Adding filtering by absolute contrast

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

@@ -777,7 +777,7 @@ public class ObjectLocation {
 		}
 		
 		// min_weight = 10.0
-		// Starting from very center remove fartherst (first or last) pixel,
+		// Starting from very center remove farthest (first or last) pixel,
 		// until remaining weight drops below min_weight or sw0[]*(1-frac_outliers).
 		// weight of the previous radius may fall also, but likely not too much
 		for (int nr = 1; nr < sw.length; nr++) {

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

@@ -18,6 +18,8 @@ import java.time.LocalDateTime;
 import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.Calendar;
+import java.util.Collections;
+import java.util.Comparator;
 import java.util.HashMap;
 import java.util.List;
 import java.util.Properties;
@@ -1855,6 +1857,248 @@ public class OrthoMap implements Comparable <OrthoMap>, Serializable{
 		return convolved;
 	}
 	
+	/**
+	 * Calculate absolute contrast of the pattern
+	 * @param data extracted square image with the object exactly
+	 *             in the center
+	 * @param ipattern square pattern array corresponding to data. 1 means 
+	 *                 average (w/o outliers) and add, 2 - average and subtract
+	 * @param outliers_frac - fraction of outliers to remove while averaging
+	 * @param debug show debug images
+	 * @return difference between average in-pattern (1) and outside (2) average
+	 *         values  
+	 */
+	public static double getAbsoluteContrast(
+			double [] data,
+			int    [] ipattern,
+			double    outliers_frac,
+			boolean   debug) {
+		if (debug) {
+			int size = (int) Math.sqrt(data.length);
+			ShowDoubleFloatArrays.showArrays(
+					data,
+					size,
+					size,
+					"extracted_data");
+			
+		}
+		ArrayList<ArrayList<Integer>> lists = new ArrayList<ArrayList<Integer>>();
+		for (int i = 0; i < 2; i++) {
+			lists.add(new ArrayList<Integer>());
+		}
+		double [] swd = new double [2],sw = new double [2], avg= new double[2], fracw=new double[2];
+		for (int n = 0; n < swd.length; n++) {
+			ArrayList<Integer> list = lists.get(n);
+			int n1 = n+1;
+			for (int i = 0; i < ipattern.length; i++) if (ipattern[i] == n1){
+				sw[n] += 1;
+				swd[n]+= data[i];
+				list.add(i);
+			}
+			avg[n] = swd[n]/sw[n];
+			fracw[n] = (1.0-outliers_frac) * sw[n];
+		}
+		if (debug) {
+			System.out.println("getAbsoluteContrast() before outliers: avg[0] ="+avg[0]+", avg[1]="+avg[1]+", avg[0]-avg[1]="+(avg[0]-avg[1]));
+		}
+		if (outliers_frac > 0) {
+			for (int n = 0; n < swd.length; n++) {
+				ArrayList<Integer> list = lists.get(n);
+				Collections.sort(list, new Comparator<Integer>() {
+					@Override
+					public int compare(Integer lhs, Integer rhs) {
+						double rhsd = data[rhs];
+						double lhsd = data[lhs];
+						return (rhsd > lhsd) ? -1 : (rhsd < lhsd) ? 1 : 0;
+					}
+				});
+				while (sw[n] >= fracw[n]) {
+					int indx_first = list.get(0);
+					int indx_last = list.get(list.size()-1);
+					boolean remove_first = Math.abs(data[indx_first] - avg[n]) > Math.abs(data[indx_last] - avg[n]);
+					int indx_worst = remove_first? indx_first : indx_last;
+					double d = data[indx_worst];
+					double sw_new = sw[n] - 1.0;
+					avg[n] = (avg[n] * sw[n] - d)/sw_new;
+					sw[n] = sw_new;
+					list.remove(remove_first ? 0 : list.size()-1);
+				}
+			}
+		}
+		if (debug) {
+			int    [] ipattern1 = new int [ipattern.length];
+			for (int n = 0; n < lists.size(); n++) {
+				ArrayList<Integer> list = lists.get(n);
+				for (Integer i: list) {
+					ipattern1[i] = n+1;
+				}
+			}
+			int [][] ipatterns = {ipattern, ipattern1};
+			double [][] dbg_img = new double [2][ipattern.length];
+			for (int n = 0; n < ipatterns.length; n++) {
+				for (int i= 0; i < ipatterns[n].length; i++) if (ipatterns[n][i] != 0){
+					switch (ipatterns[n][i]) {
+					case 1: dbg_img[n][i] = 1.0; break;
+					case 2: dbg_img[n][i] = -1.0; break;
+					}
+				}
+			}
+			int size = (int) Math.sqrt(ipattern.length);
+			ShowDoubleFloatArrays.showArrays(
+					dbg_img,
+					size,
+					size,
+					true,
+					"integer_patterns_before_after");
+		}
+		if (debug) {
+			System.out.println("getAbsoluteContrast() after outliers: avg[0] ="+avg[0]+", avg[1]="+avg[1]+", avg[0]-avg[1]="+(avg[0]-avg[1]));
+		}
+		return avg[0]-avg[1];
+	}
+	
+	/**
+	 * From existing pattern (only for simple dark main scene)
+	 * create two zones to calculate average (w/o outliers) inside
+	 * the pattern and around it. Mark inner with 1, outer - 2, keep
+	 * other 0. Then later find 2 averages (removing outliers) and their
+	 * difference - absolute contrast.
+	 * @param patterns set of square patterns, first [0] for full pattern,
+	 *                 others - for half-patterns cut in different directions. 
+	 * @param edge_frac consider in-pattern if normalized value (normalized by
+	 *                  the value with maximal absolute value) is above
+	 *                  1-edge_frac, completely out if it is below edge_frac.
+	 * @param oversize scale patterns by this value to create outer area (marked 2)
+	 * @param debug  show debug images
+	 * @return integer array corresponding to the original patterns. 1 means
+	 *         "in-patter" (average w/o outliers and add), 2 means "around pattern"-
+	 *         average w/o outliers and subtract.
+	 */
+	public static int[][] getIntPatterns(
+			double [][] patterns,
+			double edge_frac, // 0.15
+			double oversize,
+			boolean debug) {
+		double low_thresh = edge_frac;
+		double high_thresh = 1.0 - edge_frac;
+		int size = (int) Math.sqrt(patterns[0].length);
+		double xc = size/2;
+		double yc = size/2;
+		int [][] ipatterns = new int [patterns.length][patterns[0].length];
+		double amax = 0;
+		double absmax = 0;
+		for (int i = 0; i < patterns[0].length; i++) {
+			double d = patterns[0][i];
+			double ad = Math.abs(d);
+			if (ad > absmax) {
+				absmax = ad;
+				amax = d;
+			}
+		}
+		double scale = 1.0/amax;
+		double [][] npatterns = new double [patterns.length][patterns[0].length];
+		for (int n = 0; n < patterns.length; n++) {
+			for (int i = 0; i < patterns[n].length; i++) {
+				npatterns[n][i] = patterns[n][i] * scale;
+			}
+		}
+		// create full pattern first
+		int num_1 = 0, num_2=0;
+		for (int y=0; y < size; y++) {
+			double ys= yc+ (y-yc)/oversize;
+			for (int x=0; x < size; x++) {
+				int indx = y*size+x;
+				if (npatterns[0][indx] > high_thresh) {
+					ipatterns[0][indx] = 1;
+					num_1++;
+				} else if (npatterns[0][indx] <= low_thresh) {// interpolate scaled version, between - keep zero
+					double xs = xc+ (x-xc)/oversize;
+					// interpolate
+					int iys = (int) Math.floor(ys);
+					double fys = ys-iys;
+					int ixs = (int) Math.floor(xs);
+					double fxs = xs-ixs;
+					int sindx = iys*size+ixs;
+					double sd0 = 
+							(1-fys)*(1-fxs)*npatterns[0][sindx] + 
+							(1-fys)*(  fxs)*npatterns[0][sindx+1] + 
+							(  fys)*(1-fxs)*npatterns[0][sindx+size] + 
+							(  fys)*(  fxs)*npatterns[0][sindx+size+1]; 
+					if (sd0 > high_thresh) {
+						ipatterns[0][indx] = 2;
+						num_2++;
+					}
+				}
+			}
+		}
+		if ((num_1 == 0) || (num_2==0)) {
+			System.out.println("getIntPatterns(): wrong pattern or parameters: num_1="+num_1+", num2="+num_2);
+			return null;
+		}
+		// Other patterns
+		for (int n = 1; n < npatterns.length; n++) {
+			for (int y=0; y < size; y++) {
+				double ys= yc+ (y-yc)/oversize;
+				for (int x=0; x < size; x++) {
+					int indx = y*size+x;
+					if (ipatterns[0][indx] == 1) {
+						if (npatterns[n][indx]/npatterns[0][indx] > 0.5) {
+							ipatterns[n][indx] = ipatterns[0][indx]; //= 1
+						}
+					} else if (ipatterns[0][indx] == 2) {
+						double xs = xc+ (x-xc)/oversize;
+						// interpolate
+						int iys = (int) Math.floor(ys);
+						double fys = ys-iys;
+						int ixs = (int) Math.floor(xs);
+						double fxs = xs-ixs;
+						int sindx = iys*size+ixs;
+						double sd0 = 
+								(1-fys)*(1-fxs)*npatterns[0][sindx] + 
+								(1-fys)*(  fxs)*npatterns[0][sindx+1] + 
+								(  fys)*(1-fxs)*npatterns[0][sindx+size] + 
+								(  fys)*(  fxs)*npatterns[0][sindx+size+1]; 
+						
+						double sdn = 
+								(1-fys)*(1-fxs)*npatterns[n][sindx] + 
+								(1-fys)*(  fxs)*npatterns[n][sindx+1] + 
+								(  fys)*(1-fxs)*npatterns[n][sindx+size] + 
+								(  fys)*(  fxs)*npatterns[n][sindx+size+1]; 
+						if (sdn/sd0 > 0.5) {
+							ipatterns[n][indx] = ipatterns[0][indx]; // =2
+						}
+					}
+				}
+			}
+		}
+		if (debug) {
+			ShowDoubleFloatArrays.showArrays(
+					npatterns,
+					size,
+					size,
+					true,
+					"normalized_patterns");
+			double [][] dbg_img = new double [ipatterns.length][ipatterns[0].length];
+			for (int n = 0; n < ipatterns.length; n++) {
+				for (int i= 0; i < ipatterns[n].length; i++) if (ipatterns[n][i] != 0){
+					switch (ipatterns[n][i]) {
+					case 1: dbg_img[n][i] = 1.0; break;
+					case 2: dbg_img[n][i] = -1.0; break;
+					}
+				}
+			}
+			ShowDoubleFloatArrays.showArrays(
+					dbg_img,
+					size,
+					size,
+					true,
+					"integer_patterns");
+		}
+		return ipatterns;
+	}
+	
+	
+	
 	public static double [] extractKernel(
 			double [] data,
 			int       kernel_radius,

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

@@ -1976,6 +1976,8 @@ public class OrthoMapsCollection  implements Serializable{
 		double [][][] corrs_out =     new double[indices.length][][]; 
 		double [][][] convolve_out =  new double[indices.length][][]; 
 		double [][][] corr_patterns = new double[indices.length][][];
+		int    [][][] icorr_patterns= new int[indices.length][][]; // will only be used for main !
+		
 		double [][][] filtered_corrs = new double[indices.length][][];		
 		int [] zoomout = new int[indices.length];
 		ImagePlus [] imp_corrs = new ImagePlus[indices.length];
@@ -2066,8 +2068,17 @@ public class OrthoMapsCollection  implements Serializable{
 							kernels_all[scene_num],      // final double [] kernel,
 							corr_size);                  // final int width)
 				}
-				
 			}
+			if (scene_num == 0) {
+				double oversize = 1.8;
+				double edge_frac = 0.25;
+				icorr_patterns[scene_num] =  OrthoMap.getIntPatterns(
+						corr_patterns[scene_num], // double [][] patterns,
+						edge_frac,                // double edge_frac, // 0.15
+						oversize,                 // double oversize,
+						true);                    // boolean debug);
+			}
+
 		}
 		// Splitting - above done for both scenes, below - just for the main one
 		for (int scene_num = 0; scene_num < indices.length; scene_num++) { // will probably just use first one, second - derivative
@@ -2200,6 +2211,7 @@ public class OrthoMapsCollection  implements Serializable{
 					num_non_overlap++;
 				}
 			}
+			
 			if (num_non_overlap > 0) {
 				System.out.println("Removed "+num_non_overlap+" objects outside of the scenes overlap, "+match_sort.size()+" remain");
 			}
@@ -2226,6 +2238,7 @@ public class OrthoMapsCollection  implements Serializable{
 						System.out.print(",");
 					}
 				}
+				
 			}
 //			boolean remove_dc = true;
 			if (scene_num == 0) {
@@ -2353,6 +2366,18 @@ public class OrthoMapsCollection  implements Serializable{
 							imps_extracted_corr, // ImagePlus[]           imps_extracted_corr, // may be null - will not be displayed
 							imps_extracted_corr_half); // ImagePlus[]           imps_extracted_corr_half
 				}
+				double [] abs_contrast = new double [match_sort.size()];
+				double    outliers_frac = 0.3;
+				for (int i = 0; i < match_sort.size(); i++) {
+					int indx =match_sort.get(i);
+					ItemMatch match = matches_list.get(indx);
+					int best_patt= match.getPatternMatch(gops[scene_num]).getBestSub();
+					abs_contrast[i] = OrthoMap.getAbsoluteContrast(
+							extracted_objects[scene_num][i],         // double [] data,
+							icorr_patterns[scene_num][best_patt-1], //int    [] ipattern,
+							outliers_frac,                        // double    outliers_frac,
+							true);                                // boolean   debug);
+				}	
 				// Correlate second scene only for selected fragments
 				for (int scene_other = 1; scene_other < indices.length; scene_other++) { // normally just 1
 					filter_data[scene_other] = new double[match_sort.size()][2][]; // [scene][max][0-full, 1 - half][0- max, 1 - area, 2 - distance]