More debugging

src/main/java/com/elphel/imagej/correction/Eyesis_Correction.java

@@ -129,6 +129,7 @@ import com.elphel.imagej.tileprocessor.SymmVector;
 import com.elphel.imagej.tileprocessor.TwoQuadCLT;
 import com.elphel.imagej.tileprocessor.lwoc.LwirWorld;
 import com.elphel.imagej.vegetation.VegetationModel;
+import com.elphel.imagej.vegetation.VegetationSegment;
 
 import ij.CompositeImage;
 import ij.IJ;
@@ -863,6 +864,7 @@ public class Eyesis_Correction implements PlugIn, ActionListener {
 			addButton("Process Merged", panelOrange, color_process);
 			addButton("Vegetation LMA", panelOrange, color_process);
 			addButton("Combine LMA Segments", panelOrange, color_process);
+			addButton("Generate LWIR target", panelOrange, color_process);
 			plugInFrame.add(panelOrange);
 		}
 		plugInFrame.pack();
@@ -5805,6 +5807,8 @@ public class Eyesis_Correction implements PlugIn, ActionListener {
 					SYNC_COMMAND, // // SyncCommand  SYNC_COMMAND,
 					CLT_PARAMETERS, //CLTParameters    clt_parameters,
 					true); //boolean combine_segments);			
+		} else if (label.equals("Generate LWIR target")) {
+			VegetationSegment.generateSineTarget();	
 		}
 		//
 	}

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

@@ -871,8 +871,8 @@ min_str_neib_fpn	0.35
 	public double    terr_rms_diff =           1e-8; // 0.0001; virtually forever
 	public int       terr_last_series =       -1;  // Last LMA adjustment series (<0 - to the terr_num_iters.length -1)
 	public int []    terr_num_iters =        {30}; //sequence on numbers of iterations
-	public boolean   terr_only_special =       true; // special sequences for terrain-only tiles
-	public boolean   terr_only_pix =           true; // force per-pixel terrain elevation in terrain-only mode, overwrite fits_disable[TVAO_TERR_ELEV_PIX]
+///	public boolean   terr_only_special =       true; // special sequences for terrain-only tiles
+///	public boolean   terr_only_pix =           true; // force per-pixel terrain elevation in terrain-only mode, overwrite fits_disable[TVAO_TERR_ELEV_PIX]
 	public int       terr_only_series =       -1;   // similar to terr_last_series but for terrain-only mode (<0 - length of terr_only_num_iters)
 	public int []    terr_only_num_iters =   {25};  // number of iterations
 	
@@ -2246,8 +2246,8 @@ min_str_neib_fpn	0.35
 		gd.addStringField ("Maximal iterations", intsToString(terr_num_iters), 40, "Maximal number of LMA iterations per series, 1 or several values.");
 
 		gd.addMessage     ("Terrain-only LMA");
-		gd.addCheckbox    ("Terrain-only mode",     terr_only_special,           "Treat terrain-only tiles differently (below).");
-		gd.addCheckbox    ("Adjust pixel elevation",terr_only_pix,               "Force per-pixel terrain elevation adjustment in terrain-only mode.");
+///		gd.addCheckbox    ("Terrain-only mode",     terr_only_special,           "Treat terrain-only tiles differently (below).");
+///		gd.addCheckbox    ("Adjust pixel elevation",terr_only_pix,               "Force per-pixel terrain elevation adjustment in terrain-only mode.");
 		gd.addNumericField("Terrain-only iterations",terr_only_series, 0,3,"",   "Last LMA series in terrain-only mode, -1 - to last available in the sequence below.");
 		gd.addStringField ("Maximal iterations", intsToString(terr_only_num_iters), 40, "Maximal number of LMA iterations per series, 1 or several values.");
 		
@@ -3041,8 +3041,8 @@ min_str_neib_fpn	0.35
 		terr_last_series =   (int) gd.getNextNumber();// int    
 		terr_num_iters =           StringToInts(gd.getNextString());
 		
-		terr_only_special =        gd.getNextBoolean();// boolean
-		terr_only_pix =            gd.getNextBoolean();// boolean
+///		terr_only_special =        gd.getNextBoolean();// boolean
+///		terr_only_pix =            gd.getNextBoolean();// boolean
 		terr_only_series =   (int) gd.getNextNumber();// int    
 		terr_only_num_iters =      StringToInts(gd.getNextString());
 		
@@ -3811,8 +3811,8 @@ min_str_neib_fpn	0.35
 		properties.setProperty(prefix+"terr_last_series",            terr_last_series+"");        // int
 		properties.setProperty(prefix+"terr_num_iters",              intsToString(terr_num_iters)+"");  // int []
 		
-		properties.setProperty(prefix+"terr_only_special",           terr_only_special+"");     // boolean
-		properties.setProperty(prefix+"terr_only_pix",               terr_only_pix+"");     // boolean
+///		properties.setProperty(prefix+"terr_only_special",           terr_only_special+"");     // boolean
+///		properties.setProperty(prefix+"terr_only_pix",               terr_only_pix+"");     // boolean
 		properties.setProperty(prefix+"terr_only_series",            terr_only_series+"");       // int    
 		properties.setProperty(prefix+"terr_only_num_iters",         intsToString(terr_only_num_iters)+"");  // int []
 		
@@ -4596,8 +4596,8 @@ min_str_neib_fpn	0.35
 		if (properties.getProperty(prefix+"terr_num_iter")!=           null) terr_num_iters=new int[] {Integer.parseInt(properties.getProperty(prefix+"terr_num_iter"))};
 		if (properties.getProperty(prefix+"terr_num_iters")!=          null) terr_num_iters=StringToInts((String) properties.getProperty(prefix+"terr_num_iters"));
 		
-		if (properties.getProperty(prefix+"terr_only_special")!=       null) terr_only_special=Boolean.parseBoolean(properties.getProperty(prefix+"terr_only_special"));
-		if (properties.getProperty(prefix+"terr_only_pix")!=           null) terr_only_pix=Boolean.parseBoolean(properties.getProperty(prefix+"terr_only_pix"));
+///		if (properties.getProperty(prefix+"terr_only_special")!=       null) terr_only_special=Boolean.parseBoolean(properties.getProperty(prefix+"terr_only_special"));
+///		if (properties.getProperty(prefix+"terr_only_pix")!=           null) terr_only_pix=Boolean.parseBoolean(properties.getProperty(prefix+"terr_only_pix"));
 		if (properties.getProperty(prefix+"terr_only_series")!=        null) terr_only_series=Integer.parseInt(properties.getProperty(prefix+"terr_only_series"));
 		if (properties.getProperty(prefix+"terr_only_num_iters")!=     null) terr_only_num_iters=StringToInts((String) properties.getProperty(prefix+"terr_only_num_iters"));
 		
@@ -5344,8 +5344,8 @@ min_str_neib_fpn	0.35
 		imp.terr_last_series =                   this.terr_last_series;                           
 		imp.terr_num_iters =                     this.terr_num_iters.clone();
 		
-		imp.terr_only_special =                  this.terr_only_special;                           
-		imp.terr_only_pix =                      this.terr_only_pix;                           
+///		imp.terr_only_special =                  this.terr_only_special;                           
+///		imp.terr_only_pix =                      this.terr_only_pix;                           
 		imp.terr_only_series =                   this.terr_only_series;                           
 		imp.terr_only_num_iters =                this.terr_only_num_iters.clone();
 

src/main/java/com/elphel/imagej/vegetation/VegetationModel.java

@@ -1584,9 +1584,9 @@ public class VegetationModel {
 			fits_disable[i] =      clt_parameters.imp.terr_fits_disable[i].clone();
 		}
 		
-		boolean [][] terr_only_fits_disable = new boolean[clt_parameters.imp.terr_only_fits_disable.length][];
-		for (int i = 0; i < terr_only_fits_disable.length; i++) {
-			terr_only_fits_disable[i] =      clt_parameters.imp.terr_only_fits_disable[i].clone();
+		boolean [][] fits_disable_terronly = new boolean[clt_parameters.imp.terr_only_fits_disable.length][];
+		for (int i = 0; i < fits_disable_terronly.length; i++) {
+			fits_disable_terronly[i] =   clt_parameters.imp.terr_only_fits_disable[i].clone();
 		}
 		
 		double    reg_weights =       clt_parameters.imp.terr_reg_weights;         // 0.25;        // fraction of the total weight used for regularization
@@ -1599,8 +1599,8 @@ public class VegetationModel {
 		int       last_series =       clt_parameters.imp.terr_last_series;         // -1;   // 100;
 		if (last_series < 0) last_series = num_iters.length - 1; 
 		
-		boolean   terr_only_special = clt_parameters.imp.terr_only_special;        // true;  // special sequences for terrain-only tiles
-		boolean   terr_only_pix =     clt_parameters.imp.terr_only_pix;            // true;  // force per-pixel terrain elevation in terrain-only mode, overwrite fits_disable[TVAO_TERR_ELEV_PIX]
+///		boolean   terr_only_special = clt_parameters.imp.terr_only_special;        // true;  // special sequences for terrain-only tiles
+///		boolean   terr_only_pix =     clt_parameters.imp.terr_only_pix;            // true;  // force per-pixel terrain elevation in terrain-only mode, overwrite fits_disable[TVAO_TERR_ELEV_PIX]
 		int       terr_only_series =  clt_parameters.imp.terr_only_series;         //  -1;   // similar to terr_last_series but for terrain-only mode (<0 - length of terr_only_num_iters)
 		int []    terr_only_num_iters=clt_parameters.imp.terr_only_num_iters;      // {25};  // number of iterations
 		if (terr_only_series < 0) terr_only_series = terr_only_num_iters.length - 1; 
@@ -2144,6 +2144,7 @@ public class VegetationModel {
 					fit_terr_elev,     // final boolean            fit_terr_elev,					
 					fit_terr_elev_pix, // final boolean            fit_terr_elev_pix,					
 					thisOrLast(step_restore, fits_disable), // fits_disables[0], // final boolean []         fit_disable,
+					thisOrLast(step_restore, fits_disable_terronly),//			final boolean []         fits_disable_terronly,
 					reg_weights,       // final double             reg_weights,        // fraction of the total weight used for regularization
 					alpha_loss,        // final double             alpha_loss,         // alpha quadratic growing loss for when out of [0,1] range
 					alpha_loss_lin,    // final double             alpha_loss_lin, // alpha linear growing loss for when out of [0,1] range and below minimal vegetation alpha
@@ -2190,8 +2191,8 @@ public class VegetationModel {
 			        ttop_rel_rad,   // final double             ttop_rel_rad,   // 0.25;  // Relative (to the top height) sample ring radius
 			        ttop_frac,      // final double             ttop_frac,      // 0.5;   // Minimal fraction of the ring pixels below sample level
 			        ttop_rem_rad,   // final double             ttop_rem_rad,   // 0.25;  // Relative (to the top height) remove transparency radius
-			        terr_only_special,// final boolean          terr_only_special,//true; // special sequences for terrain-only tiles
-			        terr_only_pix,  // final boolean            terr_only_pix,    //true; // force per-pixel terrain elevation in terrain-only mode, overwrite fits_disable[TVAO_TERR_ELEV_PIX]
+///			        terr_only_special,// final boolean          terr_only_special,//true; // special sequences for terrain-only tiles
+///			        terr_only_pix,  // final boolean            terr_only_pix,    //true; // force per-pixel terrain elevation in terrain-only mode, overwrite fits_disable[TVAO_TERR_ELEV_PIX]
 					boost_parallax, // final double             boost_parallax,     // increase weight of scene with maximal parallax relative to the reference scene
 					max_parallax,   //final double              max_parallax,  // do not consider maximal parallax above this (consider it a glitch) 
 					debugLevel,          // final int           debugLevel);
@@ -2204,7 +2205,7 @@ public class VegetationModel {
 				continue;
 			}
 			/// Handle terrain-only tiles
-			if ((vegetationLMA.getWoiVeg() == null) && terr_only_special) {
+			if (vegetationLMA.getWoiVeg() == null) {// && terr_only_special) {
 				last_series = terr_only_series;
 				num_iters = terr_only_num_iters;
 			}
@@ -2329,9 +2330,13 @@ public class VegetationModel {
 			}
 	  		step_restore++;
 	  		for (; step_restore <= last_series; step_restore++) {
-//	  			vegetationLMA.fits_disable[VegetationLMA.TVAO_ELEVATION] = fits_disable[step_restore][VegetationLMA.TVAO_ELEVATION];
-	  			vegetationLMA.fits_disable[VegetationLMA.TVAO_ELEVATION] =thisOrLast(step_restore,fits_disable)[VegetationLMA.TVAO_ELEVATION];
-	  			vegetationLMA.fits_disable[VegetationLMA.TVAO_TERR_ELEV] =thisOrLast(step_restore,fits_disable)[VegetationLMA.TVAO_TERR_ELEV];
+	  			for (int i = 0; i < VegetationLMA.TVAO_TYPES; i++) {
+	  				vegetationLMA.fits_disable[i] =    thisOrLast(step_restore,fits_disable)[i];
+	  			}
+///	  			vegetationLMA.fits_disable[VegetationLMA.TVAO_ELEVATION] =    thisOrLast(step_restore,fits_disable)[VegetationLMA.TVAO_ELEVATION];
+///	  			vegetationLMA.fits_disable[VegetationLMA.TVAO_TERR_ELEV] =    thisOrLast(step_restore,fits_disable)[VegetationLMA.TVAO_TERR_ELEV];
+///	  			vegetationLMA.fits_disable[VegetationLMA.TVAO_TERR_ELEV_PIX] =thisOrLast(step_restore,fits_disable)[VegetationLMA.TVAO_TERR_ELEV_PIX];
+	  			vegetationLMA.fits_disable[VegetationLMA.TVAO_TERR_ELEV] |= !vegetationLMA.fits_disable[VegetationLMA.TVAO_TERR_ELEV_PIX]; 
 				if (thisOrLast(step_restore,recalc_weights)) {
 					System.out.println ("---- Recalculating weights from transparency");
 					String dbg_title= (!tile_woi && (debugLevel > -2)) ? ("transparency_"+step_restore) : null;