refactoring

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

@@ -1512,7 +1512,7 @@ public class VegetationLMA {
 		for (int n = 0; n < 4; n++) {
 			for (int i = 0; (i < indices[n].length) && (i < par_index[n].length); i++) {
 				int indx = i;
-				if (n < 3) {
+				if (n < TVAO_SCENE_OFFSET) {
 					int w = i % woi.width;
 					int h = i / woi.width;
 					indx = (h + woi.y) * full.width + (w + woi.x);
@@ -1520,7 +1520,11 @@ public class VegetationLMA {
 				int pindx = par_index[n][indx];
 				indices[n][i] =  pindx;
 				if (pindx < 0) {
-					data[n][i] = tvao[n][indx];
+					if (n == TVAO_SCENE_OFFSET) {
+						data[n][i] = Double.NaN;
+					} else {
+						data[n][i] = tvao[n][indx];
+					}
 				} else {
 					data[n][i] = vector[pindx];
 				}
@@ -1644,9 +1648,17 @@ public class VegetationLMA {
 				}
 			}
 			// Trim data to actiual
-			int num_pars_scenes =           Integer.parseInt((String) imp_pars.getProperty("NUM_PARS_SCENES"));
-			double [] scene_offsets = new double [num_pars_scenes];
-			System.arraycopy(data[3], 0, scene_offsets, 0, num_pars_scenes);
+//			int num_pars_scenes =           Integer.parseInt((String) imp_pars.getProperty("NUM_PARS_SCENES"));
+//			double [] scene_offsets = new double [num_pars_scenes];
+			double [] scene_offsets = new double [num_scenes];
+			System.arraycopy(data[TVAO_SCENE_OFFSET], 0, scene_offsets, 0, scene_offsets.length);
+			// temporary patch, later they will be NaNs already - Already done !
+			for (int i = 0; i < scene_offsets.length; i++) {
+				if (indices[TVAO_SCENE_OFFSET][i] < 0) {
+					data[TVAO_SCENE_OFFSET][i] = Double.NaN;
+				}
+			}
+			
 			for (int n = 0; n < 3; n++) {
 				if (woi.width * woi.height < data[n].length ) {
 					double [] d = new double [woi.width * woi.height];
@@ -1655,8 +1667,6 @@ public class VegetationLMA {
 				}
 			}
 			data[3] = scene_offsets;
-			
-			
 		} else {
 			this.woi = woi;
 			diff_offsets =              Boolean.parseBoolean((String) imp_pars.getProperty("DIFF_OFFSETS"));
@@ -2030,7 +2040,7 @@ public class VegetationLMA {
 					woi); // Rectangle file_woi)
 			segments[n] = new VegetationSegment(
 					woi, // Rectangle   woi,
-					tvao[3], // datadouble []   scene_offsets,
+					tvao[TVAO_SCENE_OFFSET], // datadouble []   scene_offsets,
 					new double [][] {tvao[0],tvao[1],tvao[2]}); // double [][]  tva) {} {}
 		}
 		// sort in line-scan order

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

@@ -8,7 +8,7 @@ public class VegetationSegment {
 	public double [][] tva;
 	public VegetationSegment(
 			Rectangle   woi,
-			double []   scene_offsets,
+			double []   scene_offsets, // has NaNs
 			double [][]  tva) {
 		this.woi = woi;
 		this.scene_offsets = scene_offsets;