Rename pixel size property to match bioio-base

[aswallace]

Link to Relevant Issue

This pull request resolves #14 : The physical_pixel_sizes property was not being updated on scene changes.
Requires the change in bioio-devs/bioio-base#27 for the property to actually reset

Description of Changes

Rename existing _px_sizes property to match _physical_pixel_sizes from bioio-base. This will make it so that when the property is reset from the base class (i.e., when the scene changes), pixel sizes will be recalculated in the LIF reader.

Testing

Verified that the existing tests still pass. Have not added a new unit test yet, but am open to doing so if needed.

Tested manually by reproducing the issue, as follows:

img_bio = BioImage(lif_path_str, reader=bioio_lif.Reader)

img_bio.set_scene(scene1_name)
print(f"scene 1: {img_bio.physical_pixel_sizes}")

img_bio.set_scene(scene2_name)
# pixel size previously would have remained the same, but now updates to the new pixel size
print(f"scene 2: {img_bio.physical_pixel_sizes}") 

[evamaxfield]

All tests pass and seems fine with me! Thanks!

[BrianWhitneyAI]

Nice!

[toloudis]

Is performance ok if you change scene, get pixel size, change scene, get pixel size, etc?

[aswallace]

Is performance ok if you change scene, get pixel size, change scene, get pixel size, etc?

I did some extremely basic timeit tests on one of our multi-scene LIF files on Vast (~260 GB, 80 scenes) where I just did lif.set_scene(scene), print(lif.physical_pixel_sizes) multiple times and checked time in between. TBF, I'm not completely sure what factors impact time, so my choices may or may not make sense:

In case indexing matters, I switched between scenes that were not adjacent (e.g., 3 to 78 to 24). With the changes applied to bioio-lif and bioio-base, the first time a scene was accessed it took 1-30 secs to change to that new scene and get/print pixel size. When the code was re-run with the same scenes, it took less than a second to switch and get/print pixel size.

As a reference, for both versions of the code (with and w/o changes) it took me 5-18 minutes to run _read_immediate for the first time (which also re-calculates pixel size, though its time shouldn't be affected by these PRs), and then ~3 seconds to re-run if a scene had been accessed before

Worth noting that I'm testing this on vpn to access Vast files, so my times may not accurately reflect running on local files.

[toloudis]

We might just want a new issue ticket to see if we can/should make this faster. I don't have a good sense of how important LIF files will be moving forward within AICS.