Add DefaultSmooth and DefaultSharpen Ops

Adapted from the implementations created by Barry Dezonia

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

@@ -6,13 +6,13 @@
  * %%
  * Redistribution and use in source and binary forms, with or without
  * modification, are permitted provided that the following conditions are met:
- * 
+ *
  * 1. Redistributions of source code must retain the above copyright notice,
  *    this list of conditions and the following disclaimer.
  * 2. Redistributions in binary form must reproduce the above copyright notice,
  *    this list of conditions and the following disclaimer in the documentation
  *    and/or other materials provided with the distribution.
- * 
+ *
  * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
  * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
  * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
@@ -136,7 +136,7 @@ public <I extends RealType<I>, O extends RealType<O>> O addPoissonNoise(
 
 	/**
 	 * Executes a bilateral filter on the given arguments.
-	 * 
+	 *
 	 * @param in
 	 * @param out
 	 * @param sigmaR
@@ -757,7 +757,7 @@ RandomAccessibleInterval<V> dog(final RandomAccessibleInterval<T> in,
 
 	/**
 	 * Executes the "Frangi Vesselness" filter operation on the given arguments.
-	 * 
+	 *
 	 * @param in - input image
 	 * @param out - output image
 	 * @param spacing - n-dimensional array indicating the physical distance
@@ -1245,6 +1245,19 @@ public <T extends RealType<T>> RandomAccessibleInterval<T> partialDerivative(
 		return result;
 	}
 
+	// -- Sharpen
+
+	/** Executes the "sharpen" filter operation on the given arguments. */
+	@OpMethod(op = net.imagej.ops.filter.sharpen.DefaultSharpen.class)
+	public <T extends RealType<T>> RandomAccessibleInterval<T> sharpen(
+		final RandomAccessibleInterval<T> in)
+	{
+		@SuppressWarnings("unchecked")
+		final RandomAccessibleInterval<T> result =
+			(RandomAccessibleInterval<T>) ops().run(Ops.Filter.Sharpen.class, in);
+		return result;
+	}
+
 	/** Executes the "sigma" filter operation on the given arguments. */
 	@OpMethod(op = net.imagej.ops.filter.sigma.DefaultSigmaFilter.class)
 	public <T extends RealType<T>> IterableInterval<T> sigma(
@@ -1271,6 +1284,19 @@ public <T extends RealType<T>> IterableInterval<T> sigma(
 		return result;
 	}
 
+	// -- Smooth
+
+	/** Executes the "sharpen" filter operation on the given arguments. */
+	@OpMethod(op = net.imagej.ops.filter.smooth.DefaultSmooth.class)
+	public <T extends RealType<T>> RandomAccessibleInterval<T> smooth(
+		final RandomAccessibleInterval<T> in)
+	{
+		@SuppressWarnings("unchecked")
+		final RandomAccessibleInterval<T> result =
+			(RandomAccessibleInterval<T>) ops().run(Ops.Filter.Smooth.class, in);
+		return result;
+	}
+
 	// -- Sobel
 
 	@OpMethod(op = net.imagej.ops.filter.sobel.SobelRAI.class)

src/main/java/net/imagej/ops/filter/sharpen/DefaultSharpen.java

@@ -0,0 +1,132 @@
+
+package net.imagej.ops.filter.sharpen;
+
+import net.imagej.Extents;
+import net.imagej.Position;
+import net.imagej.ops.Ops;
+import net.imagej.ops.special.function.AbstractUnaryFunctionOp;
+import net.imglib2.Cursor;
+import net.imglib2.FinalInterval;
+import net.imglib2.RandomAccess;
+import net.imglib2.RandomAccessible;
+import net.imglib2.RandomAccessibleInterval;
+import net.imglib2.algorithm.neighborhood.Neighborhood;
+import net.imglib2.algorithm.neighborhood.RectangleNeighborhood;
+import net.imglib2.algorithm.neighborhood.RectangleNeighborhoodFactory;
+import net.imglib2.algorithm.neighborhood.RectangleShape.NeighborhoodsAccessible;
+import net.imglib2.type.numeric.RealType;
+import net.imglib2.util.Util;
+import net.imglib2.view.Views;
+
+import org.scijava.plugin.Plugin;
+
+/**
+ * Op rendition of the SharpenDataValues plugin written by Barry Dezonia
+ *
+ * @author Gabe Selzer
+ */
+@Plugin(type = Ops.Filter.Sharpen.class)
+public class DefaultSharpen<T extends RealType<T>> extends
+	AbstractUnaryFunctionOp<RandomAccessibleInterval<T>, RandomAccessibleInterval<T>>
+	implements Ops.Filter.Sharpen
+{
+
+	final double[] kernel = { -1, -1, -1, -1, 12, -1, -1, -1, -1 };
+	double scale;
+
+	@Override
+	public RandomAccessibleInterval<T> calculate(
+		final RandomAccessibleInterval<T> input)
+	{
+		final RandomAccessibleInterval<T> output = ops().copy().rai(input);
+
+		final long[] planeDims = new long[input.numDimensions() - 2];
+		for (int i = 0; i < planeDims.length; i++)
+			planeDims[i] = input.dimension(i + 2);
+		final Extents extents = new Extents(planeDims);
+		final Position planePos = extents.createPosition();
+		if (planeDims.length == 0) {
+			computePlanar(planePos, input, output);
+		}
+		else {
+			while (planePos.hasNext()) {
+				planePos.fwd();
+				computePlanar(planePos, input, output);
+			}
+
+		}
+		return output;
+	}
+
+	private void computePlanar(final Position planePos,
+		final RandomAccessibleInterval<T> input,
+		final RandomAccessibleInterval<T> output)
+	{
+		// TODO can we just set scale to 4?
+		scale = 0;
+		for (final double d : kernel)
+			scale += d;
+
+		final T type = Util.getTypeFromInterval(input);
+
+		final long[] imageDims = new long[input.numDimensions()];
+		input.dimensions(imageDims);
+
+		// create all objects needed for NeighborhoodsAccessible
+		RandomAccessibleInterval<T> slicedInput = ops().copy().rai(input);
+		for (int i = planePos.numDimensions() - 1; i >= 0; i--) {
+			slicedInput = Views.hyperSlice(slicedInput, input.numDimensions() - 1 - i,
+				planePos.getLongPosition(i));
+		}
+
+		final RandomAccessible<T> refactoredInput = Views.extendMirrorSingle(
+			slicedInput);
+		final RectangleNeighborhoodFactory<T> factory = RectangleNeighborhood
+			.factory();
+		final FinalInterval neighborhoodSpan = new FinalInterval(new long[] { -1,
+			-1 }, new long[] { 1, 1 });
+
+		final NeighborhoodsAccessible<T> neighborhoods =
+			new NeighborhoodsAccessible<>(refactoredInput, neighborhoodSpan, factory);
+
+		// create cursors and random accesses for loop.
+		final Cursor<T> cursor = Views.iterable(input).localizingCursor();
+		final RandomAccess<T> outputRA = output.randomAccess();
+		for (int i = 0; i < planePos.numDimensions(); i++) {
+			outputRA.setPosition(planePos.getLongPosition(i), i + 2);
+		}
+		final RandomAccess<Neighborhood<T>> neighborhoodsRA = neighborhoods
+			.randomAccess();
+
+		int algorithmIndex = 0;
+		double sum;
+		final double[] n = new double[9];
+		while (cursor.hasNext()) {
+			cursor.fwd();
+			if (cursor.getLongPosition(0) == 14 && cursor.getLongPosition(1) == 0)
+				System.out.println("Hit 14");
+			neighborhoodsRA.setPosition(cursor);
+			final Neighborhood<T> current = neighborhoodsRA.get();
+			final Cursor<T> neighborhoodCursor = current.cursor();
+
+			algorithmIndex = 0;
+			sum = 0;
+			while (algorithmIndex < n.length) {
+				neighborhoodCursor.fwd();
+				n[algorithmIndex++] = neighborhoodCursor.get().getRealDouble();
+			}
+
+			for (int i = 0; i < kernel.length; i++) {
+				sum += kernel[i] * n[i];
+			}
+
+			double value = sum / scale;
+
+			outputRA.setPosition(cursor.getLongPosition(0), 0);
+			outputRA.setPosition(cursor.getLongPosition(1), 1);
+			if (value > type.getMaxValue()) value = type.getMaxValue();
+			if (value < type.getMinValue()) value = type.getMinValue();
+			outputRA.get().setReal(value);
+		}
+	}
+}

src/main/java/net/imagej/ops/filter/smooth/DefaultSmooth.java

@@ -0,0 +1,131 @@
+
+package net.imagej.ops.filter.smooth;
+
+import net.imagej.Extents;
+import net.imagej.Position;
+import net.imagej.ops.Ops;
+import net.imagej.ops.special.function.AbstractUnaryFunctionOp;
+import net.imglib2.Cursor;
+import net.imglib2.FinalInterval;
+import net.imglib2.RandomAccess;
+import net.imglib2.RandomAccessible;
+import net.imglib2.RandomAccessibleInterval;
+import net.imglib2.algorithm.neighborhood.Neighborhood;
+import net.imglib2.algorithm.neighborhood.RectangleNeighborhood;
+import net.imglib2.algorithm.neighborhood.RectangleNeighborhoodFactory;
+import net.imglib2.algorithm.neighborhood.RectangleShape.NeighborhoodsAccessible;
+import net.imglib2.type.numeric.RealType;
+import net.imglib2.util.Util;
+import net.imglib2.view.Views;
+
+import org.scijava.plugin.Plugin;
+
+/**
+ * Op rendition of the SmoothDataValues plugin written by Barry Dezonia
+ *
+ * @author Gabe Selzer
+ */
+@Plugin(type = Ops.Filter.Smooth.class)
+public class DefaultSmooth<T extends RealType<T>> extends
+	AbstractUnaryFunctionOp<RandomAccessibleInterval<T>, RandomAccessibleInterval<T>>
+	implements Ops.Filter.Smooth
+{
+
+	final double[] kernel = { 1, 1, 1, 1, 1, 1, 1, 1, 1 };
+	double scale;
+
+	@Override
+	public RandomAccessibleInterval<T> calculate(
+		final RandomAccessibleInterval<T> input)
+	{
+		final RandomAccessibleInterval<T> output = ops().copy().rai(input);
+
+		final long[] planeDims = new long[input.numDimensions() - 2];
+		for (int i = 0; i < planeDims.length; i++)
+			planeDims[i] = input.dimension(i + 2);
+		final Extents extents = new Extents(planeDims);
+		final Position planePos = extents.createPosition();
+		if (planeDims.length == 0) {
+			computePlanar(planePos, input, output);
+		}
+		else {
+			while (planePos.hasNext()) {
+				planePos.fwd();
+				computePlanar(planePos, input, output);
+			}
+
+		}
+		return output;
+	}
+
+	private void computePlanar(final Position planePos,
+		final RandomAccessibleInterval<T> input,
+		final RandomAccessibleInterval<T> output)
+	{
+		// TODO can we just set scale to 4?
+		scale = 0;
+		for (final double d : kernel)
+			scale += d;
+
+		final T type = Util.getTypeFromInterval(input);
+
+		final long[] imageDims = new long[input.numDimensions()];
+		input.dimensions(imageDims);
+
+		// create all objects needed for NeighborhoodsAccessible
+		RandomAccessibleInterval<T> slicedInput = ops().copy().rai(input);
+		for (int i = planePos.numDimensions() - 1; i >= 0; i--) {
+			slicedInput = Views.hyperSlice(slicedInput, input.numDimensions() - 1 - i,
+				planePos.getLongPosition(i));
+		}
+
+		final RandomAccessible<T> refactoredInput = Views.extendMirrorSingle(
+			slicedInput);
+		final RectangleNeighborhoodFactory<T> factory = RectangleNeighborhood
+			.factory();
+		final FinalInterval neighborhoodSpan = new FinalInterval(new long[] { -1,
+			-1 }, new long[] { 1, 1 });
+
+		final NeighborhoodsAccessible<T> neighborhoods =
+			new NeighborhoodsAccessible<>(refactoredInput, neighborhoodSpan, factory);
+
+		// create cursors and random accesses for loop.
+		final Cursor<T> cursor = Views.iterable(input).localizingCursor();
+		final RandomAccess<T> outputRA = output.randomAccess();
+		for (int i = 0; i < planePos.numDimensions(); i++) {
+			outputRA.setPosition(planePos.getLongPosition(i), i + 2);
+		}
+		final RandomAccess<Neighborhood<T>> neighborhoodsRA = neighborhoods
+			.randomAccess();
+
+		int algorithmIndex = 0;
+		double sum;
+		final double[] n = new double[9];
+		while (cursor.hasNext()) {
+
+			cursor.fwd();
+			neighborhoodsRA.setPosition(cursor);
+			final Neighborhood<T> current = neighborhoodsRA.get();
+			final Cursor<T> neighborhoodCursor = current.cursor();
+
+			algorithmIndex = 0;
+			sum = 0;
+			while (algorithmIndex < n.length) {
+				neighborhoodCursor.fwd();
+				n[algorithmIndex++] = neighborhoodCursor.get().getRealDouble();
+			}
+
+			for (int i = 0; i < kernel.length; i++) {
+				sum += kernel[i] * n[i];
+			}
+
+			double value = sum / scale;
+
+			outputRA.setPosition(cursor.getLongPosition(0), 0);
+			outputRA.setPosition(cursor.getLongPosition(1), 1);
+			if (value > type.getMaxValue()) value = type.getMaxValue();
+			if (value < type.getMinValue()) value = type.getMinValue();
+			outputRA.get().setReal(value);
+		}
+	}
+}

src/main/templates/net/imagej/ops/Ops.list

@@ -122,7 +122,9 @@ namespaces = ```
 		[name: "paddingIntervalCentered",        iface: "PaddingIntervalCentered"],
 		[name: "paddingIntervalOrigin",          iface: "PaddingIntervalOrigin"],
 		[name: "tubeness",                       iface: "Tubeness"],
+		[name: "sharpen",                        iface: "Sharpen"],
 		[name: "sigma",                          iface: "Sigma",               aliases: ["sigmaFilter", "filterSigma"]],
+		[name: "smooth",                       iface: "Smooth"],
 		[name: "sobel",                          iface: "Sobel"],
 		[name: "variance",                       iface: "Variance",            aliases: ["varianceFilter", "filterVariance", "var", "varFilter", "filterVar"]],
 		[name: "frangiVesselness",			 iface: "FrangiVesselness"],