Cleaning up, creating a single method to do all target processing

src/main/java/com/elphel/imagej/tileprocessor/Correlation2d.java

@@ -2442,6 +2442,9 @@ public class Correlation2d {
 			}
 		}
 		double mx = data[imax];
+		if (mx < 0) {
+			return null; //negative maximum
+		}
 		int ix0 = imax % data_width;
 		int iy0 = imax / data_width;
 		if (exclude_margins) {
@@ -2523,6 +2526,9 @@ public class Correlation2d {
 				x0 += sx / s0;
 				y0 += sy / s0;
 				frac = s0 / (s0 + s_other);
+				if (Double.isNaN(s0)) {
+					return null; // all negative
+				}
 			}
 		}
 		if (calc_fraction) {
@@ -2530,12 +2536,18 @@ public class Correlation2d {
 			if (debug){
 				System.out.println("getMaxXYCm() -> "+rslt[0]+":"+rslt[1] +" ("+rslt[2]+"), frac = " + rslt[3]);
 			}
+			if (Double.isNaN(rslt[0]) || Double.isNaN(rslt[1]) || Double.isNaN(rslt[2])) {
+				System.out.println("getMaxXYCm():NaN");
+			}
 			return rslt;
 		} else {
 			double [] rslt = {x0 - center_xy, y0 - center_xy, mx};
 			if (debug){
 				System.out.println("getMaxXYCm() -> "+rslt[0]+":"+rslt[1] +" ("+rslt[2]+")");
 			}
+			if (Double.isNaN(rslt[0]) || Double.isNaN(rslt[1]) || Double.isNaN(rslt[2])) {
+				System.out.println("getMaxXYCm():NaN");
+			}
 			return rslt;
 		}
 	}

src/main/java/com/elphel/imagej/tileprocessor/IntersceneMatchParameters.java

@@ -708,6 +708,8 @@ min_str_neib_fpn	0.35
     public int      cuas_corr_offset =    20;     // offset between motion detection pairs
     public boolean  cuas_half_step =     false;   // half step (=cuas_corr_offset/2) when scanning for motion
     public int      cuas_max_range =     2;       // how far to extend local max: 1 3x3 neighbors, 2 - 5x5 neighbs
+    public int      cuas_num_cycles =    10;      // number of cycles of testing and removing bad targets 
+    
     // boosting weight of moving targets
     public double   cuas_speed_min =     0.2;     // minimal pixels per range (per cuas_corr_offset)
     public double   cuas_speed_pref =    0.5;     // preferable speed (boost weights for faster targets)
@@ -753,6 +755,8 @@ min_str_neib_fpn	0.35
 	public boolean  cuas_ra_background = true; // apply running average to the background of the moving targets (false - use high-noise no-averaged images
 	// which files to save in the model directory:
 
+	public int      cuas_iter_show =        1; // Maximal enhancement iteration to show intermediate result (0 - none) 
+	public boolean  cuas_2d_save_show =  true; // save/show 2D correlation  
 	public boolean  cuas_intermed_low =  true; // save intermediate vector fields and target coordinates from the LMA (80x64 layers) 
 	public boolean  cuas_intermed_high = true; // save pixel-resolution accumulated images (640x512) 
 	public boolean  cuas_save_mono =     true; // save 32-bit monochrome target+backgrounds Tiffs (before optional scaling)
@@ -2183,6 +2187,8 @@ min_str_neib_fpn	0.35
 				"Reduce step for motion detection = offset/2, if false = offset.");
 		gd.addNumericField("Local max range",                        this.cuas_max_range, 0,3,"",
 				"While filtering local correlation maximums: 1 - 3x3 neighbors, 2 - 5x5 ones.");
+		gd.addNumericField("Number of enhancement cycles",           this.cuas_num_cycles, 0,3,"",
+				"Number of cycles of testing and removing bad targets from compoetition with weaker neighbors.");
 
 		gd.addMessage("=== Moving target filtering ===");
 		gd.addNumericField("Minimal speed",                          this.cuas_speed_min, 5,8,"ppr",
@@ -2260,7 +2266,7 @@ min_str_neib_fpn	0.35
 				"Taget mask to replace static background with moving target.");
 		gd.addNumericField("Mask transition width",                 this.cuas_mask_blur, 5,8,"pix",
 				"Transition between opaque and transparent mask.");
-		gd.addCheckbox ("Mask round",                    this.cuas_mask_round,
+		gd.addCheckbox ("Mask round",                               this.cuas_mask_round,
 				"Use round mask. Unchesked - use sharp square mask without any transition.");
 		
 		gd.addNumericField("Targets icon type",                     this.cuas_target_type, 0,3,"",
@@ -2274,6 +2280,10 @@ min_str_neib_fpn	0.35
 				"Apply running average to the background of the moving targets (false - use high-noise no-averaged images.");
 
 		gd.addMessage("=== Saving intermediate and final images and video ===");
+		gd.addNumericField("Maximal iteration to save/show",        this.cuas_iter_show, 0,3,"",
+				"Maximal enhancement iteration to save/ show intermediate result (0 - none).");
+		gd.addCheckbox ("Save/show 2D correlations",                this.cuas_2d_save_show,
+				"Save and optionally show 2D correlations.");
 		gd.addCheckbox ("Save tile-resolution intermediate images", this.cuas_intermed_low,
 				"Save intermediate vector fields and target coordinates from the LMA (80x64 layers).");
 		gd.addCheckbox ("Save pixel-resolution intermediate images",this.cuas_intermed_high,
@@ -3243,6 +3253,8 @@ min_str_neib_fpn	0.35
 		this.cuas_corr_offset =   (int) gd.getNextNumber();
 		this.cuas_half_step =           gd.getNextBoolean();
 		this.cuas_max_range =     (int) gd.getNextNumber();
+		this.cuas_num_cycles =    (int) gd.getNextNumber();
+		
 		this.cuas_speed_min =           gd.getNextNumber();
 		this.cuas_speed_pref =          gd.getNextNumber();
 		this.cuas_speed_boost =         gd.getNextNumber();
@@ -3282,6 +3294,8 @@ min_str_neib_fpn	0.35
 		this.cuas_scale2x =             gd.getNextBoolean();
 		this.cuas_ra_background =       gd.getNextBoolean();
 
+		this.cuas_iter_show=      (int) gd.getNextNumber();
+		this.cuas_2d_save_show =        gd.getNextBoolean();
 		this.cuas_intermed_low =        gd.getNextBoolean();
 		this.cuas_intermed_high =       gd.getNextBoolean();
 		this.cuas_save_mono =           gd.getNextBoolean();
@@ -4172,6 +4186,7 @@ min_str_neib_fpn	0.35
 		properties.setProperty(prefix+"cuas_corr_offset",     this.cuas_corr_offset+"");    // int
         properties.setProperty(prefix+"cuas_half_step",       this.cuas_half_step+"");      // boolean
 		properties.setProperty(prefix+"cuas_max_range",       this.cuas_max_range+"");      // int
+		properties.setProperty(prefix+"cuas_num_cycles",      this.cuas_num_cycles+"");     // int
 
 		properties.setProperty(prefix+"cuas_speed_min",       this.cuas_speed_min+"");      // double
 		properties.setProperty(prefix+"cuas_speed_pref",      this.cuas_speed_pref+"");     // double
@@ -4212,6 +4227,8 @@ min_str_neib_fpn	0.35
 		properties.setProperty(prefix+"cuas_scale2x",         this.cuas_scale2x+"");        // boolean
 		properties.setProperty(prefix+"cuas_ra_background",   this.cuas_ra_background+"");  // boolean
 
+		properties.setProperty(prefix+"cuas_iter_show",       this.cuas_iter_show+"");       // int
+		properties.setProperty(prefix+"cuas_2d_save_show",    this.cuas_2d_save_show+"");   // boolean
 		properties.setProperty(prefix+"cuas_intermed_low",    this.cuas_intermed_low+"");   // boolean
 		properties.setProperty(prefix+"cuas_intermed_high",   this.cuas_intermed_high+"");  // boolean
 		properties.setProperty(prefix+"cuas_save_mono",       this.cuas_save_mono+"");      // boolean
@@ -5074,6 +5091,7 @@ min_str_neib_fpn	0.35
 		if (properties.getProperty(prefix+"cuas_corr_offset")!=null)     this.cuas_corr_offset=Integer.parseInt(properties.getProperty(prefix+"cuas_corr_offset"));
 		if (properties.getProperty(prefix+"cuas_half_step")!=null)       this.cuas_half_step=Boolean.parseBoolean(properties.getProperty(prefix+"cuas_half_step"));
 		if (properties.getProperty(prefix+"cuas_max_range")!=null)       this.cuas_max_range=Integer.parseInt(properties.getProperty(prefix+"cuas_max_range"));
+		if (properties.getProperty(prefix+"cuas_num_cycles")!=null)      this.cuas_num_cycles=Integer.parseInt(properties.getProperty(prefix+"cuas_num_cycles"));
 
 		if (properties.getProperty(prefix+"cuas_speed_min")!=null)       this.cuas_speed_min=Double.parseDouble(properties.getProperty(prefix+"cuas_speed_min"));
 		if (properties.getProperty(prefix+"cuas_speed_pref")!=null)      this.cuas_speed_pref=Double.parseDouble(properties.getProperty(prefix+"cuas_speed_pref"));
@@ -5115,6 +5133,8 @@ min_str_neib_fpn	0.35
 		if (properties.getProperty(prefix+"cuas_scale2x")!=null)         this.cuas_scale2x=Boolean.parseBoolean(properties.getProperty(prefix+"cuas_scale2x"));
 		if (properties.getProperty(prefix+"cuas_ra_background")!=null)   this.cuas_ra_background=Boolean.parseBoolean(properties.getProperty(prefix+"cuas_ra_background"));
 
+		if (properties.getProperty(prefix+"cuas_iter_show")!=null)       this.cuas_iter_show=Integer.parseInt(properties.getProperty(prefix+"cuas_iter_show"));
+		if (properties.getProperty(prefix+"cuas_2d_save_show")!=null)    this.cuas_2d_save_show=Boolean.parseBoolean(properties.getProperty(prefix+"cuas_2d_save_show"));
 		if (properties.getProperty(prefix+"cuas_intermed_low")!=null)    this.cuas_intermed_low=Boolean.parseBoolean(properties.getProperty(prefix+"cuas_intermed_low"));
 		if (properties.getProperty(prefix+"cuas_intermed_high")!=null)   this.cuas_intermed_high=Boolean.parseBoolean(properties.getProperty(prefix+"cuas_intermed_high"));
 		if (properties.getProperty(prefix+"cuas_save_mono")!=null)       this.cuas_save_mono=Boolean.parseBoolean(properties.getProperty(prefix+"cuas_save_mono"));
@@ -5978,6 +5998,7 @@ min_str_neib_fpn	0.35
 		imp.cuas_corr_offset =      this.cuas_corr_offset;
 		imp.cuas_half_step =        this.cuas_half_step;
 		imp.cuas_max_range =        this.cuas_max_range;
+		imp.cuas_num_cycles =       this.cuas_num_cycles;
 		imp.cuas_speed_min =        this.cuas_speed_min;
 		imp.cuas_speed_pref =       this.cuas_speed_pref;
 		imp.cuas_speed_boost =      this.cuas_speed_boost;
@@ -6017,6 +6038,8 @@ min_str_neib_fpn	0.35
 		imp.cuas_scale2x =    		this.cuas_scale2x;    
 		imp.cuas_ra_background =    this.cuas_ra_background;
 
+		imp.cuas_iter_show=         this.cuas_iter_show;
+		imp.cuas_2d_save_show =     this.cuas_2d_save_show;
 		imp.cuas_intermed_low =     this.cuas_intermed_low;
 		imp.cuas_intermed_high =    this.cuas_intermed_high;
 		imp.cuas_save_mono =        this.cuas_save_mono;

src/main/java/com/elphel/imagej/tileprocessor/QuadCLTCPU.java

@@ -19688,136 +19688,5 @@ public class QuadCLTCPU {
 		  }
 		  return;
 	  }
-	  /*
-		public static void copyJP4src(
-				final CLTParameters   clt_parameters,
-				final QuadCLT []      quadCLTs,
-				final int []          range, // [earlies, latest]
-				final boolean         skip_existing,
-				final boolean         search_KML,
-				final int             debugLevel) { // throws Exception
-		    final Thread[] threads = ImageDtt.newThreadArray();
-		    final AtomicInteger ai = new AtomicInteger(range[0]);
-		    for (int ithread = 0; ithread < threads.length; ithread++) {
-		    	threads[ithread] = new Thread() {
-		    		public void run() {
-		    			for (int nScene = ai.getAndIncrement(); nScene <= range[1]; nScene = ai.getAndIncrement()) {
-		    				quadCLTs[nScene].copyJP4src(
-		    						clt_parameters, // CLTParameters clt_parameters,
-		    						skip_existing,  // boolean                                  skip_existing,
-		    						search_KML,     // boolean                                  search_KML,
-		    						debugLevel);     // final int                                debugLevel) // throws Exception
-		    			}
-		    		}
-		    	};
-		    }		      
-		    ImageDtt.startAndJoin(threads);
-		    return;
-		}
-	  
-		public void copyJP4src(
-				CLTParameters clt_parameters,
-				boolean                                  skip_existing,
-				boolean                                  search_KML,
-				final int                                debugLevel) // throws Exception
-		{
-			int min_dbg = 0;
-			String [] sourceFiles= correctionsParameters.getSourcePaths();
-			String set_name = getImageName();
-			
-			SetChannels [] set_channels = setChannels(set_name,debugLevel); // only for specified image timestamp
-
-			ArrayList<String> path_list = new ArrayList<String>();
-			if (set_channels != null) for (int i = 0; i < set_channels.length; i++) {
-				for (int fn:set_channels[i].file_number) {
-					path_list.add(sourceFiles[fn]);
-				}
-			}
-			// For RGB/LWIR call twice (separate for each modality)
-			String jp4_copy_path= correctionsParameters.selectX3dDirectory(
-					set_name, // quad timestamp. Will be ignored if correctionsParameters.use_x3d_subdirs is false
-					correctionsParameters.jp4SubDir,
-					true,  // smart,
-					true);  //newAllowed, // save
-			File dir = (new File(jp4_copy_path)); // .getParentFile();
-			boolean already_copied = false;
-			if (!dir.exists()){
-				dir.mkdirs();
-				if (debugLevel >= min_dbg) System.out.println("Created "+dir);
-			} else if (skip_existing) {
-				if (dir.list().length > 0) {
-					already_copied = true;
-				}
-			}
-//			if (clt_parameters.imp.ims_use) {
-//				setupIMS(
-//						clt_parameters, // CLTParameters clt_parameters,
-//						skip_existing,  // boolean skip_existing,
-//						 debugLevel);   // int     debugLevel);
-//			}
-			if (search_KML && (set_channels !=null)) { // TODO: make it look in both MAIN and AUX. Look in only the same scene?
-				writeKml(
-						debugLevel ); // also generated with x3d model
-			}
-			if (already_copied) {
-				if (debugLevel >= min_dbg) System.out.println("Skipping existing directory "+dir);
-				return;
-			}
-			for (String fname:path_list) {
-				if (fname.contains(set_name)) { // only files containing set name // TODO:improve
-					File file = new File(fname);
-					try {
-						Files.copy(
-								(file).toPath(),
-								(new File(jp4_copy_path + Prefs.getFileSeparator()+file.getName())).toPath(),
-								StandardCopyOption.REPLACE_EXISTING);
-						if (debugLevel >= min_dbg) System.out.println("Copied "+fname+" -> "+dir);
-					} catch (IOException e) {
-						// TODO Auto-generated catch block
-						System.out.println("Failed to copy "+fname+" -> "+dir);
-					}
-				}
-			}
-			if (debugLevel >= min_dbg) System.out.println("jp4_copy_path = "+jp4_copy_path);
-		}
-	  @Deprecated
-		public void setupIMS( // not needed, restoreNoModel() and restoreFromModel call restoreIMS
-				CLTParameters clt_parameters,
-				boolean skip_existing, // for now not used
-				int     debugLevel) {
-			if (!clt_parameters.imp.ims_use) {
-				return;
-			}
-			int min_dbg = 0;
-			String jp4_copy_path= correctionsParameters.selectX3dDirectory(
-					getImageName(), // quad timestamp. Will be ignored if correctionsParameters.use_x3d_subdirs is false
-					correctionsParameters.jp4SubDir,
-					true,  // smart,
-					true);  //newAllowed, // save
-			File dir = (new File(jp4_copy_path)); // .getParentFile();
-			boolean already_copied = false; // FIXME?
-			if (!dir.exists()){
-				dir.mkdirs();
-				if (debugLevel >= min_dbg) System.out.println("Created "+dir);
-			} else if (skip_existing) {
-				if (dir.list().length > 0) {
-					already_copied = true;
-				}
-			}
-			String ims_path = dir.getParent() + Prefs.getFileSeparator()+getImageName()+correctionsParameters.imsSuffix;
-			double [] saved_offset =  readImsOffset(
-					ims_path, // String ims_path,
-					debugLevel); // int debugLevel)
-			if ((saved_offset == null) || (saved_offset[0] != clt_parameters.imp.ims_offset) || (saved_offset[1] != clt_parameters.imp.gmt_plus)) {
-				saveIms(
-						clt_parameters.imp.ims_offset,
-						clt_parameters.imp.gmt_plus,   //  double gmt_plus,
-						ims_path,
-						debugLevel);
-			}
-
-		}
-	  
-	  */
-
+	
 }

src/main/java/com/elphel/imagej/tileprocessor/TDCorrTile.java

@@ -522,7 +522,7 @@ public class TDCorrTile {
 								null,            // boolean [] fpn_mask,
 								false,           // boolean    ignore_border, // only if fpn_mask != null - ignore tile if maximum touches fpn_mask
 								false);          // boolean   debug)
-						if (mv[2] > min_str) {
+						if ((mv != null) && (mv[2] > min_str)) {
 							vector_field[iTile] = new double [] {mv[0], mv[1], mv[2]-min_str, mv[3]};
 						}
 					}