Restrict units to what is defined in NGFF schema

[melissalinkert]

Fixes #288.

This lists valid space and time units per https://ngff.openmicroscopy.org/latest/#axes-md, and rejects anything not included in those lists. As indicated in #144, pixel is one of several units that are supported by OME-XML schema but not NGFF.

I debated whether to implement this by defining NGFF schema units, or defining just units that don't overlap between the two schemas (as in #144 (comment)). I think the former approach is going to be easier to keep up to date, but happy to hear other opinions.

With the test data mentioned in #288, bioformats2raw --debug mri.ome.tiff mri.zarr should log that pixel units are being omitted, and mri.zarr/0/.zattrs should show no unit attribute for anything under axes.

[sbesson]

Using bioformats2raw 0.10.1, I was able to reproduce the original issue either using the Fiji workflow described in #288 (Open the MRI sample and export as OME-TIFF) or a synthetic sample file like test&physicalSizeX=1pixel&physicalSizeY=1pixel.fake. In both cases, the conversion generates a Zarr dataset where the unit of the x and y the physical axes are expressed in pixel.

With a build of bioformats2raw including this PR, the Zarr datasets generated by the conversion are binary identical except for the physical axes which are now unitless

sbesson@Sebastien-GS-MacBook-Pro-2025 bioformats2raw % diff -ur test.zarr test_pr289.zarr 
diff -ur test.zarr/0/.zattrs test_pr289.zarr/0/.zattrs
--- test.zarr/0/.zattrs	2025-09-04 08:46:45
+++ test_pr289.zarr/0/.zattrs	2025-09-04 08:54:26
@@ -14,11 +14,9 @@
       "name" : "z",
       "type" : "space"
     }, {
-      "unit" : "pixel",
       "name" : "y",
       "type" : "space"
     }, {
-      "unit" : "pixel",
       "name" : "x",
       "type" : "space"
     } ],
sbesson@Sebastien-GS-MacBook-Pro-2025 bioformats2raw % diff -ur mri.zarr mri_pr289.zarr   
diff -ur mri.zarr/0/.zattrs mri_pr289.zarr/0/.zattrs
--- mri.zarr/0/.zattrs	2025-09-04 08:45:28
+++ mri_pr289.zarr/0/.zattrs	2025-09-04 08:54:19
@@ -11,15 +11,12 @@
       "name" : "c",
       "type" : "channel"
     }, {
-      "unit" : "pixel",
       "name" : "z",
       "type" : "space"
     }, {
-      "unit" : "pixel",
       "name" : "y",
       "type" : "space"
     }, {
-      "unit" : "pixel",
       "name" : "x",
       "type" : "space"
     } ],

The proposed changes are consistent with the discussion in #144 and feels like a reasonable approach given the behavior of other tools in the NGFF ecosystem. /cc @ome/ngff

Could we add a unit test using fake files to capture the expected behavior?

[melissalinkert]

The proposed changes are consistent with the discussion in #144 and feels like a reasonable approach given the behavior of other tools in the NGFF ecosystem. /cc @ome/ngff

Looks like the team mention might not have worked (maybe due to different organization?) - cc @joshmoore.

Could we add a unit test using fake files to capture the expected behavior?

Done in 4b39f7e.