Bug: AVIReader: ArrayIndexOutOfBoundsException

[omero-qa]

​http://qa.openmicroscopy.org.uk/qa/feedback/7450/

Comment: AVI saved from Canon PC1249. Failed to import with 5.x daily build.

java.lang.ArrayIndexOutOfBoundsException: Array index out of range: 0
	at java.util.Vector.get(Vector.java:694)
	at loci.formats.in.AVIReader.initFile(AVIReader.java:338)
	at loci.formats.FormatReader.setId(FormatReader.java:1333)
	at loci.formats.ImageReader.setId(ImageReader.java:762)
	at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:564)
	at loci.formats.ChannelFiller.setId(ChannelFiller.java:263)
	at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:564)
	at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:274)
	at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:564)
	at loci.formats.Memoizer.setId(Memoizer.java:399)
	at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:564)
	at ome.formats.importer.ImportCandidates.singleFile(ImportCandidates.java:414)
	at ome.formats.importer.ImportCandidates.handleFile(ImportCandidates.java:596)
	at ome.formats.importer.ImportCandidates.execute(ImportCandidates.java:371)
	at ome.formats.importer.ImportCandidates.<init>(ImportCandidates.java:229)
	at ome.formats.importer.ImportCandidates.<init>(ImportCandidates.java:180)
	at org.openmicroscopy.shoola.env.data.OMEROGateway.getImportCandidates(OMEROGateway.java:6455)
	at org.openmicroscopy.shoola.env.data.OmeroImageServiceImpl.importFile(OmeroImageServiceImpl.java:1170)
	at org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter.importFile(ImagesImporter.java:77)
	at org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter.access$000(ImagesImporter.java:53)
	at org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter$1.doCall(ImagesImporter.java:102)
	at org.openmicroscopy.shoola.env.data.views.BatchCall.doStep(BatchCall.java:144)
	at org.openmicroscopy.shoola.util.concur.tasks.CompositeTask.doStep(CompositeTask.java:226)
	at org.openmicroscopy.shoola.env.data.views.CompositeBatchCall.doStep(CompositeBatchCall.java:126)
	at org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.exec(ExecCommand.java:165)
	at org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.run(ExecCommand.java:276)
	at org.openmicroscopy.shoola.util.concur.tasks.AsyncProcessor$Runner.run(AsyncProcessor.java:91)
	at java.lang.Thread.run(Thread.java:680)

[rleigh]

Looks like

    if (bmpCompression == JPEG) {
      long fileOff = offsets.get(0).longValue();

is accessing offsets before any elements have been added. None appear to have been added in readChunk() for this file (attached to the QA report).

[mlinkert]

Moving to 5.1.1 for triage.

[mlinkert]

QA 11011 is related in that the frame count is incorrect.

[mlinkert]

Fixed with ​https://github.com/openmicroscopy/bioformats/pull/1832

[Melissa Linkert <melissa@…>]

(In [0b3c3886cbbcae6b4f8324251ab0dc1351e87b08/bioformats.git] on branch develop) AVI: read the optional index table (idx1)

Some videos use an index table to specify the offsets to each plane,
instead of using the plane data streams in order. This allows for
looping and/or key frame re-use. See
​https://msdn.microsoft.com/en-us/library/windows/desktop/dd318181(v=vs.85).aspx

Fixes #11264.