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Task #10623 (closed)

Opened 11 years ago

Closed 11 years ago

Bug: > 4 GB Amira files not read correctly

Reported by:	omero-qa	Owned by:	mlinkert
Priority:	minor	Milestone:	OMERO-4.4.7
Component:	Bio-Formats	Version:	n.a.
Keywords:	n.a.	Cc:	ilya.belevich@…
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/4983/

Comment: there is a problem with reading large (>4Gb) AmiraMesh? files with bio-formats reader

java.lang.IllegalArgumentException: Negative position
	at sun.nio.ch.FileChannelImpl.read(Unknown Source)
	at loci.common.NIOByteBufferProvider.allocateDirect(NIOByteBufferProvider.java:133)
	at loci.common.NIOByteBufferProvider.allocate(NIOByteBufferProvider.java:118)
	at loci.common.NIOFileHandle.buffer(NIOFileHandle.java:532)
	at loci.common.NIOFileHandle.seek(NIOFileHandle.java:254)
	at loci.common.RandomAccessInputStream.seek(RandomAccessInputStream.java:140)
	at loci.formats.in.AmiraReader.openBytes(AmiraReader.java:108)
	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:885)
	at ome.formats.importer.ImportLibrary.importData(ImportLibrary.java:810)
	at ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:586)
	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)

See the file in amira/ilya/.

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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