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Bug 244 - Jython import oddity
Jython import oddity
Status: RESOLVED WORKSFORME
Product: Fiji
Classification: Unclassified
Component: Plugins
unspecified
PC Linux
: P4 normal
Assigned To: ImageJ Bugs Mailing List
Depends on:
Blocks:
 
Reported: 2010-11-05 11:04 CDT by Mark Longair
Modified: 2011-04-13 18:52 CDT
1 user (show)

See Also:
Description Mark Longair 2010-11-05 11:04:17 CDT 
We've noticed a strange problem when importing classes in Jython.
To reproduce the problem, open the Jython Interpreter and try "import Jama":

  Starting Jython ...All ImageJ and java.lang and TrakEM2 classes imported.
  ... done.
  >>> import Jama
  Traceback (most recent call last):
    File "<string>", line 1, in <module>
  ImportError: No module named Jama

	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.PyException.<init>(PyException.java:61)
	at org.python.core.Py.ImportError(Py.java:264)
	at org.python.core.imp.import_first(imp.java:672)
	at org.python.core.imp.import_name(imp.java:756)
	at org.python.core.imp.importName(imp.java:806)
	at org.python.core.ImportFunction.__call__(__builtin__.java:1232)
	at org.python.core.PyObject.__call__(PyObject.java:367)
	at org.python.core.__builtin__.__import__(__builtin__.java:1202)
	at org.python.core.__builtin__.__import__(__builtin__.java:1185)
	at org.python.core.imp.importOne(imp.java:817)
	at org.python.pycode._pyx29.f$0(<string>:1)
	at org.python.pycode._pyx29.call_function(<string>)
	at org.python.core.PyTableCode.call(PyTableCode.java:165)
	at org.python.core.PyCode.call(PyCode.java:18)
	at org.python.core.Py.runCode(Py.java:1204)
	at org.python.core.Py.exec(Py.java:1248)
	at org.python.util.PythonInterpreter.exec(PythonInterpreter.java:172)
	at Jython.Jython_Interpreter.eval(Jython_Interpreter.java:93)
	at common.AbstractInterpreter.execute(AbstractInterpreter.java:659)
	at common.AbstractInterpreter$ExecuteCode.run(AbstractInterpreter.java:559)

However, if you try importing a specific class from that module, that works, and
subsequently trying "import Jama" will then work:

  >>> from Jama import Matrix as JMatrix
  
  >>> import Jama

  >>> print Jama
  <java package Jama 0x1>

.... so there's a workaround, but the initial "import Jama" failing is confusing at
the least.

regards,
mark

Information about your version of Java - this information is useful for the Fiji developers:

  os.arch => i386
  os.name => Linux
  os.version => 2.6.32-25-generic
  java.version => 1.6.0_21
  java.vendor => Sun Microsystems Inc.
  java.runtime.name => Java(TM) SE Runtime Environment
  java.runtime.version => 1.6.0_21-b06
  java.vm.name => Java HotSpot(TM) Client VM
  java.vm.version => 17.0-b16
  java.vm.vendor => Sun Microsystems Inc.
  java.vm.info => mixed mode
  java.awt.graphicsenv => sun.awt.X11GraphicsEnvironment
  java.specification.name => Java Platform API Specification
  java.specification.version => 1.6
  sun.cpu.endian => little
  sun.desktop => gnome
  file.separator => /

The up-to-date check says: You wanted never to be reminded.

Information about the version of each plugin:

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Comment 1 Johannes Schindelin 2010-11-05 12:50:50 CDT 
A quick and dirty way may be something similar to this:

PySystem.registry.remove(PySystemState.PYTHON_CACHEDIR_SKIP); PySystemState.packageManager =
  new SysPackageManager(new File(System.getProperty("fiji.dir"), "python-cache"),
  PySystemState.registry);

The problem here is that you cannot really reinitalize the system state, but a couple of things are global (probably by mistake), so it might work with this convoluted code.
Comment 2 Johannes Schindelin 2011-03-23 15:33:42 CDT 
Does the work-around "fix" the issue?
Comment 3 Johannes Schindelin 2011-04-13 18:52:27 CDT 
The "work-around" does not fix the issue. But this here code works:

        from Jama import *