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Task #10228 (closed)

Opened 7 years ago

Closed 6 years ago

Last modified 6 years ago

Bug: ND2 file corrupt on import, not viewable with FS

Reported by:	omero-qa	Owned by:	mlinkert
Priority:	minor	Milestone:	OMERO-4.4.7
Component:	Bio-Formats	Version:	n.a.
Keywords:	n.a.	Cc:	han.steve.sw@…
Resources:	n.a.	Referenced By:	n.a.
References:	n.a.	Remaining Time:	n.a.
Sprint:	Bugs Fixing

Description

This file imports with OMERO 4.4.5+ (howe), but the image looks visibly corrupt. Also imports with develop/FS (gretzky), but is not viewable at all (may be an FS performance issue).

https://www.openmicroscopy.org/qa2/qa2/qa/feedback/4836/

Comment: trying to import a nd2 file to colombus

java.lang.ArithmeticException: / by zero
	at loci.formats.in.NativeND2Reader.initFile(NativeND2Reader.java:498)
	at loci.formats.FormatReader.setId(FormatReader.java:914)
	at loci.formats.DelegateReader.setId(DelegateReader.java:176)
	at loci.formats.ImageReader.setId(ImageReader.java:596)
	at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:448)
	at loci.formats.ChannelFiller.setId(ChannelFiller.java:179)
	at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:448)
	at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:205)
	at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:448)
	at ome.formats.importer.ImportLibrary.open(ImportLibrary.java:219)
	at ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:398)
	at ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:340)
	at ome.formats.importer.gui.ImportHandler.importImages(ImportHandler.java:182)
	at ome.formats.importer.gui.ImportHandler.access$100(ImportHandler.java:45)
	at ome.formats.importer.gui.ImportHandler$2.run(ImportHandler.java:97)
	at java.util.concurrent.Executors$RunnableAdapter.call(Unknown Source)
	at java.util.concurrent.FutureTask$Sync.innerRun(Unknown Source)
	at java.util.concurrent.FutureTask.run(Unknown Source)
	at java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.access$201(Unknown Source)
	at java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(Unknown Source)
	at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
	at java.lang.Thread.run(Unknown Source)

References

Change History (5)

comment:1 Changed 7 years ago by rleigh

Component changed from from QA to Bio-Formats
Summary changed from BUG:Feedback 4836 to Bug: ND2 file corrupt on import, not viewable with FS

comment:2 Changed 7 years ago by rleigh

The file is viewable with FS, it was just big so needed pyramids to be generated. Same corruption as with 4.4.5.

comment:3 Changed 6 years ago by mlinkert

Owner changed from rleigh to mlinkert

comment:4 Changed 6 years ago by mlinkert

Resolution set to fixed
Status changed from new to closed

Fixed with: https://github.com/openmicroscopy/bioformats/pull/408

comment:5 Changed 6 years ago by jmoore

Milestone changed from Unscheduled to OMERO-4.5
Sprint set to Bugs Fixing

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