Worked on 100m

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

@@ -1161,6 +1161,7 @@ adjusted affines[1] for a pair: 1694564291_293695/1694564778_589341
 					return null;
 				}
 				int pair = 0;
+				boolean flip_pair = false;
 				if (fp.npoints > 2)  { // select pair
 					int [][] pairs = new int [fp.npoints/2][2];
 					for (int j = 0; j < pairs.length; j++) {
@@ -1174,19 +1175,22 @@ adjusted affines[1] for a pair: 1694564291_293695/1694564778_589341
 
 					GenericJTabbedDialog gds = new GenericJTabbedDialog("Select image pair from the image",1200,400);
 					gds.addChoice("Image pair in the marked image:", choices, choices[choices.length-1]);
+					gds.addCheckbox    ("Flip order", false, "Match first to second.");
 					gds.showDialog();
 					if (gds.wasCanceled()) return null;
 					pair= gds.getNextChoiceIndex();
+					flip_pair = gds.getNextBoolean();
 				}
 				
 				
 				double [][] points_xy= new double [2][2];
 				int [] pair_slices = new int[2];
-				for (int n = 0; n < points_xy.length; n++) {
+				for (int nn = 0; nn < points_xy.length; nn++) {
+					int n= flip_pair? (points_xy.length-nn-1) : nn;
 					int p = 2 * pair + n; // fp.npoints-2+n;
-					points_xy[n][0] = fp.xpoints[p];
-					points_xy[n][1] = fp.ypoints[p];
-					pair_slices[n] = pRoi.getPointPosition(p); // works
+					points_xy[nn][0] = fp.xpoints[p];
+					points_xy[nn][1] = fp.ypoints[p];
+					pair_slices[nn] = pRoi.getPointPosition(p); // works
 				}
 				PairwiseOrthoMatch match= new PairwiseOrthoMatch();
 				match.affine = new double[][] {

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

@@ -1787,6 +1787,7 @@ public class OrthoMapsCollection  implements Serializable{
 		
 		// filters
 		boolean       filt_keep =       false; // list filtered out, but actually keep them
+		boolean       filt_keep_pre =   false; // Keep pre first filter
 		boolean       filt_atonce =     false; // apply main/second together, false - first filter main only
 		double        filt_frac_max =   0.6;   // 0.5;  // measure are at fraction of max
 		double [][]   filt_max_radius = {{1.0,1.0},{1.2,1.2}}; // {1.0,1.0}}; // [second/main][full/half] - inactive now
@@ -1801,7 +1802,7 @@ public class OrthoMapsCollection  implements Serializable{
 		double        filt_height =     0.2; // allow extra negative offset parallel to image offset, corresponding to object above ground
 //		double []     filt_full_half_frac = {0.7, 0.5}; // second probably not needed, it is for main
 		double []     filt_full_half_frac = {0.675, 0.5}; // second probably not needed, it is for main
-		double []     filt_roundness =      {0.6,   0.0}; // second currently is not calculated/ used
+		double []     filt_roundness =      {0.58, 0.0}; //{0.6, 0.0}; // second currently is not calculated/ used 215 mine1 0.059618
 		double        filt_abs_contrast = 80.0; // 50.0;
 		double        filt_abs_easepart = 1.0; // 1.0-no ease for low AGL. Allow lower absolute contrast for partial patterns (high AGL)
 		boolean       convolve_after =    false; // true for old kernel tuning (kernel decimation before convolution)
@@ -1816,15 +1817,24 @@ public class OrthoMapsCollection  implements Serializable{
 				filt_abs_contrast = 75;
 				filt_abs_easepart = 0.85;
 				phaseCoeff[0] =     0.9;
+				phaseCoeff[1] =     0.9;
 //				adv_radius =       20; // pix?
 			} else { // 100m defaults
-				min_corrs[0] =      0.009; // 119;
+				min_corrs =   new double[]{0.007,0.006};
 				abs_edge_frac =     0.35;
 				abs_oversize =      2.2;		
 				filt_abs_contrast = 60;
 				filt_abs_easepart = 0.85;
 				phaseCoeff[0] =     0.9;
+				phaseCoeff[1] =     0.9;
 				abs_force_round =   true;
+				filt_max_radius = new double [][] {{0.6,0.3}, {1.0,1.0}}; // {1.0,1.0}}; // [second/main][full/half] - inactive now
+				filt_elongation = new double [][] {{1.4,1.5}, {1.7,1.7}};
+				filt_frac_max =     0.7;
+				filt_dist = new double[]{5.0,2.5};  // full offset and perpendicular to images offsets
+				filt_roundness[0] = 0.58; // 0.6;214-213_1694565491_890936-1694565488_589836 is 0.589
+				filt_other_frac = new double [] {0.75,0.68};// no pixels around max at filt_other_rad should be higher than this fraction of max
+
 //				adv_radius =       20; // pix?
 			}
 		}
@@ -1864,6 +1874,7 @@ public class OrthoMapsCollection  implements Serializable{
 		
 		gd.addTab("Filters","Filtering results to reduce false positives");
 		gd.addCheckbox    ("Keep filtered out",                 filt_keep, "List filtered out, but actaually keep them.");
+		gd.addCheckbox    ("Keep pre-filter",                   filt_keep_pre, "Keep even before the first scene filter.");
 		gd.addCheckbox    ("Apply filters at once",             filt_atonce, "If false, first filter by main scene only, do not process secondary scene if main failed.");
 		gd.addNumericField("Peak hight fraction",               filt_frac_max,     5,7,"","Fraction of the peak hight for eigenvlues (radius and elongation).");
 		gd.addNumericField("Max radius, main, full",            filt_max_radius[0][0],  5,7,"pix","Maximal peak cross-section average radius at certain height.");		
@@ -1921,6 +1932,7 @@ public class OrthoMapsCollection  implements Serializable{
 		abs_obscure_frac =     gd.getNextNumber();
 		
 		filt_keep=             gd.getNextBoolean();
+		filt_keep_pre=         gd.getNextBoolean();		
 		filt_atonce=           gd.getNextBoolean();
 		filt_frac_max=         gd.getNextNumber();
 		filt_max_radius[0][0]= gd.getNextNumber();
@@ -1972,6 +1984,7 @@ public class OrthoMapsCollection  implements Serializable{
 				abs_obscure_warm,    // boolean       abs_obscure_warm, // =  true; // obscured can only be by warmer objects 
 				abs_obscure_frac,    // double        abs_obscure_frac, //  0.25; // obscured threshold between center and outer 
 				filt_keep,           // boolean       filt_keep,
+				filt_keep_pre,       //	boolean       filt_keep_pre,
 				filt_atonce,         // boolean       filt_atonce,
 				filt_frac_max,       // double        frac_max,  // measure are at fraction of max			
 				filt_max_radius,     // double [][]   filt_max_radius,
@@ -2014,6 +2027,7 @@ public class OrthoMapsCollection  implements Serializable{
 			boolean       abs_obscure_warm, // =  true; // obscured can only be by warmer objects 
 			double        abs_obscure_frac, //  0.25; // obscured threshold between center and outer 
 			boolean       filt_keep,
+			boolean       filt_keep_pre,
 			boolean       filt_atonce,
 			double        frac_max,  // measure are at fraction of max			
 			double [][]   filt_max_radius,
@@ -2451,7 +2465,6 @@ public class OrthoMapsCollection  implements Serializable{
 							center_xy,  // double [] center_xy,
 							extr_size,  // int       size,
 							corrs_out[scene_num][best_patt], // double [] src_img,
-//							bestcorr[scene_num], // double [] src_img,
 							width);     // int width)
 					// combine from scratch, best[] uses thresholding inside
 					if (combine_full[0]) {
@@ -2470,42 +2483,7 @@ public class OrthoMapsCollection  implements Serializable{
 							frac_max, // double    frac_max)
 							filt_other_rad, // double    other_radius,
 							debugLevel);                   // final int       debugLevel) {
-					/*
-					// extract main scene data, needed for the absolute contrast calculations, no display
-					showExtractedImages( // scene_num == 0 here
-							null, // ortho_maps[indices[scene_num]].getName()+"-prefilter", // String prefix
-							scene_num,          //int                   scene_num,
-							//sort_pattern_index, // int                   sort_pattern_index,
-							extr_size,          // int                   extr_size,
-							gops[scene_num],                // GroundObjectPattern   gop,
-							matches_list,       // ArrayList <ItemMatch> matches_list,
-							match_sort,         // ArrayList<Integer>    match_sort,
-							extracted_objects,  // double[][][]          extracted_objects, // may be null - will not be generated
-							null,               // 							extract_display,    // double[][][]          extract_display,   // may be null - will not be displayed 
-							dmulti,             // double[][]            dmulti,
-							width,              // int                   width,
-							remove_dc,          // boolean               remove_dc,
-							null,               // imps_extracted,     //ImagePlus[]           imps_extracted, // may be null - will not be displayed
-							debugLevel);        // int                   debugLevel
-					*/
 				}
-				/*
-				// calculate absolute contrasts for all patterns, update best_sub modes: 0 - keep, 1 - keep type, 2 keep type and if half +/-1 
-				setAbsoluteContrasts(
-						abs_force_round,    // boolean       abs_force_round,
-						abs_mode,           // int                   mode, //  0 - keep, 1 keep type and if half +/-1, 2 - keep type, 3 - any
-						abs_invert,         // boolean               neg_better, // more negative is difference - stronger result
-						abs_outliers_frac,  // double outliers_frac,
-						abs_obscure_warm,   // boolean       abs_obscure_warm, // =  true; // obscured can only be by warmer objects 
-						abs_obscure_frac,   // double        abs_obscure_frac, //  0.25; // obscured threshold between center and outer 
-						gops[scene_num],    // GroundObjectPattern   gop,
-						matches_list,       // ArrayList <ItemMatch> matches_list,
-						match_sort,         // ArrayList<Integer>    match_sort,
-						extracted_objects[scene_num], //double[][]            extracted_objects, // for this scene
-						icorr_patterns[scene_num], // int [][]              ipatterns,
-						extracted_masked[scene_num], // double [][]           masked_src, // if not null, will return masked extracted objects
-						debugLevel); // int                   debugLevel
-				*/
 				double [] scene_xy_offset =   {centers[last_scene][0]-centers[0][0],centers[last_scene][1]-centers[0][1]};
 				boolean [] removed = null;
 				double    scene_agl = gops[last_scene].getAGL(); // second scene agl
@@ -2556,14 +2534,14 @@ public class OrthoMapsCollection  implements Serializable{
 					}
 					
 				}
-				if (!filt_atonce) {
+				if (!filt_atonce) { // first filter using scene 1 only
 					boolean[] filt_main_other = new boolean [indices.length]; //{true,false};
 					filt_main_other[0] = true;
 					//int num_removed = 
 					// filt_abs_contrast
 					// filt_abs_easepart
 					removed = filterCandidates(
-							filt_keep,          // boolean       filt_keep,
+							filt_keep_pre,          // boolean       filt_keep,
 							filt_main_other,    // new boolean []        filt_main_other,
 							min_corrs,          // double []             min_corrs, // one per
 							min_corr_full_rel,  // double                min_corr_full_rel,
@@ -2584,7 +2562,7 @@ public class OrthoMapsCollection  implements Serializable{
 							matches_list,       // ArrayList <ItemMatch> matches_list,
 							match_sort,         // ArrayList<Integer>    match_sort,
 							debugLevel);        // int                   debugLevel )
-					if (!filt_keep && (removed.length > match_sort.size())) { // decimate data arrays
+					if (!filt_keep_pre && (removed.length > match_sort.size())) { // decimate data arrays
 						for (int sn = 0; sn < filter_data.length; sn++) {
 							filter_data[sn] =       removeFilteredOut (filter_data[sn], removed);
 							extracted_objects[sn] = removeFilteredOut (extracted_objects[sn], removed);
@@ -2592,11 +2570,8 @@ public class OrthoMapsCollection  implements Serializable{
 							extr_corr[sn] =         removeFilteredOut (extr_corr[sn], removed);
 							extr_corr_half[sn] =    removeFilteredOut (extr_corr_half[sn], removed);
 						}
-//						best_patt_indx = removeFilteredOut(best_patt_indx, removed);
 						removed = new boolean [match_sort.size()];
 					}
-					
-//					System.out.println(num_removed+ "scenes filtered out, "+match_sort.size()+" candidates remain");
 				}
 				if (indices.length > 1) { // for a multi-scene show after filtering by the first scene
 					// show extracted scenes after some were optionally removed by the main scene filters
@@ -2862,7 +2837,13 @@ public class OrthoMapsCollection  implements Serializable{
 						"(First value is the total offset in pixels, second accounts for parallax.) "+
 						" filt_height="+filt_height+ " meters.");
 				System.out.println("filt_other_rad="+filt_other_rad+"pix,  filt_other_frac=["+filt_other_frac[0]+", "+filt_other_frac[1]+"],"+
-						" filt_full_half_frac=["+filt_full_half_frac[0]+", "+filt_full_half_frac[1]+"].");
+						" filt_full_half_frac=["+filt_full_half_frac[0]+", "+filt_full_half_frac[1]+"], filt_roundness="+filt_roundness[0]+".");
+				System.out.println("filt_abs_contrast="+filt_abs_contrast+", filt_abs_easepart="+filt_abs_easepart);
+				System.out.println("abs_edge_frac="+abs_edge_frac+", abs_oversize="+abs_oversize+
+						", abs_force_round="+abs_force_round+", abs_mode="+abs_mode+", abs_invert="+abs_invert);
+				System.out.println("abs_outliers_frac="+abs_outliers_frac+", abs_obscure_warm="+abs_obscure_warm+
+						", abs_obscure_frac="+abs_obscure_frac);
+				
 				if (indices.length > 1) {
 					System.out.println("Second image is offset by dx="+scene_xy_offset[0]+", dy="+scene_xy_offset[1]+", dist="+
 							Math.sqrt(scene_xy_offset[0]*scene_xy_offset[0]+scene_xy_offset[1]*scene_xy_offset[1])+" pix");