updated version working

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

@@ -175,7 +175,7 @@ public class ComboMatch {
 		boolean display_pairs =            false;
 		boolean create_map =               false;
 		boolean create_equalize =          false;
-		boolean use_saved_collection = false; // true; // false;
+		boolean use_saved_collection = true; // false;
 		boolean save_collection =      false; // true;
 		boolean process_correlation = true; // use false to save new version of data
 		int     num_tries_fit =       10;
@@ -339,7 +339,7 @@ public class ComboMatch {
 				maps_collection = OrthoMapsCollection.readOrthoMapsCollection (orthoMapsCollection_path);
 			} catch (ClassNotFoundException | IOException e) {
 				use_files_list = true;
-				System.out.println("Saved data not found: "+orthoMapsCollection_path+", building from a list "+files_list_path);
+				System.out.println("Saved data not found (or is corrupt): "+orthoMapsCollection_path+", building from a list "+files_list_path);
 			}
 			//files_list_path
 			if (!use_files_list) {
@@ -361,10 +361,12 @@ public class ComboMatch {
 		}
 		
 		if (import_export) {
-			return updateImportExport(
+			boolean OK = updateImportExport(
 					omtch_img_set, // String files_base
 					maps_collection); //						OrthoMapsCollection maps_collection
-
+			if (!OK) {
+				return false;
+			}
 		}
 		
 		
@@ -867,7 +869,7 @@ public class ComboMatch {
 			maps_collection.processComboMap(
 					clt_parameters, // CLTParameters    clt_parameters,
 					debugLevel);
-			return true;
+//			return true; // need to save AGL?
 		}
 		
 		// for all modes - needed for create_overlaps || process_correlation || render_match || pattern_match
@@ -2689,7 +2691,7 @@ adjusted affines[1] for a pair: 1694564291_293695/1694564778_589341
 		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 files metadata",      update_lla,     "Re-read files metadata (if it was modified), needed to calculate AGL.");
 		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.");
@@ -2726,7 +2728,7 @@ adjusted affines[1] for a pair: 1694564291_293695/1694564778_589341
 		if (update_lla) {
 			System.out.println("Updating map files metadata");
 			maps_collection.updateLLA();
-			maps_collection.updateNumberScenes();
+//			maps_collection.updateNumberScenes(); It is very long
 			maps_collection.updateSfmGain();
 		}
 		if (update_kernel_patterns) {
@@ -2807,14 +2809,14 @@ adjusted affines[1] for a pair: 1694564291_293695/1694564778_589341
 					}
 				}
 			}
-			maps_collection.updateNumberScenes();
+//			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,
+					affines2_path,
 					null,            // scenes0,
 					null,            // ArrayList<AltitudeMismatchKernel> kernels,
 					null,            // ArrayList<GroundObjectPattern>    patterns);
@@ -2823,6 +2825,7 @@ adjusted affines[1] for a pair: 1694564291_293695/1694564778_589341
 					null,            // ArrayList<AffineImport>           affine_import,
 					affine2_import); // ArrayList<Affine2Import>          affine2_import) {
 			int num_updated_affines = 0;
+			int num_new_affines = 0;
 			for (Affine2Import affine2Import: affine2_import) {
 				OrthoMap map =  maps_collection.getMap(affine2Import.name1);
 				if (map != null) {
@@ -2831,6 +2834,7 @@ adjusted affines[1] for a pair: 1694564291_293695/1694564778_589341
 						if (overwrite_affine || !pom.isAffineNonTrivial()) {
 							pom.setOverlap(affine2Import.overlap);
 							pom.setAffine(affine2Import.affine); // does not clone - OK
+							num_updated_affines++;
 						}						
 					} else {
 						OrthoMap map2 =  maps_collection.getMap(affine2Import.name2);
@@ -2841,15 +2845,12 @@ adjusted affines[1] for a pair: 1694564291_293695/1694564778_589341
 								Double.NaN,             // double rms,
 								zoom_lev,               // int zoom_lev,
 								affine2Import.overlap); // double overlap)
+						map.setMatch(map2.getName(), pom);
+						num_new_affines++;
 					}
-
-
 				}
-
-
-
-
 			}
+			System.out.println("Updated "+num_updated_affines+" pairwise affines, setup new "+num_new_affines+" matches. Specified "+affine2_import.size()+" matches.");
 		}
 
 		if (update_bl_bc) {

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

@@ -201,16 +201,16 @@ public class OrthoMap implements Comparable <OrthoMap>, Serializable{
 	}
 
 	public int getWidth() {
-		return getImageData().getWidth(); // orig_width;
+		return getImage().getWidth(); // orig_width;
 	}
 	public int getHeight() {
-		return getImageData().getHeight(); //orig_height;
+		return getImage().getHeight(); //orig_height;
 	}
 	public int getAltWidth() {
-		return getAltData().getWidth(); // orig_width;
+		return getAlt().getWidth(); // orig_width;
 	}
 	public int getAltHeight() {
-		return getAltData().getHeight(); //orig_height;
+		return getAlt().getHeight(); //orig_height;
 	}
 	
 	public void setMatch(

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

@@ -62,8 +62,9 @@ public class OrthoMapsCollection  implements Serializable{
 	
 	public static final int VERSION_PRE_ORIENT =  100;
 	public static final int VERSION_POST_ORIENT = 101;
+	public static final int VERSION_ORANGE =      102;
 	
-	public static int       LATEST_VERSION = VERSION_POST_ORIENT; // 100; // use when read from .list
+	public static int       LATEST_VERSION = VERSION_ORANGE; // 100; // use when read from .list
 ///	public transient int    current_version = LATEST_VERSION;
 	public static int       CURRENT_VERSION = LATEST_VERSION;
 	
@@ -341,14 +342,19 @@ public class OrthoMapsCollection  implements Serializable{
 				System.out.println("updateLLa(): n="+n);
 			}
 			ortho_maps[n].updateLLA();
+			IJ.showStatus("Updating LLA "+n+" of "+ortho_maps.length);
+			IJ.showProgress(1.0*n/ortho_maps.length);
 		}
 		updateAGL();
 	}
 	
 	public void updateAGL() {
 		for (int n = 0; n < ortho_maps.length; n++) {
+			IJ.showStatus("Updating AGL "+n+" of "+ortho_maps.length);
 			ortho_maps[n].agl = Double.NaN;
 			ortho_maps[n].agl = ortho_maps[n].getAGL();
+			IJ.showProgress(1.0*n/ortho_maps.length);
+			
 		}		
 	}
 	
@@ -7122,7 +7128,11 @@ public class OrthoMapsCollection  implements Serializable{
 			for (int nscene=0; nscene<indices.length; nscene++) {
 				int indx = indices[nscene];
 				System.out.println("Scene="+indx+", agl="+ortho_maps[indx].getAGL());
+				
 				double [] qorient = ortho_maps[indx].getQOrinet(); // QuatUtils.invert(ortho_maps[indx].getQOrinet());
+				if (qorient == null) {
+					qorient = new double [] {1,0,0,0};
+				}
 				final int src_width = ortho_maps[indx].getImageData().width;   // assuming same image size for alt and texture
 				final int src_height = ortho_maps[indx].getImageData().height; // assuming same image size for alt and texture
 				final double [] image_data = ortho_maps[indx].getImageData().getDData();

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

@@ -49,9 +49,13 @@ public class PairwiseOrthoMatch implements Serializable {
 	
 	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]);
+		if (jtj == null) {
+			oos.writeObject(Double.NaN);
+		} else {
+			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);
@@ -64,14 +68,19 @@ public class PairwiseOrthoMatch implements Serializable {
 	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];
+		readjtj:
+			for (int i = 0; i < jtj.length; i++) {
+				for (int j = i; j < jtj[i].length; j++) {
+					jtj[i][j] = (Double) ois.readObject();
+					if (Double.isNaN(jtj[0][0]) && (i==0) && (j==0)) {
+						jtj=null;
+						break readjtj;
+					}
+					if (j > i) {
+						jtj[j][i] = jtj[i][j];
+					}
 				}
 			}
-		}
 //		overlap = (Double) ois.readObject();
 //		equalize1to0 = new double[] {1,0};
 //		equalize1to0 = (double[]) ois.readObject();
@@ -79,8 +88,8 @@ public class PairwiseOrthoMatch implements Serializable {
 //		alt_data = (double[]) ois.readObject();
 //		}
 //		if (OrthoMapsCollection.CURRENT_VERSION >= OrthoMapsCollection.VERSION_POST_ORIENT) {
-		quat= (double[]) ois.readObject();
-		qaffine = (double[][]) ois.readObject();
+//		quat= (double[]) ois.readObject();
+//		qaffine = (double[][]) ois.readObject();
 //		}		
 		
 	}