import view causes ModuleNotFoundError: No module named 'zarr.storage'

[kirbyju]

Please see kirbyju/TCIA_Notebooks#30 for details. Note that I found a workaround (reinstalling zarr packages), but plan to keep the issue open there until the root cause is fixed in itkwidgets.

Thanks,
Justin

[thewtex]

xref: kirbyju/TCIA_Notebooks#31

[fedorov]

@thewtex latest zarr package is no longer a prerelease but (presumably) stable 3.0.2 (see https://github.com/zarr-developers/zarr-python/releases/tag/v3.0.2).

Import of itkwidgets with the latest zarr fails with the error below. Downgrade to zarr 2.18.4 fixes the issue.

AttributeError                            Traceback (most recent call last)
<ipython-input-1-156ffb6e299b> in <cell line: 0>()
      1 import itk
----> 2 from itkwidgets import view
      3 # Pydicom-Seg is a layer on top of pydicom that handles DICOM SEG objects.
      4 import pydicom
      5 import pydicom_seg

1 frames
/usr/local/lib/python3.11/dist-packages/itkwidgets/imjoy.py in register_itkwasm_imjoy_codecs()
     47 
     48     api.registerCodec({'name': 'itkwasm-image', 'type': itkwasm.Image, 'encoder': encode_itkwasm_image})
---> 49     api.registerCodec({'name': 'zarr-store', 'type': zarr.storage.BaseStore, 'encoder': encode_zarr_store})
     50 
     51 

AttributeError: module 'zarr.storage' has no attribute 'BaseStore'

[thewtex]

@fedorov @kirbyju 👍 yes, thanks for the ping 🙏 . I release itkwidgets 1.0a55 that includes this zarr version constraint until we support Zarr 3.

[fedorov]

@thewtex with 1.0a55, viewer does not work at all in Colab. I will submit a separate issue.