[ImageJ-bugs] [Bug 890] python broke after latest update

[bugzilla at fiji.sc]

http://fiji.sc/bugzilla/show_bug.cgi?id=890

--- Comment #6 from Kaitlin Snider <kaitlin.snider87 at gmail.com> ---
I am still having this issue.  Tried the fix of downloading Jython 2.5.2 and
saving the lib in Fiji.app/jars.  I'm getting this error:

Started Batch_Script.py at Sat Aug 16 10:04:35 EDT 2014
Traceback (most recent call last):
  File "D:\Google Drive\Fiji\Fiji.app\plugins\Batch_Script.py", line 10, in
<module>
    flist = os.listdir(dir1);
    at com.kenai.jaffl.provider.jffi.AsmRuntime.marshal(AsmRuntime.java:167)

    at org.python.posix.WindowsLibC$jaffl$0.stat$raw(Unknown Source)

    at org.python.posix.WindowsLibC$jaffl$0.stat(Unknown Source)

    at org.python.posix.BaseNativePOSIX.stat(BaseNativePOSIX.java:200)

    at org.python.posix.LazyPOSIX.stat(LazyPOSIX.java:207)

    at org.python.modules.posix.PosixModule.listdir(PosixModule.java:480)

    at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)

    at
sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)

    at
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)

    at java.lang.reflect.Method.invoke(Method.java:597)


java.lang.IncompatibleClassChangeError: java.lang.IncompatibleClassChangeError:
Found class com.kenai.jffi.InvocationBuffer, but interface was expected

    at org.python.core.PyException.fillInStackTrace(PyException.java:70)
    at java.lang.Throwable.<init>(Throwable.java:181)
    at java.lang.Exception.<init>(Exception.java:29)
    at java.lang.RuntimeException.<init>(RuntimeException.java:32)
    at org.python.core.PyException.<init>(PyException.java:46)
    at org.python.core.PyException.<init>(PyException.java:43)
    at org.python.core.Py.JavaError(Py.java:495)
    at org.python.core.Py.JavaError(Py.java:488)
    at
org.python.core.PyReflectedFunction.__call__(PyReflectedFunction.java:188)
    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._pyx5.f$0(D:\Google
Drive\Fiji\Fiji.app\plugins\Batch_Script.py:20)
    at org.python.pycode._pyx5.call_function(D:\Google
Drive\Fiji\Fiji.app\plugins\Batch_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.scijava.plugins.scripting.jython.JythonScriptEngine.eval(JythonScriptEngine.java:76)
    at org.scijava.script.ScriptModule.run(ScriptModule.java:175)
    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$2.call(DefaultThreadService.java:164)
    at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:303)
    at java.util.concurrent.FutureTask.run(FutureTask.java:138)
    at
java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:886)
    at
java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:908)
    at java.lang.Thread.run(Thread.java:662)
Caused by: java.lang.IncompatibleClassChangeError: Found class
com.kenai.jffi.InvocationBuffer, but interface was expected
    at com.kenai.jaffl.provider.jffi.AsmRuntime.marshal(AsmRuntime.java:167)
    at org.python.posix.WindowsLibC$jaffl$0.stat$raw(Unknown Source)
    at org.python.posix.WindowsLibC$jaffl$0.stat(Unknown Source)
    at org.python.posix.BaseNativePOSIX.stat(BaseNativePOSIX.java:200)
    at org.python.posix.LazyPOSIX.stat(LazyPOSIX.java:207)
    at org.python.modules.posix.PosixModule.listdir(PosixModule.java:480)
    at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    at
sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
    at
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
    at java.lang.reflect.Method.invoke(Method.java:597)
    at
org.python.core.PyReflectedFunction.__call__(PyReflectedFunction.java:186)
    ... 19 more

This happens with a simple batch script:

#Name the directory MANUALLY write in the folder on the next line
dir1 = "C:\\Users\\Stormcrow\\Google Drive\\Research\\Circ Rhythms\\Obrietan
Lab\\Techniques\\Analysis\\DRAQ ROI Analysis\\14-8-1 Optimized\\"

#And check:
print("The folder is: " + dir1);

#List all files in the directory
import os

flist = os.listdir(dir1);

#And check:
print("The files within this folder are: ")
for fname in flist:
    print fname

#Run a plugin on each file
from ij import IJ

for fname in flist:
    imp = IJ.openImage(dir1+fname)
    imp.show()
#Insert Plugin below - use record macro if necessary to get "Name"
    i = IJ.getImage()
    IJ.run("DRAQ ROIs wo TWS")
    print(fname + " completed processing", "")

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