Added full image model rendering

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

@@ -137,6 +137,7 @@ import com.elphel.imagej.tileprocessor.TwoQuadCLT;
 import com.elphel.imagej.tileprocessor.lwoc.LwirWorld;
 import com.elphel.imagej.vegetation.VegetationModel;
 //import com.elphel.imagej.vegetation.VegetationSegment;
+import com.elphel.imagej.vegetation.VegetationSynthesis;
 
 import ij.CompositeImage;
 import ij.IJ;
@@ -871,6 +872,7 @@ public class Eyesis_Correction implements PlugIn, ActionListener {
 			addButton("Process Merged", panelOrange, color_process);
 			addButton("Vegetation LMA", panelOrange, color_process);
 			addButton("Combine LMA Segments", panelOrange, color_process);
+			addButton("Render synthetic", panelOrange, color_process);
 			addButton("Generate LWIR target", panelOrange, color_process);
 //			addButton("Test LDLT Cholesky", panelOrange, color_process);
 			addButton("Test LLT Cholesky",  panelOrange, color_process);
@@ -5820,6 +5822,11 @@ public class Eyesis_Correction implements PlugIn, ActionListener {
 					SYNC_COMMAND, // // SyncCommand  SYNC_COMMAND,
 					CLT_PARAMETERS, //CLTParameters    clt_parameters,
 					true); //boolean combine_segments);	
+		} else if (label.equals("Render synthetic")) {
+			VegetationSynthesis.testSynthetic(
+					SYNC_COMMAND, // // SyncCommand  SYNC_COMMAND,
+					CLT_PARAMETERS, // CLTParameters    clt_parameters,
+					DEBUG_LEVEL);   // final int debugLevel
 		/*	
 		} else if (label.equals("Test LDLT Cholesky")) {
 			ImagePlus imp_sel = WindowManager.getCurrentImage();

src/main/java/com/elphel/imagej/cuas/CorrectionFPN.java

@@ -256,13 +256,13 @@ public class CorrectionFPN {
 					  for (int nsens = ai.getAndIncrement(); nsens < num_sens; nsens = ai.getAndIncrement()) {
 						  for (int nscene = 0; nscene < num_scenes; nscene++) {
 							  System.arraycopy(
-									  rowcol_data2[2 * nsens + 0],
+									  rowcol_data2[nsens + 0],
 									  nscene*img_width,
 									  rows[nscene][nsens], // data[0][nsens],
 									  0,
 									  width);
 							  System.arraycopy(
-									  rowcol_data2[2 * nsens + 1],
+									  rowcol_data2[nsens + num_sens],
 									  nscene*img_width,
 									  cols[nscene][nsens], // data[1][nsens],
 									  0,

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

@@ -805,6 +805,7 @@ public class QuadCLTCPU {
 	 * Read (try to read) this first, maybe parent is not needed (yet)
 	 * @param clt_parameters
 	 * @param ignore_this do not merge this sequence CLT data, only use parent's cumulative
+	 * @param use_parent_dsi - use parent DSI even if this exists 
 	 * @param ref_clt
 	 * @param full_path
 	 * @param single_first true: read single first, cumulative second, false - read cumulative first 
@@ -814,6 +815,7 @@ public class QuadCLTCPU {
 	public static QuadCLT restoreCenterClt(
 			CLTParameters   clt_parameters,
 			boolean         ignore_this,
+			boolean         use_parent_dsi,
 			QuadCLT         ref_clt , // latest
 			String          full_path, // if non-null, use it instead of ref_clt
 			boolean         single_first, // true: read single first, cumulative second 
@@ -915,11 +917,14 @@ public class QuadCLTCPU {
 				System.out.println("restoreCenterClt(): parent directory is not provided, and this model data does not exist - bailing out.");
 				return null;
 		}		
-		if (center_CLT == null) { // so parent parentCuasData and parent_dsi both exist
+		if (use_parent_dsi || (center_CLT == null)) { // so parent parentCuasData and parent_dsi both exist
 			// Create new center_CLT
+			if (center_CLT == null) {
 				center_CLT = new QuadCLT(ref_clt, center_name);
 				center_CLT.setImagePath(cdir.getPath()); // *********************		
 				cdir.mkdirs();
+				cuasData = parentCuasData; // will be collapsed in one place
+			}
 			center_CLT.setDSIFromCombo(parent_dsi); // set center DSI from parent
 			String rslt_suffix = "-INTER-INTRA";
 			if (!clt_parameters.correlate_lma){
@@ -934,7 +939,7 @@ public class QuadCLTCPU {
 					center_CLT.getTilesX(),                       // int         width,
 					center_CLT.getTilesY());                      // int         height)
 			center_CLT.setDSIFromCombo(parent_dsi);
-			cuasData = parentCuasData; // will be collapsed in one place
+//			cuasData = parentCuasData; // will be collapsed in one place
 		} else { // if (center_CLT == null) { 
 			if (parentCuasData != null) { // both exist - combine
 				boolean en_create = true;
@@ -4645,13 +4650,13 @@ public class QuadCLTCPU {
     			DSI_SUFFIXES[INDEX_INTER_LMA], // String suffix, // "-DSI_COMBO", "-DSI_MAIN" (DSI_COMBO_SUFFIX, DSI_MAIN_SUFFIX)
     			null, // double [][] dsi, // if null - just check file exists
     			true); // boolean silent);
-    	if (num_slices >= 0) {
+/*    	if (num_slices >= 0) {
     		return true;
     	}
     	num_slices = restoreDSI(
     			DSI_SUFFIXES[INDEX_INTER], // String suffix, // "-DSI_COMBO", "-DSI_MAIN" (DSI_COMBO_SUFFIX, DSI_MAIN_SUFFIX)
     			null, // double [][] dsi, // if null - just check file exists
-    			true); // boolean silent);
+    			true); // boolean silent); */
     	return num_slices >= 0;
     }
 

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

@@ -43,8 +43,8 @@ public class VegetationLMA {
 	public static final int TVAO_VEGETATION =       1;
 	public static final int TVAO_ALPHA =            2;
 	public static final int TVAO_ELEVATION =        3;
-	public static final int TVAO_TERR_ELEV =        4;
-	public static final int TVAO_TERR_ELEV_PIX =    5;
+	public static final int TVAO_TERR_ELEV =        4; // common for all the tile
+	public static final int TVAO_TERR_ELEV_PIX =    5; // per-pixel terrain elevation
 	public static final int TVAO_SCENE_OFFSET =     6;
 	public static final int TVAO_TYPES =            TVAO_SCENE_OFFSET + 1;
 	
@@ -439,7 +439,7 @@ public class VegetationLMA {
 		return;
 	}
 	
-	private static double [][][] getScalesXY(
+	public static double [][][] getScalesXY(
 			final double [][][] scales_mag_dir) {
 		final int num_scenes = scales_mag_dir.length;
 		final int num_pixels = scales_mag_dir[0].length;

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

@@ -92,6 +92,14 @@ public class VegetationModel {
 	public String        src_dir = null;
 	public String        src_title = null;
 
+	public String [] getSceneNames() {
+		return scene_names;
+	}
+	
+	public double [][] getTerrainScenesRendered(){
+		return terrain_scenes_render;
+	}
+	
 	
 	public double [][] tva;
 	int                step_restore;
@@ -1481,7 +1489,7 @@ public class VegetationModel {
 		
 		
 //		boolean  
-		tile_woi =                    clt_parameters.imp.terr_tile_woi;            // scan woi_enclosing, false - run a single woi_last
+		tile_woi =                    clt_parameters.imp.terr_tile_woi || combine_segments; // 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

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

@@ -98,7 +98,7 @@ public class VegetationSegment {
 		int out_length = out_woi.width*out_woi.height;
 		int accum_indx = segments.length;
 		String [] top_titles = {"terrain","vegetation","alpha","elevation","terrain_elevation","confidence"};
-		double [][][] preview_data = new double [top_titles.length][accum_indx+1][out_length];
+		double [][][] preview_data = new double [top_titles.length][accum_indx+1][out_length]; // Java heap space
 		String [] titles = new String[accum_indx+1];
 		for (int ns = 0; ns < segments.length; ns++) {
 			Rectangle woi =     segments[ns].woi; // for confidence and limits for terrain