prepared elevation data, starting elevation LMA fitting

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.testVegetationLMA(
+			VegetationModel.processVegetationLMA(
 					CLT_PARAMETERS, //CLTParameters    clt_parameters,
 					false); //boolean combine_segments);			
 		} else if (label.equals("Combine LMA Segments")) {
-			VegetationModel.testVegetationLMA(
+			VegetationModel.processVegetationLMA(
 					CLT_PARAMETERS, //CLTParameters    clt_parameters,
 					true); //boolean combine_segments);			
 		}

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

@@ -760,7 +760,9 @@ min_str_neib_fpn	0.35
 	public double    terr_difference =        100.0; // vegetation is 100 warmer (target)
 	public double    terr_pull_cold =          0.001;  // pull vegetations to warm, terrain to cold
 	
-	public double    terr_alpha_dflt =         0.5;
+	
+	public double    terr_alpha_contrast =     1.0; // initial alpha contrast (>=1.0)
+	public double    terr_alpha_dflt =         0.5; // now unused
 	public double    terr_alpha_loss =       100.0;
 	public double    terr_alpha_offset =       0.0;
 	public double    terr_alpha_lpf =          2.5;  // pull to average of 4 neighbors
@@ -775,6 +777,7 @@ min_str_neib_fpn	0.35
 	public double    terr_veget_lpf =          0.2;  // pull vegetation to average of 4 neighbors (very small - maybe not needed)
 	public double    terr_terr_pull0 =         0.05; // pull terrain to zero (makes sense with UM
 	public double    terr_veget_pull0 =        0.05; // pull vegetation to zero (makes sense with UM
+	public double    terr_scenes_pull0 =       1.0;  // pull average scene offset to zero
 
 	// LMA parameters        
 	public double    terr_boost_parallax =     3.0;  //
@@ -2013,15 +2016,19 @@ min_str_neib_fpn	0.35
 		gd.addNumericField("Min influenced scenes",terr_min_scenes, 0,3,  "",   "Minimal number of scenes (inside woi) vegetation pixel must influence.");
 		gd.addNumericField("Minimal samples/scene",terr_min_samples_scene, 0,3,"","Minimal samples per scene used for fitting (skip scene if less).");
 		gd.addNumericField("Minimum scenes used",  terr_min_total_scenes, 0,3,"", "Minimal total number of scenes used (skip segment if less).");
+		
 		gd.addNumericField("Minimal pixels fitted",terr_min_pixels, 0,3,"",   "Minimal number of terrain and vegetation pixels used for fitting in this segment(skip segment if less).");
 		gd.addCheckbox    ("Start by temperature", terr_warm_veget,     "Start with vegetation warmer than terrain.");
 		gd.addNumericField("Warmest terrain",      terr_warmest, 5,7,"", 	"Above - vegetation. below - terrain.");
 		gd.addNumericField("Initial split",        terr_initial_split, 5,7,"", 	"Initial alpha: terrain 0.0+, vegetation 1.0-.");
 		gd.addNumericField("Min. split fraction",  terr_min_split_frac, 5,7,"", "minimal modality fraction to use split by temperature (otherwise use default alpha).");
 		gd.addNumericField("Vegetation warmer",    terr_difference, 5,7,"", 	"Pull vegetation to be this warmer.");
+		
 		gd.addNumericField("Pull terrain cold",    terr_pull_cold, 5,7,"", 	"Pull vegetations to warm, terrain to cold.");
+		gd.addNumericField("Alpha initial contrast",terr_alpha_contrast, 5,7,"","Initial alpha contrast (>= 1.0).");
 		gd.addNumericField("Defalt alpha",         terr_alpha_dflt, 5,7,"", 	"Default vegetation alpha.");
 		gd.addNumericField("Alpha loss",           terr_alpha_loss, 5,7,"", 	"Alpha quadratic growing loss for when out of [0,1] range");
+		
 		gd.addNumericField("Alpha offset",         terr_alpha_offset, 5,7,"",   "Start alpha losses above 0.0 and below 1.0 by this value.");
 		gd.addNumericField("Alpha diffusion",      terr_alpha_lpf, 5,7,"", 	    "Alpha diffusion to 4 ortho neighbors.");
 		gd.addCheckbox    ("Alpha piece-linear",   terr_alpha_piece_linear,     "Piece-linear alpha (_/\u203E, false - 0.0-cosine-1.0.");
@@ -2035,6 +2042,7 @@ min_str_neib_fpn	0.35
 		gd.addNumericField("Vegetation diffusion", terr_veget_lpf, 5,7,"", 		"LPF for vegetation pixels (diffusion to 4 neighbors).");
 		gd.addNumericField("Terrain pull zero",    terr_terr_pull0, 5,7,"",		"Terrain pixels pull to 0 (makes sense with UM).");
 		gd.addNumericField("Vegetation pull zero", terr_veget_pull0, 5,7,"",	"Vegetation pixels pull to 0 (makes sense with UM).");
+		gd.addNumericField("Pull scene offset",    terr_scenes_pull0, 5,7,"",	"Pull average scene offset to zero.");
 	
 		gd.addMessage     ("LMA parameters");
 		gd.addNumericField("Boost parallax",       terr_boost_parallax, 5,7,"",	"Increase weight of scenes that have high parallax to the reference one.");
@@ -2721,6 +2729,7 @@ min_str_neib_fpn	0.35
 		terr_min_split_frac =      gd.getNextNumber();// double 
 		terr_difference =          gd.getNextNumber();// double
 		terr_pull_cold =           gd.getNextNumber();// double 
+		terr_alpha_contrast =      gd.getNextNumber();// double 
 		terr_alpha_dflt =          gd.getNextNumber();// double 
 		terr_alpha_loss =          gd.getNextNumber();// double 
 		terr_alpha_offset =        gd.getNextNumber();// double 
@@ -2737,7 +2746,7 @@ min_str_neib_fpn	0.35
 		terr_veget_lpf =           gd.getNextNumber();// double 
 		terr_terr_pull0 =          gd.getNextNumber();// double 
 		terr_veget_pull0 =         gd.getNextNumber();// double 
-
+		terr_scenes_pull0 =        gd.getNextNumber();// double
 		terr_boost_parallax =      gd.getNextNumber();// double 
 		terr_max_parallax =        gd.getNextNumber();// double 
 		terr_hifreq_weight =       gd.getNextNumber();// double
@@ -3392,6 +3401,8 @@ min_str_neib_fpn	0.35
 		properties.setProperty(prefix+"terr_difference",             terr_difference+"");         // double 
 				
 		properties.setProperty(prefix+"terr_pull_cold",              terr_pull_cold+"");          // double 
+		properties.setProperty(prefix+"terr_alpha_contrast",         terr_alpha_contrast+"");     // double 
+		
 		properties.setProperty(prefix+"terr_alpha_dflt",             terr_alpha_dflt+"");         // double 
 		properties.setProperty(prefix+"terr_alpha_loss",             terr_alpha_loss+"");         // double 
 		properties.setProperty(prefix+"terr_alpha_offset",           terr_alpha_offset+"");       // double 
@@ -3406,6 +3417,7 @@ min_str_neib_fpn	0.35
 		properties.setProperty(prefix+"terr_veget_lpf",              terr_veget_lpf+"");          // double 
 		properties.setProperty(prefix+"terr_terr_pull0",             terr_terr_pull0+"");         // double 
 		properties.setProperty(prefix+"terr_veget_pull0",            terr_veget_pull0+"");        // double
+		properties.setProperty(prefix+"terr_scenes_pull0",           terr_scenes_pull0+"");       // double
 
 		properties.setProperty(prefix+"terr_boost_parallax",         terr_boost_parallax+"");     // double 
 		properties.setProperty(prefix+"terr_max_parallax",           terr_max_parallax+"");       // double 
@@ -4082,6 +4094,8 @@ min_str_neib_fpn	0.35
 		
 		if (properties.getProperty(prefix+"terr_difference")!=         null) terr_difference=Double.parseDouble(properties.getProperty(prefix+"terr_difference"));
 		if (properties.getProperty(prefix+"terr_pull_cold")!=          null) terr_pull_cold=Double.parseDouble(properties.getProperty(prefix+"terr_pull_cold"));
+		if (properties.getProperty(prefix+"terr_alpha_contrast")!=     null) terr_alpha_contrast=Double.parseDouble(properties.getProperty(prefix+"terr_alpha_contrast"));
+		
 		if (properties.getProperty(prefix+"terr_alpha_dflt")!=         null) terr_alpha_dflt=Double.parseDouble(properties.getProperty(prefix+"terr_alpha_dflt"));
 		if (properties.getProperty(prefix+"terr_alpha_loss")!=         null) terr_alpha_loss=Double.parseDouble(properties.getProperty(prefix+"terr_alpha_loss"));
 		if (properties.getProperty(prefix+"terr_alpha_offset")!=       null) terr_alpha_offset=Double.parseDouble(properties.getProperty(prefix+"terr_alpha_offset"));
@@ -4097,6 +4111,7 @@ min_str_neib_fpn	0.35
 		if (properties.getProperty(prefix+"terr_veget_lpf")!=          null) terr_veget_lpf=Double.parseDouble(properties.getProperty(prefix+"terr_veget_lpf"));
 		if (properties.getProperty(prefix+"terr_terr_pull0")!=         null) terr_terr_pull0=Double.parseDouble(properties.getProperty(prefix+"terr_terr_pull0"));
 		if (properties.getProperty(prefix+"terr_veget_pull0")!=        null) terr_veget_pull0=Double.parseDouble(properties.getProperty(prefix+"terr_veget_pull0"));
+		if (properties.getProperty(prefix+"terr_scenes_pull0")!=       null) terr_scenes_pull0=Double.parseDouble(properties.getProperty(prefix+"terr_scenes_pull0"));
 
 		if (properties.getProperty(prefix+"terr_boost_parallax")!=     null) terr_boost_parallax=Double.parseDouble(properties.getProperty(prefix+"terr_boost_parallax"));
 		if (properties.getProperty(prefix+"terr_max_parallax")!=       null) terr_max_parallax=Double.parseDouble(properties.getProperty(prefix+"terr_max_parallax"));
@@ -4741,6 +4756,7 @@ min_str_neib_fpn	0.35
 		imp.terr_min_split_frac =                this.terr_min_split_frac;
 		imp.terr_difference =                    this.terr_difference;		
 		imp.terr_pull_cold =                     this.terr_pull_cold; 
+		imp.terr_alpha_contrast =                this.terr_alpha_contrast; 
 		imp.terr_alpha_dflt =                    this.terr_alpha_dflt;                           
 		imp.terr_alpha_loss =                    this.terr_alpha_loss;                           
 		imp.terr_alpha_offset =                  this.terr_alpha_offset;                           
@@ -4756,6 +4772,7 @@ min_str_neib_fpn	0.35
 		imp.terr_veget_lpf =                     this.terr_veget_lpf;                           
 		imp.terr_terr_pull0 =                    this.terr_terr_pull0;                           
 		imp.terr_veget_pull0 =                   this.terr_veget_pull0; 
+		imp.terr_scenes_pull0 =                  this.terr_scenes_pull0;
 
 		imp.terr_boost_parallax =                this.terr_boost_parallax;                           
 		imp.terr_max_parallax =                  this.terr_max_parallax;   

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

@@ -6368,7 +6368,7 @@ public class OpticalFlow {
 //			int [] first_last = quadCLTs[ref_index].getFirstLastIndex(quadCLTs);
 			QuadCLT [] quadCLT_tail = new QuadCLT [quadCLTs.length - earliest_scene];
 			System.arraycopy(quadCLTs, earliest_scene, quadCLT_tail, 0, quadCLT_tail.length);
-			VegetationModel.test_vegetation(
+			VegetationModel.prepareVegetationData(
 					clt_parameters,                // CLTParameters  clt_parameters,
 					quadCLT_tail,                  // QuadCLT []     quadCLTs,
 					ref_index-earliest_scene,      // int            ref_index,

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

@@ -8786,6 +8786,27 @@ ImageDtt.startAndJoin(threads);
 	 * @return                data array made of input data with replaced NaN limited by
 	 *                        optional prohibit array and amount of growth. 
 	 */
+
+	public static double [] fillNaNs(
+			final double []  data,
+			final boolean [] prohibit,
+			int              width,
+			final int        grow,
+			double           diagonal_weight, // relative to ortho
+			int              num_passes,
+			final double     max_rchange) //  = 0.01
+	{
+		return fillNaNs(
+				data,            // final double []  data,
+				null,            // final double []  data_nan,
+				prohibit,        // final boolean [] prohibit_in,
+		        width,           // int              width,
+				grow,            // final int        grow,
+				diagonal_weight, //double           diagonal_weight, // relative to ortho
+				num_passes,      // int              num_passes,
+				max_rchange,     // final double     max_rchange, //  = 0.01
+				ImageDtt.THREADS_MAX);     // final int        threadsMax)
+	}
 	public static double [] fillNaNs(
 			final double []  data,
 			final boolean [] prohibit,