problems with running macros from the command line

[Albert Cardona]

Dear all,

I would like to run ImageJ in a headless environment (no Desktop, no X.org, no
Aqua, just plain old tty) to take advantage of a cluster.

According to the ij.ImageJ class, one can run macros without GUI like:

-batch path [arg]
    Runs a macro in batch (no GUI) mode, passing it an optional argument.
    ImageJ exits when the macro finishes.

I setup a simple macro in the file macros/any.txt :

macro 'Test' {
        setBatchMode(true);
        print("Hello");
        for (i=0; i<10; i++) {
                print(i);
        }
}

So I run:

$ java -classpath ij.jar ij.ImageJ macros/any.txt

When run in an xterm (a desktop environment exists), it prints without
problems to the xterm.

But when run from a tty, nothing prints except one like:

Gtk-warning **: cannot open display


Then I tried to use the RunMacro class from
rsb.info.nih.gov/ij/plugins/download/jars/macro-runner.zip with the command:

$ java -classpath ij.jar:. RunMacro macros/any.txt

From an xterm, again, no problem. From a tty I get a nasty class loader
exception:

Exception in thread "main" java.lang.NoClassDefFoundError: while resolving
class: RunMacro
   at java.lang.VMClassLoader.resolveClass(java.lang.Class)
(/usr/lib/libgcj.so.5.0.0)
   at java.lang.Class.initializeClass() (/usr/lib/libgcj.so.5.0.0)
   at java.lang.Class.forName(java.lang.String, boolean,
java.lang.ClassLoader) (/usr/lib/libgcj.so.5.0.0)
   at java.lang.Class.forName(java.lang.String) (/usr/lib/libgcj.so.5.0.0)
   at gnu.gcj.runtime.FirstThread.run() (/usr/lib/libgcj.so.5.0.0)
   at _Jv_ThreadRun(java.lang.Thread) (/usr/lib/libgcj.so.5.0.0)
   at _Jv_RunMain(java.lang.Class, byte const, int, byte const, boolean)
(/usr/lib/libgcj.so.5.0.0)
   at __gcj_personality_v0 (/home/cardona/bin/ImageJ/java.version=1.4.2)
   at __libc_start_main (/lib/tls/libc-2.3.4.so)
   at _Jv_RegisterClasses (/home/cardona/bin/ImageJ/java.version=1.4.2)
Caused by: java.lang.ClassNotFoundException: java.lang.StringBuilder not found
in [file:./, file:ij.jar, file:/usr/share/java/libgcj-3.4.5.jar, file:./,
core:/]
   at java.net.URLClassLoader.findClass(java.lang.String)
(/usr/lib/libgcj.so.5.0.0)
   at gnu.gcj.runtime.VMClassLoader.findClass(java.lang.String)
(/usr/lib/libgcj.so.5.0.0)
   at java.lang.ClassLoader.loadClass(java.lang.String, boolean)
(/usr/lib/libgcj.so.5.0.0)
   at _Jv_FindClass(_Jv_Utf8Const, java.lang.ClassLoader)
(/usr/lib/libgcj.so.5.0.0)
   at java.lang.Class.forName(java.lang.String, boolean,
java.lang.ClassLoader) (/usr/lib/libgcj.so.5.0.0)
   at _Jv_BytecodeVerifier.verify_instructions_0() (/usr/lib/libgcj.so.5.0.0)
   at _Jv_VerifyMethod(_Jv_InterpMethod) (/usr/lib/libgcj.so.5.0.0)
   at _Jv_PrepareClass(java.lang.Class) (/usr/lib/libgcj.so.5.0.0)
   at _Jv_WaitForState(java.lang.Class, int) (/usr/lib/libgcj.so.5.0.0)
   at java.lang.VMClassLoader.linkClass0(java.lang.Class)
(/usr/lib/libgcj.so.5.0.0)
   at java.lang.VMClassLoader.resolveClass(java.lang.Class)
(/usr/lib/libgcj.so.5.0.0)
   ...9 more



So: is this a java limitation (that it needs a display), or is it an ImageJ
limitation? Sounds like a java limitation. Is there any workaround? Any java
virtual machines that can run headless?

I have found that one can specify the -Djava.awt.headless=true in the command
line, but that doesn't help ImageJ in any way when run from a tty.

Thanks for any ideas.

Albert

[Kurt De Vos]

I get the same behavior:

Exception in thread "main" java.awt.HeadlessException:
No X11 DISPLAY variable was set, but this program performed an  
operation which requires it.
         at java.awt.GraphicsEnvironment.checkHeadless(Unknown Source)
         at java.awt.MenuComponent.<init>(Unknown Source)
         at java.awt.MenuItem.<init>(Unknown Source)
         at java.awt.MenuItem.<init>(Unknown Source)
         at java.awt.Menu.<init>(Unknown Source)
         at java.awt.Menu.<init>(Unknown Source)
         at ij.Menus.addMenuBar(Menus.java:87)
         at ij.IJ.init(IJ.java:333)
         at ij.IJ.runMacroFile(IJ.java:93)
         at ij.ImageJ.main(ImageJ.java:471)
With this error info, it should be possibel to customize ij to run  
gui free.

kurt

On 4 Oct 2006, at 16:46, Albert Cardona wrote:

> -Djava.awt.headless=true

*--*--*--*--*--*--*--*--*--*--*--*--*--*
University of Sheffield
Academic Neurology Unit
Division of Genomic Medicine
E Floor, Medical School
Beech Hill Road
Sheffield
S10 2RX
United Kingdom

Tel: ++44 (0) 114 271 2473
Fax: ++44 (0) 114 226 1201
Email: [hidden email]
*--*--*--*--*--*--*--*--*--*--*--*--*--*

[Wayne Rasband]

You can work around this problem by installing Xvfb, the X window
virtual frame buffer. I had to install it on the ImageJ server to get
the example servlet at http://rsb.info.nih.gov:8080/index.html to work.

-wayne

On Oct 4, 2006, at 12:26 PM, Kurt De Vos wrote:

> I get the same behavior:
>
> Exception in thread "main" java.awt.HeadlessException:
> No X11 DISPLAY variable was set, but this program performed an
> operation which requires it.
>         at java.awt.GraphicsEnvironment.checkHeadless(Unknown Source)
>         at java.awt.MenuComponent.<init>(Unknown Source)
>         at java.awt.MenuItem.<init>(Unknown Source)
>         at java.awt.MenuItem.<init>(Unknown Source)
>         at java.awt.Menu.<init>(Unknown Source)
>         at java.awt.Menu.<init>(Unknown Source)
>         at ij.Menus.addMenuBar(Menus.java:87)
>         at ij.IJ.init(IJ.java:333)
>         at ij.IJ.runMacroFile(IJ.java:93)
>         at ij.ImageJ.main(ImageJ.java:471)
> With this error info, it should be possibel to customize ij to run gui
> free.
>
> kurt
>
> On 4 Oct 2006, at 16:46, Albert Cardona wrote:
>
>> -Djava.awt.headless=true
>
> *--*--*--*--*--*--*--*--*--*--*--*--*--*
> University of Sheffield
> Academic Neurology Unit
> Division of Genomic Medicine
> E Floor, Medical School
> Beech Hill Road
> Sheffield
> S10 2RX
> United Kingdom
>
> Tel: ++44 (0) 114 271 2473
> Fax: ++44 (0) 114 226 1201
> Email: [hidden email]
> *--*--*--*--*--*--*--*--*--*--*--*--*--*
>

[dscho]

Hi,

On Wed, 4 Oct 2006, Albert Cardona wrote:

> $ java -classpath ij.jar ij.ImageJ macros/any.txt

Did you forget "-batch"?

I found a trick which makes it work here: set DISPLAY to empty:

$ DISPLAY= java -classpath ij.jar ij.ImageJ -batch macros/any.txt

Having said that, I think it is a bug to try to initialize X11 headlessly.

Ciao,
Dscho

[Albert Cardona]

Hi Dscho,

No, I only forgot "-batch" when writing the email to the list (since I can't
copy, or not easily, from the tty).


> I found a trick which makes it work here: set DISPLAY to empty:
>
> $ DISPLAY= java -classpath ij.jar ij.ImageJ -batch macros/any.txt


I have tried this, and nothing prints in a tty. Perhaps the job is done but
lost, I would have to setup a different kind of macro for that (a macro that
does I/O of some sort).

>
> Having said that, I think it is a bug to try to initialize X11 headlessly.


I don't quite understand what you mean. The java is buggy and shouldn't init
awt and swing peers when headless?

Albert

[dscho]

Hi,

On Wed, 4 Oct 2006, Albert Cardona wrote:

> > I found a trick which makes it work here: set DISPLAY to empty:
> >
> > $ DISPLAY= java -classpath ij.jar ij.ImageJ -batch macros/any.txt
>
>
> I have tried this, and nothing prints in a tty.

I am running Linux, so I have a couple of text consoles. If I run your
macro there, with "DISPLAY=", it prints "Hello" and the numbers from 0 to
9.

> > Having said that, I think it is a bug to try to initialize X11 headlessly.
>
> I don't quite understand what you mean. The java is buggy and shouldn't
> init awt and swing peers when headless?

Java should init AWT (and possibly Swing, even if it is not used in
ImageJ), but it should not try to access the contents of the environment
variable DISPLAY, if it is not set. The latter is the Java bug I meant.
 
Ciao,
Dscho