Add getStructuringElementBoundingBox() for Shapes (#27)

* Shape(s): add getStructuringElementBoundingBox()

* Shape: add documentation

* Shape: add def getStructuringElementBoundingBox()

Thanks @stelfrich

Author: stelfrich

src/main/java/net/imglib2/algorithm/neighborhood/CenteredRectangleShape.java

@@ -40,6 +40,7 @@
 import net.imglib2.RandomAccessibleInterval;
 import net.imglib2.algorithm.neighborhood.RectangleShape.NeighborhoodsAccessible;
 import net.imglib2.algorithm.neighborhood.RectangleShape.NeighborhoodsIterableInterval;
+import net.imglib2.util.Intervals;
 import net.imglib2.util.Util;
 
 /**
@@ -152,4 +153,17 @@ private Interval createSpan()
 		}
 		return new FinalInterval( min, max );
 	}
+
+	@Override
+	public Interval getStructuringElementBoundingBox(final int numDimensions) {
+		final long[] a = new long[numDimensions];
+		final long[] b = new long[numDimensions];
+
+		for (int i = 0; i < numDimensions; ++i) {
+			a[i] = span[i] * -1;
+			b[i] = span[i];
+		}
+
+		return Intervals.union(new FinalInterval(a, a), new FinalInterval(b, b));
+	}
 }

src/main/java/net/imglib2/algorithm/neighborhood/DiamondShape.java

@@ -33,11 +33,13 @@
  */
 package net.imglib2.algorithm.neighborhood;
 
+import java.util.Arrays;
 import java.util.Iterator;
 
 import net.imglib2.AbstractEuclideanSpace;
 import net.imglib2.AbstractInterval;
 import net.imglib2.Cursor;
+import net.imglib2.FinalInterval;
 import net.imglib2.FlatIterationOrder;
 import net.imglib2.Interval;
 import net.imglib2.IterableInterval;
@@ -203,4 +205,15 @@ public int numDimensions()
 		}
 
 	}
+
+	@Override
+	public Interval getStructuringElementBoundingBox(final int numDimensions) {
+		final long[] min = new long[numDimensions];
+		Arrays.fill(min, -getRadius());
+
+		final long[] max = new long[numDimensions];
+		Arrays.fill(max, getRadius());
+
+		return new FinalInterval(min, max);
+	}
 }

src/main/java/net/imglib2/algorithm/neighborhood/DiamondTipsShape.java

@@ -33,11 +33,13 @@
  */
 package net.imglib2.algorithm.neighborhood;
 
+import java.util.Arrays;
 import java.util.Iterator;
 
 import net.imglib2.AbstractEuclideanSpace;
 import net.imglib2.AbstractInterval;
 import net.imglib2.Cursor;
+import net.imglib2.FinalInterval;
 import net.imglib2.FlatIterationOrder;
 import net.imglib2.Interval;
 import net.imglib2.IterableInterval;
@@ -205,4 +207,15 @@ public int numDimensions()
 		}
 
 	}
+
+	@Override
+	public Interval getStructuringElementBoundingBox(final int numDimensions) {
+		final long[] min = new long[numDimensions];
+		Arrays.fill(min, -getRadius());
+
+		final long[] max = new long[numDimensions];
+		Arrays.fill(max, getRadius());
+
+		return new FinalInterval(min, max);
+	}
 }

src/main/java/net/imglib2/algorithm/neighborhood/HorizontalLineShape.java

@@ -38,12 +38,14 @@
 import net.imglib2.AbstractEuclideanSpace;
 import net.imglib2.AbstractInterval;
 import net.imglib2.Cursor;
+import net.imglib2.FinalInterval;
 import net.imglib2.FlatIterationOrder;
 import net.imglib2.Interval;
 import net.imglib2.IterableInterval;
 import net.imglib2.RandomAccess;
 import net.imglib2.RandomAccessible;
 import net.imglib2.RandomAccessibleInterval;
+import net.imglib2.util.Intervals;
 
 /**
  * A {@link Shape} representing finite, centered, symmetric lines, that are
@@ -243,4 +245,16 @@ public int numDimensions()
 		}
 
 	}
+
+	@Override
+	public Interval getStructuringElementBoundingBox(final int numDimensions) {
+		final long[] a = new long[numDimensions];
+		final long[] b = new long[numDimensions];
+
+		a[dim] = -span;
+		b[dim] = span;
+
+		return Intervals.union(new FinalInterval(a, a), new FinalInterval(b, b));
+	}
+
 }

src/main/java/net/imglib2/algorithm/neighborhood/HyperSphereShape.java

@@ -34,11 +34,13 @@
 
 package net.imglib2.algorithm.neighborhood;
 
+import java.util.Arrays;
 import java.util.Iterator;
 
 import net.imglib2.AbstractEuclideanSpace;
 import net.imglib2.AbstractInterval;
 import net.imglib2.Cursor;
+import net.imglib2.FinalInterval;
 import net.imglib2.FlatIterationOrder;
 import net.imglib2.Interval;
 import net.imglib2.IterableInterval;
@@ -187,4 +189,15 @@ public RandomAccess< Neighborhood< T >> randomAccess( final Interval interval )
 			return new HyperSphereNeighborhoodRandomAccess< T >( source, radius, factory, interval );
 		}
 	}
+
+	@Override
+	public Interval getStructuringElementBoundingBox(final int numDimensions) {
+		final long[] min = new long[numDimensions];
+		Arrays.fill(min, -getRadius());
+
+		final long[] max = new long[numDimensions];
+		Arrays.fill(max, getRadius());
+
+		return new FinalInterval(min, max);
+	}
 }

src/main/java/net/imglib2/algorithm/neighborhood/PairOfPointsShape.java

@@ -33,17 +33,20 @@
  */
 package net.imglib2.algorithm.neighborhood;
 
+import java.util.Arrays;
 import java.util.Iterator;
 
 import net.imglib2.AbstractEuclideanSpace;
 import net.imglib2.AbstractInterval;
 import net.imglib2.Cursor;
+import net.imglib2.FinalInterval;
 import net.imglib2.FlatIterationOrder;
 import net.imglib2.Interval;
 import net.imglib2.IterableInterval;
 import net.imglib2.RandomAccess;
 import net.imglib2.RandomAccessible;
 import net.imglib2.RandomAccessibleInterval;
+import net.imglib2.util.Intervals;
 import net.imglib2.util.Util;
 
 /**
@@ -201,4 +204,13 @@ public int numDimensions()
 		}
 	}
 
+	@Override
+	public Interval getStructuringElementBoundingBox(final int numDimensions) {
+		final long[] zeroMin = new long[numDimensions];
+		Arrays.fill(zeroMin, 0);
+
+		return Intervals.union(new FinalInterval(zeroMin, zeroMin),
+			new FinalInterval(offset, offset));
+	}
+
 }

src/main/java/net/imglib2/algorithm/neighborhood/PeriodicLineShape.java

@@ -38,12 +38,14 @@
 import net.imglib2.AbstractEuclideanSpace;
 import net.imglib2.AbstractInterval;
 import net.imglib2.Cursor;
+import net.imglib2.FinalInterval;
 import net.imglib2.FlatIterationOrder;
 import net.imglib2.Interval;
 import net.imglib2.IterableInterval;
 import net.imglib2.RandomAccess;
 import net.imglib2.RandomAccessible;
 import net.imglib2.RandomAccessibleInterval;
+import net.imglib2.util.Intervals;
 import net.imglib2.util.Util;
 
 /**
@@ -243,4 +245,17 @@ public int numDimensions()
 		}
 	}
 
+	@Override
+	public Interval getStructuringElementBoundingBox(final int numDimensions) {
+		final long[] a = new long[numDimensions];
+		final long[] b = new long[numDimensions];
+
+		for (int i = 0; i < numDimensions; ++i) {
+			a[i] = increments[i] * -getSpan();
+			b[i] = increments[i] * getSpan();
+		}
+
+		return Intervals.union(new FinalInterval(a, a), new FinalInterval(b, b));
+	}
+
 }

src/main/java/net/imglib2/algorithm/neighborhood/RectangleShape.java

@@ -34,6 +34,7 @@
 
 package net.imglib2.algorithm.neighborhood;
 
+import java.util.Arrays;
 import java.util.Iterator;
 
 import net.imglib2.AbstractEuclideanSpace;
@@ -224,4 +225,16 @@ public RandomAccess< Neighborhood< T >> randomAccess( final Interval interval )
 			return new RectangleNeighborhoodRandomAccess< T >( source, span, factory, interval );
 		}
 	}
+
+	@Override
+	public Interval getStructuringElementBoundingBox( final int numDimensions )
+	{
+		final long[] min = new long[ numDimensions ];
+		Arrays.fill( min, -getSpan() );
+
+		final long[] max = new long[ numDimensions ];
+		Arrays.fill( max, getSpan() );
+
+		return new FinalInterval( min, max );
+	}
 }

src/main/java/net/imglib2/algorithm/neighborhood/Shape.java

@@ -34,12 +34,17 @@
 
 package net.imglib2.algorithm.neighborhood;
 
+import java.util.stream.LongStream;
+
 import net.imglib2.Cursor;
+import net.imglib2.FinalInterval;
+import net.imglib2.Interval;
 import net.imglib2.IterableInterval;
 import net.imglib2.RandomAccess;
 import net.imglib2.RandomAccessible;
 import net.imglib2.RandomAccessibleInterval;
 import net.imglib2.Sampler;
+import net.imglib2.util.ConstantUtils;
 
 /**
  * A factory for Accessibles on {@link Neighborhood Neighborhoods}.
@@ -48,6 +53,46 @@
  */
 public interface Shape
 {
+
+	/**
+	 * Get the bounding box for a {@link Shape} with {@code numDimensions}
+	 * dimensions.
+	 * <p>
+	 * Providing {@code numDimensions} is required since the input from which
+	 * {@link Neighborhood neighborhoods} are generated is not known yet. The
+	 * bounding box is described by an {@link Interval} with the center of the
+	 * bounding box located at zero.
+	 * </p>
+	 * <p>
+	 * The values of this bounding box should only be used to determine the extent
+	 * of the {@link Shape}, ignoring the absolute {@link Interval#min(int) min}
+	 * and {@link Interval#max(int) max} values.
+	 * </p>
+	 * 
+	 * @param numDimensions dimensions of the {@link Shape}
+	 * @return an {@link Interval} that describes the bounding box of a
+	 *         {@link Shape}
+	 */
+	public default Interval getStructuringElementBoundingBox( final int numDimensions )
+	{
+		final RandomAccessible< Object > accessible = ConstantUtils.constantRandomAccessible( null, numDimensions );
+		final RandomAccess< Neighborhood< Object > > access = neighborhoodsRandomAccessible( accessible ).randomAccess();
+		access.setPosition( new long[ numDimensions ] );
+		final long[] min = LongStream.generate( () -> Long.MAX_VALUE ).limit( numDimensions ).toArray();
+		final long[] max = LongStream.generate( () -> Long.MIN_VALUE ).limit( numDimensions ).toArray();
+		for ( final Cursor< Object > cursor = access.get().localizingCursor(); cursor.hasNext(); )
+		{
+			cursor.fwd();
+			for ( int d = 0; d < numDimensions; ++d )
+			{
+				final long pos = cursor.getLongPosition( d );
+				min[ d ] = Math.min( pos, min[ d ] );
+				max[ d ] = Math.max( pos, max[ d ] );
+			}
+		}
+		return new FinalInterval( min, max );
+	}
+
 	/**
 	 * Get an {@link IterableInterval} that contains all {@link Neighborhood
 	 * Neighborhoods} of the source image.

src/test/java/net/imglib2/algorithm/neighborhood/CenteredRectangleShapeTest.java

@@ -33,8 +33,15 @@
  */
 package net.imglib2.algorithm.neighborhood;
 
+import static org.junit.Assert.assertTrue;
+
+import net.imglib2.FinalInterval;
+import net.imglib2.Interval;
 import net.imglib2.algorithm.neighborhood.CenteredRectangleShape;
 import net.imglib2.algorithm.neighborhood.Shape;
+import net.imglib2.util.Intervals;
+
+import org.junit.Test;
 
 public class CenteredRectangleShapeTest extends AbstractShapeTest
 {
@@ -57,4 +64,12 @@ protected boolean isInside( final long[] pos, final long[] center )
 		return true;
 
 	}
+
+	@Test
+	public void testStructuringElementBoundingBox() {
+		Interval boundingBox = shape.getStructuringElementBoundingBox(img
+			.numDimensions());
+		assertTrue(Intervals.equals(boundingBox, new FinalInterval(new long[] { -2,
+			-3, -1 }, new long[] { 2, 3, 1 })));
+	}
 }