Working, before adding low-elevation*alpha losses

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

@@ -1450,6 +1450,8 @@ public class VegetationModel {
 		boolean   fit_scenes =        clt_parameters.imp.terr_fit_scenes;     // true;  // adjust scene offsets (start from 0 always?)
 		boolean   fit_elevations =    clt_parameters.imp.terr_fit_elevations; // false; // adjust elevation pixels (not yet implemented)
 		
+		boolean [] fit_disable =      clt_parameters.imp.terr_fit_disable.clone();  
+		
 		double    reg_weights =       clt_parameters.imp.terr_reg_weights;         // 0.25;        // fraction of the total weight used for regularization
 		double    lambda =            clt_parameters.imp.terr_lambda;              // 5.0; // 0.1;
 		double    lambda_scale_good = clt_parameters.imp.terr_lambda_scale_good;   // 0.5;
@@ -1480,7 +1482,12 @@ public class VegetationModel {
 		
 		boolean     show_final_result = !tile_woi; // true; (maybe make saving results in tiled mode?
 
-		
+		boolean   recalc_weights =        clt_parameters.imp.terr_recalc_weights ;      //false; // recalculate weight depending on terrain visibility
+		double    transparency_opaque =   1.0 - clt_parameters.imp.terr_recalc_opaque ; // 0.9;  // above is opaque  
+		double    transparency_pedestal = clt_parameters.imp.terr_recalc_pedestal ;     // 0.05; // weight of opaque tiles  
+		double    transparency_frac =     clt_parameters.imp.terr_recalc_frac ;         // 1.0;  // increase weight for far pixels (double if scale differece == this)  
+		double    transparency_dist =     clt_parameters.imp.terr_recalc_dist ;         // 0.05; // weight of opaque tiles  
+		boolean   recalc_average =        clt_parameters.imp.terr_recalc_average ;      //false; // apply transparency to average mismatch
 		
 //clt_parameters.imp.; // 		
 		
@@ -2005,6 +2012,7 @@ public class VegetationModel {
 					fit_alpha,      // final boolean            adjust_alpha,
 					fit_scenes,     // final boolean            adjust_scenes,
 					fit_elevations, // final boolean            adjust_elevations,
+					fit_disable,    // final boolean []         fit_disable,  
 					reg_weights,   // final double             reg_weights,        // fraction of the total weight used for regularization
 					alpha_loss,    // final double             alpha_loss,         // quadratic loss when alpha reaches -1.0 or 2.0 
 					alpha_offset,  // final double             alpha_offset,       // quadratic loss when alpha reaches -1.0 or 2.0
@@ -2059,6 +2067,15 @@ public class VegetationModel {
 						par_path, // String        path,
 						true,     // boolean       keep_settings,
 						null);    // Rectangle [] file_wois);      //  if not null, should be Rectangle[2] {woi_veg,woi} - will return woi data and not input parameters to this instance
+				if (recalc_weights) {
+					vegetationLMA.applyTransparency(
+							null,                  // final double []   vector,
+							transparency_opaque,   // final double      transparency_opaque,
+							transparency_pedestal, // final double      transparency_pedestal,
+							transparency_frac,     // final double      transparency_frac,
+							transparency_dist,     // final double      transparency_dist,			
+							recalc_average);       // final boolean     recalc_average);
+				}
 			}
 			// old 
 			if ("RESTORE".equals(par_path)) {
@@ -2074,7 +2091,7 @@ public class VegetationModel {
 				}
 			}
 			
-			if ((show_final_result) && (debugLevel > 0)) {
+			if ((show_final_result) && (debugLevel > -2)) { // 0)) {
 				String reconstructed_title = reference_scene+"-reconstructed-initial";
 				vegetationLMA.showYfX(
 						null, // double [] vector,
@@ -2127,6 +2144,16 @@ public class VegetationModel {
 
 	  			elev_pull0 *= 0.01;
 	  			vegetationLMA.elevation_pull0 = elev_pull0;
+	  			
+				if (recalc_weights) {
+					vegetationLMA.applyTransparency(
+							null,                  // final double []   vector,
+							transparency_opaque,   // final double      transparency_opaque,
+							transparency_pedestal, // final double      transparency_pedestal,
+							transparency_frac,     // final double      transparency_frac,
+							transparency_dist,     // final double      transparency_dist,			
+							recalc_average);       // final boolean     recalc_average);				}
+				}
 	  			if (debugLevel > -3) {
 	  				lma_rslt= vegetationLMA.runLma( // <0 - failed, >=0 iteration number (1 - immediately)
 	  						lambda,           // double lambda,           // 0.1