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Task #10234 (closed)

Opened 11 years ago

Closed 11 years ago

Last modified 11 years ago

Bug: truncated .fits files cannot be imported

Reported by: omero-qa Owned by: mlinkert
Priority: minor Milestone: OMERO-4.4.7
Component: Bio-Formats Version: n.a.
Keywords: n.a. Cc: jacques.pecreaux@…
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/4825/

Comment: Importing a fits file created on an andor iXon+ with software iXon (now named solis). This file contain an inherent bug: the fits file is announced to be of its maximum size (about 4096) but is in fact shorter since acquisition was interupted. It seems to fool the importer since it do import a large number of plane before crashing

java.lang.IllegalArgumentException
	at java.nio.Buffer.position(Buffer.java:218)
	at loci.common.NIOFileHandle.buffer(NIOFileHandle.java:535)
	at loci.common.NIOFileHandle.seek(NIOFileHandle.java:254)
	at loci.common.RandomAccessInputStream.seek(RandomAccessInputStream.java:140)
	at loci.formats.in.FitsReader.openBytes(FitsReader.java:87)
	at loci.formats.ImageReader.openBytes(ImageReader.java:414)
	at loci.formats.ChannelFiller.openBytes(ChannelFiller.java:197)
	at loci.formats.ChannelSeparator.openBytes(ChannelSeparator.java:226)
	at loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:317)
	at loci.formats.MinMaxCalculator.openBytes(MinMaxCalculator.java:273)
	at ome.formats.importer.ImportLibrary.writeDataTileBased(ImportLibrary.java:876)
	at ome.formats.importer.ImportLibrary.importData(ImportLibrary.java:801)
	at ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:577)
	at org.openmicroscopy.shoola.env.data.OMEROGateway.importImage(OMEROGateway.java:6443)
	at org.openmicroscopy.shoola.env.data.OmeroImageServiceImpl.importFile(OmeroImageServiceImpl.java:1250)
	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:662)

See also QA 4827.

Change History (3)

comment:1 Changed 11 years ago by mlinkert

  • Owner changed from mlinkert-x to mlinkert

comment:2 Changed 11 years ago by mlinkert

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

comment:3 Changed 11 years ago by jmoore

  • Component changed from from QA to Bio-Formats
  • Milestone changed from Unscheduled to OMERO-4.5
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