Implemented UM, before chenging alpha to cos

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

@@ -55,8 +55,12 @@ public class VegetationLMA {
 	public double             alpha_loss;
 	public double             alpha_offset =    0; // if >0,  start losses above 0.0 and below 1.0;
 	public double             alpha_lpf =       0;
-	public double             terr_lpf =       0;
+	public double             terr_lpf =        0;
 	public double             veget_lpf =       0;
+	public double             boost_parallax =  1;
+	public double             um_sigma =        0;       // just use in debug image names
+	public double             um_weight =       0;
+	
 	// data used to calculate lpf pull of the alpha pixel to average of four neighbors. Below similar (weaker pull) for terrain and vegetation
 	// to smooth areas where there is no data from available images. 
 	public int [][]           alpha_neibs;   // corresponds to parameters for alpha (num_pars_vegetation_alpha), each has 4 ortho neibs, -1 - border, >= 0
@@ -69,8 +73,8 @@ public class VegetationLMA {
 	
 	public int                debug_index;
 	public double [][]        debug_image;
-	public static double []   debug_alpha_scales = {100,150};
-	public String             debug_path = "/media/elphel/SSD3-4GB/lwir16-proc/berdich3/debug/vegetation/lma/";
+	public static double []   debug_alpha_scales = {0,50}; // {100,150};
+	public String             debug_path = "/media/elphel/SSD3-4GB/lwir16-proc/berdich3/debug/vegetation/lma_um/";
 	
 	public int []             indices;
 	public int [][]           cpairs =          null;
@@ -127,14 +131,20 @@ public class VegetationLMA {
 			final double             terr_lpf,       // pull terrain to average of 4 neighbors (very small)
 			final double             veget_lpf,      // pull vegetation to average of 4 neighbors (very small - maybe not needed)
 			final double             boost_parallax, // increase weight of scene with maximal parallax relative to the reference scene
+			final double             um_sigma,       // just use in debug image names
+			final double             um_weight,
 			final String             parameters_read_path, 
 			final int                debugLevel) {
-		this.woi =          woi;
-		this.alpha_loss =   alpha_loss;
-		this.alpha_offset = alpha_offset;
-		this.alpha_lpf =    alpha_lpf;
-		this.terr_lpf =     terr_lpf;
-		this.veget_lpf =    veget_lpf;
+		this.woi =            woi;
+		this.alpha_loss =     alpha_loss;
+		this.alpha_offset =   alpha_offset;
+		this.alpha_lpf =      alpha_lpf;
+		this.terr_lpf =       terr_lpf;
+		this.veget_lpf =      veget_lpf;
+		this.boost_parallax = boost_parallax;
+		this.um_sigma =       um_sigma;      // just use in debug image names
+		this.um_weight =      um_weight;
+
 		final double []     scene_weights = setupSceneWeights(
 				boost_parallax); // double boost_parallax)
 		int     min_scenes_uses = min_scenes;
@@ -509,7 +519,10 @@ public class VegetationLMA {
 			if (debug_level > -2) { //
 				String  save_dir =    debug_path;
 				String  debug_title = "parameters_vector-x"+woi.x+"-y"+woi.y+"-w"+woi.width+"-h"+woi.height;
-				debug_title +="-al"+alpha_loss+"-alo"+alpha_offset+"-alp"+alpha_lpf+"-tl"+terr_lpf+"-vl"+veget_lpf;
+				debug_title +="-al"+alpha_loss+"-alo"+alpha_offset+"-alp"+alpha_lpf+"-tl"+terr_lpf+"-vl"+veget_lpf+"-bp"+boost_parallax;
+				if (um_weight > 0) {
+					debug_title +="-um"+um_sigma+"_"+um_weight;
+				}
 				boolean save_all =    (debug_image != null);
 				boolean show_this =   debug_level > 3;
 				boolean show_all =    debug_level > 4;
@@ -683,8 +696,8 @@ public class VegetationLMA {
 		double [][] terrain_weights_max = getTerrainWeights(
 				threshold_terrain, // final double      alpha_threshold, // discard images with too low transparency
 				vector);           // final double []   vector)
-		double [] terrain_masked =  tvas[0].clone();
-		double [] vegetation_masked =  tvas[0].clone();
+		double [] terrain_masked =     tvas[0].clone();
+		double [] vegetation_masked =  tvas[1].clone();
 		for (int i = 0; i < terrain_masked.length; i++) {
 			if (!(terrain_weights_max[0][i] >= min_terrain))      terrain_masked[i] = Double.NaN;
 			if (!(terrain_weights_max[1][i] >= min_max_terrain)) terrain_masked[i] = Double.NaN;