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Task #12864 (closed)

Opened 9 years ago

Closed 9 years ago

Last modified 9 years ago

Bug: LeicaSCNReader IndexOutOfBoundsException

Reported by: omero-qa Owned by: mlinkert
Priority: minor Milestone: OMERO-5.1.4
Component: from QA Version: 5.1.1
Keywords: n.a. Cc: pognonec@…
Resources: n.a. Referenced By: n.a.
References: n.a. Remaining Time: 0.0d
Sprint: n.a.

Description

https://www.openmicroscopy.org/qa2/qa/feedback/11049/

Comment: This file is from a Leica virtual slide scanner. Strangely, it is the only one from 14 scans from the same batch to be rejected by Omero.

java.lang.IndexOutOfBoundsException: Index: 3, Size: 3
	at java.util.ArrayList.rangeCheck(ArrayList.java:653)
	at java.util.ArrayList.get(ArrayList.java:429)
	at loci.formats.in.LeicaSCNReader.initStandardMetadata(LeicaSCNReader.java:322)
	at loci.formats.in.BaseTiffReader.initMetadata(BaseTiffReader.java:95)
	at loci.formats.in.BaseTiffReader.initFile(BaseTiffReader.java:542)
	at loci.formats.FormatReader.setId(FormatReader.java:1395)
	at loci.formats.ImageReader.setId(ImageReader.java:835)
	at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:651)
	at loci.formats.ChannelFiller.setId(ChannelFiller.java:223)
	at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:651)
	at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:289)
	at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:651)
	at loci.formats.Memoizer.setId(Memoizer.java:614)
	at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:651)
	at ome.formats.importer.ImportCandidates.singleFile(ImportCandidates.java:414)
	at ome.formats.importer.ImportCandidates.handleFile(ImportCandidates.java:570)
	at ome.formats.importer.ImportCandidates.execute(ImportCandidates.java:371)
	at ome.formats.importer.ImportCandidates.<init>(ImportCandidates.java:229)
	at ome.formats.importer.ImportCandidates.<init>(ImportCandidates.java:180)
	at org.openmicroscopy.shoola.env.data.OMEROGateway.getImportCandidates(OMEROGateway.java:6849)
	at org.openmicroscopy.shoola.env.data.OmeroImageServiceImpl.importFile(OmeroImageServiceImpl.java:1174)
	at org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter.importFile(ImagesImporter.java:79)
	at org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter.access$000(ImagesImporter.java:55)
	at org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter$1.doCall(ImagesImporter.java:104)
	at org.openmicroscopy.shoola.env.data.views.BatchCall.doStep(BatchCall.java:144)
	at org.openmicroscopy.shoola.util.concur.tasks.CompositeTask.doStep(CompositeTask.java:226)
	at org.openmicroscopy.shoola.env.data.views.CompositeBatchCall.doStep(CompositeBatchCall.java:126)
	at org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.exec(ExecCommand.java:165)
	at org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.run(ExecCommand.java:276)
	at org.openmicroscopy.shoola.util.concur.tasks.AsyncProcessor$Runner.run(AsyncProcessor.java:91)
	at java.lang.Thread.run(Thread.java:745)

Change History (4)

comment:1 Changed 9 years ago by mlinkert

  • Milestone changed from Unscheduled to 5.1.4

comment:2 Changed 9 years ago by mlinkert

  • Resolution set to fixed
  • Status changed from new to closed

comment:3 Changed 9 years ago by Melissa Linkert <melissa@…>

  • Remaining Time set to 0

(In [dcad0e408a8ffff2999e721e905a64dfd7f06c7b/bioformats.git] on branch develop) Leica SCN: do not report more resolutions than there are IFDs

Fixes #12864.

comment:4 Changed 9 years ago by jamoore

  • Milestone changed from 5.1.4 to OMERO-5.1.4

Splitting 5.1.4 due to milestone decoupling

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