Weka Segmentation: block GUI while saving data.
Merge branch 'trainable-seg-gui'
Fix_Updater.js: allow setting ij.dir from versioned ij.jar files

Signed-off-by: Johannes Schindelin <johannes.schindelin@gmx.de>
Fix_Updater.js: IJ.error() already stops the script

... therefore we do not have to throw an exception, too.

Signed-off-by: Johannes Schindelin <johannes.schindelin@gmx.de>
Allow Fix_Updater.js to be started from unpacked .class files

When starting ImageJA via 'mvn exec:java', it is started from the
classes in target/classes/, not a .jar file.

Signed-off-by: Johannes Schindelin <johannes.schindelin@gmx.de>
Merge remote-tracking branch 'origin/track-mate'
Weka Segmentation: fixed bug on adaptedRandIndexStats3D that was miscalculating the index results due to an integer division.
Merge branch 'master' of fiji.sc:/srv/git/fiji
Merge branch 'trainable-seg-gui'
Add a primitive Javassist-based performance profiler

This profiler is loosely modeled on the ideas of OProfile, but uses
Javassist to instrument the loaded classes.

The gist: every instrumented method is added to a list, and gets two
static fields in the same class: the call count and the total amount
of time spent in the method (or in methods called from there).

Unfortunately, it seems that the precision with which Java can measure
CPU time per thread is a bit crude: in my tests, the granularity is
five milliseconds.

To use it, call fiji.PerformanceProfiler as main class with the "real
main class" and its arguments as parameters.

But it is a start at something we can use, re-use and enhance.

Signed-off-by: Johannes Schindelin <johannes.schindelin@gmx.de>
PerformanceProfiler: allow the profiled code to interact with the profiler

With this commit, the callee can call setActive(), isActive() and report().

Signed-off-by: Johannes Schindelin <johannes.schindelin@gmx.de>
Merge branch 'master' of github.com:fiji/fiji
IJHacker: PluginInstaller moved to another package

... without deprecation, too :-(

Signed-off-by: Johannes Schindelin <johannes.schindelin@gmx.de>
Weka Segmentation: fixed same bug about the integer division and removed log messages.
Merge branch 'master' of fiji.sc:/srv/git/fiji
Make RedirectErrAndOut more future-proof

It looks as if Wayne will pick this up for ImageJ 1.x. We do not want
ImageJ 1.x and Fiji interfere, but play along nicely instead.

Signed-off-by: Johannes Schindelin <johannes.schindelin@gmx.de>
Merge branch 'master' of github.com:fiji/fiji
Weka Segmentation: updated general information comments.
Weka Segmentation: added general information comments, removed unused imports and corrected typo.
Weka Segmentation: corrected integer division for 2D case and removed log message.