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Bug 1216 - Jython script crashes
Jython script crashes
Status: RESOLVED FIXED
Product: Fiji
Classification: Unclassified
Component: Plugins
unspecified
PC Windows
: P4 normal
Assigned To: ImageJ Bugs Mailing List
Depends on:
Blocks:
 
Reported: 2016-01-14 05:05 CST by Felix
Modified: 2016-01-26 11:43 CST
3 users (show)

See Also:
Description Felix 2016-01-14 05:05:07 CST 
When I try to run Plugins>Registration>Correct 3D drift
the following error occurs:

org.python.core.PyException: null
	at org.python.core.Py.ImportError(Py.java:304) ~[jython-shaded-2.5.3.jar:2.5.3]
	at org.python.core.imp.import_logic(imp.java:790) ~[jython-shaded-2.5.3.jar:2.5.3]
	at org.python.core.imp.import_module_level(imp.java:842) ~[jython-shaded-2.5.3.jar:2.5.3]
	at org.python.core.imp.importName(imp.java:917) ~[jython-shaded-2.5.3.jar:2.5.3]
	at org.python.core.ImportFunction.__call__(__builtin__.java:1220) ~[jython-shaded-2.5.3.jar:2.5.3]
	at org.python.core.PyObject.__call__(PyObject.java:357) ~[jython-shaded-2.5.3.jar:2.5.3]
	at org.python.core.__builtin__.__import__(__builtin__.java:1173) ~[jython-shaded-2.5.3.jar:2.5.3]
	at org.python.core.imp.importFromAs(imp.java:1011) ~[jython-shaded-2.5.3.jar:2.5.3]
	at org.python.core.imp.importFrom(imp.java:987) ~[jython-shaded-2.5.3.jar:2.5.3]
	at org.python.pycode._pyx0.f$0(C:\Users\Public\Fiji.app\plugins\Scripts\Plugins\Registration\Correct_3D_drift.py:298) ~[na:na]
	at org.python.pycode._pyx0.call_function(C:\Users\Public\Fiji.app\plugins\Scripts\Plugins\Registration\Correct_3D_drift.py) ~[na:na]
	at org.python.core.PyTableCode.call(PyTableCode.java:165) ~[jython-shaded-2.5.3.jar:2.5.3]
	at org.python.core.PyCode.call(PyCode.java:18) ~[jython-shaded-2.5.3.jar:2.5.3]
	at org.python.core.Py.runCode(Py.java:1275) ~[jython-shaded-2.5.3.jar:2.5.3]
	at org.scijava.plugins.scripting.jython.JythonScriptEngine.eval(JythonScriptEngine.java:76) ~[scripting-jython-0.2.4.jar:0.2.4]
	at org.scijava.script.ScriptModule.run(ScriptModule.java:173) ~[scijava-common-2.50.1.jar:2.50.1]
	at org.scijava.module.ModuleRunner.run(ModuleRunner.java:167) [scijava-common-2.50.1.jar:2.50.1]
	at org.scijava.module.ModuleRunner.call(ModuleRunner.java:126) [scijava-common-2.50.1.jar:2.50.1]
	at org.scijava.module.ModuleRunner.call(ModuleRunner.java:65) [scijava-common-2.50.1.jar:2.50.1]
	at org.scijava.thread.DefaultThreadService$2.call(DefaultThreadService.java:191) [scijava-common-2.50.1.jar:2.50.1]
	at java.util.concurrent.FutureTask.run(FutureTask.java:266) [na:1.8.0_66]
	at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) [na:1.8.0_66]
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617) [na:1.8.0_66]
	at java.lang.Thread.run(Thread.java:745) [na:1.8.0_66]

Information about your version of Java:

  os.arch => amd64
  os.name => Windows 7
  os.version => 6.1
  java.version => 1.8.0_66
  java.vendor => Oracle Corporation
  java.runtime.name => Java(TM) SE Runtime Environment
  java.runtime.version => 1.8.0_66-b18
  java.vm.name => Java HotSpot(TM) 64-Bit Server VM
  java.vm.version => 25.66-b18
  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 => 1.8
  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:\Program Files\Java\jdk1.8.0_66/jre
  imagej.dir => C:\Users\Public\Fiji.app

Information about the version of each plugin:

Activated update sites:
ImageJ: http://update.imagej.net/ (last check:20151222031554)
Fiji: http://update.fiji.sc/ (last check:20151222052403)
Java-8: http://sites.imagej.net/Java-8/ (last check:20160107181822)

Files not up-to-date:
  d290c110 (LOCAL_ONLY) 20151218154910 jars/commons-io-2.4.jar
  c6325009 (LOCAL_ONLY) 20151218154940 jars/omero/imagej-omero-0.3.2.jar
  1445b008 (LOCAL_ONLY) 20151218154949 jars/omero/omero-client-5.1.2-ice35.jar
  2f2a824f (LOCAL_ONLY) 20151218154950 jars/omero/scijava-log-slf4j-1.0.0.jar
  928ffe97 (LOCAL_ONLY) 20151218154912 plugins/Adapt__v1.146.jar
  8808d802 (LOCAL_ONLY) 20151218154909 plugins/BioVoxxel_Plugins.jar
  bae2315e (LOCAL_ONLY) 20151218154910 plugins/Data_Analysis.jar
  4c4c0e80 (LOCAL_ONLY) 20151218154912 plugins/IA_Class_Library_v1.123.jar
  1edfbfde (LOCAL_ONLY) 20151215213624 plugins/Imaris/ImarisBridgeUtils.jar
  eb679ca0 (LOCAL_ONLY) 20151215213624 plugins/Imaris/Imaris_Bridge.jar
  1c348610 (LOCAL_ONLY) 20151218154911 plugins/Particle_Tracker_Library_v1.125.jar
  fe58c8cc (LOCAL_ONLY) 20151218154643 plugins/jars/nanozoomer-1.0.0.jar
  8e8db316 20151218154907 plugins/mcib3d-suite/mcib3d-core.jar
  a4ccc1f2 20151218154907 plugins/mcib3d-suite/mcib3d_plugins.jar
Comment 1 Felix 2016-01-14 05:15:44 CST 
I tried with a fresh installation. in java 6 it works. However if I remove the java folder, do an update, enable the java8 update site and apply the update it won't run either. 

the error message is a bit different though:

Traceback (most recent call last):
  File "C:\Users\meyenhof\DOWNLO~1\Fiji.app\plugins\Scripts\Plugins\Registration\Correct_3D_drift.py", line 16, in <module>
    from javax.vecmath import Point3i
ImportError: No module named vecmath
Comment 2 Jan Eglinger 2016-01-14 06:01:00 CST 
(In reply to Felix from comment #1)
>     from javax.vecmath import Point3i
> ImportError: No module named vecmath

This was fixed by Curtis Rueden in the source already:
https://github.com/fiji/fiji/commit/d0d02ce8d9bce59c4b2db03cfaaf4ca597701d23#diff-45e7679c76ad4b96797e8409766cf6d9

But it doesn't seem to be available from the Java-8 update site yet.
Comment 3 Curtis Rueden 2016-01-26 11:43:56 CST 
I uploaded the latest version of Correct 3D Drift to the Java-8 update site, which should work with the new Java-8-compatible version of Java 3D.

This version of the script also has some new features contributed by Christian Tischer; see https://github.com/fiji/fiji/pull/137

Give it a try and let us know how it works for you.