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

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

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

/**
 * Implements a percentile threshold method by Doyle.
 *
 * @author Barry DeZonia
 * @author Gabriel Landini
 * @implNote op names='threshold.percentile', priority='100.'
 */
public class ComputePercentileThreshold<T extends RealType<T>> extends
	AbstractComputeThresholdHistogram<T>
{

	/**
	 * @param hist the {@link Histogram1d}
	 * @return the Percentile threshold value
	 */
	@Override
	public long computeBin(final Histogram1d<T> hist) {
		final var histogram = hist.toLongArray();
		return computeBin(histogram);
	}

	/**
	 * W. Doyle,"Operation useful for similarity-invariant pattern
	 * recognition,"<br>
	 * Journal of the Association for Computing Machinery, vol. 9,pp.<br>
	 * 259-267,<br>
	 * 1962.<br>
	 * ported to ImageJ plugin by G.Landini from Antti Niemisto's Matlab<br>
	 * code<br>
	 * (relicensed BSD 2-12-13)<br>
	 * Original Matlab code Copyright (C) 2004 Antti Niemisto<br>
	 * See http://www.cs.tut.fi/~ant/histthresh/ for an excellent slide<br>
	 * presentation and the original Matlab code.
	 */
	public static long computeBin(final long[] histogram) {
        var threshold = -1;
		final var ptile = 0.5; // default fraction of foreground pixels
		final var avec = new double[histogram.length];

		for (var i = 0; i < histogram.length; i++)
			avec[i] = 0.0;

		final var total = partialSum(histogram, histogram.length - 1);
        var temp = 1.0;
		for (var i = 0; i < histogram.length; i++) {
			avec[i] = Math.abs((partialSum(histogram, i) / total) - ptile);
			// IJ.log("Ptile["+i+"]:"+ avec[i]);
			if (avec[i] < temp) {
				temp = avec[i];
				threshold = i;
			}
		}
		return threshold;
	}

	private static double partialSum(final long[] y, final int j) {
		double x = 0;
		for (var i = 0; i <= j; i++)
			x += y[i];
		return x;
	}

}
