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Patch ZipStore for write_image and write_multiscale method using Dask arrays with storage_options #399

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@snibbor snibbor commented Aug 26, 2024

Dear all,

Thank you for your work on this project. I am excited to use OME-Zarr in my research. However, I wanted the option to write OME-Zarr to a Zip container, as this format is more convenient for transferring data to remote storage in my workflows.

From reading previous issues and posts, I see that the standard for archiving OME-Zarr images is still under discussion.
#363
#298
https://forum.image.sc/t/saving-volumetric-data-with-voxel-size-colormap-annotations/85537

During my initial attempts to use ZipStore with the write_image and write_multiscale methods, I encountered failures when using Dask arrays, particularly when the chunks parameter was included in storage_options. The issue stemmed from a duplicate key error in the da.to_zarr method.

To resolve this, I removed the storage_options arguments when working with ZipStore. My tests show that omitting the chunks from storage_options does not affect the chunk size for Dask arrays. I have also verified that all other tests in test_writer.py pass with this change.

Please let me know if there is a better way to do this. I am still learning about the more intricate aspects of Zarr stores and Dask, but I am eager to contribute to and utilize OME-Zarr in my research.

Thank you again,

Jack

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codecov bot commented Aug 28, 2024

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 85.85%. Comparing base (56f72b0) to head (b58d550).

Additional details and impacted files
@@            Coverage Diff             @@
##           master     #399      +/-   ##
==========================================
+ Coverage   85.44%   85.85%   +0.40%     
==========================================
  Files          13       13              
  Lines        1539     1541       +2     
==========================================
+ Hits         1315     1323       +8     
+ Misses        224      218       -6     

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