Add offset 1 to label ids

* This is needed, since all ids (i.e. spot ids, branch spot ids, track ids) in Mastodon are counted zero based and thus the label zero could not be differentiated from the background, which is also set to zero in the export

src/main/java/org/mastodon/mamut/segment/SegmentUsingEllipsoidsController.java

@@ -48,6 +48,9 @@
 
 public class SegmentUsingEllipsoidsController
 {
+
+	public static final int LABEL_ID_OFFSET = 1;
+
 	private static final Logger logger = LoggerFactory.getLogger( MethodHandles.lookup().lookupClass() );
 
 	private final Model model;
@@ -185,16 +188,16 @@ private int getLabelId( final Spot spot, final LabelOptions option )
 		switch ( option )
 		{
 		case SPOT_ID:
-			return spot.getInternalPoolIndex();
+			return spot.getInternalPoolIndex() + LABEL_ID_OFFSET;
 		case BRANCH_SPOT_ID:
 			BranchSpot ref = model.getBranchGraph().vertexRef();
 			int branchSpotId = model.getBranchGraph().getBranchVertex( spot, ref ).getInternalPoolIndex();
 			model.getBranchGraph().releaseRef( ref ); // NB: optional, but increases performance, when this method is called often
-			return branchSpotId;
+			return branchSpotId + LABEL_ID_OFFSET;
 		case TRACK_ID:
 			if ( trackIdProjection == null )
 				trackIdProjection = getTrackIDFeatureProjection( context, model );
-			return ( int ) trackIdProjection.value( spot );
+			return ( int ) trackIdProjection.value( spot ) + LABEL_ID_OFFSET;
 		default:
 			throw new IllegalArgumentException( "Unknown label option: " + option );
 		}

src/test/java/org/mastodon/mamut/segment/SegmentUsingEllipsoidsControllerTest.java

@@ -27,7 +27,6 @@
 import java.util.List;
 
 import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertNotEquals;
 import static org.junit.Assert.assertThrows;
 
 public class SegmentUsingEllipsoidsControllerTest
@@ -47,8 +46,7 @@ public void setUp()
 	{
 		model = new Model();
 		ModelGraph modelGraph = model.getGraph();
-		modelGraph.addVertex(); // NB: dummy vertex with internal pool index 0
-		spot = modelGraph.addVertex(); // NB: internal pool index is 1
+		spot = modelGraph.addVertex();
 		ModelBranchGraph modelBranchGraph = model.getBranchGraph();
 		modelBranchGraph.graphRebuilt();
 		branchSpot = modelBranchGraph.getBranchVertex( spot, modelBranchGraph.vertexRef() );
@@ -78,9 +76,10 @@ public void testSaveEllipsoidSegmentationToFile() throws IOException
 		SCIFIOImgPlus< IntType > imgTrack = getIntTypeSCIFIOImgPlus( imgOpener, outputTrack );
 
 		// check that the spot id / branchSpot id / track id is used as value in the center of the spot
-		assertEquals( spot.getInternalPoolIndex(), imgSpot.getAt( center ).get() );
-		assertEquals( branchSpot.getInternalPoolIndex(), imgBranchSpot.getAt( center ).get() );
-		assertEquals( 1, imgTrack.getAt( center ).get() );
+		assertEquals( spot.getInternalPoolIndex() + SegmentUsingEllipsoidsController.LABEL_ID_OFFSET, imgSpot.getAt( center ).get() );
+		assertEquals(
+				branchSpot.getInternalPoolIndex() + SegmentUsingEllipsoidsController.LABEL_ID_OFFSET, imgBranchSpot.getAt( center ).get() );
+		assertEquals( SegmentUsingEllipsoidsController.LABEL_ID_OFFSET, imgTrack.getAt( center ).get() );
 		// check that there is no value set outside the ellipsoid of the spot
 		long[] corner = new long[] { 0, 0, 0 };
 		assertEquals( 0, imgSpot.getAt( corner ).get() );