile OutputFile_MannequinValuesFromModel_Right_Leg ={
+   SepSign = ",";
+   SepSpaceAutoOnOff = Off;
+   Header.TitleSectionOnOff = Off;
+   Header.ConstSectionOnOff = Off;
+   Header.ConstSectionSaveOptionsOnOff = Off;
+   Header.VarSectionOnOff = Off;
+   FileName = TEMP_PATH+"/"+ MOCAP_TEST_FILENAME_PREFIX + MOCAP_OUTPUT_FILENAME_PREFIX + Main.ModelSetup.TrialSpecificData.TrialFileName + "-MannequinValuesFromModel-Right-Leg.txt";
+   Values = {
+      &..BodyModel.MannequinValuesFromModel.AnyFolder_Posture.AnyFolder_Right.AnyVar_HipFlexion,
+      &..BodyModel.MannequinValuesFromModel.AnyFolder_Posture.AnyFolder_Right.AnyVar_HipAbduction,
+      &..BodyModel.MannequinValuesFromModel.AnyFolder_Posture.AnyFolder_Right.AnyVar_HipExternalRotation,
+      &..BodyModel.MannequinValuesFromModel.AnyFolder_Posture.AnyFolder_Right.AnyVar_KneeFlexion,
+      &..BodyModel.MannequinValuesFromModel.AnyFolder_Posture.AnyFolder_Right.AnyVar_KneeFlexion,
+      &..BodyModel.MannequinValuesFromModel.AnyFolder_Posture.AnyFolder_Right.AnyVar_KneeFlexion,
+    };
+};
+#endif
+
+#if BM_LEG_LEFT & BM_LEG_MODEL_IS_TLEM
+AnyOutputFile OutputFile_MannequinValuesFromModel_Left_Leg ={
+   SepSign = ",";
+   SepSpaceAutoOnOff = Off;
+   Header.TitleSectionOnOff = Off;
+   Header.ConstSectionOnOff = Off;
+   Header.ConstSectionSaveOptionsOnOff = Off;
+   Header.VarSectionOnOff = Off;
+   FileName = TEMP_PATH+"/"+ MOCAP_TEST_FILENAME_PREFIX + MOCAP_OUTPUT_FILENAME_PREFIX + Main.ModelSetup.TrialSpecificData.TrialFileName + "-MannequinValuesFromModel-Left-Leg.txt";
+   Values = {
+      &..BodyModel.MannequinValuesFromModel.AnyFolder_Posture.AnyFolder_Left.AnyVar_HipFlexion,
+      &..BodyModel.MannequinValuesFromModel.AnyFolder_Posture.AnyFolder_Left.AnyVar_HipAbduction,
+      &..BodyModel.MannequinValuesFromModel.AnyFolder_Posture.AnyFolder_Left.AnyVar_HipExternalRotation,
+      &..BodyModel.MannequinValuesFromModel.AnyFolder_Posture.AnyFolder_Left.AnyVar_KneeFlexion,
+      &..BodyModel.MannequinValuesFromModel.AnyFolder_Posture.AnyFolder_Left.AnyVar_KneeFlexion,
+      &..BodyModel.MannequinValuesFromModel.AnyFolder_Posture.AnyFolder_Left.AnyVar_KneeFlexion,
+    };
+};
+#endif
+
+#if BM_ARM_RIGHT == ON
+AnyOutputFile OutputFile_MannequinValuesFromModel_Right_Arm ={
+   SepSign = ",";
+   SepSpaceAutoOnOff = Off;
+   Header.TitleSectionOnOff = Off;
+   Header.ConstSectionOnOff = Off;
+   Header.ConstSectionSaveOptionsOnOff = Off;
+   Header.VarSectionOnOff = Off;
+   FileName = TEMP_PATH+"/"+ MOCAP_TEST_FILENAME_PREFIX + MOCAP_OUTPUT_FILENAME_PREFIX + Main.ModelSetup.TrialSpecificData.TrialFileName + "-MannequinValuesFromModel-Right-Arm.txt";
+   Values = {
+      &..BodyModel.MannequinValuesFromModel.AnyFolder_Posture.AnyFolder_Right.AnyVar_SternoClavicularProtraction,
+      &..BodyModel.MannequinValuesFromModel.AnyFolder_Posture.AnyFolder_Right.AnyVar_SternoClavicularElevation,
+      &..BodyModel.MannequinValuesFromModel.AnyFolder_Posture.AnyFolder_Right.AnyVar_GlenohumeralFlexion,
+      &..BodyModel.MannequinValuesFromModel.AnyFolder_Posture.AnyFolder_Right.AnyVar_GlenohumeralAbduction,
+      &..BodyModel.MannequinValuesFromModel.AnyFolder_Posture.AnyFolder_Right.AnyVar_GlenohumeralExternalRotation,
+      &..BodyModel.MannequinValuesFromModel.AnyFolder_Posture.AnyFolder_Right.AnyVar_ElbowFlexion,
+      &..BodyModel.MannequinValuesFromModel.AnyFolder_Posture.AnyFolder_Right.AnyVar_ElbowPronation,
+    };
+};
+#endif
+
+#if BM_ARM_LEFT == ON
+AnyOutputFile OutputFile_MannequinValuesFromModel_Left_Arm ={
+   SepSign = ",";
+   SepSpaceAutoOnOff = Off;
+   Header.TitleSectionOnOff = Off;
+   Header.ConstSectionOnOff = Off;
+   Header.ConstSectionSaveOptionsOnOff = Off;
+   Header.VarSectionOnOff = Off;
+   FileName = TEMP_PATH+"/"+ MOCAP_TEST_FILENAME_PREFIX + MOCAP_OUTPUT_FILENAME_PREFIX + Main.ModelSetup.TrialSpecificData.TrialFileName + "-MannequinValuesFromModel-Left-Arm.txt";
+   Values = {
+      &..BodyModel.MannequinValuesFromModel.AnyFolder_Posture.AnyFolder_Left.AnyVar_SternoClavicularProtraction,
+      &..BodyModel.MannequinValuesFromModel.AnyFolder_Posture.AnyFolder_Left.AnyVar_SternoClavicularElevation,
+      &..BodyModel.MannequinValuesFromModel.AnyFolder_Posture.AnyFolder_Left.AnyVar_GlenohumeralFlexion,
+      &..BodyModel.MannequinValuesFromModel.AnyFolder_Posture.AnyFolder_Left.AnyVar_GlenohumeralAbduction,
+      &..BodyModel.MannequinValuesFromModel.AnyFolder_Posture.AnyFolder_Left.AnyVar_GlenohumeralExternalRotation,
+      &..BodyModel.MannequinValuesFromModel.AnyFolder_Posture.AnyFolder_Left.AnyVar_ElbowFlexion,
+      &..BodyModel.MannequinValuesFromModel.AnyFolder_Posture.AnyFolder_Left.AnyVar_ElbowPronation,
+    };
+};
+#endif
+
+#endif
 
 }; //JointAngleOutputs
 

Tools/AnyMocap/LoadMannquinValuesForInitialConditions.any

@@ -0,0 +1,133 @@
+AnyFolder SetMannequinValues = {
+
+  #define _ANYMOCAP_JOINT_ANGLE_WARNING_MSG_
+
+  AnyFolder Trunk = {
+    #include "InterpolateJointAngleData.any"
+    FileReader.FileName ??= TEMP_PATH+"/"+ MOCAP_TEST_FILENAME_PREFIX + MOCAP_OUTPUT_FILENAME_PREFIX + Main.ModelSetup.TrialSpecificData.TrialFileName + "-MannequinValuesFromModel-Trunk.txt";
+    FileReader.Data0 = zeros(NumElemOf(Main.Studies.MarkerTracking.JointAngleOutputs.OutputFile_MannequinValuesFromModel_Trunk.Values), FileReader.Length0 );
+  };
+  AnyFolder RightLeg = {
+    #include "InterpolateJointAngleData.any"
+    FileReader.FileName ??= TEMP_PATH+"/"+ MOCAP_TEST_FILENAME_PREFIX + MOCAP_OUTPUT_FILENAME_PREFIX + Main.ModelSetup.TrialSpecificData.TrialFileName + "-MannequinValuesFromModel-Right-Leg.txt";
+    FileReader.Data0 = zeros(NumElemOf(Main.Studies.MarkerTracking.JointAngleOutputs.OutputFile_MannequinValuesFromModel_Right_Leg.Values), FileReader.Length0 );
+  };
+  AnyFolder LeftLeg = {
+    #include "InterpolateJointAngleData.any"
+    FileReader.FileName ??= TEMP_PATH+"/"+ MOCAP_TEST_FILENAME_PREFIX + MOCAP_OUTPUT_FILENAME_PREFIX + Main.ModelSetup.TrialSpecificData.TrialFileName + "-MannequinValuesFromModel-Left-Leg.txt";
+    FileReader.Data0 = zeros(NumElemOf(Main.Studies.MarkerTracking.JointAngleOutputs.OutputFile_MannequinValuesFromModel_Left_Leg.Values), FileReader.Length0 );
+  };
+  AnyFolder RightArm = {
+    #include "InterpolateJointAngleData.any"
+    FileReader.FileName ??= TEMP_PATH+"/"+ MOCAP_TEST_FILENAME_PREFIX + MOCAP_OUTPUT_FILENAME_PREFIX + Main.ModelSetup.TrialSpecificData.TrialFileName + "-MannequinValuesFromModel-Right-Arm.txt";
+    FileReader.Data0 = zeros(NumElemOf(Main.Studies.MarkerTracking.JointAngleOutputs.OutputFile_MannequinValuesFromModel_Right_Arm.Values), FileReader.Length0 );
+  };
+  AnyFolder LeftArm = {
+    #include "InterpolateJointAngleData.any"
+    FileReader.FileName ??= TEMP_PATH+"/"+ MOCAP_TEST_FILENAME_PREFIX + MOCAP_OUTPUT_FILENAME_PREFIX + Main.ModelSetup.TrialSpecificData.TrialFileName + "-MannequinValuesFromModel-Left-Arm.txt";
+    FileReader.Data0 = zeros(NumElemOf(Main.Studies.MarkerTracking.JointAngleOutputs.OutputFile_MannequinValuesFromModel_Left_Arm.Values), FileReader.Length0 );
+  };
+
+
+  #undef _ANYMOCAP_JOINT_ANGLE_WARNING_MSG_
+
+   AnyVar time ??= DesignVar(Trunk.InterpolatedData.T[0]);
+
+  AnyFolder LoadedMannequinValues = {
+    //This controls the position of the pelvi wrt. to the global reference frame
+    AnyVar PelvisPosX = .Trunk.InterpolatedData(.time)[0];
+    AnyVar PelvisPosY = .Trunk.InterpolatedData(.time)[1];
+    AnyVar PelvisPosZ = .Trunk.InterpolatedData(.time)[2];
+
+    //This controls the rotation of the pelvis wrt. to the global reference frame
+    AnyVar PelvisRotX = .Trunk.InterpolatedData(.time)[3];
+    AnyVar PelvisRotY = .Trunk.InterpolatedData(.time)[4];
+    AnyVar PelvisRotZ = .Trunk.InterpolatedData(.time)[5];
+
+    // These variables control the rotation of the thorax wrt the
+    // pelvis    
+    AnyVar PelvisThoraxExtension = .Trunk.InterpolatedData(.time)[6]; 
+    AnyVar PelvisThoraxLateralBending = .Trunk.InterpolatedData(.time)[7]; 
+    AnyVar PelvisThoraxRotation = .Trunk.InterpolatedData(.time)[8];        
+
+    AnyVar PelvisT12Extension = .Trunk.InterpolatedData(.time)[9];  
+
+    AnyFolder Right = {
+      AnyVar SternoClavicularProtraction = ..RightArm.InterpolatedData(..time)[0];
+      AnyVar SternoClavicularElevation = ..RightArm.InterpolatedData(..time)[1];
+      AnyVar GlenohumeralFlexion = ..RightArm.InterpolatedData(..time)[2];
+      AnyVar GlenohumeralAbduction = ..RightArm.InterpolatedData(..time)[3];
+      AnyVar GlenohumeralExternalRotation = ..RightArm.InterpolatedData(..time)[4];
+      AnyVar ElbowFlexion = ..RightArm.InterpolatedData(..time)[5];
+      AnyVar ElbowPronation = ..RightArm.InterpolatedData(..time)[6];
+      AnyVar HipFlexion = ..RightLeg.InterpolatedData(..time)[0];
+      AnyVar HipAbduction = ..RightLeg.InterpolatedData(..time)[1];
+      AnyVar HipExternalRotation = ..RightLeg.InterpolatedData(..time)[2];
+      AnyVar KneeFlexion = ..RightLeg.InterpolatedData(..time)[3];
+      AnyVar AnklePlantarFlexion = ..RightLeg.InterpolatedData(..time)[4];
+      AnyVar SubTalarEversion = ..RightLeg.InterpolatedData(..time)[5];
+    };
+    AnyFolder Left = {
+      AnyVar SternoClavicularProtraction = ..LeftArm.InterpolatedData(..time)[0];
+      AnyVar SternoClavicularElevation = ..LeftArm.InterpolatedData(..time)[1];
+      AnyVar GlenohumeralFlexion = ..LeftArm.InterpolatedData(..time)[2];
+      AnyVar GlenohumeralAbduction = ..LeftArm.InterpolatedData(..time)[3];
+      AnyVar GlenohumeralExternalRotation = ..LeftArm.InterpolatedData(..time)[4];
+      AnyVar ElbowFlexion = ..LeftArm.InterpolatedData(..time)[5];
+      AnyVar ElbowPronation = ..LeftArm.InterpolatedData(..time)[6];
+      AnyVar HipFlexion = ..LeftLeg.InterpolatedData(..time)[0];
+      AnyVar HipAbduction = ..LeftLeg.InterpolatedData(..time)[1];
+      AnyVar HipExternalRotation = ..LeftLeg.InterpolatedData(..time)[2];
+      AnyVar KneeFlexion = ..LeftLeg.InterpolatedData(..time)[3];
+      AnyVar AnklePlantarFlexion = ..LeftLeg.InterpolatedData(..time)[4];
+      AnyVar SubTalarEversion = ..LeftLeg.InterpolatedData(..time)[5];
+    };
+  };
+ AnyOperationSetValue SetInitialPositions = {
+    #define _LOAD_MANNEQUIN_VALUES(PREFIX) \
+        &.PREFIX.PelvisPosX, \
+        &.PREFIX.PelvisPosY, \
+        &.PREFIX.PelvisPosZ, \
+        &.PREFIX.PelvisRotX, \
+        &.PREFIX.PelvisRotY, \
+        &.PREFIX.PelvisRotZ, \
+        &.PREFIX.PelvisThoraxExtension, \
+        &.PREFIX.PelvisThoraxLateralBending, \
+        &.PREFIX.PelvisThoraxRotation, \
+        &.PREFIX.PelvisT12Extension, \
+        &.PREFIX.Right.SternoClavicularProtraction, \
+        &.PREFIX.Right.SternoClavicularElevation, \
+        &.PREFIX.Right.GlenohumeralFlexion, \
+        &.PREFIX.Right.GlenohumeralAbduction, \
+        &.PREFIX.Right.GlenohumeralExternalRotation, \
+        &.PREFIX.Right.ElbowFlexion, \
+        &.PREFIX.Right.ElbowPronation, \
+        &.PREFIX.Right.HipFlexion, \
+        &.PREFIX.Right.HipAbduction, \
+        &.PREFIX.Right.HipExternalRotation, \
+        &.PREFIX.Right.KneeFlexion, \
+        &.PREFIX.Right.AnklePlantarFlexion, \
+        &.PREFIX.Right.SubTalarEversion, \
+        &.PREFIX.Left.SternoClavicularProtraction, \
+        &.PREFIX.Left.SternoClavicularElevation, \
+        &.PREFIX.Left.GlenohumeralFlexion, \
+        &.PREFIX.Left.GlenohumeralAbduction, \
+        &.PREFIX.Left.GlenohumeralExternalRotation, \
+        &.PREFIX.Left.ElbowFlexion, \
+        &.PREFIX.Left.ElbowPronation, \
+        &.PREFIX.Left.HipFlexion, \
+        &.PREFIX.Left.HipAbduction, \
+        &.PREFIX.Left.HipExternalRotation, \
+        &.PREFIX.Left.KneeFlexion, \
+        &.PREFIX.Left.AnklePlantarFlexion, \
+        &.PREFIX.Left.SubTalarEversion
+
+    Source = {_LOAD_MANNEQUIN_VALUES(LoadedMannequinValues) };
+    Target = {_LOAD_MANNEQUIN_VALUES(...HumanModel.Mannequin.Posture)};
+    };
+
+    #undef _LOAD_MANNEQUIN_VALUES
+
+
+ };
+

Tools/AnyMocap/ModelSetup.any

@@ -89,6 +89,7 @@ ModelSetup = {
  //(dynamic or standing refereces)
  #include "SaveLoadParameters.any"
 
+
  #include "ModelViews.any"  
 
 
@@ -124,6 +125,12 @@ ModelSetup = {
          + Main.ModelSetup.TrialSpecificData.TrialFileName + "_InverseDynamicStudy.anydata.h5")
        };
     };
+
+   #if MOCAP_MANNEQUIN_OUTPUT == ON
+   // Operations to set the mannequin values from a file 
+   #include "LoadMannquinValuesForInitialConditions.any"
+   #endif
+
  }; // Macros