[Question] How are coords stored in h5?

[GeniusAng]

What's your question?

I've discovered a bug. I randomly downloaded ten TCGA-BRCA WSIs for experimentation and set the --patch_size to 256. However, in the TRIDENT-main/trident_processed/20x_256px_0px_overlap/patches directory, only the first coordinate file has a spacing of 256, while the remaining nine files have a spacing of 512. Why is that?

Moreover, when I set the --patch_size to 512, the first image has a spacing of 512, but the remaining nine images have a spacing of 1024. Why did the spacing double for all but the first image?
Here are the first ten coordinates I read. The first line corresponds to the first image, and the second line corresponds to the second image:

10 coords: [(768, 4096), (768, 4352), (768, 4608), (768, 4864), (1024, 3584), (1024, 3840), (1024, 4096), (1024, 4352), (1024, 4608), (1024, 4864)]
10 coords: [(3072, 49664), (3072, 50176), (3072, 51712), (3072, 52224), (3072, 52736), (3584, 49152), (3584, 49664), (3584, 50176), (3584, 50688), (3584, 51712)]

As you can see, the difference in the second line is 512(such as 52736-52224=512), not 256.
What could be causing this? I'm seeking an explanation!

[guillaumejaume]

TRIDENT is closely following OpenSlide API. Coordinates are always with respect to the highest magnification. So a 256x256-px patching at 20x for a 40x WSI is a 512x512 patch on the 40x reference coordinate. Maybe your 1st image is a 20x image, and the others are 40x. Feel free to inspect the attrs in the h5 as well as the attributes of the WSI object to better understand how patching works.