debugging, started refreshing ground plane

src/main/java/com/elphel/imagej/tileprocessor/Correlation2d.java

@@ -2632,7 +2632,7 @@ public class Correlation2d {
 		int imax= 0;
 		for (int i= 1; i < data.length;i++) {
 			if (Double.isNaN(data[i])) {
-				System.out.println("NaN in getMaxXYCmEig()");
+				System.out.println("NaN in getMaxXYCmEig() 1");
 				return null;
 			}
 			if (data[i] > data[imax]) {
@@ -2765,7 +2765,7 @@ public class Correlation2d {
 		int imax= 0;
 		for (int i= 1; i < data.length;i++) {
 			if (Double.isNaN(data[i])) {
-				System.out.println("NaN in getMaxXYCmEig()");
+				System.out.println("NaN in getMaxXYCmEig() 2");
 				return null;
 			}
 			if (data[i] > data[imax]) {

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

@@ -314,12 +314,19 @@ public class Interscene {
 			// set pointers
 			String cent_ts = quadCLTs[cent_index].getImageName();
 			quadCLTs[latest_scene2].setRefPointer(cent_ts); // write pointer to center scene to reference scene
+			quadCLTs[latest_scene2].saveInterProperties( // save properties for interscene processing (extrinsics, ers, ...)  // null pointer
+					null, // String path,             // full name with extension or w/o path to use x3d directory
+					debugLevel+1);
+
    			if (latest_scene2 != ref_index) {
 				System.out.println("*** setInitialOrientationsCenterIms(): assumed that latest_scene2("+latest_scene2+
 						") == ref_index ("+ref_index+"), but they are different. Decide what to do - see EstimateSceneRange.getPrescanRange(). ***");
 				System.out.println("The problem is that the center index will have pointers to the first and last, but the last will not have a pointrer back.");
 
 				quadCLTs[ref_index].setRefPointer(cent_ts); // write pointer to center scene to reference scene
+				quadCLTs[ref_index].saveInterProperties( // save properties for interscene processing (extrinsics, ers, ...)  // null pointer
+						null, // String path,             // full name with extension or w/o path to use x3d directory
+						debugLevel+1);
 			}
 			// Here we a
 			quadCLTs[cent_index].setFirstLastPointers(quadCLTs[earliest_scene2],quadCLTs[latest_scene2]);// set first/last to center scene

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

@@ -4972,7 +4972,7 @@ public class OpticalFlow {
 		
     	
 		
-		QuadCLT center_CLT = null;
+		QuadCLT center_CLT = null; // used for CUAS - rotation center
 		// See if build_ref_dsi is needed
 		if (!build_ref_dsi) {
 			// try reading full
@@ -5144,7 +5144,8 @@ public class OpticalFlow {
 									false, // boolean all_properties,//				null, // Properties properties,   // if null - will only save extrinsics)
 									debugLevel);
 							first_last_index = try_ref_scene.getFirstLastIndex(quadCLTs);
-							if (first_last_index == null) {
+							
+							if (first_last_index == null) { // [-1,-1] - OK
 								//							if ((first_last_index == null) ||(first_last_index[0] < 0) || (first_last_index[1] < 0)) {
 								force_initial_orientations = true;
 							}
@@ -5319,11 +5320,11 @@ public class OpticalFlow {
 				}
 			} else {
 
-				if (center_reference) {
+				if (center_reference) { // check if initial orientation is needed. last_index may be the actual "center" as provided by caller
 					int center_index =quadCLTs[last_index].getReferenceIndex(null);
 					if (center_index == -1) {
 						force_initial_orientations = true;
-					} else {
+					} else { // always -2
 						QuadCLT try_ref_scene = (QuadCLT) quadCLT_main.spawnNoModelQuadCLT( // will conditionImageSet
 								quadCLTs[last_index].getReferenceTimestamp(), // set_channels[last_index].set_name,
 								clt_parameters,
@@ -5497,7 +5498,7 @@ public class OpticalFlow {
 					} else {
 						System.out.println ("1.no update, spawning only over null");
 					}
-					//				if (ref_index)
+					//	Improve - only read from the earliest to the last
 					for (int scene_index =  last_index; scene_index >= earliest_scene ; scene_index--) {
 						if (scene_index != ref_index) {
 							// to include ref scene photometric calibration
@@ -6401,7 +6402,7 @@ public class OpticalFlow {
 						debugLevel); // int debugLevel)
 		    }
 		}
-		boolean test_ground = false; // true;
+		boolean test_ground = true; // false; // true;
 		if (test_ground) {
 			final boolean   use_lma =         clt_parameters.gmap_use_lma ; // true;  // ;
 			final double    discard_low =     clt_parameters.gmap_discard_low ; //0.01;  // fraction of all pixels

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

@@ -1818,6 +1818,10 @@ public class QuadCLTCPU {
      * @return index of the reference scene in the provided scenes array or negative on error
      */
     public int getReferenceIndex(QuadCLTCPU [] scenes) {
+    	// saving existing data by providing a self-reference (is it needed)
+ //   	if ((timestamp_reference == null) && (timestamp_first != null) && (timestamp_last != null)) {
+ //   		timestamp_reference = getImageName();
+ //   	}
     	if (timestamp_reference != null) {
     		if (scenes != null) {
     			for (int i = 0; i < scenes.length; i++) if (scenes[i] != null){
@@ -2613,7 +2617,7 @@ public class QuadCLTCPU {
     }
     
     
-     public double [][] getGroundNoIms(
+     public double [][] getGroundNoIms( // return to_ground_xyzatr;
     		CLTParameters clt_parameters,
     		boolean       use_lma,
     		boolean       use_parallel_proj,
@@ -2624,7 +2628,7 @@ public class QuadCLTCPU {
     		double        discard_rdisp,  // discard above/below this fraction of average height
     		double        pix_size,       // in meters
     		int           max_image_width,// increase pixel size as a power of 2 until image fits
-    		double []     x0y0,        // initialize to double[2] to return width, height
+    		double []     x0y0,           // initialize to double[2] to return width, height
     		int []        whs,            // initialize to int[3] to return {width, height, scale reduction}
     		int debug_level
     		) {
@@ -2833,7 +2837,7 @@ public class QuadCLTCPU {
     	return to_ground_xyzatr; // from the camera coordinates to in-plane coordiantes
     }
 
-    public double [][] getGroundIms(
+    public double [][] getGroundIms( // return to_ground_xyzatr;
     		CLTParameters clt_parameters,
     		boolean       use_lma,
     		boolean       use_parallel_proj,    		
@@ -2912,7 +2916,7 @@ public class QuadCLTCPU {
     	double    min_disparity = 0.2;
     	double    max_disparity = 15;
     	double [][] xy_range = new double[3][]; 
-    	double agl = getAGL(
+    	double agl = getAGL( // not used for the parallel projection
     			dls[use_lma?1:0].clone(), // double [] ref_disparity,
     			dls[2],                   // double [] ref_strength,
     			scene_abs_atr_enu,        // double [] reference_atr,