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Task #9650 (closed)

Opened 12 years ago

Closed 12 years ago

Last modified 11 years ago

Bug: AVIReader fails to import MSVideo codec compressed AVIs

Reported by: rleigh Owned by: mlinkert
Priority: major Milestone: OMERO-4.4.7
Component: Bio-Formats Version: n.a.
Keywords: n.a. Cc:
Resources: n.a. Referenced By: n.a.
References: n.a. Remaining Time: n.a.
Sprint: 2012-11-20 (2)

Description

Data in from_skyking/avi/roger

I get different exceptions depending upon the file.

java.lang.ArrayIndexOutOfBoundsException: 788376
	at loci.formats.codec.MSVideoCodec.decompress(MSVideoCodec.java:233)
	at loci.formats.in.AVIReader.uncompress(AVIReader.java:409)
	at loci.formats.in.AVIReader.openBytes(AVIReader.java:206)
	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:873)
	at ome.formats.importer.ImportLibrary.importData(ImportLibrary.java:798)
	at ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:574)
	at org.openmicroscopy.shoola.env.data.OMEROGateway.importImage(OMEROGateway.java:6410)
	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:679)

	at org.openmicroscopy.shoola.env.data.OMEROGateway.importImage(OMEROGateway.java:6459)
	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:679)
Caused by: java.lang.ArrayIndexOutOfBoundsException: 788376
	at loci.formats.codec.MSVideoCodec.decompress(MSVideoCodec.java:233)
	at loci.formats.in.AVIReader.uncompress(AVIReader.java:409)
	at loci.formats.in.AVIReader.openBytes(AVIReader.java:206)
	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:873)
	at ome.formats.importer.ImportLibrary.importData(ImportLibrary.java:798)
	at ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:574)
	at org.openmicroscopy.shoola.env.data.OMEROGateway.importImage(OMEROGateway.java:6410)
	... 11 more

java.lang.ArrayIndexOutOfBoundsException

	at org.openmicroscopy.shoola.env.data.OMEROGateway.importImage(OMEROGateway.java:6459)
	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:679)
Caused by: java.lang.ArrayIndexOutOfBoundsException

Attachments (1)

Screen shot 2012-10-30 at 09.48.41.png​ (1.3 MB) - added by rleigh 11 years ago.
Insight vs QuickTime?

Download all attachments as: .zip

Change History (5)

comment:1 Changed 12 years ago by mlinkert

  • Sprint set to 2012-11-20 (2)

comment:2 Changed 12 years ago by mlinkert

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

PR filed: ​https://github.com/openmicroscopy/bioformats/pull/191

Changed 11 years ago by rleigh

Insight vs QuickTime?

comment:3 Changed 11 years ago by rleigh

I was looking a bit more closely at the above screenshot. I initially thought that the bioformats read image was pixellated with a 4x4 block size, but it looks (at least in some places) like the horizontal bands should perhaps just be inverted--the jagged edges of sloping/diagonal features would become smooth edges if each band was flipped?

comment:4 Changed 11 years ago by mlinkert

Yep, you're right - reversing the order of the rows in each of the 4x4 blocks seems to do the trick. PR updated.

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