Remove option to include intensity in the segmentation

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

@@ -11,12 +11,9 @@
 import net.imagej.ImgPlus;
 import net.imagej.axis.Axes;
 import net.imagej.axis.AxisType;
-import net.imglib2.RandomAccessible;
-import net.imglib2.RandomAccessibleInterval;
 import net.imglib2.cache.img.DiskCachedCellImg;
 import net.imglib2.cache.img.DiskCachedCellImgFactory;
 import net.imglib2.cache.img.DiskCachedCellImgOptions;
-import net.imglib2.converter.RealTypeConverters;
 import net.imglib2.img.Img;
 import net.imglib2.img.display.imagej.ImageJFunctions;
 import net.imglib2.realtransform.AffineTransform3D;
@@ -89,12 +86,9 @@ protected SegmentUsingEllipsoidsController(
 	 * Renders ellipsoids of all timepoints into an ImageJ image using the selected {@link LabelOptions} and saves it to a file.
 	 * @param labelOption the {@link LabelOptions} to use
 	 * @param file the file to save the image to
-	 * @param withBackground whether to keep the background of the image
 	 * @param showResult whether to show the result in ImageJ
 	 */
-	public void saveEllipsoidSegmentationToFile(
-			final LabelOptions labelOption, final File file, boolean withBackground, boolean showResult
-	)
+	public void saveEllipsoidSegmentationToFile( final LabelOptions labelOption, final File file, boolean showResult )
 	{
 		if ( file == null )
 			throw new IllegalArgumentException( "Cannot write ellipsoid segmentation to file. Given file is null." );
@@ -116,8 +110,6 @@ public void saveEllipsoidSegmentationToFile(
 			source.getSourceTransform( timepointId, 0, transform );
 			IntervalView< IntType > frame = Views.hyperSlice( img, 3, timepointId );
 			AbstractSource< IntType > frameSource = new RandomAccessibleIntervalSource<>( frame, new IntType(), transform, "Segmentation" );
-			if ( withBackground )
-				addBackground( timepointId, frameSource );
 			final EllipsoidIterable< IntType > ellipsoidIterable = new EllipsoidIterable<>( frameSource );
 			segmentAllSpotsOfTimepoint( ellipsoidIterable, labelOption, timepointId, frames );
 		}
@@ -144,13 +136,6 @@ private ReentrantReadWriteLock.ReadLock getReadLock( LabelOptions labelOption )
 		}
 	}
 
-	private void addBackground( int timepointId, AbstractSource< IntType > sliceSource )
-	{
-		RandomAccessible< RealType< ? > > bdvRandomAccessible = source.getSource( timepointId, 0 );
-		RandomAccessibleInterval< IntType > sliceRai = sliceSource.getSource( 0, 0 );
-		RealTypeConverters.copyFromTo( bdvRandomAccessible, sliceRai );
-	}
-
 	private void segmentAllSpotsOfTimepoint(
 			final EllipsoidIterable< ? extends RealType< ? > > iterable, final LabelOptions option, final int timepointId, final int frames
 	)

src/main/java/org/mastodon/mamut/segment/ui/SegmentUsingEllipsoidsView.java

@@ -25,10 +25,6 @@ public class SegmentUsingEllipsoidsView implements Command
 	@Parameter(label = "Show result in ImageJ window")
 	private boolean showResult;
 
-	@SuppressWarnings("unused")
-	@Parameter(label = "Keep background")
-	private boolean withBackground;
-
 	@SuppressWarnings("unused")
 	@Parameter
 	private MamutAppModel appModel;
@@ -42,6 +38,6 @@ public void run()
 	{
 		SegmentUsingEllipsoidsController controller = new SegmentUsingEllipsoidsController( appModel, context );
 		LabelOptions selectedOption = LabelOptions.getByName( option );
-		controller.saveEllipsoidSegmentationToFile( selectedOption, saveTo, showResult, withBackground );
+		controller.saveEllipsoidSegmentationToFile( selectedOption, saveTo, showResult );
 	}
 }

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

@@ -47,7 +47,8 @@ public void setUp()
 	{
 		model = new Model();
 		ModelGraph modelGraph = model.getGraph();
-		spot = modelGraph.addVertex();
+		modelGraph.addVertex(); // NB: dummy vertex with internal pool index 0
+		spot = modelGraph.addVertex(); // NB: internal pool index is 1
 		ModelBranchGraph modelBranchGraph = model.getBranchGraph();
 		modelBranchGraph.graphRebuilt();
 		branchSpot = modelBranchGraph.getBranchVertex( spot, modelBranchGraph.vertexRef() );
@@ -67,24 +68,24 @@ public void testSaveEllipsoidSegmentationToFile() throws IOException
 		File outputSpot = getTempFile( "resultSpot" );
 		File outputBranchSpot = getTempFile( "resultBranchSpot" );
 		File outputTrack = getTempFile( "resultTrack" );
-		segmentUsingEllipsoidsController.saveEllipsoidSegmentationToFile( LabelOptions.SPOT_ID, outputSpot, true, false );
-		segmentUsingEllipsoidsController.saveEllipsoidSegmentationToFile( LabelOptions.BRANCH_SPOT_ID, outputBranchSpot, true, false );
-		segmentUsingEllipsoidsController.saveEllipsoidSegmentationToFile( LabelOptions.TRACK_ID, outputTrack, true, false );
+		segmentUsingEllipsoidsController.saveEllipsoidSegmentationToFile( LabelOptions.SPOT_ID, outputSpot, false );
+		segmentUsingEllipsoidsController.saveEllipsoidSegmentationToFile( LabelOptions.BRANCH_SPOT_ID, outputBranchSpot, false );
+		segmentUsingEllipsoidsController.saveEllipsoidSegmentationToFile( LabelOptions.TRACK_ID, outputTrack, false );
 
 		ImgOpener imgOpener = new ImgOpener( context );
 		SCIFIOImgPlus< IntType > imgSpot = getIntTypeSCIFIOImgPlus( imgOpener, outputSpot );
 		SCIFIOImgPlus< IntType > imgBranchSpot = getIntTypeSCIFIOImgPlus( imgOpener, outputBranchSpot );
 		SCIFIOImgPlus< IntType > imgTrack = getIntTypeSCIFIOImgPlus( imgOpener, outputTrack );
 
-		// check that the random content has been replaced by the spot id in the center of the spot
+		// 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( 0, imgTrack.getAt( center ).get() );
-		// check that the random content has NOT been replaced outside the ellipsoid of the spot
+		assertEquals( 1, imgTrack.getAt( center ).get() );
+		// check that there is no value set outside the ellipsoid of the spot
 		long[] corner = new long[] { 0, 0, 0 };
-		assertNotEquals( spot.getInternalPoolIndex(), imgSpot.getAt( corner ).get() );
-		assertNotEquals( branchSpot.getInternalPoolIndex(), imgBranchSpot.getAt( corner ).get() );
-		assertNotEquals( 0, imgTrack.getAt( corner ).get() );
+		assertEquals( 0, imgSpot.getAt( corner ).get() );
+		assertEquals( 0, imgBranchSpot.getAt( corner ).get() );
+		assertEquals( 0, imgTrack.getAt( corner ).get() );
 	}
 
 	private static SCIFIOImgPlus< IntType > getIntTypeSCIFIOImgPlus( ImgOpener imgOpener, File outputSpot )
@@ -110,9 +111,9 @@ public void testExceptions() throws IOException
 		file.deleteOnExit();
 		assertThrows(
 				IllegalArgumentException.class,
-				() -> controller.saveEllipsoidSegmentationToFile( LabelOptions.SPOT_ID, null, true, false )
+				() -> controller.saveEllipsoidSegmentationToFile( LabelOptions.SPOT_ID, null, false )
 		);
-		assertThrows( IllegalArgumentException.class, () -> controller.saveEllipsoidSegmentationToFile( null, file, true, false ) );
+		assertThrows( IllegalArgumentException.class, () -> controller.saveEllipsoidSegmentationToFile( null, file, false ) );
 	}
 
 	private static AbstractSource< IntType > createRandomSource()