Weka Segmentation: fixed bug that was making the Rand calculations crashed whenever the number of objects was larger than 2^15 (the "short" pixels in ImageJ are signed and needed to be converted).
Merge branch 'trainable-seg-gui'
Merge branch 'master' of fiji.sc:/srv/git/fiji
Weka Segmentation: facilitate use of more than 5 classes in the GUI.
Weka Segmentation: add random colors to traces when the number of classes is larger than 5 (current maximum).
Weka Segmentation: change way to treat trace colors when the number of classes is larger than 5 (use golden angle).
Make Fiji-daily pass again

Signed-off-by: Johannes Schindelin <johannes.schindelin@gmx.de>
Make Fiji-daily pass again

Signed-off-by: Johannes Schindelin <johannes.schindelin@gmx.de>
Fix Find Jar For Class for use as plugin

When this developer changed the Beanshell script to be able to be
run from the command-line, he forgot to test whether things still
work when the script is called via ImageJ's menu.

Signed-off-by: Johannes Schindelin <johannes.schindelin@gmx.de>
TrackMate_: fix bug preventing track merging and splitting in some cases

Noticed by Jan Brocher:
We were using the POSITION_T to check if 2 spots were in the next or
previous frame when determining if they are elligible to a splitting or
merging event.
This would of course fail as soon as the time calibration put more than 1
in units of time between frames. For instance a frame interval of 5
seconds would make any splitting or merging events not-detected.

The proper way to do it is to use the FRAME feature of each spot, which
correctly reports the frame number, whatever is the physical frame
interval.

While at it, use the FRAME feature anywhere we can.
Signed-off-by: Jean-Yves Tinevez <jean-yves.tinevez@pasteur.fr>
TrackMate_: accept XML from v >= 2.0.0

Signed-off-by: Jean-Yves Tinevez <jean-yves.tinevez@pasteur.fr>
TrackMate_: protect the 3D TrackMate viewer against empty frames

Signed-off-by: Jean-Yves Tinevez <jean-yves.tinevez@pasteur.fr>
TrackMate_: optimize startup of the 3D viewer a bit

Signed-off-by: Jean-Yves Tinevez <jean-yves.tinevez@pasteur.fr>
StartupMacros: discover and run macros in macros/AutoRun/

The biggest shortcoming of the StartupMacros mechanism (which
it shares with the macro interpreter's Ext.* mechanism as well as
with the HandleExtraFileTypes class) is that there can be only one
file. There is no easy way that you can augment it locally.

Instead of forcing users to have their own, locally-modified
StartupMacros file that will be forever stale, change our StartupMacros
so that it discovers all macros stored as .ijm files in macros/AutoRun/
and runs them, in alphabetical order (for consistency).

Users who need to install macros upon startup (e.g. for keyboard
shortcuts) can always call

	run("Install...", "install=[" + getDirectory("imagej")
		+ "/macros/my-shortcuts.ijm]");

Signed-off-by: Johannes Schindelin <johannes.schindelin@gmx.de>
Merge remote-tracking branch 'github/master'
Prepare fiji-scripting for ImageJ 1.47n

ImageJ 1.47n brings its own scripting support for Jython and Beanshell.
As it is inconsistent with the other scripting languages supported by
Fiji, we need to override it.

Signed-off-by: Johannes Schindelin <johannes.schindelin@gmx.de>
Move JNI Example files in preparation for Mavenization

Signed-off-by: Johannes Schindelin <johannes.schindelin@gmx.de>
Add a pom.xml file for the JNI_Example project

Signed-off-by: Johannes Schindelin <johannes.schindelin@gmx.de>
Ignore Maven products in the JNI_Example

Signed-off-by: Johannes Schindelin <johannes.schindelin@gmx.de>
Fix compiler warnings identified in JNI_Example.c

These warnings are only now apparent due to NAR's default options.

Signed-off-by: Johannes Schindelin <johannes.schindelin@gmx.de>