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TheJacksonLaboratory / ezomero

A module with convenience functions for writing Python code that interacts with OMERO.
GNU General Public License v2.0
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ezimport doesn't support OME-NGFF #97

Closed will-moore closed 7 months ago

will-moore commented 9 months ago

Describe the bug See discussion at https://forum.image.sc/t/images-batch-import-into-a-dataset-in-omero-using-ezomero-2-1-0/89529/17 In order to recognise OME-Zarr images, Bio-Formats needs to check more than the default depth of directories. So we need to pass that argument to the importer e.g. --depth=10.

Also, once the import has completed, finding those images via clientPath at https://github.com/TheJacksonLaboratory/ezomero/blob/25e40c3936b82e16dac09358f6a7d24efbf22e01/ezomero/_importer.py#L304 fails because there is no file with image.zarr as the clientPath because this is just a directory.

To Reproduce

ezomero.ezimport(conn=conn, target="my_image.zarr", dataset=123)

Expected behavior Import should work as for other images, with image IDs returned and Image placed into Dataset.

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erickmartins commented 9 months ago

As mentioned in #98, this probably won't be a priority for now, but passing extra arguments through to the CLI importer should be straightforward, and creating an extra case for zarrs should also be ok.