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Task #12919 (closed)

Opened 9 years ago

Closed 8 years ago

BUG:SlidebookReader ArrayIndexOutOfBoundsException

Reported by: omero-qa Owned by:
Priority: minor Milestone: Unscheduled
Component: Bio-Formats Version: 5.1.2
Keywords: SlidebookReader Cc: kimmo.tanhuanpaa@…
Resources: n.a. Referenced By: n.a.
References: n.a. Remaining Time: n.a.
Sprint: n.a.

Description

​https://www.openmicroscopy.org/qa2/qa2/qa/feedback/11119/

java.lang.ArrayIndexOutOfBoundsException: 0
	at loci.formats.in.SlidebookReader.initFile(SlidebookReader.java:634)
	at loci.formats.FormatReader.setId(FormatReader.java:1426)
	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:650)
	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:6772)
	at org.openmicroscopy.shoola.env.data.OmeroImageServiceImpl.importFile(OmeroImageServiceImpl.java:1033)
	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)

	at org.openmicroscopy.shoola.env.data.util.StatusLabel.update(StatusLabel.java:673)
	at ome.formats.importer.ImportCandidates.safeUpdate(ImportCandidates.java:530)
	at ome.formats.importer.ImportCandidates.singleFile(ImportCandidates.java:465)
	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:6772)
	at org.openmicroscopy.shoola.env.data.OmeroImageServiceImpl.importFile(OmeroImageServiceImpl.java:1033)
	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)
Caused by: java.lang.ArrayIndexOutOfBoundsException: 0
	at loci.formats.in.SlidebookReader.initFile(SlidebookReader.java:634)
	at loci.formats.FormatReader.setId(FormatReader.java:1426)
	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:650)
	at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:651)
	at ome.formats.importer.ImportCandidates.singleFile(ImportCandidates.java:414)
	... 16 more

Change History (7)

comment:1 Changed 9 years ago by mlinkert

  • Component changed from from QA to Bio-Formats
  • Milestone changed from Unscheduled to 5.1.4
  • Owner changed from mlinkert-x to mlinkert

comment:2 Changed 9 years ago by jamoore

  • Milestone changed from 5.1.4 to B-F-5.1.4

Splitting 5.1.4 due to milestone decoupling

comment:3 Changed 9 years ago by sbesson

  • Milestone changed from B-F-5.1.4 to BF-5.1.5

comment:5 Changed 8 years ago by mlinkert

  • Keywords SlidebookReader added
  • Owner mlinkert deleted

Expect this to take substantial time given the state of Slidebook support. Closing as wontfix or needsfunding would be OK with me.

comment:6 Changed 8 years ago by sbesson

  • Milestone changed from B-F-5.2.0 to Unscheduled

comment:7 Changed 8 years ago by sbesson

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

As of Bio-Formats 5.2.0, recent Slidebook files can be opened on all platforms using the 3i Slidebook reader. As this reader is completely externalized from Bio-Formats and fully maintained by 3i (see ​https://www.intelligent-imaging.com/techanswers.php#SLDinFiji), closing all these tickets with wontfix.

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