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IndexError('list index out of range') for SPW

Open joshmoore opened this issue 3 years ago • 0 comments

The SPW images exported via omero zarr export works in napari:

$ napari https://minio-dev.openmicroscopy.org/idr/idr0001-graml-sysgro/pr59_nested/2551.zarr/A/5/0

But not the plate itself (visible in vizarr with nested PR): https://deploy-preview-85--vizarr.netlify.app/?source=https://minio-dev.openmicroscopy.org/idr/idr0001-graml-sysgro/pr59_nested/2551.zarr

Trying to open a nested plate with this PR (same error with the 'nested' plate above, or an older v0.1 plate):

$ napari https://s3.embassy.ebi.ac.uk/idr/zarr/v0.1/plates/422.zarr
10:51:46 ERROR PluginError: Error in plugin 'ome_zarr', hook 'napari_get_reader'
  Cause was: IndexError('list index out of range')
    in file: /Users/wmoore/Desktop/ZARR/ome-zarr-py/ome_zarr/reader.py
    at line: 513
     author: The Open Microscopy Team
    package: ome-zarr
        url: https://github.com/ome/ome-zarr-py
    version: 0.0.18.dev0

This also fails using the current master branch (c3f641d) but with a different error:

$ napari https://s3.embassy.ebi.ac.uk/idr/zarr/v0.1/plates/422.zarr
10:50:25 ERROR PluginError: Error in plugin 'ome_zarr', hook 'napari_get_reader'
  Cause was: ArrayNotFoundError("array not found at path %r' ''")
    in file: /opt/anaconda3/envs/napari/lib/python3.9/site-packages/zarr/core.py
    at line: 186
     author: The Open Microscopy Team
    package: ome-zarr
        url: https://github.com/ome/ome-zarr-py
    version: 0.0.18.dev0

And in fact it's not working for any of the older versions of ome-zarr-py that I've tried, so I don't know when it last worked (or what version of napari etc).

Originally posted by @will-moore in https://github.com/ome/ome-zarr-py/issues/75#issuecomment-823161570

joshmoore avatar Apr 24 '21 09:04 joshmoore