Commit c8f99e6d authored by Andrey Filippov's avatar Andrey Filippov
Browse files

Worked on 100m

parent dc9a97a8

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

+8 −4
Original line number Diff line number Diff line
@@ -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

+26 −45
Original line number Diff line number Diff line
@@ -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");