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Task #13144 (new)

Opened 4 years ago

Last modified 14 months ago

Bug: Minimal Tiff Reader - Index out of bounds exception

Reported by: dgault Owned by:
Priority: minor Milestone: Unscheduled
Component: Bio-Formats Version: BIo-Formats-5.1.5
Keywords: MinimalTiffReader, our-fault Cc: m.porter@…
Resources: n.a. Referenced By: n.a.
References: n.a. Remaining Time: n.a.
Sprint: n.a.

Description

Bug has been reported in QA-16978
https://www.openmicroscopy.org/qa2/qa/feedback/16978/

Issue can be reproduced with the sample file provide, index out of bounds exception is thrown in the tiff parser as the metadata for images 8 onwards in the series appear to be incorrect (starts expecting multiple channels and incorrect looking numRows and row length).

java.lang.RuntimeException?: Failure response on import!
Category: ::omero::grid::ImportRequest?
Name: import-request-failure
Parameters: {stacktrace=java.lang.ArrayIndexOutOfBoundsException?

at loci.formats.tiff.TiffParser?.getSamples(TiffParser?.java:1025)
at loci.formats.tiff.TiffParser?.getSamples(TiffParser?.java:785)
at loci.formats.in.MinimalTiffReader?.openBytes(MinimalTiffReader?.java:299)

Change History (5)

comment:1 Changed 4 years ago by mlinkert

  • Sprint Bugs Fixing deleted
  • Summary changed from Minimal Tiff Reader - Index out of bounds exception to Bug: Minimal Tiff Reader - Index out of bounds exception
  • Type changed from Bug to Task

comment:2 Changed 4 years ago by mlinkert

  • Component set to Bio-Formats
  • Keywords MinimalTiffReader added
  • Milestone changed from OMERO-4.4.7 to 5.x
  • Version set to BIo-Formats-5.1.5

NB: changed ticket type and milestone so that this shows up in ticket reports.

comment:3 Changed 4 years ago by jamoore

  • Milestone changed from 5.x to Unscheduled

comment:4 Changed 4 years ago by mlinkert

  • Keywords our-fault added
  • Owner dgault deleted

Confirmed that this is still an issue with latest develop; the exception can be reproduced with 'showinf -range 8 8 16978/P-TRE_12_R3D_D3D-Part1.tif'

The problem is that the channel count and rows per strip changes after the first 8 planes, as can be confirmed by the output of tiffdump. MinimalTiffReader/BaseTiffReader? currently assume that all planes have the same dimensions and channel counts, so this likely means that the planes will need to be split into two series based upon the channel count.

comment:5 Changed 14 months ago by mlinkert

https://github.com/openmicroscopy/bioformats/pull/3202 is a prerequisite but not sufficient to fix this case.

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