[ome-users] Bug report on opening rec file

[Jan Eglinger]

For the record: here is the forum post Giedrius refers to:

http://forum.imagej.net/t/opening-rec-file/423?u=imagejan

Cheers,
Jan


On 27.11.2015 14:39, Giedrius Zirgulis wrote:
> Dear all,
>
> I am analyzing CT scans of concrete samples using FIJI program. The aim
> is to track cracks in the concrete. Recently we receive a file in *.rec
> format, from company who operates industrial CT scanner RayScan 250E. I
> was not able to open the file using bio-formats plugin no matter what
> setting I have tried (e.g. crop on import). I have applied with this
> issue  to ImageJ forum and I was advised to report the problem directly
> to Openmicroscopy (one user noticed too large pixel size in metadata file).
>
> */This is the error message:/*
>
> (Fiji Is Just) ImageJ 2.0.0-rc-43/1.50e; Java 1.6.0_24 [64-bit]; Windows
> 7 6.1; 624MB of 6029MB (10%)
>
> java.lang.IllegalArgumentException: Array size too large: 628172145 x
> 628172145 x 1
>
>                  at loci.common.DataTools.safeMultiply32(DataTools.java:850)
>
>                  at loci.common.DataTools.allocate(DataTools.java:824)
>
>                  at
> loci.formats.ChannelSeparator.openBytes(ChannelSeparator.java:155)
>
>                  at
> loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:335)
>
>                  at
> loci.formats.DimensionSwapper.openBytes(DimensionSwapper.java:233)
>
>                  at
> loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:335)
>
>                  at
> loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:335)
>
>                  at
> loci.plugins.util.ImageProcessorReader.openProcessors(ImageProcessorReader.java:186)
>
>                  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:111)
>
>                  at loci.plugins.in.Importer.readPixels(Importer.java:149)
>
>                  at loci.plugins.in.Importer.run(Importer.java:86)
>
>                  at loci.plugins.LociImporter.run(LociImporter.java:78)
>
>                  at ij.IJ.runUserPlugIn(IJ.java:212)
>
>                  at ij.IJ.runPlugIn(IJ.java:176)
>
>                  at ij.Executer.runCommand(Executer.java:136)
>
>                  at ij.Executer.run(Executer.java:65)
>
>                  at java.lang.Thread.run(Thread.java:662)
>
> */Version information:/*
>
>                  ImageJ 1.50e
>
>                  Java 1.6.0_24 (64-bit)
>
>                  Bioformats version information attached as .tif
>
> */Non-working file located here:/*
>
> https://www.dropbox.com/sh/l0wva3glzyyz7n5/AAAkWB8ltxvArd2Gpry6LzOZa?dl=0
>
> */Metadata:/*
>
> SizeT
>
> 	
>
> 1
>
> SizeX
>
> 	
>
> 6.28E+08
>
> SizeY
>
> 	
>
> 6.28E+08
>
> SizeZ
>
> 	
>
> 6.28E+08
>
> Alpha angle
>
> 	
>
> 2.09E-16
>
> Angle #1
>
> 	
>
> 2.09E-16
>
> Angle #2
>
> 	
>
> 2.09E-16
>
> Angle #3
>
> 	
>
> 2.09E-16
>
> Angle #4
>
> 	
>
> 2.09E-16
>
> Angle #5
>
> 	
>
> 2.09E-16
>
> Angle #6
>
> 	
>
> 2.09E-16
>
> Beta angle
>
> 	
>
> 2.09E-16
>
> Gamma angle
>
> 	
>
> 2.09E-16
>
> Label #01
>
> 	
>
> q%q%q%q%q%q%q%q%q%q%q%q%q%q%q%q%q%q%q%q%q%q%q%q%q%q%q%q%q%q%q%q%q%q%q%q%q%q%q%q%
>
> Label #02
>
> 	
>
> q%q%q%q%q%q%q%q%q%q%q%q%q%q%q%q%q%q%q%q%q%q%q%q%q%q%q%q%q%q%q%q%q%q%q%q%q%q%q%q%
>
> Label #03
>
> 	
>
> q%q%q%q%q%q%q%q%q%q%q%q%q%q%q%q%q%q%q%q%q%q%q%q%q%q%q%q%q%q%q%q%q%q%q%q%q%q%q%q%
>
> Label #04
>
> 	
>
> q%q%q%q%q%q%q%q%q%q%q%q%q%q%q%q%q%q%q%q%q%q%q%q%q%q%q%q%q%q%q%q%q%q%q%q%q%q%q%q%
>
> Label #05
>
> 	
>
> q%q%q%q%q%q%q%q%q%q%q%q%q%q%q%q%q%q%q%q%q%q%q%q%q%q%q%q%q%q%q%q%q%q%q%q%q%q%q%q%
>
> Label #06
>
> 	
>
> q%q%q%q%q%q%q%q%q%q%q%q%q%q%q%q%q%q%q%q%q%q%q%q%q%q%q%q%q%q%q%q%q%q%q%q%q%q%q%q%
>
> Label #07
>
> 	
>
> q%q%q%q%q%q%q%q%q%q%q%q%q%q%q%q%q%q%q%q%q%q%q%q%q%q%q%q%q%q%q%q%q%q%q%q%q%q%q%q%
>
> Label #08
>
> 	
>
> q%q%q%q%q%q%q%q%q%q%q%q%q%q%q%q%q%q%q%q%q%q%q%q%q%q%q%q%q%q%q%q%q%q%q%q%q%q%q%q%
>
> Label #09
>
> 	
>
> q%q%q%q%q%q%q%q%q%q%q%q%q%q%q%q%q%q%q%q%q%q%q%q%q%q%q%q%q%q%q%q%q%q%q%q%q%q%q%q%
>
> Label #10
>
> 	
>
> q%q%q%q%q%q%q%q%q%q%q%q%q%q%q%q%q%q%q%q%q%q%q%q%q%q%q%q%q%q%q%q%q%q%q%q%q%q%q%q%
>
> Lens
>
> 	
>
> 9585
>
> Location
>
> 	
>
> M:\Fibres\CT
> scans\KTU_CT\CT_2\betonas_su_trukiu_prefilt_IF-5_3_small_20151125131342\betonas_su_trukiu_prefilt_IF-5_3_small_20151125131342.rec
>
> Maximum pixel value
>
> 	
>
> 2.09E-16
>
> Mean pixel value
>
> 	
>
> 2.09E-16
>
> Minimum pixel value
>
> 	
>
> 2.09E-16
>
> ND1
>
> 	
>
> 9585
>
> ND2
>
> 	
>
> 9585
>
> Number of useful labels
>
> 	
>
> 6.28E+08
>
> Pixel size (X)
>
> 	
>
> 3.33E-29
>
> Pixel size (Y)
>
> 	
>
> 3.33E-29
>
> Pixel size (Z)
>
> 	
>
> 3.33E-29
>
> Series type
>
> 	
>
> unknown
>
> VD1
>
> 	
>
> 9585
>
> VD2
>
> 	
>
> 9585
>
> The company who operates the CT scanner opens files using Avizo Fire
> software.
>
> I have tried various possible settings and various alternative
> opensource softwares.  My apologies if it is still an issue of my
> inexperience.
>
> Best regards,
>
> Giedrius Zirgulis
>
>