NCZarr does not read images produced by multiscale-spatial-image

[dzenanz]

I used the following Python code to convert an image into Zarr format:

from multiscale_spatial_image import to_multiscale, itk_image_to_multiscale, Methods
import itk
import zarr
import sys


def print_help_and_exit(exit_code=1):
    print(f'This is a standalone executable. Invoke it as {sys.argv[0]} input.nrrd output.zarr')
    exit(exit_code)


if __name__ == '__main__':
    if len(sys.argv) != 3:
        print_help_and_exit()
    image = itk.imread(sys.argv[1])

    # Generate Multiscale Image With itk_image_to_multiscale
    axis_units = {dim: "millimeters" for dim in ("x", "y", "z")}
    method = Methods.ITK_GAUSSIAN
    scale_factors = [2, 2]  # isotropic scale factors
    name = 'image'

    itk.auto_progress(0)
    multiscale_image = itk_image_to_multiscale(
        image,
        scale_factors=scale_factors,
        anatomical_axes=True,
        axis_units=axis_units,
        method=method,
        name=name,
    )

    store = zarr.storage.DirectoryStore(sys.argv[2], dimension_separator='/')
    multiscale_image.to_zarr(store)
    print(f'Successfully converted {sys.argv[1]} to {sys.argv[2]}')
else:
    print_help_and_exit()

multiscale-spatial-image is available on GitHub: https://github.com/spatial-image/multiscale-spatial-image.

Images.zip

NCZarr has trouble opening it:

dzenan@corista:~/tester$ /usr/local/bin/ncdump -h file:///media/xeonatorC/Misc/Tester/CBCT_crop1ms.zarr#mode=zarr,file
/usr/local/bin/ncdump: file:///media/xeonatorC/Misc/Tester/CBCT_crop1ms.zarr#mode=zarr,file: NetCDF: internal library error; Please contact Unidata support

Interestingly, if I zip up the resulting directory using 7-zip, NCZarr seems to open it:

dzenan@corista:~/tester$ /usr/local/bin/ncdump -h file:///media/xeonatorC/Misc/Tester/CBCT_crop1ms.zip#mode=zarr,file
netcdf CBCT_crop1ms {
}

Furthermore, both dir and zip fail if I remove the ,file from the "url":

dzenan@corista:~/tester$ /usr/local/bin/ncdump -h file:///media/xeonatorC/Misc/Tester/CBCT_crop1ms.zarr#mode=zarr
Killed
dzenan@corista:~/tester$ /usr/local/bin/ncdump -h file:///media/xeonatorC/Misc/Tester/CBCT_crop1ms.zip#mode=zarr
Killed

Ubuntu 22.04.1 LTS, GCC 11.2.0, netCDF main at b03988e.

[DennisHeimbigner]

This may be the same problem I am encountering at #2474
I think the problem has to do with using '/' as dimension separator.

[DennisHeimbigner]

The problem is that you have an attribute of the form below.
I have no idea about how to interpret it and I do not even think it is
technically a legal Zarr attribute. I have a fix of sorts for this, but
it is in the master branch only, and is not in the 4.9.0 release.
Also, it assumes that the attribute value is a dictionary, not an array of arrays.

 "direction": [
        [
            1.0,
            0.0,
            0.0
        ],
        [
            0.0,
            1.0,
            0.0
        ],
        [
            0.0,
            0.0,
            1.0
        ]
    ]

[DennisHeimbigner]

THis issue appears to be essentially the same as #2474, so comments there will generally apply here.

[dzenanz]

Closing in favor of #2474.