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Bug 608 - ZVI import error
ZVI import error
Status: RESOLVED FIXED
Product: Fiji
Classification: Unclassified
Component: Plugins
unspecified
PC Linux
: P4 major
Assigned To: ImageJ Bugs Mailing List
Depends on:
Blocks:
 
Reported: 2013-05-17 13:17 CDT by Gennady Nikitin
Modified: 2013-06-11 14:40 CDT
2 users (show)

See Also:
Description Gennady Nikitin 2013-05-17 13:17:39 CDT 
After recent update, ZVI import stopped working properly - the channels are confused, meaning that true image from certain channel could be replaced by the image from another channel, which therefore gets duplicated.

Information about your version of Java:

  os.arch => amd64
  os.name => Linux
  os.version => 3.8.0-22-generic
  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.X11GraphicsEnvironment
  java.specification.name => Java Platform API Specification
  java.specification.version => 1.6
  sun.cpu.endian => little
  sun.desktop => null
  file.separator => /

The up-to-date check says: REMIND_LATER

Information relevant to JAVA_HOME related problems:

  JAVA_HOME is set to: /media/B/Distr/Biology/Fiji.app/java/linux-amd64/jdk1.6.0_24//jre
  ij.dir => /media/B/Distr/Biology/Fiji.app

Information about the version of each plugin:

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  5a50a9eb8531ebf052814bb0a0026b662edd4072 20130225172412 plugins/mpicbg_-0.6.0-SNAPSHOT.jar
  7f36dd01e6b9a9cb4f4fefaea24c2d9d0d74db68 20130515222448 plugins/ome-xml.jar
  5e32d936ba53c22ba6b70e5eee3992a361bc2ff8 20130225172412 plugins/panorama_.jar
  96b34801f469d1286e10b0b4871d07752cb1ef0c 20130225172412 plugins/readme.txt
  044f3fef66023d33fc2238491669a0eae280156f 20130225172412 plugins/register_virtual_stack_slices-2.0.0-SNAPSHOT.jar
  4d7eaf239c033d305a464a06c3e64c68d096c7e1 20130225172412 plugins/registration_3d.jar
  34b7341db33b0142f13cc98e5ad6bb104421fec6 20130225172412 retro/backport-util-concurrent-3.1.jar
  8759ba201e6dfa1dfc40f34eb5b332a6a73c3516 20130417005432 retro/retrotranslator-runtime-1.2.9.jar
  a6d5a3b297b4ba3ba2f2d1baa0c5da631fdf86c0 20130417005433 retro/retrotranslator-transformer-1.2.9.jar
  d7160d38a0b805381cb0c0dcedd60e197e247897 20130225172412 scripts/InstallJava3D.m
  05a92a3c3f518ec50976326bf16a8a8858af2183 20130225172412 scripts/IsJava3DInstalled.m
  ff34d026692414ecd743ba34e828780c8614ea8d 20130225172412 scripts/Matlab3DViewerDemo_1.m
  25be149fecd1f6551b9b0ad53946642db65d5a4e 20130225172412 scripts/Matlab3DViewerDemo_2.m
  cb529b6c4fb0505e6e58f8d18fa8f81fc86ebe82 20130225172412 scripts/Matlab3DViewerDemo_3.m
  53d2da73a4a560c41f3c4493d1377c56fe84106c 20130225172412 scripts/Matlab3DViewerIntroduction.m
  4bb342fa00a9d96bda9fd36c8e7df515bbfa8b60 20130225172412 scripts/Miji.m
  868cd43462fefc57c310656d4b35a028f0bda4f4 20130225172412 scripts/Miji_Test.m
  dc94c3a32b5edb3106ad7f2c7c68a852d064089a 20130225172412 scripts/bfopen.m
Comment 1 Melissa Linkert 2013-05-22 17:21:13 CDT 
Does following these instructions:

http://fiji.sc/bugzilla/﷒0﷓

solve the problem?
Comment 2 Gennady Nikitin 2013-05-28 12:05:11 CDT 
No, I have updated everything, loci-common.jar is marked as up-to-date, and I get this while trying to open .zvi:

(Fiji Is Just) ImageJ 1.47q; Java 1.6.0_24 [64-bit]; Linux 3.8.0-22-generic; 30MB of 33979MB (<1%)
 
java.lang.NoClassDefFoundError: ome/scifio/common/Region
	at loci.formats.in.HamamatsuVMSReader.<init>(HamamatsuVMSReader.java:80)
	at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
	at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:39)
	at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:27)
	at java.lang.reflect.Constructor.newInstance(Constructor.java:513)
	at java.lang.Class.newInstance0(Class.java:355)
	at java.lang.Class.newInstance(Class.java:308)
	at loci.formats.ImageReader.<init>(ImageReader.java:133)
	at loci.plugins.util.LociPrefs.makeImageReader(LociPrefs.java:84)
	at loci.plugins.in.ImportProcess.createBaseReader(ImportProcess.java:594)
	at loci.plugins.in.ImportProcess.initializeReader(ImportProcess.java:472)
	at loci.plugins.in.ImportProcess.execute(ImportProcess.java:142)
	at loci.plugins.in.Importer.showDialogs(Importer.java:141)
	at loci.plugins.in.Importer.run(Importer.java:79)
	at loci.plugins.LociImporter.run(LociImporter.java:81)
	at ij.IJ.runUserPlugIn(IJ.java:194)
	at ij.IJ.runPlugIn(IJ.java:160)
	at ij.IJ.runPlugIn(IJ.java:149)
	at HandleExtraFileTypes.openImage(HandleExtraFileTypes.java:421)
	at HandleExtraFileTypes.run(HandleExtraFileTypes.java:57)
	at ij.IJ.runUserPlugIn(IJ.java:194)
	at ij.IJ.runPlugIn(IJ.java:160)
	at ij.IJ.runPlugIn(IJ.java:149)
	at ij.io.Opener.openWithHandleExtraFileTypes(Opener.java:435)
	at ij.io.Opener.openImage(Opener.java:307)
	at ij.io.Opener.openImage(Opener.java:330)
	at ij.io.Opener.open(Opener.java:143)
	at ij.RecentOpener.run(RecentOpener.java:19)
	at java.lang.Thread.run(Thread.java:662)
Caused by: java.lang.ClassNotFoundException: ome.scifio.common.Region
	at java.net.URLClassLoader$1.run(URLClassLoader.java:202)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.net.URLClassLoader.findClass(URLClassLoader.java:190)
	at java.lang.ClassLoader.loadClass(ClassLoader.java:307)
	at fiji.FijiClassLoader.loadClass(FijiClassLoader.java:266)
	at fiji.FijiClassLoader.loadClass(FijiClassLoader.java:217)
	at fiji.FijiClassLoader.loadClass(FijiClassLoader.java:212)
	... 29 more
Comment 3 Curtis Rueden 2013-05-28 13:24:01 CDT 
> Caused by: java.lang.ClassNotFoundException: ome.scifio.common.Region

That error message indicates a mismatch between versions., so it is likely that the updater did not fully upgrade your entire installation.

If you have not customized your Fiji installation, it will probably be easier to just download a new version from http://fiji.sc/Downloads.

If you would rather upgrade your existing Fiji, please run Help > Update Fiji, click Advanced Mode, and make sure there are no locally modified files (using the "View locally modified files only" View Option). If you have any locally modified files that you did not modify on purpose, please "Install / Update" them.

Please also check "View uninstalled files only" to make sure you are not missing any files, and "View local-only files" to make sure you don't have any other JARs lying around -- both of those lists should be empty. If you have any "uninstalled files" you can install them, and if you have any "local-only files" that you didn't put there on purpose you can delete them.
Comment 4 Gennady Nikitin 2013-05-28 15:13:01 CDT 
So after I downloaded the version from the site (actually, i tried it before also), I got again the wrong channels issue.

As for locally modified files - I updated everything, so there were no more, however the error of opening still occurs.

Anyway, the mess with the channels (4.4.9-dev version of LOCI plugin) is more problematic for me. I solved this problem by finding the older distributive archive of Fiji from March 2013, which actually for some reason has LOCI 4.5-dev version. So the update somehow downgrades the vesion of LOCI?.. Because for sure, with LOCI 4.5-dev version there is no such issue with confused channels.

Thank you for your help.
Comment 5 Curtis Rueden 2013-05-29 11:39:30 CDT 
> I solved this problem by finding the older distributive archive of
> Fiji from March 2013, which actually for some reason has LOCI 4.5-dev
> version. So the update somehow downgrades the vesion of LOCI?..
> Because for sure, with LOCI 4.5-dev version there is no such issue
> with confused channels.

The switch to the "4.4 stable" code happened earlier this month:

    https://groups.google.com/d/msg/fiji-devel/wSjsqZ-uEX0/fU4pdoks_HYJ

The OMERO development team requested that we stop publishing unstable/development code (i.e., the 4.5.x develop branch) to Fiji, in favor of only stable/released code (i.e., 4.4.x stable releases), and we were finally able to accommodate this request after resolving some technical obstacles. Starting with version 4.4.9, Fiji will ship only release versions of Bio-Formats, and Bio-Formats will migrate to its own update site later this year.

> So after I downloaded the version from the site (actually, i tried it
> before also), I got again the wrong channels issue.

I am very sorry to hear that the 4.4.x version of Bio-Formats has this channels bug. While we would love to address this issue in the Fiji context, with Fiji shipping only release versions now, the best we can do is to suggest reporting it to the ome-users mailing list at:

    http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users/
Comment 6 Curtis Rueden 2013-06-11 14:37:27 CDT 
A fix for this ZVI channels bug is now pending:
https://github.com/openmicroscopy/bioformats/pull/544

Should be available in Fiji later when the next stable version of Bio-Formats is released.
Comment 7 Gennady Nikitin 2013-06-11 14:40:56 CDT 
Thank you very much for your help!