Integrating atlas validation in wrapup.py

[viktorpm]

Description

This PR integrates our atlas validation functions in the wrapup section of atlas packaging.

What is this PR

• Bug fix
• Addition of a new feature
• Other

Why is this PR needed?

Currently, we run the validation functions on finalised atlases. We want to integrate this step with atlas generation to see if an atlas is valid or not immediately.

References

?

How has this PR been tested?

Locally on

• whs_sd_rat.py
• princeton_mouse.py
• admba_3d_dev_mouse.py
• axolotl_atlas.py
• cavefish_atlas.py
• humanatlas.py

Is this a breaking change?

No

Does this PR require an update to the documentation?

Possibly

Checklist:

• The code has been tested locally
• Tests have been added to cover all new functionality (unit & integration)
• The documentation has been updated to reflect any changes
• The code has been formatted with pre-commit

[viktorpm]

Example output for whs_sd_rat.py:

No mesh file exists for: {'name': 'spiral ganglion', 'acronym': 'SpG', 'id': 162, 'structure_id_path': [10000, 1049, 162], 'rgb_triplet': (185, 255, 233)}, ignoring it
In the end, 1 structures with mesh are kept
Finalising atlas
Running atlas validation on whs_sd_rat_39um_v1.2
passed validate_atlas_files
passed catch_missing_structures
passed catch_missing_mesh_files
failed validate_mesh_matches_image_extents: ('Mesh coordinate 955.5 and annotation coordinate 0.0', 'differ by more than 10 times pixel size 39.0')
passed open_for_visual_check
passed validate_checksum
passed validate_image_dimensions
passed validate_additional_references
Saving compressed atlas data at: /home/plattnerv/brainglobe_workingdir/whs_sd_rat/whs_sd_rat_39um_v1.2.tar.gz

Process finished with exit code 0

Catches known error.

[alessandrofelder]

Lovely.

Two small comments for simplification :)

[alessandrofelder]

Thanks @viktorpm

Sorry - I wasn't clear enough in my description of the changes I suggested, which (if I am right??) would significantly simplify the code even further. (Let's chat if you have questions!).

[alessandrofelder]

Suggested change

	atlas: BrainGlobeAtlas, custom_atlas_path: Path = None
	atlas: BrainGlobeAtlas

[alessandrofelder]

Suggested change

	if custom_atlas_path is None:
	atlas_path = (
	Path(get_brainglobe_dir()) / f"{atlas.atlas_name}_v"
	f"{get_local_atlas_version(atlas.atlas_name)}"
	)
	else:
	atlas_path = custom_atlas_path
	obj_path = Path(atlas_path / "meshes")
	obj_path = Path(atlas.root_dir/ "meshes")

This is what I had in mind (and for other functions for which this PRs adds a custom_atlas_path parameter.

[alessandrofelder]

If we do the changes I suggested, this can just be a list of functions (without atlas_to_validate or atlas_to_validate.root_dir!) and we can just call func(atlas_to_validate) below