Detect mines with morning/evenimg pair

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

@@ -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_nov3_50-75",
 				"/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 orthoMapsCollection_path = "/media/elphel/SSD3-4GB/lwir16-proc/ortho_videos/maps_nov3_50-75.data";
 //maps_nov3_50-75		
@@ -148,10 +148,11 @@ public class ComboMatch {
 		boolean use_saved_collection = true; // false;
 		boolean save_collection = true;
 		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 render_match =        true;
+		boolean render_match =        false; // true;
 
-		boolean pattern_match =       false;
+		boolean pattern_match =       true; // false;
 		
 		boolean bounds_to_indices =   true;
 		int     temp_mode =           1;
@@ -166,10 +167,13 @@ public class ComboMatch {
 		
 		
 		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    ("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.");
+//		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    ("Render match", render_match, "Render a pair of matched images.");
 		
@@ -215,6 +219,7 @@ public class ComboMatch {
 		use_saved_collection =     gd.getNextBoolean();
 		save_collection =          gd.getNextBoolean();
 		process_correlation=       gd.getNextBoolean();
+		num_tries_fit =      (int) gd.getNextNumber();
 		update_match=              gd.getNextBoolean();
 		render_match=              gd.getNextBoolean();
 		
@@ -728,10 +733,10 @@ public class ComboMatch {
 				double [][][] affines = {affine0,affine1};
 				int [] zooms = {initial_zoom, min_zoom_lev, 1000,1000}; // make automatic
 				double scale = 2.0; // scale vectors when warping;
-				int num_tries  = 5;
+//				int num_tries  = 5; // make configurable
 				if (!process_correlation) {
 					zooms = new int[] {min_zoom_lev, 1000};
-					num_tries = 0;
+					num_tries_fit = 0;
 					update_match = false;
 				}
 				debugLevel = 0;
@@ -750,7 +755,7 @@ public class ComboMatch {
 							frac_remove,    // double           frac_remove, //  =        0.25
 							metric_error, // 			double           metric_error,
 							ignore_prev_rms, // boolean ignore_prev_rms,
-							num_tries,      //  = 5int              num_tries, //  = 5
+							num_tries_fit,      //  = 5int              num_tries, //  = 5
 							true, // boolean          calc_warp,
 							batch_mode,     // boolean          batch_mode,
 							gpu_pair,      // String []        gpu_spair,
@@ -814,6 +819,7 @@ public class ComboMatch {
         		// TODO Auto-generated catch block
         		e.printStackTrace();
         	}
+        	System.out.println("Saved data to "+ orthoMapsCollection_path);
         }
         return true;
 	}
@@ -942,7 +948,7 @@ adjusted affines[1] for a pair: 1694564291_293695/1694564778_589341
     				ImageDtt.THREADS_MAX, // int       threadsMax,
     				debugLevel);          // int       debug_level)
     	}		
-		if (debugLevel > 0) {
+		if (debugLevel > 1) {
 			String [] dbg_titles = {"x-raw","x_filled","y-raw","y_filled"};
 			double [][] dbg_img = {vf[0], vf_filled[0],vf[1], vf_filled[1]};
     		ShowDoubleFloatArrays.showArrays(

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

+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

+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

@@ -10,6 +10,8 @@ import com.elphel.imagej.common.ShowDoubleFloatArrays;
 import com.elphel.imagej.tileprocessor.Correlation2d;
 import com.elphel.imagej.tileprocessor.TileNeibs;
 
+import Jama.EigenvalueDecomposition;
+import Jama.Matrix;
 import ij.ImagePlus;
 import ij.gui.PointRoi;
 
@@ -80,6 +82,240 @@ public class ObjectLocation {
 		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(
 			double [] data_in,