Patch ZipStore for write_image and write_multiscale method using Dask arrays with storage_options #399
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
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