[ome-users] java.lang.illegalArgumentException: Negative position error reporting

[Jeong, Young J. (MU-Student)]

??Hello to whom it may concern,

I have initially posted this on imageJ group user page and someone commented this error may be due to bugs... So here is what I did and what I got afterward.

 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)?



ImageJ 2.0.0-rc-15/1.49m; Java 1.6.0_24 [64-bit] and updated every plugins before use.


All the related files are listed below...

Scan1_v1 - security catalog: 2927282 KB

Scan1_v1.cat - HDR file: 54 KB

Scan1_v1.ct - IMG file: 16515072 KB

Scan1_v1.ct.img - HDR file: 55 KB

v1.CTrecon - txt document: 2KB


I have attached a few screenshot of what I did in word files. I am not sure if I did something completely wrong.. or something...


The response will be really appreciated.


Thank you,


Youngjae Jeong


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