Cleaning up, improving results

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

@@ -327,7 +327,29 @@ public class ComboMatch {
 					"patterns_r20.0_e25.0_ir10.0_ie8.0_is0.0_or45.0_oe20.0_os-1.0_h8_w0.6_s-60.0_200x200.tif",
 					"patterns_r20.0_e25.0_ir10.0_ie8.0_is0.0_or40.0_oe20.0_os-1.0_h8_w0.6_s-60.0_200x200.tif",
 					"patterns_r20.0_e25.0_ir10.0_ie8.0_is0.0_or35.0_oe15.0_os-1.0_h8_w0.6_s-60.0_200x200.tif",
-					"patterns_r20.0_e20.0_ir10.0_ie8.0_is0.0_or35.0_oe15.0_os-1.0_h8_w0.6_s-60.0_200x200.tif"
+					"patterns_r20.0_e20.0_ir10.0_ie8.0_is0.0_or35.0_oe15.0_os-1.0_h8_w0.6_s-60.0_200x200.tif",
+					"patterns_r30.0_e15.0_ir15.0ie8.0_is-0.05_h8_w0.6_s-200.0_200x200.tiff", // morning used
+					"--- 30, 28 edge 10 --",
+					"patterns_r30.0_e10.0_ir15.0_ie8.0_is-0.05_or42.0_oe6.0_os0.0_h8_w0.6_s-200.0_200x200.tif",
+					"patterns_r30.0_e10.0_ir15.0_ie8.0_is-0.3_or42.0_oe6.0_os0.0_h8_w0.6_s-200.0_200x200.tif",
+					"patterns_r28.0_e10.0_ir15.0_ie8.0_is-0.05_or42.0_oe6.0_os0.0_h8_w0.6_s-200.0_200x200.tif",
+					"patterns_r28.0_e10.0_ir15.0_ie8.0_is-0.3_or42.0_oe6.0_os0.0_h8_w0.6_s-200.0_200x200.tif",
+					"--- 26, 32 edge 10 --",
+					"patterns_r26.0_e10.0_ir15.0_ie8.0_is-0.05_or42.0_oe6.0_os0.0_h8_w0.6_s-200.0_200x200.tif",
+					"patterns_r26.0_e10.0_ir15.0_ie8.0_is-0.3_or42.0_oe6.0_os0.0_h8_w0.6_s-200.0_200x200.tif",
+//					"patterns_r32.0_e10.0_ir15.0_ie8.0_is-0.05_or42.0_oe6.0_os0.0_h8_w0.6_s-170.0_200x200.tif",
+					"patterns_r32.0_e10.0_ir15.0_ie8.0_is-0.05_or42.0_oe6.0_os0.0_h8_w0.6_s-200.0_200x200.tif",
+					"patterns_r32.0_e10.0_ir15.0_ie8.0_is-0.3_or42.0_oe6.0_os0.0_h8_w0.6_s-200.0_200x200.tif",
+					"---- 30, 26 edge 6 ---",
+					"patterns_r30.0_e6.0_ir15.0_ie8.0_is-0.05_or42.0_oe6.0_os0.0_h8_w0.6_s-200.0_200x200.tif",
+					"patterns_r30.0_e6.0_ir15.0_ie8.0_is-0.3_or42.0_oe6.0_os0.0_h8_w0.6_s-200.0_200x200.tif",
+					"patterns_r26.0_e6.0_ir15.0_ie8.0_is-0.05_or42.0_oe6.0_os0.0_h8_w0.6_s-200.0_200x200.tif",
+					"patterns_r26.0_e6.0_ir15.0_ie8.0_is-0.3_or42.0_oe6.0_os0.0_h8_w0.6_s-200.0_200x200.tif",
+					"---- 30, 26 edge 8 ---",					
+					"patterns_r30.0_e8.0_ir15.0_ie8.0_is-0.05_or42.0_oe6.0_os0.0_h8_w0.6_s-200.0_200x200.tif",
+					"patterns_r30.0_e8.0_ir15.0_ie8.0_is-0.3_or42.0_oe6.0_os0.0_h8_w0.6_s-200.0_200x200.tif",
+					"patterns_r26.0_e8.0_ir15.0_ie8.0_is-0.05_or42.0_oe6.0_os0.0_h8_w0.6_s-200.0_200x200.tif",
+					"patterns_r26.0_e8.0_ir15.0_ie8.0_is-0.3_or42.0_oe6.0_os0.0_h8_w0.6_s-200.0_200x200.tif"
 					};
 			
 			
@@ -399,9 +421,39 @@ public class ComboMatch {
 			for (ObjectLocation ol: object_list) {
 				System.out.println(ol.name+": "+ol.xy_meters[0]+"/"+ol.xy_meters[1]);
 			}
+			int [] indices = null;
+			int [][] bounds = maps_collection.getBoundsPixels( // should be for rectified, {-bounds[0][0], -bounds[0][1]} - exact center
+					zool_lev_objects,
+					indices); 
+			int width =  bounds[0][1] - bounds[0][0]; // bounds[x][0] - negative 
+			int height = bounds[1][1] - bounds[1][0];
+			if ((width != imp_sel.getWidth()) || (height != imp_sel.getHeight())) {
+				System.out.println("Marked image ("+imp_sel.getWidth()+"x"+imp_sel.getHeight()+") does not match the full map size ("+
+						width+"x"+height+"), will try just for a pair of the first two slices");
+				String [] labels = imp_sel.getStack().getSliceLabels();
+				indices = new int [2];
+				for (int i = 0; i < indices.length; i++) {
+					indices[i] = maps_collection.getIndex(labels[i].substring(0, 17));
+				}
+				bounds = maps_collection.getBoundsPixels( // should be for rectified, {-bounds[0][0], -bounds[0][1]} - exact center
+						zool_lev_objects,
+						indices);
+				width =  bounds[0][1] - bounds[0][0]; // bounds[x][0] - negative 
+				height = bounds[1][1] - bounds[1][0];
+				if ((width != imp_sel.getWidth()) || (height != imp_sel.getHeight())) {
+					System.out.println("Marked image ("+imp_sel.getWidth()+"x"+imp_sel.getHeight()+") does not match the 2-image map size ("+
+							width+"x"+height+") either.Giving up");
+					return false;
+				} else {
+					System.out.println("Marked image ("+imp_sel.getWidth()+"x"+imp_sel.getHeight()+") does match the 2-image map size ("+
+							width+"x"+height+"). Using it.");
+				}
+			}
+			
 			maps_collection.reverseRender(
 					object_list,        // ArrayList<ObjectLocation> objects,
-					zool_lev_objects);   // int         zoom_level){
+					zool_lev_objects,   // int         zoom_level){
+					indices);           // int []      indices){ // null or selected image indices
 			System.out.println("Object coordinates in source images: ");
 			for (ObjectLocation ol: object_list) {
 				System.out.println(ol.name+": "+ol.getPixels()[0]+"/"+ol.getPixels()[1]);
@@ -416,11 +468,14 @@ public class ComboMatch {
 						extr_size);
 
 			}
+
 			ImagePlus imp_obj = ShowDoubleFloatArrays.makeArrays(
 					object_stack,
 					extr_size,
 					extr_size,
-					OrthoMap.removeKnownExtension(imp_sel.getTitle())+"-OBJECT_"+extr_size+"x"+extr_size+".tiff",				
+					OrthoMap.removeKnownExtension(imp_sel.getTitle())+
+					OrthoMap.removeKnownExtension(pattern_file)+":"+sub_pattern_index+
+					"-OBJECT_"+extr_size+"x"+extr_size+".tiff",				
 					object_titles); // test_titles,
 			imp_obj.show();
 			
@@ -448,8 +503,10 @@ public class ComboMatch {
 			}
 			double [] kernel =  OrthoMap.getConvolutionKernel(default_kernel);
 			double [][] centers = new double [object_stack.length][];
+			
+			double [][] corr_ret = new double [object_stack.length][corr_size*corr_size];
 			for (int i = 0; i < object_stack.length; i++) {
-				String    dbg_prefix = "corr_patt_"+i;
+				String    dbg_prefix = "corr_patt_"+i+"-"+OrthoMap.removeKnownExtension(pattern_file)+":"+sub_pattern_index;
 				ObjectLocation ol = object_list.get(i);
 				centers[i] = ObjectLocation.getPatternCenter(
 						object_stack[i], // double [] data,
@@ -460,6 +517,7 @@ public class ComboMatch {
 						min_corr,        // double    min_corr,
 						radius_search,   // int       radius_search,
 						radius_centroid, // int       radius_centroid,
+						corr_ret[i],     //double [] corr_ret, // null or double[corr_size*corr_size]
 						dbg_prefix,      // String    dbg_prefix,
 						debugLevel);     // int       debugLevel)
 				System.out.println(i+": center at "+centers[i][0]+"/"+centers[i][1]+", strength="+centers[i][2]);
@@ -470,6 +528,35 @@ public class ComboMatch {
 				roi.addPoint(centers[i][0]+extr_size/2, centers[i][1]+extr_size/2, i+1); // ,1);
 			}
 			imp_obj.setRoi(roi);
+			// calculate statistics for cor_ret[i]
+			double [][] stats = new double [object_stack.length][];
+			double search_rad = 15.0;
+			double frac_max =   0.5;
+			double other_rad = 25;
+			for (int i = 0; i < object_stack.length; i++) {
+				double [] a_cent= {corr_size/2+centers[i][0],corr_size/2+centers[i][1]};
+				stats[i]=ObjectLocation.getMaxLocArea(
+						corr_ret[i], // double [] data, // square data
+						a_cent, // centers[i],  // double [] cent_xy, // if null, use center of the square
+						search_rad,  // double    radius, // search for maximum within this radius
+						frac_max,    // double    frac_max,
+						other_rad,
+						0);          // int       debugLevel) 
+			}
+			
+			System.out.println("\nUsing pattern file: "+pattern_path+", subpattern="+sub_pattern_index);
+			System.out.println(String.format("%2s (%9s): %7s %7s %7s %7s %7s %7s %17s",
+					"#","  X/Y  ","strengh", "radius", " elong ", " dist ", "  dx  ","  dy  ",
+					"image timestamp"));
+			for (int i = 0; i < object_stack.length; i++) {
+				ObjectLocation ol =  object_list.get(i);
+				System.out.println(String.format("%2d (%4d/%4d): %7.5f %7.3f %7.3f %7.3f %7.3f %7.3f %17s",
+						i, ol.getPixels()[0], ol.getPixels()[1],
+						stats[i][0],stats[i][1],stats[i][2],stats[i][3],stats[i][4]+centers[i][0],stats[i][5]+centers[i][1],
+						ol.getName()));
+			}
+			System.out.println();
+			
 			if (only_correlate) {
 				System.out.println("testPatternCorrelate(): correlation DONE, only_correlate is set to true, exiting");
 				return true;
@@ -797,7 +884,8 @@ public class ComboMatch {
 					}
 					if (render_match) {
 						ImagePlus imp_img_pair = 	maps_collection.renderMulti (
-								"multi_"+gpu_spair[0]+"-"+gpu_spair[1]+"-zoom_"+min_zoom_lev+"_"+zoom_lev, // String      title,
+								//_zoom<integer> is needed for opening with "Extract Objects" command
+								"multi_"+gpu_spair[0]+"-"+gpu_spair[1]+"_zoom"+min_zoom_lev+"_"+zoom_lev, // String      title,
 								false,             // boolean     use_alt,
 								gpu_pair,          // int []        indices, // null or which indices to use (normally just 2 for pairwise comparison)
 								bounds_to_indices, // boolean       bounds_to_indices,
@@ -824,6 +912,11 @@ public class ComboMatch {
         return true;
 	}
 	
+	public void printSceneStats() {
+		
+	}
+	
+	
 		/*
     	double [][] affine1 = {
     			{1,0,0},
@@ -1056,7 +1149,10 @@ adjusted affines[1] for a pair: 1694564291_293695/1694564778_589341
 				int nSlices = stack_scenes.getSize();
 				String [] scene_names = new String [nSlices];
 				for (int n = 0; n < scene_names.length; n++) {
-					scene_names[n] = stack_scenes.getSliceLabel(n+1).substring(0,17);
+					scene_names[n] = stack_scenes.getSliceLabel(n+1);
+					if (scene_names[n].length() >= 17) {
+						scene_names[n] = scene_names[n].substring(0,17);
+					}
 				}
 				PointRoi pRoi = (PointRoi) imp.getRoi();
 				FloatPolygon fp = pRoi.getContainedFloatPoints();

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

@@ -125,6 +125,7 @@ public class ObjectLocation {
 	 * @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
+	 * @param other_radius measure maximal disconnected pixel fraction of the maximum within this radius
 	 * @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 
 	 */
@@ -133,12 +134,14 @@ public class ObjectLocation {
 			double [] cent_xy, // if null, use center of the square
 			double    radius, // search for maximum within this radius
 			double    frac_max,
+			double    other_radius,
 			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,
+				other_radius,
 				debugLevel);
 		if (rslt != null) {
 			return rslt;
@@ -152,6 +155,7 @@ public class ObjectLocation {
 			double [] cent_xy, // if null, use center of the square
 			double    radius, // search for maximum within this radius
 			double    frac_max,
+			double    other_radius,
 			int       debugLevel) {
 		boolean   debug = debugLevel > 1;
 		int size = (int) Math.sqrt(data.length);
@@ -201,8 +205,11 @@ public class ObjectLocation {
 				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];
+		int best_x = best_indx % size;
+		int best_y = best_indx / size;
+		double xc = best_x - cent_xy[0];
+		double yc = best_y - cent_xy[1];
+		
 
 		double s0=0, sx=0, sy=0, sx2 = 0, sy2=0, sxy = 0;
 		for (int i = 0; i < clusters.length; i++) {
@@ -233,6 +240,35 @@ public class ObjectLocation {
 		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]);
+		double max_other = 0.0;
+		if (other_radius > 0) { // only calculate if asked for
+			double or2 = other_radius*other_radius;
+			min_x = Math.max(1, (int) Math.floor(best_x-other_radius));
+			min_y = Math.max(1, (int) Math.floor(best_y-other_radius));
+			max_x = Math.min(size-2, (int) Math.ceil(best_x+other_radius));
+			max_y = Math.min(size-2, (int) Math.ceil(best_y+other_radius));
+			for (int y = min_y; y <= max_y; y++) { // do not search on very edges
+				double dy = (y-best_y);
+				double y2 = dy*dy;
+				if (y2 < or2) {
+					for (int x = min_x; x <= max_x; x++) {
+						double dx = x - best_x;
+						double r2 = y2 + dx*dx;
+						if (r2 < or2) {
+							int indx = y * size + x;
+							if (clusters[indx] != center_cluster) { // only disconnected from the central area
+								double d = data[indx];
+								if (d > max_other) {
+									max_other = d;
+								}
+							}
+						}
+					}
+				}
+			}
+			max_other /= best_d;
+		}
+		
 		if (debug) {
 			System.out.println("\ncenter offset ["+(sx/s0)+","+(sy/s0)+"] , from center: ["+cent_offs[0]+","+cent_offs[1]+"]");
 			System.out.println("Covariance matrix:");
@@ -241,11 +277,11 @@ public class ObjectLocation {
 			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]));
+			System.out.println(String.format("best_d=%7.5f, rad=%6.3f, elong=%6.3f, dist=%6.3f, dx=%6.3f, dy=%6.3f, mo=%5.3f",
+					best_d, eff_rad, elong, dist, cent_offs[0], cent_offs[1], max_other));
 		}
 		
-		return new double [] {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], max_other} ;
 	}
 
 	
@@ -326,6 +362,7 @@ public class ObjectLocation {
 			double    min_corr,
 			int       radius_search,
 			int       radius_centroid,
+			double [] corr_ret, // null or double[corr_size*corr_size]
 			String    dbg_prefix,
 			int       debugLevel){
 		int refine = 1;
@@ -393,6 +430,9 @@ public class ObjectLocation {
 				false,            // final boolean   convolve,   // convolve, not correlate
 				phaseCoeff,       // final double    phaseCoeff,
 				debugLevel);      // final int       debugLevel)
+		if (corr_ret != null) {
+			System.arraycopy(corr_out, 0, corr_ret, 0, corr_out.length);
+		}
 		int data_width = 2 *radius_search + 1;
 		int offs = corr_size/2 - radius_search;
 		

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

@@ -3841,7 +3841,7 @@ public class OrthoMap implements Comparable <OrthoMap>, Serializable{
 											if (ipix1 >= 0) {
 												bestcorr[ipix1] = corrs[patt][ipix1];
 												if (combine_full) {
-													bestcorr[ipix1] *= corrs[full_patt_indx][ipix1]/corrs[full_patt_indx][ipix];
+													bestcorr[ipix1] *= Math.max(0, corrs[full_patt_indx][ipix1]/corrs[full_patt_indx][ipix]);
 												}
 												bestpatt[ipix1] = patt;
 											}