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SVS: IndexOutOfBoundsException when opening lower resolutions

Open dgault opened this issue 3 years ago • 1 comments

Issue was raised on forum thread https://forum.image.sc/t/cannot-import-svs-file-using-bioformats/71840

A sample file reproducing the issue can be found at GDC (tested with BF 6.10.1)

Exception in thread "BioFormats-ThumbLoader" java.lang.IndexOutOfBoundsException: Index: 0, Size: 0
	at java.util.ArrayList.rangeCheck(ArrayList.java:657)
	at java.util.ArrayList.get(ArrayList.java:433)
	at loci.formats.in.MinimalTiffReader.openBytes(MinimalTiffReader.java:303)
	at loci.formats.in.SVSReader.openBytes(SVSReader.java:173)

The exception does not appear to occur with the highest level resolution and is likely linked to sub-resolution issues with the SVS reader

dgault avatar Sep 20 '22 12:09 dgault

This issue has been mentioned on Image.sc Forum. There might be relevant details there:

https://forum.image.sc/t/cannot-import-svs-file-using-bioformats/71840/2

imagesc-bot avatar Sep 20 '22 12:09 imagesc-bot

Issue appears to have been resolved by https://github.com/ome/bioformats/pull/3962 I will configure the sample file from this issue and add it to the data repo as a follow up.

dgault avatar Apr 06 '23 19:04 dgault