Detect mines with morning/evenimg pair (25c2bbf2) · Commits · Elphel / imagej-elphel

src/main/java/com/elphel/imagej/orthomosaic/ComboMatch.java

+14 −8

Original line number	Original line	Diff line number	Diff line
	@@ -104,7 +104,7 @@ public class ComboMatch {
	"/media/elphel/SSD3-4GB/lwir16-proc/ortho_videos/maps_19_sep13_25-50-75-100m",		"/media/elphel/SSD3-4GB/lwir16-proc/ortho_videos/maps_19_sep13_25-50-75-100m",
	"/media/elphel/SSD3-4GB/lwir16-proc/ortho_videos/maps_nov3_50-75",		"/media/elphel/SSD3-4GB/lwir16-proc/ortho_videos/maps_nov3_50-75",
	"/media/elphel/SSD3-4GB/lwir16-proc/ortho_videos/maps_sep12-50m"};		"/media/elphel/SSD3-4GB/lwir16-proc/ortho_videos/maps_sep12-50m"};
			int default_list_choice = 0; // files_lists_paths.length-1;
	// String files_list_path = "/media/elphel/SSD3-4GB/lwir16-proc/ortho_videos/maps_nov3_50-75.list";		// String files_list_path = "/media/elphel/SSD3-4GB/lwir16-proc/ortho_videos/maps_nov3_50-75.list";
	// String orthoMapsCollection_path = "/media/elphel/SSD3-4GB/lwir16-proc/ortho_videos/maps_nov3_50-75.data";		// String orthoMapsCollection_path = "/media/elphel/SSD3-4GB/lwir16-proc/ortho_videos/maps_nov3_50-75.data";
	//maps_nov3_50-75		//maps_nov3_50-75
	@@ -148,10 +148,11 @@ public class ComboMatch {
	boolean use_saved_collection = true; // false;		boolean use_saved_collection = true; // false;
	boolean save_collection = true;		boolean save_collection = true;
	boolean process_correlation = true; // use false to save new version of data		boolean process_correlation = true; // use false to save new version of data
			int num_tries_fit = 10;
	boolean update_match = true; // use false to save new version of data		boolean update_match = true; // use false to save new version of data
	boolean render_match = true;		boolean render_match = false; // true;

	boolean pattern_match = false;		boolean pattern_match = true; // false;

	boolean bounds_to_indices = true;		boolean bounds_to_indices = true;
	int temp_mode = 1;		int temp_mode = 1;
	@@ -166,10 +167,13 @@ public class ComboMatch {


	GenericJTabbedDialog gd = new GenericJTabbedDialog("Set image pair",1200,900);		GenericJTabbedDialog gd = new GenericJTabbedDialog("Set image pair",1200,900);
	gd.addChoice ("Files list/data path (w/o extension):", files_lists_paths, files_lists_paths[files_lists_paths.length-1]);		gd.addChoice ("Files list/data path (w/o extension):", files_lists_paths, files_lists_paths[default_list_choice]);
	gd.addCheckbox ("Use saved maps collection", use_saved_collection, "If false - use files list.");		gd.addCheckbox ("Use saved maps collection", use_saved_collection, "If false - use files list.");
	gd.addCheckbox ("Save maps collection", save_collection, "Save maps collection to be able to restore.");		gd.addCheckbox ("Save maps collection", save_collection, "Save maps collection to be able to restore.");
	gd.addCheckbox ("Process correlations", process_correlation, "false to skip to just regenerate new save file.");		gd.addCheckbox ("Process correlations", process_correlation, "false to skip to just regenerate new save file.");
			// int num_tries_fit = 10;
			gd.addNumericField("Num tries fit", num_tries_fit, 0,4,"", "Try matching images this number of times");

	gd.addCheckbox ("Update match if calculated", update_match, "Will update correlation match for a pair if found.");		gd.addCheckbox ("Update match if calculated", update_match, "Will update correlation match for a pair if found.");
	gd.addCheckbox ("Render match", render_match, "Render a pair of matched images.");		gd.addCheckbox ("Render match", render_match, "Render a pair of matched images.");

	@@ -215,6 +219,7 @@ public class ComboMatch {
	use_saved_collection = gd.getNextBoolean();		use_saved_collection = gd.getNextBoolean();
	save_collection = gd.getNextBoolean();		save_collection = gd.getNextBoolean();
	process_correlation= gd.getNextBoolean();		process_correlation= gd.getNextBoolean();
			num_tries_fit = (int) gd.getNextNumber();
	update_match= gd.getNextBoolean();		update_match= gd.getNextBoolean();
	render_match= gd.getNextBoolean();		render_match= gd.getNextBoolean();

	@@ -728,10 +733,10 @@ public class ComboMatch {
	double [][][] affines = {affine0,affine1};		double [][][] affines = {affine0,affine1};
	int [] zooms = {initial_zoom, min_zoom_lev, 1000,1000}; // make automatic		int [] zooms = {initial_zoom, min_zoom_lev, 1000,1000}; // make automatic
	double scale = 2.0; // scale vectors when warping;		double scale = 2.0; // scale vectors when warping;
	int num_tries = 5;		// int num_tries = 5; // make configurable
	if (!process_correlation) {		if (!process_correlation) {
	zooms = new int[] {min_zoom_lev, 1000};		zooms = new int[] {min_zoom_lev, 1000};
	num_tries = 0;		num_tries_fit = 0;
	update_match = false;		update_match = false;
	}		}
	debugLevel = 0;		debugLevel = 0;
	@@ -750,7 +755,7 @@ public class ComboMatch {
	frac_remove, // double frac_remove, // = 0.25		frac_remove, // double frac_remove, // = 0.25
	metric_error, // double metric_error,		metric_error, // double metric_error,
	ignore_prev_rms, // boolean ignore_prev_rms,		ignore_prev_rms, // boolean ignore_prev_rms,
	num_tries, // = 5int num_tries, // = 5		num_tries_fit, // = 5int num_tries, // = 5
	true, // boolean calc_warp,		true, // boolean calc_warp,
	batch_mode, // boolean batch_mode,		batch_mode, // boolean batch_mode,
	gpu_pair, // String [] gpu_spair,		gpu_pair, // String [] gpu_spair,
	@@ -814,6 +819,7 @@ public class ComboMatch {
	// TODO Auto-generated catch block		// TODO Auto-generated catch block
	e.printStackTrace();		e.printStackTrace();
	}		}
			System.out.println("Saved data to "+ orthoMapsCollection_path);
	}		}
	return true;		return true;
	}		}
	@@ -942,7 +948,7 @@ adjusted affines[1] for a pair: 1694564291_293695/1694564778_589341
	ImageDtt.THREADS_MAX, // int threadsMax,		ImageDtt.THREADS_MAX, // int threadsMax,
	debugLevel); // int debug_level)		debugLevel); // int debug_level)
	}		}
	if (debugLevel > 0) {		if (debugLevel > 1) {
	String [] dbg_titles = {"x-raw","x_filled","y-raw","y_filled"};		String [] dbg_titles = {"x-raw","x_filled","y-raw","y_filled"};
	double [][] dbg_img = {vf[0], vf_filled[0],vf[1], vf_filled[1]};		double [][] dbg_img = {vf[0], vf_filled[0],vf[1], vf_filled[1]};
	ShowDoubleFloatArrays.showArrays(		ShowDoubleFloatArrays.showArrays(

src/main/java/com/elphel/imagej/orthomosaic/ItemMatch.java

0 → 100644

+97 −0

Original line number	Original line	Diff line number	Diff line
			package com.elphel.imagej.orthomosaic;
			import java.util.ArrayList;
			import java.util.Collections;
			import java.util.Comparator;
			import java.util.HashMap;

			public class ItemMatch {
			public double [] combo_pxy; // combo image {pixel_x, pixel_y}
			public double [] lla; // add later
			public HashMap<String, ItemPatternMatch> pattern_matches = new HashMap<String, ItemPatternMatch>();

			public ItemMatch (double [] combo_pxy) {
			this.combo_pxy = combo_pxy;
			}

			public double [] getXY() {
			return combo_pxy;
			}
			public int [] getIntXY() {
			return new int [] {(int) Math.round(combo_pxy[0]), (int) Math.round(combo_pxy[1])};
			}

			public void addPatternMatches(
			GroundObjectPattern groundObjectPattern,
			double [] matches,
			int best_sub) {
			String pattern_path = groundObjectPattern.getPatternPath();
			ItemPatternMatch match = pattern_matches.get(pattern_path);
			if (match == null) {
			match = new ItemPatternMatch(groundObjectPattern);
			pattern_matches.put(pattern_path, match);
			}
			match.setMatches(matches);
			match.setBestSub(best_sub);
			}

			public ItemPatternMatch getPatternMatch(GroundObjectPattern groundObjectPattern) {
			return getPatternMatch(groundObjectPattern.getPatternPath());
			}

			public ItemPatternMatch getPatternMatch(String pattern_path) {
			return pattern_matches.get(pattern_path);
			}

			public double [] getMatchValues(String pattern_path) {
			ItemPatternMatch match = pattern_matches.get(pattern_path);
			if (match == null) {
			System.out.println("No matches found for pattern "+pattern_path);
			return null;
			}
			return match.getMatches();
			}
			public double [] getMatchValues(GroundObjectPattern groundObjectPattern) {
			return getMatchValues(groundObjectPattern.getPatternPath());
			}

			public double getMatchValue(String pattern_path, int indx) {
			ItemPatternMatch match = pattern_matches.get(pattern_path);
			if (match == null) {
			System.out.println("No matches found for pattern "+pattern_path);
			return Double.NaN;
			}
			return match.getMatch(indx);
			}

			public double getMatchValue(GroundObjectPattern groundObjectPattern, int indx) {
			return getMatchValue(groundObjectPattern.getPatternPath(), indx);
			}

			public static ArrayList<Integer> sortByMatch(
			ArrayList<ItemMatch> match_list,
			GroundObjectPattern groundObjectPattern,
			int indx){
			String pattern_path = groundObjectPattern.getPatternPath();
			return sortByMatch(match_list, pattern_path, indx);
			}

			public static ArrayList<Integer> sortByMatch(
			ArrayList<ItemMatch> match_list,
			String pattern_path,
			int indx){
			ArrayList<Integer> result_list= new ArrayList<Integer>(match_list.size());
			for (int i = 0; i < match_list.size(); i++) {
			result_list.add(i);
			}
			Collections.sort(result_list, new Comparator<Integer>() {
			@Override
			public int compare(Integer lhs, Integer rhs) {
			double rhsd = match_list.get(rhs).getMatchValue(pattern_path, indx);
			double lhsd = match_list.get(lhs).getMatchValue(pattern_path, indx);
			return (rhsd > lhsd) ? 1 : (rhsd < lhsd) ? -1 : 0; // recreasing
			}
			});
			return result_list;
			}

			}

src/main/java/com/elphel/imagej/orthomosaic/ItemPatternMatch.java

0 → 100644

+52 −0

Original line number	Original line	Diff line number	Diff line
			package com.elphel.imagej.orthomosaic;

			import java.util.Arrays;

			public class ItemPatternMatch {
			// public String pattern_path;
			public double [] sub_matches; // array of sub-pattern match qualities. [0] - is usually combo, [1] - full pattern, [2+] - obscured
			public int best_sub = -1; // best subpattern
			public GroundObjectPattern groundObjectPattern;
			public ItemPatternMatch(GroundObjectPattern groundObjectPattern) {
			this.groundObjectPattern = groundObjectPattern;
			}
			public void setMatches(double [] matches) {
			sub_matches = matches;
			}
			public void setMatch(int indx, double match_value) {
			if (sub_matches == null) {
			sub_matches = new double [indx+1];
			Arrays.fill(sub_matches, Double.NaN);
			} else if (sub_matches.length <= indx) {
			double [] old_matches = sub_matches;
			sub_matches = new double [indx+1];
			Arrays.fill(sub_matches, Double.NaN);
			System.arraycopy(old_matches, 0, sub_matches, 0, old_matches.length);
			}
			sub_matches[indx] = match_value;
			}

			public void setBestSub(int sub) {
			best_sub = sub;
			}

			public int getBestSub() {
			return best_sub;
			}

			public double getMatch(int indx) {
			if ((sub_matches == null) \|\| (sub_matches.length <= indx)) {
			return Double.NaN;
			}
			return sub_matches[indx];
			}

			public double [] getMatches() {
			return sub_matches;
			}
			public GroundObjectPattern getGroundObjectPattern() {
			return groundObjectPattern;
			}
			}

src/main/java/com/elphel/imagej/orthomosaic/ObjectLocation.java

+236 −0

Original line number	Original line	Diff line number	Diff line
	@@ -10,6 +10,8 @@ import com.elphel.imagej.common.ShowDoubleFloatArrays;
	import com.elphel.imagej.tileprocessor.Correlation2d;		import com.elphel.imagej.tileprocessor.Correlation2d;
	import com.elphel.imagej.tileprocessor.TileNeibs;		import com.elphel.imagej.tileprocessor.TileNeibs;

			import Jama.EigenvalueDecomposition;
			import Jama.Matrix;
	import ij.ImagePlus;		import ij.ImagePlus;
	import ij.gui.PointRoi;		import ij.gui.PointRoi;

	@@ -80,6 +82,240 @@ public class ObjectLocation {
	return dcrop;		return dcrop;
	}		}

			public static double [] extractObjectImage(
			double [] center_xy,
			int size,
			double [] src_img,
			int width) {
			int height = src_img.length / width;
			double [] dcrop = new double [size*size];
			Arrays.fill(dcrop, Double.NaN);
			int hsize = size/2;
			int [] xy = {(int) Math.round(center_xy[0]), (int) Math.round(center_xy[1])};
			boolean has_NaN=false;
			for (int y = 0; y < size; y++) {
			int src_y = y - hsize + xy[1];
			if ((src_y >= 0) && (y < height)) {
			for (int x = 0; x < size; x++) {
			int src_x = x - hsize + xy[0];
			if ((src_x >= 0) && (x < width)) {
			double d = src_img[src_x + src_y * width];
			dcrop[x + size * y] = d;
			has_NaN \|= Double.isNaN(d);
			} else {
			has_NaN=true;
			}
			}
			} else {
			has_NaN=true;
			}
			}
			if (has_NaN) {
			TileNeibs tn = new TileNeibs(size,size);
			OrthoMap.fillNaNs(
			dcrop, // double [] data,
			tn, // TileNeibs tn,
			3); // int min_neibs)
			}
			return dcrop;
			}
			/**
			* Search for maximum within specified radius from the center or specified offset from the center
			* @param data square data
			* @param cent_xy offset from the square center to search
			* @param radius search for maximum within this radius
			* @param frac_max fraction of maximum to measure area
			* @return {maximum, area, dist, x, y}. No interpolation yet, each returned value is integer.
			* Returns null if no local maximum within area. x,y are offsets from the (provided) center
			*/
			public static double [] getMaxLocAreaNaN(
			double [] data, // square data
			double [] cent_xy, // if null, use center of the square
			double radius, // search for maximum within this radius
			double frac_max,
			int debugLevel) {
			double [] rslt = getMaxLocArea(
			data, // square data
			cent_xy, // if null, use center of the square
			radius, // search for maximum within this radius
			frac_max,
			debugLevel);
			if (rslt != null) {
			return rslt;
			} else {
			return new double[] {Double.NaN,Double.NaN,Double.NaN,Double.NaN,Double.NaN,Double.NaN};
			}
			}

			public static double [] getMaxLocArea(
			double [] data, // square data
			double [] cent_xy, // if null, use center of the square
			double radius, // search for maximum within this radius
			double frac_max,
			int debugLevel) {
			boolean debug = debugLevel > 1;
			int size = (int) Math.sqrt(data.length);
			if (cent_xy == null) {
			cent_xy = new double [] {size/2, size/2};
			}
			double maxr2 = radius * radius;
			double best_d = 0;
			int best_indx = -1;
			int min_x = Math.max(1, (int) Math.floor(cent_xy[0]-radius));
			int min_y = Math.max(1, (int) Math.floor(cent_xy[1]-radius));
			int max_x = Math.min(size-2, (int) Math.ceil(cent_xy[0]+radius));
			int max_y = Math.min(size-2, (int) Math.ceil(cent_xy[1]+radius));
			for (int y = min_y; y <= max_y; y++) { // do not search on very edges
			double dy = (y-cent_xy[1]);
			double y2 = dy*dy;
			if (y2 < maxr2) {
			for (int x = min_x; x <= max_x; x++) {
			double dx = x - cent_xy[0];
			double r2 = y2 + dx*dx;
			if (r2 < maxr2) {
			int indx = y * size + x;
			double d = data[indx];
			if (d > best_d) {
			best_indx = indx;
			best_d = d;
			}
			}
			}
			}
			}
			// is it local max?
			if ((data[best_indx - 1] > best_d) \|\| (data[best_indx + 1] > best_d) \|\|
			(data[best_indx - size] > best_d) \|\| (data[best_indx + size] > best_d)) {
			return null; // on the edge, not a local max
			}

			boolean [] above_thresh = new boolean [data.length];
			double thresh = best_d * frac_max;
			for (int i = 0; i < data.length; i++) {
			above_thresh[i] = data[i] > thresh;
			}

			int [] clusters = (new TileNeibs(size,size)).enumerateClusters(
			above_thresh, // boolean [] tiles,
			null, // int [] num_clusters,
			false); // boolean ordered)
			int center_cluster = clusters[best_indx];

			double xc = best_indx % size - cent_xy[0];
			double yc = best_indx / size - cent_xy[1];

			double s0=0, sx=0, sy=0, sx2 = 0, sy2=0, sxy = 0;
			for (int i = 0; i < clusters.length; i++) {
			if (clusters[i] == center_cluster) {
			double y = i / size - (yc + cent_xy[1]); //(yc + cent_xy[1]) - absolute, from (0,0)
			double x = i % size - (xc + cent_xy[0]);
			double w = data[i]-thresh;
			s0 += w;
			sx += w * x;
			sy += w * y;
			sx2 += w * x * x;
			sy2 += w * y * y;
			sxy += w * x * y;
			}
			}
			double cxx = sx2 - sx * sx / s0, cyy= sy2 - sy * sy / s0, cxy = sxy - sx * sy / s0;
			/*
			* sum(Mi*(Xi-avg(X))^2) = SX2 - SX^2/S0
			* sum(Mi*(Yi-avg(Y))^2) = SY2 - SY^2/S0
			* sum(Mi(Xi-avg(X)(Yi-avg(Y))) = SXY - SX*SY / S0
			*/
			Matrix covar = new Matrix(new double[][] {{cxx, cxy},{cxy,cyy}});
			double [] cent_offs = {sx/s0 + xc,sy/s0 + yc};
			EigenvalueDecomposition eig = covar.eig();

			double [] eigval = {eig.getD().get(0, 0),eig.getD().get(1, 1)};
			Arrays.sort(eigval); // ascending
			double elong = Math.sqrt(eigval[1]/eigval[0]);
			double eff_rad = Math.sqrt(Math.sqrt(eigval[1]*eigval[0]));
			double dist = Math.sqrt(cent_offs[0]cent_offs[0] + cent_offs[1]cent_offs[1]);
			if (debug) {
			System.out.println("\ncenter offset ["+(sx/s0)+","+(sy/s0)+"] , from center: ["+cent_offs[0]+","+cent_offs[1]+"]");
			System.out.println("Covariance matrix:");
			covar.print(8, 6);
			System.out.println("eig.getV()");
			eig.getV().print(8, 6);
			System.out.println("eig.getD()");
			eig.getD().print(8, 6);
			System.out.println(String.format("best_d=%7.5f, rad=%6.3f, elong=%6.3f, dist=%6.3f, dx=%6.3f, dy=%6.3f",
			best_d, eff_rad, elong, dist, cent_offs[0], cent_offs[1]));
			}

			return new double [] {best_d, eff_rad, elong, dist, cent_offs[0], cent_offs[1]} ;
			}


			public static double [] getMaxLocAreaInt(
			double [] data, // square data
			double [] cent_xy, // if null, use center of the square
			double radius, // search for maximum within this radius
			double frac_max) {
			int size = (int) Math.sqrt(data.length);
			if (cent_xy == null) {
			cent_xy = new double [] {size/2, size/2};
			}
			double maxr2 = radius * radius;
			double best_d = 0;
			int best_indx = -1;
			int min_x = Math.max(1, (int) Math.floor(cent_xy[0]-radius));
			int min_y = Math.max(1, (int) Math.floor(cent_xy[1]-radius));
			int max_x = Math.min(size-2, (int) Math.ceil(cent_xy[0]+radius));
			int max_y = Math.min(size-2, (int) Math.ceil(cent_xy[1]+radius));
			for (int y = min_y; y <= max_y; y++) { // do not search on very edges
			double dy = (y-cent_xy[1]);
			double y2 = dy*dy;
			if (y2 < maxr2) {
			for (int x = min_x; x <= max_x; x++) {
			double dx = x - cent_xy[0];
			double r2 = y2 + dx*dx;
			if (r2 < maxr2) {
			int indx = y * size + x;
			double d = data[indx];
			if (d > best_d) {
			best_indx = indx;
			best_d = d;
			}
			}
			}
			}
			}
			// is it local max?
			if ((data[best_indx - 1] > best_d) \|\| (data[best_indx + 1] > best_d) \|\|
			(data[best_indx - size] > best_d) \|\| (data[best_indx + size] > best_d)) {
			return null; // on the edge, not a local max
			}

			boolean [] above_thresh = new boolean [data.length];
			double thresh = best_d * frac_max;
			for (int i = 0; i < data.length; i++) {
			above_thresh[i] = data[i] > thresh;
			}

			int [] clusters = (new TileNeibs(size,size)).enumerateClusters(
			above_thresh, // boolean [] tiles,
			null, // int [] num_clusters,
			false); // boolean ordered)
			int center_cluster = clusters[best_indx];
			double area_max = 0.0;
			for (int i = 0; i < clusters.length; i++) {
			if (clusters[i] == center_cluster) {
			area_max += 1;
			}
			}
			double x_max = best_indx % size - cent_xy[0];
			double y_max = best_indx / size - cent_xy[1];
			double dist = Math.sqrt(y_max * y_max + x_max * x_max);
			return new double [] {best_d, area_max, dist, x_max, y_max} ;


			}




	public static double [] getPatternCenter(		public static double [] getPatternCenter(
	double [] data_in,		double [] data_in,

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