Cleaned up/implemented generation of the scene stats and combo images

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

@@ -148,11 +148,12 @@ public class ComboMatch {
 		int gpu_width=  clt_parameters.imp.rln_gpu_width; // 3008;
 		int gpu_height= clt_parameters.imp.rln_gpu_height; // 3008;
 		int zoom_lev = -3; // 0; // +1 - zoom in twice, -1 - zoom out twice
-		boolean show_map_stats =      false;      
-		boolean show_combo_map =      false; // true;
-		boolean show_combo_mask =     false; // generate image mas (where it is defined)_
-		boolean use_alt =             false;
-		boolean show_centers =        true;
+//		boolean show_map_stats =      false;      
+		boolean show_combo =          false; // true;
+		
+//		boolean show_combo_mask =     false; // generate image mas (where it is defined)_
+//		boolean use_alt =             false;
+//		boolean show_centers =        true;
 		boolean use_saved_collection = true; // false;
 		boolean save_collection =     true;
 		boolean process_correlation = true; // use false to save new version of data
@@ -212,11 +213,11 @@ public class ComboMatch {
 				"GPU image width");
 		gd.addNumericField("GPU image height",             gpu_height,  0,4,"",
 				"GPU image height");
-		gd.addCheckbox    ("Show transformation centers",      show_centers, "Mark verticals from the UAS on the ground.");
-		gd.addCheckbox    ("Show statistics for ortho images", show_map_stats, "Generate and show statistics for ortho maps.");
-		gd.addCheckbox    ("Show combo image map",             show_combo_map, "Load and process altitude maps.");
-		gd.addCheckbox    ("Show combo image mask",            show_combo_mask, "Display combo binary image.");
-		gd.addCheckbox    ("Show altitude combo image", use_alt, "Load and process altitude maps.");
+//		gd.addCheckbox    ("Show transformation centers",      show_centers, "Mark verticals from the UAS on the ground.");
+//		gd.addCheckbox    ("Show statistics for ortho images", show_map_stats, "Generate and show statistics for ortho maps.");
+		gd.addCheckbox    ("Show combo maps/stats",             show_combo, "Generate/save combo maps and stats.");
+//		gd.addCheckbox    ("Show combo image mask",            show_combo_mask, "Display combo binary image.");
+//		gd.addCheckbox    ("Show altitude combo image", use_alt, "Load and process altitude maps.");
 		gd.addNumericField("Remove fraction of worst matches",   frac_remove,  3,7,"",	"When fitting scenes remove this fraction of worst match.");
 		gd.addNumericField("Maximal metric error",      metric_error,  3,7,"m",	"Maximal tolerable fitting error caused by elevation variations.");
 		if (use_marked_image ) {
@@ -257,11 +258,11 @@ public class ComboMatch {
 
 		OrthoMap.setGPUWidthHeight(gpu_width,gpu_height);
 		
-		show_centers =              gd.getNextBoolean();
-		show_map_stats =            gd.getNextBoolean();
-		show_combo_map =            gd.getNextBoolean();
-		show_combo_mask =           gd.getNextBoolean();
-		use_alt =                   gd.getNextBoolean();
+//		show_centers =              gd.getNextBoolean();
+//		show_map_stats =            gd.getNextBoolean();
+		show_combo =            gd.getNextBoolean();
+//		show_combo_mask =           gd.getNextBoolean();
+//		use_alt =                   gd.getNextBoolean();
 
 //		gpu_spair[0] =              gd.getNextString();
 //		gpu_spair[1] =              gd.getNextString();
@@ -741,48 +742,9 @@ public class ComboMatch {
         // which pair to compare
 //		String [] gpu_spair = {names[gpu_ipair[0]],names[gpu_ipair[1]]}; 
 		int [] origin = new int[2];
-		ImagePlus imp_img = null;
-		if (show_map_stats) {
-			boolean ok = maps_collection.showScenesStats(false); // boolean select_all)
-			if (!ok) {
-				return false;
-			}
-			
-//			System.out.println("Exiting after generating stats");
-//			return true; // do not process anything else
-		}
-		if (show_combo_map) {
-			imp_img = 	maps_collection.renderMulti (
-					"multi_zoom"+zoom_lev, // String      title,
-					OrthoMapsCollection.MODE_IMAGE,  // int           mode,    // 0 - regular image, 1 - altitudes, 2 - black/white mask       // boolean     use_alt,
-					show_centers,      // boolean     show_centers,
-					zoom_lev,          // int         zoom_level,
-					temp_mode,         // int         temp_mode, // 0 - do nothing, 1 - equalize average,2 - try to correct
-					origin);           // int []      origin){
-			imp_img.show();
-		}
-		ImagePlus imp_alt = null;
-		if (use_alt) {
-			imp_alt =maps_collection.renderMulti (
-					"multi_alt_zoom"+zoom_lev, // String      title,
-//					true,              // boolean     use_alt,
-					OrthoMapsCollection.MODE_ALT,  // int           mode,    // 0 - regular image, 1 - altitudes, 2 - black/white mask       // boolean     use_alt,
-					show_centers,      // boolean     show_centers,
-					zoom_lev,          // int         zoom_level,
-					0,                 // int         temp_mode, // 0 - do nothing, 1 - equalize average,2 - try to correct
-					origin);           // int []      origin){
-			imp_alt.show();
-		}
-		if (show_combo_mask) {
-			imp_alt =maps_collection.renderMulti (
-					"multi_alt_zoom"+zoom_lev, // String      title,
-//					true,              // boolean     use_alt,
-					OrthoMapsCollection.MODE_MASK,  // int           mode,    // 0 - regular image, 1 - altitudes, 2 - black/white mask       // boolean     use_alt,
-					show_centers,      // boolean     show_centers,
-					zoom_lev,          // int         zoom_level,
-					0,                 // int         temp_mode, // 0 - do nothing, 1 - equalize average,2 - try to correct
-					origin);           // int []      origin){
-			imp_alt.show();
+		if (show_combo) { // now all modes, and stats?
+			maps_collection.processComboMap(debugLevel);
+			return true;
 		}
         if (process_correlation || render_match || pattern_match) {
 //        	int [] gpu_pair;
@@ -953,8 +915,6 @@ public class ComboMatch {
         					}
         				}
 
-
-
         				if (pattern_match) {
         					ImagePlus imp_pat_match = maps_collection.patternMatchDualWrap (
         							gpu_pair, // int []        indices, // null or which indices to use (normally just 2 for pairwise comparison)
@@ -974,7 +934,7 @@ public class ComboMatch {
         							temp_mode,         // int           temp_mode, // 0 - do nothing, 1 - equalize average,2 - try to correct
         							affines,           // double [][][] affines, // null or [indices.length][2][3]
         							warp,              // FineXYCorr    warp,
-        							show_centers,      // boolean     show_centers,
+        							true,              // show_centers,      // boolean     show_centers,
         							min_zoom_lev,      // int         zoom_level,
         							origin);           // int []      origin){
         					imp_img_pair.show();

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

@@ -200,6 +200,16 @@ public class ItemMatch {
 		return match.getMatch(indx);
 	}
 
+	public double getMatchBestValue(String pattern_path) {
+		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.getBestMatchValue();
+	}
+
+	
 	
 	
 	/**
@@ -212,6 +222,17 @@ public class ItemMatch {
 		return getMatchValue(groundObjectPattern.getPatternPath());
 	}
 	
+	/**
+	 * Return actual best correlation value regardless of where best subpattern index
+	 * points to - it may be forced to point to the full pattern by absolute contrast
+	 * @param groundObjectPattern
+	 * @return maximal correlation value amoong the full pattern and all half-patterns.
+	 */
+	public double getMatchBestValue(GroundObjectPattern groundObjectPattern) {
+		return getMatchBestValue(groundObjectPattern.getPatternPath());
+	}
+	
+	
 	
 	public double getMatchValue(String pattern_path) {
 		int indx = getPatternMatch(pattern_path).getBestSub(); // -1;
@@ -231,6 +252,7 @@ public class ItemMatch {
 			int                  indx){
 		String pattern_path = groundObjectPattern.getPatternPath();
 		return sortByMatch(match_list, pattern_path, keep_removed, indx);
+		
 	}
 	
 	public static ArrayList<Integer> sortByMatch(
@@ -238,6 +260,9 @@ public class ItemMatch {
 			String               pattern_path,
 			boolean              keep_removed,
 			int                  indx){
+		if (indx < 0) {
+			return sortByBestMatch (match_list, pattern_path, keep_removed);
+		}
 		double large_enough = 1.0;
 		ArrayList<Integer> result_list= new ArrayList<Integer>(match_list.size());
 		for (int i = 0; i < match_list.size(); i++) {
@@ -258,6 +283,32 @@ public class ItemMatch {
 		return result_list;
 	}
 	
+	public static ArrayList<Integer> sortByBestMatch(
+			ArrayList<ItemMatch> match_list,
+			String               pattern_path,
+			boolean              keep_removed){
+		double large_enough = 1.0;
+		ArrayList<Integer> result_list= new ArrayList<Integer>(match_list.size());
+		for (int i = 0; i < match_list.size(); i++) {
+			if (keep_removed || !match_list.get(i).isRemoved()) {
+				result_list.add(i);
+			}
+		}
+		Collections.sort(result_list, new Comparator<Integer>() {
+			@Override
+			public int compare(Integer lhs, Integer rhs) {
+				ItemMatch rhsm = match_list.get(rhs);
+				ItemMatch lhsm = match_list.get(lhs);
+				double rhsd = rhsm.getMatchBestValue(pattern_path) - (rhsm.isRemoved() ? large_enough:0 );
+				double lhsd = lhsm.getMatchBestValue(pattern_path) - (lhsm.isRemoved() ? large_enough:0 );
+				return (rhsd > lhsd) ? 1 : (rhsd < lhsd) ? -1 : 0; // decreasing
+			}
+		});
+		return result_list;
+	}
+	
+	
+	
 	public static void setExtractedObjects(
 			int                   scene_num,
 			int                   extr_size,

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

@@ -41,6 +41,25 @@ public class ItemPatternMatch {
 		}
 		return sub_matches[indx];
 	}
+	/**
+	 * Return actual largest value of full and all half patterns, regardless of best_sub which can point
+	 * to full pattern even if the correlation value is larger for partial 
+	 * @return
+	 */
+	public double getBestMatchValue() { //
+		if (sub_matches == null) {
+			return Double.NaN;
+		}
+		double best = 0;
+		for (int i = 1; i < sub_matches.length; i++) {
+			if (sub_matches[i] > best) {
+				best = sub_matches[i];
+			}
+		}
+		return best;
+	}
+	
+	
 	
 	public double [] getMatches() {
 		return sub_matches;

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

@@ -2165,7 +2165,7 @@ public class OrthoMap implements Comparable <OrthoMap>, Serializable{
 			}
 		}
 		
-		double threshold = obscure_frac * avg[0] + (1.0 - obscure_frac) * avg[1];
+		double threshold = (1.0 - obscure_frac) * avg[0] + obscure_frac * avg[1];
 		double over_thresh = (avg[0] < avg[1]) ? (zone3_min_max[0] - threshold) : (threshold - zone3_min_max[1]);