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saalfeldlab / n5-ij

ImageJ convenience layer for N5
BSD 2-Clause "Simplified" License
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OME-Zarr containers do not parse when nested inside other paths #71

Closed krokicki closed 4 months ago

krokicki commented 6 months ago

When using the "Open N5" dialog if I select an OME-Zarr it parses quickly and correctly: Screenshot 2024-03-01 at 1 45 48 PM

But if I create an empty folder and put the OME-Zarr inside, and point "Open N5" to that containing folder, it gets stuck on the "Parsing..." step for several minutes and then eventually just presents the underlying directory structure:

Screenshot 2024-03-01 at 1 54 44 PM

There are no errors generated.

bogovicj commented 6 months ago

This is happening because the plugin tries to infer the type of storage format (n5,zarr,hdf5). In this case, it guessed that the folder you pointed to is an n5 container. A release we are preparing now will allow you to specify the storage format.

In your case zarr:/Users/rokickik/Desktop/test. However, if the test folder does not contain a .zgroup it will fail, since it is not a valid zarr store. Hope that's clear. I'll leave this open until the next release.

krokicki commented 6 months ago

Makes sense. I just want to add that my actual use case is that I have a folder filled with various n5's and zarr's and it would be nice to be able to see everything that can be opened. I expected "Detect datasets" to find both the n5's and the zarr's, but it only finds the n5's right now.

bogovicj commented 6 months ago

Gotcha. Simultaneous listing / interaction with containers of different types is out-of-scope for this plugin. Maybe in the scope of the tool you started at that hackathon!?

bogovicj commented 4 months ago

Closing because out-of-scope.