Merge branch 'master' of ssh://fiji.sc/srv/git/fiji
TrackMate_: changed the deiusgn for the detectors

Again, changed the plugin design, taking inspiration from some walks on
Saint-Palais beach.

The goal is to concile, even clumsily, the ability to run the plugin
from a script and a GUI in a simple manner, and to extend this plugin,
for a script, and for the GUI.

This design decouples a bit the complexity of the GUI from the script
part, and concentrate clumsiness in a single class: the detector
provider. It manages the list of the available detectors for the GUI,
and manages save to & load from XML.

Someone only wanted to extend for scripts does not have to deal with all
these, and still use TrackMate with his own detectors.
Signed-off-by: Jean-Yves Tinevez <jeanyves.tinevez@gmail.com>
Merge remote-tracking branch 'origin/master' into track-mate
TrackMate_: spots now store the frame they are found in.

Signed-off-by: Jean-Yves Tinevez <jeanyves.tinevez@gmail.com>
TrackMate4_: WIP: moving the trackers to the provider design

Like we did for the detectors.
Signed-off-by: Jean-Yves Tinevez <jeanyves.tinevez@gmail.com>
TrackMate_: WIP2: moving the trackers to the provider design

Signed-off-by: Jean-Yves Tinevez <jeanyves.tinevez@gmail.com>
TrackMate_: WIP3: moving the trackers to the provider design

Signed-off-by: Jean-Yves Tinevez <jean-yves.tinevez@pasteur.fr>
TrackMate_: WIP4: moving the trackers to the provider design

Signed-off-by: Jean-Yves Tinevez <jeanyves.tinevez@gmail.com>
TrackMate_: an imglib2 util to get a cropped view of an Img as an Img

Signed-off-by: Jean-Yves Tinevez <jeanyves.tinevez@gmail.com>
TrackMate_: mov the trackers to the provider design

CAREFUL: Test tests fail but I have no energy left today.
Signed-off-by: Jean-Yves Tinevez <jeanyves.tinevez@gmail.com>
TrackMate_: fix JUnit tests

Signed-off-by: Jean-Yves Tinevez <jeanyves.tinevez@gmail.com>
TrackMate_: the TrackMate_ class is now an Imglib2 algorithm

Only compile tested!
Signed-off-by: Jean-Yves Tinevez <jeanyves.tinevez@gmail.com>
Adding old files
Mask respects the fit curve option
Foreground (target) color is now always non-zero
Fixed DoSpikeSupretion
 - targetpoints were never compared in stair checks
 - DoSpikeSupressio is no longer an option, as it is relatively fast
Code cleaning
TrackMate_: deleting a spot or an edge removes them from selection

Signed-off-by: Jean-Yves Tinevez <jean-yves.tinevez@pasteur.fr>
TrackMate_: fix visibility of de novo tracks

When completely new tracks were added to the model manually (new spots,
and new links between only these spots), these tracks were deemed as
invisible by default.
This commit fixes this bad behavior. To avoid having visible tracks of 1
spot (every time we add a new spot manually), we impose the size of nde
novo tracks to be at least 2 to be visible.
Signed-off-by: Jean-Yves Tinevez <jeanyves.tinevez@gmail.com>
on 2.3
	- Descriptors printed to a dedicated table
	- Sholl decay is calculated by default
	- Fix bug in cv calculation
	- Impose valid parameters, rather than keep prompting the user (buggy)
    - Progress bar is more informative
    - Major code cleaning
    - Minor fixes
Version 2.3a
    - Fixed bug introduced in 2.3 that caused  -1 tagged pixels to be counted
    - Fixed rounding in mask drawing
    - Center ROI is dislayed on mask
    - Plot is named after analyzed image
    - Organized order of Table columns
    - showStatus more informative