Tutorial snippet updates (#23)

* Tutorial snippet updates

* Tutorial images and text changes

* Tutorial snippets in Getting started

* Tutorial snippets in Modeling the human body

* Created whole folders for snippet files

* Update tests

* Used cmd.exe to create lib in ci test

* Merge commit '118df158da292f4b7f185ff8d0172692779da1e9'

* Updates to tutorial Modeling the Human Body. New folder structure

* Final updates to the first 4 tutorials.

* Update file paths in lesson1.md

* rename1

* rename2

* Tutorial updates - file structure, images and more

* Update file path in lesson2.md

---------

Co-authored-by: Jacob Hilmar Adamsen <[email protected]>
Co-authored-by: Morten Enemark Lund <[email protected]>

.github/workflows/build.yaml

@@ -66,17 +66,31 @@ jobs:
       - uses: actions/checkout@v4
         with:
           fetch-depth: 0
+          path: tutorials
+      - uses: actions/checkout@v4
+        with:
+          repository: anybody/ammr
+          ref: master
+          path: ammr
+
+      - shell: cmd
+        run: | 
+            echo #include "%GITHUB_WORKSPACE%/ammr/libdef.any" > libdef.any
 
+          
       - uses: prefix-dev/[email protected]
         with:
           cache: true
           cache-write: ${{ github.event_name == 'push' && github.ref_name == 'master' }}
           environments: test
+          manifest-path: tutorials/pixi.toml
           activate-environment: true
 
       - name: Test Snippets
         if: ${{ !github.event.pull_request.head.repo.fork && github.repository == 'anybody/tutorials' }}
-        run: pytest
+        run: |
+          cd tutorials
+          pytest
         env:
           RLM_LICENSE: ${{ secrets.LICENSE_TEST_SERVER }}
           RLM_LICENSE_PASSWORD: ${{ secrets.LICENSE_TEST_SERVER_PASSWORD }}

A_Getting_started/Snippets/lesson2/MyStandingHuman-1/Model/BodyModelConfiguration.any

@@ -0,0 +1,15 @@
+#path __BM_PLUGIN_FILE__ "BodyModelConfiguration.any"
+#define BM_CONFIG_PLUGIN __BM_PLUGIN_FILE__
+
+// -----------------------------------------------------------------------------------
+// The BodyModel configuration can be modified using BodyModel GUI plugin
+// or by manually editing this file.
+//
+// Please see this this file for more information on the options:
+// #path HTML_DOC "<AMMR_PATH_DOC>/bm_config/index.html"
+// -----------------------------------------------------------------------------------
+
+#define BM_MANNEQUIN_DRIVER_DEFAULT ON
+
+// Enable the TLEM2 lower extremity model
+#define BM_LEG_MODEL _LEG_MODEL_TLEM2_

A_Getting_started/Snippets/lesson2/MyStandingHuman-1/Model/DrawSettings.any

@@ -0,0 +1,149 @@
+
+DrawSettings ={
+
+
+  //This is the color definitions of the nodes and segments
+ Colors = {
+  AnyBodyRed = {149/256,51/256,55/256};    //AnyBody standard red
+  AnyBodyGreen = {47/256,131/256,80/256};  //AnyBody standard green
+  AnyBodyBlue = {82/256,85/256,111/256};   //AnyBody standard blue
+  AnyBodyYellow= {235/256,197/256,17/256}; //AnyBody standard yellow
+  AnyBodyPaleYellow = {248/256,204/256,115/256}; //AnyBody standard pale yellow
+AnyBodyGrey = {153/256,153/256,153/256};    //AnyBody standard grey
+
+  Nodes = AnyBodyPaleYellow; 
+  Segments =  AnyBodyPaleYellow; 
+};
+
+  Muscle ={ 
+    RGB = .Colors.AnyBodyRed;
+    Visible =On;
+    DrawScaleOnOff =Off;
+    Bulging =0.0;
+    ColorScale =1.0;
+    RGBColorScale = {0.957031, 0.785156, 0.785156};
+    MaxStress = 2500000.000000; //N/m^2 //This number is for graphics only!
+    Opacity =1.0;
+    DrawScale = 
+    {
+      EnableCreasing = Off;
+      CreasingAngle = 0.524;
+      EnableWireframe = Off;
+      EnableSmoothing = On;
+      Param = 0.0;
+      ParamArray = {0.0, 0.167, 0.333, 0.5, 0.667, 0.833, 1.0};
+      RGBArray = {{0.0, 0.0, 0.6}, {0.0, 0.0, 1.0}, {0.0, 1.0, 1.0}, {0.0, 1.0, 0.0}, {1.0, 1.0, 0.0}, {1.0, 0.0, 0.0}, {0.6, 0.0, 0.0}};
+      OpacityArray = {1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0};
+    };
+  }; 
+
+
+    BonesOpacity ={
+
+    GlobalCoef = 1;
+
+    Skull = 1*GlobalCoef;
+    Thorax = 1*GlobalCoef;
+    Pelvis = 1*GlobalCoef;
+    Sacrum = 1*GlobalCoef;
+    L5 = 1*GlobalCoef;
+    L4 = 1*GlobalCoef;
+    L3 = 1*GlobalCoef;
+    L2 = 1*GlobalCoef;
+    L1 = 1*GlobalCoef;
+
+    RightFoot = 1*GlobalCoef;
+    RightShank = 1*GlobalCoef;
+    RightThigh = 1*GlobalCoef;
+
+    LeftFoot = 1*GlobalCoef;
+    LeftShank = 1*GlobalCoef;
+    LeftThigh = 1*GlobalCoef;
+
+
+    RightClavicula = 1*GlobalCoef;
+    RightScapula = 1*GlobalCoef;
+    RightHumerus = 1*GlobalCoef;
+    RightUlna = 1*GlobalCoef;
+    RightRadius = 1*GlobalCoef;
+    RightHand = 1*GlobalCoef;
+
+    LeftClavicula = 1*GlobalCoef;
+    LeftScapula = 1*GlobalCoef;
+    LeftHumerus = 1*GlobalCoef;
+    LeftUlna = 1*GlobalCoef;
+    LeftRadius = 1*GlobalCoef;
+    LeftHand = 1*GlobalCoef;
+
+
+    // For leg TD only.
+    RightTalus = 1*GlobalCoef;
+    RightPatella = 1*GlobalCoef;
+
+    LeftTalus = 1*GlobalCoef;
+    LeftPatella = 1*GlobalCoef;
+
+
+    // For detailed cervical model only.
+    C1 = 1*GlobalCoef;
+    C2 = 1*GlobalCoef;
+    C3 = 1*GlobalCoef;
+    C4 = 1*GlobalCoef;
+    C5 = 1*GlobalCoef;
+    C6 = 1*GlobalCoef;
+    C7 = 1*GlobalCoef;
+  };
+
+
+
+  SegmentAxes ={
+    RGB ={0,0,1};
+    ScaleXYZ ={0.0001,0.00001,0.00001};
+  };
+  BML ={
+    ScaleXYZ ={0.0006,0.0006,0.0006};
+    RGB = .Colors.AnyBodyBlue;
+  };
+  JointAxesProximal = {
+    RGB = .Colors.AnyBodyRed;
+    ScaleXYZ = {0.015,0.015,0.015};
+  };
+  JointAxesDistal = {
+    RGB = .Colors.AnyBodyGreen;
+    ScaleXYZ = {0.01,0.01,0.01};
+  };
+
+
+  SegmentNodes ={
+    ScaleXYZ ={0.0005,0.0005,0.0005};
+    RGB = .Colors.AnyBodyRed;
+  };
+  WrapGeometry ={
+    RGB ={1,1,1};
+  };
+
+     DrawSettingsSupport={
+    Lin={ 
+        ScaleFactor=0.004; 
+       RGB = {0,0,1};
+      Thickness = 0.004;
+      HeadThickness = 2*Thickness;
+      HeadLength = 3*Thickness;
+    };
+    Rot={ 
+       ScaleFactor=0.08; 
+      RGB = {1,0,0};
+       Thickness = 0.075;
+       HeadThickness = 2*Thickness;
+       HeadLength = 5*Thickness;
+    };
+  };
+
+
+  Marker={
+  Color={0,0,1};
+  Radius=0.00;
+
+  };
+
+}; //DrawSettings

A_Getting_started/Snippets/lesson2/MyStandingHuman-1/Model/Environment.any

@@ -0,0 +1,25 @@
+AnyFolder Environment = {
+  //^ Environment files are used to include objects surrounding human,
+  //^ e.g. global reference frame
+
+  AnyFixedRefFrame GlobalRef = 
+  {
+    AnyDrawRefFrame drw={ScaleXYZ=0.3*{1,1,1};};
+
+    AnyRefNode RightFootPrint = {
+      //^ Positioning of the right foot. 
+      //^ Ground-foot constraints can be excluded with: #define EXCLUDE_FOOT_CONSTRAINTS
+      sRel = HeelPosition; 
+      ARel = RotMat({0,0,0}, ToeDirection, {0,10,0});
+      AnyDrawRefFrame drw = {RGB = {0,0.7,0}; ScaleXYZ = 0.1*{1,1,1};};
+    };
+
+    AnyRefNode LeftFootPrint = {
+      //^ Positioning of the right foot. 
+      //^ Ground-foot constraints can be excluded with: #define EXCLUDE_FOOT_CONSTRAINTS
+      sRel = HeelPosition;
+      ARel = RotMat({0,0,0}, ToeDirection, {0,10,0});
+      AnyDrawRefFrame drw = {RGB = {0,0.7,0}; ScaleXYZ = 0.1*{1,1,1};};
+    };    
+  };  
+};

A_Getting_started/Snippets/lesson2/MyStandingHuman-1/Model/GRFPrediction.any

@@ -0,0 +1,47 @@
+
+  //-------- GRFPrediction for the right leg
+  // See: #include "<ANYBODY_PATH_AMMR>/Tools/GRFPrediction/FootPlateConditionalContact.any" 
+  FootPlateConditionalContact GRF_Prediction_Right(
+  NORMAL_DIRECTION = "Y",
+  NUMBER_OF_NODES = 25,
+  NODES_FOLDER = FootNodes,
+  PLATE_BASE_FRAME = Main.Model.Environment.GlobalRef,
+  GLOBAL_REF = Main.Model.Environment.GlobalRef,
+  SHOW_TRIGGER_VOLUME = ON
+  ) =
+  {
+    CreateFootContactNodes25 FootNodes(
+      foot_ref=Main.HumanModel.BodyModel.Right.Leg.Seg.Foot
+    ) = {};
+
+    // Additional force plate settings
+    Settings = 
+    {
+      LimitDistHigh = 0.025; // Vertical height
+      FrictionCoefficient = 0.8;
+    };
+  };
+
+
+  //-------- GRFPrediction for the right leg
+  // See: #include "<ANYBODY_PATH_AMMR>/Tools/GRFPrediction/FootPlateConditionalContact.any" 
+  FootPlateConditionalContact GRF_Prediction_Left(
+  NORMAL_DIRECTION = "Y",
+  NUMBER_OF_NODES = 25,
+  NODES_FOLDER = FootNodes,
+  PLATE_BASE_FRAME = Main.Model.Environment.GlobalRef,
+  GLOBAL_REF = Main.Model.Environment.GlobalRef,
+  SHOW_TRIGGER_VOLUME = ON
+  ) =
+  {
+    CreateFootContactNodes25 FootNodes(
+      foot_ref=Main.HumanModel.BodyModel.Left.Leg.Seg.Foot
+    ) = {};
+
+    Settings = 
+    {
+      LimitDistHigh = 0.025;
+      FrictionCoefficient = 0.8;
+    };
+  };
+

A_Getting_started/Snippets/lesson2/MyStandingHuman-1/Model/JointsAndDrivers.any

@@ -0,0 +1,82 @@
+
+// Center of Mass drivers can be excluded
+// by setting #define EXCLUDE_COM_BALANCE_DRIVERS
+#ifndef EXCLUDE_COM_BALANCE_DRIVERS
+
+   //Constraint the collective CoM to be right above the GlobalRef
+   AnyKinDriver CenterOfMassDriver = {
+     AnyKinMeasure& CoM = ..BodyModel.Interface.CenterOfMass;
+     AnyFunConst Position = {
+       Value = Main.Model.CenterOfMassXZ;
+     };
+     MeasureOrganizer = {0,2};  // Only the x and z directions
+     Reaction.Type = {Off,Off};
+
+   };
+   // Ankles are assigned a lower weight so most of the
+   // center of mass balancing will happen at the ankle joint. 
+   Main.Model.DefaultMannequinDrivers.DefaultWeakDriverWeight = 0.01;
+   Main.Model.DefaultMannequinDrivers.AnkleDriverLeftFlexion.WeakDriverWeight = 0.001;
+   Main.Model.DefaultMannequinDrivers.AnkleDriverRightFlexion.WeakDriverWeight = 0.001;
+
+#endif
+
+
+
+// Foot driver constraints can be excluded
+// by setting #define EXCLUDE_FOOT_CONSTRAINTS
+#ifndef EXCLUDE_FOOT_CONSTRAINTS
+
+  // Default drivers for the pelvis position is set to zero 
+  // since foot drivers determine the position of the model
+  Main.Model.DefaultMannequinDrivers.PelvisGroundDriverPosX.WeakDriverWeight = 0;
+  Main.Model.DefaultMannequinDrivers.PelvisGroundDriverPosY.WeakDriverWeight = 0;
+  Main.Model.DefaultMannequinDrivers.PelvisGroundDriverPosZ.WeakDriverWeight = 0;
+  Main.Model.DefaultMannequinDrivers.PelvisGroundDriverRotX.WeakDriverWeight = 0;
+  Main.Model.DefaultMannequinDrivers.PelvisGroundDriverRotY.WeakDriverWeight = 0;
+  Main.Model.DefaultMannequinDrivers.PelvisGroundDriverRotZ.WeakDriverWeight = 0;
+
+
+  AnyFolder Right = 
+  {   
+    AnyKinEq HeelFloorContraint = {     
+      AnyKinLinear HeelMeasure = {
+        AnyRefFrame &FootPrint = Main.Model.Environment.GlobalRef.RightFootPrint;
+        AnyRefFrame &Heel = Main.HumanModel.BodyModel.Right.Leg.Seg.Foot.HeelContactNodeLow;
+      };
+      Reaction.Type = {Off,Off,Off};
+    }; 
+
+    AnyKinEq ToeDirectionContraint =
+    {
+      AnyKinLinear ToeDirection = {
+        AnyRefFrame &FootPrint = Main.Model.Environment.GlobalRef.RightFootPrint;
+        AnyRefFrame &Heel = Main.HumanModel.BodyModel.Right.Leg.Seg.Foot.BigToeNode;
+      };
+      MeasureOrganizer = {1,2}; // Only y,z direction
+      Reaction.Type = {Off,Off};
+    };
+  };
+
+  AnyFolder Left = 
+  {    
+    AnyKinEq HeelFloorContraint = {     
+      AnyKinLinear HeelMeasure = {
+        AnyRefFrame &FootPrint = Main.Model.Environment.GlobalRef.LeftFootPrint;
+        AnyRefFrame &Heel = Main.HumanModel.BodyModel.Left.Leg.Seg.Foot.HeelContactNodeLow;
+      };
+      Reaction.Type = {Off,Off,Off};
+    }; 
+
+    AnyKinEq ToeDirectionContraint =
+    {
+      AnyKinLinear ToeDirection = {
+        AnyRefFrame &FootPrint = Main.Model.Environment.GlobalRef.LeftFootPrint;
+        AnyRefFrame &Heel = Main.HumanModel.BodyModel.Left.Leg.Seg.Foot.BigToeNode;
+      };
+      MeasureOrganizer = {1,2}; // Only y,z direction
+      Reaction.Type = {Off,Off};
+    };
+  };
+
+#endif