combining processing, minor debugging and cleaning up

src/main/java/com/elphel/imagej/cameras/EyesisCorrectionParameters.java

@@ -138,8 +138,9 @@ public class EyesisCorrectionParameters {
     	public String x3dSubdirSuffix=         "";
 
   		// CLT 3d batch parameters
-    	public boolean process_main_sources = false;
-    	public boolean process_aux_sources =  true;
+    	public boolean process_main_sources = false; // not yet used
+    	public boolean process_aux_sources =  true; // not yet used
+    	public int     kml_sensors=                0xffffffff; // all sensors 
     	
     	public int     rig_batch_adjust_main = 0;
     	public int     rig_batch_adjust_aux =  0;
@@ -305,6 +306,7 @@ public class EyesisCorrectionParameters {
   			cp.process_main_sources=    this.process_main_sources;
   			cp.process_aux_sources=     this.process_aux_sources;
   			
+  			cp.kml_sensors=             this.kml_sensors;
   			cp.rig_batch_adjust_main=   this.rig_batch_adjust_main;
   			cp.rig_batch_adjust_aux=	this.rig_batch_adjust_aux;
   			cp.rig_batch_adjust_rig=	this.rig_batch_adjust_rig;
@@ -508,6 +510,8 @@ public class EyesisCorrectionParameters {
     		properties.setProperty(prefix+"process_main_sources",  this.process_main_sources+"");
     		properties.setProperty(prefix+"process_aux_sources",   this.process_aux_sources+"");
 
+    		properties.setProperty(prefix+"kml_sensors",           this.kml_sensors+"");
+
     		properties.setProperty(prefix+"rig_batch_adjust_main", this.rig_batch_adjust_main+"");
     		properties.setProperty(prefix+"rig_batch_adjust_aux",  this.rig_batch_adjust_aux+"");
     		properties.setProperty(prefix+"rig_batch_adjust_rig",  this.rig_batch_adjust_rig+"");
@@ -693,6 +697,8 @@ public class EyesisCorrectionParameters {
 			if (properties.getProperty(prefix+"process_main_sources")!= null) this.process_main_sources=Boolean.parseBoolean(properties.getProperty(prefix+"process_main_sources"));
 			if (properties.getProperty(prefix+"process_aux_sources")!= null)  this.process_aux_sources=Boolean.parseBoolean(properties.getProperty(prefix+"process_aux_sources"));
 
+  		    if (properties.getProperty(prefix+"kml_sensors")!=null) this.kml_sensors=Integer.parseInt(properties.getProperty(prefix+"kml_sensors"));
+  		    
   		    if (properties.getProperty(prefix+"rig_batch_adjust_main")!=null) this.rig_batch_adjust_main=Integer.parseInt(properties.getProperty(prefix+"rig_batch_adjust_main"));
   		    if (properties.getProperty(prefix+"rig_batch_adjust_aux")!=null)  this.rig_batch_adjust_aux=Integer.parseInt(properties.getProperty(prefix+"rig_batch_adjust_aux"));
   		    if (properties.getProperty(prefix+"rig_batch_adjust_rig")!=null)  this.rig_batch_adjust_rig=Integer.parseInt(properties.getProperty(prefix+"rig_batch_adjust_rig"));
@@ -1086,6 +1092,8 @@ public class EyesisCorrectionParameters {
     		gd.addCheckbox    ("Process main camera source images (false - ignore)",   this.process_main_sources); // 20c
     		gd.addCheckbox    ("Process AUX camera source images (false - ignore)",    this.process_aux_sources); // 20d
   			
+			gd.addNumericField("Bitmask of channels were to look for GPS data",                            this.kml_sensors,  0);
+
 			gd.addNumericField("Repeat main camera field adjustment (early, before rig)",                  this.rig_batch_adjust_main,  0);
 			gd.addNumericField("Repeat aux camera field adjustment  (early, before rig)",                  this.rig_batch_adjust_aux,   0);
 			gd.addNumericField("Repeat 2-quad camera rig field adjustment  (early, before late main/aux)", this.rig_batch_adjust_rig,   0);
@@ -1226,6 +1234,8 @@ public class EyesisCorrectionParameters {
     		this.process_main_sources=              gd.getNextBoolean(); // 20c
     		this.process_aux_sources=               gd.getNextBoolean(); // 20d
 
+    		this.kml_sensors =                (int) gd.getNextNumber();
+
     		this.rig_batch_adjust_main =      (int) gd.getNextNumber();
 			this.rig_batch_adjust_aux =       (int) gd.getNextNumber();
 			this.rig_batch_adjust_rig =       (int) gd.getNextNumber();
@@ -1289,7 +1299,7 @@ public class EyesisCorrectionParameters {
     		return (this.sourcePaths!=null)?this.sourcePaths:empty;
     	}
 
-    	public int getChannelFromTiff(String path, String suffix){
+    	public static int getChannelFromTiff(String path, String suffix){
     		int indexSuffix=path.length()-suffix.length();
     		int indexLastDash=indexSuffix-1; // in jp4 it will be underscore, not dash? Or should we change that?
     		while ((indexLastDash>0) &&

src/main/java/com/elphel/imagej/gpu/GpuQuad.java

@@ -838,6 +838,10 @@ public class GpuQuad{ // quad camera description
 		}
 		float [] fbayer = new float [bayer_data[0][0].length];
 		for (int ncam = 0; ncam < bayer_data.length; ncam++) {
+			if (bayer_data[ncam][0] == null) {
+				System.out.println("BUG!! bayer_data["+ncam+"][0] == null");
+				continue;
+			}
 			for (int i = 0; i <  bayer_data[ncam][0].length; i++) {
 				fbayer[i] = (float) (bayer_data[ncam][0][i]); //  + bayer_data[ncam][1][i] + bayer_data[ncam][2][i]);
 				for (int j = 1; j < bayer_data[ncam].length; j++) {

src/main/java/com/elphel/imagej/readers/ImagejJp4Tiff.java

@@ -649,19 +649,20 @@ public class ImagejJp4Tiff {
 			return center;
 		}
 		System.out.println ("Discontinuities remain, will fix by clusters");
-		fixByClusters(
+		boolean OK = fixByClusters(
 				width,
 				height,
 				FIXCH6_BIT,         // int    bad_bit,
 				idata,              // int [] data)
 				(dbg_img != null)); // boolean debug)
+		System.out.println ("FixByClusters -> "+OK);
 		for (int i = 0; i < idata.length; i++) {
 			pixels[i+640] = idata[i];
 		}
 		return center;
 	}
 
-	public boolean fixByClusters(
+	public static boolean fixByClusters(
 			int    width,
 			int    height,
 			int    bad_bit,
@@ -733,6 +734,9 @@ public class ImagejJp4Tiff {
 				}
 				if (ndir == 1) {
 					indx++;
+					if (indx >= clusters.length) { // start from the beginning
+						indx -= clusters.length;
+					}
 				}
 			}
 			if (ntry >= (2*clusters.length)) {

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

@@ -2467,6 +2467,9 @@ public class ImageDtt extends ImageDttCPU {
 			final boolean             use_partial,     // find motion vectors for individual pairs, false - for sum only
 			final double              centroid_radius, // 0 - use all tile, >0 - cosine window around local max
 			final int                 n_recenter,      // when cosine window, re-center window this many times
+			final double              td_weight,    // mix correlations accumulated in TD with 
+			final double              pd_weight,    // correlations (post) accumulated in PD
+			final boolean             td_nopd_only, // only use TD accumulated data if no safe PD is available for the tile.
 			final double              min_str,         //  = 0.25;
 			final double              min_str_sum,     // = 0.8; // 5;
 			final int                 min_neibs,       //   2;	   // minimal number of strong neighbors (> min_str)
@@ -2658,19 +2661,52 @@ public class ImageDtt extends ImageDttCPU {
 							}
 						}
 						// now calculate only for composite
-						double [] mv = Correlation2d.getMaxXYCm(
+						double [] mv_pd = new double [3];
+						double [] mv_td = new double [3];
+						if (pd_weight > 0.0) {
+							mv_pd = Correlation2d.getMaxXYCm(
 								corrs[corrs.length-1], // double [] data,
 								corr_size,             // int       data_width,      //  = 2 * transform_size - 1;
 								centroid_radius,       // double    radius, // 0 - all same weight, > 0 cosine(PI/2*sqrt(dx^2+dy^2)/rad)
 								n_recenter,            // int       refine, //  re-center window around new maximum. 0 -no refines (single-pass)
 								false);                // boolean   debug)
-						if (mv != null) {
-							if (mv[2] < min_str) {
-								mv = null;
+							if (mv_pd != null) {
+								if (mv_pd[2] < min_str) {
+									mv_pd = null;
+								} else {
+									mv_pd[2] -= min_str;
+								}
+							}
+						}
+						if (td_weight > 0.0) {
+							mv_td = Correlation2d.getMaxXYCm(
+								corrs[corrs.length-2], // double [] data,
+								corr_size,             // int       data_width,      //  = 2 * transform_size - 1;
+								centroid_radius,       // double    radius, // 0 - all same weight, > 0 cosine(PI/2*sqrt(dx^2+dy^2)/rad)
+								n_recenter,            // int       refine, //  re-center window around new maximum. 0 -no refines (single-pass)
+								false);                // boolean   debug)
+							if (mv_td != null) {
+								if (mv_td[2] < min_str_sum) {
+									mv_td = null;
 								} else {
-								mv[2] -= min_str;
+									mv_td[2] -= min_str_sum;
 								}
 							}
+						}
+						if ((mv_td != null) || (mv_pd != null)) {
+							double [] mv = new double[3];
+							if (mv_pd != null) {
+								mv = mv_pd;
+								mv[2] *= pd_weight;
+								if ((mv_td != null) && !td_nopd_only) {  // mix
+									mv[0] = (mv[0] * pd_weight + mv_td[0] * td_weight)/ (pd_weight + td_weight);
+									mv[1] = (mv[1] * pd_weight + mv_td[1] * td_weight)/ (pd_weight + td_weight);
+									mv[2] += mv_td[2] * td_weight;
+								} // mix
+							} else { // (mv_pd == null) &&  (mv_td != null)  below
+								mv = mv_td;
+								mv[2] *= td_weight;
+							}
 							if (mv != null) {
 								if (pXpYD == null) {
 									coord_motion[0][nTile] = mv;
@@ -2683,6 +2719,7 @@ public class ImageDtt extends ImageDttCPU {
 							}
 						}
 					}
+				}
 			};
 		}
 		startAndJoin(threads);

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

@@ -620,7 +620,7 @@ public class IntersceneLma {
 		pure_weight = s_pure/full_weight;
 		final double s = 1.0/asum_weight.sum();
 		if (Double.isNaN(s)) {
-			System.out.println("normalizeWeights(): s == NaN");
+			System.out.println("normalizeWeights(): s == NaN : 1");
 		}
 		ai.set(0);
 		for (int ithread = 0; ithread < threads.length; ithread++) {
@@ -673,7 +673,7 @@ public class IntersceneLma {
 		pure_weight = sum_weight_pure/full_weight;
 		final double s = 1.0/full_weight;
 		if (Double.isNaN(s)) {
-			System.out.println("normalizeWeights(): s == NaN");
+			System.out.println("normalizeWeights(): s == NaN  : 2");
 		}
 		ai.set(0);
 		for (int ithread = 0; ithread < threads.length; ithread++) {

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

@@ -50,6 +50,12 @@ public class IntersceneMatchParameters {
 	public  double  centroid_radius =               4.0;   // 
 	public  int     n_recenter =                    2;     // when cosine window, re-center window this many times
 	// filtering motion vectors
+	// TD accumulation of the inter-scene correlations  demonstrated artifacts (horizontally offset by 8 pixels
+	// false maximum that is sharper than the real one. Still not understood - maybe float precision related. 
+	public  double  td_weight =                     0.5;   // mix correlations accumulated in TD with 
+	public  double  pd_weight =                     0.5;   // correlations (post) accumulated in PD
+	public  boolean td_nopd_only =                  true;  // only use TD accumulated data if no safe PD is available for the tile.
+
 	public  double  min_str =                       0.25;  // minimal correlation strength for all but TD-accumulated layer
 	public  double  min_str_sum =                   0.8;	  // minimal correlation strength for TD-accumulated layer
 	public  int     min_neibs =                     2;	   // minimal number of strong neighbors (> min_str)
@@ -132,6 +138,14 @@ public class IntersceneMatchParameters {
 		gd.addNumericField("Refine centroids",                       this.n_recenter, 0,5,"",
 				"Repeat centroids after moving the window center to the new centroid location this many times (0 - calculate once)");
 
+		gd.addMessage  ("Mixing TD and PD accumulation of 2d correlations");
+		gd.addNumericField("TD-accumulated weight",                  this.td_weight, 5,7,"",
+				"Mix argmax from TD-accumulated correlation.");
+		gd.addNumericField("PD-accumulated weight",                  this.pd_weight, 5,7,"",
+				"Mix argmax from PD-accumulated correlation.");
+		gd.addCheckbox ("TD when no PD only",                        this.td_nopd_only,
+				"Use argmax from TD only if PD data is not available for this tile.");
+		
 		gd.addMessage  ("Filtering motion vectors");
 		gd.addNumericField("Minimal correlation strength (non-sum)", this.min_str, 5,7,"",
 				"Minimal correlation strength for individual correlation and for pixel-domain averaged one. Weeker tiles results are removed.");
@@ -223,6 +237,11 @@ public class IntersceneMatchParameters {
 		this.run_poly =                 gd.getNextBoolean();
 		this.centroid_radius =          gd.getNextNumber();
 		this.n_recenter =         (int) gd.getNextNumber();
+
+		this.td_weight =                gd.getNextNumber();
+		this.pd_weight =                gd.getNextNumber();
+		this.td_nopd_only =             gd.getNextBoolean();
+		
 		this.min_str =                  gd.getNextNumber();
 		this.min_str_sum =              gd.getNextNumber();
 		this.min_neibs =          (int) gd.getNextNumber();
@@ -275,6 +294,11 @@ public class IntersceneMatchParameters {
 		properties.setProperty(prefix+"run_poly",             this.run_poly+"");            // boolean
 		properties.setProperty(prefix+"centroid_radius",      this.centroid_radius+"");     // double
 		properties.setProperty(prefix+"n_recenter",           this.n_recenter+"");          // int
+		
+		properties.setProperty(prefix+"td_weight",            this.td_weight+"");           // double
+		properties.setProperty(prefix+"pd_weight",            this.pd_weight+"");           // double
+		properties.setProperty(prefix+"td_nopd_only",         this.td_nopd_only+"");        // boolean
+		
 		properties.setProperty(prefix+"min_str",              this.min_str+"");             // double
 		properties.setProperty(prefix+"min_str_sum",          this.min_str_sum+"");         // double
 		properties.setProperty(prefix+"min_neibs",            this.min_neibs+"");           // int
@@ -323,6 +347,11 @@ public class IntersceneMatchParameters {
 		if (properties.getProperty(prefix+"run_poly")!=null)             this.run_poly=Boolean.parseBoolean(properties.getProperty(prefix+"run_poly"));
 		if (properties.getProperty(prefix+"centroid_radius")!=null)      this.centroid_radius=Double.parseDouble(properties.getProperty(prefix+"centroid_radius"));
 		if (properties.getProperty(prefix+"n_recenter")!=null)           this.n_recenter=Integer.parseInt(properties.getProperty(prefix+"n_recenter"));
+		
+		if (properties.getProperty(prefix+"td_weight")!=null)            this.td_weight=Double.parseDouble(properties.getProperty(prefix+"td_weight"));
+		if (properties.getProperty(prefix+"pd_weight")!=null)            this.pd_weight=Double.parseDouble(properties.getProperty(prefix+"pd_weight"));
+		if (properties.getProperty(prefix+"td_nopd_only")!=null)         this.td_nopd_only=Boolean.parseBoolean(properties.getProperty(prefix+"td_nopd_only"));
+		
 		if (properties.getProperty(prefix+"min_str")!=null)              this.min_str=Double.parseDouble(properties.getProperty(prefix+"min_str"));
 		if (properties.getProperty(prefix+"min_str_sum")!=null)          this.min_str_sum=Double.parseDouble(properties.getProperty(prefix+"min_str_sum"));
 		if (properties.getProperty(prefix+"min_neibs")!=null)            this.min_neibs=Integer.parseInt(properties.getProperty(prefix+"min_neibs"));
@@ -373,6 +402,11 @@ public class IntersceneMatchParameters {
 		imp.run_poly              = this.run_poly;
 		imp.centroid_radius       = this.centroid_radius;
 		imp.n_recenter            = this.n_recenter;
+		
+		imp.td_weight             = this.td_weight;
+		imp.pd_weight             = this.pd_weight;
+		imp.td_nopd_only          = this.td_nopd_only;
+
 		imp.min_str               = this.min_str;
 		imp.min_str_sum           = this.min_str_sum;
 		imp.min_neibs             = this.min_neibs;

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

@@ -3907,7 +3907,7 @@ public class OpticalFlow {
 					null, // QuadCLT quadCLT_aux,
 					clt_parameters, // EyesisCorrectionParameters.DCTParameters dct_parameters,
 					true, // boolean                                  skip_existing,
-					false, // boolean                                  search_KML,
+					true, // false, // boolean                                  search_KML,
 					debugLevel);
 			quadCLTs[ref_index] = (QuadCLT) quadCLT_main.spawnNoModelQuadCLT( // will conditionImageSet
 					set_channels[ref_index].set_name,
@@ -3971,7 +3971,7 @@ public class OpticalFlow {
 						null, // QuadCLT quadCLT_aux,
 						clt_parameters, // EyesisCorrectionParameters.DCTParameters dct_parameters,
 						true, // boolean                                  skip_existing,					
-						false, // boolean                                  search_KML,
+						true, // false, // boolean                                  search_KML,
 						debugLevel);
 			} // split cycles to remove output clutter
 		} // if (build_ref_dsi) {
@@ -4061,6 +4061,9 @@ public class OpticalFlow {
 							quadCLTs[ref_index].getImageName() + "/" + scene_QuadClt.getImageName()+
 							" Done. RMS="+lma_rms[0]+", maximal so far was "+maximal_series_rms);
 				}
+				if (scene_index == 25) {
+					System.out.println("scene_index == 25");
+				}
 				/*
 			if (delete_scene_asap) {
 				scenes[i+1] = null;
@@ -9682,10 +9685,11 @@ public double[][] correlateIntersceneDebug( // only uses GPU and quad
 		if (ref_scene.getGPU() != null) {
 			ref_scene.getGPU().setGpu_debug_level(debug_level - 4); // monitor GPU ops >=-1
 		}
-		final double disparity_corr = 0.00; // (z_correction == 0) ? 0.0 : geometryCorrection.getDisparityFromZ(1.0/z_correction);
-		double [][] dsrbg_ref= ref_scene.getDSRBG();
+		final double disparity_corr = 0.0; // (z_correction == 0) ? 0.0 : geometryCorrection.getDisparityFromZ(1.0/z_correction);
+//		double [][] dsrbg_ref= ref_scene.getDSRBG();
+		double [][] dls= ref_scene.getDLS();
 		double [][] ref_pXpYD = transformToScenePxPyD( // full size - [tilesX*tilesY], some nulls
-				dsrbg_ref[0],  // final double []   disparity_ref, // invalid tiles - NaN in disparity (maybe it should not be masked by margins?)
+				dls[0],  // final double []   disparity_ref, // invalid tiles - NaN in disparity (maybe it should not be masked by margins?)
 				ZERO3,         // final double []   scene_xyz, // camera center in world coordinates
 				ZERO3,         // final double []   scene_atr, // camera orientation relative to world frame
 				ref_scene,     // final QuadCLT     scene_QuadClt,
@@ -9713,7 +9717,7 @@ public double[][] correlateIntersceneDebug( // only uses GPU and quad
 		//setupERS() will be inside transformToScenePxPyD()
 		 */
 		double [][] scene_pXpYD = transformToScenePxPyD( // will be null for disparity == NaN, total size - tilesX*tilesY
-				dsrbg_ref[0], // final double []   disparity_ref, // invalid tiles - NaN in disparity (maybe it should not be masked by margins?)
+				dls[0], // final double []   disparity_ref, // invalid tiles - NaN in disparity (maybe it should not be masked by margins?)
 				scene_xyz,    // final double []   scene_xyz, // camera center in world coordinates
 				scene_atr,    // final double []   scene_atr, // camera orientation relative to world frame
 				scene,        // final QuadCLT     scene_QuadClt,
@@ -9804,6 +9808,9 @@ public double[][] correlateIntersceneDebug( // only uses GPU and quad
 					clt_parameters.imp.use_partial,    // final boolean             use_partial,     // find motion vectors for individual pairs, false - for sum only
 					clt_parameters.imp.centroid_radius,// final double              centroid_radius, // 0 - use all tile, >0 - cosine window around local max
 					clt_parameters.imp.n_recenter,     // final int                 n_recenter,      // when cosine window, re-center window this many times
+					clt_parameters.imp.td_weight,      // final double  td_weight,    // mix correlations accumulated in TD with 
+					clt_parameters.imp.pd_weight,      // final double  pd_weight,    // correlations (post) accumulated in PD
+					clt_parameters.imp.td_nopd_only,   // final boolean td_nopd_only, // only use TD accumulated data if no safe PD is available for the tile.
 					clt_parameters.imp.min_str,        // final double              min_str,         //  = 0.25;
 					clt_parameters.imp.min_str_sum,    // final double              min_str_sum,     // = 0.8; // 5;
 					clt_parameters.imp.min_neibs,      // final int                 min_neibs,       //   2;	   // minimal number of strong neighbors (> min_str)

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

@@ -14214,9 +14214,42 @@ public class QuadCLTCPU {
 			  if (imp.getProperty("ALTITUDE")  != null) gps_lla[2] =Double.parseDouble((String) imp.getProperty("ALTITUDE"));
 			  return true;
 		  }
+		  if (imp.getProperty("STD_GPS_Latitude")  != null) {
+			  gps_lla = new double[3];
+			  for (int i = 0; i < 3; i++) {
+				  gps_lla[i] = Double.NaN;
+			  }
+			  if (imp.getProperty("STD_GPS_Latitude")  != null) gps_lla[0] =parseDegreeMinSec((String) imp.getProperty("STD_GPS_Latitude"));
+			  if (imp.getProperty("STD_GPS_Longitude")  != null) gps_lla[1] =parseDegreeMinSec((String) imp.getProperty("STD_GPS_Longitude"));
+			  if (imp.getProperty("STD_GPS_Altitude")  != null) gps_lla[2] =parseStringToEndString((String) imp.getProperty("STD_GPS_Altitude"),"m");
+			  return true;
+		  }
 		  return false; // not used in lwir
 	  }
 
+	  static double parseDegreeMinSec(String s) {
+		  int indx_degree = s.indexOf("\u00B0");
+		  int indx_minute  = s.indexOf("\u2032");
+		  if (indx_minute < 0) {
+			  indx_minute  = s.indexOf("'");
+		  }
+		  int indx_second  = s.indexOf("\u2033");
+		  if (indx_second < 0) {
+			  indx_second  = s.indexOf("\"");
+		  }
+		  double degrees =  Double.parseDouble(s.substring(0,indx_degree));
+		  double min_sec = Double.parseDouble(s.substring(indx_degree+1, indx_minute))/60.0 +
+				  Double.parseDouble(s.substring(indx_minute+1, indx_second))/3600.0;
+		  if (degrees < 0) {
+			  return degrees - min_sec;
+		  } else {
+			  return degrees + min_sec;
+		  }
+	  }
+	  static double parseStringToEndString(String s, String end_string) {
+		  int indx_end = s.indexOf(end_string);
+		  return Double.parseDouble(s.substring(0, indx_end));
+	  }
 
 	  public boolean writeKml( // USED in lwir
 			  String image_name,
@@ -14227,12 +14260,18 @@ public class QuadCLTCPU {
 		  }
 		  String [] sourceFiles_main=correctionsParameters.getSourcePaths();
 		  SetChannels [] set_channels = setChannels(image_name,debugLevel); // only for specified image timestamp
+		  int kml_sensors = correctionsParameters.kml_sensors;	
 
 		  ArrayList<String> path_list = new ArrayList<String>();
 		  for (int i = 0; i < set_channels.length; i++) {
-			  for (int fn:set_channels[i].file_number) {
-				  path_list.add(sourceFiles_main[fn]);
+			  for (int nchn = 0; nchn < set_channels[i].file_number.length; nchn++) {
+				  if ((kml_sensors & (1 << nchn)) != 0) {
+					  path_list.add(sourceFiles_main[set_channels[i].file_number[nchn]]);
+				  }
 			  }
+///			  for (int fn:set_channels[i].file_number) {
+///				  path_list.add(sourceFiles_main[fn]);
+///			  }
 		  }
 		  for (String fname:path_list) {
 			  System.out.println("writeKml(): "+fname);

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

@@ -3137,6 +3137,11 @@ if (debugLevel > -100) return true; // temporarily !
 				return;
 			}
 		}
+		if (search_KML && (set_channels_main !=null)) { // TODO: make it look in both MAIN and AUX. Look in only the same scene?
+			quadCLT_main.writeKml(
+					set_name,
+					debugLevel ); // also generated with x3d model
+		}
 		for (String fname:path_list) {
 			if (fname.contains(set_name)) { // only files containing set name // TODO:improve
 				File file = new File(fname);
@@ -3152,11 +3157,6 @@ if (debugLevel > -100) return true; // temporarily !
 				}
 			}
 		}
-		if (search_KML && (set_channels_main !=null)) { // TODO: make it look in both MAIN and AUX. Look in only the same scene?
-			quadCLT_main.writeKml(
-					set_name,
-					debugLevel ); // also generated with x3d model
-		}
 		System.out.println("jp4_copy_path = "+jp4_copy_path);
 		//		  System.out.println("Do something useful here");
 	}

src/main/java/com/elphel/imagej/x3d/export/X3dOutput.java

@@ -284,6 +284,7 @@ public class X3dOutput {
 		addTextElement(kmlDoc, el_Camera, "heading",   String.format("%f",0.0));
 		addTextElement(kmlDoc, el_Camera, "tilt",      String.format("%f",90.0));
 		addTextElement(kmlDoc, el_Camera, "roll",      String.format("%f",0.0));
+		addTextElement(kmlDoc, el_Camera, "altitudeMode", "clampToGround");
 		if (icon_path != null) {
 			Element el_Icon = addElement(kmlDoc, el_PhotoOverlay, "Icon");
 			addTextElement(kmlDoc, el_Icon, "href",  icon_path);
@@ -296,6 +297,7 @@ public class X3dOutput {
 		addTextElement(kmlDoc, el_OriginalData, "heading",   String.format("%f",0.0));
 		addTextElement(kmlDoc, el_OriginalData, "tilt",      String.format("%f",90.0));
 		addTextElement(kmlDoc, el_OriginalData, "roll",      String.format("%f",0.0));
+		addTextElement(kmlDoc, el_OriginalData, "altitudeMode", "clampToGround");
 
 		try {
 			// write the content into xml file