JonkerVolgenant WIP. A bare skeleton.

Signed-off-by: Jean-Yves Tinevez <jean-yves.tinevez@pasteur.fr>
Release v2.2.0-rc4

Signed-off-by: Jean-Yves Tinevez <jeanyves.tinevez@gmail.com>
Merge branch 'master' of ssh://github.com/fiji/TrackMate
Merge branch 'master' of ssh://github.com/fiji/TrackMate
Code style changes.

Signed-off-by: Jean-Yves Tinevez <jean-yves.tinevez@pasteur.fr>
Make the ImagePlusChooser more reusable.

Signed-off-by: Jean-Yves Tinevez <jean-yves.tinevez@pasteur.fr>
Make the loading plugin more reusable.

Signed-off-by: Jean-Yves Tinevez <jean-yves.tinevez@pasteur.fr>
An importer for ICY track XML files.

Just point the TrackMate loader to an ICY tracks XML file, and it will
do the loading. All available features will be re-calculated on loading.
You also need to specify a target ImagePlus.
Signed-off-by: Jean-Yves Tinevez <jean-yves.tinevez@pasteur.fr>
LoadICYTrackPlugIn: remove unneeded code.

Signed-off-by: Jean-Yves Tinevez <jean-yves.tinevez@pasteur.fr>
Merge branch 'master' of ssh://github.com/fiji/TrackMate
Let pom-imagej manage which SCIFIO version we use

Signed-off-by: Johannes Schindelin <johannes.schindelin@gmx.de>
Let pom-imagej manage which ImageJ 1.x version we use

Signed-off-by: Johannes Schindelin <johannes.schindelin@gmx.de>
No more Sezpoz!

We retired Sezpoz a *long* time ago. ;-)

Signed-off-by: Johannes Schindelin <johannes.schindelin@gmx.de>
There is no need to override the managed ImgLib2 versions anymore

Signed-off-by: Johannes Schindelin <johannes.schindelin@gmx.de>
Add an explicit SCIFIO dependency

We use it directly, so we should not rely on transitive dependencies.

Signed-off-by: Johannes Schindelin <johannes.schindelin@gmx.de>
Disallow default penalties from being modified

When the map containing the default penalties is used directly, that means
that it gets modified when adding penalties. As a consequence, subsequent
runs will inherit settings from whatever previous run.

In particular with the LAPTrackerTest, this wreaked havoc because the
first test added penalties for the mean intensity while the second test
did not even provide the mean intensity, resulting in a nasty
NullPointerException.

Thanks, Jeniece Jenkins.

Signed-off-by: Johannes Schindelin <johannes.schindelin@gmx.de>
Merge branch 'master' of ssh://github.com/fiji/TrackMate
Really no more Sezpoz!

The original commit b5850ca1(No more Sezpoz!) got reverted by accident.

Signed-off-by: Johannes Schindelin <johannes.schindelin@gmx.de>
Let pom-imagej manage the JFreeChart and ImgLib2-ij versions

Signed-off-by: Johannes Schindelin <johannes.schindelin@gmx.de>
Minor typos in track quality analyzer.

Signed-off-by: Jean-Yves Tinevez <jean-yves.tinevez@pasteur.fr>