ImageJ java.lang.IllegalArgumentException: Negative position error

[Youngjae Jeong]

​Hello all,

I recently have started to figure out how to use imageJ to analyze the uCT scans of bone geometry. The size of raw file is quite large, which is about 16GB. Because of lare size of the file, it gives me an error with memory issue. So what I have tried next is to open up file by specifying the range of images. The size of file is 2048x2048; 2016 planes. It shows me an image when I have selected 1(Z begin)-250(Z End) with 1 for Z step. The problem arise when I have tried to select beyond 250 and it gives me following messages.

The file I am opening is ct.img.hdr file and this scan was done by inveon uCT scan. The disc image file (.ct) is ~16GB


(Fiji Is Just) ImageJ 2.0.0-rc-15/1.49m; Java 1.6.0_24 [64-bit]; Windows NT (unknown) 6.2; 527MB of 2977MB (17%)
 
 java.lang.IllegalArgumentException: Negative position
  at sun.nio.ch.FileChannelImpl.read(FileChannelImpl.java:600)
  at loci.common.NIOByteBufferProvider.allocateDirect(NIOByteBufferProvider.java:131)
  at loci.common.NIOByteBufferProvider.allocate(NIOByteBufferProvider.java:116)
  at loci.common.NIOFileHandle.buffer(NIOFileHandle.java:551)
  at loci.common.NIOFileHandle.seek(NIOFileHandle.java:273)
  at loci.common.RandomAccessInputStream.seek(RandomAccessInputStream.java:154)
  at loci.formats.in.InveonReader.openBytes(InveonReader.java:118)
  at loci.formats.ChannelFiller.openBytes(ChannelFiller.java:193)
  at loci.formats.ChannelSeparator.openBytes(ChannelSeparator.java:222)
  at loci.formats.ChannelSeparator.openBytes(ChannelSeparator.java:155)
  at loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:313)
  at loci.formats.DimensionSwapper.openBytes(DimensionSwapper.java:243)
  at loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:313)
  at loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:313)
  at loci.plugins.util.ImageProcessorReader.openProcessors(ImageProcessorReader.java:190)
  at loci.plugins.in.ImagePlusReader.readProcessors(ImagePlusReader.java:416)
  at loci.plugins.in.ImagePlusReader.readPlanes(ImagePlusReader.java:380)
  at loci.plugins.in.ImagePlusReader.readImage(ImagePlusReader.java:277)
  at loci.plugins.in.ImagePlusReader.readImages(ImagePlusReader.java:238)
  at loci.plugins.in.ImagePlusReader.readImages(ImagePlusReader.java:216)
  at loci.plugins.in.ImagePlusReader.openImagePlus(ImagePlusReader.java:114)
  at loci.plugins.in.Importer.readPixels(Importer.java:150)
  at loci.plugins.in.Importer.run(Importer.java:89)
  at loci.plugins.LociImporter.run(LociImporter.java:81)
  at ij.IJ.runUserPlugIn(IJ.java:202)
  at ij.IJ.runPlugIn(IJ.java:166)
  at ij.IJ.runPlugIn(IJ.java:155)
  at HandleExtraFileTypes.openImage(HandleExtraFileTypes.java:421)
  at HandleExtraFileTypes.run(HandleExtraFileTypes.java:57)
  at ij.IJ.runUserPlugIn(IJ.java:202)
  at ij.IJ.runPlugIn(IJ.java:166)
  at ij.IJ.runPlugIn(IJ.java:155)
  at ij.io.Opener.openWithHandleExtraFileTypes(Opener.java:483)
  at ij.io.Opener.openImage(Opener.java:361)
  at ij.plugin.FolderOpener.run(FolderOpener.java:114)
  at ij.IJ.runPlugIn(IJ.java:172)
  at ij.Executer.runCommand(Executer.java:131)
  at ij.Executer.run(Executer.java:64)
  at java.lang.Thread.run(Thread.java:662)


I am kinda naive on java.script and imageJ as well. Can anyone tell me what I am doing wrong?? or any reason of this error?


Thank you,

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[ctrueden]

Hi Youngjae,

>  java.lang.IllegalArgumentException: Negative position
>   at sun.nio.ch.FileChannelImpl.read(FileChannelImpl.java:600)
>   at loci.common.NIOByteBufferProvider.allocateDirect(
NIOByteBufferProvider.java:131)

Looks like a bug in the Bio-Formats library.

Please report this bug to the Bio-Formats team:
http://openmicroscopy.org/info/bio-formats/about/bug-reporting.html

Regards,
Curtis

On Wed, Dec 17, 2014 at 4:05 PM, Youngjae Jeong <[hidden email]>
wrote:

>
> ​Hello all,
>
> I recently have started to figure out how to use imageJ to analyze the uCT
> scans of bone geometry. The size of raw file is quite large, which is about
> 16GB. Because of lare size of the file, it gives me an error with memory
> issue. So what I have tried next is to open up file by specifying the range
> of images. The size of file is 2048x2048; 2016 planes. It shows me an image
> when I have selected 1(Z begin)-250(Z End) with 1 for Z step. The problem
> arise when I have tried to select beyond 250 and it gives me following
> messages.
>
> The file I am opening is ct.img.hdr file and this scan was done by inveon
> uCT scan. The disc image file (.ct) is ~16GB
>
>
> (Fiji Is Just) ImageJ 2.0.0-rc-15/1.49m; Java 1.6.0_24 [64-bit]; Windows
> NT (unknown) 6.2; 527MB of 2977MB (17%)
>
>  java.lang.IllegalArgumentException: Negative position
>   at sun.nio.ch.FileChannelImpl.read(FileChannelImpl.java:600)
>   at
> loci.common.NIOByteBufferProvider.allocateDirect(NIOByteBufferProvider.java:131)
>   at
> loci.common.NIOByteBufferProvider.allocate(NIOByteBufferProvider.java:116)
>   at loci.common.NIOFileHandle.buffer(NIOFileHandle.java:551)
>   at loci.common.NIOFileHandle.seek(NIOFileHandle.java:273)
>   at
> loci.common.RandomAccessInputStream.seek(RandomAccessInputStream.java:154)
>   at loci.formats.in.InveonReader.openBytes(InveonReader.java:118)
>   at loci.formats.ChannelFiller.openBytes(ChannelFiller.java:193)
>   at loci.formats.ChannelSeparator.openBytes(ChannelSeparator.java:222)
>   at loci.formats.ChannelSeparator.openBytes(ChannelSeparator.java:155)
>   at loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:313)
>   at loci.formats.DimensionSwapper.openBytes(DimensionSwapper.java:243)
>   at loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:313)
>   at loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:313)
>   at
> loci.plugins.util.ImageProcessorReader.openProcessors(ImageProcessorReader.java:190)
>   at
> loci.plugins.in.ImagePlusReader.readProcessors(ImagePlusReader.java:416)
>   at loci.plugins.in.ImagePlusReader.readPlanes(ImagePlusReader.java:380)
>   at loci.plugins.in.ImagePlusReader.readImage(ImagePlusReader.java:277)
>   at loci.plugins.in.ImagePlusReader.readImages(ImagePlusReader.java:238)
>   at loci.plugins.in.ImagePlusReader.readImages(ImagePlusReader.java:216)
>   at
> loci.plugins.in.ImagePlusReader.openImagePlus(ImagePlusReader.java:114)
>   at loci.plugins.in.Importer.readPixels(Importer.java:150)
>   at loci.plugins.in.Importer.run(Importer.java:89)
>   at loci.plugins.LociImporter.run(LociImporter.java:81)
>   at ij.IJ.runUserPlugIn(IJ.java:202)
>   at ij.IJ.runPlugIn(IJ.java:166)
>   at ij.IJ.runPlugIn(IJ.java:155)
>   at HandleExtraFileTypes.openImage(HandleExtraFileTypes.java:421)
>   at HandleExtraFileTypes.run(HandleExtraFileTypes.java:57)
>   at ij.IJ.runUserPlugIn(IJ.java:202)
>   at ij.IJ.runPlugIn(IJ.java:166)
>   at ij.IJ.runPlugIn(IJ.java:155)
>   at ij.io.Opener.openWithHandleExtraFileTypes(Opener.java:483)
>   at ij.io.Opener.openImage(Opener.java:361)
>   at ij.plugin.FolderOpener.run(FolderOpener.java:114)
>   at ij.IJ.runPlugIn(IJ.java:172)
>   at ij.Executer.runCommand(Executer.java:131)
>   at ij.Executer.run(Executer.java:64)
>   at java.lang.Thread.run(Thread.java:662)
>
>
> I am kinda naive on java.script and imageJ as well. Can anyone tell me
> what I am doing wrong?? or any reason of this error?
>
>
> Thank you,
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

... [show rest of quote]

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[Youngjae Jeong]

Thanks for the reply. I just reported as you have suggested.

Youngjae Jeong


________________________________________
From: ImageJ Interest Group <[hidden email]> on behalf of Curtis Rueden <[hidden email]>
Sent: Thursday, December 18, 2014 1:09 PM
To: [hidden email]
Subject: Re: ImageJ java.lang.IllegalArgumentException: Negative position error

Hi Youngjae,

>  java.lang.IllegalArgumentException: Negative position
>   at sun.nio.ch.FileChannelImpl.read(FileChannelImpl.java:600)
>   at loci.common.NIOByteBufferProvider.allocateDirect(
NIOByteBufferProvider.java:131)

Looks like a bug in the Bio-Formats library.

Please report this bug to the Bio-Formats team:
http://openmicroscopy.org/info/bio-formats/about/bug-reporting.html

Regards,
Curtis

On Wed, Dec 17, 2014 at 4:05 PM, Youngjae Jeong <[hidden email]>
wrote:

>
> ​Hello all,
>
> I recently have started to figure out how to use imageJ to analyze the uCT
> scans of bone geometry. The size of raw file is quite large, which is about
> 16GB. Because of lare size of the file, it gives me an error with memory
> issue. So what I have tried next is to open up file by specifying the range
> of images. The size of file is 2048x2048; 2016 planes. It shows me an image
> when I have selected 1(Z begin)-250(Z End) with 1 for Z step. The problem
> arise when I have tried to select beyond 250 and it gives me following
> messages.
>
> The file I am opening is ct.img.hdr file and this scan was done by inveon
> uCT scan. The disc image file (.ct) is ~16GB
>
>
> (Fiji Is Just) ImageJ 2.0.0-rc-15/1.49m; Java 1.6.0_24 [64-bit]; Windows
> NT (unknown) 6.2; 527MB of 2977MB (17%)
>
>  java.lang.IllegalArgumentException: Negative position
>   at sun.nio.ch.FileChannelImpl.read(FileChannelImpl.java:600)
>   at
> loci.common.NIOByteBufferProvider.allocateDirect(NIOByteBufferProvider.java:131)
>   at
> loci.common.NIOByteBufferProvider.allocate(NIOByteBufferProvider.java:116)
>   at loci.common.NIOFileHandle.buffer(NIOFileHandle.java:551)
>   at loci.common.NIOFileHandle.seek(NIOFileHandle.java:273)
>   at
> loci.common.RandomAccessInputStream.seek(RandomAccessInputStream.java:154)
>   at loci.formats.in.InveonReader.openBytes(InveonReader.java:118)
>   at loci.formats.ChannelFiller.openBytes(ChannelFiller.java:193)
>   at loci.formats.ChannelSeparator.openBytes(ChannelSeparator.java:222)
>   at loci.formats.ChannelSeparator.openBytes(ChannelSeparator.java:155)
>   at loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:313)
>   at loci.formats.DimensionSwapper.openBytes(DimensionSwapper.java:243)
>   at loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:313)
>   at loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:313)
>   at
> loci.plugins.util.ImageProcessorReader.openProcessors(ImageProcessorReader.java:190)
>   at
> loci.plugins.in.ImagePlusReader.readProcessors(ImagePlusReader.java:416)
>   at loci.plugins.in.ImagePlusReader.readPlanes(ImagePlusReader.java:380)
>   at loci.plugins.in.ImagePlusReader.readImage(ImagePlusReader.java:277)
>   at loci.plugins.in.ImagePlusReader.readImages(ImagePlusReader.java:238)
>   at loci.plugins.in.ImagePlusReader.readImages(ImagePlusReader.java:216)
>   at
> loci.plugins.in.ImagePlusReader.openImagePlus(ImagePlusReader.java:114)
>   at loci.plugins.in.Importer.readPixels(Importer.java:150)
>   at loci.plugins.in.Importer.run(Importer.java:89)
>   at loci.plugins.LociImporter.run(LociImporter.java:81)
>   at ij.IJ.runUserPlugIn(IJ.java:202)
>   at ij.IJ.runPlugIn(IJ.java:166)
>   at ij.IJ.runPlugIn(IJ.java:155)
>   at HandleExtraFileTypes.openImage(HandleExtraFileTypes.java:421)
>   at HandleExtraFileTypes.run(HandleExtraFileTypes.java:57)
>   at ij.IJ.runUserPlugIn(IJ.java:202)
>   at ij.IJ.runPlugIn(IJ.java:166)
>   at ij.IJ.runPlugIn(IJ.java:155)
>   at ij.io.Opener.openWithHandleExtraFileTypes(Opener.java:483)
>   at ij.io.Opener.openImage(Opener.java:361)
>   at ij.plugin.FolderOpener.run(FolderOpener.java:114)
>   at ij.IJ.runPlugIn(IJ.java:172)
>   at ij.Executer.runCommand(Executer.java:131)
>   at ij.Executer.run(Executer.java:64)
>   at java.lang.Thread.run(Thread.java:662)
>
>
> I am kinda naive on java.script and imageJ as well. Can anyone tell me
> what I am doing wrong?? or any reason of this error?
>
>
> Thank you,
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

... [show rest of quote]

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html


--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html