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 * Image processing operations for SciJava Ops.
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package org.scijava.ops.image.threshold.isoData;

import org.scijava.ops.image.threshold.AbstractComputeThresholdHistogram;
import net.imglib2.histogram.Histogram1d;
import net.imglib2.type.numeric.RealType;

import org.scijava.ops.spi.OpExecutionException;

// NB - this plugin adapted from Gabriel Landini's code of his AutoThreshold
// plugin found in Fiji (version 1.14).

/**
 * Implements an IsoData (intermeans) threshold method by Ridler {@literal &}
 * Calvard.
 *
 * @author Barry DeZonia
 * @author Gabriel Landini
 * @implNote op names='threshold.isoData', priority='100.'
 */
public class ComputeIsoDataThreshold> extends
	AbstractComputeThresholdHistogram
{

	/**
	 * TODO
	 *
	 * @param hist the {@link Histogram1d}
	 * @return the IsoData threshold value
	 */
	@Override
	public long computeBin(final Histogram1d hist) {
		final long[] histogram = hist.toLongArray();
		return computeBin(histogram);
	}

	/**
	 * Also called intermeans

	 * Iterative procedure based on the isodata algorithm [T.W. Ridler,

	 * S. Calvard, Picture thresholding using an iterative selection method,

	 * IEEE Trans. System, Man and Cybernetics, SMC-8 (1978) 630-632.]

	 * The procedure divides the image into objects and background by taking

	 * an

	 * initial threshold, then the averages of the pixels at or below the

	 * threshold and pixels above are computed. The averages of those two

	 * values

	 * are computed, the threshold is incremented and the process is

	 * repeated

	 * until the threshold is larger than the composite average. That is,

	 * threshold = (average background + average objects)/2

	 * The code in ImageJ that implements this function is the

	 * getAutoThreshold() method in the ImageProcessor class.

	 * 

	 * From: Tim Morris ([email protected])

	 * Subject: Re: Thresholding method?

	 * posted to sci.image.processing on 1996/06/24

	 * The algorithm implemented in NIH Image sets the threshold as that

	 * grey

	 * value, G, for which the average of the averages of the grey values

	 * below and above G is equal to G. It does this by initialising G to

	 * the

	 * lowest sensible value and iterating:

	 * 

	 * L = the average grey value of pixels with intensities {@literal <} G

	 * H = the average grey value of pixels with intensities {@literal >} G

	 * is G = (L + H)/2?

	 * yes ={@literal >} exit

	 * no ={@literal >} increment G and repeat

	 * 

	 * There is a discrepancy with IJ because of slightly different methods
	 */
	public static long computeBin(final long[] histogram) {
		long l, toth, totl, h;
		int i, g = 0;
		for (i = 1; i < histogram.length; i++) {
			if (histogram[i] > 0) {
				g = i + 1;
				break;
			}
		}
		while (true) {
			l = 0;
			totl = 0;
			for (i = 0; i < g; i++) {
				totl = totl + histogram[i];
				l = l + (histogram[i] * i);
			}
			h = 0;
			toth = 0;
			for (i = g + 1; i < histogram.length; i++) {
				toth += histogram[i];
				h += (histogram[i] * i);
			}
			if (totl > 0 && toth > 0) {
				l /= totl;
				h /= toth;
				if (g == (int) Math.round((l + h) / 2.0)) break;
			}
			g++;
			if (g > histogram.length - 2) {
				throw new OpExecutionException("IsoData Threshold not found.");
			}
		}
		return g;
	}

}