[ome-users] Problem opening large NRRD volume

[Melissa Linkert]

Hi Carlos,

> > 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:

Thank you very much for reporting this problem, and for sending the
relevant dataset.  The problem will be fixed in the upcoming 4.4 release
of Bio-Formats.

Regards,
-Melissa

On Tue, Jun 12, 2012 at 03:34:58PM +0200, B Sys wrote:
> LOCI version is
> 
> LOCI Plugins for ImageJ, revision d3781f8 built 24 april 2012
> Release 4.4-DEV
> 
> On Tue, Jun 12, 2012 at 10:42 AM, B Sys <bsys.com.ar at gmail.com> wrote:
> 
> > 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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