GraphCut: changed label "potts weight" to "smoothness"
Merge branch 'contrib' into embryo-tracker
Embryo_Tracker: Commented out changes to sliders, using old LoG method.

Signed-off-by: Nick Perry <nicholas.m.perry@gmail.com>
Embryo_Tracker: new method for linking.

FrameToFrameLinker: now using Hungarian algorithm to link.
AssignmentAlgorithm: part of the Hungarian implementation
AssignmentProblem: part of the Hungarian implementation
HungarianAlgorithm: part of the Hungarian implementation

Signed-off-by: Nick Perry <nicholas.m.perry@gmail.com>
Merge branch 'contrib' of ssh://pacific.mpi-cbg.de/srv/git/fiji into contrib
Merge branch 'contrib' into embryo-tracker
Embryo_Tracker: minor GUI tweaks

Signed-off-by: Jean-Yves Tinevez <jean-yves.tinevez@pasteur.fr>
Embryo_TRacker: morphology features are now ordered

A always report the longest semi-asxes.
Important for tracking.
Signed-off-by: Jean-Yves Tinevez <jean-yves.tinevez@pasteur.fr>
Embryo_Tracker: made the ThresholdPanel generic

... if someone ever feels like re-using it, it's better not be tied to a
specific nperry feature....
Signed-off-by: Jean-Yves Tinevez <jean-yves.tinevez@pasteur.fr>
Merge branch 'embryo-tracker' of ssh://pacific.mpi-cbg.de/srv/git/fiji into embryo-tracker
Embryo_Tracker: created an interface for object tracking classes.

Changed ObjectTracker to be an interface for object tracking, which I will implement using another class.

Signed-off-by: Nick Perry <nicholas.m.perry@gmail.com>
Merge branch 'embryo-tracker' of ssh://pacific.mpi-cbg.de/srv/git/fiji into embryo-tracker
Embryo_Tracker: worked on tracking class.

FrameToFrameLinker: deleted because no longer used.
LAPTracer: implements ObjectTracker, tracks objects using Hungarian Algorithm in two steps. First step links objects -> track segments. Second step links track segments -> final tracks (allows for merge/split).

Signed-off-by: Nick Perry <nicholas.m.perry@gmail.com>
Merge branch 'embryo-tracker' of ssh://pacific.mpi-cbg.de/srv/git/fiji into embryo-tracker
Embryo_Tracker: Added to checkInput() for LAPTracker.

Signed-off-by: Nick Perry <nicholas.m.perry@gmail.com>
Embryo_Tracker: removed the TreeNode class.

No longer using DFS on a tree to solve linking problem. Using Hungarian Algorithm instead.

Signed-off-by: Nick Perry <nicholas.m.perry@gmail.com>
Embryo_Tracker: more refactoring

The spot segmentation part is now moved to a dedicated algorithm class.
When we get the Preibisch one, we can then simply use it.
Signed-off-by: Jean-Yves Tinevez <jean-yves.tinevez@pasteur.fr>
Embryo_Tracker: LAPTracker creates object linking cost matrix.

Worked on LAPTracker. Now, it can create the cost matrix for step 1, which links objects between consecutive frames. Uses the Jama library heavily.

Signed-off-by: Nick Perry <nicholas.m.perry@gmail.com>
Embryo_Tracker: changed Hungarian classes to use double[] instead of float[].

Changed the Hungarian classes written by Gary Baker to use double and double[] internally instead of float[] and float, so I could use Jama class easily.

Signed-off-by: Nick Perry <nicholas.m.perry@gmail.com>
Embryo_Tracker: LAPTracker solves track segments.

LAPTracker: step 1 works, so it finds the track segments.
ObjectTracker: deleted commented out code from when this wasn't an interface.

Signed-off-by: Nick Perry <nicholas.m.perry@gmail.com>