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ome / omero-cli-zarr

https://pypi.org/project/omero-cli-zarr/
GNU General Public License v2.0
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Fix path/to/image when exporting Plate images #146

Closed will-moore closed 12 months ago

will-moore commented 1 year ago

Fixes a bug introduced by https://github.com/ome/omero-cli-zarr/pull/144 where the well/field/image path wasn't being passed to da.to_zarr() when downsampling images during Plate export.

To test:

omero zarr export Plate:123

This bug didn't affect the export of single Images (which was tested on that PR). Without this fix, the first downsampled image 1 gets written to plate.zarr/1/.zarray and then this is not found when we try to read it to downsample again (since we're still looking in the "right" place at plate.zarr/A/1/0/1/.zarray):

Traceback (most recent call last):
  File "/Users/wmoore/opt/anaconda3/envs/omeroweb2/lib/python3.9/site-packages/zarr/core.py", line 243, in _load_metadata_nosync
    meta_bytes = self._store[mkey]
  File "/Users/wmoore/opt/anaconda3/envs/omeroweb2/lib/python3.9/site-packages/zarr/storage.py", line 1087, in __getitem__
    raise KeyError(key)
KeyError: '.zarray'
joshmoore commented 12 months ago

Since gh-147 is based on this PR, taking @dominikl's https://github.com/ome/omero-cli-zarr/pull/147#issuecomment-1688260381 as a sign-off.