[ome-users] Unable to export to jpg2000

[Melissa Linkert]

Hi Ron,

> I have been try to export images using the LOCI Bio-Formats plugin in Fiji with no success.  I can get it to work with 8-bit grayscale images but not RGB color images.  Every time I try to export it stops and an Exception window opens.  I have updated Fiji (1.47c) and Java (java 1.6.0.33 on a Mac OSX 10.6.8, and java version 7 update 7 on a Windows 7 PC) and I have installed the latest Trunk, and Daily Build (Oct 5, 2012).   The Exception files from the Mac and PC are similar and I have included both below.   My images are tiff files with RGB channels but nothing else.  I have a attached a small version of an image in jpeg format just to save space.  We do all of our image processing and analysis using Fiji, but need to send the files to collaborators as jpg2000s and I hope to batch process the conversion of tiffs to JPG2000 because we have 100s of files that need conversion.    I was able to use Photoshop to save an RGB tiff image into jp2 format, but unfortunately the Photoshop Automator does not support this function making it an impractical way to convert 100s of files.

Thank you very much for reporting this problem.  I have filed a ticket to
fix this on our issue tracking system:

http://trac.openmicroscopy.org.uk/ome/ticket/9730

As a workaround, you might consider using the Bio-Formats command line
tools to convert your files:

http://loci.wisc.edu/bio-formats/command-line-tools

...as they are not affected by this bug.

Regards,
-Melissa

On Fri, Oct 05, 2012 at 11:00:11AM -0400, paletzki wrote:
> Hello
> I have been try to export images using the LOCI Bio-Formats plugin in Fiji with no success.  I can get it to work with 8-bit grayscale images but not RGB color images.  Every time I try to export it stops and an Exception window opens.  I have updated Fiji (1.47c) and Java (java 1.6.0.33 on a Mac OSX 10.6.8, and java version 7 update 7 on a Windows 7 PC) and I have installed the latest Trunk, and Daily Build (Oct 5, 2012).   The Exception files from the Mac and PC are similar and I have included both below.   My images are tiff files with RGB channels but nothing else.  I have a attached a small version of an image in jpeg format just to save space.  We do all of our image processing and analysis using Fiji, but need to send the files to collaborators as jpg2000s and I hope to batch process the conversion of tiffs to JPG2000 because we have 100s of files that need conversion.    I was able to use Photoshop to save an RGB tiff image into jp2 format, but unfortunately the Photoshop Automator does not support this function making it an impractical way to convert 100s of files.
> 
> Any help would be greatly appreciated.
> Thanks
> Ron 
> 
> 
> Exception list from Mac
> java.lang.reflect.InvocationTargetException
> at sun.reflect.GeneratedMethodAccessor5.invoke(Unknown Source)
> at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
> at java.lang.reflect.Method.invoke(Method.java:597)
> at ij.Command.runPlugIn(Command.java:146)
> at ij.Command.runCommand(Command.java:95)
> at ij.Executer.run(Executer.java:64)
> at java.lang.Thread.run(Thread.java:680)
> Caused by: java.lang.IllegalArgumentException: Raster sun.awt.image.SunWritableRaster at 5549f0e is incompatible with ColorModel DirectColorModel: rmask=ff0000 gmask=ff00 bmask=ff amask=0
> at java.awt.image.BufferedImage.<init>(BufferedImage.java:614)
> at loci.formats.gui.AWTImageTools.constructImage(AWTImageTools.java:736)
> at loci.formats.codec.JPEG2000Codec.compress(JPEG2000Codec.java:133)
> at loci.formats.out.JPEG2000Writer.compressBuffer(JPEG2000Writer.java:130)
> at loci.formats.out.JPEG2000Writer.saveBytes(JPEG2000Writer.java:90)
> at loci.formats.FormatWriter.saveBytes(FormatWriter.java:136)
> at loci.plugins.out.Exporter.run(Exporter.java:549)
> at loci.plugins.LociExporter.run(LociExporter.java:77)
> at ij.plugin.filter.PlugInFilterRunner.processOneImage(PlugInFilterRunner.java:256)
> at ij.plugin.filter.PlugInFilterRunner.<init>(PlugInFilterRunner.java:105)
> at ij.IJ.runUserPlugIn(IJ.java:187)
> at ij.IJ.runPlugIn(IJ.java:152)
> ... 7 more
> 
> Exception list from PC
> java.lang.reflect.InvocationTargetException
> 
> 	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
> 
> 	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
> 
> 	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
> 
> 	at java.lang.reflect.Method.invoke(Method.java:597)
> 
> 	at ij.Command.runPlugIn(Command.java:146)
> 
> 	at ij.Command.runCommand(Command.java:95)
> 
> 	at ij.Executer.run(Executer.java:64)
> 
> 	at java.lang.Thread.run(Thread.java:662)
> 
> Caused by: java.lang.IllegalArgumentException: Raster sun.awt.image.SunWritableRaster at 70b9cab2 is incompatible with ColorModel DirectColorModel: rmask=ff0000 gmask=ff00 bmask=ff amask=0
> 
> 	at java.awt.image.BufferedImage.<init>(BufferedImage.java:611)
> 
> 	at loci.formats.gui.AWTImageTools.constructImage(AWTImageTools.java:736)
> 
> 	at loci.formats.codec.JPEG2000Codec.compress(JPEG2000Codec.java:133)
> 
> 	at loci.formats.out.JPEG2000Writer.compressBuffer(JPEG2000Writer.java:130)
> 
> 	at loci.formats.out.JPEG2000Writer.saveBytes(JPEG2000Writer.java:90)
> 
> 	at loci.formats.FormatWriter.saveBytes(FormatWriter.java:136)
> 
> 	at loci.plugins.out.Exporter.run(Exporter.java:549)
> 
> 	at loci.plugins.LociExporter.run(LociExporter.java:77)
> 
> 	at ij.plugin.filter.PlugInFilterRunner.processOneImage(PlugInFilterRunner.java:256)
> 
> 	at ij.plugin.filter.PlugInFilterRunner.<init>(PlugInFilterRunner.java:105)
> 
> 	at ij.IJ.runUserPlugIn(IJ.java:187)
> 
> 	at ij.IJ.runPlugIn(IJ.java:152)
> 
> 	... 8 more
> 
> Example image
> 
> 
> Ronald Paletzki, PhD
> Biologist/Contractor
> LSN/NIMH/NIH
> Bldg49/ Rm 5A36
> Bethesda, MD
> 301-443-0711
> 
> 
> 
> 
> 
> 

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