MRXS: fix PNG tile support #146
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muhanadz
approved these changes
Apr 8, 2022
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Without the PR, testing Mirax2.2-4-PNG.mrxs with:
Version = 0.4.0
Bio-Formats version = 6.8.0
throws multiple ArrayIndexOutOfBoundsException
With the PR, testing Mirax2.2-4-PNG.mrxs with:
Version = 0.4.1-SNAPSHOT
Bio-Formats version = 6.8.0
throws no exception. The output file was converted to OME-TIFF using raw2ometiff with no problems. The OME-TIFF opens and looks as expected in QuPath with multiple series and resolution pyramids.
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Fixes #124.
https://openslide.cs.cmu.edu/download/openslide-testdata/Mirax/Mirax2.2-4-PNG.zip reproduces the issue. Without this PR, attempting to convert
Mirax2.2-4-PNG.mrxsshould throwArrayIndexOutOfBoundsExceptionmany times, as noted in #124. With this PR, the same conversion should succeed, and running raw2ometiff afterwards should produce an OME-TIFF that looks reasonable in QuPath/showinf.