[ome-users] Bug report on opening rec file
Giedrius Zirgulis
giedrius.zirgulis at ntnu.no
Fri Nov 27 13:39:28 GMT 2015
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
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