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Range [X, X+X) out of bounds for length X

Open evhen14 opened this issue 2 years ago • 2 comments

Dear Bio Formats team,

unfortunately, the latest version (6.11.1 and 6.11.0) of bioformats_package.jar produces an error that I expect to be avoidable.

image Command used: ./bftools/bfconvert -no-upgrade 3546a516-a1f8-4666-a962-95be246fc54f.tiff ff.ome.tif

The input file: https://www.dropbox.com/s/m5sn4s9ag24d1uq/3546a516-a1f8-4666-a962-95be246fc54f.tiff?dl=0

evhen14 avatar Jan 23 '23 07:01 evhen14

Hi @evhen14, thank you for raising the issue and providing a sample file. I can confirm that I was able to reproduce this bug with the latest Bio-Formats release. Further investigation will be needed to find the root cause of the issue.

dgault avatar Jan 23 '23 14:01 dgault

The issue is a combination of there being 4 samples per pixel, and the image height (4200) not being a multiple of the default tile height (32) when the tiles are the full image width ("strips" in TIFF terminology).

Using something like bfconvert -tilex 512 -tiley 512 3546a516-a1f8-4666-a962-95be246fc54f.tiff output.ome.tiff should work around this problem until we have a better solution. Note that bfconvert -tilex 5600 -tiley 8 3546a516-a1f8-4666-a962-95be246fc54f.tiff output.ome.tiff will not work, as the tile height will be automatically adjusted to 16 for compliance with the TIFF specification.

melissalinkert avatar Mar 09 '23 22:03 melissalinkert