Set Omero pixel size

[jburel]

Read Ome-zarr pixel size and set Omero pixel size
This PR integrates changes suggested in BioNGFF/omero-import-utils#28 and fixes a few issues noticed while running the tests
cc @folterj

[will-moore]

We already have testing code for checking pixels sizes (since we get pixel sizes set "for free" when we import OME.xml).

See https://github.com/ome/omero-cli-zarr/blob/10df9400245a8ffdf6e6557bf0690841972e1998/test/integration/clitest/test_import.py#L60C10-L60C23 where we get 3 images imported in the Fileset and this specifies the expected pixel_size_x for each image.

So if you could add a similar list to the other samples e.g. "pixel_sizes_x": [0.36] for the 6001240 image. Most are a single image (single item list) but I think there is a bf2raw layout one which will have multiple images.

[will-moore]

Another thought: could we also set the timeIncrement too, if the Zarr has it.
https://forum.image.sc/t/how-to-correctly-set-a-timeincrement-for-omero-pixels/101600

I'm not sure we have any samples with correct Time values in the scale (which I also wanted for testing zarr in OMERO.figure), so I created #189 to export timeIncrement to zarr scale.

[jburel]

@will-moore Timeincrement can go in a follow-up PR.
The test mentioned above was initially failing. Let's quickly discuss

[will-moore]

OK let's chat... What was the test failing with?
It looks like the pixel sizes are the same in the OME.xml for that image as in the zarr scales, so this PR shouldn't change the values that get populated in OMERO.

https://ome.github.io/ome-ngff-validator/?source=https://storage.googleapis.com/jax-public-ngff/example_v2/LacZ_ctrl.zarr/2/

[jburel]

@will-moore Test adjusted to check the value

[will-moore]

Looks good 👍

[snoopycrimecop]

Conflicting PR. Removed from build OMERO-plugins-push#44. See the console output for more details.
Possible conflicts:

• PR Add labels support for import #181 will-moore 'Add labels support for import'
  • test/integration/clitest/test_import.py
• PR Revert "Remove support for Plate import" #182 will-moore 'Revert "Remove support for Plate import"'
  • test/integration/clitest/test_import.py

--conflicts Conflict resolved in build OMERO-plugins-push#45. See the console output for more details.

[will-moore]

Tested the various samples from test_import.py, importing them via CLI to merge-ci.
All had pixel sizes set as expected 👍

[jburel]

Thanks @will-moore. Merging so we can fix the conflicts