Copied affine export from lwir16 branch

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

@@ -195,6 +195,10 @@ public class ComboMatch {
                 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;
@@ -261,6 +265,10 @@ public class ComboMatch {
                                 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    ("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[].");
@@ -275,6 +283,8 @@ public class ComboMatch {
                 omtch_img_set = ComboMatch.FILES_LISTS_PATHS[gd.getNextChoiceIndex()];
                 String files_list_path =         omtch_img_set+".list";
                 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;
@@ -313,6 +323,11 @@ public class ComboMatch {
                 fix_duplicates=             gd.getNextBoolean();
                 update_bl_bc=               gd.getNextBoolean();
                 suffix_bc_bl_indx =         gd.getNextChoiceIndex();
+                
+                export_affine =             gd.getNextBoolean();
+                export_affine2 =            gd.getNextBoolean();
+                
+                
                 log_append =                gd.getNextBoolean();
                 log_path =                  gd.getNextString();
 //              READ_NO_ALT =               gd.getNextBoolean();
@@ -344,6 +359,64 @@ public class ComboMatch {
                         maps_collection.updateNumberScenes();
                         maps_collection.updateSfmGain();
                 }
+                
+                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 (export_affine || export_affine2) {
+                        return true; // do not save
+                }
+                
+                
                 if (fix_duplicates) {
                         removeDuplicateScenes (maps_collection);
                 }
@@ -358,6 +431,8 @@ public class ComboMatch {
 			}
 		}
 		
+		
+		
 		String [] names = maps_collection.getNames(); // null
 		if (object_list != null) {
 			int       corr_size =                128;