added new parameter and according changes so that limit bounds or oth…

[moerlemans]

Offsets can be taken into account when usign the dataset with annotations on mrxs files

Fixes #160

[jonasteuwen]

Can you rebase? Also, the CI/CD should pass

[jonasteuwen]

Make sure CI passes. Run it before you commit, that will also save some CI time.

[jonasteuwen]

I suggest a different way to implement this.

In the WsiAnnotations, you can make a parameter _requires_offset_to_slide_bounds, which you set to True if you read HaloXML. In the read_region you subsequently check if this variable is "True", and if so use the limit_bounds variable.

[jonasteuwen]

@moerlemans can you rebase once #201 is merged?

[moerlemans]

The problem is that the limit bounds variable is given by the slide. Which the WsiAnnotation has no access to. So this should be an argument to read region or to the init of wsi annotations. I feel like this last option would be best, initialize it to be zero and use it in read_region. The issue has only appeared for me when using halo xml, but I think it will happen with other types as well probably

[moerlemans]

rebased and made the logic according to the last comment I made.

[jonasteuwen]

@moerlemans Can you properly rebase because now you've modified 34 files?

I think you can do something like this:

Add _offset_with_slide_bounds = False to the WsiAnnotations class. Add a property with @property named offset_with_slide_bounds that returns this (so it can only be set within the class itself). Now, you can add this to the constructor of WsiAnnotations, and set it by default to False, and in the Halo constructor, you add this.

Now in the dataset class you an instance check if it is WsiAnnotations or just _offset = slide.get_scaled_slide_bounds(scaling)[0] if getattr(annotations, "offset_with_slide_bounds", False) else (0, 0) and add this to the region.

[jonasteuwen]

I think #204 fixes this

[moerlemans]

Indeed this is fixed in #204