[ome-users] Bug report on opening rec file
David Gault (Staff)
d.gault at dundee.ac.uk
Tue Dec 1 19:24:09 GMT 2015
Hi Giedrius,
Thank you for reporting this issue and providing the sample files.
I have tested these files over the past few days and although we have readers which support some .rec files, the data here appears to be formatted differently from what we had supported previously.
As such I have uploaded your sample files to our QA server and created a ticket to add support for this new format. You can view the ticket below and I have added you to the CC list so you shall receive an update for any status change to the ticket.
https://trac.openmicroscopy.org/ome/ticket/13120#ticket
With Thanks,
David Gault
On 27 Nov 2015, at 13:39, Giedrius Zirgulis <giedrius.zirgulis at ntnu.no<mailto:giedrius.zirgulis at ntnu.no>> 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
<Bio_formats.tif>_______________________________________________
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