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Bug 785 - Can't open image files in ImageJ2
Can't open image files in ImageJ2
Status: RESOLVED WONTFIX
Product: Fiji
Classification: Unclassified
Component: ImageJ2
unspecified
PC Windows
: P5 enhancement
Assigned To: ImageJ Developers Mailing List
Depends on:
Blocks:
 
Reported: 2014-06-13 08:40 CDT by stephan.junek
Modified: 2014-06-13 10:27 CDT
1 user (show)

See Also:

Description stephan.junek 2014-06-13 08:40:46 CDT
Hi all,

since upgrading to ImageJ2, I can't open any image files anymore, including images that were created and saved from Fiji. I always get the following error: 
(Fiji Is Just) ImageJ 2.0.0-rc-4/1.49b; Java 1.6.0_24 [64-bit]; Windows 7 6.1; 32MB of 18421MB (<1%)
 
java.lang.NoClassDefFoundError: Could not initialize class loci.common.NIOByteBufferProvider
	at loci.common.NIOFileHandle.<init>(NIOFileHandle.java:129)
	at loci.common.NIOFileHandle.<init>(NIOFileHandle.java:138)
	at loci.common.NIOFileHandle.<init>(NIOFileHandle.java:147)
	at loci.common.Location.getHandle(Location.java:307)
	at loci.common.Location.getHandle(Location.java:278)
	at loci.common.Location.getHandle(Location.java:268)
	at loci.common.RandomAccessInputStream.<init>(RandomAccessInputStream.java:95)
	at loci.formats.FormatReader.isThisType(FormatReader.java:539)
	at loci.formats.ImageReader.isThisType(ImageReader.java:245)
	at io.scif.bf.BioFormatsFormat$Checker.isFormat(BioFormatsFormat.java:250)
	at io.scif.services.DefaultFormatService.getFormatList(DefaultFormatService.java:289)
	at io.scif.services.DefaultFormatService.getFormat(DefaultFormatService.java:271)
	at net.imagej.DefaultDatasetService.canOpen(DefaultDatasetService.java:215)
	at net.imagej.io.DatasetIOPlugin.supportsOpen(DatasetIOPlugin.java:66)
	at org.scijava.io.DefaultIOService.getOpener(DefaultIOService.java:66)
	at net.imagej.legacy.plugin.DefaultLegacyOpener.open(DefaultLegacyOpener.java:129)
	at net.imagej.legacy.DefaultLegacyHooks.interceptFileOpen(DefaultLegacyHooks.java:434)
	at net.imagej.legacy.DefaultLegacyHooks.interceptRunPlugIn(DefaultLegacyHooks.java:156)
	at ij.IJ.runPlugIn(IJ.java)
	at ij.Executer.runCommand(Executer.java:131)
	at ij.Executer.run(Executer.java:64)
	at java.lang.Thread.run(Thread.java:662)


I also reinstalled Java (jre-8u5-windows-x64.exe), but this didn't change anything.

Looking forward to your answer!

Cheers,
Stephan.
Comment 1 Mark Hiner 2014-06-13 09:06:43 CDT
Hi Stephan,

 When reporting a bug like this, it is extremely helpful if you use the Help > Report a Bug option in Fiji. There is certainly something wrong with the state of your installation that it is unable to initialize a class distributed as part of Fiji, and that state is precisely what would be included with Help > Report a Bug.

 While version information of Fiji, ImageJ and Java are useful, they don't tell the full story of what update sites you have enabled or locally modified files you have installed. Given that this is the first report we've had of a failure like this, it seems quite likely that this is a problem with something local to your system, or an update site.

 Since this bug is already open, can you you open the Help > Report a Bug, copy the entire "Useful information about your system" text box and paste it in a new comment on this bug?

Thanks for the report,
Mark
Comment 2 stephan.junek 2014-06-13 09:08:55 CDT
Sure, here it is:

Information about your version of Java:

  os.arch => amd64
  os.name => Windows 7
  os.version => 6.1
  java.version => 1.6.0_24
  java.vendor => Sun Microsystems Inc.
  java.runtime.name => Java(TM) SE Runtime Environment
  java.runtime.version => 1.6.0_24-b07
  java.vm.name => Java HotSpot(TM) 64-Bit Server VM
  java.vm.version => 19.1-b02
  java.vm.vendor => Sun Microsystems Inc.
  java.vm.info => mixed mode
  java.awt.graphicsenv => sun.awt.Win32GraphicsEnvironment
  java.specification.name => Java Platform API Specification
  java.specification.version => 1.6
  sun.cpu.endian => little
  sun.desktop => windows
  file.separator => \

The up-to-date check says: REMIND_LATER

Information relevant to JAVA_HOME related problems:

  JAVA_HOME is set to: D:\FIJI-W~2\Fiji.app/java/win64/jdk1.6.0_24//jre
  imagej.dir => D:\FIJI-W~2\Fiji.app

Information about the version of each plugin:

Activated update sites:
ImageJ: http://update.imagej.net/ (last check:20140613041451)
Fiji: http://fiji.sc/update/ (last check:20140612230314)
MOSAIC ToolSuite: http://mosaic.mpi-cbg.de/Downloads/update/Fiji/MosaicToolsuite/ (last check:20131118104144)

Files not up-to-date:
  71331805 (LOCAL_ONLY) 20140514170519 plugins/JACoP_.jar
Comment 3 Mark Hiner 2014-06-13 10:07:59 CDT
This looks like it's the same or a highly similar problem to http://fiji.sc/bugzilla/﷒0﷓

Also in http://fiji.sc/bugzilla/﷒1﷓ it was determined that the MOSAIC suite is incompatible with Bio-Formats 5.0.2.

The MOSAIC group (http://mosaic.mpi-cbg.de/) needs to update their plugin so that it doesn't ship its own SLF4J bindings (org.slf4j.impl.StaticLoggerBinder.class, and potentially other classes are duplicated).

Marking resolved as I don't think there's anything in Fiji we will can do to handle this.

Until that plugin is fixed by its developers, I think you will just have to disable its update site.
Comment 4 stephan.junek 2014-06-13 10:27:23 CDT
Yes, removing the mosaic plugin solved the problem.

Thanks for the fast support!!

Stephan