Refactoring, bug fixing

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

@@ -5802,9 +5802,13 @@ public class Eyesis_Correction implements PlugIn, ActionListener {
 		} else if (label.equals("Process Merged")) {
 			OrangeTest.processMerged();			
 		} else if (label.equals("Vegetation LMA")) {
-			VegetationModel.testVegetationLMA(false); //boolean combine_segments);			
+			VegetationModel.testVegetationLMA(
+					CLT_PARAMETERS, //CLTParameters    clt_parameters,
+					false); //boolean combine_segments);			
 		} else if (label.equals("Combine LMA Segments")) {
-			VegetationModel.testVegetationLMA(true); //boolean combine_segments);			
+			VegetationModel.testVegetationLMA(
+					CLT_PARAMETERS, //CLTParameters    clt_parameters,
+					true); //boolean combine_segments);			
 		}
 		//
 	}

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

@@ -5687,12 +5687,18 @@ public class OpticalFlow {
 		// generates 3-d modes, colors, stereos, tiffs/videos
 		
 		// Testing vegetation, for debugging supposing that terrain layer is already set in *-INTER-INTRA-LMA.tiff - normally it is only set during 3d model generation
+		// Moved to the very end, after 3D
 		boolean test_vegetation = true;
+		/*
 		if (test_vegetation) { // limit start of the quadCLTs by reading start/end from the reference scene
+			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(
 					clt_parameters,                // CLTParameters  clt_parameters,
-					quadCLTs,       // QuadCLT []     quadCLTs,
-					ref_index,      // int            ref_index,
+					quadCLT_tail,                  // QuadCLT []     quadCLTs,
+					ref_index-earliest_scene,      // int            ref_index,
 					debugLevel);                   // int debugLevel)
 			if (videos != null) {
 				videos[0] = new String[0];
@@ -5700,7 +5706,7 @@ public class OpticalFlow {
 			// temporarily - exiting now
 			return quadCLTs[ref_index].getX3dTopDirectory();
 		}
-		
+		*/
 		
 		
 		if (generate_mapped || reuse_video) { // modifies combo_dsn_final ?
@@ -6357,6 +6363,22 @@ public class OpticalFlow {
 			
 		}
 		
+//		boolean test_vegetation = true;
+		if (test_vegetation) { // limit start of the quadCLTs by reading start/end from the reference scene
+//			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(
+					clt_parameters,                // CLTParameters  clt_parameters,
+					quadCLT_tail,                  // QuadCLT []     quadCLTs,
+					ref_index-earliest_scene,      // int            ref_index,
+					debugLevel);                   // int debugLevel)
+			if (videos != null) {
+				videos[0] = new String[0];
+			}
+			// temporarily - exiting now
+		}
+		
 		if (export_images) {
 			if (combo_dsn_final == null) {
 				combo_dsn_final =quadCLTs[ref_index].restoreComboDSI(true); // also sets quadCLTs[ref_index].dsi and blue sky