modifying parameters input

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

@@ -729,6 +729,7 @@ min_str_neib_fpn	0.35
 	public String    terr_model_path =  "/media/elphel/SSD3-4GB/lwir16-proc/berdich3/models/models_1697875868-1697879449-b/1697877487_245877/v35";
 	public String    terr_model_state = "1697877487_245877-TERR-VEG-STATE"; 
 	public String    terr_segments_dir = "sections"; 
+	public String    terr_segments_suffix = "-new"; 
 	public String    terr_par_dir =           "";      // directory path to intermediate parameters
 	public String    terr_par_file =          "";      // file name of the  intermediate parameters
 	public boolean   terr_par_restore =       false;   // restore parameters from file
@@ -815,6 +816,7 @@ min_str_neib_fpn	0.35
 	public double    terr_elev_lpf =          50.0;  // pull elevation to average of 4 neighbors
 	public double    terr_terr_pull0 =         0.1;  // pull terrain to initial (pre-adjustment) values
 	public double    terr_terr_pull_up=        0.25; // pull terrain to initial when it is colder
+	public double    terr_terr_pull_avg=       0.1;  // Pull terrain to the initial offset by the average offset of all terrain pixels  
 	public double    terr_veget_pull0 =        5.0;  // pull vegetation initial (pre-adjustment) values
 	public double    terr_elev_pull0 =         1.0;  // pull elevation to initial (pre-adjustment) values
 	public boolean   terr_elev_alpha_en =      false;// Enable loss for low vegetation with high opacity
@@ -2054,6 +2056,7 @@ min_str_neib_fpn	0.35
 		gd.addStringField ("Model path",         terr_model_path, 120, "Model directory path with version.");
 		gd.addStringField ("Model state file",   terr_model_state, 50, "Model vegetation source data (w/o extension).");
 		gd.addStringField ("Segments subdir",    terr_segments_dir, 50,"Model vegetation source data (w/o extension).");
+		gd.addStringField ("Segments suffix",    terr_segments_suffix, 50,"suffix to select from multiple versions (w/o \".par-tiff\".");
 
 		gd.addStringField ("Restore directory",  terr_par_dir, 120,     "Directory to resore initial parameters from.");
 		gd.addStringField ("Restore file",       terr_par_file, 120,    "Filename to resore initial parameters from.");
@@ -2138,7 +2141,8 @@ 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("Elevation diffusion",  terr_elev_lpf, 5,7,"", 		"LPF for elevation pixels (diffusion to 4 neighbors).");
 		gd.addNumericField("Terrain pull",         terr_terr_pull0, 5,7,"",		"Terrain pixels pull to initial (pre-adjustment) values.");
-		gd.addNumericField("Terrain pull up",      terr_terr_pull_up, 5,7,"",	"Terrain pixels pull to initial (pre-adjustment) values when it is colder than initial.");
+		gd.addNumericField("Terrain pull up",      terr_terr_pull_up, 5,7,"",	"Terrain pixels pull to initial (pre-adjustment) values when it is colder than initial (<0 - sqme as above).");
+		gd.addNumericField("Terrain pull to average",terr_terr_pull_avg, 5,7,"","Pull terrain to the initial offset by the average offset of all terrain pixels.");
 		gd.addNumericField("Vegetation pull",      terr_veget_pull0, 5,7,"",	"Vegetation pixels pull initial (pre-adjustment) values.");
 		gd.addNumericField("Elevation pull",       terr_elev_pull0, 5,7,"",  	"Elevation pixels pull to initial (pre-adjustment) values.");
 		
@@ -2824,7 +2828,7 @@ min_str_neib_fpn	0.35
 		terr_model_path =          gd.getNextString();
 		terr_model_state =         gd.getNextString();
 		terr_segments_dir =        gd.getNextString();
-		
+		terr_segments_suffix =     gd.getNextString();
 		terr_par_dir =             gd.getNextString();
 		terr_par_file =            gd.getNextString();
 		terr_par_restore =         gd.getNextBoolean(); // boolean
@@ -2898,6 +2902,7 @@ min_str_neib_fpn	0.35
 		terr_elev_lpf =            gd.getNextNumber();// double
 		terr_terr_pull0 =          gd.getNextNumber();// double 
 		terr_terr_pull_up =        gd.getNextNumber();// double 
+		terr_terr_pull_avg =       gd.getNextNumber();// double 
 		terr_veget_pull0 =         gd.getNextNumber();// double
 		terr_elev_pull0 =          gd.getNextNumber();// double
 		terr_elev_alpha_en =       gd.getNextBoolean();// boolean
@@ -3541,6 +3546,7 @@ min_str_neib_fpn	0.35
 		properties.setProperty(prefix+"terr_model_path",             terr_model_path+"");         // String
 		properties.setProperty(prefix+"terr_model_state",            terr_model_state+"");        // String
 		properties.setProperty(prefix+"terr_segments_dir",           terr_segments_dir+"");       // String
+		properties.setProperty(prefix+"terr_segments_suffix",        terr_segments_suffix+"");    // String
 		
 		properties.setProperty(prefix+"terr_par_dir",                terr_par_dir+"");            // String
 		properties.setProperty(prefix+"terr_par_file",               terr_par_file+"");           // String
@@ -3616,6 +3622,7 @@ min_str_neib_fpn	0.35
 		properties.setProperty(prefix+"terr_elev_lpf",               terr_elev_lpf+"");           // double 
 		properties.setProperty(prefix+"terr_terr_pull0",             terr_terr_pull0+"");         // double 
 		properties.setProperty(prefix+"terr_terr_pull_up",           terr_terr_pull_up+"");       // double 
+		properties.setProperty(prefix+"terr_terr_pull_avg",          terr_terr_pull_avg+"");      // double 
 		properties.setProperty(prefix+"terr_veget_pull0",            terr_veget_pull0+"");        // double
 		properties.setProperty(prefix+"terr_elev_pull0",             terr_elev_pull0+"");         // double
 		properties.setProperty(prefix+"terr_elev_alpha_en",          terr_elev_alpha_en+"");      // boolean
@@ -4282,6 +4289,7 @@ min_str_neib_fpn	0.35
 		if (properties.getProperty(prefix+"terr_model_path")!=         null) terr_model_path=(String) properties.getProperty(prefix+"terr_model_path");
 		if (properties.getProperty(prefix+"terr_model_state")!=        null) terr_model_state=(String) properties.getProperty(prefix+"terr_model_state");
 		if (properties.getProperty(prefix+"terr_segments_dir")!=       null) terr_segments_dir=(String) properties.getProperty(prefix+"terr_segments_dir");
+		if (properties.getProperty(prefix+"terr_segments_suffix")!=    null) terr_segments_suffix=(String) properties.getProperty(prefix+"terr_segments_suffix");
 
 		if (properties.getProperty(prefix+"terr_par_dir")!=            null) terr_par_dir=(String) properties.getProperty(prefix+"terr_par_dir");
 		if (properties.getProperty(prefix+"terr_par_file")!=           null) terr_par_file=(String) properties.getProperty(prefix+"terr_par_file");
@@ -4355,6 +4363,7 @@ min_str_neib_fpn	0.35
 		if (properties.getProperty(prefix+"terr_elev_lpf")!=           null) terr_elev_lpf=Double.parseDouble(properties.getProperty(prefix+"terr_elev_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_terr_pull_up")!=       null) terr_terr_pull_up=Double.parseDouble(properties.getProperty(prefix+"terr_terr_pull_up"));
+		if (properties.getProperty(prefix+"terr_terr_pull_avg")!=      null) terr_terr_pull_avg=Double.parseDouble(properties.getProperty(prefix+"terr_terr_pull_avg"));
 		if (properties.getProperty(prefix+"terr_veget_pull0")!=        null) terr_veget_pull0=Double.parseDouble(properties.getProperty(prefix+"terr_veget_pull0"));
 		if (properties.getProperty(prefix+"terr_elev_pull0")!=         null) terr_elev_pull0=Double.parseDouble(properties.getProperty(prefix+"terr_elev_pull0"));
 		if (properties.getProperty(prefix+"terr_elev_alpha_en")!=      null) terr_elev_alpha_en=Boolean.parseBoolean(properties.getProperty(prefix+"terr_elev_alpha_en"));
@@ -4993,6 +5002,7 @@ min_str_neib_fpn	0.35
 		imp.terr_model_path =                    this. terr_model_path;
 		imp.terr_model_state =                   this. terr_model_state;
 		imp.terr_segments_dir =                  this. terr_segments_dir;
+		imp.terr_segments_suffix =               this.terr_segments_suffix;
 		
 		imp.terr_par_dir =                       this. terr_par_dir;
 		imp.terr_par_file =                      this. terr_par_file;
@@ -5064,6 +5074,7 @@ min_str_neib_fpn	0.35
 		imp.terr_elev_lpf =                      this.terr_elev_lpf;
 		imp.terr_terr_pull0 =                    this.terr_terr_pull0;                           
 		imp.terr_terr_pull_up =                  this.terr_terr_pull_up;                           
+		imp.terr_terr_pull_avg =                 this.terr_terr_pull_avg;                           
 		imp.terr_veget_pull0 =                   this.terr_veget_pull0; 
 		imp.terr_elev_pull0 =                    this.terr_elev_pull0;
 		imp.terr_elev_alpha_en =                 this.terr_elev_alpha_en;

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

@@ -95,6 +95,8 @@ public class VegetationModel {
 	
 	public double [][] tva;
 	int                step_restore;
+	public boolean     tile_woi;
+	
 	
 	public final SyncCommand SYNC_COMMAND;
 	public boolean isFailed() {
@@ -1434,7 +1436,7 @@ public class VegetationModel {
 		
 		boolean   run_combine =  combine_segments; //          true;   // if true, run combining instead of LMA
 		String    segments_sub =      clt_parameters.imp.terr_segments_dir;         //
-		
+		String    segments_suffix =   clt_parameters.imp.terr_segments_suffix;
 		String    parameters_dir =    clt_parameters.imp.terr_par_dir;         //
 		String    parameters_file =   clt_parameters.imp.terr_par_file;         //
 		boolean   par_restore =       clt_parameters.imp.terr_par_restore;               // true;
@@ -1454,7 +1456,8 @@ public class VegetationModel {
 		
 		
 		
-		boolean   tile_woi =          clt_parameters.imp.terr_tile_woi;            // scan woi_enclosing, false - run a single woi_last
+//		boolean  
+		tile_woi =                    clt_parameters.imp.terr_tile_woi;            // scan woi_enclosing, false - run a single woi_last
 		Rectangle woi_enclosing =     clt_parameters.imp.terr_woi_enclos;          // new Rectangle(0,  0, 200, 160); // will be tiled, using width/height from woi_step;
 		Rectangle woi_step =          clt_parameters.imp.terr_woi_step;            // new Rectangle(10,10,20,20);
 		Rectangle woi_last =          clt_parameters.imp.terr_woi_last;            // new Rectangle(160,310,20,20); // 170
@@ -1500,7 +1503,8 @@ public class VegetationModel {
 		double    veget_lpf =         clt_parameters.imp.terr_veget_lpf;           // 0.2; //0.15; /// 0.2; //// 0.01; /// 0.1;    // pull vegetation to average of 4 neighbors (very small - maybe not needed)
 		double    elevation_lpf =     clt_parameters.imp.terr_elev_lpf;		
 		double    terr_pull0 =        clt_parameters.imp.terr_terr_pull0;          // 0.1; //0.03; ////// 0.05; ///// 0.1; //// 0.01; /// 0.2; /// 0.1;    //pull terrain to zero (makes sense with UM
-		double    terr_pull_up =      clt_parameters.imp.terr_terr_pull_up;        // 0.2; //Terrain pixels pull to initial (pre-adjustment) values when it is colder than initial.
+		double    terr_pull_up =      clt_parameters.imp.terr_terr_pull_up;        // 0.2; // Terrain pixels pull to initial (pre-adjustment) values when it is colder than initial.
+		double    terr_pull_avg =     clt_parameters.imp.terr_terr_pull_avg;       // 0.1; // Pull terrain to the initial offset by the average offset of all terrain pixels  
 		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
@@ -2027,7 +2031,8 @@ public class VegetationModel {
 		
 		if (run_combine) {
 			VegetationSegment [] segments = vegetationLMA.readAllSegments(
-					segments_dir); // String dir_path)
+					segments_dir,     // String dir_path)
+					segments_suffix); // String suffix);
 			vegetationLMA.combineSegments(
 					segments,
 					border_width,           // int                  width);
@@ -2043,6 +2048,7 @@ public class VegetationModel {
 		}
 		Rectangle woi = woi_last_done;
 		while (true) {
+			step_restore=       par_restore? clt_parameters.imp.terr_step_restore : 0;
 			woi = nextTileWoi(
 					woi_enclosing, // Rectangle enclosing,
 					woi_step, // Rectangle step,
@@ -2060,15 +2066,7 @@ public class VegetationModel {
 			} else {
 				System.out.println("===== Will process a single WOI ("+woi.x+", "+woi.y+", "+woi.width+", "+woi.height+").");
 			}
-			/*
-			boolean [][] fits_disables = new boolean [num_iters.length][];
-			for (int i = 0; i <fits_disables.length; i++) {
-				fits_disables[i] = fit_disable.clone();
-			}
-			if (!par_restore && (fits_disables.length > 1)) {
-				fits_disables[0][VegetationLMA.TVAO_ELEVATION] = true; // disable elevation adjustment for the first run 
-			}
-			*/
+
 			int num_samples = vegetationLMA.prepareLMA(
 					false,             // final boolean            keep_parameters,
 					woi,               // final Rectangle   woi,
@@ -2094,7 +2092,7 @@ public class VegetationModel {
 					alpha_scale_avg,    // final double             alpha_scale_avg, //  = 1.2; // scale average alpha (around 0.5) when pulling to it
 					alpha_push,         //  final double             alpha_push,      //  5.0;   // push from alpha==0.5
 					alpha_push_neutral, // double    alpha_push_neutral = 0.8; // alpha point from which push (closer to opaque)
-					alpha_push_center,// final double             alpha_push_center,// 1.5; // weight of center alpha pixel relative to each of the 4 ortho ones
+					alpha_push_center,  // final double             alpha_push_center,// 1.5; // weight of center alpha pixel relative to each of the 4 ortho ones
 					alpha_en_holes, // final boolean            alpha_en_holes, // Search for small semi-transparent holes, disable diffusion of local alpha minimums
 					alpha_mm_hole,  //  double    alpha_mm_hole    = 0.1; // NaN to disable. Local "almost minimum" (lower than this fraction between min and max neighbor) is not subject to alpha_lpf
 					terr_lpf,       // final double             terr_lpf,           // pull terrain to average of 4 neighbors (very small)
@@ -2102,6 +2100,7 @@ public class VegetationModel {
 					elevation_lpf,  // final double             elevation_lpf,
 					terr_pull0,     // final double             terr_pull0,     // pull terrain to initial (pre-adjustment) values
 					terr_pull_up,   // final double             terr_pull_up,   // Terrain pixels pull to initial (pre-adjustment) values when it is colder than initial.
+					terr_pull_avg,  // final double             terr_pull_avg,  // pull terrain to the initial offset by the average offset of all terrain pixels  
 					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
@@ -2136,7 +2135,7 @@ public class VegetationModel {
 					continue;
 				}
 			}
-			int num_iter = num_iters[step_restore];
+			int num_iter = num_iters[step_restore]; //
 			if (par_restore) { // always use last number of iterations - not anymore
 				par_path = parameters_dir;
 				if (!par_path.endsWith(Prefs.getFileSeparator())) {
@@ -2147,10 +2146,11 @@ public class VegetationModel {
 				vegetationLMA.restoreParametersFile( //FIXME: Not finished for real import ! 
 						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
+						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
+						null);    // double [] other_pars)
 				if (thisOrLast(step_restore,recalc_weights)) {
 					System.out.println ("---- Recalculating weights from transparency after loading parameters");
-					String dbg_title= (debugLevel > -2) ?("transparency_"+step_restore): null;
+					String dbg_title= (!tile_woi && (debugLevel > -2)) ?("transparency_"+step_restore): null;
 					vegetationLMA.applyTransparency(
 							null,                  // final double []   vector,
 							transparency_opaque,   // final double      transparency_opaque,
@@ -2234,7 +2234,7 @@ public class VegetationModel {
 	  			vegetationLMA.fits_disable[VegetationLMA.TVAO_ELEVATION] =thisOrLast(step_restore,fits_disable)[VegetationLMA.TVAO_ELEVATION];
 				if (thisOrLast(step_restore,recalc_weights)) {
 					System.out.println ("---- Recalculating weights from transparency");
-					String dbg_title= (debugLevel > -2) ? ("transparency_"+step_restore) : null;
+					String dbg_title= (!tile_woi && (debugLevel > -2)) ? ("transparency_"+step_restore) : null;
 					vegetationLMA.applyTransparency(
 							null,                  // final double []   vector,
 							transparency_opaque,   // final double      transparency_opaque,

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

@@ -7,13 +7,20 @@ public class VegetationSegment {
 	public Rectangle   woi;
 	public double []   scene_offsets;
 	public double [][] tva;
+	public double      terrain_offset;
+	public String      path;
 	public VegetationSegment(
+			String      path, 
 			Rectangle   woi_veg,
 			Rectangle   woi,
+			double terrain_offset,
 			double []   scene_offsets, // has NaNs
 			double [][]  tva) {
+		this.path = path;
 		this.woi = woi;
+		this.woi_veg = woi_veg;
 		this.scene_offsets = scene_offsets;
 		this.tva =  tva;
+		this.terrain_offset = terrain_offset;
 	}
 }