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Task #10647 (closed)

Opened 11 years ago

Closed 11 years ago

Bug: truncated LZW images not always supported

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

Description

See QA 5004 - 5006.

https://www.openmicroscopy.org/qa2/qa2/qa/feedback/5004/

Comment: Tiff-files generated with Nikon NIS-Elements 4.x

loci.formats.FormatException: java.io.EOFException: Attempting to read beyond end of file.
	at loci.formats.codec.BaseCodec.decompress(BaseCodec.java:188)
	at loci.formats.tiff.TiffCompression.decompress(TiffCompression.java:278)
	at loci.formats.tiff.TiffParser.getTile(TiffParser.java:699)
	at loci.formats.tiff.TiffParser.getSamples(TiffParser.java:878)
	at loci.formats.tiff.TiffParser.getSamples(TiffParser.java:739)
	at loci.formats.in.MinimalTiffReader.openBytes(MinimalTiffReader.java:292)
	at loci.formats.ImageReader.openBytes(ImageReader.java:414)
	at loci.formats.ChannelFiller.openBytes(ChannelFiller.java:197)
	at loci.formats.ChannelFiller.openBytes(ChannelFiller.java:189)
	at loci.formats.ChannelSeparator.openBytes(ChannelSeparator.java:197)
	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:1215)
	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:722)
Caused by: java.io.EOFException: Attempting to read beyond end of file.
	at loci.common.ByteArrayHandle.readByte(ByteArrayHandle.java:204)
	at loci.common.RandomAccessInputStream.readByte(RandomAccessInputStream.java:353)
	at loci.common.RandomAccessInputStream.read(RandomAccessInputStream.java:470)
	at loci.formats.codec.LZWCodec.decompress(LZWCodec.java:320)
	at loci.formats.codec.BaseCodec.decompress(BaseCodec.java:183)
	... 26 more

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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