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Bug 1155 - CoverMaker plugin is not working
CoverMaker plugin is not working
Status: RESOLVED FIXED
Product: Fiji
Classification: Unclassified
Component: Plugins
unspecified
Macintosh Mac OS
: P4 normal
Assigned To: ImageJ Bugs Mailing List
Depends on:
Blocks:
 
Reported: 2015-09-05 02:49 CDT by tomancak
Modified: 2015-09-24 12:57 CDT
2 users (show)

See Also:
Description tomancak 2015-09-05 02:49:47 CDT 
Something wrong with inlining Java code in Jython.

Any ideas?

Thanks a lot

PAvel


(Fiji Is Just) ImageJ 2.0.0-rc-34/1.50a; Java 1.8.0_31 [64-bit]; Mac OS X 10.8.5; 309MB of 7958MB (3%)
 
java.lang.ClassNotFoundException: weave.gen1
	at java.net.URLClassLoader$1.run(URLClassLoader.java:372)
	at java.net.URLClassLoader$1.run(URLClassLoader.java:361)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.net.URLClassLoader.findClass(URLClassLoader.java:360)
	at java.lang.ClassLoader.loadClass(ClassLoader.java:424)
	at java.lang.ClassLoader.loadClass(ClassLoader.java:357)
	at fiji.scripting.Weaver.inline(Weaver.java:185)
	at fiji.scripting.Weaver.inline(Weaver.java:93)
	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.lang.reflect.Method.invoke(Method.java:483)
	at org.python.core.PyReflectedFunction.__call__(PyReflectedFunction.java:186)
	at org.python.core.PyReflectedFunction.__call__(PyReflectedFunction.java:204)
	at org.python.core.PyObject.__call__(PyObject.java:404)
	at org.python.core.PyObject.__call__(PyObject.java:408)
	at org.python.pycode._pyx0.Inline$3(/Applications/Fiji.app/plugins/Examples/CoverMaker/Cover_Maker.py:48)
	at org.python.pycode._pyx0.call_function(/Applications/Fiji.app/plugins/Examples/CoverMaker/Cover_Maker.py)
	at org.python.core.PyTableCode.call(PyTableCode.java:165)
	at org.python.core.PyBaseCode.call(PyBaseCode.java:134)
	at org.python.core.PyFunction.__call__(PyFunction.java:317)
	at org.python.pycode._pyx0.CreateCover$4(/Applications/Fiji.app/plugins/Examples/CoverMaker/Cover_Maker.py:140)
	at org.python.pycode._pyx0.call_function(/Applications/Fiji.app/plugins/Examples/CoverMaker/Cover_Maker.py)
	at org.python.core.PyTableCode.call(PyTableCode.java:165)
	at org.python.core.PyBaseCode.call(PyBaseCode.java:184)
	at org.python.core.PyFunction.__call__(PyFunction.java:350)
	at org.python.pycode._pyx0.f$0(/Applications/Fiji.app/plugins/Examples/CoverMaker/Cover_Maker.py:334)
	at org.python.pycode._pyx0.call_function(/Applications/Fiji.app/plugins/Examples/CoverMaker/Cover_Maker.py)
	at org.python.core.PyTableCode.call(PyTableCode.java:165)
	at org.python.core.PyCode.call(PyCode.java:18)
	at org.python.core.Py.runCode(Py.java:1275)
	at org.scijava.plugins.scripting.jython.JythonScriptEngine.eval(JythonScriptEngine.java:76)
	at org.scijava.script.ScriptModule.run(ScriptModule.java:174)
	at org.scijava.module.ModuleRunner.run(ModuleRunner.java:167)
	at org.scijava.module.ModuleRunner.call(ModuleRunner.java:126)
	at org.scijava.module.ModuleRunner.call(ModuleRunner.java:65)
	at org.scijava.thread.DefaultThreadService$2.call(DefaultThreadService.java:191)
	at java.util.concurrent.FutureTask.run(FutureTask.java:266)
	at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
	at java.lang.Thread.run(Thread.java:745)


/Users/tomancak/Desktop/Desktop_2015/CoverMaker//12_9.tif
26,22
binding is: class org.python.core.PyList
Traceback (most recent call last):
  File "/Applications/Fiji.app/plugins/Examples/CoverMaker/Cover_Maker.py", line 327, in <module>
    tileName, tileIndex, cols, rows = CreateCover(ip, tilewidth, tileheight, dbpath)
  File "/Applications/Fiji.app/plugins/Examples/CoverMaker/Cover_Maker.py", line 98, in CreateCover
    cruncher = Inline(arrays)
  File "/Applications/Fiji.app/plugins/Examples/CoverMaker/Cover_Maker.py", line 48, in Inline
    return Weaver.inline(
	at java.net.URLClassLoader$1.run(URLClassLoader.java:372)
	at java.net.URLClassLoader$1.run(URLClassLoader.java:361)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.net.URLClassLoader.findClass(URLClassLoader.java:360)
	at java.lang.ClassLoader.loadClass(ClassLoader.java:424)
	at java.lang.ClassLoader.loadClass(ClassLoader.java:357)
	at fiji.scripting.Weaver.inline(Weaver.java:185)
	at fiji.scripting.Weaver.inline(Weaver.java:93)
	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.lang.reflect.Method.invoke(Method.java:483)

java.lang.ClassNotFoundException: java.lang.ClassNotFoundException: weave.gen1

Information about your version of Java:

  os.arch => x86_64
  os.name => Mac OS X
  os.version => 10.8.5
  java.version => 1.8.0_31
  java.vendor => Oracle Corporation
  java.runtime.name => Java(TM) SE Runtime Environment
  java.runtime.version => 1.8.0_31-b13
  java.vm.name => Java HotSpot(TM) 64-Bit Server VM
  java.vm.version => 25.31-b07
  java.vm.vendor => Oracle Corporation
  java.vm.info => mixed mode
  java.awt.graphicsenv => sun.awt.CGraphicsEnvironment
  java.specification.name => Java Platform API Specification
  java.specification.version => 1.8
  sun.cpu.endian => little
  sun.desktop => null
  file.separator => /

The up-to-date check says: UPDATEABLE

Information relevant to JAVA_HOME related problems:

  JAVA_HOME is set to: /Library/Java/JavaVirtualMachines/jdk1.8.0_31.jdk/Contents/Home//jre
  imagej.dir => /Applications/Fiji.app

Information about the version of each plugin:

Activated update sites:
ImageJ: http://update.imagej.net/ (last check:20150722105527)
Fiji: http://fiji.sc/update/ (last check:20150725035809)
ClearVolume: http://sites.imagej.net/ClearVolume/ (last check:20150703181607)

Files not up-to-date:
  6dc91247 (MODIFIED) 20150302111630 Contents/Info.plist
  01a6a964 (MODIFIED) 20150822172349 jars/bigdataviewer-core-1.2.1-SNAPSHOT.jar
  970f9d47 (MODIFIED) 20150705201300 jars/bigdataviewer-core-1.2.1.jar
  d294eed6 (LOCAL_ONLY) 20150804030405 jars/bigdataviewer-core-1.2.2.jar_backup.jar
  279163cd (MODIFIED) 20150607165741 plugins/bigdataviewer_fiji-1.0.13-SNAPSHOT.jar
  439ae281 (LOCAL_ONLY) 20150201153952 plugins/trackmate-1.0.0-SNAPSHOT.jar
  143a7a00 (LOCAL_ONLY) 20150201153955 plugins/trove4j-3.0.3.jar
Comment 1 Curtis Rueden 2015-09-24 12:57:16 CDT 
This issue was resolved a couple of weeks ago on Gitter, but unfortunately in a private chat room.

We worked around the issue by removing the inline Java code in favor of a call to an new external Java method.

See:
* https://github.com/fiji/fiji-lib/commit/31b922bad9e41cd92147341bf5a74481e2d9d25b
* https://github.com/fiji/fiji/commit/02c560db1de2ea1d9d814d1c71cc317d9e519aa2