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Bug 125 - TrakEM2 new blank project in Windows
TrakEM2 new blank project in Windows
Status: RESOLVED FIXED
Product: Fiji
Classification: Unclassified
Component: Plugins
unspecified
PC Windows
: P4 normal
Assigned To: ImageJ Bugs Mailing List
Depends on:
Blocks:
 
Reported: 2009-12-19 05:23 CST by Richard Fetter
Modified: 2010-04-01 11:03 CDT
2 users (show)

See Also:
Description Richard Fetter 2009-12-19 05:23:36 CST 
I'm trying to montage and analyze some raster EM images generated by Leginon using File -> New -> TrakEM2[blank].  A new project window opens, but the Log window reports a list off errors(below).  Trying to open the MRC files by dragging to the project window causes the system to hang. I have tried re-installing Fiji on my Windows XP system but this is not solving the problem.  The same Fiji installation on a Linux system works fine.

==================
ERROR:
java.lang.reflect.InvocationTargetException
	at java.awt.EventQueue.invokeAndWait(Unknown Source)
	at javax.swing.SwingUtilities.invokeAndWait(Unknown Source)
	at ini.trakem2.ControlWindow$3.run(ControlWindow.java:317)
Caused by: java.lang.NoClassDefFoundError: javax/media/j3d/Shape3D
	at java.lang.ClassLoader.defineClass1(Native Method)
	at java.lang.ClassLoader.defineClass(Unknown Source)
	at java.lang.ClassLoader.defineClass(Unknown Source)
	at fiji.FijiClassLoader.loadClass(FijiClassLoader.java:162)
	at fiji.FijiClassLoader.loadClass(FijiClassLoader.java:140)
	at fiji.FijiClassLoader.loadClass(FijiClassLoader.java:135)
	at java.lang.ClassLoader.loadClassInternal(Unknown Source)
	at ini.trakem2.ControlWindow.<init>(ControlWindow.java:78)
	at ini.trakem2.ControlWindow.<init>(ControlWindow.java:60)
	at ini.trakem2.ControlWindow$2.run(ControlWindow.java:185)
	at java.awt.event.InvocationEvent.dispatch(Unknown Source)
	at java.awt.EventQueue.dispatchEvent(Unknown Source)
	at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source)
	at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source)
	at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source)
	at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
	at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
	at java.awt.EventDispatchThread.run(Unknown Source)
Caused by: java.lang.ClassNotFoundException: javax.media.j3d.Shape3D
	at java.lang.ClassLoader.findClass(Unknown Source)
	at java.lang.ClassLoader.loadClass(Unknown Source)
	at fiji.FijiClassLoader.loadClass(FijiClassLoader.java:173)
	at fiji.FijiClassLoader.loadClass(FijiClassLoader.java:140)
	at fiji.FijiClassLoader.loadClass(FijiClassLoader.java:135)
	at java.lang.ClassLoader.loadClassInternal(Unknown Source)
	... 18 more
==> Caused by:
java.lang.NoClassDefFoundError: javax/media/j3d/Shape3D
	at java.lang.ClassLoader.defineClass1(Native Method)
	at java.lang.ClassLoader.defineClass(Unknown Source)
	at java.lang.ClassLoader.defineClass(Unknown Source)
	at fiji.FijiClassLoader.loadClass(FijiClassLoader.java:162)
	at fiji.FijiClassLoader.loadClass(FijiClassLoader.java:140)
	at fiji.FijiClassLoader.loadClass(FijiClassLoader.java:135)
	at java.lang.ClassLoader.loadClassInternal(Unknown Source)
	at ini.trakem2.ControlWindow.<init>(ControlWindow.java:78)
	at ini.trakem2.ControlWindow.<init>(ControlWindow.java:60)
	at ini.trakem2.ControlWindow$2.run(ControlWindow.java:185)
	at java.awt.event.InvocationEvent.dispatch(Unknown Source)
	at java.awt.EventQueue.dispatchEvent(Unknown Source)
	at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source)
	at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source)
	at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source)
	at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
	at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
	at java.awt.EventDispatchThread.run(Unknown Source)
Caused by: java.lang.ClassNotFoundException: javax.media.j3d.Shape3D
	at java.lang.ClassLoader.findClass(Unknown Source)
	at java.lang.ClassLoader.loadClass(Unknown Source)
	at fiji.FijiClassLoader.loadClass(FijiClassLoader.java:173)
	at fiji.FijiClassLoader.loadClass(FijiClassLoader.java:140)
	at fiji.FijiClassLoader.loadClass(FijiClassLoader.java:135)
	at java.lang.ClassLoader.loadClassInternal(Unknown Source)
	... 18 more
==> Caused by:
java.lang.ClassNotFoundException: javax.media.j3d.Shape3D
	at java.lang.ClassLoader.findClass(Unknown Source)
	at java.lang.ClassLoader.loadClass(Unknown Source)
	at fiji.FijiClassLoader.loadClass(FijiClassLoader.java:173)
	at fiji.FijiClassLoader.loadClass(FijiClassLoader.java:140)
	at fiji.FijiClassLoader.loadClass(FijiClassLoader.java:135)
	at java.lang.ClassLoader.loadClassInternal(Unknown Source)
	at java.lang.ClassLoader.defineClass1(Native Method)
	at java.lang.ClassLoader.defineClass(Unknown Source)
	at java.lang.ClassLoader.defineClass(Unknown Source)
	at fiji.FijiClassLoader.loadClass(FijiClassLoader.java:162)
	at fiji.FijiClassLoader.loadClass(FijiClassLoader.java:140)
	at fiji.FijiClassLoader.loadClass(FijiClassLoader.java:135)
	at java.lang.ClassLoader.loadClassInternal(Unknown Source)
	at ini.trakem2.ControlWindow.<init>(ControlWindow.java:78)
	at ini.trakem2.ControlWindow.<init>(ControlWindow.java:60)
	at ini.trakem2.ControlWindow$2.run(ControlWindow.java:185)
	at java.awt.event.InvocationEvent.dispatch(Unknown Source)
	at java.awt.EventQueue.dispatchEvent(Unknown Source)
	at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source)
	at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source)
	at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source)
	at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
	at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
	at java.awt.EventDispatchThread.run(Unknown Source)
==================


Information about your version of Java - this information is useful for the Fiji developers:
  os.arch => x86
  os.name => Windows XP
  os.version => 5.1
  java.version => 1.6.0_17
  java.vendor => Sun Microsystems Inc.
  java.runtime.name => Java(TM) SE Runtime Environment
  java.runtime.version => 1.6.0_17-b04
  java.vm.name => Java HotSpot(TM) Client VM
  java.vm.version => 14.3-b01
  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 => \
Comment 1 Johannes Schindelin 2009-12-19 12:12:17 CST 
You have not installed Java3D.  Your Java version tells me that you do not run with Fiji's Java, where Java3D is installed, but your own Java version (1.6.0 Update 17 instead of Fiji's 1.6.0 Update 14).

If you are running Fiji with enough privileges to add Java extensions, you can try this:

1) Open the Script Editor with File>New>Script

2) Select language "Python" in the Language menu

3) Copy these two lines:

    from ij3d import Install_J3D
    Install_J3D().run(None)

4) Select "Run" from the Run menu

This will probably take some time, but as long as the window title says "(Running)", you will have to wait.  When it is done, you probably need to restart Fiji.

Run "Plugins>3D Viewer" to see whether it worked.

Unfortunately, the output of that procedure goes to the console, which on Windows means that you will not see it unless you start Fiji from the command line with the command line option "--console".
Comment 2 Albert Cardona 2010-03-31 20:30:33 CDT 
Rick: is this error still an issue for you?

Please call "Help - Update Fiji", there have been a number of fixes in many packages.
Comment 3 Johannes Schindelin 2010-04-01 11:03:34 CDT 
I'll just assume that the issue does not exist any longer (4 months is a long enough time to say whether it's still a problem, methinks).