Fixed one more bug with the labkit importer.

When editing the whole movie, if the label of a new spot was using
the label of an existing spot in another time-point, the existing
one was removed. Because the new spot was identified as a modification
of the existing one.
The solution is to pass to the importer only the list of existing
spots in the current time-frame.

src/main/java/fiji/plugin/trackmate/gui/editor/LabkitImporter.java

@@ -34,6 +34,7 @@
 import fiji.plugin.trackmate.Model;
 import fiji.plugin.trackmate.Spot;
 import fiji.plugin.trackmate.detection.SpotRoiUtils;
+import ij.IJ;
 import net.imglib2.RandomAccessibleInterval;
 import net.imglib2.loops.LoopBuilder;
 import net.imglib2.roi.labeling.ImgLabeling;
@@ -48,6 +49,8 @@
 public class LabkitImporter< T extends IntegerType< T > & NativeType< T > >
 {
 
+	private static final boolean DEBUG = false;
+
 	private final Model model;
 
 	private final double[] calibration;
@@ -148,6 +151,7 @@ else if ( novelSpotList == null || novelSpotList.isEmpty() )
 					 * One I had in the previous spot list, but that has
 					 * disappeared. Remove it.
 					 */
+					IJ.log( " - Removed spot " + str( previousSpot ) );
 					model.removeSpot( previousSpot );
 				}
 				else
@@ -212,6 +216,9 @@ else if ( target == previousSpot )
 			else
 				throw new IllegalArgumentException( "The edge of a spot does not have the spot as source or target?!?" );
 		}
+		if ( DEBUG )
+			IJ.log( " - Modified spot " + str( previousSpot ) + " -> " + str( mainNovelSpot ) );
+
 		model.removeSpot( previousSpot );
 
 		// Deal with the other ones.
@@ -225,6 +232,9 @@ else if ( target == previousSpot )
 			s.putFeature( Spot.POSITION_T, currentTimePoint * dt );
 			s.putFeature( Spot.QUALITY, -1. );
 			model.addSpotTo( s, Integer.valueOf( currentTimePoint ) );
+
+			if ( DEBUG )
+				IJ.log( " - Added spot " + str( s ) );
 		}
 	}
 
@@ -235,6 +245,9 @@ private void addNewSpot( final Iterable< Spot > novelSpotList, final int current
 			spot.putFeature( Spot.POSITION_T, currentTimePoint * dt );
 			spot.putFeature( Spot.QUALITY, -1. );
 			model.addSpotTo( spot, Integer.valueOf( currentTimePoint ) );
+
+			if ( DEBUG )
+				IJ.log( " - Added spot " + str( spot ) );
 		}
 	}
 
@@ -276,10 +289,25 @@ private Map< Integer, List< Spot > > getSpots( final RandomAccessibleInterval< T
 		final ImgLabeling< Integer, ? > labeling = ImgLabeling.fromImageAndLabels( rai, indices );
 		final Map< Integer, List< Spot > > spots = SpotRoiUtils.from2DLabelingWithROIMap(
 				labeling,
-				labeling.minAsDoubleArray(),
+				new double[] { 0., 0. },
 				calibration,
 				simplify,
 				rai );
 		return spots;
 	}
+
+	private static final String str( final Spot spot )
+	{
+		return spot.ID() + " (" +
+				roundToN( spot.getDoublePosition( 0 ), 1 ) + ", " +
+				roundToN( spot.getDoublePosition( 1 ), 1 ) + ", " +
+				roundToN( spot.getDoublePosition( 2 ), 1 ) + ") " +
+				"@ t=" + spot.getFeature( Spot.FRAME ).intValue();
+	}
+
+	private static double roundToN( final double num, final int n )
+	{
+		final double scale = Math.pow( 10, n );
+		return Math.round( num * scale ) / scale;
+	}
 }

src/main/java/fiji/plugin/trackmate/gui/editor/LabkitLauncher.java

@@ -218,9 +218,18 @@ public void run()
 						log.setStatus( "Re-importing from Labkit..." );
 						for ( int t = 0; t < nTimepoints; t++ )
 						{
+							// The spots of this time-point:
+							final Map< Integer, Spot > spotLabelsThisFrame = new HashMap<>();
+							for ( final Integer label : spotLabels.keySet() )
+							{
+								final Spot spot = spotLabels.get( label );
+								if ( spot.getFeature( Spot.FRAME ).intValue() == t )
+									spotLabelsThisFrame.put( label, spot );
+							}
+
 							final RandomAccessibleInterval< T > novelIndexImgThisFrame = Views.hyperSlice( indexImg, timeDim, t );
 							final RandomAccessibleInterval< T > previousIndexImgThisFrame = Views.hyperSlice( previousIndexImg, timeDim, t );
-							reimporter.reimport( novelIndexImgThisFrame, previousIndexImgThisFrame, t, spotLabels );
+							reimporter.reimport( novelIndexImgThisFrame, previousIndexImgThisFrame, t, spotLabelsThisFrame );
 							log.setProgress( t / ( double ) nTimepoints );
 						}
 						log.setStatus( "" );