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<b><a class="bz_bug_link
bz_status_NEEDSINFO "
title="NEEDSINFO - Cannot run commands from the ijpb/MorphoLibJ plugin in --headless mode using --jython script option"
href="http://fiji.sc/bugzilla/show_bug.cgi?id=1107#c4">Comment # 4</a>
on <a class="bz_bug_link
bz_status_NEEDSINFO "
title="NEEDSINFO - Cannot run commands from the ijpb/MorphoLibJ plugin in --headless mode using --jython script option"
href="http://fiji.sc/bugzilla/show_bug.cgi?id=1107">bug 1107</a>
from <span class="vcard"><a class="email" href="mailto:ghv2@psu.edu" title="Greg Von Kuster <ghv2@psu.edu>"> <span class="fn">Greg Von Kuster</span></a>
</span></b>
<pre>Here is the full stack trace of the command that uses the Edge Detection plugin
available at
<a href="http://imagejdocu.tudor.lu/lib/exe/fetch.php?media=plugin:filter:edge_detection:image_edge.jar">http://imagejdocu.tudor.lu/lib/exe/fetch.php?media=plugin:filter:edge_detection:image_edge.jar</a>.
$ ImageJ-macosx --ij2 --headless --debug --jython
/Users/gvk/work/ts_install/shed_tools/localhost/repos/iuc/imagej2_edge_detection/d53f258d585f/imagej2_edge_detection/jython_script.py
/var/folders/qm/p6jt97wj4239jx8gdv7jy75m0000gn/T/tmpkNSSbb
/var/folders/qm/p6jt97wj4239jx8gdv7jy75m0000gn/T/tmp-imagej-Q8RvY3/tmpg30esn.gif
area_filter 3.0 1.0 100.0 50.0 None None None None None
/Users/gvk/Desktop/tmp5tOFP0.png None None png
Available RAM: 10164MB, using 3/4 of that: 7623MB
JRE not found in
'/Users/gvk/work/ts_install/tool_dependency_dir/fiji/20141125/iuc/package_fiji_20141125/a9ee9bebf932/jre'
JAVA_HOME contains a JRE:
'/Library/Java/JavaVirtualMachines/jdk1.8.0_20.jdk/Contents/Home//jre'
Re-executing with correct library lookup path
(/Users/gvk/work/ts_install/tool_dependency_dir/fiji/20141125/iuc/package_fiji_20141125/a9ee9bebf932/lib/macosx:/Users/gvk/work/ts_install/tool_dependency_dir/fiji/20141125/iuc/package_fiji_20141125/a9ee9bebf932/mm/macosx)
Available RAM: 10164MB, using 3/4 of that: 7623MB
JRE not found in
'/Users/gvk/work/ts_install/tool_dependency_dir/fiji/20141125/iuc/package_fiji_20141125/a9ee9bebf932/jre'
JAVA_HOME contains a JRE:
'/Library/Java/JavaVirtualMachines/jdk1.8.0_20.jdk/Contents/Home//jre'
java
-Djava.ext.dirs=/Users/gvk/work/ts_install/tool_dependency_dir/fiji/20141125/iuc/package_fiji_20141125/a9ee9bebf932/java/macosx-java3d/Home/lib/ext:/Library/Java/JavaVirtualMachines/jdk1.8.0_20.jdk/Contents/Home/jre/lib/ext:/Library/Java/Extensions:/System/Library/Java/Extensions:/System/Library/Frameworks/JavaVM.framework/Home/lib/ext
-Dpython.cachedir.skip=true
-Dplugins.dir=/Users/gvk/work/ts_install/tool_dependency_dir/fiji/20141125/iuc/package_fiji_20141125/a9ee9bebf932
-Xmx7623m -Djava.awt.headless=true -Dapple.awt.UIElement=true -Xincgc
-XX:PermSize=128m
-Djava.class.path=/Users/gvk/work/ts_install/tool_dependency_dir/fiji/20141125/iuc/package_fiji_20141125/a9ee9bebf932/jars/imagej-launcher-3.1.6.jar
-Dimagej.dir=/Users/gvk/work/ts_install/tool_dependency_dir/fiji/20141125/iuc/package_fiji_20141125/a9ee9bebf932
-Dij.dir=/Users/gvk/work/ts_install/tool_dependency_dir/fiji/20141125/iuc/package_fiji_20141125/a9ee9bebf932
-Dfiji.dir=/Users/gvk/work/ts_install/tool_dependency_dir/fiji/20141125/iuc/package_fiji_20141125/a9ee9bebf932
-Dfiji.executable=ImageJ-macosx -Dij.executable=ImageJ-macosx
-Djava.library.path=/Users/gvk/work/ts_install/tool_dependency_dir/fiji/20141125/iuc/package_fiji_20141125/a9ee9bebf932/lib/macosx:/Users/gvk/work/ts_install/tool_dependency_dir/fiji/20141125/iuc/package_fiji_20141125/a9ee9bebf932/mm/macosx
-Dij.debug=true -Dscijava.log.level=debug net.imagej.launcher.ClassLauncher
-classpath /usr/share/java/jython.jar -classpath . -ijjarpath jars -ijjarpath
plugins org.python.util.jython
/Users/gvk/work/ts_install/shed_tools/localhost/repos/iuc/imagej2_edge_detection/d53f258d585f/imagej2_edge_detection/jython_script.py
/var/folders/qm/p6jt97wj4239jx8gdv7jy75m0000gn/T/tmpkNSSbb
/var/folders/qm/p6jt97wj4239jx8gdv7jy75m0000gn/T/tmp-imagej-Q8RvY3/tmpg30esn.gif
area_filter 3.0 1.0 100.0 50.0 None None None None None
/Users/gvk/Desktop/tmp5tOFP0.png None None png
Using JAVA_HOME
/Library/Java/JavaVirtualMachines/jdk1.8.0_20.jdk/Contents/Home//jre
Work around attempt at MacOSX world domination:
/Library/Java/JavaVirtualMachines/jdk1.8.0_20.jdk/Contents/Home//jre/lib/jli/libjli.dylib
Opening Java library
/Library/Java/JavaVirtualMachines/jdk1.8.0_20.jdk/Contents/Home//jre/lib/server/libjvm.dylib
Java HotSpot(TM) 64-Bit Server VM warning: ignoring option PermSize=128m;
support was removed in 8.0
Java HotSpot(TM) 64-Bit Server VM warning: Using incremental CMS is deprecated
and will likely be removed in a future release
Adding option:
-Djava.home=/Library/Java/JavaVirtualMachines/jdk1.8.0_20.jdk/Contents/Home/
ij1.plugin.dirs: null
$HOME/.plugins: /Users/gvk/.plugins does not exist
java.lang.IllegalArgumentException: Cannot handle replace call to list in
ij.Menus's public static synchronized java.lang.String[] getPlugins()
at net.imagej.patcher.CodeHacker.replaceCallInMethod(CodeHacker.java:724)
at net.imagej.patcher.CodeHacker.replaceCallInMethod(CodeHacker.java:649)
at
net.imagej.patcher.LegacyExtensions.addExtraPlugins(LegacyExtensions.java:475)
at
net.imagej.patcher.LegacyExtensions.injectHooks(LegacyExtensions.java:175)
at net.imagej.patcher.LegacyInjector.inject(LegacyInjector.java:308)
at net.imagej.patcher.LegacyInjector.injectHooks(LegacyInjector.java:109)
at
net.imagej.patcher.LegacyEnvironment.initialize(LegacyEnvironment.java:101)
at
net.imagej.patcher.LegacyEnvironment.applyPatches(LegacyEnvironment.java:495)
at net.imagej.patcher.LegacyInjector.preinit(LegacyInjector.java:397)
at net.imagej.patcher.LegacyInjector.preinit(LegacyInjector.java:376)
at fiji.IJ1Patcher.run(IJ1Patcher.java:37)
at net.imagej.launcher.ClassLauncher.patchIJ1(ClassLauncher.java:195)
at net.imagej.launcher.ClassLauncher.run(ClassLauncher.java:154)
at net.imagej.launcher.ClassLauncher.main(ClassLauncher.java:76)
Caused by: java.lang.RuntimeException: java.io.IOException: invalid constant
type: 18 at 168
at javassist.CtClassType.getClassFile2(CtClassType.java:204)
at javassist.compiler.MemberResolver.lookupMethod(MemberResolver.java:98)
at javassist.compiler.MemberResolver.lookupMethod(MemberResolver.java:84)
at javassist.compiler.TypeChecker.atMethodCallCore(TypeChecker.java:711)
at javassist.compiler.TypeChecker.atCallExpr(TypeChecker.java:688)
at javassist.compiler.JvstTypeChecker.atCallExpr(JvstTypeChecker.java:157)
at javassist.compiler.ast.CallExpr.accept(CallExpr.java:46)
at javassist.compiler.CodeGen.doTypeCheck(CodeGen.java:242)
at javassist.compiler.CodeGen.atStmnt(CodeGen.java:330)
at javassist.compiler.ast.Stmnt.accept(Stmnt.java:50)
at javassist.compiler.CodeGen.atIfStmnt(CodeGen.java:391)
at javassist.compiler.CodeGen.atStmnt(CodeGen.java:355)
at javassist.compiler.ast.Stmnt.accept(Stmnt.java:50)
at javassist.compiler.Javac.compileStmnt(Javac.java:569)
at javassist.expr.MethodCall.replace(MethodCall.java:235)
at net.imagej.patcher.CodeHacker$7.edit(CodeHacker.java:685)
at javassist.expr.ExprEditor.loopBody(ExprEditor.java:192)
at javassist.expr.ExprEditor.doit(ExprEditor.java:91)
at javassist.CtBehavior.instrument(CtBehavior.java:679)
at
net.imagej.patcher.CodeHacker$EagerExprEditor.instrument(CodeHacker.java:1278)
at net.imagej.patcher.CodeHacker.replaceCallInMethod(CodeHacker.java:669)
... 13 more
Caused by: java.io.IOException: invalid constant type: 18 at 168
at javassist.bytecode.ConstPool.readOne(ConstPool.java:1044)
at javassist.bytecode.ConstPool.read(ConstPool.java:984)
at javassist.bytecode.ConstPool.<init>(ConstPool.java:125)
at javassist.bytecode.ClassFile.read(ClassFile.java:770)
at javassist.bytecode.ClassFile.<init>(ClassFile.java:114)
at javassist.CtClassType.getClassFile2(CtClassType.java:191)
... 33 more
java.lang.IllegalArgumentException: Cannot modify method: public void run()
at net.imagej.patcher.CodeHacker.insertAtTopOfMethod(CodeHacker.java:167)
at
net.imagej.patcher.LegacyExtensions.injectHooks(LegacyExtensions.java:229)
at net.imagej.patcher.LegacyInjector.inject(LegacyInjector.java:308)
at net.imagej.patcher.LegacyInjector.injectHooks(LegacyInjector.java:109)
at
net.imagej.patcher.LegacyEnvironment.initialize(LegacyEnvironment.java:101)
at
net.imagej.patcher.LegacyEnvironment.applyPatches(LegacyEnvironment.java:495)
at net.imagej.patcher.LegacyInjector.preinit(LegacyInjector.java:397)
at net.imagej.patcher.LegacyInjector.preinit(LegacyInjector.java:376)
at fiji.IJ1Patcher.run(IJ1Patcher.java:37)
at net.imagej.launcher.ClassLauncher.patchIJ1(ClassLauncher.java:195)
at net.imagej.launcher.ClassLauncher.run(ClassLauncher.java:154)
at net.imagej.launcher.ClassLauncher.main(ClassLauncher.java:76)
Caused by: java.lang.IllegalArgumentException: No such class:
JavaScriptEvaluator
at net.imagej.patcher.CodeHacker.getClass(CodeHacker.java:880)
at net.imagej.patcher.CodeHacker.getMethod(CodeHacker.java:906)
at net.imagej.patcher.CodeHacker.getBehavior(CodeHacker.java:896)
at net.imagej.patcher.CodeHacker.insertAtTopOfMethod(CodeHacker.java:158)
... 11 more
Caused by: javassist.NotFoundException: JavaScriptEvaluator
at javassist.ClassPool.get(ClassPool.java:450)
at net.imagej.patcher.CodeHacker.getClass(CodeHacker.java:875)
... 14 more
java.lang.IllegalArgumentException: Cannot handle app name in ij.ImageJ's
public <init>(java.applet.Applet applet, int mode)
at net.imagej.patcher.CodeHacker.replaceAppNameInCall(CodeHacker.java:445)
at
net.imagej.patcher.LegacyExtensions.insertAppNameHooks(LegacyExtensions.java:404)
at
net.imagej.patcher.LegacyExtensions.injectHooks(LegacyExtensions.java:290)
at net.imagej.patcher.LegacyInjector.inject(LegacyInjector.java:308)
at net.imagej.patcher.LegacyInjector.injectHooks(LegacyInjector.java:109)
at
net.imagej.patcher.LegacyEnvironment.initialize(LegacyEnvironment.java:101)
at
net.imagej.patcher.LegacyEnvironment.applyPatches(LegacyEnvironment.java:495)
at net.imagej.patcher.LegacyInjector.preinit(LegacyInjector.java:397)
at net.imagej.patcher.LegacyInjector.preinit(LegacyInjector.java:376)
at fiji.IJ1Patcher.run(IJ1Patcher.java:37)
at net.imagej.launcher.ClassLauncher.patchIJ1(ClassLauncher.java:195)
at net.imagej.launcher.ClassLauncher.run(ClassLauncher.java:154)
at net.imagej.launcher.ClassLauncher.main(ClassLauncher.java:76)
Caused by: java.lang.RuntimeException: java.io.IOException: invalid constant
type: 18 at 1
at javassist.CtClassType.getClassFile2(CtClassType.java:204)
at javassist.CtClassType.subtypeOf(CtClassType.java:304)
at javassist.CtClassType.subtypeOf(CtClassType.java:319)
at
javassist.compiler.MemberResolver.compareSignature(MemberResolver.java:235)
at javassist.compiler.MemberResolver.lookupMethod(MemberResolver.java:107)
at javassist.compiler.MemberResolver.lookupMethod(MemberResolver.java:84)
at javassist.compiler.TypeChecker.atMethodCallCore(TypeChecker.java:711)
at javassist.compiler.TypeChecker.atCallExpr(TypeChecker.java:688)
at javassist.compiler.JvstTypeChecker.atCallExpr(JvstTypeChecker.java:157)
at javassist.compiler.ast.CallExpr.accept(CallExpr.java:46)
at javassist.compiler.CodeGen.doTypeCheck(CodeGen.java:242)
at javassist.compiler.CodeGen.atStmnt(CodeGen.java:330)
at javassist.compiler.ast.Stmnt.accept(Stmnt.java:50)
at javassist.compiler.Javac.compileStmnt(Javac.java:569)
at javassist.expr.MethodCall.replace(MethodCall.java:235)
at net.imagej.patcher.CodeHacker$4.edit(CodeHacker.java:426)
at net.imagej.patcher.CodeHacker$4.edit(CodeHacker.java:440)
at javassist.expr.ExprEditor.loopBody(ExprEditor.java:220)
at javassist.expr.ExprEditor.doit(ExprEditor.java:91)
at javassist.CtBehavior.instrument(CtBehavior.java:679)
at
net.imagej.patcher.CodeHacker$EagerExprEditor.instrument(CodeHacker.java:1278)
at net.imagej.patcher.CodeHacker.replaceAppNameInCall(CodeHacker.java:401)
... 12 more
Caused by: java.io.IOException: invalid constant type: 18 at 1
at javassist.bytecode.ConstPool.readOne(ConstPool.java:1044)
at javassist.bytecode.ConstPool.read(ConstPool.java:984)
at javassist.bytecode.ConstPool.<init>(ConstPool.java:125)
at javassist.bytecode.ClassFile.read(ClassFile.java:770)
at javassist.bytecode.ClassFile.<init>(ClassFile.java:114)
at javassist.CtClassType.getClassFile2(CtClassType.java:191)
... 33 more
Launching main class org.python.util.jython with parameters
[/Users/gvk/work/ts_install/shed_tools/localhost/repos/iuc/imagej2_edge_detection/d53f258d585f/imagej2_edge_detection/jython_script.py,
/var/folders/qm/p6jt97wj4239jx8gdv7jy75m0000gn/T/tmpkNSSbb,
/var/folders/qm/p6jt97wj4239jx8gdv7jy75m0000gn/T/tmp-imagej-Q8RvY3/tmpg30esn.gif,
area_filter, 3.0, 1.0, 100.0, 50.0, None, None, None, None, None,
/Users/gvk/Desktop/tmp5tOFP0.png, None, None, png]
Class loader = sun.misc.Launcher$AppClassLoader@c387f44
java.lang.NullPointerException
at
net.imagej.patcher.EssentialLegacyHooks.missingSubdirectories(EssentialLegacyHooks.java:164)
at
net.imagej.patcher.EssentialLegacyHooks.missingSubdirectories(EssentialLegacyHooks.java:167)
at
net.imagej.patcher.EssentialLegacyHooks.missingSubdirectories(EssentialLegacyHooks.java:167)
at
net.imagej.patcher.EssentialLegacyHooks.missingSubdirectories(EssentialLegacyHooks.java:167)
at
net.imagej.patcher.EssentialLegacyHooks.missingSubdirs(EssentialLegacyHooks.java:146)
at ij.IJ.getClassLoader(IJ.java)
at ij.io.Opener.<clinit>(Opener.java:55)
at ij.IJ.openImage(IJ.java:1609)
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:387)
at org.python.core.PyObject.__call__(PyObject.java:391)
at
org.python.pycode._pyx0.f$0(/Users/gvk/work/ts_install/shed_tools/localhost/repos/iuc/imagej2_edge_detection/d53f258d585f/imagej2_edge_detection/jython_script.py:67)
at
org.python.pycode._pyx0.call_function(/Users/gvk/work/ts_install/shed_tools/localhost/repos/iuc/imagej2_edge_detection/d53f258d585f/imagej2_edge_detection/jython_script.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.python.util.PythonInterpreter.execfile(PythonInterpreter.java:235)
at org.python.util.jython.run(jython.java:247)
at org.python.util.jython.main(jython.java:129)
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 net.imagej.launcher.ClassLauncher.launch(ClassLauncher.java:258)
at net.imagej.launcher.ClassLauncher.run(ClassLauncher.java:184)
at net.imagej.launcher.ClassLauncher.main(ClassLauncher.java:76)
java.lang.NullPointerException
java.lang.NumberFormatException: For input string: "&median_filter_radius"
at sun.misc.FloatingDecimal.readJavaFormatString(FloatingDecimal.java:2043)
at sun.misc.FloatingDecimal.parseDouble(FloatingDecimal.java:110)
at java.lang.Double.parseDouble(Double.java:538)
at
net.imagej.patcher.HeadlessGenericDialog.getMacroParameter(HeadlessGenericDialog.java:305)
at
net.imagej.patcher.HeadlessGenericDialog.addNumericField(HeadlessGenericDialog.java:107)
at Image_Edge.EdgeDetection(Image_Edge.java:71)
at Image_Edge.run(Image_Edge.java:39)
at ij.IJ.runUserPlugIn(IJ.java:202)
at ij.IJ.runPlugIn(IJ.java:166)
at ij.Executer.runCommand(Executer.java:131)
at ij.Executer.run(Executer.java:64)
at ij.IJ.run(IJ.java:272)
at ij.IJ.run(IJ.java:323)
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:422)
at org.python.core.PyObject.__call__(PyObject.java:426)
at
org.python.pycode._pyx0.f$0(/Users/gvk/work/ts_install/shed_tools/localhost/repos/iuc/imagej2_edge_detection/d53f258d585f/imagej2_edge_detection/jython_script.py:67)
at
org.python.pycode._pyx0.call_function(/Users/gvk/work/ts_install/shed_tools/localhost/repos/iuc/imagej2_edge_detection/d53f258d585f/imagej2_edge_detection/jython_script.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.python.util.PythonInterpreter.execfile(PythonInterpreter.java:235)
at org.python.util.jython.run(jython.java:247)
at org.python.util.jython.main(jython.java:129)
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 net.imagej.launcher.ClassLauncher.launch(ClassLauncher.java:258)
at net.imagej.launcher.ClassLauncher.run(ClassLauncher.java:184)
at net.imagej.launcher.ClassLauncher.main(ClassLauncher.java:76)</pre>
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