[ome-users] Problem opening large NRRD volume

[B Sys]

Hello, I have came across a possible bug when opening a large NRRD file.
I found it when trying to open it with Fiji, so I had contacted people form
the Fiji development team. They told me that it appears to be a BioFormats
issue.

I am using Linux 64-bit (Arch Linux), but I have also seen this issue in
Ubuntu 64-bit.

You can find a bzipped version of the volume attached, which will
uncompress to approximately 3.6GB. I am still trying to find which
BioFormats version Fiji is using, but I still couldn't manage to do it.
Surely it is one of the latest, since it says that it is up-to-date.

The error message is the following:

java.lang.IllegalArgumentException: Negative position
at sun.nio.ch.FileChannelImpl.read(FileChannelImpl.java:600)
at
loci.common.NIOByteBufferProvider.allocateDirect(NIOByteBufferProvider.java:120)
at
loci.common.NIOByteBufferProvider.allocate(NIOByteBufferProvider.java:105)
at loci.common.NIOFileHandle.buffer(NIOFileHandle.java:520)
at loci.common.NIOFileHandle.seek(NIOFileHandle.java:241)
at
loci.common.RandomAccessInputStream.seek(RandomAccessInputStream.java:116)
at loci.formats.in.NRRDReader.openBytes(NRRDReader.java:150)
at loci.formats.ChannelFiller.openBytes(ChannelFiller.java:184)
at loci.formats.ChannelFiller.openBytes(ChannelFiller.java:176)
at loci.formats.ChannelSeparator.openBytes(ChannelSeparator.java:184)
at loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:304)
at loci.formats.DimensionSwapper.openBytes(DimensionSwapper.java:249)
at loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:304)
at loci.formats.MinMaxCalculator.openBytes(MinMaxCalculator.java:260)
at loci.formats.MinMaxCalculator.openBytes(MinMaxCalculator.java:252)
at loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:292)
at loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:292)
at
loci.plugins.util.ImageProcessorReader.openProcessors(ImageProcessorReader.java:188)
at loci.plugins.in.ImagePlusRea
1der.readProcessors(ImagePlusReader.java:414)
at loci.plugins.in.ImagePlusReader.readPlanes(ImagePlusReader.java:378)
at loci.plugins.in.ImagePlusReader.readImage(ImagePlusReader.java:275)
at loci.plugins.in.ImagePlusReader.readImages(ImagePlusReader.java:236)
at loci.plugins.in.ImagePlusReader.readImages(ImagePlusReader.java:214)
at loci.plugins.in.ImagePlusReader.openImagePlus(ImagePlusReader.java:112)
at loci.plugins.in.Importer.readPixels(Importer.java:148)
at loci.plugins.in.Importer.run(Importer.java:87)
at loci.plugins.LociImporter.run(LociImporter.java:79)
at ij.IJ.runUserPlugIn(IJ.java:185)
at ij.IJ.runPlugIn(IJ.java:152)
at ij.IJ.runPlugIn(IJ.java:141)
at HandleExtraFileTypes.openImage(HandleExtraFileTypes.java:375)
at HandleExtraFileTypes.run(HandleExtraFileTypes.java:53)
at ij.IJ.runUserPlugIn(IJ.java:185)
at ij.IJ.runPlugIn(IJ.java:152)
at ij.IJ.runPlugIn(IJ.java:141)
at ij.io.Opener.openWithHandleExtraFileTypes(Opener.java:413)
at ij.io.Opener.openImage(Opener.java:288)
at ij.io.Opener.openImage(Opener.java:309)
at ij.io.Opener.open(Opener.java:138)
at ij.io.Opener.openAndAddToRecent(Opener.java:224)
at ij.plugin.DragAndDrop.openFile(DragAndDrop.java:176)
at ij.plugin.DragAndDrop.run(DragAndDrop.java:152)
at java.lang.Thread.run(Thread.java:662)

Let me know if I can help in any other way,
Carlos
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