Embryo_Tracker: more refactoring in the main class

The segmenter has now some its own package
Signed-off-by: Jean-Yves Tinevez <jean-yves.tinevez@pasteur.fr>
Embryo_Tracker: stub class to display segmentation results

using the 3D viewer...
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: Spot now uses EnumMap to store Features

for performance and convenience.
Signed-off-by: Jean-Yves Tinevez <jean-yves.tinevez@pasteur.fr>
Embryo_Tracker: refactored tracking

Made separate classes for creating cost matrices, which implement a cost matrix creation interface class. Hopefully this makes the code easier to read.

Signed-off-by: Nick Perry <nicholas.m.perry@gmail.com>
Embryo_Tracker: worked on top middle submatrix of segment cost matrix.

Didn't get very far.

Signed-off-by: Nick Perry <nicholas.m.perry@gmail.com>
Embryo_Tracker: Spots now store previous and next Spot references in tracks.

To facilitate tracking, Spots now store a reference to the Spots preceding them and following them in a track.

Signed-off-by: Nick Perry <nicholas.m.perry@gmail.com>
Embryo_Tracker: initialize next/prev lists in Spots.

the arraylist holding prev/next spots in tracks weren't initialized at spot construction.

Signed-off-by: Nick Perry <nicholas.m.perry@gmail.com>
Embryo_Tracker: changed method name for Spot to addNext

No longer setNext, since it's an arraylist and I add them.

Signed-off-by: Nick Perry <nicholas.m.perry@gmail.com>
GraphCut: moved plugins.config to src directory
Embryo_Tracker: changed the Spot feature returned value

Now the Spot feature methods return Float object instead of float
primitives, so as to be able to deal with missing features (null
objects).
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
GraphCut: added support to batch process several files
Embryo_Tracker: gui to interactively treshold blobs

There is now a gui that can threshold spot display according to their
feature values.
Signed-off-by: Jean-Yves Tinevez <jean-yves.tinevez@pasteur.fr>
Embryo_Tracker: safe gaurd in Utils class

Added a safe guard in the case where we are trying to build an histogram
with no data.
Emryo_Tracker: finished implementing LAPTracker, but buggy

LAPTracker, and the two cost matrix classes used by it, are *written* but seemingly non-functional. Both cost matrices are created, and the LAP is executed on them. The results are compiled into track segments and final tracks, respectively. But the LAP for gap closing / merging / splitting doesn't finish. So something is wrong with either the Hungarian Algorithm implementation, or my cost matrix for that step.

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: adding debugging code, change BLOCKED value in tracking.

Added code in LAPTracker to print out the segments just to check if NaN works as a blocking value. It does, so now NaN is used to block parts of the cost matrix instead of positive infinity.

Signed-off-by: Nick Perry <nicholas.m.perry@gmail.com>
Embryo_Tracker: plugging the displayer in the plugin

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