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Bug 811 - Open File Error
Open File Error
Status: CLOSED FIXED
Product: Fiji
Classification: Unclassified
Component: Plugins
unspecified
PC Windows
: P4 normal
Assigned To: ImageJ Bugs Mailing List
Depends on:
Blocks:
 
Reported: 2014-06-24 13:02 CDT by nantho2
Modified: 2014-06-24 16:24 CDT
3 users (show)

See Also:

Attachments
After restarting ImageJ after updating to re-include MOSAIC (74 bytes, text/plain)
2014-06-24 14:40 CDT, nantho2
error after restart after install of MOSAIC (71.83 KB, image/png)
2014-06-24 16:06 CDT, nantho2
Show Obsolete (1) Add an attachment (proposed patch, testcase, etc.)

Description nantho2 2014-06-24 13:02:43 CDT 
Error opening tif, MOSAIC tools installed and uninstalled with change.  Error below:

(Fiji Is Just) ImageJ 2.0.0-rc-6/1.49b; Java 1.6.0_24 [64-bit]; Windows 7 6.1; 21MB of 6095MB (<1%)
 
java.lang.NoSuchMethodError: org.slf4j.helpers.MessageFormatter.format(Ljava/lang/String;Ljava/lang/Object;)Ljava/lang/String;
	at org.slf4j.impl.Log4jLoggerAdapter.debug(Log4jLoggerAdapter.java:223)
	at loci.common.NIOByteBufferProvider.<clinit>(NIOByteBufferProvider.java:88)
	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:316)
	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:130)
	at net.imagej.legacy.DefaultLegacyHooks.interceptFileOpen(DefaultLegacyHooks.java:436)
	at net.imagej.legacy.DefaultLegacyHooks.interceptRunPlugIn(DefaultLegacyHooks.java:158)
	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:20140623162553)
Fiji: http://fiji.sc/update/ (last check:20140623182555)

Files not up-to-date:
  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
  f84c20e3 20140624135744 plugins/Mosaic_ToolSuite/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
  466390a2 (LOCAL_ONLY) 20140623095348 plugins/mics_toolkit_.jar
Comment 1 Curtis Rueden 2014-06-24 13:38:47 CDT 
This sort of problem is due to a skew between library versions. In other words: two JAR files not intended to work together at their respective versions.

Can you please:
1) Press L for the Command Finder.
2) Type "find jar for class"
3) Run that command
4) Specify the argument: org.slf4j.impl.Log4jLoggerAdapter
5) Paste the contents of the Log back to this bug report
?

The result should read something like:

 The class org.slf4j.impl.Log4jLoggerAdapter was not found in ImageJ's class path

Or hopefully more like:

 The class org.slf4j.impl.Log4jLoggerAdapter is contained in C:\Users\nantho\Fiji.app\jars\some-library-x.y.z.jar

Where "some-library-x.y.z.jar" is the location of that class.
Comment 2 nantho2 2014-06-24 14:06:19 CDT 
Thanks.  The Result is:
The class org.slf4j.impl.Log4jLoggerAdapter is contained in /C:/Users/NELLYP~1/FIJI_I~2/plugins/Mosaic_ToolSuite.jar
Comment 3 Johannes Schindelin 2014-06-24 14:19:47 CDT 
> The class org.slf4j.impl.Log4jLoggerAdapter is contained in /C:/Users/NELLYP~1/FIJI_I~2/plugins/Mosaic_ToolSuite.jar

There you have the problem. You can either

- contact the maintainers of the MOSAIC update site to fix the problem (they include classes incompatible with Bio-Formats' requirements in their .jar file, making it a so-called "fat" binary), or

- you can try your luck by renaming the file to have a .zip file extension and then use your favorite ZIP tool to remove the offending files (all files in the org/slf4j/ directory tree should be in the file Fiji.app/jars/slf4j-api-1.7.6.jar file and no other .jar file in the Fiji.app/ directory tree) and then rename it back into a .jar.
Comment 4 Johannes Schindelin 2014-06-24 14:20:19 CDT 
Oh, and something must have gone wrong when you deactivated the MOSAIC update site because that file was still there...
Comment 5 Johannes Schindelin 2014-06-24 14:39:48 CDT 
Actually, I see what happened. You installed the MOSAIC tool suite manually at some stage (the report suggests March 5th 2014 short after 8am UTC which seems insanely early translated to EST, so I do not really trust that timestamp).

Now, you installed it into plugins/Mosaic_ToolSuite.jar, while the MOSAIC update site installs it into plugins/Mosaic_ToolSuite/Mosaic_ToolSuite.jar (notice the extra subdirectory?).

The fix is easy: run your updater, switch to the advanced mode, type in "mosaic" in the search box, mark the file (which should be marked as "Local-only"), click the Uninstall button and then the Apply changes button.

After that, you can follow the MOSAIC tool suite again because they already fixed the bug you reported, at least in their current version.
Comment 6 nantho2 2014-06-24 14:40:47 CDT 
Created attachment 167
After restarting ImageJ after updating to re-include MOSAIC
Comment 7 nantho2 2014-06-24 14:41:53 CDT 
clicking OK after attached image gives the following error in the Log window:
Deleting duplicate plugin: C:\Users\NELLYP~1\FIJI_I~2\plugins\Mosaic_ToolSuite.jar
Comment 8 Johannes Schindelin 2014-06-24 15:19:57 CDT 
Did you mean to attach an image? It only attached 74 bytes of text...
Comment 9 nantho2 2014-06-24 16:06:19 CDT 
Created attachment 168
error after restart after install of MOSAIC
Comment 10 nantho2 2014-06-24 16:19:31 CDT 
I looked in the jar file but the slf4j folder didn't exist. I've deleted my Fiji folder and downloaded a fresh version which appears to be working.

Thanks
Comment 11 Johannes Schindelin 2014-06-24 16:24:42 CDT 
Good that you got a working version again! Hopefully I can help better next time you have a problem.