/*
 * #%L
 * ImageJ software for multidimensional image processing and analysis.
 * %%
 * Copyright (C) 2014 - 2016 Board of Regents of the University of
 * Wisconsin-Madison, University of Konstanz and Brian Northan.
 * %%
 * 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.threshold.apply;

import net.imagej.ops.map.neighborhood.MapNeighborhoodWithCenter;
import net.imagej.ops.special.computer.AbstractUnaryComputerOp;
import net.imagej.ops.threshold.LocalThresholdMethod;
import net.imglib2.IterableInterval;
import net.imglib2.RandomAccessibleInterval;
import net.imglib2.algorithm.neighborhood.Shape;
import net.imglib2.outofbounds.OutOfBoundsFactory;
import net.imglib2.type.logic.BitType;
import net.imglib2.type.numeric.RealType;
import net.imglib2.view.Views;

import org.scijava.plugin.Parameter;

/**
 * Apply a local thresholding method to an image, optionally using a out of
 * bounds strategy.
 * 
 * @author Jonathan Hale (University of Konstanz)
 * @author Martin Horn (University of Konstanz)
 * @author Stefan Helfrich (University of Konstanz)
 */
//@Plugin(type = Ops.Threshold.Apply.class)
public class LocalThreshold<T extends RealType<T>>
	extends
	AbstractUnaryComputerOp<RandomAccessibleInterval<T>, IterableInterval<BitType>>
//	implements Ops.Threshold.Apply
{

//	@Parameter
	protected LocalThresholdMethod<T> method;

	@Parameter
	private Shape shape;

	@Parameter(required = false)
	private OutOfBoundsFactory<T, RandomAccessibleInterval<T>> outOfBounds;

	protected MapNeighborhoodWithCenter<T, BitType> mapper;	

	@SuppressWarnings("unchecked")
	@Override
	public void initialize() {
		mapper = ops().op(MapNeighborhoodWithCenter.class, out(), extend(in(),	outOfBounds), method, shape);
	}

	@Override
	public void compute1(final RandomAccessibleInterval<T> input,
		final IterableInterval<BitType> output)
	{
		mapper.compute1(extend(input, outOfBounds), output);
	}

	/**
	* Extends an input using an {@link OutOfBoundsFactory} if available,
	* otherwise returns the unchanged input.
	*
	* @param in {@link RandomAccessibleInterval} that is to be extended
	* @param outOfBounds the factory that is used for extending
	* @return {@link RandomAccessibleInterval} extended using the
	*         {@link OutOfBoundsFactory}
	*/
	public static <T> RandomAccessibleInterval<T> extend(
		final RandomAccessibleInterval<T> in,
		final OutOfBoundsFactory<T, RandomAccessibleInterval<T>> outOfBounds)
	{
		// FIXME Move this method to a static utility class
		return outOfBounds == null ? in : Views.interval((Views.extend(in,
			outOfBounds)), in);
	}
}

@@ -2354,52 +2354,8 @@
  */%0A
-//@Plugin(type = Ops.Threshold.Apply.class)%0A
 publ
@@ -2400,18 +2400,17 @@
 Type%3CT%3E%3E
-%0A%09
+ 
 extends%0A
@@ -2494,58 +2494,10 @@
 e%3E%3E%0A
-//%09implements Ops.Threshold.Apply%0A%7B%0A%0A//%09@Parameter
+%7B%0A
 %0A%09pr

Clean up code