Fiji now uses stock IJ1

[Johannes Schindelin]

Dear all,

just quickly: after working hard on this for almost two weeks, I uploaded
a plain, stock IJ1 into the Fiji Updater. What modifications we need in
ij.jar, we now apply by runtime patching using javassist
(http://fiji.sc/Javassist -- still rudimentary, will be enhanced over time
as I or others have time to do it). All the ImageJA-specific changes in
that regard have been either put into that runtime patches, or just
abolished.

This is all in the ongoing effort to streamline development.

The headless mode was implemented using runtime patching, too, although
there is now a way to write out a misc/headless.jar from the
runtime-patched classes if need be.

Unfortunately, time pressure does not allow me to reinstate the ImageJA
applet stuff, the embedded applet. So for the time being, applet users
will be stuck with a version based on 1.45q including all the
Fiji-specific stuff. Sorry.

Oh, and I am pretty confident that the WebStart system does not work right
now, if somebody needs it, please speak up, then I try to wiggle it as a
side project somewhere into my schedule.

Ciao,
Johannes

P.S.: Should there be things that I broke with the update, I am very
sorry, please file a bug with our ticket system (http://fiji.sc/bugzilla),
I'll not be reachable by mail today.

[Albert Cardona]

Hi Johannes,

nice work. This will definitely help Fiji and ImageJ 2.0 a lot.

By the way, nice tutorial on the Fiji wiki on javassist. I will use it!

Albert
--
http://albert.rierol.net
http://www.ini.uzh.ch/~acardona/

[Albert Cardona]

By the way, that made TrakEM2 not compile anymore:

...
Building in modules/TrakEM2/
Building TrakEM2_.jar <- mpicbg/trakem2/transform/TranslationModel...
./modules/TrakEM2/ini/trakem2/display/Display.java:6620:
setCurrentWindow(ij.gui.ImageWindow) in ij.WindowManager cannot be
applied to (ij.gui.ImageWindow,boolean)
WindowManager.setCurrentWindow(canvas.getFakeImagePlus().getWindow(),
true);
^
Note: Some input files use or override a deprecated API.
Note: Recompile with -Xlint:deprecation for details.
Note: Some input files use unchecked or unsafe operations.
Note: Recompile with -Xlint:unchecked for details.
1 error
Fake failed: Compile error
in rule TrakEM2_.jar <- mpicbg/trakem2/transform/TranslationModel...
in rule plugins/TrakEM2_.jar <- jars/ij.jar jars/jai_core.jar jar...
in rule all <- fiji jars/ij.jar plugins/loci_tools.jar jars/Vecto...
Publishing Javadoc

[Johannes Schindelin]

Hi Albert,

On Tue, 18 Oct 2011, Albert Cardona wrote:

> By the way, that made TrakEM2 not compile anymore:
>
> ...
> Building in modules/TrakEM2/
> Building TrakEM2_.jar <- mpicbg/trakem2/transform/TranslationModel...
> ./modules/TrakEM2/ini/trakem2/display/Display.java:6620:
> setCurrentWindow(ij.gui.ImageWindow) in ij.WindowManager cannot be
> applied to (ij.gui.ImageWindow,boolean)
> WindowManager.setCurrentWindow(canvas.getFakeImagePlus().getWindow(),
> true);
> ^

Sorry for the breakage!

Can you please remove the ", true"? ImageJ does not have a way to suppress
the recording.

For backwards compatibility, I runtime-patch that method back using the
IJHacker, but the boolean does not suppress the recording anymore. This
should fix things when running current TrakeEM2.

Thanks!
Dscho

[Albert Cardona]

2011/10/18 Johannes Schindelin <Johannes....@gmx.de>:

Ok! TrakEM2 runs fine, the error is a minor one.
I'll fix it and upload a new version.

Albert

[Johannes Schindelin]

Hi Albert,

On Tue, 18 Oct 2011, Albert Cardona wrote:

> nice work.

Thanks!

> This will definitely help Fiji and ImageJ 2.0 a lot.

I think so, too!

> By the way, nice tutorial on the Fiji wiki on javassist. I will use it!

Yes, it is really useful. Especially for that headless stuff. A more
complete solution would be possible now, basically rebuilding a headless
AWT on the fly and then runtime-patching all the plugins to use those
classes instead of AWT, but that is too huge a project for me to take on
right now :-)

But I _will_ use Javassist for some performance profiling...

Ciao,
Dscho

[Johannes Schindelin]

Hi Albert,

On Tue, 18 Oct 2011, Albert Cardona wrote:

> 2011/10/18 Johannes Schindelin <Johannes....@gmx.de>:

>
> > On Tue, 18 Oct 2011, Albert Cardona wrote:
> >
> >> By the way, that made TrakEM2 not compile anymore:
> >>
> >> ...
> >> Building in modules/TrakEM2/
> >> Building TrakEM2_.jar <- mpicbg/trakem2/transform/TranslationModel...
> >> ./modules/TrakEM2/ini/trakem2/display/Display.java:6620:
> >> setCurrentWindow(ij.gui.ImageWindow) in ij.WindowManager cannot be
> >> applied to (ij.gui.ImageWindow,boolean)
> >> � � � � � � � �WindowManager.setCurrentWindow(canvas.getFakeImagePlus().getWindow(),
> >> true);
> >> � � � � � � � � � � � � � � ^
> >
> > Sorry for the breakage!
> >
> > Can you please remove the ", true"? ImageJ does not have a way to suppress
> > the recording.
> >
> > For backwards compatibility, I runtime-patch that method back using the
> > IJHacker, but the boolean does not suppress the recording anymore. This
> > should fix things when running current TrakeEM2.
>
> Ok! TrakEM2 runs fine, the error is a minor one. I'll fix it and upload
> a new version.

Cool! And again, sorry!

Ciao,
Dscho