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Task #10699 (closed)

Opened 11 years ago

Closed 11 years ago

Bug: FV1000 reader throws NPE on missing thumbnail

Reported by:	omero-qa	Owned by:	mlinkert
Priority:	minor	Milestone:	OMERO-4.4.7
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:	n.a.

Description

https://www.openmicroscopy.org/qa2/qa2/qa/feedback/5018/

Comment: Hi all,
This is the same problem as earlier but this time with an updated OMERO.importer 4.4.6.
I'm uploading the file as requested.
Again I believe that this is due to misinformation between the metadata and the number of slices in a certain timepoint, due to early and abnormal termination of acquisition.

java.lang.NullPointerException
	at loci.formats.in.FV1000Reader.replaceExtension(FV1000Reader.java:1598)
	at loci.formats.in.FV1000Reader.initFile(FV1000Reader.java:599)
	at loci.formats.FormatReader.setId(FormatReader.java:1182)
	at loci.formats.ImageReader.setId(ImageReader.java:727)
	at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:529)
	at loci.formats.ChannelFiller.setId(ChannelFiller.java:263)
	at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:529)
	at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:274)
	at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:529)
	at ome.formats.importer.ImportLibrary.open(ImportLibrary.java:323)
	at ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:499)
	at org.openmicroscopy.shoola.env.data.OMEROGateway.importImage(OMEROGateway.java:6605)
	at org.openmicroscopy.shoola.env.data.OmeroImageServiceImpl.importFile(OmeroImageServiceImpl.java:1251)
	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(Unknown Source)

References

Change History (1)

comment:1 Changed 11 years ago by mlinkert

Component changed from from QA to Bio-Formats
Milestone changed from Unscheduled to OMERO-4.4.7
Resolution set to fixed
Status changed from new to closed

Fixed with https://github.com/openmicroscopy/bioformats/pull/478

This fix will be included in the upcoming 4.4.7 release.

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