[ome-users] Problem opening large NRRD volume

[B Sys]

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
>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.openmicroscopy.org.uk/pipermail/ome-users/attachments/20120612/e77d01e7/attachment.html>