Separate Op into integer case and realType case

This allows us to handle integer types and realTypes separately. The
reason for this is as follows:

It seems clear that we would want to allow floating point randomness
when our type allows floating points

If we always base our calculations on floating points, this results in
edge effects when we add noise to integer types. This is due to
rounding: suppose we have a pseudorandomly generated double between 0
and 2. Most IntegerTypes simply round that double to a long, integer,
    etc in setReal. Thus the probability we add 0 to the input is 0.25,
    1 to the input is 0.5, and 2 to the input is 0.25. To get around
    this case we want to generate the random number differently when we
    have an integer type.

For these reasons we have two different Ops to perform the different
noise generation and have shared logic for setting the output.

N.B. We do not allow wrapping for floating point types. This is because
we operate within the following constraint: the number after the max of
the type should map to the minimum of the type. In the case of floating
points, what then should happen to a number equal to 0.5 + the maximum
of the type? In this paradigm, we would expect it to be the minimum of
the type - 0.5; this is impossible, however, since this would be outside
of the range of the type. For this reason, we always clamp.

Author: gselzer

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

@@ -131,22 +131,44 @@ public <I extends RealType<I>, O extends RealType<O>> O addPoissonNoise(
 		return result;
 	}
 
+	// -- Uniform Noise --
+	
 	@OpMethod(op = net.imagej.ops.filter.addUniformNoise.AddUniformNoiseRealType.class)
-	public <I extends RealType<I>, O extends RealType<O>> O addUniformNoise(final O out,
+	public <I extends RealType<I>> I addUniformNoise(final I out,
 		final I in, final double rangeMin, final double rangeMax)
 	{
 		@SuppressWarnings("unchecked")
-		final O result = (O) ops().run(Ops.Filter.AddUniformNoise.class, out, in, rangeMin,
+		final I result = (I) ops().run(Ops.Filter.AddUniformNoise.class, out, in, rangeMin,
 			rangeMax);
 		return result;
 	}
 
 	@OpMethod(op = net.imagej.ops.filter.addUniformNoise.AddUniformNoiseRealType.class)
-	public <I extends RealType<I>, O extends RealType<O>> O addUniformNoise(final O out,
+	public <I extends RealType<I>> I addUniformNoise(final I out,
 		final I in, final double rangeMin, final double rangeMax, final long seed)
 	{
 		@SuppressWarnings("unchecked")
-		final O result = (O) ops().run(Ops.Filter.AddUniformNoise.class, out, in, rangeMin,
+		final I result = (I) ops().run(Ops.Filter.AddUniformNoise.class, out, in, rangeMin,
+			rangeMax, seed);
+		return result;
+	}
+	
+	@OpMethod(op = net.imagej.ops.filter.addUniformNoise.AddUniformNoiseIntegerType.class)
+	public <I extends RealType<I>> I addUniformNoise(final I out,
+		final I in, final long rangeMin, final long rangeMax)
+	{
+		@SuppressWarnings("unchecked")
+		final I result = (I) ops().run(Ops.Filter.AddUniformNoise.class, out, in, rangeMin,
+			rangeMax);
+		return result;
+	}
+	
+	@OpMethod(op = net.imagej.ops.filter.addUniformNoise.AddUniformNoiseIntegerType.class)
+	public <I extends RealType<I>> I addUniformNoise(final I out,
+		final I in, final long rangeMin, final long rangeMax, final long seed)
+	{
+		@SuppressWarnings("unchecked")
+		final I result = (I) ops().run(Ops.Filter.AddUniformNoise.class, out, in, rangeMin,
 			rangeMax, seed);
 		return result;
 	}

src/main/java/net/imagej/ops/filter/addUniformNoise/AddUniformNoiseIntegerType.java

@@ -0,0 +1,100 @@
+/*
+ * #%L
+ * ImageJ software for multidimensional image processing and analysis.
+ * %%
+ * Copyright (C) 2014 - 2018 ImageJ developers.
+ * %%
+ * 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
+ * ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDERS OR CONTRIBUTORS BE
+ * LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+ * CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
+ * SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
+ * INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
+ * CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+ * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
+ * POSSIBILITY OF SUCH DAMAGE.
+ * #L%
+ */
+
+package net.imagej.ops.filter.addUniformNoise;
+
+import java.math.BigInteger;
+
+import net.imagej.ops.Ops;
+import net.imagej.ops.special.computer.AbstractUnaryComputerOp;
+import net.imglib2.type.numeric.IntegerType;
+
+import org.scijava.Priority;
+import org.scijava.plugin.Parameter;
+import org.scijava.plugin.Plugin;
+import org.scijava.util.MersenneTwisterFast;
+
+/**
+ * Adds a pseudorandomly generated value {@code x} to a {@link IntegerType}
+ * {@code I}, such that {@code x} is (inclusively) bounded by {@code rangeMin}
+ * and {@code rangeMax} parameters, i.e. {@code rangeMin <= x <= rangeMax}.
+ * 
+ * @author Gabe Selzer
+ */
+@Plugin(type = Ops.Filter.AddUniformNoise.class, priority = Priority.HIGH)
+public class AddUniformNoiseIntegerType<I extends IntegerType<I>> extends
+	AbstractUnaryComputerOp<I, I> implements Ops.Filter.AddUniformNoise
+{
+
+	/**
+	 * The greatest that an input value can be decreased.
+	 */
+	@Parameter
+	private long rangeMin;
+
+	/**
+	 * The greatest that an input value can be <b> increased </b>
+	 */
+	@Parameter
+	private long rangeMax;
+
+	/**
+	 * If false, the Op will wrap outputs that are outside of the type bounds,
+	 * instead of clamping them
+	 */
+	@Parameter(required = false)
+	private boolean clampOutput = true;
+
+	@Parameter(required = false)
+	private long seed = 0xabcdef1234567890L;
+	private long range;
+
+	private MersenneTwisterFast rng;
+
+	@Override
+	public void initialize() {
+		if (rng == null) rng = new MersenneTwisterFast(seed);
+		if (rangeMax < rangeMin) {
+			long temp = rangeMax;
+			rangeMax = rangeMin;
+			rangeMin = temp;
+		}
+		// MersenneTwister can only generate numbers that can fit into a long.
+		range = Math.subtractExact(rangeMax + 1, rangeMin);
+	}
+
+	@Override
+	public void compute(I input, I output) {
+		final double newVal = rng.nextLong(range) + rangeMin + input
+			.getRealDouble();
+
+		AddUniformNoiseRealType.setOutput(newVal, clampOutput, output);
+	}
+
+}

src/main/java/net/imagej/ops/filter/addUniformNoise/AddUniformNoiseRealType.java

@@ -81,17 +81,39 @@ public void initialize() {
 		if (!Double.isFinite(rangeMax - rangeMin))
 			throw new IllegalArgumentException("range not allowed by op.");
 	}
-
+	
 	@Override
 	public void compute(I input, I output) {
 		final double newVal = (rangeMax - rangeMin) * rng.nextDouble(true, true) +
 			rangeMin + input.getRealDouble();
-		if (newVal > input.getMaxValue())
-			output.setReal(input.getMaxValue());
-		else if (newVal < input.getMinValue())
-			output.setReal(input.getMinValue());
-		else
-			output.setReal(newVal);
+		
+		setOutput(newVal, true, output);
+	}
+	
+	protected static <I extends RealType<I>> void setOutput(double newVal, boolean clampOutput, I output) {
+		// clamp output
+		if (clampOutput) {
+			output.setReal(Math.max(output.getMinValue(), Math.min(output.getMaxValue(),
+				newVal)));
+		}
+
+		// wrap output
+		else {
+			double outVal = newVal;
+			// when output larger than max value, add difference of output and max
+			// value to the min value
+			while (outVal > output.getMaxValue()) {
+				outVal = output.getMinValue() + (outVal - output.getMaxValue() - 1);
+			}
+			// when output smaller than min value, subtract difference of output and
+			// min value from the max value
+			while (outVal < output.getMinValue()) {
+				outVal = output.getMaxValue() - (output.getMinValue() - outVal - 1);
+			}
+
+			output.setReal(outVal);
+		}
+		
 	}
 
 }