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     ("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.addMessage     ("--- 3D reconstruction ---");
+		
+		
+		
+		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/ImageDttParameters.java

@@ -28,6 +28,7 @@ import java.util.Properties;
 import com.elphel.imagej.common.GenericJTabbedDialog;
 
 public class ImageDttParameters {
+	// "ImageDtt" tab followed by others
 	public boolean gpu_mode_debug =         true;
 	public boolean gpu_verify =             false; // verify tasks/ input data
 	public boolean corr_mode_debug =        true;
@@ -398,6 +399,7 @@ public class ImageDttParameters {
 	
 	public void dialogQuestions(GenericJTabbedDialog gd) {
 		
+		gd.addTab         ("imageDtt", "Setup extra ImageDtt parameters - eventually all will be set that way");
 		gd.addCheckbox    ("Debug CPU->GPU matching",                                         this.gpu_mode_debug,
 				"output clt_corr_partial");
 		gd.addCheckbox    ("Verify GPU input",                                                this.gpu_verify,
@@ -710,8 +712,8 @@ public class ImageDttParameters {
 		gd.addMessage("Single-tile (no lazy eye) only parameters (some are common");
 		gd.addNumericField("Cluster disparity range",                                         this.lma_disp_range,  3, 6, "pix",
 				"Disparity range to combine in one cluster (to mitigate ERS");
-//			gd.addCheckbox    ("Correlation maximum as gaussian",                                 this.lmas_gaussian,
-//					"Model correlation maximum as a Gaussian exp(-r^2)  (false - as a parabola - 1-r^2)");
+		//			gd.addCheckbox    ("Correlation maximum as gaussian",                                 this.lmas_gaussian,
+		//					"Model correlation maximum as a Gaussian exp(-r^2)  (false - as a parabola - 1-r^2)");
 		gd.addNumericField    ("Correlation maximum function type",                            this.lmas_gaussian,  0, 3, "",
 				"0 - parabola - 1-r^2, 1 -  exp(-r^2), 2 - limited parabola (>=0), 3 - limited squared parabola  (1-r^2)^2");
 
@@ -765,8 +767,8 @@ public class ImageDttParameters {
 
 		gd.addCheckbox    ("Re-run LMA after removing weak/failed tiles",                     this.lma_second,
 				"Re-run LMA with filtered tiles (see Correlation strength calculation section below)");
-//			gd.addCheckbox    ("Gaussian mode during LMA re-run",                                 this.lma_second_gaussian,
-//					"Parabola is more stable when using with un-filtered tiles, so it makes sense to use Gaussina only on filtered tiles");
+		//			gd.addCheckbox    ("Gaussian mode during LMA re-run",                                 this.lma_second_gaussian,
+		//					"Parabola is more stable when using with un-filtered tiles, so it makes sense to use Gaussina only on filtered tiles");
 		gd.addNumericField    ("Correlation maximum function typedurinf re-run",              this.lma_second_gaussian,  0, 3, "",
 				"0 - parabola - 1-r^2, 1 -  exp(-r^2), 2 - limited parabola (>=0), 3 - limited squared parabola  (1-r^2)^2."+
 				" Parabola is more stable when using with un-filtered tiles, so it makes sense to use Gaussina only on filtered tiles");
@@ -1049,7 +1051,7 @@ public class ImageDttParameters {
 		this.tilt_damp_tilt =        gd.getNextNumber();
 		this.tilt_clust_extra= (int) gd.getNextNumber();
 
-//LMA tab
+		//LMA tab
 		this.lma_disp_range =        gd.getNextNumber();
 		this.lmas_gaussian=    (int) gd.getNextNumber();
 		this.lmas_adjust_wm=         gd.getNextBoolean();
@@ -1133,6 +1135,7 @@ public class ImageDttParameters {
 
 
 	public void setProperties(String prefix,Properties properties){
+		
 		properties.setProperty(prefix+"gpu_mode_debug",       this.gpu_mode_debug+"");
 		properties.setProperty(prefix+"gpu_verify",           this.gpu_verify+"");
 		properties.setProperty(prefix+"corr_mode_debug",      this.corr_mode_debug+"");

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

@@ -193,16 +193,6 @@ public class IntersceneMatchParameters {
 	public  double  half_disparity =                5.0;   // Reduce weight twice for this disparity
 	public  double  half_avg_diff =                 0.2;   // when L2 of x,y difference from average of neibs - reduce twice
 	
-	// Photometric calibration (move elsewhere)?
-	public boolean  photo_en =                      false; // perform photogrammetric calibration to equalize pixel values
-	public int      photo_num_full =                1;     // 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
-	
-	
-	
 	// Detect initial match
 	public  double  min_ref_str =                   0.22;  // For orientations: use only tiles of the reference scene DSI_MAIN is stronger  
 	public  int     pix_step =                      4;     // Azimuth/tilt search step in pixels
@@ -258,12 +248,24 @@ public class IntersceneMatchParameters {
 	private boolean show_motion_vectors =           true;  // show calculated motion vectors
 	public  int     debug_level =                     -1;  // all renders are disable for debug_level < 0, scene "renders" for for debug_level < 1
 
-
 	// Pairwise ERS testing
 	public boolean  test_ers =                     false;
 	public  int     test_ers0 =                       -1; // try adjusting a pair of scenes with ERS. Reference scene index
 	public  int     test_ers1 =                       -1; // try adjusting a pair of scenes with ERS. Other scene index
 
+	// SKy detection/filtering
+	public  double  sky_highest_min =                -50; // lowest absolute value should not be higher (requires photometric) 
+	public  double  cold_frac =                        0.005; // this and lower will scale fom by  cold_scale
+	public  double  hot_frac =                         0.9;    // this and above will scale fom by 1.0
+	public  double  cold_scale =                       0.2;  // <=1.0. 1.0 - disables temperature dependence
+	public  double  sky_seed =                         5.0;  // start with product of strength by diff_second below this
+	public  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
+	public  int     sky_shrink =                       3;
+	public  int     seed_rows =                        5; // sky should appear in this top rows 
+	public  double  sky_lim =                         15.0; // then expand to product of strength by diff_second below this
+	public  int     sky_expand_extra =                 0; // 1?
+	public  double  min_strength =                     0.08;
+	public  int     lowest_sky_row =                  50;// appears that low - invalid, remove completely
 	
 	public boolean renderRef()            {return renderRef             (debug_level);}
 	public boolean renderScene()          {return renderScene           (debug_level);}
@@ -635,21 +637,6 @@ public class IntersceneMatchParameters {
 		gd.addNumericField("Difference from neighbors average ",     this.half_avg_diff, 5,7,"",
 				"Reduce twice for high difference from neighbors average.");
 		
-		gd.addMessage  ("Photometric calibration (move elsewhere?)");
-		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.addMessage  ("Initial search for the inter-scene match");
 		gd.addNumericField("DSI_MAIN minimal strength",              this.min_ref_str, 5,7,"",
 					"Match only tiles where DSI_MAIN is stronger than that (and has LMA).");
@@ -764,6 +751,35 @@ public class IntersceneMatchParameters {
 				"Other scene index in a scene sequence (should have a very different angular/linear velocity component)");
 		
 		
+		gd.addTab("Sky","Featureless sky areas detection and filtering (LWIR only)");
+		gd.addMessage  ("Temperature-related filtering (requires photometric calibration)");
+		gd.addNumericField("High limit of the scene coldest tile",   this.sky_highest_min, 5,7,"",
+				"Sky is normally cold. If the (globally offset) minimal scene absolutre pixel value is above - no sky in the scene (debug images still show it)");
+		gd.addNumericField("Cold level fraction",                    this.cold_frac, 5,7,"",
+				"All tiles below this percentile are considered \"cold\".");
+		gd.addNumericField("Hot level fraction",                     this.hot_frac, 5,7,"",
+				"All tiles above this percentile are considered \"hot\".");
+		gd.addNumericField("Cold FOM scale",                         this.cold_scale, 5,7,"",
+				"Multiply (strength*spread) by this value (reduce), and linearly scale up to 1.0 for hot ones.");
+		gd.addMessage  ("Generate seed tiles for the potential sky area");
+		gd.addNumericField("Seed FOM level",                         this.sky_seed, 5,7,"",
+				"Maximal FOM (strength*spread*temp_scale) level to seed sky area, temp_scale is generated from average pixel value "+
+		        "at infinity and 3 above parameters");
+		gd.addNumericField("Seed maximal disparity",                 this.lma_seed, 5,7,"pix",
+				"Seed tiles should not have LMA-found disparity above this");
+		gd.addNumericField("Shrink sky seed",                        this.sky_shrink, 0,3,"",
+				"Shrink sky seed tiles to eliminate too small (false) clusters. One shrinks in hor/vert, 2 - with diagonals, ...");
+		gd.addNumericField("Seed rows",                              this.seed_rows, 0,3,"",
+				"Sky is above and normally should appear in the top image rows. Applies after shrinking.");
+		gd.addMessage  ("Expand seed tiles");
+		gd.addNumericField("Expand FOM limit",                       this.sky_lim, 5,7,"",
+				"Expand while FOM is below this value (usually to a high-contrast skyline).");
+		gd.addNumericField("Expand extra",                           this.sky_expand_extra, 0,3,"",
+				"Additionally expand sky area after reaching threshold in the previous step.");
+		gd.addNumericField("Modify strength to be at least this",    this.min_strength, 5,7,"",
+				"Input strength has some with zero values resulting in zero FOM. Make them at least this.");
+		gd.addNumericField("Lowest sky row",                        this.lowest_sky_row, 0,3,"",
+				"Last defense - if the detected sky area reaches near-bottom of the page - it is invalid, remove it (but keep in debug images)");
 	}
 
 	public void dialogAnswers(GenericJTabbedDialog gd) {
@@ -975,13 +991,6 @@ public class IntersceneMatchParameters {
 		this.half_disparity =           gd.getNextNumber();
 		this.half_avg_diff =            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.min_ref_str =              gd.getNextNumber();
 		this.pix_step =           (int) gd.getNextNumber();
 		this.search_rad =         (int) gd.getNextNumber();
@@ -1035,6 +1044,21 @@ public class IntersceneMatchParameters {
 		this.test_ers0 =          (int) gd.getNextNumber();
 		this.test_ers1 =          (int) gd.getNextNumber();
 
+		this.sky_highest_min =          gd.getNextNumber(); 	
+		this.cold_frac =                gd.getNextNumber();       	
+		this.hot_frac =                 gd.getNextNumber();        	
+		this.cold_scale =               gd.getNextNumber();      	
+		this.sky_seed =                 gd.getNextNumber();        	
+		this.lma_seed =                 gd.getNextNumber();        	
+		this.sky_shrink =         (int) gd.getNextNumber();      	
+		this.seed_rows =          (int) gd.getNextNumber();       	
+		this.sky_lim =                  gd.getNextNumber();         	
+		this.sky_expand_extra =   (int) gd.getNextNumber();	
+		this.min_strength =             gd.getNextNumber();    
+		this.lowest_sky_row =     (int) gd.getNextNumber();
+		
+		
+		
 		if (this.weight_zero_neibs > 1.0) this.weight_zero_neibs = 1.0;
 	}
 	
@@ -1195,13 +1219,6 @@ public class IntersceneMatchParameters {
 		properties.setProperty(prefix+"half_disparity",       this.half_disparity+"");      // double
 		properties.setProperty(prefix+"half_avg_diff",        this.half_avg_diff+"");       // double
 		
-		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+"pix_step",             this.pix_step+"");            // int
 		properties.setProperty(prefix+"search_rad",           this.search_rad+"");          // int
 		properties.setProperty(prefix+"maybe_sum",            this.maybe_sum+"");           // double
@@ -1253,6 +1270,21 @@ public class IntersceneMatchParameters {
 		properties.setProperty(prefix+"test_ers0",            this.test_ers0+"");           // int
 		properties.setProperty(prefix+"test_ers1",            this.test_ers1+"");           // int
 	
+
+		properties.setProperty(prefix+"sky_highest_min",      this.sky_highest_min+"");     // double
+		properties.setProperty(prefix+"cold_frac",            this.cold_frac+"");           // double
+		properties.setProperty(prefix+"hot_frac",             this.hot_frac+"");            // double
+		properties.setProperty(prefix+"cold_scale",           this.cold_scale+"");          // double
+		properties.setProperty(prefix+"sky_seed",             this.sky_seed+"");            // double
+		properties.setProperty(prefix+"lma_seed",             this.lma_seed+"");            // double
+		properties.setProperty(prefix+"sky_shrink",           this.sky_shrink+"");          // int
+		properties.setProperty(prefix+"seed_rows",            this.seed_rows+"");           // int
+		properties.setProperty(prefix+"sky_lim",              this.sky_lim+"");             // double
+		properties.setProperty(prefix+"sky_expand_extra",     this.sky_expand_extra+"");    // int
+		properties.setProperty(prefix+"min_strength",         this.min_strength+"");        // double
+		properties.setProperty(prefix+"lowest_sky_row",       this.lowest_sky_row+"");      // int
+	
+	
 	}
 	
 	public void getProperties(String prefix,Properties properties){
@@ -1440,13 +1472,6 @@ public class IntersceneMatchParameters {
 		if (properties.getProperty(prefix+"half_disparity")!=null)       this.half_disparity=Double.parseDouble(properties.getProperty(prefix+"half_disparity"));
 		if (properties.getProperty(prefix+"half_avg_diff")!=null)        this.half_avg_diff=Double.parseDouble(properties.getProperty(prefix+"half_avg_diff"));
 		
-		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+"pix_step")!=null)             this.pix_step=Integer.parseInt(properties.getProperty(prefix+"pix_step"));
 		if (properties.getProperty(prefix+"search_rad")!=null)           this.search_rad=Integer.parseInt(properties.getProperty(prefix+"search_rad"));
 		if (properties.getProperty(prefix+"maybe_sum")!=null)            this.maybe_sum=Double.parseDouble(properties.getProperty(prefix+"maybe_sum"));
@@ -1458,8 +1483,6 @@ public class IntersceneMatchParameters {
 		if (properties.getProperty(prefix+"maybe_fom")!=null)            this.maybe_fom=Double.parseDouble(properties.getProperty(prefix+"maybe_fom"));
 		if (properties.getProperty(prefix+"sure_fom")!=null)             this.sure_fom=Double.parseDouble(properties.getProperty(prefix+"sure_fom"));
 		
-		
-		
 		if (properties.getProperty(prefix+"use_combo_dsi")!=null)        this.use_combo_dsi=Boolean.parseBoolean(properties.getProperty(prefix+"use_combo_dsi"));		
 		if (properties.getProperty(prefix+"use_lma_dsi")!=null)          this.use_lma_dsi=Boolean.parseBoolean(properties.getProperty(prefix+"use_lma_dsi"));
 
@@ -1499,6 +1522,19 @@ public class IntersceneMatchParameters {
 		if (properties.getProperty(prefix+"test_ers")!=null)             this.test_ers=Boolean.parseBoolean(properties.getProperty(prefix+"test_ers"));		
 		if (properties.getProperty(prefix+"test_ers0")!=null)            this.test_ers0=Integer.parseInt(properties.getProperty(prefix+"test_ers0"));
 		if (properties.getProperty(prefix+"test_ers1")!=null)            this.test_ers1=Integer.parseInt(properties.getProperty(prefix+"test_ers1"));
+		
+		if (properties.getProperty(prefix+"sky_highest_min")!=null)      this.sky_highest_min=Double.parseDouble(properties.getProperty(prefix+"sky_highest_min"));
+		if (properties.getProperty(prefix+"cold_frac")!=null)            this.cold_frac=Double.parseDouble(properties.getProperty(prefix+"cold_frac"));
+		if (properties.getProperty(prefix+"hot_frac")!=null)             this.hot_frac=Double.parseDouble(properties.getProperty(prefix+"hot_frac"));
+		if (properties.getProperty(prefix+"cold_scale")!=null)           this.cold_scale=Double.parseDouble(properties.getProperty(prefix+"cold_scale"));
+		if (properties.getProperty(prefix+"sky_seed")!=null)             this.sky_seed=Double.parseDouble(properties.getProperty(prefix+"sky_seed"));
+		if (properties.getProperty(prefix+"lma_seed")!=null)             this.lma_seed=Double.parseDouble(properties.getProperty(prefix+"lma_seed"));
+		if (properties.getProperty(prefix+"sky_shrink")!=null)           this.sky_shrink=Integer.parseInt(properties.getProperty(prefix+"sky_shrink"));
+		if (properties.getProperty(prefix+"seed_rows")!=null)            this.seed_rows=Integer.parseInt(properties.getProperty(prefix+"seed_rows"));
+		if (properties.getProperty(prefix+"sky_lim")!=null)              this.sky_lim=Double.parseDouble(properties.getProperty(prefix+"sky_lim"));
+		if (properties.getProperty(prefix+"sky_expand_extra")!=null)     this.sky_expand_extra=Integer.parseInt(properties.getProperty(prefix+"sky_expand_extra"));
+		if (properties.getProperty(prefix+"min_strength")!=null)         this.min_strength=Double.parseDouble(properties.getProperty(prefix+"min_strength"));
+		if (properties.getProperty(prefix+"lowest_sky_row")!=null)       this.lowest_sky_row=Integer.parseInt(properties.getProperty(prefix+"lowest_sky_row"));
 	}
 	
 	@Override
@@ -1644,13 +1680,6 @@ public class IntersceneMatchParameters {
 		imp.half_disparity        = this.half_disparity;
 		imp.half_avg_diff         = this.half_avg_diff;
 		
-		imp.photo_en              = this.photo_en;
-		imp.photo_num_full        = this.photo_num_full;
-		imp.photo_num_refines     = this.photo_num_refines;
-		imp.photo_min_strength    = this.photo_min_strength;
-		imp.photo_max_diff        = this.photo_max_diff;
-		imp.photo_debug           = this.photo_debug;
-		
 		imp.pix_step =              this.pix_step;
 		imp.search_rad =            this.search_rad;
 		imp.maybe_sum =             this.maybe_sum;
@@ -1698,6 +1727,23 @@ public class IntersceneMatchParameters {
 		imp.show_2d_correlations  = this.show_2d_correlations;
 		imp.show_motion_vectors   = this.show_motion_vectors ;
 		imp.debug_level           = this.debug_level;
+
+		imp.test_ers =              this.test_ers;         
+		imp.test_ers0 =             this.test_ers0;
+		imp.test_ers1 =             this.test_ers1;
+		
+		imp.sky_highest_min =       this.sky_highest_min;
+		imp.cold_frac =             this.cold_frac;
+		imp.hot_frac =              this.hot_frac;
+		imp.cold_scale =            this.cold_scale;
+		imp.sky_seed =              this.sky_seed;
+		imp.lma_seed =              this.lma_seed;
+		imp.sky_shrink =            this.sky_shrink;
+		imp.seed_rows =             this.seed_rows;
+		imp.sky_lim =               this.sky_lim;
+		imp.sky_expand_extra =      this.sky_expand_extra;
+		imp.min_strength =          this.min_strength;
+		imp.lowest_sky_row =        this.lowest_sky_row;
 		return imp;
 	}
 	public static long getLongColor(Color color) {
@@ -1714,56 +1760,6 @@ public class IntersceneMatchParameters {
 		}
 	}
 	
-	/*
-	public void orderStereo(){
-		boolean ordered;
-		do {
-			ordered=true;
-			for (int i = 0; i < (stereo_bases.length - 1); i++) {
-				if (stereo_bases[i+1]<stereo_bases[i]) {
-					boolean en = generate_stereo_var[i+1];
-					generate_stereo_var[i+1] = generate_stereo_var[i];
-					generate_stereo_var[i] = en;
-					double base =  stereo_bases[i+1];
-					stereo_bases[i+1] = stereo_bases[i];
-					stereo_bases[i] = base;
-					ordered = false;
-				}
-			}
-			
-		} while (!ordered);
-	}
-	public void addStereo(double base, boolean en) {
-		double [] bases = new double [stereo_bases.length + 1];
-		boolean [] ens = new boolean [stereo_bases.length + 1];
-		bases[0] = base;
-		ens[0] = en;
-		System.arraycopy(stereo_bases, 0, bases, 1,      stereo_bases.length);
-		System.arraycopy(generate_stereo_var, 0, ens, 1, stereo_bases.length);
-		stereo_bases = bases;
-		generate_stereo_var = ens;
-		orderStereo();
-	}
-	public void removeStereo(int indx) {
-		if ((indx >=0) && (indx <stereo_bases.length)) {
-			double [] bases = new double [stereo_bases.length - 1];
-			boolean [] ens = new boolean [stereo_bases.length - 1];
-			if (indx > 0) {
-				System.arraycopy(stereo_bases,        0, bases, 0, indx);
-				System.arraycopy(generate_stereo_var, 0, ens,   0, indx);
-			}
-			if (indx < (stereo_bases.length - 1)) {
-				System.arraycopy(stereo_bases,        indx+1, bases, indx, stereo_bases.length - indx - 1);
-				System.arraycopy(generate_stereo_var, indx+1, ens,   indx, stereo_bases.length - indx - 1);
-			}
-			stereo_bases = bases;
-			generate_stereo_var = ens;
-		}
-	}
-	
-
-	 */
-	
 	public void orderStereoViews(){
 		boolean ordered;
 		do {

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

@@ -153,6 +153,7 @@ public class QuadCLTCPU {
     boolean                                                is_aux = false;
     double  []                                             lwir_offsets = null; // per image subtracted values
     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,