Bug 373 – Headless support for IJ.run / GenericDialog from jython

Bug 373 - Headless support for IJ.run / GenericDialog from jython


Summary:	Headless support for IJ.run / GenericDialog from jython

Status:	RESOLVED FIXED

Product:	Fiji
Classification:	Unclassified
Component:	Plugins
Version:	unspecified
Hardware:	Macintosh Mac OS

Importance:	P4 normal
Assigned To:	Johannes Schindelin

URL:

Depends on:
Blocks:

Reported:	2011-10-19 22:52 CDT by Greg Jefferis
Modified:	2012-01-06 00:20 CST
CC List:	1 user (show)

See Also:

Description Greg Jefferis 2011-10-19 22:52:46 CDT

not sure how widespread this is, but from jython in headless mode all calls I have tried to IJ.run seem to barf. Fix would be very much appreciated,

Greg.

PS would it be possible to add a test for this? This is a classic case of getting burned by an update.

-- testheadless.py --
from ij import IJ, ImagePlus
from ij.io import Opener
# toy example to check headless can cope with IJ.run
imp = IJ.openImage('http://rsb.info.nih.gov/ij/images/blobs.gif')
IJ.run(imp, "8-bit","")
--
jefferis:src (master)$ fiji --headless -- testheadless.py 
Traceback (most recent call last):
  File "testheadless.py", line 5, in <module>
    IJ.run(imp, "8-bit","")
	at java.awt.GraphicsEnvironment.checkHeadless(GraphicsEnvironment.java:159)
	at java.awt.MenuComponent.<init>(MenuComponent.java:145)
	at java.awt.MenuItem.<init>(MenuItem.java:174)
	at java.awt.MenuItem.<init>(MenuItem.java:158)
	at java.awt.Menu.<init>(Menu.java:132)
	at java.awt.Menu.<init>(Menu.java:112)
	at ij.Menus.getMenu(Menus.java:676)
	at ij.Menus.getMenu(Menus.java:666)
	at ij.Menus.addMenuBar(Menus.java:101)
	at ij.IJ.init(IJ.java:305)
	at ij.IJ.run(IJ.java:236)
	at ij.IJ.run(IJ.java:296)
	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.awt.HeadlessException: java.awt.HeadlessException

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

  os.arch => x86_64
  os.name => Mac OS X
  os.version => 10.6.7
  java.version => 1.6.0_26
  java.vendor => Apple Inc.
  java.runtime.name => Java(TM) SE Runtime Environment
  java.runtime.version => 1.6.0_26-b03-384-10M3425
  java.vm.name => Java HotSpot(TM) 64-Bit Server VM
  java.vm.version => 20.1-b02-384
  java.vm.vendor => Apple Inc.
  java.vm.info => mixed mode
  java.awt.graphicsenv => apple.awt.CGraphicsEnvironment
  java.specification.name => Java Platform API Specification
  java.specification.version => 1.6
  sun.cpu.endian => little
  sun.desktop => null
  file.separator => /

The up-to-date check says: You wanted to be reminded later.

Information relevant to JAVA_HOME related problems:

  JAVA_HOME is set to: null
  fiji.dir => /Applications/Fiji.app

Information about the version of each plugin:

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Comment 1 Johannes Schindelin 2011-10-20 00:51:18 CDT

Very sorry for the breakage. The reason is that I completely overlooked the fact that we allow headless mode for running scripts that call into ImageJ.

For the moment, please prefix your script with

  from fiji import Headless, IJHacker, JavassistHelper
  Headless().run()
  IJHacker().run()
  JavassistHelper.defineClasses()

until I come up with a proper fix. For the moment, I am considering a change in the Fiji launcher so that it always calls a certain class first which then would run the IJHacker if ij.jar is in the classpath and Headless, too, if we're running headlessly in addition to that.

Comment 2 Johannes Schindelin 2011-10-20 02:08:26 CDT

Actually, that plan does not work (calling two main classes from the Fiji launcher), since that would break '--system'.

Comment 3 Johannes Schindelin 2012-01-06 00:20:40 CST

This should be fixed with the recent merge of the 'ij2-launcher' branch.