Enhance download paths in the examples notebooks

[GeorgeBatch]

• TIA Toolbox version: 1.5.1
• Python version: 3.11.8
• Operating System: CentOS Linux 7 (Core)

Description

In the example notebooks, the files are sometimes downloaded into the examples directory instead of the examples/tmp/ directory. The examples/tmp/ is the place for downloads since it gets cleared at the start of every notebook.

What I Did

In examples/10-wsi-registration.ipynb I changed:

fixed_img_file_name = Path("fixed_image.tif")
moving_img_file_name = Path("moving_image.tif")

to

fixed_img_file_name = global_save_dir / "fixed_image.tif"
moving_img_file_name = global_save_dir / "moving_image.tif"

I wanted to make a pull request with fixes like that.

Problem: But because of the notebook format, the metadata changes when I save the notebook. Instead of a 2-line change, GitHub sees more than 100 deletions and additions. See: GeorgeBatch@97d65b9

Possible solution: Maybe it's better to have the example notebooks saved without the outputs.

[shaneahmed]

Please go ahead and create a PR. All the notebooks are written in Colab, so if you write the notebook in Colab the metadata won't change much. You can also review the change in reviewnb. The link for reviewnb should automatically be generated when you create the PR.

[GeorgeBatch]

I was running them locally, will try in collab so metadata changes less.