need hints on debugging both classpath and jamvm to run ImageJ

[Albert Cardona]

Dear all,

I would like to run the public domain image analysis program ImageJ with GNU 
Classpath/jamvm (or any free java for that matter). I compiled both classpath 
0.92 and jamvm 1.4.3 with CFLAGS=-g and then run the program.

My system:
Powerbook Ti 3.5  1 GHz
kubuntu-ppc GNU/Linux

Some background: in ImageJ, a rectangle of an awt.Image is painted on an 
ImageCanvas that extends Canvas and lives inside an awt.Window. The repaint() 
method ends up calling the method public void paint(Graphics g) { ... }

ImageJ is an 800k AWT-only image processing application widely used in both 
academic research and industry, with a user base of literally tens of 
thousands of people, developed by the NIH and collaborators all around the 
world. Making ImageJ run with Classpath and a free VM such as jamvm has the 
potential of fostering usage of a free java. Thus my interest.

When running the distributed ImageJ ij.jar with Classpath 0.92 and jamvm, I 
run into a number of issues:
- ImageJ runs but images are colored incorrectly. For example, grayscale 
images show in a gradient of reds.
- ROIs are repainted leaving a dirty trail behind on 8-bit images. On RGB 
images, painting ROIs is VERY slow, about 20 seconds to paint a small ROI.
- clicking on an image results in the image becoming whiter and whiter.
- filling ROIs (i.e. changing the byte[] and recreating the awt.Image and 
calling repaint on the ImageCanvas (that extends awt.Canvas) doesn't repaint 
the ImageCanvas at all.
- when creating a new image with File->New->Image... , a new window for the 
image shows but the program goes into an infinite loop and has to be killed.
- closing an ImageWindow takes about 20 seconds for the checking popup to 
query about really closing it.
- when clicking 'no' in a ij.gui.YesNoCancelDialog, several popups come up 
complaing about "no images open" as if one had pushed keyboard commands 
repeatedly. Some times this leads to:
Exception during event dispatch:
java.lang.NullPointerException
   at java.awt.MenuItem.dispatchEventImpl(MenuItem.java:547)
   at java.awt.CheckboxMenuItem.dispatchEventImpl(CheckboxMenuItem.java:296)
   at java.awt.MenuComponent.dispatchEvent(MenuComponent.java:347)
   at java.awt.EventQueue.dispatchEvent(EventQueue.java:479)
   at java.awt.EventDispatchThread.run(EventDispatchThread.java:85)

Eventually ImageJ crashes or gets stuck.

Text windows though seem to work just fine.

None of this problems exist when ImageJ is run with Sun's java 1.3.1, 1.4.2, 
1.5.0 or 1.6.0 beta.


So now: what is the best way to debug both classpath and jamvm ? When running 
jamvm from ddd, I get:

Using host libthread_db library "/lib/libthread_db.so.1".
(gdb) 
run 
-Xbootclasspath/a:/home/albertca/Programming/jamvm/jamvm-local/share/classpath/glibj.zip:/home/albertca/Programming/jamvm/jamvm-local/share/classpath/tools.zip:/home/albertca/Programming/jamvm/jamvm-local/share/classpath
 
-Dgnu.classpath.boot.library.path=/home/albertca/Programming/jamvm/jamvm-local/lib/classpath
 -Xmx384Mb -classpath 
./ij.jar:./jars/colt.jar:./jars/jai_imageio.jar:./jars/jimi.jar:./jars/jpedal/additional_jars/bcprov-jdk14-119.jar:./jars/jpedal/additional_jars/jdom.jar:./jars/jpedal/pjes.jar:./jars/jpedal/14_os_jpedal.jar:./jars/jython21/jython.jar:./jars/postgresql-8.1-405.jdbc3.jar
 
ij.ImageJ
[Thread debugging using libthread_db enabled]
[New Thread 805413360 (LWP 7972)]
[New Thread 1225315568 (LWP 7975)]
[New Thread 1233704176 (LWP 7976)]

Program received signal SIGUSR1, User defined signal 1.
[Switching to Thread 805413360 (LWP 7972)]
0x0fe52f68 in clone () from /lib/libc.so.6


Meaning, the program doesn't run at all! I can't see what is different than 
running the program from the command line. Using a -classpath ij.jar only (no 
extensions to ImageJ) results in exactly the same problem.

How is one to debug GNU Classpath and/or jamvm? Or are the above GNU Classpath 
problems only?

Thanks for any hints.

Albert

-- 
Albert Cardona
Molecular Cell Developmental Biology
University of California Los Angeles
Tel +1 310 2067376