From b637c1bfd1043db19af95f9b4852c210055ae66d Mon Sep 17 00:00:00 2001
From: Alison Walter <awalter2@wisc.edu>
Date: Fri, 25 Jan 2019 22:12:33 +0100
Subject: [PATCH] Add method to add masks to labelings with default label and
 test

---
 src/main/java/net/imglib2/roi/Masks.java      | 38 +++++++++++++
 .../roi/mask/integer/MaskToLabelingTest.java  | 54 +++++++++++++++++++
 2 files changed, 92 insertions(+)

diff --git a/src/main/java/net/imglib2/roi/Masks.java b/src/main/java/net/imglib2/roi/Masks.java
index cbc137ee7..8b3aed4f8 100644
--- a/src/main/java/net/imglib2/roi/Masks.java
+++ b/src/main/java/net/imglib2/roi/Masks.java
@@ -408,6 +408,44 @@ public static < T, I extends IntegerType< I > > void addMasksToLabeling( final L
 		}
 	}
 
+	/**
+	 * Adds any {@link LabeledMaskInterval}s in the list to the provided
+	 * {@link ImgLabeling}. If a given {@link MaskInterval} is a
+	 * {@link CompositeMaskPredicate}, this method will recurse through the
+	 * children looking for {@link LabeledMaskInterval}s. And if one is found,
+	 * its label will be added to the {@code ImgLabeling} only at the locations
+	 * in the root/parent {@code CompositeMaskPredicate}. If a given
+	 * {@link MaskInterval} or part of a {@code CompositeMaskPredicate} does not
+	 * contain a label, the given default label will be set at those locations.
+	 *
+	 * @param masks
+	 *            list of potential {@link MaskInterval}s to add
+	 * @param labeling
+	 *            {@link ImgLabeling} to add labels/masks to
+	 * @param defaultLabel
+	 *            the label to assign to pixels inside the given
+	 *            {@link MaskInterval}s that do not already have labels (i.e.
+	 *            not part of a {@link LabeledMaskInterval}
+	 */
+	@SuppressWarnings( "unchecked" )
+	public static < T, I extends IntegerType< I > > void addMasksToLabeling( final List< MaskInterval > masks, final ImgLabeling< T, I > labeling, final T defaultLabel )
+	{
+		addMasksToLabeling( masks, labeling, ( Class< T > ) defaultLabel.getClass() );
+
+		final RandomAccess< LabelingType< T > > ra = labeling.randomAccess();
+		for ( final MaskInterval mi : masks )
+		{
+			final Cursor< Void > c = Regions.iterable( Masks.toRandomAccessibleInterval( mi ) ).cursor();
+			while ( c.hasNext() )
+			{
+				c.next();
+				ra.setPosition( c );
+				if ( ra.get().isEmpty() )
+					ra.get().add( defaultLabel );
+			}
+		}
+	}
+
 	/*
 	 * Empty Masks
 	 * ===============================================================
diff --git a/src/test/java/net/imglib2/roi/mask/integer/MaskToLabelingTest.java b/src/test/java/net/imglib2/roi/mask/integer/MaskToLabelingTest.java
index 1b29e3dbd..33dca8466 100644
--- a/src/test/java/net/imglib2/roi/mask/integer/MaskToLabelingTest.java
+++ b/src/test/java/net/imglib2/roi/mask/integer/MaskToLabelingTest.java
@@ -335,6 +335,60 @@ public void testDifferentDimensions()
 			assertTrue( c.next().isEmpty() );
 	}
 
+	@Test
+	public void testDefaultLabelEntireMask()
+	{
+		final MaskInterval m = createBox( new long[] { 10, 10 }, new long[] { 20, 20 } );
+		final Img< IntType > indexImg = ArrayImgs.ints( 21, 21 );
+		final ImgLabeling< String, IntType > imgLabeling = new ImgLabeling<>( indexImg );
+		final String defaultLabel = "default";
+		Masks.addMasksToLabeling( Collections.singletonList( m ), imgLabeling, defaultLabel );
+
+		final Cursor< LabelingType< String > > c = imgLabeling.cursor();
+		while ( c.hasNext() )
+		{
+			final LabelingType< String > labels = c.next();
+			if ( m.test( c ) )
+			{
+				assertTrue( labels.contains( defaultLabel ) );
+				assertEquals( 1, labels.size() );
+			}
+			else
+				assertTrue( labels.isEmpty() );
+		}
+	}
+
+	@Test
+	public void testDefaultLabelPartialMask()
+	{
+		final LabeledMaskInterval< String > labeledSphere = new LabeledMaskInterval<>( createSphere( new long[] { 10, 10 }, 5 ), "label" );
+		final MaskInterval sphere = createSphere( new long[] { 15, 13 }, 4 );
+		final MaskInterval or = labeledSphere.or( sphere );
+		final MaskInterval minus = sphere.minus( labeledSphere );
+		final String defaultLabel = "default";
+		final Img< IntType > indexImg = ArrayImgs.ints( 20, 20 );
+		final ImgLabeling< String, IntType > imgLabeling = new ImgLabeling<>( indexImg );
+		Masks.addMasksToLabeling( Collections.singletonList( or ), imgLabeling, defaultLabel );
+
+		final Cursor< LabelingType< String > > c = imgLabeling.cursor();
+		while ( c.hasNext() )
+		{
+			final LabelingType< String > labels = c.next();
+			if ( labeledSphere.test( c ) )
+			{
+				assertTrue( labels.contains( labeledSphere.getLabel() ) );
+				assertEquals( 1, labels.size() );
+			}
+			else if ( minus.test( c ) )
+			{
+				assertTrue( labels.contains( defaultLabel ) );
+				assertEquals( 1, labels.size() );
+			}
+			else
+				assertTrue( labels.isEmpty() );
+		}
+	}
+
 	// -- Helper methods --
 
 	private static MaskInterval createBox( final long[] min, final long[] max )