Array img opt neighborhoods-Leon's branch

src/main/java/net/imagej/ops/OpEnvironment.java

@@ -67,10 +67,15 @@
 import net.imagej.ops.thread.ThreadNamespace;
 import net.imagej.ops.threshold.ThresholdNamespace;
 import net.imagej.ops.transform.TransformNamespace;
+import net.imglib2.Interval;
 import net.imglib2.IterableInterval;
 import net.imglib2.RandomAccessible;
 import net.imglib2.RandomAccessibleInterval;
+import net.imglib2.algorithm.neighborhood.RectangleShape;
 import net.imglib2.algorithm.neighborhood.Shape;
+import net.imglib2.img.array.ArrayImg;
+import net.imglib2.outofbounds.OutOfBoundsFactory;
+import net.imglib2.type.NativeType;
 import net.imglib2.type.Type;
 
 import org.scijava.Contextual;
@@ -723,6 +728,19 @@ default <EI, EO> IterableInterval<EO> map(
 		return result;
 	}
 
+	/** Executes the "map" operation on the given arguments. */
+	@OpMethod(op = net.imagej.ops.map.neighborhood.DefaultMapNeighborhood.class)
+	default <EI, EO> IterableInterval<EO> map(final IterableInterval<EO> out,
+		final RandomAccessibleInterval<EI> in, final Shape shape,
+		final UnaryComputerOp<Iterable<EI>, EO> op,
+		final OutOfBoundsFactory<EI, RandomAccessibleInterval<EI>> oobFactory)
+	{
+		@SuppressWarnings("unchecked")
+		final IterableInterval<EO> result = (IterableInterval<EO>) run(
+				net.imagej.ops.Ops.Map.class, out, in, op, shape, oobFactory);
+		return result;
+	}
+
 	/** Executes the "map" operation on the given arguments. */
 	@OpMethod(
 		op = net.imagej.ops.map.neighborhood.MapNeighborhoodWithCenter.class)
@@ -737,6 +755,76 @@ default <EI, EO> IterableInterval<EO> map(
 		return result;
 	}
 
+	/** Executes the "map" operation on the given arguments. */
+	@OpMethod(
+		op = net.imagej.ops.map.neighborhood.MapNeighborhoodWithCenter.class)
+	default <EI, EO> IterableInterval<EO> map(final IterableInterval<EO> out,
+		final RandomAccessibleInterval<EI> in, final Shape shape,
+		final CenterAwareComputerOp<EI, EO> func,
+		final OutOfBoundsFactory<EI, RandomAccessibleInterval<EI>> oobFactory)
+	{
+		@SuppressWarnings("unchecked")
+		final IterableInterval<EO> result = (IterableInterval<EO>) run(
+			net.imagej.ops.Ops.Map.class, out, in, func, shape, oobFactory);
+		return result;
+	}
+
+	/** Executes the "map" operation on the given arguments. */
+	@OpMethod(
+		op = net.imagej.ops.map.neighborhood.array.MapNeighborhoodWithCenterNativeType.class)
+	default <I extends NativeType<I>, O extends NativeType<O>> ArrayImg<O, ?> map(
+		final ArrayImg<O, ?> out, final ArrayImg<I, ?> in, final RectangleShape shape,
+		final CenterAwareComputerOp<I, O> op)
+	{
+		@SuppressWarnings("unchecked")
+		final ArrayImg<O, ?> result = (ArrayImg<O, ?>) run(
+			net.imagej.ops.Ops.Map.class, out, in, shape, op);
+		return result;
+	}
+
+	/** Executes the "map" operation on the given arguments. */
+	@OpMethod(ops = {
+		net.imagej.ops.map.neighborhood.array.MapNeighborhoodNativeType.class,
+		net.imagej.ops.map.neighborhood.array.MapNeighborhoodNativeTypeExtended.class })
+	default <I extends NativeType<I>, O extends NativeType<O>> ArrayImg<O, ?> map(
+		final ArrayImg<O, ?> out, final ArrayImg<I, ?> in,
+		final RectangleShape shape, final UnaryComputerOp<Iterable<I>, O> op)
+	{
+		@SuppressWarnings("unchecked")
+		final ArrayImg<O, ?> result = (ArrayImg<O, ?>) run(
+			net.imagej.ops.Ops.Map.class, out, in, shape, op);
+		return result;
+	}
+
+	/** Executes the "map" operation on the given arguments. */
+	@OpMethod(
+		op = net.imagej.ops.map.neighborhood.array.MapNeighborhoodNativeType.class)
+	default <I extends NativeType<I>, O extends NativeType<O>> ArrayImg<O, ?> map(
+		final ArrayImg<O, ?> out, final ArrayImg<I, ?> in,
+		final RectangleShape shape, final UnaryComputerOp<Iterable<I>, O> op,
+		final Interval interval)
+	{
+		@SuppressWarnings("unchecked")
+		final ArrayImg<O, ?> result = (ArrayImg<O, ?>) run(
+			net.imagej.ops.Ops.Map.class, out, in, shape, op, interval);
+		return result;
+	}
+
+	/** Executes the "map" operation on the given arguments. */
+	@OpMethod(
+		op = net.imagej.ops.map.neighborhood.array.MapNeighborhoodNativeTypeExtended.class)
+	default
+		<I extends NativeType<I>, O extends NativeType<O>> ArrayImg<O, ?> map(
+		final ArrayImg<O, ?> out, final ArrayImg<I, ?> in, final RectangleShape shape,
+		final UnaryComputerOp<Iterable<I>, O> op,
+		final OutOfBoundsFactory<I, ?> oobFactory)
+	{
+		@SuppressWarnings("unchecked")
+		final ArrayImg<O, ?> result = (ArrayImg<O, ?>) run(
+			net.imagej.ops.Ops.Map.class, out, in, op, shape, oobFactory);
+		return result;
+	}
+
 	/** Executes the "map" operation on the given arguments. */
 	@OpMethod(op = net.imagej.ops.map.MapIterableToIterable.class)
 	default <EI, EO> Iterable<EO> map(final Iterable<EO> out,

src/main/java/net/imagej/ops/filter/AbstractCenterAwareNeighborhoodBasedFilter.java

@@ -30,11 +30,8 @@
 
 package net.imagej.ops.filter;
 
-import org.scijava.plugin.Parameter;
-
 import net.imagej.ops.Ops.Map;
 import net.imagej.ops.map.neighborhood.CenterAwareComputerOp;
-import net.imagej.ops.special.chain.RAIs;
 import net.imagej.ops.special.computer.AbstractUnaryComputerOp;
 import net.imagej.ops.special.computer.Computers;
 import net.imagej.ops.special.computer.UnaryComputerOp;
@@ -44,6 +41,8 @@
 import net.imglib2.outofbounds.OutOfBoundsBorderFactory;
 import net.imglib2.outofbounds.OutOfBoundsFactory;
 
+import org.scijava.plugin.Parameter;
+
 public abstract class AbstractCenterAwareNeighborhoodBasedFilter<I, O> extends
 	AbstractUnaryComputerOp<RandomAccessibleInterval<I>, IterableInterval<O>>
 {
@@ -62,15 +61,16 @@ public abstract class AbstractCenterAwareNeighborhoodBasedFilter<I, O> extends
 	@Override
 	public void initialize() {
 		filterOp = unaryComputer(out().firstElement());
-		map = Computers.unary(ops(), Map.class, out(), in(), shape, filterOp);
+		map = Computers.unary(ops(), Map.class, out(), in(), shape, filterOp,
+			outOfBoundsFactory);
 	}
 
 	@Override
 	public void compute1(RandomAccessibleInterval<I> input,
 		IterableInterval<O> output)
 	{
 		// map computer to neighborhoods
-		map.compute1(RAIs.extend(input, outOfBoundsFactory), output);
+		map.compute1(input, output);
 	}
 
 	/**

src/main/java/net/imagej/ops/filter/AbstractNeighborhoodBasedFilter.java

@@ -30,8 +30,6 @@
 
 package net.imagej.ops.filter;
 
-import org.scijava.plugin.Parameter;
-
 import net.imagej.ops.Ops.Map;
 import net.imagej.ops.special.computer.AbstractUnaryComputerOp;
 import net.imagej.ops.special.computer.Computers;
@@ -41,7 +39,8 @@
 import net.imglib2.algorithm.neighborhood.Shape;
 import net.imglib2.outofbounds.OutOfBoundsBorderFactory;
 import net.imglib2.outofbounds.OutOfBoundsFactory;
-import net.imglib2.view.Views;
+
+import org.scijava.plugin.Parameter;
 
 public abstract class AbstractNeighborhoodBasedFilter<I, O> extends
 	AbstractUnaryComputerOp<RandomAccessibleInterval<I>, IterableInterval<O>>
@@ -61,15 +60,15 @@ public abstract class AbstractNeighborhoodBasedFilter<I, O> extends
 	@Override
 	public void initialize() {
 		filterOp = unaryComputer(out().firstElement());
-		map = Computers.unary(ops(), Map.class, out(), in(), shape, filterOp);
+		map = Computers.unary(ops(), Map.class, out(), in(), shape, filterOp,
+			outOfBoundsFactory);
 	}
 
 	@Override
 	public void compute1(RandomAccessibleInterval<I> input,
 		IterableInterval<O> output)
 	{
-		map.compute1(Views.interval(Views.extend(input, outOfBoundsFactory), input),
-			output);
+		map.compute1(input, output);
 	}
 
 	/**

src/main/java/net/imagej/ops/map/neighborhood/AbstractMapNeighborhood.java

@@ -46,9 +46,9 @@
  * @param <PO> producer of outputs
  * @param <OP> type of {@link Op} which processes each element
  */
-public abstract class AbstractMapNeighborhood<EI, EO, PI, PO, OP extends Op>
-	extends AbstractBinaryComputerOp<PI, Shape, PO> implements
-	MapNeighborhood<EI, EO, PI, PO, OP>
+public abstract class AbstractMapNeighborhood<EI, EO, PI, PO, S extends Shape, OP extends Op>
+	extends AbstractBinaryComputerOp<PI, S, PO> implements
+	MapNeighborhood<EI, EO, PI, PO, S, OP>
 {
 
 	@Parameter

src/main/java/net/imagej/ops/map/neighborhood/DefaultMapNeighborhood.java

@@ -37,8 +37,11 @@
 import net.imglib2.RandomAccessibleInterval;
 import net.imglib2.algorithm.neighborhood.Neighborhood;
 import net.imglib2.algorithm.neighborhood.Shape;
+import net.imglib2.outofbounds.OutOfBoundsFactory;
+import net.imglib2.view.Views;
 
 import org.scijava.Priority;
+import org.scijava.plugin.Parameter;
 import org.scijava.plugin.Plugin;
 
 /**
@@ -52,9 +55,12 @@
  */
 @Plugin(type = Ops.Map.class, priority = Priority.LOW_PRIORITY)
 public class DefaultMapNeighborhood<I, O> extends
-	AbstractMapNeighborhood<I, O, RandomAccessibleInterval<I>, IterableInterval<O>, UnaryComputerOp<Iterable<I>, O>>
+	AbstractMapNeighborhood<I, O, RandomAccessibleInterval<I>, IterableInterval<O>, Shape, UnaryComputerOp<Iterable<I>, O>>
 {
 
+	@Parameter(required = false)
+	private OutOfBoundsFactory<I, RandomAccessibleInterval<I>> oobFactory;
+
 	private UnaryComputerOp<IterableInterval<Neighborhood<I>>, IterableInterval<O>> map;
 
 	@SuppressWarnings({ "rawtypes", "unchecked" })
@@ -69,7 +75,9 @@ IterableInterval.class, in1() == null ? IterableInterval.class : in2()
 	public void compute2(final RandomAccessibleInterval<I> in1, final Shape in2,
 		final IterableInterval<O> out)
 	{
-		map.compute1(in2.neighborhoodsSafe(in1), out);
+		final RandomAccessibleInterval<I> extended = oobFactory == null ? in1
+			: Views.interval(Views.extend(in1, oobFactory), in1);
+		map.compute1(in2.neighborhoodsSafe(extended), out);
 	}
 
 }

src/main/java/net/imagej/ops/map/neighborhood/MapNeighborhood.java

@@ -43,8 +43,8 @@
  * @param <EO> element type of outputs
  * @param <OP> type of {@link Op} which processes each neighborhood
  */
-public interface MapNeighborhood<EI, EO, PI, PO, OP extends Op> extends
-	BinaryComputerOp<PI, Shape, PO>, MapOp<OP>
+public interface MapNeighborhood<EI, EO, PI, PO, S extends Shape, OP extends Op>
+	extends BinaryComputerOp<PI, S, PO>, MapOp<OP>
 {
 	// NB: Marker interface.
 }

src/main/java/net/imagej/ops/map/neighborhood/MapNeighborhoodWithCenter.java

@@ -39,8 +39,11 @@
 import net.imglib2.RandomAccessibleInterval;
 import net.imglib2.algorithm.neighborhood.Neighborhood;
 import net.imglib2.algorithm.neighborhood.Shape;
+import net.imglib2.outofbounds.OutOfBoundsFactory;
+import net.imglib2.view.Views;
 
 import org.scijava.Priority;
+import org.scijava.plugin.Parameter;
 import org.scijava.plugin.Plugin;
 
 /**
@@ -55,11 +58,14 @@
  *      CenterAwareComputerOp)
  * @see CenterAwareComputerOp
  */
-@Plugin(type = Ops.Map.class, priority = Priority.LOW_PRIORITY + 1)
+@Plugin(type = Ops.Map.class, priority = Priority.LOW_PRIORITY + 21)
 public class MapNeighborhoodWithCenter<I, O> extends
-	AbstractMapNeighborhood<I, O, RandomAccessibleInterval<I>, IterableInterval<O>, CenterAwareComputerOp<I, O>>
+	AbstractMapNeighborhood<I, O, RandomAccessibleInterval<I>, IterableInterval<O>, Shape, CenterAwareComputerOp<I, O>>
 {
 
+	@Parameter(required = false)
+	private OutOfBoundsFactory<I, RandomAccessibleInterval<I>> oobFactory;
+
 	private BinaryComputerOp<IterableInterval<Neighborhood<I>>, RandomAccessibleInterval<I>, IterableInterval<O>> map;
 
 	@SuppressWarnings({ "rawtypes", "unchecked" })
@@ -73,7 +79,9 @@ public void initialize() {
 	public void compute2(final RandomAccessibleInterval<I> in1, final Shape in2,
 		final IterableInterval<O> out)
 	{
-		map.compute2(in2.neighborhoodsSafe(in1), in1, out);
+		final RandomAccessibleInterval<I> extended = oobFactory == null ? in1
+			: Views.interval(Views.extend(in1, oobFactory), in1);
+		map.compute2(in2.neighborhoodsSafe(extended), in1, out);
 	}
 
 }