package com.elphel.imagej.tileprocessor;
import java.awt.Point;
import java.awt.Rectangle;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.concurrent.atomic.AtomicInteger;

/**
 ** TileNeibs - handles walking inside rectangular area
 **
 ** Copyright (C) 2017 Elphel, Inc.
 **
 ** -----------------------------------------------------------------------------**
 **
 **  TileNeibs.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/>.
 ** -----------------------------------------------------------------------------**
 **
 */

public class TileNeibs{
	final public static int DIR_N =       0; // UP
	final public static int DIR_NE =      1;
	final public static int DIR_E =       2; // Right
	final public static int DIR_SE =      3;
	final public static int DIR_S =       4; // Down
	final public static int DIR_SW =      5;
	final public static int DIR_W =       6; // Left
	final public static int DIR_NW =      7;
	final public static int DIR_CENTER = -1;
	final public static int DIR_UP =      0; // UP
	final public static int DIR_LEFT =    2; // Right
	final public static int DIR_DOWN =    4; // Down
	final public static int DIR_RIGHT =   6; // Left
	final public static int [][] DIR_XY = {{0,-1}, {1,-1}, {1,0}, {1,1}, {0,1}, {-1,1}, {-1,0}, {-1,-1}};
	final public static int DIRS =        DIR_XY.length; //8; // total dirs
	final static int THREADS_MAX =        100;
	
	final int              sizeX;
	final int              sizeY;
	public Rectangle       inner = null;
	public Rectangle       full = null;

	public Rectangle getFullRectangle() {
		if (full == null) {
			full = new Rectangle(0,0,sizeX,sizeY);
		}
		return full;
	}
	
	public Rectangle getInnerRectangle() {
		if (inner == null) {
			inner = new Rectangle(1,1,sizeX-2, sizeY-2);
		}
		return inner;
	}
	
	int last_grown; // actual grown until died
	public int dirs = DIRS;

	public static int reverseDir(int dir) {
		if ((dir < 0) || (dir >= DIRS)) {
			return dir;
		}
		return (dir+DIRS/2) % DIRS;
	}
	
	public int getLastGrown() {
		return last_grown;
	}
	public TileNeibs(int size){
		this.sizeX = size;
		this.sizeY = size;
		this.inner = new Rectangle(1,1,size-2, size-2);
	}
	public TileNeibs(int sizeX, int sizeY){
		this.sizeX = sizeX;
		this.sizeY = sizeY;
		this.inner = new Rectangle(1,1,sizeX-2, sizeY-2);
	}
	public int numNeibs() // TODO: make configurable to
	{
		return dirs;
	}
	public int opposite(int dir){
		return (dir + dirs / 2) % dirs;
	}

	int getLength(){
		return sizeX * sizeY;
	}

	boolean isBorder(int indx) {
		int [] xy = {indx % sizeX ,indx / sizeX};
		return (xy[0]==0) || (xy[1]==0) || (xy[0]== (sizeX - 1)) || (xy[1]==(sizeY-1)); 
	}
	
	
	/**
	 * Get x,y pair from index
	 * @param indx element index
	 * @return array of {x,y}
	 */

	int [] getXY(int indx)
	{
		int [] xy = {indx % sizeX ,indx / sizeX};
		return xy;
	}
	
	int getX(int indx) {return indx % sizeX;};
	
	int getY(int indx) {return indx / sizeX;};
	
	Point getPoint(int indx) {
		return new Point (indx % sizeX, indx / sizeX);
	}
	
	public int getSizeX() {
		return sizeX;
	}
	public int getSizeY() {
		return sizeY;
	}

	/**
	 * Get element index from x and y
	 * @param x horizontal position
	 * @param y vertical position
	 * @return element linescan index
	 */

	int getIndex(int x, int y){
		if ((x < 0) || (y < 0) || (x >= sizeX) || (y >= sizeY)) return -1;
		return y * sizeX + x;
	}

	int getIndex(int [] xy){
		if ((xy[0] < 0) || (xy[1] < 0) || (xy[0] >= sizeX) || (xy[1] >= sizeY)) return -1;
		return xy[1] * sizeX + xy[0];
	}

	/**
	 * Get element index offset by dx and dy from the indx
	 * @param indx start index
	 * @param dx offset in x direction
	 * @param dy offset in y direction
	 * @return new index or -1 if leaving
	 */
	public int getNeibIndex(int indx, int dx, int dy) {
		int y = indx / sizeX + dy;
		int x = indx % sizeX + dx;
		if ((x < 0) || (y < 0 ) || (x >= sizeX) || (y >= sizeY)) return -1;
		return y * sizeX + x;
	}

	public boolean isInside (int indx, Rectangle roi) {
		if (indx < 0) return false;
		int y = indx / sizeX;
		int x = indx % sizeX;
		return (y >= roi.y) && (x >= roi.x)  || (y < roi.y + roi.height) || (x < roi.x + roi.width);
	}

	/**
	 * Get 2d element index after step N, NE, ... NW. Returns -1 if leaving array
	 * @param indx start index
	 * @param dir step direction (CW from up)
	 * @return new index or -1 if leaving
	 */
	public int getNeibIndex(int indx, int dir)
	{
		int y = indx / sizeX;
		int x = indx % sizeX;
		if (dir < 0) return indx;
		if (dir > 8) {
			System.out.println("getNeibIndex(): indx="+indx+", dir="+dir);
		}
		switch (dir){
		case 0: return (y == 0) ?                                    -1 : (indx - sizeX);
		case 1: return ((y == 0)           || ( x == (sizeX - 1))) ? -1 : (indx - sizeX + 1);
		case 2: return (                      ( x == (sizeX - 1))) ? -1 : (indx        + 1);
		case 3: return ((y == (sizeY - 1)) || ( x == (sizeX - 1))) ? -1 : (indx + sizeX + 1);
		case 4: return ((y == (sizeY - 1))                       ) ? -1 : (indx + sizeX);
		case 5: return ((y == (sizeY - 1)) || ( x == 0))           ? -1 : (indx + sizeX - 1);
		case 6: return (                      ( x == 0))           ? -1 : (indx        - 1);
		case 7: return ((y == 0)           || ( x == 0))           ? -1 : (indx - sizeX - 1);
		default: return indx;
		}
	}

	public static int getDX(int dir)
	{
		if (dir > 8) {
			System.out.println("getDX(): dir="+dir);
		}
		switch (dir){
		case 1:
		case 2:
		case 3:
			return 1;
		case 5:
		case 6:
		case 7:
			return -1;
		default:
			return 0;
		}
	}
	
	public static int getDY(int dir)
	{
		if (dir > 8) {
			System.out.println("getDY(): dir="+dir);
		}
		switch (dir){
		case 7:
		case 0:
		case 1:
			return -1;
		case 3:
		case 4:
		case 5:
			return 1;
		default:
			return 0;
		}
	}
	
	

	public static int getNumDirs(int radius) {
		if (radius < 0) {
			return 0;
		} else if (radius == 0) {
			return 1;
		} else {
			return 8 * radius;
		}
	}
	
	/**
	 * Get 2d element index after step of variable radius:
	 * radius==1 - same as getNeibIndex(int indx, int dir), 8 directions
	 * radius==2 - 16 directions (5x5 square), 0 - still up, north
	 * radius==3 - 24 directions (7x7 square)
	 * ...
	 * @param indx start index
	 * @param dir step direction (CW from up)
	 * @param radius - "distance" from the start point
	 * @return new index or -1 if leaving array in any direction
	 */

	public int getNeibIndexRadius(int indx, int dir, int radius) {
		if (radius < 2) {
			return  getNeibIndex(indx, dir);
		}
		int y = indx / sizeX;
		int x = indx % sizeX;
		if (dir > (8 * radius)) {
			System.out.println("getNeibIndex(): indx="+indx+", dir="+dir+", radius="+radius);
		}
		int dr = (dir + radius) % (8 * radius);
		int quad = dr / (2 * radius);
		int side = dr %  (2 * radius);
		switch (quad) {
		case 0:
			x = x - radius + side;
			y = y - radius;
			break;
		case 1:
			x = x + radius; 
			y = y - radius + side;
			break;
		case 2:
			x = x + radius - side; 
			y = y + radius;
			break;
		case 3:
			x = x - radius; 
			y = y + radius - side;
			break;
		}
		if ((x >= 0) && (y >= 0) && (x < sizeX) && (y < sizeY)) {
			return x + sizeX*y;
		} else {
			return -1;
		}
	}
	
	
	
	
	/**
	 * Get 2d element index after step N, NE, ... NW. Returns -1 if leaving array
	 * And 2 steps for dir = 8(N), 9(NNE),..23(NNW)
	 * @param indx start index
	 * @param dir step direction (CW from up)
	 * @return new index or -1 if leaving
	 */
	int getNeibIndex2(int indx, int dir)
	{
		int y = indx / sizeX;
		int x = indx % sizeX;
		if (dir < 0) return indx;
		if (dir > 24) {
			System.out.println("getNeibIndex(): indx="+indx+", dir="+dir);
		}
//		switch (dir % dirs){
		switch (dir){
		case  0: return (y == 0) ?                                    -1 : (indx - sizeX);
		case  1: return ((y == 0)           || ( x == (sizeX - 1))) ? -1 : (indx - sizeX + 1);
		case  2: return (                      ( x == (sizeX - 1))) ? -1 : (indx        + 1);
		case  3: return ((y == (sizeY - 1)) || ( x == (sizeX - 1))) ? -1 : (indx + sizeX + 1);
		case  4: return ((y == (sizeY - 1))                       ) ? -1 : (indx + sizeX);
		case  5: return ((y == (sizeY - 1)) || ( x == 0))           ? -1 : (indx + sizeX - 1);
		case  6: return (                      ( x == 0))           ? -1 : (indx        - 1);
		case  7: return ((y == 0)           || ( x == 0))           ? -1 : (indx - sizeX - 1);

		case  8: return ( y < 2) ?                                   -1 : (indx - 2 * sizeX);
		case  9: return ((y < 2)            || ( x > (sizeX - 2))) ? -1 : (indx - 2 * sizeX + 1);
		case 10: return ((y < 2)            || ( x > (sizeX - 3))) ? -1 : (indx - 2 * sizeX + 2);
		case 11: return ((y < 1)            || ( x > (sizeX - 3))) ? -1 : (indx - 1 * sizeX + 2);
		case 12: return (                      ( x > (sizeX - 3))) ? -1 : (indx             + 2);
		case 13: return ((y > (sizeY - 2))  || ( x > (sizeX - 3))) ? -1 : (indx + 1 * sizeX + 2);
		case 14: return ((y > (sizeY - 3))  || ( x > (sizeX - 3))) ? -1 : (indx + 2 * sizeX + 2);
		case 15: return ((y > (sizeY - 3))  || ( x > (sizeX - 2))) ? -1 : (indx + 2 * sizeX + 1);
		case 16: return ((y > (sizeY - 3))                       ) ? -1 : (indx + 2 * sizeX);
		case 17: return ((y > (sizeY - 3))  || ( x < 1))           ? -1 : (indx + 2 * sizeX - 1);
		case 18: return ((y > (sizeY - 3))  || ( x < 2))           ? -1 : (indx + 2 * sizeX - 2);
		case 19: return ((y > (sizeY - 2))  || ( x < 2))           ? -1 : (indx + 1 * sizeX - 2);
		case 20: return (                      ( x < 2))           ? -1 : (indx             - 2);
		case 21: return ((y < 1)            || ( x < 2))           ? -1 : (indx - 1 * sizeX - 2);
		case 22: return ((y < 2)            || ( x < 2))           ? -1 : (indx - 2 * sizeX - 2);
		case 23: return ((y < 2)            || ( x < 1))           ? -1 : (indx - 2 * sizeX - 1);
		default: return indx;
		}
	}



	/**
	 * Return tile segment for 50% overlap. -1 - center, 0 N, 1 - NE,... 7 - NW
	 * @param indx element index
	 * @return which of the 9 areas this element belongs
	 */
	int getSegment(int indx)
	{
		int s1x = sizeX / 4;
		int s3x = 3 * sizeX / 4;
		int s1y = sizeY / 4;
		int s3y = 3 * sizeY / 4;
		int x = indx % sizeX;
		int y = indx / sizeX;
		boolean up = y < s1y;
		boolean down = y >= s3y;
		boolean left = x < s1x;
		boolean right = x >= s3x;
		if (up){
			if (left) return 7;
			if (right) return 1;
			return 0;
		}
		if (down){
			if (left) return 5;
			if (right) return 3;
			return 4;
		}
		if (left) return 6;
		if (right) return 2;
		return -1;
	}

	/**
	 * Find if the step leaves the center half of all area
	 * @param indx start point
	 * @param dir direction
	 * @return direction to the new tile (assuming 50% overlap) or -1 if did not cross the border
	 */
	int leaveOvderlapedCenter(int indx, int dir)
	{
		int segm = getSegment(indx);
		int indx1 = getNeibIndex(indx, dir);
		if (indx1 < 0 ) {
			return -1; // should not happen
		}
		int segm1 = getSegment(indx1);
		if (segm1 == segm) return -1;
		if (segm == -1) return segm1;
		int [][] dxy = {
				{ 0, 0},
				{-1, 0},
				{-1, 1},
				{ 0, 1},
				{ 1, 1},
				{ 1, 0},
				{ 1,-1},
				{ 0,-1},
				{-1,-1}};
		int dx = dxy[segm1 + 1][1] - dxy[segm + 1][1];
		int dy = dxy[segm1 + 1][0] - dxy[segm + 1][0];
		for (int dp1 = 0; dp1 <=8; dp1++) {
			int sdx = (dx > 0) ? 1: ( (dx < 0) ? -1 : 0);
			int sdy = (dy > 0) ? 1: ( (dy < 0) ? -1 : 0);
			if ((dxy[dp1][0] == sdy) && (dxy[dp1][1] == sdx)){
				return dp1 -1;
			}
		}
		return -1; // should not happen
	}
	
	/**
	 * Invert selection in a single or multithreaded environment.
	 * @param tiles array to invert
	 * @return inverted array
	 */
	public static boolean [] invertSelection(
			final boolean [] tiles) {
		final boolean [] itiles = new boolean [tiles.length];
		invertSelection(tiles, itiles);
		return itiles;
	}

	/**
	 * Invert selection in a single or multithreaded environment. May be in-place if tiles and itiles
	 * are the same array.
	 * @param tiles  input array to be inverted
	 * @param itiles output array of the same size as the input one. May be the same as tiles
	 */
	public static void invertSelection(
			final boolean [] tiles,
			final boolean [] itiles
			) {
		boolean is_main = isMainThread();
		final Thread[] threads = is_main ? ImageDtt.newThreadArray(THREADS_MAX) : null;
		final AtomicInteger ai =  is_main ?   new AtomicInteger(0) : null;
		if (is_main) {
			ai.set(0);
			for (int ithread = 0; ithread < threads.length; ithread++) {
				threads[ithread] = new Thread() {
					public void run() {
						for (int tile = ai.getAndIncrement(); tile < tiles.length; tile = ai.getAndIncrement()) {
							itiles[tile] = !tiles[tile];
						}
					}
				};
			}		      
			ImageDtt.startAndJoin(threads);
		} else {
			for (int tile = 0; tile < tiles.length; tile++) itiles[tile] = !tiles[tile];
		}
	}

	/**
	 * And boolean array to another boolean array in a single or multithreaded environment.
	 * dst_tiles &= src_tiles
	 * @param src_tiles array to AND to another one
	 * @param dst_tiles array to be modified by AND-ing with the first one
	 */
	public static void andSelection(
			final boolean [] src_tiles,
			final boolean [] dst_tiles
			) {
		boolean is_main = isMainThread();
		final Thread[] threads = is_main ? ImageDtt.newThreadArray(THREADS_MAX) : null;
		final AtomicInteger ai =  is_main ?   new AtomicInteger(0) : null;
		if (is_main) {
			ai.set(0);
			for (int ithread = 0; ithread < threads.length; ithread++) {
				threads[ithread] = new Thread() {
					public void run() {
						for (int tile = ai.getAndIncrement(); tile < src_tiles.length; tile = ai.getAndIncrement()) {
							dst_tiles[tile] &= src_tiles[tile];
						}
					}
				};
			}		      
			ImageDtt.startAndJoin(threads);
		} else {
			for (int tile = 0; tile < src_tiles.length; tile++) dst_tiles[tile] &= src_tiles[tile];
		}
	}
	
	
	/**
	 * Shrink boolean array (single or multithreaded depending on is
	 * it called from the main thread or not) 
	 * @param shrink    see definitons for growSelection()
	 * @param tiles     selection array (should be [sizeX * sizeY])
	 * @param prohibit  optional (may be null) array of prohibited tiles (for both originating and destination)
	 */
	public void shrinkSelection(
			final int        shrink,           // grow tile selection by 1 over non-background tiles 1: 4 directions, 2 - 8 directions, 3 - 8 by 1, 4 by 1 more
			final boolean [] tiles,  
			final boolean [] prohibit)
	{
		final boolean [] itiles = invertSelection(tiles);
		growSelection(
				shrink,           // grow tile selection by 1 over non-background tiles 1: 4 directions, 2 - 8 directions, 3 - 8 by 1, 4 by 1 more
				itiles,
				prohibit);
		invertSelection(itiles, tiles);
	}

	
	/**
	 * Select outmost pixels of the selection (single or multithreaded depending on is
	 * it called from the main thread or not)
	 * @param shrink    see definitons for growSelection()
	 * @param tiles     selection array (should be [sizeX * sizeY])
	 * @param prohibit  optional (may be null) array of prohibited tiles
	 * @return tile selection of the outmost tiles of the input tiles
	 */
	public boolean [] getEdgeSelection(
			int        shrink,           // grow tile selection by 1 over non-background tiles 1: 4 directions, 2 - 8 directions, 3 - 8 by 1, 4 by 1 more
			boolean [] tiles,
			boolean [] prohibit)
	{
		final boolean [] etiles = invertSelection(tiles);
		growSelection(
				shrink,           // grow tile selection by 1 over non-background tiles 1: 4 directions, 2 - 8 directions, 3 - 8 by 1, 4 by 1 more
				etiles,
				prohibit);
		andSelection (tiles, etiles);
		return etiles;
	}
	
	public boolean [] getRidges(
			final double  [] value,
			final boolean [] en,
			final double     min_over,  // minimal center above each side
			final double     max_rel_slope) { // maximal ridge slope relative to the value if >0
		final boolean [] ridges = new boolean [sizeX * sizeY];
		final Thread[] threads =    ImageDtt.newThreadArray(THREADS_MAX);
		final AtomicInteger ai =    new AtomicInteger(0);
		ai.set(0);
		for (int ithread = 0; ithread < threads.length; ithread++) {
			threads[ithread] = new Thread() {
				public void run() {
					for (int pix = ai.getAndIncrement(); pix < value.length; pix = ai.getAndIncrement()) if ((en == null) || en[pix]){
						double d = value[pix];
						for (int dir = 0; dir < DIRS/2; dir++) {
							int pix1 = getNeibIndex(pix, dir);
							int pix2 = getNeibIndex(pix, (dir + DIRS/2) % DIRS);
							if ((pix1 >= 0) && (pix2 >=0)) {
								if ((d > value[pix1]) && (d > value[pix2]) && ((d - (value[pix1]+value[pix1])/2) > min_over)) {
									// check ridge slope in ortho direction
									if (max_rel_slope >=0) {
										int dir_ridge = (dir + DIRS/4) % DIRS;
										int pix_ridge1=getNeibIndex(pix, dir_ridge);
										int pix_ridge2=getNeibIndex(pix, (dir_ridge + DIRS/2) % DIRS);
										if ((pix_ridge1 >=0) && (pix_ridge2 >=0)) {
											double ridge_slope = Math.abs(value[pix_ridge2] - value[pix_ridge1]) / 2;
											if ((ridge_slope / d) < max_rel_slope) {
												ridges[pix] = true;
											}
										}
									} else {
										ridges[pix] = true;
										break;
									}
									break;
								}
							}
						}
					}
				}
			};
		}		      
		ImageDtt.startAndJoin(threads);
		return ridges;
	}
	
	// Not working
	public double [] getRidgeValue(
			final double  [] value,
			final boolean [] en,
			final double     var_radius) {
		final double [] ridges = new double [sizeX * sizeY];
		final int ivar_radius = (int) Math.floor(var_radius);
		final double [][] var_weights = new double [ivar_radius+1][ivar_radius+1];
		for (int i = 0; i < var_weights.length; i++) {
			for (int j = 0; j < var_weights[i].length; j++) {
				var_weights[i][j] = Math.cos(0.5*Math.PI*i/var_radius) * Math.cos(0.5*Math.PI*j/var_radius);
			}
		}
		final Thread[] threads = ImageDtt.newThreadArray(THREADS_MAX);
		final AtomicInteger ai = new AtomicInteger(0);
		Arrays.fill(ridges, Double.NaN);
		ai.set(0);
		for (int ithread = 0; ithread < threads.length; ithread++) {
			threads[ithread] = new Thread() {
				public void run() {
					for (int pix = ai.getAndIncrement(); pix < value.length; pix = ai.getAndIncrement()) if ((en == null) || en[pix]){
						if (!Double.isNaN(value[pix])) {
							int y0 = pix / sizeX;
							int x0 = pix % sizeX;
							// calculate gradient
							double sw = 0.0, swxd = 0.0, swyd = 0.0;
							for (int dvy = -ivar_radius; dvy <= ivar_radius; dvy++) {
								for (int dvx = -ivar_radius; dvx <= ivar_radius; dvx++) {
									int indx = getIndex(x0+dvx, y0+dvy);
									if (indx >= 0) {
										double d = value[indx];
										if (!Double.isNaN(d)) {
											double w = var_weights[Math.abs(dvy)][Math.abs(dvx)]; // 1.0;
											double wd = w * d;
											sw += w;
											swxd += dvx * wd;
											swyd += dvy * wd;
										}
									}
								}
							}
							if (sw > 0.0) { // always
								swxd /= sw;
								swyd /= sw;
								// normalize gradient vector 
								double l = Math.sqrt(swxd*swxd + swyd*swyd);
								if (l>0) {
									double ux = swxd/l;
									double uy = swyd/l;
									double sdt2w = 0, st4w = 0;
									for (int dvy = -ivar_radius; dvy <= ivar_radius; dvy++) {
										for (int dvx = -ivar_radius; dvx <= ivar_radius; dvx++) {
											int indx = getIndex(x0+dvx, y0+dvy);
											if (indx >= 0) {
												double d = value[indx];
												if (!Double.isNaN(d)) {
													double w = var_weights[Math.abs(dvy)][Math.abs(dvx)]; // 1.0;
													double t =   dvx * uy - dvy * ux;
													double t2 =  t * t;
													double t2w = t2 * w;
													sdt2w +=     d * t2w;
													st4w +=      t2*t2w;
												}
											}
										}
									}
									if (st4w > 0) {
										ridges[pix] = -sdt2w/st4w;
									}
								}
							}							
						}
					}
				}
			};
		}		      
		ImageDtt.startAndJoin(threads);
		return ridges;
		
	}
			
	
	
	public void growSelectionGradient( // multithreaded version
			int        grow,           // grow tile selection by 1 over non-background tiles 1: 4 directions, 2 - 8 directions, 3 - 8 by 1, 4 by 1 more
			final boolean [] tiles,
			final boolean [] prohibit,
			final double []  value,
			final double     min_incr,
			final boolean    keep_top,     // do not grow over local max
			final boolean    keep_thin_top)// do not grow over local max only if next after that is already selected
	{
		final Thread[] threads =    ImageDtt.newThreadArray(THREADS_MAX);
		final AtomicInteger ai =    new AtomicInteger(0);
		final AtomicInteger anew =  new AtomicInteger(0);
		final boolean [] src_tiles = tiles.clone(); // just in case
		final int sizeXm1 = sizeX - 1;
		final int sizeYm1 = sizeY - 1;
		final int sizeXm2 = sizeX - 2;
		final int sizeYm2 = sizeY - 2;
		// grow
		boolean hor = true;
		final int dbg_tile = -82228; // 71992; //312/112 or 61800 for 360/96
		int num_prev = 1; // as if previous pass was successful
		for (; grow > 0; grow--){
			boolean single = (grow ==1) && hor;
			System.arraycopy(tiles, 0, src_tiles, 0, tiles.length);
			anew.set(0);
			if (hor){
				ai.set(0);
				for (int ithread = 0; ithread < threads.length; ithread++) {
					threads[ithread] = new Thread() {
						public void run() {
							for (int tindx = ai.getAndIncrement(); tindx < tiles.length; tindx = ai.getAndIncrement()) {
								int tileX = tindx % sizeX;
								if ((tindx == dbg_tile) || (tindx == (dbg_tile-1))){
									System.out.println("growSelectionMulti().1: tindx="+tindx);
								}
								int tindx1= tindx + 1;
								if ((tileX < sizeXm1) && ((prohibit == null) || (!prohibit[tindx] && !prohibit[tindx1]))) {
									if (!src_tiles[tindx1] && src_tiles[tindx]){
										if (value[tindx1] >= value[tindx] + min_incr) {
											boolean add_tile = false;
											if (keep_thin_top || keep_top) {
												int tindx2= tindx1 + 1;
												if ((tileX < sizeXm2) &&
														!prohibit[tindx2] &&
														(value[tindx2] < value[tindx1])) {
													if (!keep_top && !tiles[tindx2]) {
														add_tile = true;
													}
												} else {
													add_tile = true;
												}
											} else {
												add_tile = true;
											}
											if (add_tile) {
												anew.getAndIncrement();
												tiles[tindx1] = true;
											}
										}
									}
								}
							}
						}
					};
				}		      
				ImageDtt.startAndJoin(threads);
				System.arraycopy(tiles, 0, src_tiles, 0, tiles.length);
				ai.set(0);
				for (int ithread = 0; ithread < threads.length; ithread++) {
					threads[ithread] = new Thread() {
						public void run() {
							for (int tindx = ai.getAndIncrement(); tindx < tiles.length; tindx = ai.getAndIncrement()) {
								int tileX = tindx % sizeX;
								if ((tindx == dbg_tile) || (tindx == (dbg_tile+1))){
									System.out.println("growSelectionMulti().1: tindx="+tindx);
								}
								int tindx1= tindx - 1;
								if ((tileX > 0) && ((prohibit == null) || (!prohibit[tindx] && !prohibit[tindx1]))) {
									if (!src_tiles[tindx1] && src_tiles[tindx]){
										if (value[tindx1] >= value[tindx] + min_incr) {
											boolean add_tile = false;
											if (keep_thin_top || keep_top) {
												int tindx2= tindx1 - 1;
												if ((tileX > 1) &&
														!prohibit[tindx2] &&
														(value[tindx2] < value[tindx1])) {
													if (!keep_top && !tiles[tindx2]) {
														add_tile = true;
													}
													
												} else {
													add_tile = true;
												}
											} else {
												add_tile = true;
											}
											if (add_tile) {
												anew.getAndIncrement();
												tiles[tindx1] = true;
											}
										}
									}
								}
							}
						}
					};
				}		      
				ImageDtt.startAndJoin(threads);
			}
			if (!hor || single){ // do vertically, but from previous state
				System.arraycopy(tiles, 0, src_tiles, 0, tiles.length);
				ai.set(0);
				for (int ithread = 0; ithread < threads.length; ithread++) {
					threads[ithread] = new Thread() {
						public void run() {
							for (int tindx = ai.getAndIncrement(); tindx < tiles.length; tindx = ai.getAndIncrement()) {
								int tileY = tindx / sizeX;
								if ((tindx == dbg_tile) || (tindx == (dbg_tile-sizeX))){
									System.out.println("growSelectionMulti().3: tindx="+tindx);
								}
								int tindx1= tindx + sizeX;
								if ((tileY < sizeYm1) && ((prohibit == null) || (!prohibit[tindx] && !prohibit[tindx1]))) {
									if (!src_tiles[tindx1] && src_tiles[tindx]){
										if (value[tindx1] >= value[tindx] + min_incr) {
											boolean add_tile = false;
											if (keep_thin_top || keep_top) {
												int tindx2= tindx1 + sizeX;
												if ((tileY < sizeYm2) &&
														!prohibit[tindx2] &&
														(value[tindx2] < value[tindx1])) {
													if (!keep_top && !tiles[tindx2]) {
														add_tile = true;
													}
												} else {
													add_tile = true;
												}
											} else {
												add_tile = true;
											}
											if (add_tile) {
												anew.getAndIncrement();
												tiles[tindx1] = true;
											}
										}
									}
								}
							}
						}
					};
				}		      
				ImageDtt.startAndJoin(threads);
				System.arraycopy(tiles, 0, src_tiles, 0, tiles.length);
				ai.set(0);
				for (int ithread = 0; ithread < threads.length; ithread++) {
					threads[ithread] = new Thread() {
						public void run() {
							for (int tindx = ai.getAndIncrement(); tindx < tiles.length; tindx = ai.getAndIncrement()) {
								int tileY = tindx / sizeX;
								if ((tindx == dbg_tile) || (tindx == (dbg_tile+sizeX))){
									System.out.println("growSelectionMulti().1: tindx="+tindx);
								}
								int tindx1= tindx - sizeX;
								if ((tileY > 0) && ((prohibit == null) || (!prohibit[tindx] && !prohibit[tindx1]))) {
									if (!src_tiles[tindx1] && src_tiles[tindx]){
										if (value[tindx1] >= value[tindx] + min_incr) {
											boolean add_tile = false;
											if (keep_thin_top || keep_top) {
												int tindx2= tindx1 - sizeX;
												if ((tileY > 1) &&
														!prohibit[tindx2] &&
														(value[tindx2] < value[tindx1])) {
													if (!keep_top && !tiles[tindx2]) {
														add_tile = true;
													}
												} else {
													add_tile = true;
												}
											} else {
												add_tile = true;
											}
											if (add_tile) {
												anew.getAndIncrement();
												tiles[tindx1] = true;
											}
										}
									}
								}
							}
						}
					};
				}		      
				ImageDtt.startAndJoin(threads);
			}
			hor = !hor;
			if ((anew.get() == 0) && (num_prev == 0)){
				break;
			}
			num_prev = anew.get();
		}
	}

	/**
	 * Grow pixel selection in multiple threads.
	 * @param grow     amount of growth: 1 - 1 pixel in ortho (up/down, right/left) directions,
	 *                 2 - ortho+diagonal, 3 - 2 steps in ortho, etc.
	 * @param tiles    boolean array to grow (should be [sizeX * sizeY])
	 * @param prohibit optional array (may be null) that prohibits growth (for both originating and
	 *                 destination tiles). 
	 */
	public void growSelectionMulti( // multithreaded version
			int        grow,           // grow tile selection by 1 over non-background tiles 1: 4 directions, 2 - 8 directions, 3 - 8 by 1, 4 by 1 more
			final boolean [] tiles,
			final boolean [] prohibit)
	{
		final Thread[] threads =    ImageDtt.newThreadArray(THREADS_MAX);
		final AtomicInteger ai =    new AtomicInteger(0);
		final AtomicInteger anew =  new AtomicInteger(0);
		final boolean [] src_tiles = tiles.clone(); // just in case
		final int sizeXm1 = sizeX - 1;
		final int sizeYm1 = sizeY - 1;
		// grow
		int grow0 = grow; // requested steps
		boolean hor = true;
		final int dbg_tile = -82228; // 71992; //312/112 or 61800 for 360/96
		int num_prev = 1; // as if previous pass was successful
		for (; grow > 0; grow--){
			boolean single = (grow ==1) && hor;
			System.arraycopy(tiles, 0, src_tiles, 0, tiles.length);
			anew.set(0);
			if (hor){
				ai.set(0);
				for (int ithread = 0; ithread < threads.length; ithread++) {
					threads[ithread] = new Thread() {
						public void run() {
							for (int tindx = ai.getAndIncrement(); tindx < tiles.length; tindx = ai.getAndIncrement()) {
								int tileX = tindx % sizeX;
								if ((tindx == dbg_tile) || (tindx == (dbg_tile-1))){
									System.out.println("growSelectionMulti().1: tindx="+tindx);
								}
								if ((tileX < sizeXm1) && ((prohibit == null) || (!prohibit[tindx] && !prohibit[tindx + 1]))) {
									if (!src_tiles[tindx + 1] && src_tiles[tindx]){
										anew.getAndIncrement();
										tiles[tindx + 1] = true; // |= src_tiles[tindx];
									}
								}
							}
						}
					};
				}		      
				ImageDtt.startAndJoin(threads);
				System.arraycopy(tiles, 0, src_tiles, 0, tiles.length);
				ai.set(0);
				for (int ithread = 0; ithread < threads.length; ithread++) {
					threads[ithread] = new Thread() {
						public void run() {
							for (int tindx = ai.getAndIncrement(); tindx < tiles.length; tindx = ai.getAndIncrement()) {
								int tileX = tindx % sizeX;
								if ((tindx == dbg_tile) || (tindx == (dbg_tile+1))){
									System.out.println("growSelectionMulti().2: tindx="+tindx);
								}
								if ((tileX > 0) && ((prohibit == null) || (!prohibit[tindx] && !prohibit[tindx - 1]))) {
									if (!src_tiles[tindx - 1] && src_tiles[tindx]){
										anew.getAndIncrement();
										tiles[tindx - 1] = true; // |= src_tiles[tindx];
									}
								}
							}
						}
					};
				}		      
				ImageDtt.startAndJoin(threads);
			}
			if (!hor || single){ // do vertically, but from previous state
				System.arraycopy(tiles, 0, src_tiles, 0, tiles.length);
				ai.set(0);
				for (int ithread = 0; ithread < threads.length; ithread++) {
					threads[ithread] = new Thread() {
						public void run() {
							for (int tindx = ai.getAndIncrement(); tindx < tiles.length; tindx = ai.getAndIncrement()) {
								int tileY = tindx / sizeX;
								if ((tindx == dbg_tile) || (tindx == (dbg_tile-sizeX))){
									System.out.println("growSelectionMulti().3: tindx="+tindx);
								}
								if ((tileY < sizeYm1) && ((prohibit == null) || (!prohibit[tindx] && !prohibit[tindx + sizeX]))) {
									if (!src_tiles[tindx + sizeX] && src_tiles[tindx]){
										anew.getAndIncrement();
										tiles[tindx + sizeX] = true; // |= src_tiles[tindx];
									}
								}
							}
						}
					};
				}		      
				ImageDtt.startAndJoin(threads);
				System.arraycopy(tiles, 0, src_tiles, 0, tiles.length);
				ai.set(0);
				for (int ithread = 0; ithread < threads.length; ithread++) {
					threads[ithread] = new Thread() {
						public void run() {
							for (int tindx = ai.getAndIncrement(); tindx < tiles.length; tindx = ai.getAndIncrement()) {
								int tileY = tindx / sizeX;
								if ((tindx == dbg_tile) || (tindx == (dbg_tile+sizeX))){
									System.out.println("growSelectionMulti().1: tindx="+tindx);
								}
								if ((tileY > 0) && ((prohibit == null) || (!prohibit[tindx] && !prohibit[tindx - sizeX]))) {
									if (!src_tiles[tindx - sizeX] && src_tiles[tindx]){
										anew.getAndIncrement();
										tiles[tindx - sizeX] = true; // |= src_tiles[tindx];
									}
								}
							}
						}
					};
				}		      
				ImageDtt.startAndJoin(threads);
			}
			hor = !hor;
			if ((anew.get() == 0) && (num_prev == 0)){
				break;
			}
			num_prev = anew.get();
		}
		last_grown = grow0 - grow;
	}
	
	
	
	/**
	 * Find out if the current thread is main.
	 * @return true for the main thread, false - for others
	 */
	public static boolean isMainThread() {
		return Thread.currentThread().getName().equals("main");
	}
	

	
	/**
	 * Grow pixel selection in either a single thread (if the method is called from one of
	 * concurrent threads (already used by multiple callers) or in multiple threads if the
	 * current thread is "main"
	 * @param grow     amount of growth: 1 - 1 pixel in ortho (up/down, right/left) directions,
	 *                 2 - ortho+diagonal, 3 - 2 steps in ortho, etc.
	 * @param tiles    boolean array to grow (should be [sizeX * sizeY])
	 * @param prohibit optional array (may be null) that prohibits growth (for both originating and
	 *                 destination tiles). 
	 */
	public void growSelection(
			int              grow,           // grow tile selection by 1 over non-background tiles 1: 4 directions, 2 - 8 directions, 3 - 8 by 1, 4 by 1 more
			final boolean [] tiles,
			final boolean [] prohibit)
	{
		if (grow <= 0) {
			return;
		}
		// if it is not in multithreaded mode - run multithreaded version instead;
		if (isMainThread()) {
			growSelectionMulti (
					grow,
					tiles,
					prohibit);
			return;
		}
		boolean [] src_tiles = tiles.clone(); // just in case
		// grow
		int grow0 = grow; // requested steps
		boolean hor = true;
		int num_prev = 1; // as if previous pass was successful
		for (; grow > 0; grow--){
			boolean single = (grow ==1) && hor;
			src_tiles = tiles.clone();
			int num_new = 0; // as if previous pass was successful
			if (hor){
				for (int tileY = 0; tileY < sizeY; tileY++){
					for (int tileX = 0; tileX < (sizeX - 1); tileX++){
						int tindx = tileY * sizeX + tileX;
						if ((prohibit == null) || (!prohibit[tindx] && !prohibit[tindx + 1])) {
							if (!tiles[tindx + 1] && src_tiles[tindx]){
								num_new++;
							}
							tiles[tindx + 1] |= src_tiles[tindx];
						}
					}
					for (int tileX = 1; tileX < sizeX; tileX++){
						int tindx = tileY * sizeX + tileX;
						if ((prohibit == null) || (!prohibit[tindx] && !prohibit[tindx - 1])) {
							if (!tiles[tindx - 1] && src_tiles[tindx]){
								num_new++;
							}
							tiles[tindx - 1] |= src_tiles[tindx];
						}
					}
				}
			}
			if (!hor || single){ // do vertically, but from previous state
				for (int tileX = 0; tileX < sizeX; tileX++){
					for (int tileY = 0; tileY < (sizeY - 1); tileY++){
						int tindx = tileY * sizeX + tileX;
						if ((prohibit == null) || (!prohibit[tindx] && !prohibit[tindx + sizeX])) {
							if (!tiles[tindx + sizeX] && src_tiles[tindx]){
								num_new++;
							}
							tiles[tindx + sizeX] |= src_tiles[tindx];
						}

					}
					for (int tileY = 1; tileY < sizeY; tileY++){
						int tindx = tileY * sizeX + tileX;
						if ((prohibit == null) || (!prohibit[tindx] && !prohibit[tindx - sizeX])) {
							if (!tiles[tindx - sizeX] && src_tiles[tindx]){
								num_new++;
							}
							tiles[tindx - sizeX] |= src_tiles[tindx];
						}
					}
				}
			}
			hor = !hor;
			if ((num_new == 0) && (num_prev == 0)){
				break;
			}
			num_prev = num_new;
		}
		last_grown = grow0 - grow;
	}

	public boolean [] boundShape(
			boolean [] selection,
			boolean octo)
	{
		boolean [] bound_shape = new boolean [selection.length];
		int min_x=-1, max_x=-1, min_y=-1, max_y=-1;
		int min_s=-1, max_s=-1, min_d=-1, max_d=-1;
		boolean is_set = false;
		for (int i = 0; i < selection.length; i++) if (selection[i]){
			int [] xy = getXY(i);
			int [] sd = {xy[0]+xy[1],xy[0]-xy[1]};
			if (!is_set) {
				min_x = xy[0];
				max_x = xy[0];
				min_y = xy[1];
				max_y = xy[1];
				if (octo) {
				min_s = sd[0];
				max_s = sd[0];
				min_d = sd[1];
				max_d = sd[1];
				}
				is_set = true;
			} else {
				if      (xy[0] < min_x) min_x = xy[0];
				else if (xy[0] > max_x) max_x = xy[0];
				if      (xy[1] < min_y) min_y = xy[1];
				else if (xy[1] > max_y) max_y = xy[1];
				if (octo) {
					if      (sd[0] < min_s) min_s = sd[0];
					else if (sd[0] > max_s) max_s = sd[0];
					if      (sd[1] < min_d) min_d = sd[1];
					else if (sd[1] > max_d) max_d = sd[1];
				}

			}
		}
		for (int y = min_y; y <= max_y; y++){
			for (int x = min_x; x <= max_x; x++){
				if (!octo ||
				(((x + y) >= min_s) && ((x + y) <= max_s) && ((x - y) >= min_d) && ((x - y) <= max_d))) {
					bound_shape[getIndex(x,y)] = true;

				}
			}
		}
		return bound_shape;
	}

	public static double[] getDoubleWindow(
			Rectangle window,
			double [] data,
			int data_width) {
		double [] window_data = new double [window.width * window.height];
		for (int row = 0; row < window.height; row++) {
			System.arraycopy(
					data,
					(window.y + row) * data_width + window.x,
					window_data,
					row * window.width,
					window.width);
		}
		return window_data;
	}
	
	public static void setDoubleWindow(
			Rectangle window,
			double [] window_data,
			double [] data,
			int       data_width) {
		for (int row = 0; row < window.height; row++) {
			System.arraycopy(
					window_data,
					row * window.width,
					data,
					(window.y + row) * data_width + window.x,
					window.width);
		}
	}
	

	public int [] distanceFromEdge(
			boolean [] tiles) {
		int [] dfe = new int [tiles.length];
		for (int i = 0; i < tiles.length; i++) dfe[i] = tiles[i] ? -1 : 0;
		ArrayList<Integer> front = new ArrayList<Integer>();
		int dist = 0;
		for (boolean has_empty = true; has_empty;) {
			has_empty = false;
			for (int start_indx = 0; start_indx < tiles.length; start_indx++) if (dfe[start_indx] < 0){
				has_empty = true;
				// see if it has wave front around
				boolean has_front_near = false;
				for (int d = 0; (d < dirs) && !has_front_near; d++){
					int ipx1 = 	getNeibIndex(start_indx, d);
					if ((ipx1 >= 0) && (dfe[ipx1] == dist)) {
						has_front_near = true;
					}
				}
				if (has_front_near) {
					dfe[start_indx] = dist+1;
					front.add(start_indx);
					// build wave front (may be several)
					while (!front.isEmpty()) {
						int ipx = front.remove(0);// get oldest element
						for (int d = 0; (d < dirs) && !has_front_near; d++){
							int ipx1 = 	getNeibIndex(ipx, d);
							if ((ipx1 >= 0) && (dfe[ipx1] < 0)) { // fresh cell
								// does it has front neighbor?

								for (int d1 = 0; (d1 < dirs) && !has_front_near; d1++){
									int ipx2 = 	getNeibIndex(ipx1, d1);
									if ((ipx2 >= 0) && (dfe[ipx2] == dist)) { // old front cell
										dfe[ipx1] = dist+1;
										front.add(ipx1);
										break;
									}
								}
							}
						}
					}		

				}
			}
			dist++; 
		}
		return dfe;
	}
	
	/**
	 * Enumerate clusters on rectangular area
	 * @param tiles        selected tiles, size should be sizeX * sizeY
	 * @param num_clusters if non null, will return number of clusters
	 * @param ordered      if true, order tiles from largest to smallest5
	 * @return integer array, where 0 is unused, 1+ cluster it belongs to
	 */
	public int [] enumerateClusters(
			boolean [] tiles,
			int []     num_clusters,
			boolean ordered)
	{
		int [] waves = new int [tiles.length];
		for (int i = 0; i < tiles.length; i++) waves[i] = tiles[i] ? 0: -1;
		ArrayList<Integer> front = new ArrayList<Integer>();
		int [] enum_clust = new int[tiles.length];
		int numClust = 0;
		for (int start_indx = 0; start_indx < tiles.length; start_indx++) if (waves[start_indx] == 0){ // found first pixel of a new cluster
			numClust ++;
			Integer ipx = start_indx;
			Integer ipx1;
			front.clear();
			int area = 1;
			waves[ipx] = area;
			enum_clust[ipx] = numClust;
			front.add(ipx);
			while (!front.isEmpty()) {
				ipx = front.remove(0);// get oldest element
				for (int d = 0; d < dirs; d++){
					ipx1 = 	getNeibIndex(ipx, d);
					if (ipx1 >= 0){
						if (waves[ipx1] == 0) {
							area++;
							waves[ipx1] = area;
							enum_clust[ipx1] = numClust;
							front.add(ipx1);
						}
					}
				}
			}
		}
		if (num_clusters != null) {
			num_clusters[0] = numClust;
		}
		if (!ordered) {
			return enum_clust;
		}

		// count cluster
		int []clustSizes = new int [numClust];
		for (int i = 0; i < clustSizes.length; i++) clustSizes[i] = 0;
		for (int i = 0; i < enum_clust.length; i++) if (enum_clust[i] > 0) clustSizes[enum_clust[i]-1]++;

		class Pair implements Comparable<Pair> {
			public final int index;
			public final int value;

			public Pair(int index, int value) {
				this.index = index;
				this.value = value;
			}

			@Override
			public int compareTo(Pair other) {
				return Integer.valueOf(this.value).compareTo(other.value);
			}
		}

		Pair[] pairs = new Pair[numClust];
		for (int i = 0; i < clustSizes.length; i++) pairs [i] = new Pair (i, clustSizes[i]);
		Arrays.sort(pairs);
		int [] revIndex = new int [numClust];
		for (int i = 0; i < revIndex.length; i++) revIndex [pairs[i].index] = (numClust - i); // array was in accending order
		int [] enum_clust_ordered = new int[tiles.length];
		for (int i=0; i < enum_clust_ordered.length; i++){
			enum_clust_ordered[i] = (enum_clust[i] > 0) ? revIndex[enum_clust[i] - 1] : 0;
		}
		return enum_clust_ordered;
	}
	

	/**
	 * Get tiles, connected to the seed tile
	 * @param tiles     selected tiles, size should be sizeX * sizeY
	 * @param tiles
	 * @param seedX
	 * @param seedY
	 * @return boolean array of tiles that are connected to the seed tile
	 */
	public boolean [] getConnected(
			boolean [] tiles,
			int        seedX,
			int        seedY)
	{
		int [] waves = new int [tiles.length];
		boolean [] rslt = new boolean [tiles.length];
		for (int i = 0; i < tiles.length; i++) waves[i] = tiles[i] ? 0: -1;
		ArrayList<Integer> front = new ArrayList<Integer>();
		int [] enum_clust = new int[tiles.length];
		if ((seedX < 0) || (seedY < 0) || (seedX >= sizeX) || (seedY>= sizeY) || (tiles.length != (sizeX*sizeY)) ) {
			return null;
		}
		int start_indx = seedX + seedY * sizeX;
		if (!tiles[start_indx]) {
			return rslt;
		}
		Integer ipx = start_indx;
		Integer ipx1;
		front.clear();
		int area = 1;
		waves[ipx] = area;
		rslt[ipx] = true;
		front.add(ipx);
		while (!front.isEmpty()) {
			ipx = front.remove(0);// get oldest element
			for (int d = 0; d < dirs; d++){
				ipx1 = 	getNeibIndex(ipx, d);
				if (ipx1 >= 0){
					if (waves[ipx1] == 0) {
						area++;
						waves[ipx1] = area;
						rslt[ipx1] = true;
						front.add(ipx1);
					}
				}
			}
		}
		return rslt;
	}
	
	
	public static int getMax(
			int [] data)
	{
		int mx = data[0];
		for (int i = 1; i < data.length; i++){
			if (data[i] > mx){
				mx= data[i];
			}
		}
		return mx;
	}

	public int removeFewNeibs(
			boolean [] selection, // should be the same size
			int min_neibs)
	{
		int num_total_removed=0;
		int l = getLength();
		while (true) {
			int num_removed = 0;
			boolean [] to_remove = new boolean[l];
			for (int indx = 0; indx < l; indx++) if (selection[indx]){
				int num_neibs = 0;
				label_neibs: {
					for (int dir = 0; dir < 8; dir++) {
						int indx1 = getNeibIndex(indx, dir);
						if ((indx1 >= 0) && selection[indx1]) {
							num_neibs++;
							if (num_neibs >= min_neibs) {
								break label_neibs;
							}

						}
					}
					to_remove[indx] = true;
					num_removed++;
				}
			}
			if (num_removed > 0) {
				for (int i = 0; i < l; i++) if (to_remove[i]) {
					selection[i] = false;
				}
				num_total_removed += num_removed;
			} else {
				break;
			}
		}


		return num_total_removed;
	}
	
	public boolean [] fillConcave(
			boolean [] tiles // should be the same size
			) {
		boolean [] filled = tiles.clone();
		int min_neibs = 4;
		ArrayList<Integer> front = new ArrayList<Integer>();
		for (int start_indx = 0; start_indx < tiles.length; start_indx++) if (!filled[start_indx]) {
			int nneib = 0;
			for (int dir = 0; dir < dirs; dir++) {
				int id = getNeibIndex(start_indx, dir);
				if ((id >= 0) && filled[id]) nneib++;
			}
			if (nneib >= min_neibs) {
				front.add(start_indx); // do not mark yet
				filled[start_indx] = true;
				while (!front.isEmpty()) {
					int seed = front.remove(0);// get oldest element
					for (int d = 0; d < dirs; d++){
						int indx = 	getNeibIndex(seed, d);
						if ((indx >=0) && !filled[indx]) {
							nneib = 0;
							for (int dir = 0; dir < dirs; dir++) {
								int id = getNeibIndex(indx, dir);
								if ((id >= 0) && filled[id]) nneib++;
							}
							if (nneib >= min_neibs) {
								front.add(indx); // do not mark yet
								filled[indx] = true;
							}
						}
					}
				}				
			}
		}
		return filled;
	}
	
	/**
	 * Get array of indices for all local maximums (pixels that are not less than their 8 neighbors). NaNs are considered smaller than normal values.
	 * @param data data in line-scan order, should be [sizeX*sizeY] (not verified)
	 * @param exclude_margins do not allow maximums on the outer edge of the defined rectangle 
	 * @return variable-length interger array of local maxima
	 */
	public int [] getLocalMaxes(
			double [] data,
			boolean   exclude_margins) {
		ArrayList<Integer> max_list = new ArrayList<Integer>();
		int x0 = exclude_margins ? 1 : 0;
		int y0 = exclude_margins ? 1 : 0;
		int x1 = sizeX - x0 - 1;
		int y1 = sizeY - y0 - 1;
		for (int y = y0; y <= y1; y++) {
			for (int x = x0; x <= x1; x++) {
				int ntile = y * sizeX + x;
				double d = data[ntile];
				if (!Double.isNaN(d)) {
					check_ismax: {
						for (int dir = 0; dir < DIRS; dir++) {
							int ntile1 = getNeibIndex(ntile,dir);
							if ((ntile >=0) && (data[ntile1] > d)){
								break check_ismax;
							}
						}
						max_list.add(ntile);
					}
				}
			}
		}
        return max_list.stream().mapToInt(Integer::intValue).toArray();
	}

	/**
	 * Calculate index of an absolute maximum in array, ignore NaNs. If all elements are NaN, will return -1
	 * @param data Data array, may contain NaN values
	 * @return index of a largest element (NaN is considered smaller than any normal value) or -1 if all are NaN
	 */
	public static int getAmaxTile(
			double [] data) {
		int ntile = - 1;
		double maxv = Double.NaN;
		for (int i = 0; i < data.length; i++) {
			double d = data[i];
			if (!(d <= maxv)) {
				ntile = i;
				maxv = d;
			}
		}
		return ntile;
	}

	/**
	 * Verify that this local maximum is disconnected from any tile larger it by the tiles having
	 * value of the specified fraction of the maximal value. 
	 * @param data data array
	 * @param ntile tile index
	 * @param fraction fraction of the maximal value that separates the maximum
	 * @param radius if >0, limits allowable expansion (and returns false if reached)
	 * @return true if it is an isolated maximum, false if not.
	 */
	public boolean isMaxIsolated(
			double [] data,
			int       ntile,
			double    fraction,
			int       radius) {
		if ((ntile <0) || (ntile >= data.length)) {
			return false; // outside
		}
		int xc = getX(ntile);
		int yc = getY(ntile);
		Rectangle full = getFullRectangle();
		Rectangle limits = (radius <=0) ?  null : (full.intersection(new Rectangle(xc-radius, yc-radius, 2*radius+1,2*radius+1)));
		boolean [] tried = new boolean [data.length];
		double local_max = data[ntile];
		double threshold = local_max * fraction;
		ArrayList<Integer> wave = new ArrayList<Integer>();
		wave.add(ntile);
		tried[ntile] = true;
		while (!wave.isEmpty()) {
			ntile = wave.remove(0);
			for (int dir = 0; dir < DIRS; dir++) {
				int ntile1 = getNeibIndex(ntile, dir);
				if ((ntile1 >= 0) && !tried[ntile1]) {
					tried[ntile1] = true;
					double d = data[ntile1]; // may be NaN
					if (d > local_max) {
						return false;
					} else if (d > threshold) { // NaN will result in false
						wave.add(ntile1);
						if ((limits != null) && !limits.contains(getPoint(ntile1))) {
							return false;
						}
					}
				}
			}
			
		}
		return true;
	}
	
	/**
	 * Check if the point indx is on the edge of the defined rectangle
	 * @param indx
	 * @return
	 */
	public boolean isEdge(int indx) {
		boolean isedge = !getInnerRectangle().contains(getPoint(indx));
		return isedge;
	}

	
}
