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Support Zarr stores not ending in '.zarr' #719

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berombau opened this issue Nov 15, 2023 · 4 comments · Fixed by #721
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Support Zarr stores not ending in '.zarr' #719

berombau opened this issue Nov 15, 2023 · 4 comments · Fixed by #721
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@berombau
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Reading an OME-NGFF zarr store without the usual .zarr suffix (probably not best practice but they exist) result in an error:

message: "Could not find IO for: HumanLiverH35"

Can the reader logic be updated to support this?
Or can an additional URL parameter be added like &use2D to specify the reader?
@berombau berombau mentioned this issue Nov 15, 2023
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@PaulHax
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PaulHax commented Nov 15, 2023

Thanks for the report. Your right, not good logic. For a fix, we could add another URL parameter here, say &imageName:
https://github.com/Kitware/itk-vtk-viewer/blob/master/src/index.js#L220-L232

And when imageName ends in .zarr, this becomes true:
https://github.com/Kitware/itk-vtk-viewer/blob/master/src/IO/toMultiscaleSpatialImage.js#L68

@berombau
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berombau commented Nov 15, 2023 •
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Can you give an example for a correct imageName then? Would it matter what's before the .zarr?
How about changing this regex line here. The comment appears to support my use case already, as the images I want to view are subgroups of a SpatialData .zarr store. The regex in the code does not appear to do so. It was changed in this commit to support DANDI urls.

It can be something like [./]zarr\b regexr, which should work I think.

@PaulHax
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PaulHax commented Nov 16, 2023 •
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Ah, just changing the regex would be nice. If you want to open a PR, I'll test and deploy. Otherwise I plan on touching code within a couple weeks.

(Thanks for the regexr link, very usefull.)

berombau added a commit to berombau/itk-vtk-viewer that referenced this issue Nov 16, 2023
@berombau
fix(zarrmultiscalespatialimage): support Zarr stores not ending in .zarr
79b6cb3 
The isZarr regex was updated to support .zarr/image, besides just .zarr and DANDI /zarr/.

fix Kitware#719
@berombau berombau mentioned this issue Nov 16, 2023
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PaulHax added a commit that referenced this issue Dec 20, 2023
@berombau @PaulHax
fix(zarrmultiscalespatialimage): support Zarr stores not ending in .z…
2138166 
…arr (#721)

* fix(zarrmultiscalespatialimage): support Zarr stores not ending in .zarr

The isZarr regex was updated to support .zarr/image, besides just .zarr and DANDI /zarr/.

fix #719

* fix(ZarrMultiscaleSpatialImage): add word boundary to isZarr regex

---------

Co-authored-by: Paul Elliott <paul.elliott@kitware.com>
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🎉 This issue has been resolved in version 14.47.1 🎉

The release is available on:

Your semantic-release bot 📦🚀

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fix(zarrmultiscalespatialimage): support Zarr stores not ending in .zarr berombau/itk-vtk-viewer
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@berombau @PaulHax