Reorganized some parameters, before quadratic photometric equalization

src/main/java/com/elphel/imagej/cameras/CLTParameters.java

@@ -365,6 +365,13 @@ public class CLTParameters {
 	public double     fom_inf_bonus  =    0.2; // add this to infinity FOM (if it is closer than fom_inf_range)
 	public double     fom_inf_range  =    0.8; // 0.5
 	
+	// Photometric calibration (move elsewhere)?
+	public boolean    photo_en =                      false; // perform photogrammetric calibration to equalize pixel values
+	public int        photo_num_full =                3;     // Number of full recalibrations with re-processing of the images  
+	public int        photo_num_refines =             3;     // Calibrate, remove outliers, recalibrate, ... 
+	public double     photo_min_strength =            0.0;   // maybe add to filter out weak tiles
+	public double     photo_max_diff =                40.0;  // To filter mismatches. Normal (adjusted) have RMSE ~9
+	public boolean    photo_debug =                   false; // Generate images and text
 	
 	
 	
@@ -1347,6 +1354,13 @@ public class CLTParameters {
 		properties.setProperty(prefix+"fom_inf_bonus",              this.fom_inf_bonus+"");
 		properties.setProperty(prefix+"fom_inf_range",              this.fom_inf_range+"");
 		
+		properties.setProperty(prefix+"photo_en",                   this.photo_en+"");            // boolean
+		properties.setProperty(prefix+"photo_num_full",             this.photo_num_full+"");      // int
+		properties.setProperty(prefix+"photo_num_refines",          this.photo_num_refines+"");   // int
+		properties.setProperty(prefix+"photo_min_strength",         this.photo_min_strength+"");  // double
+		properties.setProperty(prefix+"photo_max_diff",             this.photo_max_diff+"");      // double
+		properties.setProperty(prefix+"photo_debug",                this.photo_debug+"");         // boolean
+		
 		properties.setProperty(prefix+"show_textures",              this.show_textures+"");
 		properties.setProperty(prefix+"debug_filters",              this.debug_filters+"");
 
@@ -2204,6 +2218,13 @@ public class CLTParameters {
 		if (properties.getProperty(prefix+"fom_inf_bonus")!=null)                 this.fom_inf_bonus=Double.parseDouble(properties.getProperty(prefix+"fom_inf_bonus"));
 		if (properties.getProperty(prefix+"fom_inf_range")!=null)                 this.fom_inf_range=Double.parseDouble(properties.getProperty(prefix+"fom_inf_range"));
 		
+		if (properties.getProperty(prefix+"photo_en")!=null)             this.photo_en=Boolean.parseBoolean(properties.getProperty(prefix+"photo_en"));		
+		if (properties.getProperty(prefix+"photo_num_full")!=null)       this.photo_num_full=Integer.parseInt(properties.getProperty(prefix+"photo_num_full"));
+		if (properties.getProperty(prefix+"photo_num_refines")!=null)    this.photo_num_refines=Integer.parseInt(properties.getProperty(prefix+"photo_num_refines"));
+		if (properties.getProperty(prefix+"photo_min_strength")!=null)   this.photo_min_strength=Double.parseDouble(properties.getProperty(prefix+"photo_min_strength"));
+		if (properties.getProperty(prefix+"photo_max_diff")!=null)       this.photo_max_diff=Double.parseDouble(properties.getProperty(prefix+"photo_max_diff"));
+		if (properties.getProperty(prefix+"photo_debug")!=null)          this.photo_debug=Boolean.parseBoolean(properties.getProperty(prefix+"photo_debug"));		
+		
 		if (properties.getProperty(prefix+"show_textures")!=null)                 this.show_textures=Boolean.parseBoolean(properties.getProperty(prefix+"show_textures"));
 		if (properties.getProperty(prefix+"debug_filters")!=null)                 this.debug_filters=Boolean.parseBoolean(properties.getProperty(prefix+"debug_filters"));
 
@@ -2788,7 +2809,7 @@ public class CLTParameters {
 
 	public boolean showJDialog() {
 		//  			GenericDialog gd = new GenericDialog("Set CLT parameters");
-		GenericJTabbedDialog gd = new GenericJTabbedDialog("Set CLT parameters",800,900);
+		GenericJTabbedDialog gd = new GenericJTabbedDialog("Set CLT parameters",1090,900);
 		gd.addTab         ("General", "General parameters");
 		gd.addNumericField("Nominal (rectilinear) disparity between side of square cameras (pix)",              this.disparity,  3,7,"pix",
 				"Used when rendering 4 images");
@@ -2855,7 +2876,7 @@ public class CLTParameters {
 		gd.addNumericField("Calculated from correlation offset vs. actual one (not yet understood)",            this.corr_magic_scale,  3,6,"", "CM and poly");
 		gd.addNumericField("Select all-pair correlation type to use 0 - CM, 1 - poly",                          this.corr_select,  0);
 
-		gd.addTab         ("imageDtt", "Setup extra ImageDtt parameters - eventually all will be set that way");
+//		gd.addTab         ("imageDtt", "Setup extra ImageDtt parameters - eventually all will be set that way");
 		this.img_dtt.dialogQuestions(gd);
 		gd.addTab         ("Rig", "Parameters for the wide baseline rig with two quad cameras");
 		this.rig.dialogQuestions(gd);
@@ -3164,16 +3185,16 @@ public class CLTParameters {
 		gd.addNumericField("Minimal number of infinity tiles",                                 this.lyms_min_num_inf,    0,3,"",
 				"Minimal number of tiles (in all scenes total) in an infinity cluster");
 		
-		gd.addTab         ("3D", "3D reconstruction");
-
-		gd.addNumericField("Maximal channel mismatchatch for RGB cameras",                                           this.mismatch_rgb,  4,6,"counts",
+		
+		gd.addTab         ("Initial DSI", "Building initial (single-scene) DSI");
+		gd.addMessage     ("--- Filter tiles by inter-channel mismatch (requires photometic equalization) ---");
+		gd.addNumericField("Maximal channel mismatch for RGB cameras",                                               this.mismatch_rgb,  4,6,"counts",
 				"Discard correlation results during disparity sweep if channels differ more (RGB)");
-		gd.addNumericField("Maximal channel mismatchatch for LWIR cameras",                                          this.mismatch_lwir,  4,6,"counts",
+		gd.addNumericField("Maximal channel mismatch for LWIR cameras",                                              this.mismatch_lwir,  4,6,"counts",
 				"Discard correlation results during disparity sweep if channels differ more (LWIR)");
 		gd.addNumericField("Minimal correlation strength to override mismatch filter",                               this.mismatch_override,  4,6,"",
 				"Allow tiles with the really strong correlation to have large mismatch.");
-		
-		gd.addMessage     ("--- FOM for initial DSI ---");
+		gd.addMessage     ("--- FOM for initial DSI (the combination of parameters that ranges corelation results) ---");
 		gd.addNumericField("Minimal strength",                                                                       this.fom_min_strength,  4,6,"",
 				"Discard all weaker tiles (FOM=NEGATIVE_INFINITY).");
 		gd.addNumericField("Weight of residual disparity, RGB",                                                      this.fom_adisp_rgb,  4,6,"",
@@ -3188,8 +3209,30 @@ public class CLTParameters {
 				"Prevent stray FG over sky - add to FOM.");
 		gd.addNumericField("Infinity bonus disparity range",                                                         this.fom_inf_range,  4,6,"pix",
 				"Infinity range to receive FOM bonus.");
-
-		gd.addMessage     ("--- 3D reconstruction ---");
+		gd.addMessage     ("See \"Corr LMA\" tab under \"LMA (single) results filtering\" for LMA parameters");
+		gd.addMessage     ("that influence the results on the last stages of the DSI building.");
+		gd.addMessage     ("\"Sky\" tab parameters define featureless sky area detection that supplement initial DSI.");
+
+ 		gd.addTab  ("Photometric","Photometric equalization - can be performed after DSI is available)");
+ 		gd.addMessage  ("Photometric calibration is saved with the current scene (and saved with the \"Save\" command and with the reference scene.");
+ 		gd.addMessage  ("It is applied when the source files are read.");
+		gd.addCheckbox ("Enable photometric calibration",            this.photo_en,
+				"Equalize per- sensor gains and offsets. Requires disparity map. Save to reference scene and with current scene (to .corr-zml).");
+		gd.addNumericField("Full photometric (re)calibrations",      this.photo_num_full, 0,3,"pix",
+				"Full recalibratrions include re-importing raw images with updated offsets/gains");
+		gd.addNumericField("Refines",                                this.photo_num_refines, 0,3,"pix",
+				"Calculate calibration, remove outliers (e.g. FG/BG) and repeat");
+		gd.addNumericField("Minimal DSI strength",                   this.photo_min_strength, 5,7,"",
+				"Do not use weak tiles.");
+		gd.addNumericField("Maximal channel mismatch",               this.photo_max_diff, 5,7,"",
+				"Detect (and remove outliers). Adjusted images have RMSE ~9 counts.");
+		gd.addCheckbox ("Debug pphotometric calibration",            this.photo_debug,
+				"Generate debug images an text output.");
+		
+		
+		
+		
+		gd.addTab         ("3D", "3D reconstruction");
 		gd.addCheckbox    ("Show generated textures",                                                                this.show_textures);
 		gd.addCheckbox    ("show intermediate results of filtering",                                                 this.debug_filters);
 
@@ -4182,6 +4225,13 @@ public class CLTParameters {
 		this.fom_inf_bonus=         gd.getNextNumber();
 		this.fom_inf_range=         gd.getNextNumber();
 		
+ 		this.photo_en =                 gd.getNextBoolean();
+		this.photo_num_full =     (int) gd.getNextNumber();
+		this.photo_num_refines =  (int) gd.getNextNumber();
+		this.photo_min_strength =       gd.getNextNumber();
+		this.photo_max_diff =           gd.getNextNumber();
+		this.photo_debug =              gd.getNextBoolean();
+		
 		this.show_textures=         gd.getNextBoolean();
 		this.debug_filters=         gd.getNextBoolean();
 		this.min_smth=              gd.getNextNumber();

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

@@ -4038,12 +4038,12 @@ public class OpticalFlow {
     	boolean export_ml_files =            clt_parameters.imp.export_ml_files;
 
     	//boolean calibrate_photometric =      true;
-    	boolean  photo_en =                  clt_parameters.imp.photo_en; //          false; // perform photogrammetric calibration to equalize pixel values
-    	int      photo_num_full =            clt_parameters.imp.photo_num_full; //     1;    // Number of full recalibrations with re-processing of the images  
-    	int      photo_num_refines =         clt_parameters.imp.photo_num_refines; //  3;    // Calibrate, remove outliers, recalibrate, ... 
-    	double   photo_min_strength =        clt_parameters.imp.photo_min_strength; // 0.0;  // maybe add to filter out weak tiles
-    	double   photo_max_diff =            clt_parameters.imp.photo_max_diff; //    40.0;  // To filter mismatches. Normal (adjusted) have RMSE ~9
-    	boolean  photo_debug =               clt_parameters.imp.photo_debug; //       false; // Generate images and text
+    	boolean  photo_en =                  clt_parameters.photo_en; //          false; // perform photogrammetric calibration to equalize pixel values
+    	int      photo_num_full =            clt_parameters.photo_num_full; //     1;    // Number of full recalibrations with re-processing of the images  
+    	int      photo_num_refines =         clt_parameters.photo_num_refines; //  3;    // Calibrate, remove outliers, recalibrate, ... 
+    	double   photo_min_strength =        clt_parameters.photo_min_strength; // 0.0;  // maybe add to filter out weak tiles
+    	double   photo_max_diff =            clt_parameters.photo_max_diff; //    40.0;  // To filter mismatches. Normal (adjusted) have RMSE ~9
+    	boolean  photo_debug =               clt_parameters.photo_debug; //       false; // Generate images and text
     	
     	boolean show_dsi_image =             clt_parameters.imp.show_ranges && !batch_mode;
     	boolean show_images =                clt_parameters.imp.show_images && !batch_mode;
@@ -4132,11 +4132,19 @@ public class OpticalFlow {
 		final int        debugLevelInner=clt_parameters.batch_run? -2: debugLevel; // copied from TQ
 		
 		double  min_ref_str =        clt_parameters.imp.min_ref_str;
-		double sky_seed =         7.0;  // start with product of strength by diff_second below this
-		double sky_lim =         15.0; // then expand to product of strength by diff_second below this
-		double lma_seed=          2.0;  // seed - disparity_lma limit		double sky_lim  =      15.0; // then expand to product of strength by diff_second below this
-		int    sky_shrink =       6;
-		int    sky_expand_extra = 0; // 1?
+		
+ 		double sky_highest_min =     clt_parameters.imp.sky_highest_min;
+ 		double cold_frac =           clt_parameters.imp.cold_frac;
+ 		double hot_frac =            clt_parameters.imp.hot_frac;
+ 		double cold_scale =          clt_parameters.imp.cold_scale;
+ 		double sky_seed =            clt_parameters.imp.sky_seed;
+ 		double lma_seed =            clt_parameters.imp.lma_seed;
+ 		int    sky_shrink =          clt_parameters.imp.sky_shrink;
+ 		int    seed_rows =           clt_parameters.imp.seed_rows;
+ 		double sky_lim =             clt_parameters.imp.sky_lim;
+ 		int    sky_expand_extra =    clt_parameters.imp.sky_expand_extra;
+ 		double min_strength =        clt_parameters.imp.min_strength;
+ 		int    lowest_sky_row =      clt_parameters.imp.lowest_sky_row;
 		
 		boolean [] ref_blue_sky = null; // turn off "lma" in the ML output  
 		
@@ -4267,6 +4275,13 @@ public class OpticalFlow {
 							sky_lim,            // double sky_lim, //   =      15.0; // then expand to product of strength by diff_second below this
 							sky_shrink,         // int    sky_shrink, //  =       4;
 							sky_expand_extra,   // int    sky_expand_extra, //  = 100; // 1?
+							cold_scale, // =       0.2;  // <=1.0. 1.0 - disables temperature dependence
+							cold_frac, // =        0.005; // this and lower will scale fom by  cold_scale
+							hot_frac, // =         0.9;    // this and above will scale fom by 1.0
+							min_strength, // =     0.08;
+							seed_rows, // =        5; // sky should appear in this top rows 
+							lowest_sky_row,        //  =     50;// appears that low - invalid, remove completely
+							sky_highest_min,       //  =   100; // lowest absolute value should not be higher (requires photometric) 
 							dsi[TwoQuadCLT.DSI_STRENGTH_AUX], // double [] strength,
 							dsi[TwoQuadCLT.DSI_SPREAD_AUX], // double [] spread,
 							dsi[TwoQuadCLT.DSI_DISPARITY_AUX_LMA], // double [] spread,
@@ -4311,6 +4326,13 @@ public class OpticalFlow {
 							sky_lim,                               // double sky_lim, //   =      15.0; // then expand to product of strength by diff_second below this
 							sky_shrink,                            // int    sky_shrink, //  =       4;
 							sky_expand_extra,                      // int    sky_expand_extra, //  = 100; // 1?
+							cold_scale, // =       0.2;  // <=1.0. 1.0 - disables temperature dependence
+							cold_frac, // =        0.005; // this and lower will scale fom by  cold_scale
+							hot_frac, // =         0.9;    // this and above will scale fom by 1.0
+							min_strength, // =     0.08;
+							seed_rows, // =        5; // sky should appear in this top rows
+							lowest_sky_row,        //  =     50;// appears that low - invalid, remove completely
+							sky_highest_min,       //  =   100; // lowest absolute value should not be higher (requires photometric) 
 							dsi[TwoQuadCLT.DSI_STRENGTH_AUX],      // double [] strength,
 							dsi[TwoQuadCLT.DSI_SPREAD_AUX],        // double [] spread,
 							dsi[TwoQuadCLT.DSI_DISPARITY_AUX_LMA], //double [] disp_lma,

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

@@ -152,7 +152,8 @@ public class QuadCLTCPU {
     boolean [][]                                           saturation_imp = null; // (near) saturated pixels or null
     boolean                                                is_aux = false;
     double  []                                             lwir_offsets = null; // per image subtracted values
-    double []                                              lwir_scales = null;  // per image scales
+    double []                                              lwir_scales =  null;  // per image scales
+//double []                                              lwir_scales2 = null;  // per image quadratic scales
     @Deprecated
     double                                                 lwir_offset =  Double.NaN; // average of lwir_offsets[]
     // hot and cold are calculated during autoranging (when generating 4 images for restored (added lwir_offset)
@@ -442,6 +443,13 @@ public class QuadCLTCPU {
 			double sky_lim, //   =      15.0; // then expand to product of strength by diff_second below this
 			int    sky_shrink, //  =       4;
 			int    sky_expand_extra, //  = 100; // 1?
+			double cold_scale, // =       0.2;  // <=1.0. 1.0 - disables temperature dependence
+			double cold_frac, // =        0.005; // this and lower will scale fom by  cold_scale
+			double hot_frac, // =         0.9;    // this and above will scale fom by 1.0
+			double min_strength, // =     0.08;
+			int    seed_rows, // =        5; // sky should appear in this top rows 
+			int    lowest_sky_row,        //  =     50;// appears that low - invalid, remove completely
+			double sky_highest_min,       //  =   -50; // 100; // lowest absolute value should not be higher (requires photometric) 
 			int    width,
 			double [] strength,
 			double [] spread,
@@ -452,15 +460,16 @@ public class QuadCLTCPU {
 			return null;
 		}
 		double [] temp_scales = null;
+		/*
 		double cold_scale =    0.2;  // <=1.0. 1.0 - disables temperature dependence
 		double cold_frac =     0.005; // this and lower will scale fom by  cold_scale
 		double hot_frac =      0.9;    // this and above will scale fom by 1.0
 		double min_strength =  0.08;
 		int    seed_rows =     5; // sky should appear in this top rows 
-		
-		
-		int num_bins = 1000;
+		*/
+		boolean failure = false;
 		if (avg_val != null) {
+			int num_bins = 1000;
 			double min_temp = Double.NaN, max_temp=Double.NaN, avg_temp = 0;
 			int num_def = 0;
 			for (int i = 0; i < avg_val.length; i++) {
@@ -513,6 +522,10 @@ public class QuadCLTCPU {
 						break;
 					}
 				}
+				if (temp_cold > sky_highest_min) {
+					System.out.println("getBlueSky(): Coldest offset value "+temp_cold+" > "+sky_highest_min+" - invalid sky" );
+					failure = true;
+				}
 				temp_scales = new double[avg_val.length];
 				Arrays.fill(temp_scales, Double.NaN);
 				double kscale = (1.0 - cold_scale)/(temp_hot - temp_cold);
@@ -607,7 +620,16 @@ public class QuadCLTCPU {
 					"sky_selection",
 					dbg_titles); //	dsrbg_titles);
 		}
-		
+		for (int i = lowest_sky_row*width; i < sky_tiles.length; i++) {
+			if (sky_tiles[i]) {
+				System.out.println("getBlueSky(): sky area appeared too low - at row "+(i/width)+" >= "+lowest_sky_row+" removing blue sky");
+				failure = true;
+				break;
+			}
+		}
+		if (failure) { // Will still show in debug images !!!
+			Arrays.fill(sky_tiles, false);
+		}
 		return sky_tiles;
 	}
 	
@@ -625,6 +647,13 @@ public class QuadCLTCPU {
 			double sky_lim, //   =      15.0; // then expand to product of strength by diff_second below this
 			int    sky_shrink, //  =       4;
 			int    sky_expand_extra, //  = 100; // 1?
+			double cold_scale, // =       0.2;  // <=1.0. 1.0 - disables temperature dependence
+			double cold_frac, // =        0.005; // this and lower will scale fom by  cold_scale
+			double hot_frac, // =         0.9;    // this and above will scale fom by 1.0
+			double min_strength, // =     0.08;
+			int    seed_rows, // =        5; // sky should appear in this top rows
+			int    lowest_sky_row,        //  =     50;// appears that low - invalid, remove completely
+			double sky_highest_max,       //  =   100; // lowest absolute value should not be higher (requires photometric) 
 			double [] strength,
 			double [] spread,
 			double [] disp_lma,
@@ -637,6 +666,13 @@ public class QuadCLTCPU {
 				sky_lim, //   =      15.0; // then expand to product of strength by diff_second below this
 				sky_shrink, //  =       4;
 				sky_expand_extra, //  = 100; // 1?
+				cold_scale, // =       0.2;  // <=1.0. 1.0 - disables temperature dependence
+				cold_frac, // =        0.005; // this and lower will scale fom by  cold_scale
+				hot_frac, // =         0.9;    // this and above will scale fom by 1.0
+				min_strength, // =     0.08;
+				seed_rows, // =        5; // sky should appear in this top rows 
+				lowest_sky_row,        //  =     50;// appears that low - invalid, remove completely
+				sky_highest_max,       //  =   100; // lowest absolute value should not be higher (requires photometric) 
 				width,
 				strength,
 				spread,