package com.elphel.imagej.common;

/**
 **
 ** DoubleFHT - Determine simulation pattern parameters to match
 ** the acquired image
 **
 ** Copyright (C) 2010-2011 Elphel, Inc.
 **
 ** -----------------------------------------------------------------------------**
 **
 **  MatchSimulatedPattern.java is free software: you can redistribute it and/or modify
 **  it under the terms of the GNU General Public License as published by
 **  the Free Software Foundation, either version 3 of the License, or
 **  (at your option) any later version.
 **
 **  This program is distributed in the hope that it will be useful,
 **  but WITHOUT ANY WARRANTY; without even the implied warranty of
 **  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 **  GNU General Public License for more details.
 **
 **  You should have received a copy of the GNU General Public License
 **  along with this program.  If not, see <http://www.gnu.org/licenses/>.
 ** -----------------------------------------------------------------------------**
 **
 */
import java.util.ArrayList;
import java.util.Arrays;
import java.util.List;

import ij.IJ;
import ij.process.FHT;

//import ij.plugin.FFT;
//import ij.plugin.ContrastEnhancer;
//import java.awt.image.ColorModel;
//import ij.plugin.*;
public class DoubleFHT {

//	private boolean isFrequencyDomain;
	private int maxSize = 20;
	private double[] freqMask = null; // frequency mask cache, will be reused if all parameters are the same
//	private int freqMaskN=0;
//	private double freqHighPass=0;
//	private double freqLowPass=0;
	private double[] freqPass = null; // {freqHighPass,freqLowPass};
	private int maxN = -1; // undefined
	private int ln2 = -1; // undefined
	private double[] C; // TODO: make arrays for each reasonable FHT size (or use cache)
	private double[] S;
	private int[] bitrev;
	private double[] tempArr;
	public boolean showProgress = false;
	private double[][][] CS_cache = new double[maxSize][][]; // CS cache for different sizes,
	private double[][] freqMask_cache = new double[maxSize][]; // frequency mask cache, will be reused if all parameters
																// are the same
	private double[][] freqPass_cache = new double[maxSize][]; // cache for low/high frequencies
	private int[][] bitrev_cache = new int[maxSize][];
	private double[][] hamming1d = new double[maxSize][]; // will cache 1d Hamming window;
	private double[] hamming1dMin = new double[maxSize]; // will cache 1d Hamming window;
	private double[][] gaussian1d = new double[maxSize][]; // will cache 1d Gaussian window;
	private double[] gaussian1dWidths = new double[maxSize]; // will cache 1d Gaussian window;

	private double[] translateFHT = null; // cached array for sub-pixel translate
	private double[] translateFHTdXY = null;
	private int translateFHTN = 0;
	public boolean debug = false;

	public DoubleFHT() {
		this.C = null;
		this.S = null;
		for (int i = 0; i < CS_cache.length; i++) {
			this.CS_cache[i] = null;
			this.freqMask_cache[i] = null;
			this.freqPass_cache[i] = null;
			this.bitrev_cache[i] = null;
			this.hamming1d[i] = null;
			this.gaussian1d[i] = null;
			this.gaussian1dWidths[i] = -1.0;
		}

	}

	public boolean powerOf2Size(double[] data) {
		return powerOf2Size(data.length);
	}

	public boolean powerOf2Size(int len) {
		int i = 4;
		while (i < len)
			i *= 4;
		return i == len;
	}

	public void swapQuadrants(double[] data) {
		if (data == null)
			return;
		int size = (int) Math.sqrt(data.length);
		int hsize = size / 2;
		int shift03 = (size + 1) * hsize;
		int shift12 = (size - 1) * hsize;
		int i, j, index;
		double d;
		for (i = 0; i < hsize; i++)
			for (j = 0; j < hsize; j++) {
				index = i * size + j;
				d = data[index];
				data[index] = data[index + shift03];
				data[index + shift03] = d;
				index += hsize;
				d = data[index];
				data[index] = data[index + shift12];
				data[index + shift12] = d;
			}
	}

	/*
	 * Performs a forward transform, converting this image into the frequency
	 * domain. The image contained in data must be square and its width must be a
	 * power of 2.
	 */
	public boolean transform(double[] data) {
		return transform(data, false);
	}

	/*
	 * Performs an inverse transform, converting this image into the space domain.
	 * The image contained in data must be square and its width must be a power of
	 * 2.
	 */
	public boolean inverseTransform(double[] data) {
		return transform(data, true);
	}

	/*
	 * Returns an inverse transform of this image, which is assumed to be in the
	 * frequency domain.
	 */
	public boolean transform(double[] data, boolean inverse) {
		// IJ.log("transform: "+maxN+" "+inverse);
		updateMaxN(data);
		rc2DFHT(data, inverse, this.maxN);
		return true;
	}

	public double[] createFrequencyFilter(double highPass, double lowPass) {
		return createFrequencyFilter(null, highPass, lowPass);
	}

	public double[] createFrequencyFilter(double[] data, // int n,
			double highPass, double lowPass) {
		if (data != null)
			updateMaxN(data);
//		 int n;

		if ((this.freqMask != null) && (this.freqPass[0] == highPass) && (this.freqPass[1] == lowPass))
			return this.freqMask;
		this.freqMask = new double[(this.maxN + 1) * this.maxN / 2 + 1];
		double[] lo = new double[this.maxN];
		double[] hi = new double[this.maxN];
		int i, j;
		double kHi = (highPass > 0) ? (0.5 / highPass / highPass) : 0;
		double kLo = (lowPass > 0) ? (1.0 / lowPass / lowPass / this.maxN / this.maxN) : 0;
		double mx2;
//    System.out.println("createFrequencyFilter: highPass ="+highPass+ " lowPass= "+lowPass+ " kHi= "+kHi+ " kLo= "+kLo);

		for (i = 0; i < this.maxN; i++) {
			mx2 = -i * i;
			hi[i] = (kHi > 0) ? Math.exp(mx2 * kHi) : 0.0;
			lo[i] = (kLo > 0) ? Math.exp(mx2 * kLo) : 1.0;
		}
// more precise version should add data from 4 corners, below is the simple version that may have discontinuities in the middle
		for (int index = 0; index < this.freqMask.length; index++) {
			i = index / this.maxN;
			j = index % this.maxN;
			if (j > this.maxN / 2)
				j = this.maxN - j;
			this.freqMask[index] = (1.0 - hi[i] * hi[j]) * lo[i] * lo[j];
		}
		this.freqPass = new double[2];
		this.freqPass[0] = highPass;
		this.freqPass[1] = lowPass;
		return this.freqMask;
	}

	/**
	 * Shift the data by phase modification in the frequency domain
	 * 
	 * @param data square 2**N array in line scan order. Data is modified in-place
	 * @param dx   amount of the horizontal shift (left) in pixels
	 * @param dy   amount of the vertical shift (down) in pixels
	 * @return modified (shifted) data TODO: add shift+up-sample combination
	 */
	public double[] shift(double[] data, double dx, double dy) {
		return shift(data, 1, dx, dy);
	}

	/**
	 * Upsample input array by padding in the frequency domain
	 * 
	 * @param first input square power of 2 array
	 * @param scale upsample scale (power of 2)
	 * @return upsampled array, scan
	 */
	public double[] upsample(double[] first, int scale) {
		return shift(first, scale, 0.0, 0.0);
	}

	/**
	 * Upsample data and shift it by phase modification in the frequency domain
	 * 
	 * @param data  square 2**N array in line scan order. Data is modified in-place
	 * @param scale upsample scale
	 * @param dx    amount of the horizontal shift (left) in pixels (before scaling)
	 * @param dy    amount of the vertical shift (down) in pixels (before scaling)
	 * @return modified (shifted) data
	 */

	public double[] shift(double[] data, int scale, double dx, double dy) {
		if ((scale == 0) && (dx == 0.0) && (dy == 0.0))
			return data;
		updateMaxN(data);
		swapQuadrants(data);
		if (!transform(data, false))
			return null; // direct FHT
		double[] result;
		// scale first
		if (scale > 1) {
			int halfN = this.maxN / 2;
			int shift = this.maxN * (scale - 1);
			int scaledN = this.maxN * scale;
			result = new double[data.length * scale * scale];
			for (int i = 0; i < result.length; i++)
				result[i] = 0.0;
			double scale2 = scale * scale;
			for (int i = 0; i < data.length; i++) {
				int iy = i / this.maxN;
				int ix = i % this.maxN;
				if (ix > halfN)
					ix += shift;
				if (iy > halfN)
					iy += shift;
				result[scaledN * iy + ix] = scale2 * data[i];
			}
			updateMaxN(result);
		} else {
			result = data;
		}
		// now shift
		if ((dx != 0.0) || (dy != 0.0)) {
			dx *= scale;
			dy *= scale;
			double sX = 2 * Math.PI * dx / this.maxN;
			double sY = 2 * Math.PI * dy / this.maxN;
			int halfN = this.maxN / 2;
			double[] cosDX = new double[this.maxN];
			double[] sinDX = new double[this.maxN];
			double[] cosDY = new double[halfN + 1];
			double[] sinDY = new double[halfN + 1];
			for (int i = 0; i <= halfN; i++) { // need less?
				cosDX[i] = Math.cos(sX * i);
				sinDX[i] = Math.sin(sX * i);
				cosDY[i] = Math.cos(sY * i);
				sinDY[i] = Math.sin(sY * i);
			}
			for (int i = 1; i < halfN; i++) { // need less?
				cosDX[this.maxN - i] = cosDX[i];
				sinDX[this.maxN - i] = -sinDX[i];
			}
			for (int row = 0; row <= halfN; row++) {
				int rowMod = (this.maxN - row) % this.maxN;
				int maxCol = (row < halfN) ? (this.maxN - 1) : halfN;
				for (int col = 0; col <= maxCol; col++) {
					int colMod = (this.maxN - col) % this.maxN;
					int index = row * this.maxN + col;
					int indexMod = rowMod * this.maxN + colMod;
					double re = 0.5 * (data[index] + data[indexMod]);
					double im = 0.5 * (data[index] - data[indexMod]);
					if ((col == halfN) || (row == halfN))
						im = 0;
					double cosDelta = cosDX[col] * cosDY[row] - sinDX[col] * sinDY[row]; // cos(deltaX)*cos(deltaY)-sin(deltaX)*sin(deltaY)
					double sinDelta = sinDX[col] * cosDY[row] + cosDX[col] * sinDY[row]; // sin(deltaX)*cos(deltaY)+cos(deltaX)*sin(deltaY)
					double reMod = re * cosDelta - im * sinDelta;
					double imMod = re * sinDelta + im * cosDelta;
					data[index] = reMod + imMod;
					data[indexMod] = reMod - imMod;
				}
			}
		}
		if (!transform(result, true))
			return null; // inverse FHT
		swapQuadrants(result);
		return result;
	}

	/**
	 * Invert kernel for deconvolutions. Kernel is assumed to fade near edges
	 * @param data     source kernel, square, power of 2 sides. Data is destroyed
	 * @param fat_zero add to denominator to prevent noise amplification
	 * @param highPassSigma high-pass sigma to create frequency filter or 0
	 * @param lowPassSigma  low-pass sigma to create frequency filter or 0
	 * @return inverted kernel
	 */
	public double [] invert (
			double [] data,
			double fat_zero,
			double highPassSigma,
			double lowPassSigma
			) {
		double [] filter= null;
		if ((highPassSigma> 0.0) || (lowPassSigma> 0.0)) {
			updateMaxN(data);
			createFrequencyFilter(highPassSigma, lowPassSigma); // for repetitive calls will reuse mask
			filter =this.freqMask;
		}
		return invert (data, fat_zero, filter);
		
	}
	
	/**
	 * Invert kernel for deconvolutions. Kernel is assumed to fade near edges
	 * @param data     source kernel, square, power of 2 sides. Data is destroyed
	 * @param fat_zero add to denominator to prevent noise amplification
	 * @param filter low-pass/high-pass filter or null
	 * @return inverted kernel
	 */
	public double [] invert (
			double [] data, // destroyed
			double fat_zero,
			double [] filter
			) {
		updateMaxN(data);
		int size = (int) Math.sqrt(data.length);
		double nominator_FD_value = size*size; // fill FD of the nominator. what is the best value?
		double [] nominator_FD = new double[data.length];
		Arrays.fill(nominator_FD, nominator_FD_value);
		swapQuadrants(data);
		if (!transform(data,false))  return null; // direct FHT
		double [] inverted = divide(nominator_FD,data, fat_zero);
		if (filter != null) {
			multiplyByReal(inverted, filter);
		}
		transform(inverted, true); // inverse transform
		swapQuadrants(inverted);
		return inverted;
	}
	

	
	/* calculates correlation, destroys original arrays */

	public double[] correlate(double[] first, double[] second, double highPassSigma, double lowPassSigma,
			double phaseCoeff) {
		updateMaxN(first);
		createFrequencyFilter(highPassSigma, lowPassSigma); // for repetitive calls will reuse mask
		if (this.freqMask.length < first.length / 2) {
			System.out.println("Error: first.length=" + first.length + " second.length=" + second.length + " this.maxN="
					+ this.maxN + " this.freqMask.length=" + this.freqMask.length);
		}
		return correlate(first, second, phaseCoeff, this.freqMask);
	}

	public double[] correlate(double[] first, double[] second, double phaseCoeff) {
		return correlate(first, second, phaseCoeff, null);
	}

	public double[] correlate(double[] first, double[] second, double phaseCoeff, double[] filter) {
		if (phaseCoeff <= 0.0)
			return correlate(first, second, filter);
		else
			return phaseCorrelate(first, second, phaseCoeff, filter);
	}

	// asymmetrical - will divide by squared second amplitude (pattern to match)
	public double[] phaseCorrelate( // old
			double[] first, double[] second, double phaseCoeff, double[] filter) { // high/low pass filtering
		if (first.length != second.length) {
			IJ.showMessage("Error", "Correlation arrays should be the same size");
			return null;
		}
// 	    	 System.out.println("phaseCorrelate, phaseCoeff="+phaseCoeff);

		swapQuadrants(first);
		swapQuadrants(second);
		if (!transform(first, false))
			return null; // direct FHT
		if (!transform(second, false))
			return null; // direct FHT
		first = phaseMultiply(first, second, phaseCoeff); // correlation, not convolution
		if (filter != null)
			multiplyByReal(first, filter);
		transform(first, true); // inverse transform
		swapQuadrants(first);
		return first;
	}

	public double[] phaseCorrelate(double[] first, double phaseCoeff, double high_pass, double low_pass) { // high/low
																											// pass
																											// filtering
		return phaseCorrelate(first, phaseCoeff, high_pass, low_pass, null);
	}

	public double[] phaseCorrelate(double[] first, double phaseCoeff, double high_pass, double low_pass, // high/low
																											// pass
																											// filtering
			double[] fht_save) { // null-OK
		updateMaxN(first);
		double[] filter = null;
		if ((high_pass > 0) || (low_pass > 0)) {
			filter = createFrequencyFilter(high_pass, low_pass);
		}
		return phaseCorrelate(first, phaseCoeff, filter, fht_save);
	}

	public double[] phaseCorrelate( // never
			double[] first, double phaseCoeff, double[] filter) { // high/low pass filtering
		return phaseCorrelate(first, phaseCoeff, filter, null);
	}

	public double[] phaseCorrelate(double[] first, double phaseCoeff, double[] filter, // high/low pass filtering
			double[] fht_save) { // null-OK
		updateMaxN(first);
		swapQuadrants(first);
		if (!transform(first, false))
			return null; // direct FHT
		if (fht_save != null) {
			System.arraycopy(first, 0, fht_save, 0, first.length);
		}
		first = phaseMultiplyNorm(first, first, phaseCoeff); // correlation, not convolution
		if (filter != null)
			multiplyByReal(first, filter);
		transform(first, true); // inverse transform
		swapQuadrants(first);
		return first;
	}

	public double[] phaseCorrelate(double[] first, double[] second, double phaseCoeff, double highPassSigma,
			double lowPassSigma, double[] first_save, double[] second_save) { // null-OK
		updateMaxN(first);
		double[] filter = null;
		if ((highPassSigma > 0) || (lowPassSigma > 0)) {
			filter = createFrequencyFilter(highPassSigma, lowPassSigma);
		}
		return phaseCorrelate(first, second, phaseCoeff, filter, // high/low pass filtering
				first_save, second_save);

	}

	public double[] phaseCorrelate( // new
			double[] first, double[] second, double phaseCoeff, double[] filter, // high/low pass filtering
			double[] first_save, double[] second_save) { // null-OK
		if (first.length != second.length) {
			IJ.showMessage("Error", "Correlation arrays should be the same size");
			return null;
		}
		updateMaxN(first);
		swapQuadrants(first);
		swapQuadrants(second);
		if (!transform(first, false))
			return null; // direct FHT
		if (!transform(second, false))
			return null; // direct FHT
		if (first_save != null)
			System.arraycopy(first, 0, first_save, 0, first.length);
		if (second_save != null)
			System.arraycopy(second, 0, second_save, 0, second.length);

		first = phaseMultiplyNorm(first, second, phaseCoeff); // correlation, not convolution
		if (filter != null)
			multiplyByReal(first, filter);
		transform(first, true); // inverse transform
		swapQuadrants(first);
		return first;
	}

	/**
	 * Transform pattern once, and then use FD of the pattern for each overlapping
	 * image tile
	 * 
	 * @param second pattern to be transform
	 * @return transformed pattern ( the original is also modified)
	 */
	public double[] transformPattern( // new
			double[] second) { // null-OK
		updateMaxN(second);
		swapQuadrants(second);
		if (!transform(second, false))
			return null; // direct FHT
		return second;
	}

	/**
	 * Phase correlate with pattern, that is transformed separately with
	 * transformPattern()
	 * 
	 * @param first      square array to be phase-correlated, modified but not with
	 *                   result!
	 * @param secondFD   pattern already transformed to FD
	 * @param phaseCoeff 0 - regular correlation, 1.0 - pure phase correlation
	 * @param filter     frequency filter or null
	 * @param first_save null or array to accommodate FD of the first array before
	 *                   updating it with correlation
	 * @return phase correlation, first still contains original transformed!
	 */
	public double[] phaseCorrelatePattern( // new
			double[] first, double[] secondFD, double phaseCoeff, double[] filter, // high/low pass filtering
			double[] first_save) { // null-OK
		if (first.length != secondFD.length) {
			IJ.showMessage("Error", "Correlation arrays should be the same size");
			return null;
		}
		updateMaxN(first);
		swapQuadrants(first);
		if (!transform(first, false))
			return null; // direct FHT
		if (first_save != null)
			System.arraycopy(first, 0, first_save, 0, first.length);

		first = phaseMultiplyNorm(first, secondFD, phaseCoeff); // correlation, not convolution
		if (filter != null)
			multiplyByReal(first, filter);
		transform(first, true); // inverse transform
		swapQuadrants(first);
		return first;
	}

	/**
	 * Convolve with pattern, that is transformed separately with transformPattern()
	 * 
	 * @param first      square array to be phase-correlated, modified but not with
	 *                   result!
	 * @param secondFD   pattern already transformed to FD
	 * @param filter     frequency filter or null
	 * @param first_save null or array to accommodate FD of the first array before
	 *                   updating it with correlation
	 * @return convolution result, first still contains original transformed!
	 */

	public double[] convolvePattern( // new
			double[] first, double[] secondFD, double[] filter, // high/low pass filtering
			double[] first_save) { // null-OK
		if (first.length != secondFD.length) {
			IJ.showMessage("Error", "Correlation arrays should be the same size");
			return null;
		}
		updateMaxN(first);
		swapQuadrants(first);
		if (!transform(first, false))
			return null; // direct FHT
		if (first_save != null)
			System.arraycopy(first, 0, first_save, 0, first.length);
		first = multiply(first, secondFD, false); // convolution, not correlation
		if (filter != null)
			multiplyByReal(first, filter);
		transform(first, true); // inverse transform
		swapQuadrants(first);
		return first;
	}

//
	public double[] applyFreqFilter(double[] first, double[] filter) {
		if (filter == null)
			filter = this.freqMask;
		if (this.freqMask.length < first.length / 2) {
			System.out.println("Error in applyFreqFilter(): first.length=" + first.length + " this.maxN=" + this.maxN
					+ " filter.length=" + filter.length);
		}
		multiplyByReal(first, filter);
		return first;
	}

// modify - instead of a sigma - correlationHighPassSigma (0.0 - regular correlation, 1.0 - phase correlation)

	public double[] correlate(double[] first, double[] second) {
		return correlate(first, second, null);
	}

	public double[] correlate(double[] first, double[] second, double[] filter) { // high/low pass filtering
//    	 System.out.println("correlate");
		if (first.length != second.length) {
			IJ.showMessage("Error", "Correlation arrays should be the same size");
			return null;
		}
		swapQuadrants(first);
		swapQuadrants(second);
		if (!transform(first, false))
			return null; // direct FHT
		if (!transform(second, false))
			return null; // direct FHT
		first = multiply(first, second, true); // correlation, not convolution
		if (filter != null)
			multiplyByReal(first, filter);
		transform(first, true); // inverse transform
		swapQuadrants(first);
		return first;
	}

	public double[] convolve(double[] first, double[] second) {
		return convolve(first, second, null);
	}

	public double[] convolve(double[] first, double[] second, double[] filter) { // high/low pass filtering
		// System.out.println("correlate");
		if (first.length != second.length) {
			IJ.showMessage("Error", "Correlation arrays should be the same size");
			return null;
		}
		swapQuadrants(first);
		swapQuadrants(second);
		if (!transform(first, false))
			return null; // direct FHT
		if (!transform(second, false))
			return null; // direct FHT
		first = multiply(first, second, false); // convolution, not correlation
		if (filter != null)
			multiplyByReal(first, filter);
		transform(first, true); // inverse transform
		swapQuadrants(first);
		return first;
	}

	/**
	 * Translate real array (zero in the center) by a sub-pixel vector (preferably
	 * in +/- 0.5 range for each coordinate) by multiplying spectrum by the linear
	 * phase gradient. Caches array, so multiple arrays can be shifted by the same
	 * vector faster
	 * 
	 * @param data square array to be translated by a sub-pixel value. in the end it
	 *             holds FHT (before multiplication)!
	 * @param dx   translation in x-direction
	 * @param dy   translation in y direction
	 * @return modified data array, translated by specified vector (in-place)
	 */

	public double[] translateSubPixel(double[] data, double dx, double dy) {
		if (debug)
			ShowDoubleFloatArrays.showArrays(data, "source-" + IJ.d2s(dx, 3) + ":" + IJ.d2s(dy, 3));
		swapQuadrants(data);
		if (!transform(data, false))
			return null; // direct FHT
		if ((this.maxN != translateFHTN) || (dx != translateFHTdXY[0]) || (dy != translateFHTdXY[1])) {
			calcTranslateFHT(dx, dy);
		}
		if (debug)
			ShowDoubleFloatArrays.showArrays(data, "fht-source-" + IJ.d2s(dx, 3) + ":" + IJ.d2s(dy, 3));
		data = multiply(data, this.translateFHT, false); // convolution, not correlation
		if (debug)
			ShowDoubleFloatArrays.showArrays(data, "fht-multiplied-" + IJ.d2s(dx, 3) + ":" + IJ.d2s(dy, 3));
		transform(data, true); // inverse transform
		swapQuadrants(data);
		if (debug)
			ShowDoubleFloatArrays.showArrays(data, "result-" + IJ.d2s(dx, 3) + ":" + IJ.d2s(dy, 3));
		return data;
	}

	/**
	 * Calculating (and caching) FHT array for subpixel translation
	 * 
	 * @param dx translation in x-direction
	 * @param dy translation in y direction
	 */
	private void calcTranslateFHT(double dx, double dy) {
		double k = 2.0 * Math.PI / this.maxN;
		double kx = k * dx;
		double ky = k * dy;
		this.translateFHT = new double[this.maxN * this.maxN];
		double sqrt2 = Math.sqrt(2.0);
		double pi4 = Math.PI / 4;
		int hSize = this.maxN / 2;
		double a, b, p;
		int rowMod, colMod;
		for (int r = 0; r < hSize; r++) {
			rowMod = (maxN - r) % maxN;
			for (int c = 0; c < hSize; c++) {
				colMod = (maxN - c) % maxN;
				p = kx * c + ky * r;
				a = sqrt2 * Math.sin(pi4 + p);
				b = sqrt2 * Math.sin(pi4 - p);
				this.translateFHT[r * this.maxN + c] = a;
				this.translateFHT[rowMod * this.maxN + colMod] = b;
				if (c == 0) {
					this.translateFHT[r * this.maxN + c + hSize] = a;
					this.translateFHT[rowMod * this.maxN + colMod + hSize] = b;
				} else {
					p = -kx * c + ky * r;
					a = sqrt2 * Math.sin(pi4 + p);
					b = sqrt2 * Math.sin(pi4 - p);
					this.translateFHT[r * this.maxN + colMod] = a;
					this.translateFHT[rowMod * this.maxN + c] = b;
				}
			}
		}

// update cache
		this.translateFHTdXY = new double[2];
		this.translateFHTdXY[0] = dx;
		this.translateFHTdXY[1] = dy;
		this.translateFHTN = this.maxN;
		if (debug)
			ShowDoubleFloatArrays.showArrays(this.translateFHT, "translateFHT-" + IJ.d2s(dx, 3) + ":" + IJ.d2s(dy, 3));
	}

	public boolean updateMaxN(double[] data) { // was private
		if (data == null)
			return false; // do nothing
		if (!powerOf2Size(data)) {
			String msg = "Image is not power of 2 size";
			IJ.showMessage("Error", msg);
			throw new IllegalArgumentException(msg);
		}
		int n = (int) Math.sqrt(data.length);
		boolean differentSize = (n != this.maxN);
		this.maxN = n;
		if (differentSize) {
//System.out.println("Changing FFT size: old ln2="+this.ln2+" new maxN="+this.maxN);
			// save length old mask and mask parameters
			if (this.ln2 >= 0) {
				this.freqMask_cache[this.ln2] = this.freqMask;
				this.freqPass_cache[this.ln2] = this.freqPass;
			}

//			int ln2;
			for (this.ln2 = 0; maxN > (1 << this.ln2); this.ln2++)
				;
			if ((this.ln2 >= CS_cache.length) || (CS_cache[this.ln2] == null)) {
				if (this.ln2 >= CS_cache.length) {
					String msg = "Too large image, increase this.maxSize (it is now " + this.maxSize + ", wanted "
							+ this.ln2 + ")";
					IJ.showMessage("Error", msg);
					throw new IllegalArgumentException(msg);
				}
				this.freqMask_cache[this.ln2] = null;
				this.freqPass_cache[this.ln2] = new double[2];
				this.freqPass_cache[this.ln2][0] = 0.0;
				this.freqPass_cache[this.ln2][1] = 0.0;
				makeSinCosTables(this.maxN);
				this.CS_cache[this.ln2] = new double[2][];
				this.CS_cache[this.ln2][0] = this.C;
				this.CS_cache[this.ln2][1] = this.S;
				makeBitReverseTable(this.maxN);
				this.bitrev_cache[this.ln2] = this.bitrev;

			} else {
				this.C = this.CS_cache[this.ln2][0];
				this.S = this.CS_cache[this.ln2][1];
				this.bitrev = this.bitrev_cache[this.ln2];

			}
			this.freqMask = this.freqMask_cache[this.ln2]; // for the new one there will be just null
			this.freqPass = this.freqPass_cache[this.ln2];
			this.tempArr = new double[maxN];

		}
		return differentSize;

	}

	public double[] getHamming1d() {
		if (this.maxN >= 0)
			return getHamming1d(this.maxN);
		return null;
	}

	/**
	 *
	 * @param n power of 2 FHT size.
	 * @return one-dimensional array with Hamming window for low-pass frequency
	 *         filtering (maximum in the center)
	 */
	public double[] getHamming1d(int n) {
		return getHamming1d(n, 0.08); // normal Hamming window
	}

	public double[] getHamming1d(int n, double min) { // min==0.08 - normal Hamming, 0.0 - pure shifted cosine
		int ln2;
		for (ln2 = 0; n > (1 << ln2); ln2++)
			;
		if (n != (1 << ln2)) {
			String msg = "Not a power of 2 :" + n;
			IJ.showMessage("Error", msg);
			throw new IllegalArgumentException(msg);
		}
		if (ln2 >= this.hamming1d.length) {
			String msg = "Too large array length, increase this.maxSize (it is now " + this.maxSize + ", wanted " + ln2
					+ ")";
			IJ.showMessage("Error", msg);
			throw new IllegalArgumentException(msg);
		}
		if ((this.hamming1d[ln2] == null) || (this.hamming1dMin[ln2] != min)) {
			this.hamming1d[ln2] = new double[n];
			this.hamming1dMin[ln2] = min;
			double C054 = 0.5 * (1 + min);
			double C046 = 0.5 * (1 - min);
			for (int i = 0; i <= n / 2; i++)
				this.hamming1d[ln2][i] = (C054 - C046 * Math.cos((i * 2.0 * Math.PI) / n));
			for (int i = 1; i <= n / 2; i++)
				this.hamming1d[ln2][n - i] = this.hamming1d[ln2][i];
		}
		return this.hamming1d[ln2];
	}

	/**
	 * Creates one-dimensional array for low-pass filtering in the frequency domain,
	 * by multiplying by Gaussian Zero is in the center, same as for Hamming above
	 * 
	 * @param lowPass relative frequency. with lowPass==1.0, Gaussian sigma will be
	 *                sqrt(2)*Nyquist frequency (==2/n)
	 * @param n       - number of FFT points (2^2)
	 * @return one dimensional array, with 1.0 at 0, and minimum in the middle
	 */
	public double[] getGaussian1d(double lowPass) {
		return getGaussian1d(lowPass, this.maxN);
	}

	public double[] getGaussian1d(double lowPass, int n) {
		int ln2;
		for (ln2 = 0; n > (1 << ln2); ln2++)
			;
		if (n != (1 << ln2)) {
			String msg = "Not a power of 2 :" + n;
			IJ.showMessage("Error", msg);
			throw new IllegalArgumentException(msg);
		}
		if (ln2 >= this.gaussian1d.length) {
			String msg = "Too large array length, increase this.maxSize (it is now " + this.maxSize + ", wanted " + ln2
					+ ")";
			IJ.showMessage("Error", msg);
			throw new IllegalArgumentException(msg);
		}
		if (this.gaussian1d[ln2] == null) {
			this.gaussian1d[ln2] = new double[n];
			this.gaussian1dWidths[ln2] = -1.0;
		}
		if (this.gaussian1dWidths[ln2] != lowPass) {
			this.gaussian1dWidths[ln2] = lowPass;
			double kLo = (lowPass > 0) ? (1.0 / lowPass / lowPass / n / n) : 0;
			double mx2;

			for (int i = 0; i <= n / 2; i++) {
				mx2 = -i * i;
				this.gaussian1d[ln2][n / 2 - i] = (kLo > 0.0) ? Math.exp(mx2 * kLo) : 1.0;
			}
			for (int i = 1; i <= n / 2; i++)
				this.gaussian1d[ln2][n - i] = this.gaussian1d[ln2][i];
		}
		return this.gaussian1d[ln2];
	}

	private void makeSinCosTables(int maxN) {
		int ln2;
		for (ln2 = 0; maxN > (1 << ln2); ln2++)
			;
		int n = maxN / 4;
		this.C = new double[n];
		this.S = new double[n];
		double theta = 0.0;
		double dTheta = 2.0 * Math.PI / maxN;
		for (int i = 0; i < n; i++) {
			this.C[i] = Math.cos(theta);
			this.S[i] = Math.sin(theta);
			theta += dTheta;
		}
	}

	private void makeBitReverseTable(int maxN) {
		bitrev = new int[maxN];
		int nLog2 = log2(maxN);
		for (int i = 0; i < maxN; i++)
			bitrev[i] = bitRevX(i, nLog2);
	}

	/* Performs a 2D FHT (Fast Hartley Transform). */
	public void rc2DFHT(double[] x, boolean inverse, int maxN) {
		// IJ.write("FFT: rc2DFHT (row-column Fast Hartley Transform)");
		for (int row = 0; row < maxN; row++)
			dfht3(x, row * maxN, inverse, maxN);
		progress(0.4);
		transposeR(x, maxN);
		progress(0.5);
		for (int row = 0; row < maxN; row++)
			dfht3(x, row * maxN, inverse, maxN);
		progress(0.7);
		transposeR(x, maxN);
		progress(0.8);

		int mRow, mCol;
		double A, B, C, D, E;
		for (int row = 0; row <= maxN / 2; row++) { // Now calculate actual Hartley transform
			for (int col = 0; col <= maxN / 2; col++) {
				mRow = (maxN - row) % maxN;
				mCol = (maxN - col) % maxN;
				A = x[row * maxN + col]; // see Bracewell, 'Fast 2D Hartley Transf.' IEEE Procs. 9/86
				B = x[mRow * maxN + col];
				C = x[row * maxN + mCol];
				D = x[mRow * maxN + mCol];
				E = ((A + D) - (B + C)) / 2;
				x[row * maxN + col] = A - E;
				x[mRow * maxN + col] = B + E;
				x[row * maxN + mCol] = C + E;
				x[mRow * maxN + mCol] = D - E;
			}
		}
		progress(0.95);
	}

	void progress(double percent) {
		if (showProgress)
			IJ.showProgress(percent);
	}

	/* Performs an optimized 1D FHT. */
	public void dfht3(double[] x, int base, boolean inverse, int maxN) {
		int i, stage, gpNum, gpSize, numGps, Nlog2;
		int bfNum, numBfs;
		int Ad0, Ad1, Ad2, Ad3, Ad4, CSAd;
		double rt1, rt2, rt3, rt4;

		Nlog2 = log2(maxN);
		BitRevRArr(x, base, Nlog2, maxN); // bitReverse the input array
		gpSize = 2; // first & second stages - do radix 4 butterflies once thru
		numGps = maxN / 4;
		for (gpNum = 0; gpNum < numGps; gpNum++) {
			Ad1 = gpNum * 4;
			Ad2 = Ad1 + 1;
			Ad3 = Ad1 + gpSize;
			Ad4 = Ad2 + gpSize;
			rt1 = x[base + Ad1] + x[base + Ad2]; // a + b
			rt2 = x[base + Ad1] - x[base + Ad2]; // a - b
			rt3 = x[base + Ad3] + x[base + Ad4]; // c + d
			rt4 = x[base + Ad3] - x[base + Ad4]; // c - d
			x[base + Ad1] = rt1 + rt3; // a + b + (c + d)
			x[base + Ad2] = rt2 + rt4; // a - b + (c - d)
			x[base + Ad3] = rt1 - rt3; // a + b - (c + d)
			x[base + Ad4] = rt2 - rt4; // a - b - (c - d)
		}

		if (Nlog2 > 2) {
			// third + stages computed here
			gpSize = 4;
			numBfs = 2;
			numGps = numGps / 2;
			// IJ.write("FFT: dfht3 "+Nlog2+" "+numGps+" "+numBfs);
			for (stage = 2; stage < Nlog2; stage++) {
				for (gpNum = 0; gpNum < numGps; gpNum++) {
					Ad0 = gpNum * gpSize * 2;
					Ad1 = Ad0; // 1st butterfly is different from others - no mults needed
					Ad2 = Ad1 + gpSize;
					Ad3 = Ad1 + gpSize / 2;
					Ad4 = Ad3 + gpSize;
					rt1 = x[base + Ad1];
					x[base + Ad1] = x[base + Ad1] + x[base + Ad2];
					x[base + Ad2] = rt1 - x[base + Ad2];
					rt1 = x[base + Ad3];
					x[base + Ad3] = x[base + Ad3] + x[base + Ad4];
					x[base + Ad4] = rt1 - x[base + Ad4];
					for (bfNum = 1; bfNum < numBfs; bfNum++) {
						// subsequent BF's dealt with together
						Ad1 = bfNum + Ad0;
						Ad2 = Ad1 + gpSize;
						Ad3 = gpSize - bfNum + Ad0;
						Ad4 = Ad3 + gpSize;

						CSAd = bfNum * numGps;
						if (((base + Ad2) >= x.length) || ((base + Ad4) >= x.length) || (CSAd >= this.C.length)
								|| (CSAd >= this.S.length)) {

							System.out.println("dfht3 Error: ln2=" + this.ln2 + " maxN=" + this.maxN + " x.length="
									+ x.length + " this.C.length=" + this.C.length + " this.S.length=" + this.S.length
									+ " base=" + base + " Ad2=" + Ad2 + " Ad4=" + Ad4 + " CSAd=" + CSAd);
						}

						rt1 = x[base + Ad2] * C[CSAd] + x[base + Ad4] * S[CSAd];
						rt2 = x[base + Ad4] * C[CSAd] - x[base + Ad2] * S[CSAd];

						x[base + Ad2] = x[base + Ad1] - rt1;
						x[base + Ad1] = x[base + Ad1] + rt1;
						x[base + Ad4] = x[base + Ad3] + rt2;
						x[base + Ad3] = x[base + Ad3] - rt2;

					} /* end bfNum loop */
				} /* end gpNum loop */
				gpSize *= 2;
				numBfs *= 2;
				numGps = numGps / 2;
			} /* end for all stages */
		} /* end if Nlog2 > 2 */

		if (inverse) {
			for (i = 0; i < maxN; i++)
				x[base + i] = x[base + i] / maxN;
		}
	}

	void transposeR(double[] x, int maxN) {
		int r, c;
		double rTemp;

		for (r = 0; r < maxN; r++) {
			for (c = r; c < maxN; c++) {
				if (r != c) {
					rTemp = x[r * maxN + c];
					x[r * maxN + c] = x[c * maxN + r];
					x[c * maxN + r] = rTemp;
				}
			}
		}
	}

	int log2(int x) {
		int count = 15;
		while (!btst(x, count))
			count--;
		return count;
	}

	private boolean btst(int x, int bit) {
		// int mask = 1;
		return ((x & (1 << bit)) != 0);
	}

	void BitRevRArr(double[] x, int base, int bitlen, int maxN) {
		for (int i = 0; i < maxN; i++)
			tempArr[i] = x[base + bitrev[i]];
		for (int i = 0; i < maxN; i++)
			x[base + i] = tempArr[i];
	}

	private int bitRevX(int x, int bitlen) {
		int temp = 0;
		for (int i = 0; i <= bitlen; i++)
			if ((x & (1 << i)) != 0)
				temp |= (1 << (bitlen - i - 1));
		return temp & 0x0000ffff;
	}

	public int[] nonZeroAmpIndices(double[] ampMask) {
		int numNonZero = 0;
		for (int i = 0; i < ampMask.length; i++)
			if (ampMask[i] > 0.0)
				numNonZero++;
		int[] result = new int[numNonZero];
		numNonZero = 0;
		for (int i = 0; i < ampMask.length; i++)
			if (ampMask[i] > 0.0)
				result[numNonZero++] = i;
		return result;
	}

	/**
	 * Calculate feature matching quality
	 * 
	 * @param h                     FHT array
	 * @param directionAngle        direction of the linear phase gradient
	 * @param distance              Distance to the linear feature in the direction
	 *                              directionAngle (determines the phase gradient
	 *                              absolute value)
	 * @param distance              Distance to the linear feature in the direction
	 *                              directionAngle (determines the phase gradient
	 *                              absolute value)
	 * @param phaseIntegrationWidth Width of the band corresponding to the linear
	 *                              feature
	 * @param amHPhase              array with amplitudes and (modified) phases for
	 *                              each index or null. Used to mask out some of the
	 *                              points
	 * @param phaseStepCorr         Zero-based linear phase values plus these values
	 *                              approximate real phases
	 * @param bandMask              if not null, multiply amplitudes by this mask
	 * @return pair of correlation and self-RMS (to calculate relative feature
	 *         strength)
	 */
	public double[] linearFeatureStrength(double[] h, double directionAngle, double distance,
			double phaseIntegrationWidth, // zero - no limit
			int[] nonZeroIndices, double[][] amHPhase, double[] phaseStepCorr, double[] bandMask) {
		double halfWidth = (phaseIntegrationWidth > 0.0) ? phaseIntegrationWidth / 2 : this.maxN;
		double sin = Math.sin(directionAngle);
		double cos = Math.cos(directionAngle);
		int halfN = this.maxN / 2;
		double diffPhase = distance * 2 * Math.PI / this.maxN;
		double corrSum = 0.0;
		double sumSquares = 0.0;
		int numSamples = 0;
		for (int numPoint = 0; numPoint < nonZeroIndices.length; numPoint++)
			if ((amHPhase == null) || (amHPhase[numPoint][0] > 0.0)) {
				int index = nonZeroIndices[numPoint];
				int x = (index + halfN) % this.maxN - halfN;
				int y = index / this.maxN;
				double t = cos * x + sin * y;
				if (Math.abs(cos * y - sin * x) <= halfWidth) {
					int indexMod = ((this.maxN - (index / this.maxN)) % this.maxN) * this.maxN
							+ ((this.maxN - (index % this.maxN)) % this.maxN);
					double re = 0.5 * (h[index] + h[indexMod]);
					double im = 0.5 * (h[index] - h[indexMod]);
					double amp2 = re * re + im * im;
					if (bandMask != null)
						amp2 *= bandMask[numPoint];
//			    sumSquares+=((y!=0)?2:1)*amp2;
					sumSquares += amp2;
					double phase = phaseStepCorr[numPoint] + diffPhase * t;
					double cosPhase = Math.cos(phase);
					double sinPhase = Math.sin(phase);
					corrSum += re * cosPhase + im * sinPhase;
					// debugprint
					numSamples++;
					if (this.debug)
						System.out.println("   Used x=" + x + " y=" + y + " cos*y+sin*x=" + (cos * y + sin * x)
								+ "  cos=" + cos + " sin=" + sin + " t=" + t);
				} else {
					if (this.debug)
						System.out.println("Dropped x=" + x + " y=" + y + " cos*y+sin*x=" + (cos * y + sin * x)
								+ "  cos=" + cos + " sin=" + sin + " t=" + t);
				}
			}
		double[] result = { corrSum, Math.sqrt(numSamples * sumSquares) }; // second is n*RMS
		return result;
	}

	/**
	 * Reconstruct FHT of the linear feature using the masked amplitudes of the
	 * original and linear phase approximation
	 * 
	 * @param h                     FHT array
	 * @param directionAngle        direction of the linear phase gradient
	 * @param distance              Distance to the linear feature in the direction
	 *                              directionAngle (determines the phase gradient
	 *                              absolute value)
	 * @param phaseIntegrationWidth Width of the band corresponding to the linear
	 *                              feature
	 * @param nonZeroIndices        array of non-zero indices in the FHT array
	 * @param amHPhase              array with amplitudes and (modified) phases for
	 *                              each index or null. Used to mask out some of the
	 *                              points
	 * @param phaseStepCorr         Zero-based linear phase values plus these values
	 *                              approximate real phases
	 * @param bandMask              if not null, multiply amplitudes by this mask
	 * @return FHT Reconstructed array transformed to space domain with quadrants
	 *         swapped;
	 */
	public double[] reconstructLinearFeature(double[] h, double directionAngle, double distance,
			double phaseIntegrationWidth, // zero - no limit
			int[] nonZeroIndices, double[][] amHPhase, double[] phaseStepCorr, double[] bandMask) {
		double halfWidth = (phaseIntegrationWidth > 0.0) ? phaseIntegrationWidth / 2 : this.maxN;
		double sin = Math.sin(directionAngle);
		double cos = Math.cos(directionAngle);
		int halfN = this.maxN / 2;
		double diffPhase = distance * 2 * Math.PI / this.maxN;
		double[] reconstructedFHT = new double[h.length];
		for (int i = 0; i < reconstructedFHT.length; i++)
			reconstructedFHT[i] = 0.0;
		for (int numPoint = 0; numPoint < nonZeroIndices.length; numPoint++)
			if ((amHPhase == null) || (amHPhase[numPoint][0] > 0.0)) {
				int index = nonZeroIndices[numPoint];
				int x = (index + halfN) % this.maxN - halfN;
				int y = index / this.maxN;
				if (Math.abs(cos * y - sin * x) <= halfWidth) {
					int indexMod = ((this.maxN - (index / this.maxN)) % this.maxN) * this.maxN
							+ ((this.maxN - (index % this.maxN)) % this.maxN);
					double re = 0.5 * (h[index] + h[indexMod]);
					double im = 0.5 * (h[index] - h[indexMod]);
					double amp = Math.sqrt(re * re + im * im);
					if (bandMask != null)
						amp *= bandMask[numPoint];
					double t = cos * x + sin * y;
					double phase = phaseStepCorr[numPoint] + diffPhase * t;
					double reconstructedRe = amp * Math.cos(phase);
					double reconstructedIm = amp * Math.sin(phase);
					reconstructedFHT[index] = reconstructedRe + reconstructedIm;
					reconstructedFHT[indexMod] = reconstructedRe - reconstructedIm;
//			    if (this.debug)	System.out.println("reconstructLinearFeature(): x="+x+" y="+y +" index="+index+ " indexMod="+indexMod+ " re="+re+" im="+im +" amp="+amp+
//			    		" t="+t+ " phase="+ phase+" reconstructedRe="+reconstructedRe+" reconstructedIm="+reconstructedIm);

				}
			}
		transform(reconstructedFHT, true);
		swapQuadrants(reconstructedFHT);
		return reconstructedFHT; // space domain
	}

	/**
	 * Adds phase shift to stitch symmetrical around 0 areas (there is zero at 0)
	 * 
	 * @param directionAngle  perpendicular to the linear feature (direction of high
	 *                        amplitude in frequency domain)
	 * @param zeroPhase       extrapolated phase at 0 for positive direction at
	 *                        angle (half step)
	 * @param distance        Estimated distance to line (only used with
	 *                        zeroBinHalfSize)
	 * @param phaseTolerance  - if >0.0, will zero amplitude if the phase is too off
	 * @param amHPhase        [numLixel]{amplitude, phase} - phase will be modified!
	 *                        May be null - will work faster
	 * @param zeroBinHalfSize - if abs(projection) is less than zeroBinHalfSize, use
	 *                        the best (of 2 options) phase
	 * @param nonZeroIndices
	 * @return applied phase correction, added to the modified phase will result
	 *         actual phase
	 */
	public double[] compensatePhaseStep(double directionAngle, double zeroPhase, double distance, double phaseTolerance,
			double[][] amHPhase, int[] nonZeroIndices, double zeroBinHalfSize) {
		double sin = Math.sin(directionAngle);
		double cos = Math.cos(directionAngle);
		int halfN = this.maxN / 2;
		double diffPhase = distance * 2 * Math.PI / this.maxN;
		double[] phaseCorr = new double[nonZeroIndices.length];
		for (int numPoint = 0; numPoint < nonZeroIndices.length; numPoint++) {
			int index = nonZeroIndices[numPoint];
			int x = (index + halfN) % this.maxN - halfN;
			int y = index / this.maxN;
			double t = cos * x + sin * y;
			double dPhase = (t > 0) ? zeroPhase : (-zeroPhase);
			if (amHPhase != null) {
				if ((y != 0) && (Math.abs(t) < zeroBinHalfSize)) {
					double flattenedPhase = amHPhase[numPoint][1] - diffPhase * t;
					double diffPlus = flattenedPhase - zeroPhase;
					double diffMinus = flattenedPhase + zeroPhase;
					diffPlus -= (2 * Math.PI * Math.round(diffPlus / (2 * Math.PI)));
					diffMinus -= (2 * Math.PI * Math.round(diffMinus / (2 * Math.PI)));
					dPhase = (Math.abs(diffPlus) < Math.abs(diffMinus)) ? zeroPhase : (-zeroPhase);
					/*
					 * System.out.println("numPoint="+numPoint+" x="+x+" y="+y+
					 * " phase(was)="+amHPhase[numPoint][1]+ " flattenedPhase="+flattenedPhase+
					 * " diffPlus="+diffPlus+" diffMinus="+diffMinus+ " dPhase="+dPhase);
					 */
				}

				amHPhase[numPoint][1] -= dPhase;
				amHPhase[numPoint][1] -= (2 * Math.PI * Math.round(amHPhase[numPoint][1] / (2 * Math.PI)));

				double phaseError = amHPhase[numPoint][1] - diffPhase * t;
				phaseError -= (2 * Math.PI * Math.round(phaseError / (2 * Math.PI)));

				if ((phaseTolerance > 0.0) && (Math.abs(phaseError) > phaseTolerance)) {
					amHPhase[numPoint][0] = 0.0; // bad phase - make zero;
				}
			}
			phaseCorr[numPoint] = dPhase;
		}
		return phaseCorr;
	}

	public int[] getBandIndices(boolean keepDC, double ribbonWidth, double angle) {
		int halfN = this.maxN / 2;
		double halfWidth = ribbonWidth / 2;
		int length = halfN * this.maxN;
		int[] tmpIndices = new int[length];
		double sin = Math.sin(angle);
		double cos = Math.cos(angle);
		int pointNumber = 0;
		for (int index = 0; index < length; index++) {
			int x = (index + halfN) % this.maxN - halfN;
			int y = index / this.maxN;
			double t = cos * x + sin * y;
			double d = sin * x - cos * y;
			int it = (int) Math.round(Math.abs(t));
			if ((keepDC || (y > 0) || (x > 0)) && (Math.abs(d) < halfWidth) && (it < halfN)) {
				tmpIndices[pointNumber++] = index;
			}
		}
		int[] indices = new int[pointNumber];
		for (int i = 0; i < pointNumber; i++)
			indices[i] = tmpIndices[i];
		return indices;
	}

	public double[] getRibbonMask(boolean keepDC, int[] bandIndices, double ribbonWidth, double resultHighPass0,
			double angle) {
		double resultHighPass = keepDC ? 0.0 : resultHighPass0;
		int halfN = this.maxN / 2;
		double halfWidth = ribbonWidth / 2;
		double sin = Math.sin(angle);
		double cos = Math.cos(angle);
		if (sin < 0) {
			sin = -sin;
			cos = -cos;
		}
		double[] ribbonMask = new double[bandIndices.length];
		for (int iIndex = 0; iIndex < bandIndices.length; iIndex++) {
			int index = bandIndices[iIndex];
			int x = (index + halfN) % this.maxN - halfN;
			int y = index / this.maxN;
			double t = Math.abs(cos * x + sin * y);
			double d = sin * x - cos * y;
//		    int it=(int) Math.round(Math.abs(t));
			int it = (int) Math.round(t);
			if ((keepDC || (y > 0) || (x > 0)) && (Math.abs(d) < halfWidth) && (it < halfN)) {
				double w = (0.54 + 0.46 * Math.cos(Math.PI * d / halfWidth)); // (masked) amplitude;
				if (t < resultHighPass)
					w *= 0.54 + 0.46 * Math.cos(Math.PI * (resultHighPass - t) / resultHighPass);
				else if (t > (halfN - halfWidth))
					w *= 0.54 + 0.46 * Math.cos(Math.PI * (t - (halfN - halfWidth)) / halfWidth);
				ribbonMask[iIndex] = w;
//			    if (this.debug)	System.out.println("getRibbonMask(): x="+x+" y="+y +" t="+t+" d="+d +" w="+w+ " w0="+ (0.54+0.46*Math.cos(Math.PI*d/halfWidth)));
			} else {
				ribbonMask[iIndex] = 0.0;
				System.out.println("getRibbonMask(): should not get here");
			}
		}
		return ribbonMask;
	}

	/**
	 * Detect linear features in the frequency domain sample
	 * 
	 * @param ribbonWidth      Width of the band for processing phase (data inside
	 *                         will be multiplied by the Hamming filter
	 *                         perpendicular to the direction of the band
	 * @param fht              frequency-domain FHT array of the sample
	 * @param minRMSFrac       Process only frequencies with amplitude above this
	 *                         ratio of the RMS of all frequencies. (0 - do not use
	 *                         this threshold)
	 * @param minAbs           Process only frequencies with (absolute) amplitude
	 *                         above this value (0 - do not use this threshold)
	 * @param maxPhaseMismatch Maximal mismatch between the diagonal pair of 2 pixel
	 *                         pairs to consider pixels valid (distance between
	 *                         crossing diagonals)
	 * @param dispertionCost   - >0 - use phase dispersion when calculating quality
	 *                         of phase match, 0 - only weights.
	 * @param filter           Bitmask enabling different phase half-steps (+1 - 0,
	 *                         +2 - pi/2, +4 - pi, +8 - 3pi/2. Value zero allows
	 *                         arbitrary step step 0 corresponds to thin white line,
	 *                         pi - thin black line, +pi/2 - edge black-to-white in
	 *                         the direction of directionAngle, 3pi/2 -
	 *                         white-to-black in the direction of directionAngle
	 * @return array of the following values: {bestAngle, angle of the perpendicular
	 *         towards the linear feature: 0 in the direction of pixel x (right),
	 *         pi/2 - in the direction of the pixel Y (down) distance, - distance
	 *         from the sample center to the linear feature in the direction
	 *         bnestAngle (in pixels) phaseAtZero, - extrapolated phase at zero
	 *         frequency (DC) , see description of the parameter "filter" above
	 *         maxStrength}; strength of the feature (combines multiple factors)
	 */

	public double[] calcPhaseApproximation(double ribbonWidth, double[] fht, double minRMSFrac, double minAbs,
			double maxPhaseMismatch, double dispertionCost, int filter) {
		createPolarMasksIndices(ribbonWidth); // all but first time will return immediately.
		int halfN = this.maxN / 2;
		double dispersionFatZero = (dispertionCost > 0) ? (Math.PI / halfN / dispertionCost) : 0.0;
		double[][] dPHdXdY = new double[5][this.maxN * this.maxN / 2]; // amp, phase, phaseWeight, dPhase/dX, dPhase/dY
		for (int n = 0; n < dPHdXdY.length; n++)
			for (int i = 0; i < dPHdXdY[0].length; i++)
				dPHdXdY[n][i] = 0.0;
		double sum2 = 0.0;
		for (int index = 0; index < dPHdXdY[0].length; index++) {
			int indexMod = ((this.maxN - (index / this.maxN)) % this.maxN) * this.maxN
					+ ((this.maxN - (index % this.maxN)) % this.maxN);
			double re = 0.5 * (fht[index] + fht[indexMod]);
			double im = 0.5 * (fht[index] - fht[indexMod]);
//		    int x=(index+halfN)%this.maxN-halfN;
//		    int y=index/this.maxN;
			double amp2 = re * re + im * im;
			sum2 += amp2;
			dPHdXdY[0][index] = Math.sqrt(amp2);
			dPHdXdY[1][index] = Math.atan2(im, re);
		}
		double rms = Math.sqrt(sum2 / dPHdXdY[0].length);
		double thresholdAmplitude = 0.0;
		if (this.debug)
			System.out.println("calc_dPHdXdY): rms=" + rms);
		if (minRMSFrac > 0)
			thresholdAmplitude = minRMSFrac * rms;
		if ((minAbs > 0) && ((thresholdAmplitude == 0) || (thresholdAmplitude > minAbs)))
			thresholdAmplitude = minAbs;
		for (int index = 0; index < dPHdXdY[0].length; index++)
			if (dPHdXdY[0][index] < thresholdAmplitude)
				dPHdXdY[0][index] = 0.0;
		double oneThird = 1.0 / 3;
		for (int y = 0; y < (halfN - 1); y++) {
			for (int x = -halfN + 1; x < (halfN - 1); x++) {
//				int index00=y*this.maxN+(x+halfN);
				int index00 = y * this.maxN + (x + this.maxN) % this.maxN;
				int indexX0 = y * this.maxN + (x + this.maxN + 1) % this.maxN;
				int index0Y = index00 + this.maxN;
				int indexXY = (y + 1) * this.maxN + (x + this.maxN + 1) % this.maxN;
				if ((dPHdXdY[0][index00] > 0) && (dPHdXdY[0][indexX0] > 0) && (dPHdXdY[0][index0Y] > 0)
						&& (dPHdXdY[0][indexXY] > 0)) {
					double dP00X0 = dPHdXdY[1][indexX0] - dPHdXdY[1][index00];
					double dP000Y = dPHdXdY[1][index0Y] - dPHdXdY[1][index00];
					double dPX0XY = dPHdXdY[1][indexXY] - dPHdXdY[1][indexX0];
					double dP0YXY = dPHdXdY[1][indexXY] - dPHdXdY[1][index0Y];
					dP00X0 -= (2 * Math.PI) * Math.round(dP00X0 / (2 * Math.PI));
					dP000Y -= (2 * Math.PI) * Math.round(dP000Y / (2 * Math.PI));
					dPX0XY -= (2 * Math.PI) * Math.round(dPX0XY / (2 * Math.PI));
					dP0YXY -= (2 * Math.PI) * Math.round(dP0YXY / (2 * Math.PI));
					if (this.debug) {
						System.out.println(" index00=" + index00 + " indexX0=" + indexX0 + " index0Y=" + index0Y
								+ " indexXY=" + indexXY);
						System.out.println(" dPHdXdY[1][index00]=" + dPHdXdY[1][index00] + " dPHdXdY[1][indexX0]="
								+ dPHdXdY[1][indexX0] + " dPHdXdY[1][index0Y]=" + dPHdXdY[1][index0Y]
								+ " dPHdXdY[1][indexXY]=" + dPHdXdY[1][indexXY]);
						System.out.println(
								" dP00X0=" + dP00X0 + " dP000Y=" + dP000Y + " dPX0XY=" + dPX0XY + " dP0YXY=" + dP0YXY);
					}

					double curv = Math.abs((dPX0XY - dP000Y) / 2);
					if ((maxPhaseMismatch == 0) || (curv < maxPhaseMismatch)) {
						double w = Math.pow(dPHdXdY[0][index00] * dPHdXdY[0][indexX0] * dPHdXdY[0][index0Y], oneThird);
						if (this.debug)
							System.out.print(">>> x=" + x + " y=" + y + " curv=" + curv);
						dPHdXdY[2][index00] += w;
						dPHdXdY[3][index00] += w * dP00X0;
						dPHdXdY[4][index00] += w * dP000Y;
						if (this.debug)
							System.out.print(" index00=" + index00 + " w=" + w);
						w = Math.pow(dPHdXdY[0][index00] * dPHdXdY[0][indexX0] * dPHdXdY[0][indexXY], oneThird);
						dPHdXdY[2][indexX0] += w;
						dPHdXdY[3][indexX0] += w * dP00X0;
						dPHdXdY[4][indexX0] += w * dPX0XY;
						if (this.debug)
							System.out.print(" indexX0=" + indexX0 + " w=" + w);
						w = Math.pow(dPHdXdY[0][index00] * dPHdXdY[0][index0Y] * dPHdXdY[0][indexXY], oneThird);
						dPHdXdY[2][index0Y] += w;
						dPHdXdY[3][index0Y] += w * dP0YXY; // dP000Y;
						dPHdXdY[4][index0Y] += w * dP000Y; // dP0YXY;
						if (this.debug)
							System.out.print(" index0Y=" + index0Y + " w=" + w);
						w = Math.pow(dPHdXdY[0][indexX0] * dPHdXdY[0][index0Y] * dPHdXdY[0][indexXY], oneThird);
						dPHdXdY[2][indexXY] += w;
						dPHdXdY[3][indexXY] += w * dP0YXY; // dPX0XY;
						dPHdXdY[4][indexXY] += w * dPX0XY; // dP0YXY;
						if (this.debug)
							System.out.print(" indexXY=" + indexXY + " w=" + w);
					} else {
						if (this.debug)
							System.out.println(">-- x=" + x + " y=" + y + " curv=" + curv + " w=" + Math
									.pow(dPHdXdY[0][index00] * dPHdXdY[0][indexX0] * dPHdXdY[0][index0Y], oneThird));

					}

				}
			}
		}
		for (int i = 1; i < halfN; i++) {
			int j = this.maxN - i;
			if ((dPHdXdY[2][i] + dPHdXdY[2][j]) > 0.0) {
				dPHdXdY[3][i] = (dPHdXdY[3][i] * dPHdXdY[2][i] + dPHdXdY[3][j] * dPHdXdY[2][j])
						/ (dPHdXdY[2][i] + dPHdXdY[2][j]);
				dPHdXdY[4][i] = (dPHdXdY[4][i] * dPHdXdY[2][i] + dPHdXdY[4][j] * dPHdXdY[2][j])
						/ (dPHdXdY[2][i] + dPHdXdY[2][j]);
				dPHdXdY[2][i] = dPHdXdY[2][i] + dPHdXdY[2][j];
				dPHdXdY[3][j] = dPHdXdY[3][i];
				dPHdXdY[4][j] = dPHdXdY[4][i];
				dPHdXdY[2][j] = dPHdXdY[2][i];
			}
		}
		for (int index = 0; index < dPHdXdY[0].length; index++)
			if (dPHdXdY[2][index] > 0) {
				dPHdXdY[3][index] /= dPHdXdY[2][index];
				dPHdXdY[4][index] /= dPHdXdY[2][index];
			}
		// generate show image
		if (this.debug) {
			double[][] debugdPHdXdY = new double[5][this.maxN * this.maxN];
			for (int i = 0; i < debugdPHdXdY[0].length; i++) {
				int x = (i % this.maxN) - halfN;
				int y = (i / this.maxN) - halfN;
				boolean other = (y < 0);
				if (y < 0) {
					y = -y;
					x = -x;
				}
				if ((y < halfN) && (x > -halfN) && (x < halfN)) {
					int j = (x + this.maxN) % this.maxN + this.maxN * y;
					for (int n = 0; n < debugdPHdXdY.length; n++) {
						debugdPHdXdY[n][i] = (other && ((n == 1))) ? (-dPHdXdY[n][j]) : dPHdXdY[n][j];
					}
				}

			}
			String[] titles = { "amp", "phase", "weight", "d/dx", "d/dy" };
			ShowDoubleFloatArrays.showArrays(debugdPHdXdY, this.maxN, this.maxN, true, "dbgDiffPhases", titles);
		}
		int numAngles = this.polarPhaseMasks.length;
		double[] sinAngle = new double[numAngles];
		double[] cosAngle = new double[numAngles];
		double[] S0 = new double[numAngles];
		double[] SF = new double[numAngles];
		double[] SF2 = new double[numAngles];
		double[] strength = new double[numAngles];
		double[] mean = new double[numAngles];
		for (int iAngle = 0; iAngle < numAngles; iAngle++) {
			double angle = iAngle * Math.PI / numAngles;
			sinAngle[iAngle] = Math.sin(angle);
			cosAngle[iAngle] = Math.cos(angle);
			S0[iAngle] = 0.0;
			SF[iAngle] = 0.0;
			SF2[iAngle] = 0.0;
			strength[iAngle] = 0.0;
			mean[iAngle] = 0.0;
		}
		for (int index = 0; index < this.polarPhaseIndices.length; index++)
			if (dPHdXdY[2][index] > 0.0) {
				if (this.debug) {
					int x = ((index + halfN) % this.maxN) - halfN;
					int y = (index / this.maxN);
					System.out.println("\n+++ calc_dPHdXdY()x/y/ |" + x + "|" + y);
				}
				for (int iiAngle = 0; iiAngle < this.polarPhaseIndices[index].length; iiAngle++) {
					int iAngle = this.polarPhaseIndices[index][iiAngle];
					double w = this.polarPhaseMasks[iAngle][index] * dPHdXdY[2][index];
					S0[iAngle] += w;
					if (this.debug) {
						System.out.println("    calc_dPHdXdY()  iAngle/mask/weight/w: |" + "|" + iAngle + "|"
								+ this.polarPhaseMasks[iAngle][index] + "|" + dPHdXdY[2][index] + "|" + w + "|"
								+ S0[iAngle]);
					}
					double F = dPHdXdY[3][index] * cosAngle[iAngle] + dPHdXdY[4][index] * sinAngle[iAngle];
					SF[iAngle] += w * F;
					SF2[iAngle] += w * F * F;

				}
			}
		int iAngleMax = -1;
		double maxStrength = 0.0;
		for (int iAngle = 0; iAngle < numAngles; iAngle++) {
			double disp = 0;
			if (S0[iAngle] > 0.0) {
				mean[iAngle] = SF[iAngle] / S0[iAngle];
				disp = Math.sqrt(S0[iAngle] * SF2[iAngle] - SF[iAngle] * SF[iAngle]) / S0[iAngle];
// TODO: reduce dispersion influence if it is small

				strength[iAngle] = (dispersionFatZero > 0.0)
						? (dispersionFatZero * S0[iAngle] / (dispersionFatZero + disp))
						: S0[iAngle];
			}
			if (this.debug)
				System.out.println("calc_dPHdXdY(): |" + iAngle + "|" + S0[iAngle] + "|" + SF[iAngle] + "|"
						+ SF2[iAngle] + "|" + mean[iAngle] + "|" + disp + "|" + strength[iAngle]);
			if (strength[iAngle] > maxStrength) {
				maxStrength = strength[iAngle];
				iAngleMax = iAngle;
			}
		}
		if (iAngleMax < 0) {
			if (this.debug)
				System.out.println("calcPhaseApproximation(): Could not find maximal strength direction");
			return null;
		}
		double b = 0.5 * (strength[(iAngleMax + 1) % numAngles] - strength[(iAngleMax + numAngles - 1) % numAngles]);
		double a = 0.5 * (strength[(iAngleMax + 1) % numAngles] + strength[(iAngleMax + numAngles - 1) % numAngles])
				- strength[iAngleMax]; // negative
//		double x=-0.5*b/a;
		double dAngle = (-0.5 * b / a);
		double bestAngle = iAngleMax + dAngle;
		maxStrength += a * dAngle * dAngle + b * dAngle;
		if (this.debug)
			System.out.println(
					"calcPhaseApproximation(): |" + iAngleMax + "|" + dAngle + "|" + bestAngle + "|" + maxStrength);
		int secondAngle = (iAngleMax + ((dAngle < 0) ? -1 : 1) + numAngles) % numAngles;
		double secondMean = mean[secondAngle];
		if ((dAngle * (secondAngle - iAngleMax)) < 0)
			secondMean = -secondMean; // roll over
		double bestMean = mean[iAngleMax] * (1.0 - Math.abs(dAngle)) + secondMean * Math.abs(dAngle);
		if (bestMean < 0) {
			bestAngle += numAngles;
			bestMean = -bestMean;
		}
		bestAngle *= Math.PI / numAngles;
		bestAngle -= (2 * Math.PI) * Math.round(bestAngle / (2 * Math.PI));
		double distance = bestMean * this.maxN / (2 * Math.PI);

		if (this.debug)
			System.out.println(
					"calcPhaseApproximation(): bestAngle=" + bestAngle + " (" + IJ.d2s(180 * bestAngle / Math.PI, 2)
							+ "), distance=" + distance + " (bestMean=" + bestMean + "), maxStrength=" + maxStrength);
		// bin weights, Re and Im for the points with non-zero amplitude and within the
		// band in the direction angle along the direction angle
		double[][] wReIm = new double[3][halfN]; // weight/re/im
		double sin = Math.sin(bestAngle);
		double cos = Math.cos(bestAngle);
		double halfWidth = this.polarRibbonWidth / 2;
		boolean conj = (sin < 0);
		if (conj) {
			sin = -sin;
			cos = -cos;
		}

		for (int index = 0; index < dPHdXdY[0].length; index++) {
			int indexMod = ((this.maxN - (index / this.maxN)) % this.maxN) * this.maxN
					+ ((this.maxN - (index % this.maxN)) % this.maxN);
			int x = (index + halfN) % this.maxN - halfN;
			int y = index / this.maxN;
			double t = cos * x + sin * y;
			double d = sin * x - cos * y;
			int it = (int) Math.round(Math.abs(t));
			if (((y > 0) || (x > 0)) && (Math.abs(d) < halfWidth) && (it < halfN)) {
				double re = 0.5 * (fht[index] + fht[indexMod]);
				double im = 0.5 * (fht[index] - fht[indexMod]);
				if (conj)
					im = -im;
				if (t < 0) {
					im = -im;
					t = -t;
				}
				double w = dPHdXdY[0][index] * (0.54 + 0.46 * Math.cos(Math.PI * d / halfWidth)); // (masked) amplitude;
				if (t < halfWidth)
					w *= 0.54 + 0.46 * Math.cos(Math.PI * (halfWidth - t) / halfWidth);
				else if (t > (halfN - halfWidth))
					w *= 0.54 + 0.46 * Math.cos(Math.PI * (t - (halfN - halfWidth)) / halfWidth);
				wReIm[0][it] += w;
				wReIm[1][it] += w * re;
				wReIm[2][it] += w * im;
			}
		}
		if (this.debug) {
			System.out.println("calcPhaseApproximation(): binnig w/re/im along selected direction");
			for (int it = 0; it < wReIm[0].length; it++) {
				System.out.println("calcPhaseApproximation(): |" + it + "|" + wReIm[0][it] + "|" + wReIm[1][it] + "|"
						+ wReIm[2][it] + "|" + Math.atan2(wReIm[2][it], wReIm[1][it]));
			}
		}
		double[] approximatedZeroPhaseDist = approximateLinearPhase(wReIm, filter);
		if (approximatedZeroPhaseDist == null)
			return null;
		if (this.debug) {
			System.out.println("calcPhaseApproximation(): initial distance=" + distance + " updated distance="
					+ approximatedZeroPhaseDist[1] + " phase at zero=" + approximatedZeroPhaseDist[0] + " ("
					+ IJ.d2s(approximatedZeroPhaseDist[0] * 180.0 / Math.PI, 1) + ")");
			for (int it = 0; it < wReIm[0].length; it++) {
				System.out.println("calcPhaseApproximation(): |" + it + "|" + wReIm[0][it] + "|" + wReIm[1][it] + "|"
						+ wReIm[2][it] + "|" + Math.atan2(wReIm[2][it], wReIm[1][it]));
			}
		}
		distance = approximatedZeroPhaseDist[1];
		double phaseAtZero = approximatedZeroPhaseDist[0];
		double[] result = { bestAngle, distance, phaseAtZero, maxStrength };
		return result;
	}

	private double polarRibbonWidth = -1;
	private double[][] polarPhaseMasks = null;
	private int[][] polarPhaseIndices = null;

	public void createPolarMasksIndices(double ribbonWidth) { // <0 - invalidate
		if (this.polarRibbonWidth == ribbonWidth)
			return; // already set;
		this.polarRibbonWidth = ribbonWidth;
		if (ribbonWidth < 0.0) {
			this.polarPhaseMasks = null;
			this.polarPhaseIndices = null;
			return;
		}
		int halfN = this.maxN / 2;
		int length = halfN * this.maxN;
		double halfWidth = ribbonWidth / 2;

		int numAngles = (int) Math.round(Math.PI * halfN);
		this.polarPhaseMasks = new double[numAngles][length];
		this.polarPhaseIndices = new int[length][];
		for (int i = 0; i < this.polarPhaseIndices.length; i++) {
			this.polarPhaseIndices[i] = null;
			for (int iAngle = 0; iAngle < numAngles; iAngle++)
				this.polarPhaseMasks[iAngle][i] = 0.0;
		}
		for (int iAngle = 0; iAngle < numAngles; iAngle++) {
			double angle = iAngle * Math.PI / numAngles;
			double sin = Math.sin(angle);
			double cos = Math.cos(angle);
			double sumWeights = 0.0;
			for (int index = 0; index < length; index++) {
				int x = (index + halfN) % this.maxN - halfN;
				int y = index / this.maxN;
				double t = cos * x + sin * y;
				double d = sin * x - cos * y;
				if (((y > 0) || (x > 0)) && (Math.abs(d) < halfWidth) && (Math.abs(t) < halfN)) {
					this.polarPhaseMasks[iAngle][index] = 0.54 + 0.46 * Math.cos(d / halfWidth * Math.PI); // normalize
					if (Math.abs(t) > (halfN - halfWidth))
						this.polarPhaseMasks[iAngle][index] *= 0.54
								+ 0.46 * Math.cos((Math.abs(t) - (halfN - halfWidth)) / halfWidth * Math.PI);
					sumWeights += this.polarPhaseMasks[iAngle][index];
				}
			}
			sumWeights = 1.0 / sumWeights;
			for (int index = 0; index < length; index++)
				this.polarPhaseMasks[iAngle][index] *= sumWeights;
		}
		for (int index = 0; index < length; index++) {
			int numUsedAngles = 0;
			for (int iAngle = 0; iAngle < numAngles; iAngle++)
				if (this.polarPhaseMasks[iAngle][index] > 0.0)
					numUsedAngles++;
			this.polarPhaseIndices[index] = new int[numUsedAngles]; // may be 0
			int iiAngle = 0;
			for (int iAngle = 0; iAngle < numAngles; iAngle++)
				if (this.polarPhaseMasks[iAngle][index] > 0.0)
					this.polarPhaseIndices[index][iiAngle++] = iAngle;
		}

		if (this.debug) {
			double[][] debugPolarPhaseMasks = new double[numAngles + 1][this.maxN * this.maxN];
			for (int i = 0; i < debugPolarPhaseMasks[0].length; i++) {
				int x = (i % this.maxN) - halfN;
				int y = (i / this.maxN) - halfN;
				if (y < 0) {
					y = -y;
					x = -x;
				}
				if ((y < halfN) && (x > -halfN) && (x < halfN)) {
					int j = (x + this.maxN) % this.maxN + this.maxN * y;
					for (int n = 0; n < numAngles; n++) {
						debugPolarPhaseMasks[n][i] = this.polarPhaseMasks[n][j];
					}
					debugPolarPhaseMasks[numAngles][i] = this.polarPhaseIndices[j].length;
				}

			}
			String[] titles = new String[numAngles + 1];
			for (int n = 0; n < numAngles; n++)
				titles[n] = IJ.d2s(180.0 * n / numAngles, 1);
			titles[numAngles] = "usage number";
			ShowDoubleFloatArrays.showArrays(debugPolarPhaseMasks, this.maxN, this.maxN, true, "dbgDiffPhases", titles);
		}
	}

	/**
	 * Project and accumulate Re, Im on the direction perpendicular to the linear
	 * feature
	 * 
	 * @param directionAngle        direction of the perpendicular line
	 * @param phaseIntegrationWidth Disregard pixels outside of the band centered
	 *                              along directionAngle
	 * @param h                     FHT array
	 * @param nonZeroIndices        List of the above-threshold indices in the FHT
	 *                              array
	 * @return arrays of {weight, re, Im} along the line with the step equal to 1
	 *         pixel
	 */
	public double[][] binReIm(double directionAngle, double phaseIntegrationWidth, // zero - no limit
			double[] h, int[] nonZeroIndices) {
		int halfN = this.maxN / 2;
		double[][] wReIm = new double[3][halfN]; // weight/re/im
		for (int n = 0; n < wReIm.length; n++)
			for (int i = 0; i < wReIm[0].length; i++)
				wReIm[n][i] = 0.0;
		double sin = Math.sin(directionAngle);
		double cos = Math.cos(directionAngle);
		double amp, re, im;
		double halfWidth = (phaseIntegrationWidth > 0.0) ? phaseIntegrationWidth / 2 : this.maxN;
		for (int numPoint = 0; numPoint < nonZeroIndices.length; numPoint++) {
			int index = nonZeroIndices[numPoint];
			int indexMod = ((this.maxN - (index / this.maxN)) % this.maxN) * this.maxN
					+ ((this.maxN - (index % this.maxN)) % this.maxN);
			re = 0.5 * (h[index] + h[indexMod]);
			im = 0.5 * (h[index] - h[indexMod]);
			int x = (index + halfN) % this.maxN - halfN;
			int y = index / this.maxN;
			amp = Math.sqrt(re * re + im * im);
			if (y == 0)
				amp *= 0.5;
			double t = cos * x + sin * y;
			if (Math.abs(cos * y - sin * x) <= halfWidth) {
				int itl = (int) Math.floor(t);
				int ith = itl + 1;
				double wl = amp * (t - itl);
				double wh = amp * (itl + 1 - t);
				boolean conj = (itl < 0);
				if (conj) {
					itl = -itl;
					ith = -ith;
				}
				if (itl < wReIm[0].length) {
					wReIm[0][itl] += wl;
					wReIm[1][itl] += wl * re;
					if (conj)
						wReIm[2][itl] -= wl * im;
					else
						wReIm[2][itl] += wl * im;
				}
				if (ith < wReIm[0].length) {
					wReIm[0][ith] += wh;
					wReIm[1][ith] += wh * re;
					if (conj)
						wReIm[2][ith] -= wh * im;
					else
						wReIm[2][ith] += wh * im;
				}
			} else {
				System.out.println(
						"binReIm(): dropped point x=" + x + " y=" + y + " as it is too far from the center line");
			}
		}
		for (int i = 0; i < wReIm[0].length; i++) {
			if (wReIm[0][i] > 0.0) {
				wReIm[1][i] /= wReIm[0][i];
				wReIm[2][i] /= wReIm[0][i];
			}
		}
		return wReIm;
	}

	/**
	 * Linear approximate phase, optionally filtering types of features (black line,
	 * white line black-to-white edge, white-to-black edge
	 * 
	 * @param wReIm  - array of weights, Re and Im along the selected direction
	 * @param filter Bitmask enabling different phase half-steps (+1 - 0, +2 - pi/2,
	 *               +4 - pi, +8 - 3pi/2. Value zero allows arbitrary step step 0
	 *               corresponds to thin white line, pi - thin black line, +pi/2 -
	 *               edge black-to-white in the direction of directionAngle, 3pi/2 -
	 *               white-to-black in the direction of directionAngle
	 * @return pair of phase at 0 and slope expressed in distance (in pixels) from
	 *         the center to the linear feature along the selected direction (may be
	 *         negative)
	 */
	public double[] approximateLinearPhase(double[][] wReIm, int filter) {
		double[] phase = new double[wReIm[0].length];
		for (int i = 0; i < phase.length; i++)
			if (wReIm[0][i] > 0.0)
				phase[i] = Math.atan2(wReIm[2][i], wReIm[1][i]);
		double diffPhase = 0.0;
		double sumWeights = 0.0;
		for (int i = 0; i < (phase.length - 1); i++) {
			double w = wReIm[0][i] * wReIm[0][i + 1];
			if (w > 0.0) {
				double diff = phase[i + 1] - phase[i];
				if (diff > Math.PI)
					while (diff > Math.PI)
						diff -= 2 * Math.PI;
				else if (diff < -Math.PI)
					while (diff < -Math.PI)
						diff += 2 * Math.PI;
				sumWeights += w;
				diffPhase += diff * w;
			}
		}
		if (sumWeights == 0.0)
			return null;
		diffPhase /= sumWeights;
		double[] binPhases = { 0.0, Math.PI / 2, Math.PI, -Math.PI / 2 };
		double[] zeroPhaseBins = { 0.0, 0.0, 0.0, 0.0 };
		double zeroPhase = Double.NaN;
		switch (filter) {
		case 0:
			double re = 0.0, im = 0.0;
			for (int n = 0; n < phase.length; n++)
				if (wReIm[0][n] > 0.0) {
					double phZero = phase[n] - diffPhase * n;
					re += wReIm[0][n] * Math.cos(phZero);
					im += wReIm[0][n] * Math.sin(phZero);
				}
			zeroPhase = Math.atan2(im, re);
			if (Double.isNaN(zeroPhase))
				zeroPhase = 0.0; // ??
			break;
		case 1:
			zeroPhase = binPhases[0];
			break;
		case 2:
			zeroPhase = binPhases[1];
			break;
		case 4:
			zeroPhase = binPhases[2];
			break;
		case 8:
			zeroPhase = binPhases[3];
			break;
		default:
//			double [] zeroPhaseBins={0.0,0.0,0.0,0.0};
			boolean[] binEnabled = { (filter & 1) != 0, (filter & 2) != 0, (filter & 4) != 0, (filter & 8) != 0 };
			for (int n = 0; n < phase.length; n++)
				if (wReIm[0][n] > 0.0) {
					double phZero = phase[n] - diffPhase * n;
					phZero -= 2 * Math.PI * Math.floor(phZero / (2 * Math.PI)); // now in the range 0..2*PI
					double bestBinDif = 2 * Math.PI;
					int iBestBin = 0;

					for (int i = 0; i < binEnabled.length; i++)
						if (binEnabled[i]) {
							double d = phZero - binPhases[i];
							d -= 2 * Math.PI * Math.round(d / (2 * Math.PI));
							d = Math.abs(d);
							if (d < bestBinDif) {
								bestBinDif = d;
								iBestBin = i;
							}
						}
					zeroPhaseBins[iBestBin] += wReIm[0][n];
				}
			double maxBinValue = 0;
			int iMaxBin = -1;
			for (int i = 0; i < zeroPhaseBins.length; i++)
				if (zeroPhaseBins[i] > maxBinValue) {
					maxBinValue = zeroPhaseBins[i];
					iMaxBin = i;
				}
			zeroPhase = iMaxBin * 2 * Math.PI / zeroPhaseBins.length;
			if (zeroPhase > Math.PI)
				zeroPhase -= 2 * Math.PI;
		}
		double[] fullPhase = phase.clone();
		for (int i = 0; i < fullPhase.length; i++)
			if (wReIm[0][i] > 0.0) {
				double diff = fullPhase[i] - (zeroPhase + diffPhase * i);
				fullPhase[i] -= 2 * Math.PI * Math.round(diff / (2 * Math.PI));
			}
		if (this.debug) {
			for (int i = 0; i < zeroPhaseBins.length; i++)
				System.out.println("Phase    " + i + " bin: " + zeroPhaseBins[i]);
			System.out.println("Initial estimated distance to line " + (this.maxN * diffPhase / (2 * Math.PI))
					+ ", zeroPhase=" + zeroPhase);

			for (int i = 0; i < phase.length; i++)
				if (wReIm[0][i] > 0.0) {
					System.out.println(i + "|" + IJ.d2s(phase[i], 3) + "|" + IJ.d2s(fullPhase[i], 3) + "|"
							+ IJ.d2s((zeroPhase + diffPhase * i), 3));
				}
		}
// re-adjust slope (distance) after zero phase is selected
		double SFX = 0.0, SX2 = 0.0;
		for (int i = 0; i < fullPhase.length; i++)
			if (wReIm[0][i] > 0.0) {
				SFX += wReIm[0][i] * i * (fullPhase[i] - zeroPhase);
				SX2 += wReIm[0][i] * i * i;
			}
		diffPhase = SFX / SX2;
		double distance = this.maxN * diffPhase / (2 * Math.PI);
		double[] result = { zeroPhase, distance };
		if (this.debug) {
			System.out.println("Recalculated distance to line " + distance + " (slope=" + diffPhase + " rad/pix)");
		}
		return result;
	}

	public double[][] calcIndAmReIm(double[] h, int[] nonZeroIndices) {
		double[][] ampReIm = new double[3][nonZeroIndices.length];
		for (int numPoint = 0; numPoint < nonZeroIndices.length; numPoint++) {
			int index = nonZeroIndices[numPoint];
			int indexMod = ((this.maxN - (index / this.maxN)) % this.maxN) * this.maxN
					+ ((this.maxN - (index % this.maxN)) % this.maxN);
			ampReIm[1][numPoint] = 0.5 * (h[index] + h[indexMod]);
			ampReIm[2][numPoint] = 0.5 * (h[index] - h[indexMod]);
			ampReIm[0][numPoint] = Math
					.sqrt(ampReIm[1][index] * ampReIm[1][index] + ampReIm[2][index] * ampReIm[2][index]);
		}
		return ampReIm;
	}

	public double[][] calcIndAmHPhase(double[] h, int[] nonZeroIndices) {
		double re, im;
		double[][] amHPhase = new double[nonZeroIndices.length][2];
		for (int numPoint = 0; numPoint < nonZeroIndices.length; numPoint++) {
			int index = nonZeroIndices[numPoint];
			int indexMod = ((this.maxN - (index / this.maxN)) % this.maxN) * this.maxN
					+ ((this.maxN - (index % this.maxN)) % this.maxN);
			re = 0.5 * (h[index] + h[indexMod]);
			im = 0.5 * (h[index] - h[indexMod]);
			amHPhase[numPoint][0] = Math.sqrt(re * re + im * im);
			if ((index / this.maxN) > 0)
				amHPhase[numPoint][0] *= 2; // double weight
			amHPhase[numPoint][1] = Math.atan2(im, re);
			/*
			 * System.out.println("numPoint="+numPoint+" index="+nonZeroIndices[numPoint]+
			 * " x="+(nonZeroIndices[numPoint]%this.maxN)+" y="+(nonZeroIndices[numPoint]/
			 * this.maxN)+ " re="+re+" im="+im+" phase="+amHPhase[numPoint][1]);
			 */
		}
		return amHPhase;
	}

	public int updateFullCycles(int[] fullCycles, // may be modified
			double px, double py, int[] nonZeroIndices, double[][] amHPhase) {
		int numChanges = 0;
		double e = 1E-8;
		double[] linearPhase = tiltedPhase(px, py, nonZeroIndices);
		for (int numPoint = 0; numPoint < nonZeroIndices.length; numPoint++) {
//			double delta=amHPhase[numPoint][1]+fullCycles[numPoint]*2*Math.PI -linearPhase[numPoint];
			double delta = linearPhase[numPoint] - (amHPhase[numPoint][1] + fullCycles[numPoint] * 2 * Math.PI);
			if (Math.abs(delta) > (Math.PI + e)) {
				System.out.print("numPoint=" + numPoint + " index=" + nonZeroIndices[numPoint] + " x="
						+ (nonZeroIndices[numPoint] % this.maxN) + " y=" + (nonZeroIndices[numPoint] / this.maxN)
						+ " fullCycles[" + numPoint + "]: " + fullCycles[numPoint] + " -> ");
				fullCycles[numPoint] += (int) Math.round(delta / (2 * Math.PI));
				System.out.println(fullCycles[numPoint]);
				numChanges++;
			}
		}
		return numChanges;
	}

	public double calcWeightedPhaseRMS(int[] fullCycles, // may be modified
			double px, double py, int[] nonZeroIndices, double[][] ampPhase) {
		double[] linearPhase = tiltedPhase(px, py, nonZeroIndices);
		double S0 = 0.0, S2 = 0.0;
		for (int numPoint = 0; numPoint < ampPhase.length; numPoint++) {

			double delta = ampPhase[numPoint][1] + fullCycles[numPoint] * 2 * Math.PI - linearPhase[numPoint];
			S0 += ampPhase[numPoint][0];
			S2 += ampPhase[numPoint][0] * delta * delta;
			/*
			 * System.out.println("nonZeroIndices["+numPoint+"]="+nonZeroIndices[numPoint]+
			 * " x="+(nonZeroIndices[numPoint]%this.maxN)+" y="+(nonZeroIndices[numPoint]/
			 * this.maxN)+
			 * " ampPhase["+numPoint+"][0]="+ampPhase[numPoint][0]+" ampPhase["+numPoint+
			 * "][1]="+ampPhase[numPoint][1]+ " delta="+delta+" S0="+S0+" S2="+S2);
			 */
		}
		double weightedRMS = Math.sqrt(S2 / S0);
		return weightedRMS;
	}

	public double[] calcPhaseShift(int[] fullCycles, // may be modified
			int[] nonZeroIndices, double[][] ampPhase) {
//		double [] linearPhase= tiltedPhase (px, py, nonZeroIndices);
// minimize weighted RMS with a plane through (0,0)
		int halfN = this.maxN / 2;
		double SFX = 0.0, SFY = 0.0, SX2 = 0.0, SY2 = 0.0, SXY = 0.0;
		for (int numPoint = 0; numPoint < ampPhase.length; numPoint++) {
			int index = nonZeroIndices[numPoint];
			int x = (index + halfN) % this.maxN - halfN;
			int y = index / this.maxN;
			double fXY = ampPhase[numPoint][1] + Math.PI * 2 * fullCycles[numPoint];
			double w = ampPhase[numPoint][0];
			SFX += w * x * fXY;
			SFY += w * y * fXY;
			SX2 += w * x * x;
			SY2 += w * y * y;
			SXY += w * x * y;
		}
		double denominator = SXY * SXY - SX2 * SY2;
		double[] phaseTilt = { (SFY * SXY - SFX * SY2) / denominator, (SFX * SXY - SFY * SX2) / denominator };
		return phaseTilt;
	}

	public double calcPhaseShift(double px, double py, int[] fullCycles, // may be modified
			int[] nonZeroIndices, double[][] ampPhase) {
//		double [] linearPhase= tiltedPhase (px, py, nonZeroIndices);
// minimize weighted RMS with a plane through (0,0)
		int halfN = this.maxN / 2;
		double SFX = 0.0, SFY = 0.0, SX2 = 0.0, SY2 = 0.0, SXY = 0.0;
		for (int numPoint = 0; numPoint < ampPhase.length; numPoint++) {
			int index = nonZeroIndices[numPoint];
			int x = (index + halfN) % this.maxN - halfN;
			int y = index / this.maxN;
			double fXY = ampPhase[numPoint][1] + Math.PI * 2 * fullCycles[numPoint];
			double w = ampPhase[numPoint][0];
			SFX += w * x * fXY;
			SFY += w * y * fXY;
			SX2 += w * x * x;
			SY2 += w * y * y;
			SXY += w * x * y;
		}
		return (py * SFY + px * SFX - px * py * SXY) / (px * px * SX2 + py * py * SY2);
	}

	public double[] tiltedPhase(double px, double py, int[] nonZeroIndices) {
		int halfN = this.maxN / 2;
		double[] phase = new double[nonZeroIndices.length];
		for (int numPoint = 0; numPoint < nonZeroIndices.length; numPoint++) {
			int index = nonZeroIndices[numPoint];
			int x = (index + halfN) % this.maxN - halfN;
			int y = index / this.maxN;
			phase[numPoint] = px * x + py * y;
		}
		return phase;
	}

	/*
	 * public double [][] calcAmReIm (double [] h, double [] ampMask){ int rowMod,
	 * colMod; int halfN=this.maxN/2; double [][] ampReIm=new
	 * double[3][this.maxN*halfN]; for (int r =0; r<this.maxN/2; r++) { rowMod =
	 * (this.maxN - r) % this.maxN; for (int c=0; c<this.maxN; c++){ int index= r *
	 * this.maxN + c; if ((ampMask==null) || (ampMask[index]>0.0)){ colMod =
	 * (this.maxN - c) % this.maxN; int indexMod=rowMod * this.maxN + colMod;
	 * ampReIm[1][index]=0.5*(h[index]+h[indexMod]);
	 * ampReIm[2][index]=0.5*(h[index]-h[indexMod]);
	 * ampReIm[0][index]=Math.sqrt(ampReIm[1][index]*ampReIm[1][index]+ampReIm[2][
	 * index]*ampReIm[2][index]); } else { ampReIm[1][index]=0.0;
	 * ampReIm[2][index]=0.0; ampReIm[0][index]=0.0; } } } return ampReIm; }
	 */
	public double[] filterAmplitude(double[] h, boolean removeIslands, double threshold) { // relative to RMS value
		int rowMod, colMod;
		int halfN = this.maxN / 2;
		double[] amplitude = new double[this.maxN * halfN];
		double max = 0;
		int iMax = -1;
		double sum2 = 0.0;
		double amp2;
		for (int r = 0; r < this.maxN / 2; r++) {
			rowMod = (this.maxN - r) % this.maxN;
			for (int c = 0; c < this.maxN; c++) {
				int index = r * this.maxN + c;
				if (c == this.maxN / 2) {
					amplitude[index] = 0.0;
				} else {
					colMod = (this.maxN - c) % this.maxN;
					int indexMod = rowMod * this.maxN + colMod;
					if (r > 0) {
						amp2 = h[index] * h[index] + h[indexMod] * h[indexMod]; // count twice (for the second
																				// symmetrical half)
						amplitude[index] = 2.0 * amp2; // so square root will be twice
					} else {
						amp2 = 0.5 * (h[index] * h[index] + h[indexMod] * h[indexMod]);
						amplitude[index] = amp2;
					}
					sum2 += amp2;
					if (amp2 > max) {
						max = amp2;
						iMax = index;
					}
				}
			}
		}
		double minAmp2 = threshold * sum2 / (this.maxN - 1) / (this.maxN - 1);
		for (int i = 0; i < amplitude.length; i++) {
			if (amplitude[i] < minAmp2)
				amplitude[i] = 0.0;
			else
				amplitude[i] = Math.sqrt(amplitude[i]);
		}
		int numDefined = 0;
		if (this.debug) {
			for (int i = 0; i < amplitude.length; i++)
				if (amplitude[i] > 0.0)
					numDefined++;
			System.out.println(
					"quadraticAmplitude(): number of defined cells=" + numDefined + " ( of " + amplitude.length + ")");
		}

		if (removeIslands) {
			boolean[] confirmed = new boolean[amplitude.length];
			for (int i = 0; i < confirmed.length; i++)
				confirmed[i] = false;
			int[][] dirs = { { 1, 0 }, { 1, 1 }, { 0, 1 }, { -1, 1 }, { -1, 0 }, { -1, -1 }, { 0, -1 }, { 1, -1 } };
			List<Integer> ampList = new ArrayList<Integer>(confirmed.length);
			int x = (iMax + halfN) % this.maxN - halfN;
			int y = iMax / this.maxN;
			Integer Index = iMax;
			ampList.add(Index);
			confirmed[Index] = true;
			while (ampList.size() > 0) {
				int index = ampList.remove(0);
				x = (index + halfN) % this.maxN - halfN;
				y = index / this.maxN;
				for (int iDir = 0; iDir < dirs.length; iDir++) {
					int x1 = x + dirs[iDir][0];
					int y1 = y + dirs[iDir][1];
					if (y1 < 0) {
						y1 = -y1;
						x1 = -x1;
					}
					if ((x1 > -halfN) && (x1 < halfN) && (y1 >= 0) && (y1 < halfN)) {
						Index = (x1 + this.maxN) % this.maxN + this.maxN * y1;
						if (!confirmed[Index] && (amplitude[Index] > 0.0)) {
							confirmed[Index] = true;
							ampList.add(Index);
						}
					}
				}
			}
			for (int i = 0; i < amplitude.length; i++) {
				if (!confirmed[i])
					amplitude[i] = 0.0;
			}
			if (this.debug) {
				numDefined = 0;
				for (int i = 0; i < amplitude.length; i++)
					if (amplitude[i] > 0.0)
						numDefined++;
				System.out.println("quadraticAmplitude(): number of remaining cells=" + numDefined + " ( of "
						+ amplitude.length + ")");
			}
		}
		/*
		 * if (this.debug){ ShowDoubleFloatArrays.showArrays( amplitude, this.maxN,
		 * halfN, "fltAmp"); double [] debugAmplitude=new double [this.maxN*this.maxN];
		 * for (int i=0;i<debugAmplitude.length;i++){ debugAmplitude[i]=0.0; int x=
		 * (i%this.maxN)-halfN; int y= (i/this.maxN)-halfN; if (y<0) { y=-y; x=-x; } if
		 * ((y<halfN) && (x>-halfN) && ( x<halfN)){ int j= (x+this.maxN)%this.maxN +
		 * this.maxN*y; debugAmplitude[i]=amplitude[j]; if (y>0) debugAmplitude[i]*=0.5;
		 * }
		 * 
		 * } ShowDoubleFloatArrays.showArrays( debugAmplitude, this.maxN, this.maxN,
		 * "fltAmp"); }
		 */
		return amplitude;
	}

	public double[] quadraticAmplitude(double[] amplitude, boolean removeIslands, double threshold) { // relative to RMS
																										// value
		int halfN = this.maxN / 2;
		double[] result = new double[3]; // CX2, CY2, CXY
		for (int i = 0; i < result.length; i++)
			result[i] = 0.0;
		double s = 0.0;
		double amp;
		for (int r = 0; r < this.maxN / 2; r++) {
			for (int c = 0; c < this.maxN; c++)
				if (c != this.maxN / 2) {
					int index = r * this.maxN + c;
					amp = amplitude[index];
					s += amp;
					int x = ((c + halfN) % this.maxN) - halfN;
					result[0] += amp * x * x;
					result[1] += amp * r * r;
					result[2] += amp * x * r;
				}
		}
		s *= halfN * halfN; // normalize so result will be related to pixels, not to the FFT size
		for (int i = 0; i < result.length; i++)
			result[i] /= s;
		return result;
	}

	/*
	 * public double [] quadraticAmplitude( double [] h){ int rowMod, colMod;
	 * double[] result = new double[3]; // CX2, CY2, CXY for (int
	 * i=0;i<result.length;i++) result[i]=0.0; double s=0.0; double amp; int
	 * halfN=this.maxN/2; for (int r =0; r<this.maxN/2; r++) { rowMod = (this.maxN -
	 * r) % this.maxN; for (int c=0; c<this.maxN; c++) if (c!=this.maxN/2){ colMod =
	 * (this.maxN - c) % this.maxN; int index= r * this.maxN + c; int
	 * indexMod=rowMod * this.maxN + colMod;
	 * amp=Math.sqrt(0.5*(h[index]*h[index]+h[indexMod]*h[indexMod])); if (r>0)
	 * amp*=2; // count twice (for the second symmetrical half) s+=amp; int
	 * x=((c+halfN)%this.maxN)-halfN; result[0]+=amp*x*x; result[1]+=amp*r*r;
	 * result[2]+=amp*x*r; } } s*=halfN*halfN; // normalize so result will be
	 * related to pixels, not to the FFT size for (int i=0;i<result.length;i++)
	 * result[i]/=s; return result; }
	 */
	public double[] ellipseAmplitude(double[] quadratic) {
		double[] result = new double[3]; // angle (clockwise from X, large half-diameter, small/large ratio
		double alpha = 0.5 * Math.atan2(2 * quadratic[2], quadratic[0] - quadratic[1]); // 1/2*atan(2*Sxy/(sx2-sy2))
		double cos = Math.cos(alpha), sin = Math.sin(alpha);
		double I1 = sin * sin * quadratic[0] + cos * cos * quadratic[1] - 2 * cos * sin * quadratic[2];
		double I2 = cos * cos * quadratic[0] + sin * sin * quadratic[1] + 2 * cos * sin * quadratic[2];
		boolean rot = (I1 > I2);
		result[0] = alpha + (rot ? Math.PI : 0);
		result[1] = Math.sqrt(rot ? I1 : I2);
		result[2] = Math.sqrt(rot ? (I2 / I1) : (I1 / I2));
		return result;
	}

	public double[] multiply(double[] h1, double[] h2, boolean conjugate) {
		int rowMod, colMod;
		double h2e, h2o;
		double[] product = new double[maxN * maxN];
		for (int r = 0; r < maxN; r++) {
			rowMod = (maxN - r) % maxN;
			for (int c = 0; c < maxN; c++) {
				colMod = (maxN - c) % maxN;
				h2e = (h2[r * maxN + c] + h2[rowMod * maxN + colMod]) / 2;
				h2o = (h2[r * maxN + c] - h2[rowMod * maxN + colMod]) / 2;
				if (conjugate)
					product[r * maxN + c] = h1[r * maxN + c] * h2e - h1[rowMod * maxN + colMod] * h2o;
				else
					product[r * maxN + c] = h1[r * maxN + c] * h2e + h1[rowMod * maxN + colMod] * h2o;
			}
		}
		return product;
	}

	public double[] phaseMultiply(double[] h1, double[] h2, double phaseCoeff) {
		int rowMod, colMod;
		double h2e, h2o, d;
		double[] product = new double[maxN * maxN];
		for (int r = 0; r < maxN; r++) {
			rowMod = (maxN - r) % maxN;
			for (int c = 0; c < maxN; c++) {
				colMod = (maxN - c) % maxN;
				h2e = (h2[r * maxN + c] + h2[rowMod * maxN + colMod]) / 2;
				h2o = (h2[r * maxN + c] - h2[rowMod * maxN + colMod]) / 2;
				d = phaseCoeff * (h2e * h2e + h2o * h2o) + (1.0 - phaseCoeff);
				product[r * maxN + c] = (h1[r * maxN + c] * h2e - h1[rowMod * maxN + colMod] * h2o) / d;
			}
		}
		return product;
	}

	public double[] phaseMultiplyNorm(double[] h1, double[] h2, double phaseCoeff) {
		int size = maxN;
		int size2 = size >> 1;
		int size21 = size * size2;
		int rowMod, colMod, base, baseMod;
		double h2e, h2o;
		double[] product = new double[size * size];
		for (int r = 0; r < size; r++) {
			rowMod = (size - r) % size;
			for (int c = 0; c < size; c++) {
				colMod = (size - c) % size;
				h2e = (h2[r * size + c] + h2[rowMod * size + colMod]) / 2;
				h2o = (h2[r * size + c] - h2[rowMod * size + colMod]) / 2;
				product[r * size + c] = (h1[r * size + c] * h2e - h1[rowMod * size + colMod] * h2o);
			}
		}
		double[] amplitude = calculateAmplitudeHalf(product);
		double avg_ampl = 0.0;
		for (int row = 1; row < size2; row++) {
			base = row * size;
			for (int col = 0; col < size; col++) {
				avg_ampl += amplitude[col + base];
			}
		}
		avg_ampl *= 2;
		for (int col = 0; col < size; col++) {
			avg_ampl += amplitude[col] + amplitude[col + size21];
		}
		avg_ampl /= size * size;
		double aoffs = (1.0 - phaseCoeff) * avg_ampl;
		double ampl;
		for (int row = 0; row <= size2; row++) {
			base = row * size;
			rowMod = (size - row) % size;
			baseMod = rowMod * size;
			for (int col = 0; col < size; col++) {
				ampl = phaseCoeff * amplitude[col + base] + aoffs;
				product[col + base] /= ampl;
				if ((row > 0) && (row < size2)) {
					colMod = (size - col) % size;
					product[colMod + baseMod] /= ampl;
				}
			}
		}
		return product;
	}

// Multiply by real array (i.e. filtering in frequency domain). Array m length should be at least maxN*maxN/2+1
	public void multiplyByReal(double[] h, double[] m) {
		int rowMod, colMod;
		int index = 0, indexM;
		for (int r = 0; r < maxN; r++) {
			rowMod = (maxN - r) % maxN;
			for (int c = 0; c < maxN; c++) {
				colMod = (maxN - c) % maxN;
				indexM = rowMod * maxN + colMod;
				if (indexM > index)
					indexM = index;
				h[index] *= m[indexM];
				index++;
			}
		}
	}

	/* nothing to prevent division by small values */
	/*
	 * Returns the image resulting from the point by point Hartley division of this
	 * image by the specified image. Both images are assumed to be in the frequency
	 * domain. Division in the frequency domain is equivalent to deconvolution in
	 * the space domain.
	 */
	public double[] divide(double[] h1, double[] h2) {
		int rowMod, colMod;
		double mag, h2e, h2o;
		double[] result = new double[maxN * maxN];
		for (int r = 0; r < maxN; r++) {
			rowMod = (maxN - r) % maxN;
			for (int c = 0; c < maxN; c++) {
				colMod = (maxN - c) % maxN;
				mag = h2[r * maxN + c] * h2[r * maxN + c] + h2[rowMod * maxN + colMod] * h2[rowMod * maxN + colMod];
				if (mag < 1e-20)
					mag = 1e-20;
				h2e = (h2[r * maxN + c] + h2[rowMod * maxN + colMod]);
				h2o = (h2[r * maxN + c] - h2[rowMod * maxN + colMod]);
				double tmp = (h1[r * maxN + c] * h2e - h1[rowMod * maxN + colMod] * h2o);
				result[r * maxN + c] = tmp / mag;
			}
		}
		return result;
	}

	public double[] divide(double[] h1, double[] h2, double fat_zero) {
		int rowMod, colMod;
		double mag, h2e, h2o;
		double fz2 = fat_zero * fat_zero;
		double[] result = new double[maxN * maxN];
		for (int r = 0; r < maxN; r++) {
			rowMod = (maxN - r) % maxN;
			for (int c = 0; c < maxN; c++) {
				colMod = (maxN - c) % maxN;
				mag = h2[r * maxN + c] * h2[r * maxN + c] + h2[rowMod * maxN + colMod] * h2[rowMod * maxN + colMod]
						+ fz2;
				if (mag < 1e-20)
					mag = 1e-20;
				h2e = (h2[r * maxN + c] + h2[rowMod * maxN + colMod]);
				h2o = (h2[r * maxN + c] - h2[rowMod * maxN + colMod]);
				double tmp = (h1[r * maxN + c] * h2e - h1[rowMod * maxN + colMod] * h2o);
				result[r * maxN + c] = tmp / mag;
			}
		}
		return result;
	}

	
	
	public double[] setReal(double[] amp) { // only first half used
		double[] result = new double[maxN * maxN];
		int rowMod, colMod;
		for (int r = 0; r < maxN / 2; r++) {
			rowMod = (maxN - r) % maxN;
			for (int c = 0; c < maxN; c++) {
				colMod = (maxN - c) % maxN;
				result[r * maxN + c] = amp[r * maxN + c];
				result[rowMod * maxN + colMod] = amp[r * maxN + c];
			}
		}
		return result;
	}

	public double[] calculateAmplitude(double[] fht) {
		int size = (int) Math.sqrt(fht.length);
		double[] amp = new double[size * size];
		for (int row = 0; row < size; row++) {
			amplitude(row, size, fht, amp);
		}
		swapQuadrants(amp);
		return amp;
	}

	public double[] calculateAmplitudeNoSwap(double[] fht) {
		int size = (int) Math.sqrt(fht.length);
		double[] amp = new double[size * size];
		for (int row = 0; row < size; row++) {
			amplitude(row, size, fht, amp);
		}
		return amp;
	}

	public static double[] calculatePhaseNoSwap(double[] fht) {
		int size = (int) Math.sqrt(fht.length);
		double[] phs = new double[size * size];
		for (int row = 0; row < size; row++) {
			phase(row, size, fht, phs);
		}
		return phs;
	}

	public double[] calculatePhase(double[] fht) {
		int size = (int) Math.sqrt(fht.length);
		double[] phs = new double[size * size];
		for (int row = 0; row < size; row++) {
			phase(row, size, fht, phs);
		}
		swapQuadrants(phs);
		return phs;
	}

	public double[] calculateAmplitudeHalf(double[] fht) {
		int size = (int) Math.sqrt(fht.length);
		int size2 = (size >> 1) + 1;
		double[] amp = new double[size * size2];
		for (int row = 0; row < size2; row++) {
			amplitude(row, size, fht, amp);
		}
		return amp;
	}

	public double[] calculateAmplitude2(double[] fht) {
		int size = (int) Math.sqrt(fht.length);
		double[] amp = new double[size * size];
		for (int row = 0; row < size; row++) {
			amplitude2(row, size, fht, amp);
		}
		swapQuadrants(amp);
		return amp;
	}

	/* Amplitude of one row from 2D Hartley Transform. */
	void amplitude(int row, int size, double[] fht, double[] amplitude) {
		int base = row * size;
		int l;
		for (int c = 0; c < size; c++) {
			l = ((size - row) % size) * size + (size - c) % size;
			amplitude[base + c] = Math.sqrt(fht[base + c] * fht[base + c] + fht[l] * fht[l]);
		}
	}

	static void phase(int row, int size, double[] fht, double[] phase) {
		int base = row * size;
		int l;
		for (int c = 0; c < size; c++) {
			l = ((size - row) % size) * size + (size - c) % size;
			double re = 0.5 * (fht[base + c] + fht[l]);
			double im = 0.5 * (fht[base + c] - fht[l]);
			phase[base + c] = Math.atan2(im, re);
			;
		}
	}

	/* Squared amplitude of one row from 2D Hartley Transform. */
	void amplitude2(int row, int size, double[] fht, double[] amplitude) {
		int base = row * size;
		int l;
		for (int c = 0; c < size; c++) {
			l = ((size - row) % size) * size + (size - c) % size;
			amplitude[base + c] = fht[base + c] * fht[base + c] + fht[l] * fht[l];
		}
	}

// Other FHT-related methods moved here
	/*
	 * converts FHT results (frequency space) to complex numbers of
	 * [fftsize/2+1][fftsize]
	 */
	public double[][][] FHT2FFTHalf(FHT fht, int fftsize) {
		float[] fht_pixels = (float[]) fht.getPixels();
		double[][][] fftHalf = new double[(fftsize >> 1) + 1][fftsize][2];
		int row1, row2, col1, col2;

		for (row1 = 0; row1 <= (fftsize >> 1); row1++) {
			row2 = (fftsize - row1) % fftsize;
			for (col1 = 0; col1 < fftsize; col1++) {
				col2 = (fftsize - col1) % fftsize;
				fftHalf[row1][col1][0] = 0.5 * (fht_pixels[row1 * fftsize + col1] + fht_pixels[row2 * fftsize + col2]);
				fftHalf[row1][col1][1] = 0.5 * (fht_pixels[row2 * fftsize + col2] - fht_pixels[row1 * fftsize + col1]);
			}
		}
		return fftHalf;
	}

	public double[][][] FHT2FFTHalf(double[] fht_pixels, int fftsize) {
		double[][][] fftHalf = new double[(fftsize >> 1) + 1][fftsize][2];
		int row1, row2, col1, col2;

		for (row1 = 0; row1 <= (fftsize >> 1); row1++) {
			row2 = (fftsize - row1) % fftsize;
			for (col1 = 0; col1 < fftsize; col1++) {
				col2 = (fftsize - col1) % fftsize;
				fftHalf[row1][col1][0] = 0.5 * (fht_pixels[row1 * fftsize + col1] + fht_pixels[row2 * fftsize + col2]);
				fftHalf[row1][col1][1] = 0.5 * (fht_pixels[row2 * fftsize + col2] - fht_pixels[row1 * fftsize + col1]);
			}
		}
		return fftHalf;
	}

	/*
	 * converts FFT arrays of complex numbers of [fftsize/2+1][fftsize] to FHT
	 * arrays
	 */
	public float[] floatFFTHalf2FHT(double[][][] fft, int fftsize) {
		float[] fht_pixels = new float[fftsize * fftsize];
		int row1, row2, col1, col2;
		for (row1 = 0; row1 <= (fftsize >> 1); row1++) {
			row2 = (fftsize - row1) % fftsize;
			for (col1 = 0; col1 < fftsize; col1++) {
				col2 = (fftsize - col1) % fftsize;
				fht_pixels[row1 * fftsize + col1] = (float) (fft[row1][col1][0] - fft[row1][col1][1]);
				fht_pixels[row2 * fftsize + col2] = (float) (fft[row1][col1][0] + fft[row1][col1][1]);
			}
		}
		return fht_pixels;
	}

	public double[] FFTHalf2FHT(double[][][] fft, int fftsize) {
		double[] fht_pixels = new double[fftsize * fftsize];
		int row1, row2, col1, col2;
		for (row1 = 0; row1 <= (fftsize >> 1); row1++) {
			row2 = (fftsize - row1) % fftsize;
			for (col1 = 0; col1 < fftsize; col1++) {
				col2 = (fftsize - col1) % fftsize;
				fht_pixels[row1 * fftsize + col1] = fft[row1][col1][0] - fft[row1][col1][1];
				fht_pixels[row2 * fftsize + col2] = fft[row1][col1][0] + fft[row1][col1][1];
			}
		}
		return fht_pixels;
	}

	// Uses just first half and one line
	public double[] FFTHalf2FHT(double[][] fft, int fftsize) {
		double[] fht_pixels = new double[fftsize * fftsize];
		int row1, row2, col1, col2;
		for (row1 = 0; row1 <= (fftsize >> 1); row1++) {
			row2 = (fftsize - row1) % fftsize;
			for (col1 = 0; col1 < fftsize; col1++) {
				col2 = (fftsize - col1) % fftsize;
				fht_pixels[row1 * fftsize + col1] = fft[0][row1 * fftsize + col1] - fft[1][row1 * fftsize + col1];
				fht_pixels[row2 * fftsize + col2] = fft[0][row1 * fftsize + col1] + fft[1][row1 * fftsize + col1];
			}
		}
		return fht_pixels;
	}

	/* Amplitude/phase related methods */
	public double[] interpolateFHT(double[] fht0, // first FHT array
			double[] fht1, // second FHT array
			double ratio) { // array of interpolation points - 0.0 - fht0, 1.0 - fht1
		double[] points = { ratio };
		double[][] results = interpolateFHT(fht0, // first FHT array
				fht1, // second FHT array
				points, // array of interpolation points - 0.0 - fht0, 1.0 - fht1
				true); // do not clone 0.0 and 1.0 (ends)
		return results[0];
	}

	/*
	 * returns array of interpolated FHTs between fht0 and fht1, endpoints if
	 * present (0.0, 1.0) are referenced, not cloned
	 */
	public double[][] interpolateFHT(double[] fht0, // first FHT array
			double[] fht1, // second FHT array
			double[] points) { // array of interpolation points - 0.0 - fht0, 1.0 - fht1
		return interpolateFHT(fht0, // first FHT array
				fht1, // second FHT array
				points, // array of interpolation points - 0.0 - fht0, 1.0 - fht1
				false); // do not clone 0.0 and 1.0 (ends)
	}

	public double[][] interpolateFHT(double[] fht0, // first FHT array
			double[] fht1, // second FHT array
			double[] points, // array of interpolation points - 0.0 - fht0, 1.0 - fht1
			boolean cloneTrivial) {
		double[] fht_div = divide(fht1, fht0);
		int size = (int) Math.sqrt(fht0.length);
		int hsize = size / 2;
		double[][][] aphase = new double[hsize + 1][size][2];
		double[][][] amp01 = new double[hsize + 1][size][2]; /* squared amplitudes of fht0 and fht1 */
		double[][] phase = new double[hsize + 1][size]; /* +/-pi phase of the first array */
		double[][][] fft0 = FHT2FFTHalf(fht0, size);
		double[][][] fft1 = FHT2FFTHalf(fht1, size);
		double[][][] fft_div = FHT2FFTHalf(fht_div, size);
		int i, j, k;
		double a, c, p;
		/* use mul for amplitudes, div - for phases */
		for (i = 0; i <= hsize; i++)
			for (j = 0; j < size; j++) {
				amp01[i][j][0] = fft0[i][j][0] * fft0[i][j][0] + fft0[i][j][1] * fft0[i][j][1];
				amp01[i][j][1] = fft1[i][j][0] * fft1[i][j][0] + fft1[i][j][1] * fft1[i][j][1];
				if (amp01[i][j][0] > 0.0)
					phase[i][j] = Math.atan2(fft0[i][j][1], fft0[i][j][0]);
				else
					phase[i][j] = 0.0;
				aphase[i][j][0] = amp01[i][j][0] * amp01[i][j][1]; // product of squared amplitudes is OK for phase
																	// restorations, we just need to know where
																	// amplitudes are higher
				a = fft_div[i][j][0] * fft_div[i][j][0] + fft_div[i][j][1] * fft_div[i][j][1];
				if (a > 0.0)
					aphase[i][j][1] = Math.atan2(fft_div[i][j][1], fft_div[i][j][0]);
				else
					aphase[i][j][1] = 0.0;
			}
		aphase[0][0][1] = 0.0;
		/* calculate full phases */
		fullPhase(aphase);
		double[][] result = new double[points.length][];
		for (k = 0; k < result.length; k++) {
			if (points[k] == 0.0)
				result[k] = cloneTrivial ? fht0.clone() : fht0;
			else if (points[k] == 1.0)
				result[k] = cloneTrivial ? fht1.clone() : fht1;
			else { /* interpolate */
				c = points[k];
				for (i = 0; i <= hsize; i++)
					for (j = 0; j < size; j++) {
						if ((amp01[i][j][0] == 0.0) || (amp01[i][j][1] == 0.0))
							a = 0.0;
						/*
						 * Extrapolation is defined here only in the direction of decreasing of the
						 * spectral amplitudes (outside, to the wider PSF), so additional limit to
						 * prevent division of small values
						 */
						/*
						 * Seems to work, possible improvements: 1-filter spectrum in high-freq areas. 2
						 * - use farther inner points for farther approximation
						 */

						else if ((c < 0.0) && (amp01[i][j][0] > amp01[i][j][1]))
							a = Math.sqrt(amp01[i][j][0]);
						else if ((c > 1.0) && (amp01[i][j][0] < amp01[i][j][1]))
							a = Math.sqrt(amp01[i][j][1]);
						else
							a = Math.pow(amp01[i][j][0], 0.5 * (1.0 - c)) * Math.pow(amp01[i][j][1], 0.5 * c);
						p = phase[i][j] + c * aphase[i][j][1];
						fft0[i][j][0] = a * Math.cos(p);
						fft0[i][j][1] = a * Math.sin(p);
					}
				result[k] = FFTHalf2FHT(fft0, size);
			}
		}
		return result;
	}

	/**
	 *
	 * @param fht          FHT data
	 * @param fullCentered - if false - returns minimal (size*(size/2-1) arrays, if
	 *                     true - fills the full square arrays and swaps quadrants
	 * @return 2-d array, first index: 0 - amplitude, 1 - phase. second index range
	 *         depends on fullCentered
	 */
	public double[][] fht2AmpHase(double[] fht, boolean fullCentered) {
		int size = (int) Math.sqrt(fht.length);
		int hsize = size / 2;
		double[][][] fft = FHT2FFTHalf(fht, size);
		double[][] aphase = new double[2][size * (fullCentered ? size : (hsize + 1))];
		int index = 0;
		double a;
		for (int i = 0; i <= hsize; i++)
			for (int j = 0; j < size; j++) {
				a = Math.sqrt(fft[i][j][0] * fft[i][j][0] + fft[i][j][1] * fft[i][j][1]);
				aphase[0][index] = a;
				aphase[1][index++] = (a > 0.0) ? Math.atan2(fft[i][j][1], fft[i][j][0]) : 0.0;
			}
		if (fullCentered) {
			for (int i = 1; i < hsize; i++)
				for (int j = 0; j < size; j++) {
					int j1 = (size - j) % size;
					aphase[0][(size - i) * size + j] = aphase[0][i * size + j1];
					aphase[1][(size - i) * size + j] = -aphase[1][i * size + j1];
				}
			swapQuadrants(aphase[0]);
			swapQuadrants(aphase[1]);
		}
		return aphase;
	}

	public double[][] fht2ReIm(double[] fht, boolean fullCentered) {
		int size = (int) Math.sqrt(fht.length);
		int hsize = size / 2;
		double[][][] fft = FHT2FFTHalf(fht, size);
		double[][] reIm = new double[2][size * (fullCentered ? size : (hsize + 1))];
		int index = 0;
		for (int i = 0; i <= hsize; i++)
			for (int j = 0; j < size; j++) {
				reIm[0][index] = fft[i][j][0];
				reIm[1][index++] = fft[i][j][1];
			}
		if (fullCentered) {
			for (int i = 1; i < hsize; i++)
				for (int j = 0; j < size; j++) {
					int j1 = (size - j) % size;
					reIm[0][(size - i) * size + j] = reIm[0][i * size + j1];
					reIm[1][(size - i) * size + j] = -reIm[1][i * size + j1];
				}
			swapQuadrants(reIm[0]);
			swapQuadrants(reIm[1]);
		}
		return reIm;
	}

	/*
	 * replace +/-pi phase with the full phase, using amplitude to guide grouth of
	 * the covered area, so amplitude and phase does not need to be a pair from the
	 * same FFT array
	 */
	public void fullPhase(double[][][] aphase) {
		int size = aphase[0].length;
		int hsize = aphase.length - 1;
		boolean[][] map = new boolean[hsize + 1][size];
		int i, j;
		aphase[0][0][1] = 0.0;
		int ix, iy, ix1, iy1, ix1n, iy1n;
		List<Integer> pixelList = new ArrayList<Integer>(100);
		Integer Index;
		int[][] dirs = { { -1, 0 }, { -1, -1 }, { 0, -1 }, { 1, -1 }, { 1, 0 }, { 1, 1 }, { 0, 1 }, { -1, 1 } };
		ix = 0;
		iy = 0;
		int clusterSize = 0;
		boolean noNew = true;
		int maxX = 0;
		int maxY = 0;
		int oldX = 0;
		int oldY = 0;
		boolean oldConj = false;
		int listIndex;
		Index = iy * size + ix;
		pixelList.clear();
		pixelList.add(Index);
		clusterSize++;
		map[iy][ix] = true;
		noNew = true;
		double phase, oldPhase, fullCyclesPhase;
		double maxValue = -1.0;

		while (pixelList.size() > 0) {
			/* Find maximal new neighbor */
			maxValue = -1.0;
			listIndex = 0;
			while (listIndex < pixelList.size()) {
				Index = pixelList.get(listIndex);
				iy = Index / size;
				ix = Index % size;
				noNew = true;
				for (j = 0; j < 8; j++) {
					ix1 = (ix + dirs[j][0] + size) % size;
					iy1 = (iy + dirs[j][1] + size) % size;
					if ((iy1 > hsize) || (((iy1 == 0) || (iy1 == hsize)) && (ix1 > hsize))) {
						ix1n = (size - ix1) % size;
						iy1n = (size - iy1) % size;
					} else { /* But phase will be opposite sign */
						ix1n = ix1;
						iy1n = iy1;
					}
					if (!map[iy1n][ix1n]) {
						noNew = false;
						if (aphase[iy1n][ix1n][0] > maxValue) {
							maxValue = aphase[iy1n][ix1n][0];
							maxX = ix1n;
							maxY = iy1n;
//      if (DEBUG_LEVEL>4)      System.out.println(" amplPhase(): iy="+iy+ " ix="+ix+" maxY="+maxY+" maxX="+maxX);
						}
					}
				}
				if (noNew)
					pixelList.remove(listIndex); // remove current list element
				else
					listIndex++; // increase list index
			}

			if (pixelList.size() == 0)
				break;
			/*
			 * To calculate the phase - find already processed neighbor with the highest
			 * amplitude
			 */
			maxValue = -1.0;
			for (j = 0; j < 8; j++) {
				ix1 = (maxX + dirs[j][0] + size) % size;
				iy1 = (maxY + dirs[j][1] + size) % size;
				if ((iy1 > hsize) || (((iy1 == 0) || (iy1 == hsize)) && (ix1 > hsize))) {
					ix1n = (size - ix1) % size;
					iy1n = (size - iy1) % size;
				} else { /* But phase will be opposite sign */
					ix1n = ix1;
					iy1n = iy1;
				}
				if (map[iy1n][ix1n]) {
					if (aphase[iy1n][ix1n][0] > maxValue) {
						maxValue = aphase[iy1n][ix1n][0];
						oldX = ix1n;
						oldY = iy1n;
						oldConj = (iy1 != iy1n) || (ix1 != ix1n); // point on the other half (conjugate)

					}
				}
			}

			/* Calculate the phase from the closest neighbor */
			oldPhase = (oldConj ? -1 : 1) * aphase[oldY][oldX][1];
			fullCyclesPhase = 2 * Math.PI * Math.floor(oldPhase / (2 * Math.PI) + 0.5);
			oldPhase -= fullCyclesPhase; // +/- pi
			phase = aphase[maxY][maxX][1];
			if ((phase - oldPhase) > Math.PI)
				fullCyclesPhase -= 2 * Math.PI;
			else if ((oldPhase - phase) > Math.PI)
				fullCyclesPhase += 2 * Math.PI;
			aphase[maxY][maxX][1] += fullCyclesPhase;
			/*
			 * if (DEBUG_LEVEL>3) {
			 * System.out.println(" amplPhase():Old:["+oldConj+"] ("+pixelList.size()+")  "
			 * +oldX+":"+oldY+" "+IJ.d2s(aphase[oldY][oldX][0],2)+":"+
			 * IJ.d2s(aphase[oldY][oldX][1],2)+
			 * " New:"+maxX+":"+maxY+" "+IJ.d2s(aphase[maxY][maxX][0],2)+":"+
			 * IJ.d2s(aphase[maxY][maxX][1],2)+
			 * " Diff="+IJ.d2s((aphase[maxY][maxX][1]-(oldConj?-1:1)*aphase[oldY][oldX][1]),
			 * 2)); }
			 */
			/* Add this new point to the list */
			Index = maxY * size + maxX;
			pixelList.add(Index);
			clusterSize++;
			map[maxY][maxX] = true;
		} // end of while (pixelList.size()>0)
		/* Fix remaining phases for y=0 and y=hsize */
		for (i = 1; i < hsize; i++) {
			aphase[0][size - i][1] = -aphase[0][i][1];
			aphase[hsize][size - i][1] = -aphase[hsize][i][1];
		}
	}

}
