Muscle modeling updates (#40)

* Updates to Muscle Modeling Tutorial

* Update of intro image in Muscle Modeling

* Added label to Chapter for reference

---------

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

Author: melund

Muscle_modeling/_static/intro/image1.jpeg

@@ -1,6 +1,7 @@
 ::: {rst-class} break
 :::
 
+(MuscleModeling)=
 # Muscle Modeling
 
 This tutorial introduces the many facilities for modeling muscles in the

Muscle_modeling/_static/intro/image1.png

@@ -3,7 +3,11 @@
 
 # Introduction to Muscle Modeling
 
-![Muscles back](_static/intro/image1.jpeg)
+```{image} _static/intro/image1.png
+:alt: Muscles back
+:align: center
+:width: 50%
+```
 
 Muscles are the actuators of living bodies. They are activated by the
 central nervous system (CNS) by a complicated electro-chemical process.
@@ -15,14 +19,14 @@ the user to the necessary muscle forces in a process known as inverse
 dynamics. To do so, the system must know the properties of the muscles
 involved, and this is where muscle modeling comes into the picture.
 
-AnyBody contains four different muscle models ranging from simple to
-more complicated physiological behavior. The simplest model just assumes
-a constant strength of the muscle regardless of its working conditions.
-The more complicated models take such conditions as current length,
-contraction velocity, fiber length, pennation angle, tendon elasticity,
-and stiffness of passive tissues into account. Please refer to the
-AnyScript Reference Manual (Find it in AnyBody->Help) for concise
-information about the available muscle models:
+AnyBody contains four different muscle models ranging from simple to more
+complicated physiological behavior. The simplest model just assumes a constant
+strength of the muscle regardless of its working conditions. The more
+complicated models take such conditions as current length, contraction velocity,
+fiber length, pennation angle, tendon elasticity, and stiffness of passive
+tissues into account. Please refer to the AnyScript Reference Manual (Find it in
+AnyBody->Help->AnyScript Reference) for concise information about the available
+muscle models:
 
 1. AnyMuscleModel - assuming constant strength of the muscle
 2. AnyMuscleModel3E - a three element model taking serial and parallel

Muscle_modeling/index.md

@@ -73,7 +73,10 @@ Main = {
 When you load the model, open a model view window, and run the
 SetInitialConditions operation, you should get the following picture:
 
-![simple model](_static/lesson1/image1.jpeg)
+```{image} _static/lesson1/image1.jpeg
+:alt: simple model
+:align: center
+```
 
 The model has a driver, so you can run the kinematic analysis and see
 the movement. The arm flexes about the origin of the red reference
@@ -95,7 +98,10 @@ If you pick the Classes tab in the right-hand side of the window, then
 you will get access to the class tree. Expand the tree as shown in the
 picture until you get to the AnyMuscleModel.
 
-![class tree](_static/lesson1/image2.png)
+```{image} _static/lesson1/image2.png
+:alt: class tree
+:align: center
+```
 
 Notice that this class has three derived classes. These are more
 advanced muscle models, and we shall get to those later. However for the
@@ -185,23 +191,26 @@ 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:
 
-![class tree AnyMuscleViaPoint](_static/lesson1/image3.png)
+```{image} _static/lesson1/image3.png
+:alt: class tree AnyMuscleViaPoint
+:align: center
+```
 
 ```AnyScriptDoc
 AnyMuscleModel SimpleModel = {
-      F0 = 100;
-      //Lf0 = 0;
-      //Vol0 = 0;
-   };
-
-   § AnyMuscleViaPoint <ObjectName> = {
-      //RefFrames = ;
-      //Surfaces = ;
-      AnyMuscleModel &<Insert name0> = <Insert object reference (or full object definition)>;
-      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!
-    };§
+   F0 = 100;
+   //Lf0 = 0;
+   //Vol0 = 0;
+};
+
+§ AnyMuscleViaPoint <ObjectName> = {
+   //RefFrames = ;
+   //Surfaces = ;
+   AnyMuscleModel &<Insert name0> = <Insert object reference (or full object definition)>;
+   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!
+   };§
 ```
 
 Let us start by filling out what we can and removing what we have no use
@@ -265,13 +274,19 @@ 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>`):
 
-![simple model with muscle](_static/lesson1/image4.jpeg)
+```{image} _static/lesson1/image4.jpeg
+:alt: simple model with muscle
+:align: center
+```
 
 Notice that the muscle is now able to balance the gravity, and we are
 able to run the InverseDynamicAnalysis. If you try it out and
 subsequently open a chart view, you are able to plot the muscle force:
 
-![muscle force](_static/lesson1/image5.png)
+```{image} _static/lesson1/image5.png
+:alt: muscle force
+:align: center
+```
 
 The muscle force is the item Fm in the list of properties you can plot
 for a muscle. As you can see, lots of other properties are available,

Muscle_modeling/intro.md

@@ -14,13 +14,19 @@ AnyDrawMuscle drw = {};
 It obviously does not contain much, so every setting is at its default
 value leading to the following display of the muscle:
 
-![simple model with muscle](_static/lesson2/image1.jpeg)
+```{image} _static/lesson2/image1.jpeg
+:alt: simple model with muscle
+:align: center
+```
 
 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:
 
-![class tree AnyDrawMuscle](_static/lesson2/image2.gif)
+```{image} _static/lesson2/image2.gif
+:alt: class tree AnyDrawMuscle
+:align: center
+```
 
 Erase the previous AnyDrawMuscle, right-click the AnyDrawMuscle in the
 tree view, and insert an instance:
@@ -130,7 +136,10 @@ how the muscle force goes up drastically with the reduced moment arm:
 Consequently the muscle now bulges more towards the end of the movement
 than it does in the beginning:
 
-![Chart view Muscle1.Fm](_static/lesson2/image3.gif)
+```{image} _static/lesson2/image3.gif
+:alt: Chart view Muscle1.Fm
+:align: center
+```
 
 The muscle thickness does not have to reflect force. Choosing other
 values for the Bulging property will give other results:
@@ -162,7 +171,10 @@ AnyDrawMuscle drw = {
 When you reload and run the InverseDynamicAnalysis, you will notice that
 the red shade of the muscle changes as its activity grows:
 
-![Simple model two positions](_static/lesson2/image4.jpeg)
+```{image} _static/lesson2/image4.jpeg
+:alt: Simple model two positions
+:align: center
+```
 
 When the activity is zero, the color defaults to a rather pale red. You
 can control this "initial" value of the scaled color through the

Muscle_modeling/lesson1.md

@@ -24,12 +24,18 @@ Anatomically, via point muscles are mostly found in the lower
 extremities and in the spine, while the arms and shoulders almost
 exclusively have wrapping muscles.
 
-![Old leg Muscle wrapping](_static/lesson3/image1.jpeg)
+```{image} _static/lesson3/image1.jpeg
+:alt: Old leg Muscle wrapping
+:align: center
+```
 
 *Most muscles in the legs can be modeled
 reasonably with via point muscles.*
 
-![Deltoid muscles](_static/lesson3/image2.jpeg)
+```{image} _static/lesson3/image2.jpeg
+:alt: Deltoid muscles
+:align: center
+```
 
 *The deltoid muscle wraps over the head
 of the humerus.*
@@ -125,7 +131,10 @@ AnyMuscleViaPoint Muscle1 = {
 
 The figure below shows the result:
 
-![Simpel model with via point muscle](_static/lesson3/image3.jpeg)
+```{image} _static/lesson3/image3.jpeg
+:alt: Simple model with via point muscle
+:align: center
+```
 
 A muscle can pass through an unlimited number of via points, and the
 points can be attached to different segments. This can be used to create

Muscle_modeling/lesson2.md

@@ -83,7 +83,10 @@ insertion point of the cylinder is at {0, 0, 0.2} corresponding exactly
 to half of the length of the cylinder of 0.4. This causes the cylinder
 to be inserted symmetrically about the xy plane as illustrated below:
 
-![wrapcylinder](_static/lesson4/image1.jpeg)
+```{image} _static/lesson4/image1.jpeg
+:alt: Wrap cylinder
+:align: center
+```
 
 The cylinder direction is always z in the coordinate direction of the
 object that the cylinder is inserted into. So, if the cylinder does not
@@ -109,7 +112,10 @@ AnyRefNode CylCenter = {
 
  Which causes the cylinder to rotate 20 degrees about the y axis.
 
-![wrap cylinder rotated](_static/lesson4/image2.jpeg)
+```{image} _static/lesson4/image2.jpeg
+:alt: Wrap cylinder rotated
+:align: center
+```
 
 There are a couple of things to notice about the cylinder: First of all
 the graphics looks like the cylinder is faceted. This is not really the
@@ -242,7 +248,10 @@ It is time to see what we have done. If you load the model and run the
 InverseDynamics analysis (and have done everything right), you will see
 the model moving through a sequence of positions like this:
 
-![wrap cylinder with via point sequence](_static/lesson4/image3.jpeg)
+```{image} _static/lesson4/image3.jpeg
+:alt: Wrap cylinder with via point sequence
+:align: center
+```
 
 As mentioned above, wrapping muscles can also have via points. In fact,
 we can easily change the via point muscle, Muscle1,  to wrap over the
@@ -269,7 +278,10 @@ to change the type from AnyMuscleViaPoint to AnyMuscleShortestPath and
 insert the wrapping surface and the StringMesh specification. This gives
 us the following result:
 
-![wrap cylinder two muscles](_static/lesson4/image4.jpeg)
+```{image} _static/lesson4/image4.jpeg
+:alt: Wrap cylinder two muscles
+:align: center
+```
 
 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
@@ -339,7 +351,10 @@ Step button rather than the run button. This will show you how the
 system uses the InitWrapVectors to pull the muscle to the other side of
 the cylinder:
 
-![wrap cylinder Init wrap vectors](_static/lesson4/image5.jpeg)
+```{image} _static/lesson4/image5.jpeg
+:alt: Wrap cylinder Init wrap vectors
+:align: center
+```
 
 If you keep pressing the step button you will see how the muscle now
 wraps on the other side of the cylinder.