An importer for Fernando Amat TGMM tracking results.

WIP.
Signed-off-by: Jean-Yves Tinevez <jeanyves.tinevez@gmail.com>
A static util to ask for a folder.

Signed-off-by: Jean-Yves Tinevez <jeanyves.tinevez@gmail.com>
TGMM import: take a list of transforms.

Signed-off-by: Jean-Yves Tinevez <jeanyves.tinevez@gmail.com>
TGMMImporter: be more verbose.

Signed-off-by: Jean-Yves Tinevez <jean-yves.tinevez@pasteur.fr>
State that we want Doubles and not Floats in display parameters.

Signed-off-by: Jean-Yves Tinevez <jean-yves.tinevez@pasteur.fr>
Fix a bug in TGMM importer causing the wrong transform to be used.

We were using the transform at timepoint t when we should have used the
transform at timepoint frame[t].
Signed-off-by: Jean-Yves Tinevez <jean-yves.tinevez@pasteur.fr>
More of these double to floats cast problems.

Signed-off-by: Jean-Yves Tinevez <jean-yves.tinevez@pasteur.fr>
TGMMImporter: extract a rough spot radius.

Tried to derive it from the precision matrix, but obviously it does not
work well. I am not sure I understand well how I should do.
Signed-off-by: Jean-Yves Tinevez <jean-yves.tinevez@pasteur.fr>
More float vs double problems.

Signed-off-by: Jean-Yves Tinevez <jean-yves.tinevez@pasteur.fr>
More float vs double problems.

Signed-off-by: Jean-Yves Tinevez <jean-yves.tinevez@pasteur.fr>
Merge branch 'fernando-import' of github.com:fiji/TrackMate into fernando-import
Embryonic action for the analysis of track branches.

Signed-off-by: Jean-Yves Tinevez <jean-yves.tinevez@pasteur.fr>
SparseCostMatrix: add an extra check to verify we are not out of bounds.

Signed-off-by: Jean-Yves Tinevez <jean-yves.tinevez@pasteur.fr>
Embryonic sparse LAP tracker as in Jaquaman et al. 2008.

Right now there is the embryonic frame-to-frame linking support. it
copies what Nick did for the non sparse version, which copies the utrack
software rathter than the paper itself.

SparseLinker is as far as I want today.
Signed-off-by: Jean-Yves Tinevez <jean-yves.tinevez@pasteur.fr>
Add utility methods to SparseCostMatrix.

Signed-off-by: Jean-Yves Tinevez <jean-yves.tinevez@pasteur.fr>
Rename and finalize the SparseLinker.

Signed-off-by: Jean-Yves Tinevez <jean-yves.tinevez@pasteur.fr>
Embryonic sparse LAP tracker integrated into TrackMate.

Does not generate track - BUG.
Just meant to do the frame to frame tracking.
Signed-off-byy Jean-Yves Tinevez <jean-yves.tinevez@pasteur.fr>
Fix a bug in the GUI: not echoing error messages when tracking fails.

Signed-off-by: Jean-Yves Tinevez <jeanyves.tinevez@gmail.com>
Fix two bugs in SparseFrameToFrameLinker.

- The graph was not instantiated.
- We were passing the wrong settings map.
Signed-off-by: Jean-Yves Tinevez <jeanyves.tinevez@gmail.com>
Increase the sparsity in the frame-to-frame linking.

If a source does not have any non-infinite cost, then we do not include
it in the sparse matrix to compute assignments. Then, we do a little
gymnastic so that the assignments we return are indexes into the
original source list.
Signed-off-by: Jean-Yves Tinevez <jeanyves.tinevez@gmail.com>