CLI add_image not working for 2D data

mobie / mobie-utils-python

Python tools for MoBIE

MIT License

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Closed martinschorb closed 6 months ago

martinschorb commented 7 months ago

Hi,

when running add_image from CLI, the chunks parameter gets checked for 3D -> failure for 2D data.

... mobie/import_data/utils.py", line 156, in ensure_volume
    assert chunks[0] == 1, f"{chunks}"
           ^^^^^^^^^^^^^^

martinschorb commented 7 months ago

OK, found (and fixed) the reason.

Default file format in add_image is still bdv.n5. There is no such command line parameter, that's why it is chosen when running from CLI.

Three options exist to fix the problem:

make ome.zarr the default for all add_image.
implicitely select ome.zarr when calling add_image in the main function when run from CL
add a CL parameter for file type

constantinpape commented 7 months ago

Is it now working after merging #128 @martinschorb ?

constantinpape commented 6 months ago

Can you check if this is working now @martinschorb ?

martinschorb commented 6 months ago

runs now.