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Task #9600 (closed)

Opened 12 years ago

Closed 12 years ago

Bug: Some Ultraview datasets do not open

Reported by: omero-qa Owned by: mlinkert
Priority: blocker Milestone: OMERO-4.4.4
Component: Bio-Formats Version: n.a.
Keywords: n.a. Cc: helio.roque@…
Resources: n.a. Referenced By: n.a.
References: n.a. Remaining Time: n.a.
Sprint: 2012-09-25 (5)

Description

The source of the problem seems to be having some pixels files that contain a single Z section mixed with some pixels files that contain all of the Z sections for a particular timepoint. See the file listing in the QA comment.

​http://qa.openmicroscopy.org.uk/qa/feedback/4625/

Comment: Even choosing the htm file the dataset still fails.

java.lang.ArrayIndexOutOfBoundsException: 6698
	at loci.formats.in.PerkinElmerReader.initFile(PerkinElmerReader.java:385)
	at loci.formats.FormatReader.setId(FormatReader.java:1105)
	at loci.formats.ImageReader.setId(ImageReader.java:695)
	at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:505)
	at loci.formats.ChannelFiller.setId(ChannelFiller.java:263)
	at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:505)
	at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:274)
	at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:505)
	at ome.formats.importer.ImportLibrary.open(ImportLibrary.java:310)
	at ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:486)
	at org.openmicroscopy.shoola.env.data.OMEROGateway.importImage(OMEROGateway.java:6335)
	at org.openmicroscopy.shoola.env.data.OmeroImageServiceImpl.importFile(OmeroImageServiceImpl.java:1248)
	at org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter.importFile(ImagesImporter.java:85)
	at org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter.access$000(ImagesImporter.java:54)
	at org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter$1.doCall(ImagesImporter.java:110)
	at org.openmicroscopy.shoola.env.data.views.BatchCall.doStep(BatchCall.java:144)
	at org.openmicroscopy.shoola.util.concur.tasks.CompositeTask.doStep(CompositeTask.java:226)
	at org.openmicroscopy.shoola.env.data.views.CompositeBatchCall.doStep(CompositeBatchCall.java:126)
	at org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.exec(ExecCommand.java:165)
	at org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.run(ExecCommand.java:276)
	at org.openmicroscopy.shoola.util.concur.tasks.AsyncProcessor$Runner.run(AsyncProcessor.java:91)
	at java.lang.Thread.run(Thread.java:680)

Change History (3)

comment:1 Changed 12 years ago by mlinkert

  • Component changed from from QA to Bio-Formats
  • Milestone changed from Unscheduled to OMERO-4.4.4
  • Priority changed from minor to major
  • Sprint set to 2012-09-25 (5)

comment:2 Changed 12 years ago by jmoore

  • Priority changed from major to blocker

Elevating to blocker if it's to be included in 4.4.4

comment:3 Changed 12 years ago by mlinkert

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

See: ​https://github.com/openmicroscopy/bioformats/pull/144

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