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Task #9340 (closed)

Opened 7 years ago

Closed 7 years ago

Bug: BMP file does not open correctly

Reported by:	omero-qa	Owned by:	mlinkert
Priority:	minor	Milestone:	OMERO-4.4.4
Component:	Bio-Formats	Version:	n.a.
Keywords:	n.a.	Cc:	cwood1967@…
Resources:	n.a.	Referenced By:	n.a.
References:	n.a.	Remaining Time:	n.a.
Sprint:	n.a.

Description

http://qa.openmicroscopy.org.uk/qa/feedback/4538/

Comment: Bitmap File won't import

java.lang.IllegalArgumentException
	at java.nio.Buffer.position(Buffer.java:218)
	at loci.common.NIOFileHandle.buffer(NIOFileHandle.java:513)
	at loci.common.NIOFileHandle.skipBytes(NIOFileHandle.java:375)
	at loci.common.RandomAccessInputStream.skipBytes(RandomAccessInputStream.java:387)
	at loci.formats.in.BMPReader.openBytes(BMPReader.java:129)
	at loci.formats.FormatReader.openBytes(FormatReader.java:739)
	at loci.formats.ImageReader.openBytes(ImageReader.java:387)
	at loci.formats.ChannelFiller.getLookupTableComponentCount(ChannelFiller.java:267)
	at loci.formats.ChannelFiller.setId(ChannelFiller.java:250)
	at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:488)
	at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:257)
	at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:488)
	at ome.formats.importer.ImportLibrary.open(ImportLibrary.java:312)
	at ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:488)
	at org.openmicroscopy.shoola.env.data.OMEROGateway.importImage(OMEROGateway.java:6402)
	at org.openmicroscopy.shoola.env.data.OmeroImageServiceImpl.importFile(OmeroImageServiceImpl.java:1228)
	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$1.doCall(ImagesImporter.java:111)
	at org.openmicroscopy.shoola.env.data.views.BatchCall.doStep(BatchCall.java:144)
	at org.openmicroscopy.shoola.util.concur.tasks.CompositeTask.doStep(CompositeTask.java:226)
	at org.openmicroscopy.shoola.env.data.views.CompositeBatchCall.doStep(CompositeBatchCall.java:126)
	at org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.exec(ExecCommand.java:165)
	at org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.run(ExecCommand.java:274)
	at org.openmicroscopy.shoola.util.concur.tasks.AsyncProcessor$Runner.run(AsyncProcessor.java:91)
	at java.lang.Thread.run(Thread.java:680)

This error shouldn't occur with 4.4.0, but the image still looks incorrect, likely due to a non-standard usage of byte padding.

References

Change History (2)

comment:1 Changed 7 years ago by mlinkert

Milestone changed from Unscheduled to OMERO-4.4.1

comment:2 Changed 7 years ago by mlinkert

Component changed from from QA to Bio-Formats
Resolution set to fixed
Status changed from new to closed

Fixed with: https://github.com/melissalinkert/bioformats/commit/1fcf980435f6a5a2d550f6b1373ec3219e5ee334

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