/*
 * #%L
 * ImageJ software for multidimensional image processing and analysis.
 * %%
 * Copyright (C) 2009 - 2014 Board of Regents of the University of
 * Wisconsin-Madison, Broad Institute of MIT and Harvard, and Max Planck
 * Institute of Molecular Cell Biology and Genetics.
 * %%
 * 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
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 */

package imagej.ops.threshold;

import imagej.ops.Copyable;
import imagej.ops.Op;
import imagej.ops.OpService;
import imagej.ops.misc.MinMax;

import java.util.List;

import net.imglib2.IterableInterval;
import net.imglib2.histogram.Histogram1d;
import net.imglib2.histogram.Real1dBinMapper;
import net.imglib2.type.numeric.RealType;

import org.scijava.ItemIO;
import org.scijava.plugin.Parameter;

/**
 * An algorithm for thresholding an image into two classes of pixels from its
 * histogram.
 */
public abstract class ThresholdMethod<T extends RealType<T>> implements Op,
	Copyable
{

	@Parameter
	private IterableInterval<T> img;

	@Parameter(required = false)
	private Histogram1d<T> hist;

	@Parameter
	private OpService opService;

	@Parameter(type = ItemIO.OUTPUT)
	private T threshold;

	@Override
	public void run() {
		if (hist == null) {
			hist = createHistogram();
		}

		threshold = img.firstElement().createVariable();

		getThreshold(hist, threshold);
	}

	private final Histogram1d<T> createHistogram() {
		final List<Object> res = (List<Object>) opService.run(new MinMax<T>(), img);
		return new Histogram1d<T>(new Real1dBinMapper<T>(((T) res.get(0))
			.getRealDouble(), ((T) res.get(1)).getRealDouble(), 256, false));
	}

	/**
	 * Calculates the threshold index from an unnormalized histogram of data.
	 * Returns -1 if the threshold index cannot be found.
	 */
	protected abstract void getThreshold(Histogram1d<T> histogram, T threshold);

	@Override
	public abstract ThresholdMethod<T> copy();

}

@@ -2175,17 +2175,24 @@
 Op,%0A
-%09
+        
 Copyable
 %0A%7B%0A%0A
@@ -2191,13 +2191,16 @@
 able
-%0A%7B%0A%0A%09
+ %7B%0A%0A    
 @Par
@@ -2198,33 +2198,36 @@
 %0A    @Parameter%0A
-%09
+    
 private Iterable
@@ -2248,70 +2248,12 @@
 g;%0A%0A
-%09@Parameter(required = false)%0A%09private Histogram1d%3CT%3E hist;%0A%0A%09
+    
 @Par
@@ -2259,17 +2259,20 @@
 rameter%0A
-%09
+    
 private 
@@ -2293,17 +2293,20 @@
 rvice;%0A%0A
-%09
+    
 @Paramet
@@ -2330,17 +2330,20 @@
 OUTPUT)%0A
-%09
+    
 private 
@@ -2356,17 +2356,20 @@
 shold;%0A%0A
-%09
+    
 @Overrid
@@ -2366,25 +2366,28 @@
   @Override%0A
-%09
+    
 public void 
@@ -2398,33 +2398,31 @@
 ) %7B%0A
-%09%09if (hist == null) %7B%0A%09%09%09
+        Histogram1d%3CT%3E 
 hist
@@ -2447,15 +2447,17 @@
 ();%0A
-%09%09%7D%0A%0A%09%09
+%0A        
 thre
@@ -2502,18 +2502,24 @@
 ble();%0A%0A
-%09%09
+        
 getThres
@@ -2541,21 +2541,27 @@
 shold);%0A
-%09%7D%0A%0A%09
+    %7D%0A%0A    
 private 
@@ -2601,18 +2601,24 @@
 ram() %7B%0A
-%09%09
+        
 final Li
@@ -2633,16 +2633,32 @@
 t%3E res =
+%0A               
  (List%3CO
@@ -2664,17 +2664,16 @@
 Object%3E)
- 
 opServic
@@ -2701,18 +2701,24 @@
 , img);%0A
-%09%09
+        
 return n
@@ -2758,21 +2758,37 @@
 pper%3CT%3E(
+%0A                
 ((T)
- 
 res.get(
@@ -2794,12 +2794,8 @@
 (0))
-%0A%09%09%09
 .get
@@ -2811,14 +2811,29 @@
 e(),
+%0A               
  ((T)
- 
 res.
@@ -2875,18 +2875,27 @@
 ));%0A
-%09%7D%0A%0A%09/**%0A%09
+    %7D%0A%0A    /**%0A    
  * C
@@ -2964,17 +2964,20 @@
 f data.%0A
-%09
+    
  * Retur
@@ -3026,14 +3026,20 @@
 nd.%0A
-%09 */%0A%09
+     */%0A    
 prot
@@ -3112,17 +3112,20 @@
 hold);%0A%0A
-%09
+    
 @Overrid
@@ -3130,9 +3130,12 @@
 ide%0A
-%09
+    
 publ

remove optional (required=false) parameter from ThresholdMethod