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Bug 1239 - Java 3D not working properly
Java 3D not working properly
Status: RESOLVED FIXED
Product: Fiji
Classification: Unclassified
Component: Plugins
unspecified
PC Windows
: P4 normal
Assigned To: ImageJ Bugs Mailing List
Depends on:
Blocks:
 
Reported: 2016-03-07 11:16 CST by Adam Ostrowski
Modified: 2016-04-25 16:30 CDT
3 users (show)

See Also:
Description Adam Ostrowski 2016-03-07 11:16:40 CST 
I'm experiencing significant JAVA version incompatibility issues. Starting from the fact, that one of the most important PlugIns I use, OMERO connect plugin requires Java 1.7 or higher. The version supplied with Fiji is 1.6, so I disabled it forcing the programme to use the system version. This allows some plugins to run, but the ones requiring Java 3D will not function. I had the IT department install the new Java 3D, but the problem persists. the exact error report is as follows:

version = 1.5
Exception occurred in RenderingErrorListener:
java.lang.RuntimeException
	at ij3d.ImageWindow3D$ErrorListener.errorOccurred(ImageWindow3D.java:330)
	at javax.media.j3d.VirtualUniverse.notifyRenderingErrorListeners(VirtualUniverse.java:1329)
	at javax.media.j3d.NotificationThread.processNotifications(NotificationThread.java:90)
	at javax.media.j3d.NotificationThread.run(NotificationThread.java:107)
nFrames = 1

Please provide an up to date and functional java version or a solution to these problems.
Thanks!

Information about your version of Java:

  os.arch => amd64
  os.name => Windows 7
  os.version => 6.1
  java.version => 1.7.0_60
  java.vendor => Oracle Corporation
  java.runtime.name => Java(TM) SE Runtime Environment
  java.runtime.version => 1.7.0_60-b19
  java.vm.name => Java HotSpot(TM) 64-Bit Server VM
  java.vm.version => 24.60-b09
  java.vm.vendor => Oracle Corporation
  java.vm.info => mixed mode
  java.awt.graphicsenv => sun.awt.Win32GraphicsEnvironment
  java.specification.name => Java Platform API Specification
  java.specification.version => 1.7
  sun.cpu.endian => little
  sun.desktop => windows
  file.separator => \

The up-to-date check says: UP_TO_DATE

Information relevant to JAVA_HOME related problems:

  JAVA_HOME is set to: C:\Program Files\Java\jdk1.7.0_60/jre
  imagej.dir => D:\Fiji.app

Information about the version of each plugin:

Activated update sites:
ImageJ: http://update.imagej.net/ (last check:20160217150804)
Fiji: http://update.fiji.sc/ (last check:20160218135537)
Bio-Formats: http://sites.imagej.net/Bio-Formats/ (last check:20160216022645)

Files not up-to-date:
  6a7750c0 (OBSOLETE_UNINSTALLED) 20150814165554 jars/ffmpeg-2.6.1-0.11-android-arm.jar
  fd2b5490 (OBSOLETE_UNINSTALLED) 20150814165554 jars/ffmpeg-2.6.1-0.11-android-x86.jar
  4653bdb4 (OBSOLETE_UNINSTALLED) 20150814165554 jars/ffmpeg-2.6.1-0.11-linux-x86.jar
  977eac28 (OBSOLETE_UNINSTALLED) 20150814165554 jars/ffmpeg-2.6.1-0.11-linux-x86_64.jar
  8e223ac3 (OBSOLETE_UNINSTALLED) 20150814165556 jars/ffmpeg-2.6.1-0.11-macosx-x86_64.jar
  ccd3679d (OBSOLETE_UNINSTALLED) 20150814165556 jars/ffmpeg-2.6.1-0.11-windows-x86.jar
  a314dfd6 (OBSOLETE_UNINSTALLED) 20150814165556 jars/ffmpeg-2.6.1-0.11-windows-x86_64.jar
  c295a4c5 (OBSOLETE_UNINSTALLED) 20150814165558 jars/jdom-2.0.2.jar
  64241209 (OBSOLETE_UNINSTALLED) 20150814165558 jars/jdom-contrib.jar
  ec17890b (LOCAL_ONLY) 20150731184018 plugins/OMERO.insight-ij-5.2.2-ice35-b17/libs/JHotDraw.jar
  91ece67d (LOCAL_ONLY) 20131203192004 plugins/OMERO.insight-ij-5.2.2-ice35-b17/libs/JWlz.jar
  36cb5c0a (LOCAL_ONLY) 20150731184018 plugins/OMERO.insight-ij-5.2.2-ice35-b17/libs/TableLayout.jar
  7c4005e7 (LOCAL_ONLY) 20050801112630 plugins/OMERO.insight-ij-5.2.2-ice35-b17/libs/axis-wsdl4j.jar
  364315a9 (LOCAL_ONLY) 20060423071656 plugins/OMERO.insight-ij-5.2.2-ice35-b17/libs/axis.jar
  3370a633 (LOCAL_ONLY) 20070427153948 plugins/OMERO.insight-ij-5.2.2-ice35-b17/libs/axis2-saaj.jar
  34b7341d (LOCAL_ONLY) 20071111222848 plugins/OMERO.insight-ij-5.2.2-ice35-b17/libs/backport-util-concurrent.jar
  85606650 (LOCAL_ONLY) 20160228171404 plugins/OMERO.insight-ij-5.2.2-ice35-b17/libs/blitz-javadoc.jar
  fdca3ab2 (LOCAL_ONLY) 20160228171326 plugins/OMERO.insight-ij-5.2.2-ice35-b17/libs/blitz-sources.jar
  a97a8e83 (LOCAL_ONLY) 20160228171410 plugins/OMERO.insight-ij-5.2.2-ice35-b17/libs/blitz.jar
  189f61fa (LOCAL_ONLY) 20150805084902 plugins/OMERO.insight-ij-5.2.2-ice35-b17/libs/bufr.jar
  6b2c6ea5 (LOCAL_ONLY) 20160228171140 plugins/OMERO.insight-ij-5.2.2-ice35-b17/libs/common-javadoc.jar
  0d0bc024 (LOCAL_ONLY) 20160228171138 plugins/OMERO.insight-ij-5.2.2-ice35-b17/libs/common-sources.jar
  d838ddf7 (LOCAL_ONLY) 20160228171140 plugins/OMERO.insight-ij-5.2.2-ice35-b17/libs/common.jar
  66c7ae94 (LOCAL_ONLY) 20051122180848 plugins/OMERO.insight-ij-5.2.2-ice35-b17/libs/commons-beanutils.jar
  940245e0 (LOCAL_ONLY) 20111203023826 plugins/OMERO.insight-ij-5.2.2-ice35-b17/libs/commons-codec.jar
  64d8a654 (LOCAL_ONLY) 20060622224518 plugins/OMERO.insight-ij-5.2.2-ice35-b17/libs/commons-collections.jar
  86ab9004 (LOCAL_ONLY) 20061203183312 plugins/OMERO.insight-ij-5.2.2-ice35-b17/libs/commons-digester.jar
  9e9eb622 (LOCAL_ONLY) 20051122180920 plugins/OMERO.insight-ij-5.2.2-ice35-b17/libs/commons-discovery.jar
  d59d3e4c (LOCAL_ONLY) 20080120204418 plugins/OMERO.insight-ij-5.2.2-ice35-b17/libs/commons-io.jar
  f6139801 (LOCAL_ONLY) 20100225012342 plugins/OMERO.insight-ij-5.2.2-ice35-b17/libs/commons-lang.jar
  fa9b8239 (LOCAL_ONLY) 20130516220522 plugins/OMERO.insight-ij-5.2.2-ice35-b17/libs/commons-logging.jar
  60a83b54 (LOCAL_ONLY) 20150731184018 plugins/OMERO.insight-ij-5.2.2-ice35-b17/libs/commons-validator.jar
  15958f82 (LOCAL_ONLY) 20100519160622 plugins/OMERO.insight-ij-5.2.2-ice35-b17/libs/ehcache-core.jar
  27410488 (LOCAL_ONLY) 20061120225932 plugins/OMERO.insight-ij-5.2.2-ice35-b17/libs/filters.jar
  e33cecc2 (LOCAL_ONLY) 20150805084958 plugins/OMERO.insight-ij-5.2.2-ice35-b17/libs/grib.jar
  2cd0d04c (LOCAL_ONLY) 20140422224746 plugins/OMERO.insight-ij-5.2.2-ice35-b17/libs/guava.jar
  85c28658 (LOCAL_ONLY) 20150731184018 plugins/OMERO.insight-ij-5.2.2-ice35-b17/libs/hibernate-jpa-2.0-api.jar
  0c6e277e (LOCAL_ONLY) 20131003214258 plugins/OMERO.insight-ij-5.2.2-ice35-b17/libs/httpclient.jar
  9f61e37d (LOCAL_ONLY) 20130729170622 plugins/OMERO.insight-ij-5.2.2-ice35-b17/libs/httpcore.jar
  d216e98a (LOCAL_ONLY) 20131003214348 plugins/OMERO.insight-ij-5.2.2-ice35-b17/libs/httpmime.jar
  1911c9e1 (LOCAL_ONLY) 20140427224424 plugins/OMERO.insight-ij-5.2.2-ice35-b17/libs/ice-glacier2.jar
  b1d709fb (LOCAL_ONLY) 20140427224658 plugins/OMERO.insight-ij-5.2.2-ice35-b17/libs/ice-grid.jar
  c49b8fa2 (LOCAL_ONLY) 20140427230042 plugins/OMERO.insight-ij-5.2.2-ice35-b17/libs/ice-storm.jar
  53aa5393 (LOCAL_ONLY) 20140427224510 plugins/OMERO.insight-ij-5.2.2-ice35-b17/libs/ice.jar
  ad406214 (LOCAL_ONLY) 20140308072144 plugins/OMERO.insight-ij-5.2.2-ice35-b17/libs/ij.jar
  4679e275 (LOCAL_ONLY) 20080217174132 plugins/OMERO.insight-ij-5.2.2-ice35-b17/libs/ini4j.jar
  62d77e4e (LOCAL_ONLY) 20100520024410 plugins/OMERO.insight-ij-5.2.2-ice35-b17/libs/java-getopt.jar
  c827227f (LOCAL_ONLY) 20100821185944 plugins/OMERO.insight-ij-5.2.2-ice35-b17/libs/java-image-scaling.jar
  86d3432e (LOCAL_ONLY) 20060717130958 plugins/OMERO.insight-ij-5.2.2-ice35-b17/libs/jaxrpc-api.jar
  07f15e96 (LOCAL_ONLY) 20140724173642 plugins/OMERO.insight-ij-5.2.2-ice35-b17/libs/jcommon.jar
  c4eeeb8f (LOCAL_ONLY) 20140731143446 plugins/OMERO.insight-ij-5.2.2-ice35-b17/libs/jfreechart.jar
  d5e85b0e (LOCAL_ONLY) 20150702170156 plugins/OMERO.insight-ij-5.2.2-ice35-b17/libs/jhdf5.jar
  34d3c097 (LOCAL_ONLY) 20111221222152 plugins/OMERO.insight-ij-5.2.2-ice35-b17/libs/jna.jar
  4c09d41c (LOCAL_ONLY) 20130308142342 plugins/OMERO.insight-ij-5.2.2-ice35-b17/libs/joda-time.jar
  4a754817 (LOCAL_ONLY) 20140504150434 plugins/OMERO.insight-ij-5.2.2-ice35-b17/libs/kryo.jar
  10d5cf34 (LOCAL_ONLY) 20060103173402 plugins/OMERO.insight-ij-5.2.2-ice35-b17/libs/log4j.jar
  94e94459 (LOCAL_ONLY) 20160212105654 plugins/OMERO.insight-ij-5.2.2-ice35-b17/libs/lwf-stubs.jar
  ab8ff4ee (LOCAL_ONLY) 20120719222102 plugins/OMERO.insight-ij-5.2.2-ice35-b17/libs/metadata-extractor.jar
  16b765c2 (LOCAL_ONLY) 20120531142650 plugins/OMERO.insight-ij-5.2.2-ice35-b17/libs/minlog.jar
  ac2a30fb (LOCAL_ONLY) 20160228171134 plugins/OMERO.insight-ij-5.2.2-ice35-b17/libs/model-psql-javadoc.jar
  a3b473a5 (LOCAL_ONLY) 20160228171126 plugins/OMERO.insight-ij-5.2.2-ice35-b17/libs/model-psql-sources.jar
  decae9ed (LOCAL_ONLY) 20160228171134 plugins/OMERO.insight-ij-5.2.2-ice35-b17/libs/model-psql.jar
  66de339f (LOCAL_ONLY) 20140821163824 plugins/OMERO.insight-ij-5.2.2-ice35-b17/libs/native-lib-loader.jar
  a51a31db (LOCAL_ONLY) 20131008220038 plugins/OMERO.insight-ij-5.2.2-ice35-b17/libs/netcdf.jar
  aff28c0e (LOCAL_ONLY) 20131010232536 plugins/OMERO.insight-ij-5.2.2-ice35-b17/libs/objenesis.jar
  18382f06 (LOCAL_ONLY) 20140427165354 plugins/OMERO.insight-ij-5.2.2-ice35-b17/libs/ome-java.jar
  7af6ddeb (LOCAL_ONLY) 20100312205702 plugins/OMERO.insight-ij-5.2.2-ice35-b17/libs/perf4j.jar
  81555875 (LOCAL_ONLY) 20111221222232 plugins/OMERO.insight-ij-5.2.2-ice35-b17/libs/platform.jar
  4ef2cfd3 (LOCAL_ONLY) 20091215081538 plugins/OMERO.insight-ij-5.2.2-ice35-b17/libs/poi.jar
  eedc0cd9 (LOCAL_ONLY) 20080930100254 plugins/OMERO.insight-ij-5.2.2-ice35-b17/libs/serializer.jar
  5085d943 (LOCAL_ONLY) 20140205223714 plugins/OMERO.insight-ij-5.2.2-ice35-b17/libs/slf4j-api.jar
  083137a4 (LOCAL_ONLY) 20160212105624 plugins/OMERO.insight-ij-5.2.2-ice35-b17/libs/specification.jar
  ba32bfdf (LOCAL_ONLY) 20100520023746 plugins/OMERO.insight-ij-5.2.2-ice35-b17/libs/swingx.jar
  36cdef55 (LOCAL_ONLY) 20080930100254 plugins/OMERO.insight-ij-5.2.2-ice35-b17/libs/xalan.jar
  93f166fd (LOCAL_ONLY) 20061007140232 plugins/OMERO.insight-ij-5.2.2-ice35-b17/libs/xercesImpl.jar
  a5c15945 (LOCAL_ONLY) 20120703121340 plugins/OMERO.insight-ij-5.2.2-ice35-b17/libs/xmpcore.jar
  a00ae789 (LOCAL_ONLY) 20160228171826 plugins/OMERO.insight-ij-5.2.2-ice35-b17/omero_ij.jar
Comment 1 Curtis Rueden 2016-03-07 12:26:09 CST 
Please download the latest version of Fiji which comes bundled with Java 8 and has the Java-8 update site enabled. It bundles of a new version of Java 3D which works with Java 8. Hopefully this configuration will also be compatible with the OMERO plugin.
Comment 2 Adam Ostrowski 2016-03-08 12:56:55 CST 
I tried downloading the most current version directly from the Fiji website. Unfortunately the zip packages are broken and will not unpack on windows or Linux machine. This applies to both windows and Linux distributions. I did not try a Mac.
Comment 3 Curtis Rueden 2016-03-08 13:14:21 CST 
> Unfortunately the zip packages are broken and will not unpack on windows
> or Linux machine. This applies to both windows and Linux distributions.

When did you try this? Yesterday, I updated the Fiji downloads to be served from downloads.imagej.net instead of jenkins.imagej.net, which I was expecting would solve this exact problem for many users overseas.

Then, earlier today, our web server had some brief minutes of downtime a couple hours ago -- perhaps you were bitten by that downtime, which cut off your downloads.

Could you please try downloading one more time? You can browse all the latest Fiji packages here, including approximate file sizes:

 http://downloads.imagej.net/fiji/latest/

If the downloads are still not completing successfully, we'll have to do some additional troubleshooting on the server side.
Comment 4 Adam Ostrowski 2016-03-09 06:07:00 CST 
I just downloaded the new package form the server you supplied. The package unpacks fine, but the programme crashes upon startup. Is there a logfile I could look up and/or supply?
Comment 5 Jan Eglinger 2016-03-09 06:20:14 CST 
(In reply to Adam Ostrowski from comment #4)
> I just downloaded the new package form the server you supplied. The package
> unpacks fine, but the programme crashes upon startup.

There was another bug preventing ImageJ from starting up beyond showing the initial splash screen:
http://fiji.sc/bugzilla/﷒0﷓

Could you try to do the following from the Command Prompt (on Windows):

cd %temp%
rm *.stub

Then try again running ImageJ-win64.exe.
Comment 6 Adam Ostrowski 2016-03-09 06:30:24 CST 
Yes, the file was there and getting rid of it allowed Fiji to start. The plugins also work now.

Before all this kicked off I tried running the updated with the Java site ticked, but after the update I couldn't launch the programme anymore. I wonder if that temporary file was to blame for that too.
I still have the folder with the previous version of Fiji, so I could check that if you'd like.
Comment 7 Curtis Rueden 2016-04-25 16:30:05 CDT 
Closing, since it sounds like all is working for you now.

If you have any continuing issues, please feel free to file a new issue, or reach out to us on the ImageJ forum -- http://forum.imagej.net/