Tested LMA equalization, some bug fixes

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

@@ -159,6 +159,8 @@ public class ComboMatch {
 		boolean create_overlaps =     false;
 		boolean equalize_overlaps =   false;
 		boolean create_map =          false;
+		boolean create_equalize =     false;
+		
 //		boolean show_combo_mask =     false; // generate image mas (where it is defined)_
 //		boolean use_alt =             false;
 //		boolean show_centers =        true;
@@ -194,7 +196,7 @@ public class ComboMatch {
 		}
 		
 		
-		GenericJTabbedDialog gd = new GenericJTabbedDialog("Set image pair",1200,700);
+		GenericJTabbedDialog gd = new GenericJTabbedDialog("Set image pair",1200,800);
 		gd.addChoice      ("Files list/data path (w/o extension):", files_lists_paths, files_lists_paths[default_list_choice]);
 		gd.addCheckbox    ("Use saved maps collection", use_saved_collection, "If false - use files list.");
 		gd.addCheckbox    ("Save maps collection", save_collection, "Save maps collection to be able to restore.");
@@ -235,6 +237,7 @@ public class ComboMatch {
 		gd.addCheckbox    ("Create overlap pairs",             create_overlaps, "Create scene pairs overlaps.");
 		gd.addCheckbox    ("Equalize overlap pairs",           equalize_overlaps, "Equalize intensities in overlaps.");
 		gd.addCheckbox    ("Create map",                       create_map, "Create combined map from pairwise matches.");
+		gd.addCheckbox    ("Equalize intensities",             create_equalize, "Create map intensities equalization 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.");
@@ -263,6 +266,7 @@ public class ComboMatch {
 		String orthoMapsCollection_path =files_lists_paths[choice_index]+".data";
 		use_saved_collection =     gd.getNextBoolean();
 		save_collection =          gd.getNextBoolean();
+		String orthoMapsCollection_savepath = save_collection?orthoMapsCollection_path:null;
 		process_correlation=       gd.getNextBoolean();
 		num_tries_fit =      (int) gd.getNextNumber();
 		update_match=              gd.getNextBoolean();
@@ -292,6 +296,7 @@ public class ComboMatch {
 		create_overlaps =           gd.getNextBoolean();
 		equalize_overlaps =         gd.getNextBoolean();
 		create_map =                gd.getNextBoolean();
+		create_equalize =           gd.getNextBoolean();
 		frac_remove =               gd.getNextNumber();
 		metric_error=               gd.getNextNumber();
 		if (use_marked_image ) { // will only be used if found and asked
@@ -778,20 +783,28 @@ public class ComboMatch {
 			OrthoMultiLMA.buildOrthoMap(
 					clt_parameters,            // CLTParameters       clt_parameters,
 					maps_collection, // OrthoMapsCollection maps_collection
-					orthoMapsCollection_path); // String orthoMapsCollection_path
+					orthoMapsCollection_savepath); // String orthoMapsCollection_path
 			return true;
 		}
-    	
+
+		if (create_equalize) {
+			OrthoEqualizeLMA.buildEqualize(
+					clt_parameters,            // CLTParameters       clt_parameters,
+					maps_collection, // OrthoMapsCollection maps_collection
+					orthoMapsCollection_savepath); // String orthoMapsCollection_path
+			return true;
+		}
+		
 		if (create_overlaps) {
 			boolean ok =maps_collection.getIntersectedPairs(
 					clt_parameters, // CLTParameters    clt_parameters,
-					orthoMapsCollection_path); // String orthoMapsCollection_path);
+					orthoMapsCollection_savepath); // String orthoMapsCollection_path);
 			return ok; // Just exit, do not try other commands.  if (!ok) return false;
 		}
 		if (equalize_overlaps) {
 			boolean ok =maps_collection.equalizeIntersectedPairs(
 					clt_parameters, // CLTParameters    clt_parameters,
-					orthoMapsCollection_path); // String orthoMapsCollection_path);
+					orthoMapsCollection_savepath); // String orthoMapsCollection_path);
 			return ok; // Just exit, do not try other commands.  if (!ok) return false;
 		}
 		

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

@@ -117,6 +117,9 @@ public class OrthoMap implements Comparable <OrthoMap>, Serializable{
 	public transient double                     sfm_gain = Double.NaN;     // maximal SfM gain of this map
 	public transient double []                  equalize = {1,0}; // rectified value = equalize[0]*source_value+equalize[1]
 	private void writeObject(ObjectOutputStream oos) throws IOException {
+		// temporary fix:
+//		double [][] affine_clone = {affine[0].clone(), affine[1].clone()};
+//		affine = affine_clone;
 		oos.defaultWriteObject();
 		oos.writeObject(path);
 	//	oos.writeObject(scenes_path);
@@ -511,7 +514,7 @@ public class OrthoMap implements Comparable <OrthoMap>, Serializable{
 	}
 	
 	public void setAffine(double [][] affine) {
-		this.affine = affine;
+		this.affine = new double[][] {affine[0].clone(),affine[1].clone()};
 	}
 	public double [][] getAffine(){
 		return affine;

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

@@ -4893,7 +4893,7 @@ public class OrthoMapsCollection  implements Serializable{
 			int debugLevel) {
 		int [] indices = getScenesSelection(
 				null, // boolean select_all,
-				" to process"); // String purpose)
+				" to process/display"); // String purpose)
 		if (indices == null) {
 			return false;
 		}
@@ -4907,7 +4907,7 @@ public class OrthoMapsCollection  implements Serializable{
 			int [] indices,
 			int debugLevel) {
 		boolean show_map_stats =      false;      
-		boolean show_combo_map =      false; // true;
+		boolean show_combo_map =      true;  // false; // true;
 		boolean show_alt_map =        false;
 		boolean show_combo_mask =     false; // generate image mas (where it is defined)
 		boolean show_frames =         false;
@@ -4920,6 +4920,8 @@ public class OrthoMapsCollection  implements Serializable{
 		boolean show_centers =        true;
 		boolean bounds_to_indices =   true;
 		boolean merge_layers =        false;  // instead of individuals
+		boolean ignore_affines =      false;
+		boolean ignore_equalize =     false;
 
 		String        save_top_dir =      "/media/elphel/NVME/lwir16-proc/ortho_videos/debug/sept12-13/pattern_match/";
 		String        sub_dir =           "combo_maps";
@@ -4942,10 +4944,15 @@ public class OrthoMapsCollection  implements Serializable{
 		gd.addNumericField("Margins",                    margins,  0,4,"",
 				"Add margins around images");
 
-  		gd.addCheckbox    ("Show transformation centers",      show_centers, "Mark verticals from the UAS on the ground.");
-		gd.addCheckbox    ("Bounds to selected images", bounds_to_indices, "Set combo image bounds to selected images only. False - all images.");
-		gd.addCheckbox    ("Merge layers",                     merge_layers, "Generate composite binary image.");
+  		gd.addCheckbox    ("Show transformation centers",show_centers, "Mark verticals from the UAS on the ground.");
+		gd.addCheckbox    ("Bounds to selected images",  bounds_to_indices, "Set combo image bounds to selected images only. False - all images.");
+		gd.addCheckbox    ("Merge layers",               merge_layers, "Generate composite binary image.");
 
+		gd.addCheckbox    ("Ignore affines",             ignore_affines, "Ignore available affines, use unity.");
+		gd.addCheckbox    ("Ignore equalization",        ignore_equalize, "Ignore available intensity equalization, use unity.");
+
+		
+		
 		gd.addStringField ("Pattern match save directory",      save_top_dir, 120, "Top directory to save combo maps");
 		gd.addStringField ("Save subdirectory",                 sub_dir, 80, "Subdirectory for versions of the same scene/pair of scenes");
 		gd.addCheckbox    ("Show generated images",             show_images, "Display generated images.");
@@ -4968,7 +4975,8 @@ public class OrthoMapsCollection  implements Serializable{
 		show_centers =       gd.getNextBoolean();
 		bounds_to_indices =  gd.getNextBoolean();
 		merge_layers =       gd.getNextBoolean();
-
+		ignore_affines =     gd.getNextBoolean();
+		ignore_equalize =    gd.getNextBoolean();
 		save_top_dir=        gd.getNextString();
 		sub_dir=             gd.getNextString();
 		show_images=         gd.getNextBoolean();
@@ -5015,13 +5023,22 @@ public class OrthoMapsCollection  implements Serializable{
 			int [] wh =     new int[2];
 			int [] origin = new int[2];
 			double [][] centers = show_centers? (new double [indices.length][]): null;
+			double [][][] affines = null;
+			if (ignore_affines) {
+				affines = new double [indices.length][2][3];
+				for (int i = 0; i < indices.length; i++) {
+					affines[i][0][0] = 1;
+					affines[i][1][1] = 1;
+				}
+			}
+			
 			double [][] dmulti = renderMultiDouble (
 					null,              // double [][]   ground_planes, // null - images, non-null altitudes. use new double[2][3] for old way alt
 					indices,           // int []        indices, // null or which indices to use (normally just 2 for pairwise comparison)
 					bounds_to_indices, // boolean       bounds_to_indices,
-					null,              // affines,    // double [][][] affines, // null or [indices.length][2][3]
+					affines,           // null,            // affines,    // double [][][] affines, // null or [indices.length][2][3]
 					null,              // double [][]   equalize,
-					true,              // boolean       ignore_equalize,
+					ignore_equalize,   // true,              // boolean       ignore_equalize,
 					null,              // warp,       // FineXYCorr    warp,,
 					zoom_lev,          // int         zoom_level,
 					wh,                // int []      wh,

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

@@ -19,6 +19,9 @@ public class PairwiseOrthoMatch implements Serializable {
 
 	public PairwiseOrthoMatch() {
 		
+	}
+	public double getOverlap() {
+		return overlap;
 	}
 	public PairwiseOrthoMatch(
 			double [][] affine,