Debugging OrthoMultiLMA

src/main/java/com/elphel/imagej/orthomosaic/ComboMatch.java

@@ -157,6 +157,7 @@ public class ComboMatch {
 //		boolean show_map_stats =      false;      
 		boolean show_combo =          false; // true;
 		boolean create_overlaps =     false;
+		boolean create_map =          false;
 //		boolean show_combo_mask =     false; // generate image mas (where it is defined)_
 //		boolean use_alt =             false;
 //		boolean show_centers =        true;
@@ -231,6 +232,7 @@ public class ComboMatch {
 //		gd.addCheckbox    ("Show statistics for ortho images", show_map_stats, "Generate and show statistics for ortho maps.");
 		gd.addCheckbox    ("Show combo maps/stats",            show_combo, "Generate/save combo maps and stats.");
 		gd.addCheckbox    ("Create overlap pairs",             create_overlaps, "Create scene pairs overlaps.");
+		gd.addCheckbox    ("Create map",                       create_map, "Create combined map from pairwise matches.");
 //		gd.addCheckbox    ("Show combo image mask",            show_combo_mask, "Display combo binary image.");
 //		gd.addCheckbox    ("Show altitude combo image", use_alt, "Load and process altitude maps.");
 		gd.addNumericField("Remove fraction of worst matches",   frac_remove,  3,7,"",	"When fitting scenes remove this fraction of worst match.");
@@ -286,6 +288,7 @@ public class ComboMatch {
 		
 		show_combo =                gd.getNextBoolean();
 		create_overlaps =           gd.getNextBoolean();
+		create_map =                gd.getNextBoolean();
 		frac_remove =               gd.getNextNumber();
 		metric_error=               gd.getNextNumber();
 		if (use_marked_image ) { // will only be used if found and asked
@@ -768,6 +771,13 @@ public class ComboMatch {
     		} // final int debugLevel);
     	}
 
+		if (create_map) {
+			OrthoMultiLMA.buildOrthoMap(
+					clt_parameters,            // CLTParameters       clt_parameters,
+					maps_collection, // OrthoMapsCollection maps_collection
+					orthoMapsCollection_path); // String orthoMapsCollection_path
+			return true;
+		}
     	
 		if (create_overlaps) {
 			boolean ok =maps_collection.getIntersectedPairs(

src/main/java/com/elphel/imagej/orthomosaic/OrthoPairLMA.java

@@ -720,7 +720,7 @@ public class OrthoPairLMA {
 	}
 	
 	
-	private double [][] getWJtJlambda( // USED in lwir
+	private double [][] getWJtJlambda(
 			final double      lambda,
 			final double [][] jt)
 	{
@@ -766,7 +766,6 @@ public class OrthoPairLMA {
 			final double [][] jt, // should be null or initialized with [vector.length][]
 			final int         debug_level)
 	{
-//		final double [][] affine = {{vector[0],vector[1],vector[4]},{vector[2],vector[3],vector[5]}};
 		final double [] fx = new double [weights.length]; // weights.length]; : weights.length :
 		if (jt != null) {
 			for (int i = 0; i < jt.length; i++) {

src/main/java/com/elphel/imagej/tileprocessor/Corr2dLMA.java

@@ -2583,7 +2583,7 @@ public class Corr2dLMA {
 			fx[i] = this.weights[i] * d;
 			rms += fx[i]*d; // sum of weights
 		}
-		rms_pure = Math.sqrt(rms)/this.pure_weight;
+		rms_pure = Math.sqrt(rms)/this.pure_weight; // Not Math.sqrt(rms/this.pure_weight)? 
 		for (int i = num_samples; i < num_points; i++) {
 			double d = (values[i] - fx[i]);
 			fx[i] = this.weights[i] * d;