done refactoring, starting debugging

src/main/java/com/elphel/imagej/orthomosaic/Affine2Import.java

+package com.elphel.imagej.orthomosaic;
+
+public class Affine2Import {
+	public static final String AFFINE2_TAG = "AFFINE2";	
+	public static final int    AFFINE2_LEN = 10;
+	public String name1;
+	public String name2;
+	public double overlap;
+	public double [][] affine;
+	public static boolean matches(String [] tokens) {
+		return ((tokens.length == AFFINE2_LEN) && AFFINE2_TAG.equals(tokens[0]));
+	}
+	public Affine2Import(
+			String [] tokens) {
+		if (!matches(tokens)) {
+			throw new IllegalArgumentException ("Not Affine2Import tokens");
+		}
+		int indx = 1;
+		name1 = tokens[indx++];
+		name2 = tokens[indx++];
+		overlap = Double.parseDouble(tokens[indx++]);
+		affine = new double [2][3];
+		for (int i = 0; i < affine.length; i++) {
+			for (int j = 0; j < affine[i].length; j++) {
+				affine[i][j] = Double.parseDouble(tokens[indx++]);
+			}
+		}
+	}
+}

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

+package com.elphel.imagej.orthomosaic;
+
+public class AffineImport {
+	public static final String AFFINE_TAG = "AFFINE";
+	public static final int    AFFINE_LEN = 8;
+	public String name;
+	public double [][] affine;
+	public static boolean matches(String [] tokens) {
+		return ((tokens.length == AFFINE_LEN) && AFFINE_TAG.equals(tokens[0]));
+	}
+	public AffineImport(
+			String [] tokens) {
+		if (!matches(tokens)) {
+			throw new IllegalArgumentException ("Not AffineImport tokens");
+		}
+		int indx = 1;
+		name = tokens[indx++];
+		affine = new double [2][3];
+		for (int i = 0; i < affine.length; i++) {
+			for (int j = 0; j < affine[i].length; j++) {
+				affine[i][j] = Double.parseDouble(tokens[indx++]);
+			}
+		}
+	}
+	
+// String[] tokens	
+}

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

@@ -43,6 +43,7 @@ import ij.gui.PointRoi;
 import ij.process.FloatPolygon;
 
 public class ComboMatch {
+	public static final String [] SUFFIXES_BL_BC=     {"","-BL","-BC"};
 	public static GPUTileProcessor GPU_TILE_PROCESSOR = null;
 	public static GpuQuad   GPU_QUAD_AFFINE = null;
 	public static ImagePlus imp_src1 = null;
@@ -174,9 +175,6 @@ public class ComboMatch {
 		boolean display_pairs =            false;
 		boolean create_map =               false;
 		boolean create_equalize =          false;
-                
-                
-                
 		boolean use_saved_collection = false; // true; // false;
 		boolean save_collection =      false; // true;
 		boolean process_correlation = true; // use false to save new version of data
@@ -191,23 +189,24 @@ public class ComboMatch {
 		boolean restore_temp =        true;
 		double  frac_remove  =        clt_parameters.imp.pmtch_frac_remove; //   0.15;
 		double  metric_error =        clt_parameters.imp.pmtch_metric_err; // 0.05; // 0.02;//  2 cm
-                boolean update_files =        false;
-                boolean update_lla =          false; // re-read file metadata
-                boolean update_kernel_patterns = false;
-                boolean update_bl_bc =        false;
-                boolean export_affine =       false; // export per-scene affines
-                boolean export_affine2 =      false; // export per-pair affines
+		
+		boolean import_export =       false;
+//		boolean update_files =        false;
+//		boolean update_lla =          false; // re-read file metadata
+//		boolean update_kernel_patterns = false;
+//		boolean update_bl_bc =        false;
+//		boolean export_affine =       false; // export per-scene affines
+//		boolean export_affine2 =      false; // export per-pair affines
 
 
 		boolean fix_duplicates =      false;
-                String [] suffixes_bl_bc=     {"","-BL","-BC"};
 		boolean log_append =           clt_parameters.imp.pwise_log_append;
 		String log_path =              clt_parameters.imp.pwise_log_path;
 		String omtch_img_set =         clt_parameters.imp.omtch_img_set;
 		
 //		boolean READ_NO_ALT =          false; // to read older format data file where pairs do not have alt_data[]
 		
-		int  suffix_bc_bl_indx =   2;
+//		int  suffix_bc_bl_indx =   2;
 		if (!use_marked_image) {
 			process_correlation=false; // use already adjusted by default
 		}
@@ -217,12 +216,10 @@ public class ComboMatch {
 		}
 		
 		GenericJTabbedDialog gd = new GenericJTabbedDialog("Set image pair",1200,900);
-//		gd.addChoice      ("Files list/data path (w/o extension):", FILES_LISTS_PATHS, FILES_LISTS_PATHS[default_list_choice]);
 		gd.addChoice      ("Files list/data path (w/o extension):", FILES_LISTS_PATHS, omtch_img_set);
 		gd.addCheckbox    ("Use saved maps collection ", use_saved_collection, " (if available). If false - use files list.");
 		gd.addCheckbox    ("Save maps collection", save_collection, "Save maps collection to be able to restore.");
 		gd.addCheckbox    ("Process correlations", process_correlation, "false to skip to just regenerate new save file.");
-//		int num_tries_fit =           10;
 		gd.addNumericField("Num tries fit",        num_tries_fit,  0,4,"", "Try matching images this number of times");
 
 		gd.addCheckbox    ("Update match if calculated", update_match, "Will update correlation match for a pair if found.");
@@ -254,28 +251,29 @@ public class ComboMatch {
 		if (use_marked_image ) {
 			gd.addCheckbox    ("Use marked image data",   true, "Use markes from the selected image");
 		}
-                gd.addCheckbox    ("Update scene files",        update_files, "Re-read files as specified in .list file, possibly changing versions");
-                gd.addCheckbox    ("Update files metadata",     update_lla, "Re-read files metadata (if it was modified)");
-                gd.addCheckbox    ("Update kernels/patterns",   update_kernel_patterns, "Re-read kernels and patterns from *.list file");
+		gd.addCheckbox    ("Import/Export operations",  import_export, "Import/export and update operations");
+//		gd.addCheckbox    ("Update scene files",        update_files, "Re-read files as specified in .list file, possibly changing versions");
+//		gd.addCheckbox    ("Update files metadata",     update_lla, "Re-read files metadata (if it was modified)");
+//		gd.addCheckbox    ("Update kernels/patterns",   update_kernel_patterns, "Re-read kernels and patterns from *.list file");
 		gd.addCheckbox    ("Remove duplicate scenes",   fix_duplicates, "Remove scenes with the same timestamp");
 
-		gd.addCheckbox    ("Update BC/BL suffix",       update_bl_bc,
-				"Change source filenames to use -BC for bicubic, -BL - for bilinear, or empty - for old bilinear files");
-		gd.addChoice("BL/BC suffix:",        
-                                suffixes_bl_bc,
-                                suffixes_bl_bc[suffix_bc_bl_indx],
-                                "Select interpolation mode of the source files: old bilinear (empty), bilinear (-BL), or bicubic (-BC)", 0);
+//		gd.addCheckbox    ("Update BC/BL suffix",       update_bl_bc,
+//				"Change source filenames to use -BC for bicubic, -BL - for bilinear, or empty - for old bilinear files");
+//		gd.addChoice("BL/BC suffix:",        
+//				SUFFIXES_BL_BC,
+//				SUFFIXES_BL_BC[suffix_bc_bl_indx],
+//				"Select interpolation mode of the source files: old bilinear (empty), bilinear (-BL), or bicubic (-BC)", 0);
 
-                gd.addCheckbox    ("Export scene affines",      export_affine,  "Export per-scene affines in text format for migration.");
-                gd.addCheckbox    ("Export pairs affines",      export_affine2, "Export per-pair  affines in text format for migration.");
+//		gd.addCheckbox    ("Export scene affines",      export_affine,  "Export per-scene affines in text format for migration.");
+//		gd.addCheckbox    ("Export pairs affines",      export_affine2, "Export per-pair  affines in text format for migration.");
 
 		gd.addCheckbox    ("Write log file",            log_append, "Enable writing log file with matching results.");
 		gd.addStringField ("Log file full path",        log_path, 150, "Path of the log file to be appended.");     
-//          gd.addCheckbox    ("Read no-alt data (old)",    READ_NO_ALT, "Read older format data file where pairs do not have alt_data[].");
+		//          gd.addCheckbox    ("Read no-alt data (old)",    READ_NO_ALT, "Read older format data file where pairs do not have alt_data[].");
 
 
 
-//		update_kernel_patterns
+		//		update_kernel_patterns
 		gd.showDialog();
 		if (gd.wasCanceled()) return false;
 
@@ -285,6 +283,7 @@ public class ComboMatch {
 		String orthoMapsCollection_path =omtch_img_set+".data";
 		String affines_path =            omtch_img_set+".affines"; // for export per-scene affines
 		String affines2_path =           omtch_img_set+".affines2"; // for export per-pair affines
+		
 		use_saved_collection =     gd.getNextBoolean();
 		save_collection =          gd.getNextBoolean();
 		String orthoMapsCollection_savepath = save_collection?orthoMapsCollection_path:null;
@@ -317,15 +316,16 @@ public class ComboMatch {
 		if (use_marked_image ) { // will only be used if found and asked
 			use_marked_image=       gd.getNextBoolean();
 		}
-                update_files=               gd.getNextBoolean();
-                update_lla=                 gd.getNextBoolean();
-                update_kernel_patterns=     gd.getNextBoolean();
+		import_export =             gd.getNextBoolean();
+//		update_files=               gd.getNextBoolean();
+//		update_lla=                 gd.getNextBoolean();
+//		update_kernel_patterns=     gd.getNextBoolean();
 		fix_duplicates=             gd.getNextBoolean();
-                update_bl_bc=               gd.getNextBoolean();
-                suffix_bc_bl_indx =         gd.getNextChoiceIndex();
+//		update_bl_bc=               gd.getNextBoolean();
+//		suffix_bc_bl_indx =         gd.getNextChoiceIndex();
 
-                export_affine =             gd.getNextBoolean();
-                export_affine2 =            gd.getNextBoolean();
+//		export_affine =             gd.getNextBoolean();
+//		export_affine2 =            gd.getNextBoolean();
 
 
 		log_append =                gd.getNextBoolean();
@@ -343,13 +343,13 @@ public class ComboMatch {
 			}
 			//files_list_path
 			if (!use_files_list) {
-				if (update_kernel_patterns) {
-                                        maps_collection.updateKernels(files_list_path);
-                                        maps_collection.updatePatterns(files_list_path);
-                                }
-                                if (update_files) {
-                                        maps_collection.updateFiles(files_list_path);
-                                }
+//				if (update_kernel_patterns) {
+//					maps_collection.updateKernels(files_list_path);
+//					maps_collection.updatePatterns(files_list_path);
+//				}
+//				if (update_files) {
+//					maps_collection.updateFiles(files_list_path);
+//				}
 			}
 		} else {
 			use_files_list = true;
@@ -360,6 +360,15 @@ public class ComboMatch {
 			maps_collection.updateSfmGain();
 		}
 		
+		if (import_export) {
+			return updateImportExport(
+					omtch_img_set, // String files_base
+					maps_collection); //						OrthoMapsCollection maps_collection
+
+		}
+		
+		
+		/*
 		if (export_affine) {
 			StringBuffer sb = new StringBuffer();
 			for (OrthoMap omap :  maps_collection.ortho_maps) {
@@ -415,22 +424,23 @@ public class ComboMatch {
 		if (export_affine || export_affine2) {
 			return true; // do not save
 		}
-                
+*/
 
 		if (fix_duplicates) {
 			removeDuplicateScenes (maps_collection);
 		}
 
+/*		
 		if (update_bl_bc) {
 			boolean OK = updateBlBcFileNames(
-					suffixes_bl_bc[suffix_bc_bl_indx], // String suffix,
+					SUFFIXES_BL_BC[suffix_bc_bl_indx], // String suffix,
 					"-FLAT",// String before,
 					maps_collection); // OrthoMapsCollection maps_collection)
 			if (!OK) {
 				System.out.println("Failed to update filenames for different interpolation mode");
 			}
 		}
-		
+		*/
 		
 		
 		String [] names = maps_collection.getNames(); // null
@@ -608,7 +618,7 @@ public class ComboMatch {
 				}
 			}
 			
-			maps_collection.reverseRender(
+			maps_collection.reverseRender( // assuming image, not alt
 					object_list,        // ArrayList<ObjectLocation> objects,
 					zool_lev_objects,   // int         zoom_level){
 					indices);           // int []      indices){ // null or selected image indices
@@ -843,12 +853,12 @@ public class ComboMatch {
 		//getTemperature()
 		// get all temperatures
 		maps_collection.getAllTemperatures();
-		if (update_lla) {
-			System.out.println("Updating map files metadata");
-			maps_collection.updateLLa();
-			maps_collection.updateNumberScenes();
-			maps_collection.updateSfmGain();
-		}
+//		if (update_lla) {
+//			System.out.println("Updating map files metadata");
+//			maps_collection.updateLLA();
+//			maps_collection.updateNumberScenes();
+//			maps_collection.updateSfmGain();
+//		}
 		
         // which pair to compare
 //		String [] gpu_spair = {names[gpu_ipair[0]],names[gpu_ipair[1]]}; 
@@ -2652,5 +2662,210 @@ adjusted affines[1] for a pair: 1694564291_293695/1694564778_589341
 		}
 	}
 	
+	public static boolean updateImportExport(
+			String files_base,
+			OrthoMapsCollection maps_collection) {
+		if  (maps_collection == null) {
+			throw new IllegalArgumentException ("maps_collection is not initialized!");
+		}
+		int  suffix_bc_bl_indx =   2;
+		boolean update_files =           false;
+		boolean update_lla =             false; // re-read file metadata
+		boolean update_kernel_patterns = false;
+		boolean update_bl_bc =           false;
+		boolean export_affine =          false; // export per-scene affines
+		boolean export_affine2 =         false; // export per-pair affines
+		boolean overwrite_affine =       false;
+		boolean import_affine =          false; // export per-scene affines
+		boolean import_affine2 =         false; // export per-pair affines
+		String files_list_path =         files_base+".list";
+//		String orthoMapsCollection_path =omtch_img_set+".data";
+		String affines_path =            files_base+".affines"; // for export per-scene affines
+		String affines2_path =           files_base+".affines2"; // for export per-pair affines
+
+
+		GenericJTabbedDialog gd = new GenericJTabbedDialog("Select Update, Import or Export operations",1200,900);
+		gd.addStringField ("List file full path",        files_list_path, 150, "Path to read/update directories and GEO files.");     
+		gd.addStringField ("Scene affines full path",    affines_path, 150, "Path to import/export scenes affines.");     
+		gd.addStringField ("Pairwise affines full path", affines2_path, 150, "Path to import/export scenes pairs affines.");     
+		gd.addCheckbox    ("Update scene files",         update_files,   "Re-read files as specified in .list file, possibly changing versions");
+		gd.addCheckbox    ("Update files metadata",      update_lla,     "Re-read files metadata (if it was modified)");
+		gd.addCheckbox    ("Update kernels/patterns",    update_kernel_patterns, "Re-read kernels and patterns from *.list file");
+		gd.addCheckbox    ("Export scene affines",       export_affine,  "Export per-scene affines in text format for migration.");
+		gd.addCheckbox    ("Export pairs affines",       export_affine2, "Export per-pair  affines in text format for migration.");
+		
+		gd.addCheckbox    ("Overwrite affines on import",overwrite_affine, "Overwrite existing non-trivial affines on import.");
+		gd.addCheckbox    ("Import scene affines",       import_affine,  "Export per-scene affines in text format for migration.");
+		gd.addCheckbox    ("Import pairs affines",       import_affine2, "Export per-pair  affines in text format for migration.");
+		gd.addCheckbox    ("Update BC/BL suffix",        update_bl_bc,
+				"Change source filenames to use -BC for bicubic, -BL - for bilinear, or empty - for old bilinear files");
+		gd.addChoice("BL/BC suffix:",        
+				SUFFIXES_BL_BC,
+				SUFFIXES_BL_BC[suffix_bc_bl_indx],
+				"Select interpolation mode of the source files: old bilinear (empty), bilinear (-BL), or bicubic (-BC)", 0);
+		gd.showDialog();
+		if (gd.wasCanceled()) return false;
+		files_list_path =           gd.getNextString();
+		affines_path =              gd.getNextString();
+		affines2_path =             gd.getNextString();
+   		update_files=               gd.getNextBoolean();
+		update_lla=                 gd.getNextBoolean();
+		update_kernel_patterns=     gd.getNextBoolean();
+		export_affine =             gd.getNextBoolean();
+		export_affine2 =            gd.getNextBoolean();
+		overwrite_affine =          gd.getNextBoolean();
+		import_affine =             gd.getNextBoolean();
+		import_affine2 =            gd.getNextBoolean();
+		update_bl_bc=               gd.getNextBoolean();
+		suffix_bc_bl_indx =         gd.getNextChoiceIndex();
+		
+		if (update_files) {
+			maps_collection.updateFiles(files_list_path);
+			maps_collection.updateNumberScenes(); // number of scenes in each sequence
+		}
+		if (update_lla) {
+			System.out.println("Updating map files metadata");
+			maps_collection.updateLLA();
+			maps_collection.updateNumberScenes();
+			maps_collection.updateSfmGain();
+		}
+		if (update_kernel_patterns) {
+			maps_collection.updateKernels(files_list_path);
+			maps_collection.updatePatterns(files_list_path);
+		}
+		
+		if (export_affine) {
+			StringBuffer sb = new StringBuffer();
+			for (OrthoMap omap :  maps_collection.ortho_maps) {
+				String name = omap.getName();
+				double [][] affine = omap.getAffine();
+				if (affine != null) {
+					sb.append(String.format("AFFINE %s %11.8f  %11.8f  %11.8f  %11.8f  %11.8f  %11.8f\n",
+							name, affine[0][0], affine[0][1], affine[0][2], affine[1][0], affine[1][1], affine[1][2]));
+				}
+			}
+			CalibrationFileManagement.saveStringToFile (
+					affines_path,          //String path,
+					sb.toString(), // data,
+					false); // boolean append)
+		}
+
+		if (export_affine2) {
+			StringBuffer sb = new StringBuffer();
+			ArrayList<Point> pairs_list = new ArrayList<Point>(); 
+			for (OrthoMap map : maps_collection.ortho_maps) {
+				for (String other_name: map.pairwise_matches.keySet()) {
+					pairs_list.add(new Point(
+							maps_collection.getIndex(map.getName()),
+							maps_collection.getIndex(other_name)));
+				}
+			}
+			Collections.sort(pairs_list, new Comparator<Point>() {
+				@Override
+				public int compare(Point lhs, Point rhs) {
+					return (rhs.x > lhs.x) ? -1 : (rhs.x < lhs.x) ? 1 :
+						((rhs.y > lhs.y) ? -1 : (rhs.y < lhs.y) ? 1 : 0); // increasing
+				}
+			});
+			for (Point pair: pairs_list) {
+				PairwiseOrthoMatch pom = maps_collection.ortho_maps[pair.x].getMatch(
+						maps_collection.ortho_maps[pair.y].getName(), false); // undef_only || nan_rms);
+						if ((pom !=null) && pom.isDefined()) {
+							double overlap = pom.overlap;
+							double [][] affine = pom.getAffine();
+							sb.append(String.format("AFFINE2 %s %s %11.8f  %11.8f  %11.8f  %11.8f  %11.8f  %11.8f  %11.8f\n",
+									maps_collection.ortho_maps[pair.x].getName(),
+									maps_collection.ortho_maps[pair.y].getName(),
+									overlap,
+									affine[0][0], affine[0][1], affine[0][2], affine[1][0], affine[1][1], affine[1][2]));
+						}
+			}
+			CalibrationFileManagement.saveStringToFile (
+					affines2_path,          //String path,
+					sb.toString(), // data,
+					false); // boolean append)
+		}
+
+		if (import_affine) {
+			ArrayList<AffineImport> affine_import = new ArrayList<AffineImport>();
+			OrthoMapsCollection.getPathsAndScenesFromSourceList(
+					affines_path,
+					null, // scenes0,
+					null,       // ArrayList<AltitudeMismatchKernel> kernels,
+					null,      // ArrayList<GroundObjectPattern>    patterns);
+					null, // ArrayList<ModelRegex>             model_regexes,
+					null,   // String []                         regex_use) {
+					affine_import,          // ArrayList<AffineImport>           affine_import,
+					null);         // ArrayList<Affine2Import>          affine2_import) {
+			int num_updated_affines = 0;
+			for (AffineImport affineImport: affine_import) {
+				OrthoMap map =  maps_collection.getMap(affineImport.name);
+				if (map != null) {
+					if (overwrite_affine || !map.isAffineNonTrivial()) {
+						map.setAffine(affineImport.affine);
+						num_updated_affines++;
+					}
+				}
+			}
+			maps_collection.updateNumberScenes();
+			System.out.println("Updated "+num_updated_affines+" affines of "+affine_import.size()+" specified. There are "+
+			maps_collection.ortho_maps.length+" maps in the system.");
+		}
+		if (import_affine2) {
+			ArrayList<Affine2Import> affine2_import = new ArrayList<Affine2Import>();
+			OrthoMapsCollection.getPathsAndScenesFromSourceList(
+					affines_path,
+					null,            // scenes0,
+					null,            // ArrayList<AltitudeMismatchKernel> kernels,
+					null,            // ArrayList<GroundObjectPattern>    patterns);
+					null,            // ArrayList<ModelRegex>             model_regexes,
+					null,            // String []                         regex_use) {
+					null,            // ArrayList<AffineImport>           affine_import,
+					affine2_import); // ArrayList<Affine2Import>          affine2_import) {
+			int num_updated_affines = 0;
+			for (Affine2Import affine2Import: affine2_import) {
+				OrthoMap map =  maps_collection.getMap(affine2Import.name1);
+				if (map != null) {
+					PairwiseOrthoMatch pom = map.getMatch(affine2Import.name2,true);
+					if (pom != null) {
+						if (overwrite_affine || !pom.isAffineNonTrivial()) {
+							pom.setOverlap(affine2Import.overlap);
+							pom.setAffine(affine2Import.affine); // does not clone - OK
+						}						
+					} else {
+						OrthoMap map2 =  maps_collection.getMap(affine2Import.name2);
+						int zoom_lev = Math.min(map.getOriginalZoomLevel(), map2.getOriginalZoomLevel());
+						pom= new PairwiseOrthoMatch(
+								affine2Import.affine,   // double [][] affine,
+								null,                   // double [][] jtj,
+								Double.NaN,             // double rms,
+								zoom_lev,               // int zoom_lev,
+								affine2Import.overlap); // double overlap)
+					}
+
+
+				}
+
+
+
+
+			}
+		}
+
+		if (update_bl_bc) {
+			boolean OK = updateBlBcFileNames(
+					SUFFIXES_BL_BC[suffix_bc_bl_indx], // String suffix,
+					"-FLAT",// String before,
+					maps_collection); // OrthoMapsCollection maps_collection)
+			if (!OK) {
+				System.out.println("Failed to update filenames for different interpolation mode");
+			}
+		}
+		
+		return true;
+	}
+	
+	
+	
 	
 }

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

@@ -238,6 +238,10 @@ public class FloatImageData implements Serializable  {
 		return extra_zoom[0];
 	}
 	
+	public double needZoomIn() {
+		return needZoomIn(pix_meters);
+	}
+	
 	public int getZoomLevel() {
 		return zoom_lev;
 	}

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

@@ -106,54 +106,57 @@ public class OrthoMap implements Comparable <OrthoMap>, Serializable{
 	
 	
 	public static final String ALT_SUFFIX = "-ALT";
-	public transient String                     name;  // timestamp
-	public transient double                     ts;
-	public transient String                     path;        // full path to the model directory (including /vXX?)
-	public double []                            lla;      // lat/long/alt
-	public LocalDateTime                        dt;
+	public           String                       path;        // full path to the model directory (including /vXX?)
+//	public  double []                  lla;      // lat/long/alt
+//	public LocalDateTime                        dt;
 	// affine convert (input) rectified coordinates (meters) relative to vert_meters to source image
 	// coordinates relative to vert_meters
 	public           double [][]                  affine = new double[][] {{1,0,0},{0,1,0}}; // relative to vert_meters[], positive Y is down (as in images)
-	public transient double [][]                ers_affine = new double[][] {{1,0},{0,1}}; // orientation only for remaining ERS, positive Y is down (as in images)
-	public transient FloatImageData             orig_image;
-	public transient FloatImageData             alt_image;
-	public int                                  orig_zoom_level;
-	public boolean                              orig_zoom_valid;
-	public double                               need_extra_zoom;
+	public           double [][]                  ers_affine = new double[][] {{1,0},{0,1}}; // orientation only for remaining ERS, positive Y is down (as in images)
+	public           FloatImageData               orig_image;
+	public           FloatImageData               alt_image;
+//	public int                                  orig_zoom_level;
+//	public boolean                              orig_zoom_valid;
+//	public double                               need_extra_zoom;
 	public           double                       averageRawPixel = Double.NaN; // measure of scene temperature
-	transient HashMap <Integer, FloatImageData> images;
 	HashMap          <String, PairwiseOrthoMatch> pairwise_matches;
-	public transient SensorTemperatureData[]    temp_data;
-	public transient double                     agl = Double.NaN;
-	public transient int                        num_scenes = -1;;   // number of scenes that made up this image
-	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]
-	public transient double []                  qorient = null; // quternion representing orientation+scale of the scene
+	public           SensorTemperatureData[]      temp_data;
+	public           double                       agl = Double.NaN;
+	public           int                          num_scenes = -1;;   // number of scenes that made up this image
+	public           double                       sfm_gain = Double.NaN;     // maximal SfM gain of this map
+	public           double []                    equalize = {1,0}; // rectified value = equalize[0]*source_value+equalize[1]
+	public           double []                    qorient = null; // quternion representing orientation+scale of the scene
+// really transient	
+	transient HashMap <Integer, FloatImageData> images;
+	public transient String                     name;  // timestamp
+	public transient double                       ts;
+
+	
 
 	private void writeObject(ObjectOutputStream oos) throws IOException {
 		oos.defaultWriteObject();
-		oos.writeObject(path);
-		oos.writeObject(temp_data); // temporary, while transient
-		oos.writeObject(agl);
-		oos.writeObject(num_scenes);
-		oos.writeObject(sfm_gain);
-		oos.writeObject(equalize);
-		oos.writeObject(qorient);
+//		oos.writeObject(path);
+//		oos.writeObject(temp_data); // temporary, while transient
+//		oos.writeObject(agl);
+//		oos.writeObject(num_scenes);
+//		oos.writeObject(sfm_gain);
+//		oos.writeObject(equalize);
+//		oos.writeObject(qorient);
 	}
 	
 	private void readObject(ObjectInputStream ois) throws ClassNotFoundException, IOException {
 		ois.defaultReadObject();
-		path = (String) ois.readObject();
+//		path = (String) ois.readObject();
 		name = getNameFromPath(path);
 		ts= Double.parseDouble(name.replace("_", "."));
-		temp_data = (SensorTemperatureData[]) ois.readObject();
-		agl = (double)  ois.readObject();
-		num_scenes = (int) ois.readObject();
-		sfm_gain = (double) ois.readObject();
-		equalize = (double []) ois.readObject();
-		if (OrthoMapsCollection.CURRENT_VERSION >= OrthoMapsCollection.VERSION_POST_ORIENT) {
-			qorient = (double[]) ois.readObject();
-		}
+//		temp_data = (SensorTemperatureData[]) ois.readObject();
+//		agl = (double)  ois.readObject();
+//		num_scenes = (int) ois.readObject();
+//		sfm_gain = (double) ois.readObject();
+//		equalize = (double []) ois.readObject();
+//		if (OrthoMapsCollection.CURRENT_VERSION >= OrthoMapsCollection.VERSION_POST_ORIENT) {
+//			qorient = (double[]) ois.readObject();
+//		}
 		images = new HashMap <Integer, FloatImageData>(); // field images was not saved
 //		averageImagePixel = Double.NaN; // average image pixel value (to combine with raw)
 		
@@ -229,7 +232,16 @@ public class OrthoMap implements Comparable <OrthoMap>, Serializable{
 		if (with_undefined || match.isDefined()) return match;
 		return null;
 	}
-
+	public static boolean isAffineNonTrivial(double [][] affine) {
+		if (affine == null) {
+			return false;
+		}
+		return ( affine[0][0] != 1.0) || (affine[0][1] != 0.0)  || (affine[0][2] != 0.0) ||
+				(affine[1][0] != 0.0) || (affine[1][1] != 1.0)  || (affine[1][2] != 0.0);
+	}
+	public boolean isAffineNonTrivial() {
+		return isAffineNonTrivial(this.affine);
+	}
 	
 	
 	public PairwiseOrthoMatch getMatch(String name) {
@@ -252,7 +264,8 @@ public class OrthoMap implements Comparable <OrthoMap>, Serializable{
 	}
 	
 	public int getOriginalZoomLevel() {
-		return orig_zoom_level;
+		return getImage().getZoomLevel(); // image, not altitude!
+//		return orig_zoom_level;
 	}
 // Generate ALT image path from the GEO
 	public static String getAltPath(String path) {
@@ -494,7 +507,7 @@ public class OrthoMap implements Comparable <OrthoMap>, Serializable{
 		
 		// initialize and read Exif for the images
 		orig_image = new FloatImageData(path);
-		dt = orig_image.getDT();
+//		dt = orig_image.getDT();
 		/*
 		
 		Properties imp_prop = null;
@@ -551,7 +564,7 @@ public class OrthoMap implements Comparable <OrthoMap>, Serializable{
 				return false;
 			}
 			orig_image = new FloatImageData(path);
-			dt = orig_image.getDT();
+//			dt = orig_image.getDT();
 		}
 		if (alt_image != null) {
 			String alt_path = getAltPath(path);
@@ -577,7 +590,7 @@ public class OrthoMap implements Comparable <OrthoMap>, Serializable{
 				return null;
 			}
 			orig_image = new FloatImageData(path);
-			dt = orig_image.getDT();
+//			dt = orig_image.getDT();
 		}
 		return orig_image;
 	}
@@ -654,7 +667,8 @@ public class OrthoMap implements Comparable <OrthoMap>, Serializable{
 		return ts;
 	}
 	public LocalDateTime getLocalDateTime() {
-		return dt;
+		return getImage().getDT();
+//		return dt;
 	}
 	
 	public String getName() {
@@ -974,11 +988,11 @@ public class OrthoMap implements Comparable <OrthoMap>, Serializable{
 			return false;
 		}
 		if (!orig_image.isZoomValid()) {
-			System.out.println("Original zoom level is invalid, need_extra_zoom = "+need_extra_zoom);
+			System.out.println("Original zoom level is invalid, need_extra_zoom = "+orig_image.needZoomIn());
 			return false;
 		}
 		if (zoom_level > orig_image.getZoomLevel()) {
-			System.out.println("Requested zoom level is too high ("+zoom_level+" > "+orig_zoom_level+")");
+			System.out.println("Requested zoom level is too high ("+zoom_level+" > "+orig_image.getZoomLevel()+")");
 			return false;
 		}
 		if (images.get(zoom_level) != null) {
@@ -1085,7 +1099,7 @@ public class OrthoMap implements Comparable <OrthoMap>, Serializable{
 		final float [] felev = src_elev.readFData(); 
 		final double [] elev = new double [tilesX*tilesY];
 		Arrays.fill(elev, Double.NaN);
-		final int diff_zoom_lev = zoom_level-orig_zoom_level;
+		final int diff_zoom_lev = zoom_level-getAlt().getZoomLevel(); // orig_zoom_level;
 		final double scale = 1.0/getScale (diff_zoom_lev); //	int zoom_lev);
 		
 		final Thread[] threads = ImageDtt.newThreadArray();

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

@@ -84,33 +84,35 @@ public class OrthoMapsCollection  implements Serializable{
 			"kernelsDirectory", "patternsDirectory"};
 	public static final String [] NAME_FH = {"full","half"};
 	public static final String [] NAME_MO = {"main","other"};
+	
+	public            OrthoMap []                       ortho_maps;
+	private           HashMap<String,ModelRegex>        model_regexes;
+	private           String                            current_model_regex="";
+	private           ArrayList<AltitudeMismatchKernel> kernels;
+	private           ArrayList<GroundObjectPattern>    patterns;
+	
+	// real transient:
 	public  transient long                              version = -1;
-	OrthoMap []                                 ortho_maps;
-	// remove some transients
-	transient HashMap<Double,Integer>           map_index;
-	transient HashMap<String,Integer>           map_index_string;
-	transient ArrayList<AltitudeMismatchKernel> kernels;
-	transient ArrayList<GroundObjectPattern>    patterns;
-	transient HashMap<String,ModelRegex>        model_regexes;
-	transient String                            current_model_regex="";
+	private transient HashMap<Double,Integer>           map_index;
+	private transient HashMap<String,Integer>           map_index_string;
 	
 	
 	private void writeObject(ObjectOutputStream oos) throws IOException { // ?
 		oos.defaultWriteObject();
 		oos.writeObject(AltitudeMismatchKernel.getKernelsDirectory());
-		oos.writeObject(kernels);
+//		oos.writeObject(kernels);
 		oos.writeObject(GroundObjectPattern.getPatternsDirectory());		
-		oos.writeObject(patterns);
+//		oos.writeObject(patterns);
 //		oos.writeObject(path);
 		// ortho_maps is not transient
 	}
-	@SuppressWarnings("unchecked")
+//	@SuppressWarnings("unchecked")
 	private void readObject(ObjectInputStream ois) throws ClassNotFoundException, IOException {
 		ois.defaultReadObject();
 		AltitudeMismatchKernel.setKernelsDirectory((String) ois.readObject());
-		kernels = (ArrayList<AltitudeMismatchKernel>) ois.readObject();
+//		kernels = (ArrayList<AltitudeMismatchKernel>) ois.readObject();
 		GroundObjectPattern.setPatternsDirectory((String) ois.readObject());
-		patterns = (ArrayList<GroundObjectPattern>)   ois.readObject();
+//		patterns = (ArrayList<GroundObjectPattern>)   ois.readObject();
 		
 		reindex(); // will recreate map_index, map_index_string
 		// lla is not transient
@@ -131,7 +133,10 @@ public class OrthoMapsCollection  implements Serializable{
 					kernels,       // ArrayList<AltitudeMismatchKernel> kernels,
 					patterns,      // ArrayList<GroundObjectPattern>    patterns);
 					model_regexes, // ArrayList<ModelRegex>             model_regexes,
-					regex_use_p); // String []                         regex_use) {
+					regex_use_p,   // String []                         regex_use) {
+					null,          // ArrayList<AffineImport>           affine_import,
+					null);         // ArrayList<Affine2Import>          affine2_import) {
+
 			current_model_regex = regex_use_p[0];
 			paths = ModelRegex.removeDuplicatesSort(paths);        
 			String [] orig_paths = paths.clone();
@@ -169,7 +174,7 @@ public class OrthoMapsCollection  implements Serializable{
 					if (indx >= 0) {
 						OrthoMap omap = orthoMapsCollection.ortho_maps[indx];
 						omap.orig_image = new FloatImageData(path); // always replace (nothing to preserve
-						omap.dt = omap.orig_image.getDT(); // just in case?
+///						omap.dt = omap.orig_image.getDT(); // just in case?
 						// see if alt image is already initialized
 						if (omap.alt_image != null) {
 							FloatImageData alt_image = OrthoMap.getAlt(path);
@@ -201,6 +206,7 @@ public class OrthoMapsCollection  implements Serializable{
 					Arrays.sort(ortho_maps); // mixed old+new, previous scene numbers will no longer be valui
 					orthoMapsCollection.ortho_maps = ortho_maps; 
 					orthoMapsCollection.reindex();
+					
 				} else {
 					System.out.println("No new scenes added");
 				}
@@ -218,6 +224,11 @@ public class OrthoMapsCollection  implements Serializable{
 		}
 	}
 	
+	public OrthoMap getMap(String name) {
+		int indx = getIndex(name);
+		if (indx < 0) return null;
+		return ortho_maps[indx];
+	}
 	
 	public static double [][] unityAffine() {
 		return new double [][] {{1,0,0},{0,1,0}};
@@ -243,7 +254,9 @@ public class OrthoMapsCollection  implements Serializable{
 					kernels, // ArrayList<AltitudeMismatchKernel> kernels,
 					null,    // ArrayList<GroundObjectPattern>    patterns);
 					null,    // ArrayList<ModelRegex>             model_regexes,
-					null);   // String []                         regex_use) {
+					null,    // String []                         regex_use) {
+					null,    // ArrayList<AffineImport>           affine_import,
+					null);   // ArrayList<Affine2Import>          affine2_import) {
 		} else {
 			System.out.println("updateKernels(): path should end with \".list\"");
 		}
@@ -259,7 +272,9 @@ public class OrthoMapsCollection  implements Serializable{
 					null,     // ArrayList<AltitudeMismatchKernel> kernels,
 					patterns, // ArrayList<GroundObjectPattern>    patterns);
 					null,     // ArrayList<ModelRegex>             model_regexes,
-					null);   // String []                         regex_use) {
+					null,     // String []                         regex_use) {
+					null,     // ArrayList<AffineImport>           affine_import,
+					null);    // ArrayList<Affine2Import>          affine2_import) {
 					
 		} else {
 			System.out.println("updatePatterns(): path should end with \".list\"");
@@ -297,6 +312,7 @@ public class OrthoMapsCollection  implements Serializable{
 			map_index.put(ortho_maps[i].getTimeStamp(), i);
 			map_index_string.put(ortho_maps[i].name,i);
 		}
+//		updateNumberScenes();
 		return ortho_maps.length;
 	}
 	
@@ -319,7 +335,7 @@ public class OrthoMapsCollection  implements Serializable{
 		}
 	}
 	
-	public void updateLLa() { // make automatic by saving/testing file modification stamp?
+	public void updateLLA() { // make automatic by saving/testing file modification stamp?
 		for (int n = 0; n < ortho_maps.length; n++) {
 			if (n == 530) {
 				System.out.println("updateLLa(): n="+n);
@@ -362,7 +378,9 @@ public class OrthoMapsCollection  implements Serializable{
 			ArrayList<AltitudeMismatchKernel> kernels,
 			ArrayList<GroundObjectPattern>    patterns,
 			HashMap<String,ModelRegex>        model_regexes,
-			String []                         regex_use) {
+			String []                         regex_use,
+			ArrayList<AffineImport>           affine_import,
+			ArrayList<Affine2Import>          affine2_import) {
 		List<String> lines;
 		List<String> rel_files = new ArrayList<String>(); 
 		Path seq_path = Paths.get(files_list);
@@ -404,7 +422,6 @@ public class OrthoMapsCollection  implements Serializable{
 								tokens[3],
 								LocalDateTime.parse(tokens[4])));
 					}
-					
 				} else if ((tokens.length > 0) && (tokens[0].toUpperCase().equals("REGEX"))) {
 					if ((model_regexes != null) && (tokens.length > 4)) {
 						model_regexes.put(tokens[1],new  ModelRegex(
@@ -417,6 +434,15 @@ public class OrthoMapsCollection  implements Serializable{
 					if ((regex_use != null) && (tokens.length > 1)) {
 						regex_use[0] = tokens[1];
 					}
+				} else if ((tokens.length > 0) && AffineImport.matches(tokens)) {
+					if (affine_import != null) {
+						affine_import.add(new AffineImport(tokens));
+					}
+				} else if ((tokens.length > 0) && Affine2Import.matches(tokens)) {
+					if (affine2_import != null) {
+						affine2_import.add(new Affine2Import(tokens));
+					}
+					
 				} else if ((tokens.length == 1) && (tokens[0].length() > 0)) {
 					rel_files.add(tokens[0]);
 				}
@@ -639,7 +665,7 @@ public class OrthoMapsCollection  implements Serializable{
 		for (ObjectLocation ol: objects) {
 			int nmap =getIndex(ol.getName());
 			final double scale = 1.0/OrthoMap.getPixelSizeMeters(zoom_level);
-			final double src_scale = 1.0/OrthoMap.getPixelSizeMeters(ortho_maps[nmap].orig_zoom_level); // pix per meter
+			final double src_scale = 1.0/OrthoMap.getPixelSizeMeters(ortho_maps[nmap].getImage().getZoomLevel()); // pix per meter
 			double [][] mbounds = ortho_maps[nmap].getBoundsMeters(true); // keep original bounds
 			double [] enu_offset = ortho_maps[reference_index].enuOffsetTo(ortho_maps[nmap]);
 			double [] scaled_out_center = { // xy center to apply affine to
@@ -921,7 +947,9 @@ public class OrthoMapsCollection  implements Serializable{
 			final double [][] affine = (affines !=null) ? affines[indx]: ortho_maps[nmap].affine; // only here use provided
 			Arrays.fill(fpixels[findx], Float.NaN);
 			final double scale = 1.0/OrthoMap.getPixelSizeMeters(zoom_level);
-			final double src_scale = 1.0/OrthoMap.getPixelSizeMeters(ortho_maps[nmap].orig_zoom_level); // pix per meter
+//			final int orig_zoom_level = getOriginalZoomLevel()
+			final int orig_zoom_level = use_alt? ortho_maps[nmap].getAlt().getZoomLevel(): ortho_maps[nmap].getImage().getZoomLevel();
+			final double src_scale = 1.0/OrthoMap.getPixelSizeMeters(orig_zoom_level); // pix per meter
 //			double [][] mbounds = ortho_maps[nmap].getBoundsMeters(true); // keep original bounds
 			double [][] mbounds = ortho_maps[nmap].getBoundsMeters(true,affine); // keep original bounds
 			double [] enu_offset = ortho_maps[indices[0]].enuOffsetTo(ortho_maps[nmap]);
@@ -1082,7 +1110,9 @@ public class OrthoMapsCollection  implements Serializable{
 			final double [] equalize = ignore_equalize ? null:((equalize_in != null) ? equalize_in[indx] : ortho_maps[nmap].equalize);
 			Arrays.fill(dpixels[findx], Float.NaN);
 			final double scale = 1.0/OrthoMap.getPixelSizeMeters(zoom_level);
-			final double src_scale = 1.0/OrthoMap.getPixelSizeMeters(ortho_maps[nmap].orig_zoom_level); // pix per meter
+			final int orig_zoom_level = use_alt? ortho_maps[nmap].getAlt().getZoomLevel(): ortho_maps[nmap].getImage().getZoomLevel();
+			final double src_scale = 1.0/OrthoMap.getPixelSizeMeters(orig_zoom_level); // pix per meter
+//			final double src_scale = 1.0/OrthoMap.getPixelSizeMeters(ortho_maps[nmap].orig_zoom_level); // pix per meter
 		// metric bounds of the rectified image relative to its origin
 ///			double [][] mbounds = ortho_maps[nmap].getBoundsMeters(true); // keep original bounds
 			double [][] mbounds = ortho_maps[nmap].getBoundsMeters(true,affine); // keep original bounds
@@ -1195,10 +1225,14 @@ public class OrthoMapsCollection  implements Serializable{
 
 	
 	public int getIndex(String sindx) {
-		return map_index_string.get(sindx);
+		Integer indx = map_index_string.get(sindx);
+		if (indx == null) {
+			return -1;
+		}
+		return indx;
 	}
 	
-	
+	/*
 	public float [][] getPaddedPairGPU(
 			String [] spair,
 			int       zoom_lev){
@@ -1221,6 +1255,7 @@ public class OrthoMapsCollection  implements Serializable{
 		}
 		return gpu_pair_img;
 	}
+	*/
 	
     
 	public PairwiseOrthoMatch SpiralMatch (
@@ -2375,36 +2410,11 @@ public class OrthoMapsCollection  implements Serializable{
 		// try reading current_version, if fails - restart without it (for older formats)
 		FileInputStream fileInputStream  = new FileInputStream(path);
 		ObjectInputStream objectInputStream  = new ObjectInputStream(fileInputStream);
-		int current_version = -1;
-		OrthoMapsCollection orthoMapsCollection = null;
-		PairwiseOrthoMatch.READ_NO_ALT = true; // reading old version
-		Object obj = objectInputStream.readObject(); // reads OrthoMapsCollection
-		/* // do not handle that intermediate version 
-		try {
-			obj = objectInputStream.readObject(); // reads OrthoMapsCollection
-		} catch (Exception e) {
-			// TODO Auto-generated catch block
-			e.printStackTrace();
-			fileInputStream.reset();
-			System.out.println("readOrthoMapsCollection(): error reading stream, using current_version="+current_version);
-			PairwiseOrthoMatch.READ_NO_ALT = false; // reading new version
-			obj = objectInputStream.readObject(); // reads OrthoMapsCollection
-		}
-        */
-		PairwiseOrthoMatch.READ_NO_ALT = false; // reading new version
-		if (obj instanceof OrthoMapsCollection) {
-			orthoMapsCollection = (OrthoMapsCollection) obj;
-			System.out.println("readOrthoMapsCollection(): got old version, using current_version="+current_version);
-		} else {
-			current_version = (int) obj;
+		int current_version = (int) objectInputStream.readObject(); // reads OrthoMapsCollection
 		OrthoMapsCollection.CURRENT_VERSION = current_version; // trying here 08.29.2024 - before orthoMapsCollection exists
 		System.out.println("readOrthoMapsCollection(): got current_version="+current_version);
-			PairwiseOrthoMatch.READ_NO_ALT = false; // reading new version
-			orthoMapsCollection = (OrthoMapsCollection) objectInputStream.readObject();
-		}
-		
+		OrthoMapsCollection orthoMapsCollection = (OrthoMapsCollection) objectInputStream.readObject();
 		objectInputStream.close();
-///		orthoMapsCollection.current_version = current_version;
 		System.out.println("readOrthoMapsCollection(): got orthoMapsCollection, current_version="+current_version);
 		return orthoMapsCollection;
 	}
@@ -2412,10 +2422,7 @@ public class OrthoMapsCollection  implements Serializable{
 	public void writeOrthoMapsCollection (String path) throws IOException {
 		FileOutputStream fileOutputStream = new FileOutputStream(path);
 		ObjectOutputStream objectOutputStream = new ObjectOutputStream(fileOutputStream);
-		
-///   	current_version = LATEST_VERSION;
  		objectOutputStream.writeObject(LATEST_VERSION); // current_version);
-		
 		objectOutputStream.writeObject(this);
 	    objectOutputStream.flush();
 	    objectOutputStream.close();

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

@@ -32,20 +32,61 @@ import Jama.Matrix;
 
 public class PairwiseOrthoMatch implements Serializable {
 	private static final long serialVersionUID = 1L;
-	public static boolean  READ_NO_ALT = false; // to read old format w/o alt data ( not final!)
+//	public static boolean  READ_NO_ALT = false; // to read old format w/o alt data ( not final!)
 	private          double [][] affine = new double[2][3];
-	public transient double [][] jtj =    new double [6][6];
 	public           int         zoom_lev;
 	public           double      rms = Double.NaN;
-	public transient double      overlap = 0.0;
-	public transient double []   alt_data = null;
-	public transient double []   equalize1to0 = {1,0}; // value1 = equalize2to1[0]*value2+equalize2to1[1]
-	public transient double []   quat = null; // relative orientation of the second scene (ERS affine removed). Will be eventually saved 
-	public transient double [][] qaffine = null; // affine relative to rotated scenes 
+	public           double      overlap = 0.0;
+	public           double []   alt_data = null;
+	public           double []   equalize1to0 = {1,0}; // value1 = equalize2to1[0]*value2+equalize2to1[1]
+	public           double []   quat = null; // relative orientation of the second scene (ERS affine removed). Will be eventually saved 
+	public           double [][] qaffine = null; // affine relative to rotated scenes 
+	// real transient
+	public transient double [][] jtj =    new double [6][6];
 	// below - not saved/restored
 	public transient boolean     ok = false; // not saved/restored
 	public transient int []      nxy = null; // not saved, just to communicate for logging
 	
+	private void writeObject(ObjectOutputStream oos) throws IOException {
+		oos.defaultWriteObject();
+		for (int i = 0; i < jtj.length; i++) {
+			for (int j = i; j < jtj[i].length; j++) {
+				oos.writeObject(jtj[i][j]);
+			}
+		}
+//		oos.writeObject(overlap);
+//		oos.writeObject(equalize1to0);
+//		oos.writeObject(alt_data);
+//		oos.writeObject(quat);
+//		oos.writeObject(qaffine);
+		
+	}
+	private void readObject(ObjectInputStream ois) throws ClassNotFoundException, IOException {
+		ois.defaultReadObject();
+		jtj = new double [6][6]; // readObject does not use constructor!
+		for (int i = 0; i < jtj.length; i++) {
+			for (int j = i; j < jtj[i].length; j++) {
+				jtj[i][j] = (Double) ois.readObject();
+				if (j > i) {
+					jtj[j][i] = jtj[i][j];
+				}
+			}
+		}
+//		overlap = (Double) ois.readObject();
+//		equalize1to0 = new double[] {1,0};
+//		equalize1to0 = (double[]) ois.readObject();
+//		if (!READ_NO_ALT) {
+//		alt_data = (double[]) ois.readObject();
+//		}
+//		if (OrthoMapsCollection.CURRENT_VERSION >= OrthoMapsCollection.VERSION_POST_ORIENT) {
+		quat= (double[]) ois.readObject();
+		qaffine = (double[][]) ois.readObject();
+//		}		
+		
+	}
+	
+	
+	
 	public double [] getQuaternion() {
 		return quat;
 	}
@@ -95,6 +136,11 @@ public class PairwiseOrthoMatch implements Serializable {
 	public boolean isDefined() {
 		return affine != null;
 	}
+	
+	public boolean isAffineNonTrivial() {
+		return OrthoMap.isAffineNonTrivial(this.affine);
+	}
+
 	public double [] getEqualize2to1() {
 		return equalize1to0;
 	}
@@ -298,42 +344,5 @@ public class PairwiseOrthoMatch implements Serializable {
 		this.affine= affine;
 	}
 	
-	private void writeObject(ObjectOutputStream oos) throws IOException {
-		oos.defaultWriteObject();
-		for (int i = 0; i < jtj.length; i++) {
-			for (int j = i; j < jtj[i].length; j++) {
-				oos.writeObject(jtj[i][j]);
-			}
-		}
-		oos.writeObject(overlap);
-		oos.writeObject(equalize1to0);
-		oos.writeObject(alt_data);
-		oos.writeObject(quat);
-		oos.writeObject(qaffine);
-		
-	}
-	private void readObject(ObjectInputStream ois) throws ClassNotFoundException, IOException {
-		ois.defaultReadObject();
-		jtj = new double [6][6]; // readObject does not use constructor!
-		for (int i = 0; i < jtj.length; i++) {
-			for (int j = i; j < jtj[i].length; j++) {
-				jtj[i][j] = (Double) ois.readObject();
-				if (j > i) {
-					jtj[j][i] = jtj[i][j];
-				}
-			}
-		}
-		overlap = (Double) ois.readObject();
-//		equalize1to0 = new double[] {1,0};
-		equalize1to0 = (double[]) ois.readObject();
-		if (!READ_NO_ALT) {
-			alt_data = (double[]) ois.readObject();
-		}
-		if (OrthoMapsCollection.CURRENT_VERSION >= OrthoMapsCollection.VERSION_POST_ORIENT) {
-			quat= (double[]) ois.readObject();
-			qaffine = (double[][]) ois.readObject();
-		}		
-		
-	}
 	//private void readObjectNoData() throws ObjectStreamException; // used to modify default values
 }