Muscle modeling updates

Muscle_modeling/lesson1.md

@@ -76,6 +76,7 @@ SetInitialConditions operation, you should get the following picture:
 ```{image} _static/lesson1/image1.jpeg
 :alt: simple model
 :align: center
+:width: 40%
 ```
 
 The model has a driver, so you can run the kinematic analysis and see
@@ -101,6 +102,7 @@ picture until you get to the AnyMuscleModel.
 ```{image} _static/lesson1/image2.png
 :alt: class tree
 :align: center
+:width: 45%
 ```
 
 Notice that this class has three derived classes. These are more
@@ -187,14 +189,8 @@ simpler muscles of the body, primarily those in the extremities and the
 spine. You can, in fact, make a pretty decent model of the legs entirely
 with via point muscles.
 
-Place the cursor right after the end brace of the musle model,
-right-click the AnyMuscleViaPoint class in the tree, and insert an
-instance of it:
-
-```{image} _static/lesson1/image3.png
-:alt: class tree AnyMuscleViaPoint
-:align: center
-```
+Place the cursor right after the end brace of the musle model, in the Class
+List scroll down to find AnyMuscleViaPoint and insert an instance of it:
 
 ```AnyScriptDoc
 AnyMuscleModel SimpleModel = {
@@ -203,14 +199,19 @@ AnyMuscleModel SimpleModel = {
    //Vol0 = 0;
 };
 
-§ AnyMuscleViaPoint <ObjectName> = {
-   //RefFrames = ;
-   //Surfaces = ;
-   AnyMuscleModel &<Insert name0> = <Insert object reference (or full object definition)>;
+§AnyViaPointMuscle <ObjectName> = 
+{
+   //viewForce.Visible = Off;
+   //MetabModel = Null;
+   //FatigueModel = Null;
+   //MuscleModel = Null;
+   //viewMuscle.Visible = Off;
    AnyRefFrame &<Insert name0> = <Insert object reference (or full object definition)>;
    AnyRefFrame &<Insert name1> = <Insert object reference (or full object definition)>;
-   //AnyRefFrame &<Insert name2> = <Insert object reference (or full object definition)>; You can make any number of these objects!
-   };§
+   //AnyRefFrame &<Insert name2> = <Insert object reference (or full object definition)>;
+   //AnyRefFrame &<Insert name3> = <Insert object reference (or full object definition)>; You can make any number of AnyRefFrame objects!
+   AnyMuscleModel &<Insert name0> = <Insert object reference (or full object definition)>;
+};§
 ```
 
 Let us start by filling out what we can and removing what we have no use
@@ -272,11 +273,13 @@ Notice that we have added an AnyDrawMuscle object to the definition.
 Like other classes in AnyScript, muscles are not drawn in the Model View
 window unless you specifically ask for it. When you load the model and
 run the SetInitialConditions study you will get the following picture
-(if your model does not load, and you cannot find the error, {download}`clickhere to download a model that works <Downloads/MuscleDemo.1.any>`):
+(if your model does not load, and you cannot find the error, 
+{download}`click here to download a model that works <Downloads/MuscleDemo.1.any>`):
 
 ```{image} _static/lesson1/image4.jpeg
 :alt: simple model with muscle
 :align: center
+:width: 40%
 ```
 
 Notice that the muscle is now able to balance the gravity, and we are

Muscle_modeling/lesson2.md

@@ -17,18 +17,13 @@ value leading to the following display of the muscle:
 ```{image} _static/lesson2/image1.jpeg
 :alt: simple model with muscle
 :align: center
+:width: 40%
 ```
 
-Let us play around with the settings a bit. An easy way to display all
-the settings is to discard our manually defined AnyDrawMuscle object and
-insert a template from the class tree instead:
-
-```{image} _static/lesson2/image2.gif
-:alt: class tree AnyDrawMuscle
-:align: center
-```
-
-Erase the previous AnyDrawMuscle, right-click the AnyDrawMuscle in the
+Let us play around with the settings a bit. An easy way to display all the
+settings is to discard our manually defined AnyDrawMuscle object and insert a
+template from the class list instead. Find the AnyDrawMuscle object in the Class
+List, erase the previous AnyDrawMuscle, right-click the AnyDrawMuscle in the
 tree view, and insert an instance:
 
 ```AnyScriptDoc
@@ -174,6 +169,7 @@ the red shade of the muscle changes as its activity grows:
 ```{image} _static/lesson2/image4.jpeg
 :alt: Simple model two positions
 :align: center
+:width: 80%
 ```
 
 When the activity is zero, the color defaults to a rather pale red. You

Muscle_modeling/lesson3.md

@@ -27,6 +27,7 @@ exclusively have wrapping muscles.
 ```{image} _static/lesson3/image1.jpeg
 :alt: Old leg Muscle wrapping
 :align: center
+:width: 25%
 ```
 
 *Most muscles in the legs can be modeled
@@ -35,6 +36,7 @@ reasonably with via point muscles.*
 ```{image} _static/lesson3/image2.jpeg
 :alt: Deltoid muscles
 :align: center
+:width: 25%
 ```
 
 *The deltoid muscle wraps over the head
@@ -134,6 +136,7 @@ The figure below shows the result:
 ```{image} _static/lesson3/image3.jpeg
 :alt: Simple model with via point muscle
 :align: center
+:width: 40%
 ```
 
 A muscle can pass through an unlimited number of via points, and the

Muscle_modeling/lesson4.md

@@ -65,15 +65,14 @@ statement, and change the cylinder parameters as shown below:
   AnyRefNode CylCenter = {
     sRel = {0, 0, -0.2};
 
-   §AnySurfCylinder WrapSurf = {
-      Radius = 0.15;
-      Length = 0.4;
-      //CapRatio = 0.1;
-      //CapRatio2 = 0.1;
-      AnyDrawParamSurf drw = {};
+    §AnySurfCylinder WrapSurf = {
+        Radius = 0.15;
+        Length = 0.4;
+        //CapRatio = 0.1;
+        //CapRatio2 = 0.1;
+        AnyDrawParamSurf drw = {};
     };§
   };
-
 };  // Global reference frame
 ```
 
@@ -86,6 +85,7 @@ to be inserted symmetrically about the xy plane as illustrated below:
 ```{image} _static/lesson4/image1.jpeg
 :alt: Wrap cylinder
 :align: center
+:width: 60%
 ```
 
 The cylinder direction is always z in the coordinate direction of the
@@ -115,6 +115,7 @@ AnyRefNode CylCenter = {
 ```{image} _static/lesson4/image2.jpeg
 :alt: Wrap cylinder rotated
 :align: center
+:width: 60%
 ```
 
 There are a couple of things to notice about the cylinder: First of all
@@ -258,13 +259,13 @@ we can easily change the via point muscle, Muscle1,  to wrap over the
 cylinder even though it also has a via point:
 
 ```AnyScriptDoc
-Any§ShortestPath§Muscle Muscle1 = {
+§AnyMuscleShortestPath§ Muscle1 = {
   AnyMuscleModel &Model = .SimpleModel;
   AnyRefFrame &Orig = .GlobalRef.M1Origin;
   AnyRefFrame &Via = .Arm.ViaPoint;
-§ AnySurface &srf = .GlobalRef.CylCenter.WrapSurf;§
+  §AnySurface &srf = .GlobalRef.CylCenter.WrapSurf;§
   AnyRefFrame &Ins = .Arm.M1Insertion;
- §SPLine.StringMesh = 20;§
+  §SPLine.StringMesh = 20;§
   AnyDrawMuscle drw = {
     Bulging = 2;
     ColorScale = 1;
@@ -281,16 +282,14 @@ us the following result:
 ```{image} _static/lesson4/image4.jpeg
 :alt: Wrap cylinder two muscles
 :align: center
+:width: 70%
 ```
 
 As you can see, both muscles are now wrapping over the cylinder, and we
 can run the InverseDynamics analysis. It seems to work, but the system
 provides the following warning:
 
-`WARNING - Via-point 'Main.MyModel.GlobalRef.M1Origin' on
-'Main.MyModel.Muscle1.SPLine'`
-`is located below the wrapping surface
-'Main.MyModel.GlobalRef.CylCenter.WrapSurf'.`
+`WARNING(OBJ.MCH.KIN7): MuscleDemo.Ini.any(75): Muscle1.SPLine: Penetration of surface: WrapSurf: Via-point 'M1Origin' on 'SPLine' is located below the wrapping surface'WrapSurf`
 
 This is a warning that you will see rather frequently when working with
 complex models with wrapping. The warning comes when one of the end
@@ -328,7 +327,7 @@ AnyMuscleShortestPath Muscle2 = {
   AnySurface &srf = .GlobalRef.CylCenter.WrapSurf;
   AnyRefFrame &Ins = .Arm.M2Insertion;
   SPLine.StringMesh = 20;
- §SPLine.InitWrapPosVectors = {{-0.2, -0.2, 0}, {-0.05, -0.2, 0}};§
+  §SPLine.InitWrapPosVectors = {{-0.2, -0.2, 0}, {-0.05, -0.2, 0}};§
   AnyDrawMuscle drw = {
     Bulging = 2;
     ColorScale = 1;
@@ -354,6 +353,7 @@ the cylinder:
 ```{image} _static/lesson4/image5.jpeg
 :alt: Wrap cylinder Init wrap vectors
 :align: center
+:width: 60%
 ```
 
 If you keep pressing the step button you will see how the muscle now