intermediate, before changing alpha pull

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

@@ -5802,11 +5802,11 @@ public class Eyesis_Correction implements PlugIn, ActionListener {
 		} else if (label.equals("Process Merged")) {
 			OrangeTest.processMerged();			
 		} else if (label.equals("Vegetation LMA")) {
-			VegetationModel.processVegetationLMA(
+			VegetationModel.processVegetation(
 					CLT_PARAMETERS, //CLTParameters    clt_parameters,
 					false); //boolean combine_segments);			
 		} else if (label.equals("Combine LMA Segments")) {
-			VegetationModel.processVegetationLMA(
+			VegetationModel.processVegetation(
 					CLT_PARAMETERS, //CLTParameters    clt_parameters,
 					true); //boolean combine_segments);			
 		}

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

@@ -1277,7 +1277,7 @@ public class VegetationModel {
 	
 	
 	
-	public static void processVegetationLMA(
+	public static void processVegetation(
 			CLTParameters    clt_parameters,
 			boolean combine_segments) 
 	{
@@ -1296,7 +1296,7 @@ public class VegetationModel {
 		VegetationModel vegetationModel = new VegetationModel(
 				model_directory, // String dir,
 				model_state_file); // String title)
-		vegetationModel.testVegetationLMA(
+		vegetationModel.processVegetationLMA(
 				combine_segments, // boolean combine_segments,
 				clt_parameters, // CLTParameters      clt_parameters,
 				-1); // int                debugLevel) {
@@ -1369,7 +1369,7 @@ public class VegetationModel {
 		}
 	}
 	
-	public void testVegetationLMA(
+	public void processVegetationLMA(
 			boolean            combine_segments,
 			CLTParameters      clt_parameters,
 			int                debugLevel) {
@@ -1418,7 +1418,13 @@ public class VegetationModel {
 //		double    terr_difference =   clt_parameters.imp.terr_difference;          // Pull vegetation to be this warmer
 //		double    terr_pull_cold =    clt_parameters.imp.terr_pull_cold;           // pull vegetations to warm, terrain to cold
 		double    elevation_radius =  clt_parameters.imp.terr_elevation_radius;    // Radius of elevation/vegetation influence 
-		double    alpha_initial_contrast = clt_parameters.imp.terr_alpha_contrast; // initial alpha contrast (>=1.0)
+//		double    alpha_initial_contrast = clt_parameters.imp.terr_alpha_contrast; // initial alpha contrast (>=1.0)
+
+		double    alpha_sigma =       clt_parameters.imp.terr_alpha_sigma;         // 8.0;  // Initial alpha: Gaussian blur sigma to find local average for vegetation temperature.
+		double    alpha_init_min=     clt_parameters.imp.terr_alpha_init_min;      // 0.7;  // Initial alpha: fraction for transparent 
+		double    alpha_init_max=     clt_parameters.imp.terr_alpha_init_max;      // 0.9;  // Initial alpha: fraction for opaque 
+        double    alpha_init_offs=    clt_parameters.imp.terr_alpha_init_offs;     // 0.01; // Initial alpha: opaque/transparent offset from 1.0/0.0 
+        
 		double    default_alpha =     clt_parameters.imp.terr_alpha_dflt;          //  0.5; //  0.8;
 		double    alpha_loss =        clt_parameters.imp.terr_alpha_loss;          //100.0; // 10.0; /// 100.0; // 10.0;  // 10000.0; // 1000.0; // 100.; // 10.0;         // quadratic loss when alpha reaches -1.0 or 2.0 
 		double    alpha_offset =      clt_parameters.imp.terr_alpha_offset;        //  0.0; // 0.02; // 0.03;    // if >0,  start losses above 0.0 and below 1.0;
@@ -1436,6 +1442,10 @@ public class VegetationModel {
 		double    terr_pull0 =        clt_parameters.imp.terr_terr_pull0;          // 0.05; //0.03; ////// 0.05; ///// 0.1; //// 0.01; /// 0.2; /// 0.1;    //pull terrain to zero (makes sense with UM
 		double    veget_pull0 =       clt_parameters.imp.terr_veget_pull0;         // 0.05; //0.1; // 0.03; ////// 0.05; ///// 0.1; //// 0.01; /// 0.1;    // pull vegetation to zero (makes sense with UM
 		double    elev_pull0 =        clt_parameters.imp.terr_elev_pull0; 
+	    boolean   elev_alpha_en=      clt_parameters.imp.terr_elev_alpha_en; // false;// Enable loss for low vegetation with high opacity
+	    double    elev_alpha =        clt_parameters.imp.terr_elev_alpha;    // 1.0;  // multiply alpha by under-low elevation for loss
+	    double    elev_alpha_pwr =    clt_parameters.imp.terr_elev_alpha_pwr;    // 1.0;  // multiply alpha by under-low elevation for loss
+	    double    low_veget =         clt_parameters.imp.terr_low_veget;     // 2.0;  // (pix) Elevation considered low (lower loss for high alpha)
 		double    scenes_pull0 =      clt_parameters.imp.terr_scenes_pull0;        // 1.0
 		
 		// LMA parameters        
@@ -1488,29 +1498,11 @@ public class VegetationModel {
 		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.; // 		
-		
-		
 		boolean restore_mode =   false;
 		boolean save_par_files = true; // false;
-//		boolean diff_mode = true;
-		
-//		String segments_dir = "/media/elphel/SSD3-4GB/lwir16-proc/berdich3/debug/vegetation/segments_new/";
 		String segments_dir = getSegmentsDir(segments_sub);
-		
-//		boolean   next_run =      false;
 		boolean   read_pars =     false; // true; /// false; /// true; //   false; // true;
 		
-		
-		
-
-		
-
-		// combine  parameters
-		
-		
-		
 		// debug feature to read to continue - needs to be cleaned up/replaced
 		String  parameters_path = "/media/elphel/SSD3-4GB/lwir16-proc/berdich3/debug/vegetation/essential/parameters_vector_data_x143-y317-w35-h35-al100.0-alo0.0-alp10.0-alin-tl0.2-vl0.01-tp0.01-vp0.01-bp5.0-um1.0_0.8.tiff";
 
@@ -1552,7 +1544,6 @@ public class VegetationModel {
 						titles_laplacian,                     // String []    titles, // all slices*frames titles or just slice titles or null
 						new String[] {"source","laplacian"},                     // String []    frame_titles, // frame titles or null
 						true);                            // boolean      show)
-
 			}
 		}
 
@@ -1933,21 +1924,21 @@ public class VegetationModel {
 			
 
 		} // if ((elevations == null) || (scale_dirs == null)){
-		
-		
-		// directions should not be averaged over scenes as the flight direction may change
-		
-//		if (debugLevel < 1000) {
-//			return; // 
-//		}
-		
-		
-//		initial_transparent = initial_split;
-//		initial_opaque =      1.0 - initial_split;
-		
+		/*
 		VegetationLMA vegetationLMA = new VegetationLMA (
 				this,
-				alpha_initial_contrast); // double alpha_initial_contrast)
+				alpha_initial_contrast, // double alpha_initial_contrast)
+				debugLevel); // int debugLevel) 
+		*/
+		VegetationLMA vegetationLMA = new VegetationLMA (
+				this,
+				alpha_init_offs,  // 0.01; // double    alpha_offs,
+				alpha_init_min,   // 0.7;  // double    alpha_min,
+				alpha_init_max,   // 0.9;  // double    alpha_max,
+				alpha_sigma, // 8.0;  // double    alpha_sigma,
+				debugLevel); // int debugLevel) 
+		
+		
 		if (debugLevel > -2) {
 			double [][] dbg_img = {
 					vegetationLMA.tvao[VegetationLMA.TVAO_TERRAIN],
@@ -2030,6 +2021,10 @@ public class VegetationModel {
 					terr_pull0,     // final double             terr_pull0,     // pull terrain to initial (pre-adjustment) values
 					veget_pull0,    // final double             veget_pull0,    // pull vegetation to initial (pre-adjustment) values
 					elev_pull0,     // final double             elev_pull0,     // pull elevation to initial (pre-adjustment) values
+					elev_alpha_en,  // final boolean            elev_alpha_en,  // false; // Enable loss for low vegetation with high opacity
+					elev_alpha,     // final double             elev_alpha,     // 1.0;   // multiply alpha by under-low elevation for loss
+					elev_alpha_pwr, // final double             elev_alpha_pwr, // 2.0;  // raise alpha to this power (when alpha > 0)
+					low_veget,      // final double             low_veget,      // 2.0;   // (pix) Elevation considered low (lower loss for high alpha)
 					scenes_pull0,   // final double             scenes_pull0,
 					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)