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Test xarray compatible datasets #35

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joshmoore opened this issue May 26, 2022 · 1 comment
Open

Test xarray compatible datasets #35

joshmoore opened this issue May 26, 2022 · 1 comment
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@joshmoore
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Testing the zarr from spatial-image/multiscale-spatial-image#32:

Exception in thread "main" java.lang.ArrayIndexOutOfBoundsException: -1
	at loci.formats.in.ZarrReader.getOptimalTileHeight(ZarrReader.java:130)
	at loci.formats.ImageReader.getOptimalTileHeight(ImageReader.java:753)
	at loci.formats.ReaderWrapper.getOptimalTileHeight(ReaderWrapper.java:585)
	at loci.formats.tools.ImageInfo.readCoreMetadata(ImageInfo.java:577)
	at loci.formats.tools.ImageInfo.testRead(ImageInfo.java:1048)

chunks are [64, 64, 64]. However, since this dataset follows ome/ngff#114 we might should handle this separately from this PR.

Originally posted by @joshmoore in #31 (comment)

@joshmoore
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From @dgault:

Proposed 0.5 changes From Josh's comment #31 (comment), I have only taken a quick look but this seem like a pretty major breaking change and certainly not for this PR. The metadata appears to have different values for shape and chunks. Currently we are reading the shape values via JZarr.

Also, @thewtex has merged the related PR:
spatial-image/multiscale-spatial-image#32 (comment)

@joshmoore joshmoore self-assigned this May 26, 2022
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