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Bug 791 - .jpg open error
.jpg open error
Status: RESOLVED FIXED
Product: Fiji
Classification: Unclassified
Component: Plugins
unspecified
PC Windows
: P4 normal
Assigned To: ImageJ Bugs Mailing List
Depends on:
Blocks:
 
Reported: 2014-06-16 08:04 CDT by nantho2
Modified: 2014-06-19 08:41 CDT
3 users (show)

See Also:
Description nantho2 2014-06-16 08:04:50 CDT 
Also, standard image files are not opening.  I recieved the following error for opening a jpg (drag and drop did nothing and I needed to go to Open in the menus):

(Fiji Is Just) ImageJ 2.0.0-rc-4/1.49b; Java 1.6.0_24 [64-bit]; Windows 7 6.1; 26MB of 6095MB (<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:201)
	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)

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: C:\Users\NELLYP~1\Fiji\Fiji.app/java/win64/jdk1.6.0_24//jre
  imagej.dir => C:\Users\NELLYP~1\Fiji\Fiji.app

Information about the version of each plugin:

Activated update sites:
ImageJ: http://update.imagej.net/ (last check:20140610174546)
Fiji: http://fiji.sc/update/ (last check:20140610180938)
MOSAIC ToolSuite: http://mosaic.mpi-cbg.de/Downloads/update/Fiji/MosaicToolsuite/ (last check:20131118044144)

Files not up-to-date:
  28dd47da (MODIFIED) 20140616085853 jars/imagej-common-0.7.3.jar
  e50da8f6 (MODIFIED) 20140616085853 jars/imagej-updater-0.3.7.jar
  af8c5783 (MODIFIED) 20140616085852 jars/scifio-0.15.1.jar
  86b72a38 (MODIFIED) 20140616085852 jars/scijava-common-2.23.0.jar
  2eca2c1e (LOCAL_ONLY) 20140521105355 macros/BatchMacro.ijm
  728a17e6 (LOCAL_ONLY) 20131122172305 macros/Macro.ijm
  cb9e3fee (LOCAL_ONLY) 20140512131332 plugins/Differentials_m_.jar
  0bbd60b1 (LOCAL_ONLY) 20140217105204 plugins/Intravital_Microscopy_Toolbox.ijm
  94ff9125 (LOCAL_ONLY) 20140305083011 plugins/Mosaic_ToolSuite.jar
  113d8ccc (LOCAL_ONLY) 20130815165830 plugins/PhiOverlay.jar
  68fa4608 (LOCAL_ONLY) 20130814125912 plugins/Radial_Profile.class
  100e7398 (LOCAL_ONLY) 20050928181804 plugins/SurfaceJ_.class
  276637c9 (LOCAL_ONLY) 20050928181804 plugins/VolumeJ_.class
Comment 1 Mark Hiner 2014-06-16 09:06:47 CDT 
This looks like the same stack trace as http://fiji.sc/bugzilla/﷒0﷓ and is not format-specific.

Please note that the Bio-Formats importer is a plugin and not part of the core ImageJ2 image I/O.

In this case, both the Bio-Formats Importer and File > Open (or drag and drop) are failing because they are both using Bio-Formats. The Bio-Formats Importer uses it implicitly, and SCIFIO/ImageJ2 provide an I/O plugin that uses Bio-Formats for File > Open and drag and drop.

So we are seeing a common exception likely because of the MOSAIC ToolSuite's conflict with Bio-Formats, which both I/O mechanisms are using.

Please go through the following steps and see if your problem is resolved:
1) Help > Update Fiji to ensure your Fiji is up to date
2) Try opening your data again, with the MOSAIC ToolSuite update site still enabled.
3) If 2) fails, disable the MOSAIC ToolSuite
4) Attempt opening your data again.

Let us know how that goes.

Thanks,
Mark
Comment 2 Johannes Schindelin 2014-06-17 17:21:31 CDT 
Neil, did you have a chance to follow Mark's instructions yet?
Comment 3 nantho2 2014-06-18 16:14:47 CDT 
I've gone back to the old version, and haven't had a chance to see if it still happens, but I'm a little confused, this is a bug opening a jpg...
The bug I submitted prior to this was for the bio format plugin, but when I couldn't open any image I submitted another.

Thanks
Neil
Comment 4 Johannes Schindelin 2014-06-18 16:49:17 CDT 
Neil, I do not want to be pushy, but clarify that we are *really* working very hard on ImageJ2. I mean, really, really hard.

If you could help us by following Mark's simple instructions and helping us getting this bug fixed, great.

If you cannot spare those five minutes, then I am afraid I will have to close this ticket because we have way too much on our plates already, it is a little unfair to try to make us work even more. Besides, we simply cannot perform the feedback required for a successful bugfix. That really requires a *little* bit of effort also on the bug reporter's side.

So, what is it? Closing time or feedback time?
Comment 5 Mark Hiner 2014-06-18 17:52:12 CDT 
Neil,

 To clarify, you opened http://fiji.sc/bugzilla/﷒0﷓. I closed it as a duplicate of http://fiji.sc/bugzilla/﷒1﷓ - which was a conflict of Bio-Formats with the MOSAIC ToolSuite.

 I believe this bug is similarly a duplicate but left it open until you could confirm it.. it has nothing to do with being a .jpg. ImageJ2 uses SCIFIO for file input/output, which has a Bio-Formats plugin. So all open operations with SCIFIO enabled will at least trigger a format check with Bio-Formats, which as I said had a conflict with the MOSAIC ToolSuite.

 I do believe this was fixed by the MOSAIC developers, as we close #772, so the steps for you to try in my first message should still fix things for you.
Comment 6 nantho2 2014-06-18 21:16:53 CDT 
I updated Fiji, and then clicked Manage update sites, and checked the MOSAIC ToolSuite (I assume this is what you meant by "with the MOSAIC ToolSuite update site still enabled", but certainly didn't want to waste your time by asking), and applied that update.  The jpg now opened.  I uninstalled the MOSIC ToolSuite through the updates and tried again and it still worked.

Something along the lines fixed the issue.
Comment 7 Johannes Schindelin 2014-06-19 08:41:22 CDT 
Neil, thank you for taking the time to help us make Fiji/ImageJ2 better. The fix is most likely the same Mark referred to: the MOSAIC update site (which you identified correctly, of course) shipped an outdated version of a Bio-Formats component until recently. It was fixed only very recently, hence your issue. Happy it got resolved!