Inverse Dynamics of Muscle Systems and other changes

[JacobAdamsen]

• Updates of Inverse Dynamics of Muscle Systems tutorial
  - Updated all images
  - Change of some text formulations and wordings
  - Update of equation insertion method
  - Secured all models run and give reasonable results
  - NOT a complete update of the tutorial. Could still use extra changes/updates of the general content and use of code
  snippets for AnyBody model
• Marked tutorial The Mechanical Elements as deleted
• made the new Mechanical Tutorial visible

[gemini-code-assist]

Hello @JacobAdamsen, I'm Gemini Code Assist¹! I'm currently reviewing this pull request and will post my feedback shortly. In the meantime, here's a summary to help you and other reviewers quickly get up to speed!

Summary of Changes

This pull request focuses on updating the Inverse Dynamics of Muscle Systems tutorial, marking the 'The Mechanical Elements' tutorial as deleted, and renaming 'Making Things Move' to 'Motion Capture movement'. The tutorial updates include image replacements, text revisions, equation insertion method updates, and ensuring models run with reasonable results. A key change involves modifying the muscle model's constant strength in calibration.any.

Highlights

• Inverse Dynamics Tutorial Update: The 'Inverse Dynamics of Muscle Systems' tutorial has been updated with new images, revised text, and improved equation formatting. Models are now verified to run correctly.
• Tutorial Deletion: The tutorial 'The Mechanical Elements' has been marked as deleted.
• Tutorial Renaming: The tutorial 'Making Things Move' has been renamed to 'Motion Capture Movement'.
• Muscle Model Strength Modification: The F0 parameter in the AnyMuscleModel within calibration.any has been changed from 600 to 400.

Changelog

Click here to see the changelog

• MuscleRecruitment/Downloads/calibration.any
  • Modified the F0 parameter (muscle strength) in the AnyMuscleModel from 600 to 400. This change affects the simple muscle model's constant strength.
• MuscleRecruitment/Inverse_dynamics.md
  • Removed the caution_old_tutorial caution box.
  • Replaced the image insertion method from ![alt text](path/to/image) to the sphinx {image} path/to/image :alt: alt text :align: center :width: 40% format for better control over image attributes.
  • Minor text changes for clarity and flow.
• MuscleRecruitment/lesson1.md
  • Removed the caution_old_tutorial caution box.
  • Updated the equation formatting to use equation* environments for better rendering.
  • Minor text changes for clarity and flow.
  • Replaced the image insertion method from ![alt text](path/to/image) to the sphinx {image} path/to/image :alt: alt text :align: center :width: 50% format for better control over image attributes.
  • Added the location of the muscle force in the Chart view as Main.MyStudy.Output.Model.M1.Fm
• MuscleRecruitment/lesson2.md
  • Removed the caution_old_tutorial caution box.
  • Updated the equation formatting to use equation* environments for better rendering.
  • Minor text changes for clarity and flow.
  • Replaced the image insertion method from ![alt text](path/to/image) to the sphinx {image} path/to/image :alt: alt text :align: center :width: 80% format for better control over image attributes.
• MuscleRecruitment/lesson3.md
  • Removed the caution_old_tutorial caution box.
  • Updated the image insertion method from ![alt text](path/to/image) to the sphinx {image} path/to/image :alt: alt text :align: center :width: 90% format for better control over image attributes.
  • Added a note about expected Notices during model loading.
  • Updated the location of the muscle activity in the Chart view as Main.Bike2D.Study.Output.Model.Leg2D.Right.Mus
  • Minor text changes for clarity and flow.
• MuscleRecruitment/lesson4.md
  • Removed the caution_old_tutorial caution box.
  • Updated the image insertion method from ![alt text](path/to/image) to the sphinx {image} path/to/image :alt: alt text :align: center :width: 90% format for better control over image attributes.
  • Minor text changes for clarity and flow.
• MuscleRecruitment/lesson5.md
  • Removed the caution_old_tutorial caution box.
  • Updated the image insertion method from ![alt text](path/to/image) to the sphinx {image} path/to/image :alt: alt text :align: center :width: 90% format for better control over image attributes.
  • Updated the location of the max muscle activity in the Chart view as Main.Bike2D.Study.Output.MaxMuscleActivity
  • Minor text changes for clarity and flow.
• MuscleRecruitment/lesson6.md
  • Removed the caution_old_tutorial caution box.
  • Updated the equation formatting to use equation* environments for better rendering.
  • Updated the image insertion method from ![alt text](path/to/image) to the sphinx {image} path/to/image :alt: alt text :align: center :width: 90% format for better control over image attributes.
  • Added references to Praagman et al.
  • Minor text changes for clarity and flow.
• MuscleRecruitment/lesson_calibration.md
  • Updated the image insertion method from ![alt text](path/to/image) to the sphinx {image} path/to/image :alt: alt text :align: center format for better control over image attributes.
  • Updated the link to the arm2d example.
  • Updated the link to the Muscle Modeling tutorial.
  • Minor text changes for clarity and flow.
• The_mechanical_elements/index.md
  • Marked the tutorial as deleted by adding '(Deleted)' to the title.
  • Kept the caution_old_tutorial caution box.
• Tutorials.md
  • Renamed 'Making_things_move/index' to 'Motion_Capture_Movement/index'.
• core-tutorial-descriptions.txt
  • Renamed 'Making things move' to 'Motion Capture Movement'.

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A tutorial's plight,
Images updated, text tight,
Knowledge takes new form.

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[gemini-code-assist]

Code Review

The pull request updates the Inverse Dynamics of Muscle Systems tutorial with new images, text revisions, and an updated equation insertion method. It also marks the 'The Mechanical Elements' tutorial as deleted and renames 'Making Things Move' to 'Motion Capture movement'. Overall, the changes seem well-organized and contribute to improving the tutorial's clarity and accuracy.

Summary of Findings

• Calibration Model F0 Value: The F0 value in the calibration model was changed from 600 to 400. It's important to verify that this change is intentional and doesn't negatively impact the model's behavior or accuracy. This change has a high potential to affect the results of the tutorial.
• Image Insertion Method: The pull request updates the image insertion method in the markdown files. While this improves the formatting, it's important to ensure that the new method is compatible with all rendering engines and that the images are displayed correctly across different platforms.

Merge Readiness

The pull request includes several updates to the tutorials, including image updates, text revisions, and method updates. Before merging, it's important to ensure that the changes are thoroughly tested and that the tutorials still function as expected. Given the potential impact of the F0 value change in the calibration model, I recommend addressing the high severity comment before merging. I am unable to directly approve this pull request, and users should have others review and approve this code before merging.

[melund]

@JacobAdamsen Is this PR ready to be merged? I now you write that it is not a complete update, but should we merge it anyway?