Next snapshot, working onpairs selection and LMA map

src/main/java/com/elphel/imagej/correction/Eyesis_Correction.java

@@ -849,6 +849,7 @@ public class Eyesis_Correction implements PlugIn, ActionListener {
 			addButton("Read Tiff",  panelLWIRWorld, color_process);
 			addButton("Test video",  panelLWIRWorld, color_process);
 			addButton("Ortho Pairs",  panelLWIRWorld, color_process);
+			addButton("Manual pair",  panelLWIRWorld, color_process);
 			addButton("Extract Objects",  panelLWIRWorld, color_process);
 			addButton("Mismatched resolutions",  panelLWIRWorld, color_process);
 			addButton("Generate DATI",  panelLWIRWorld, color_process);
@@ -5709,7 +5710,7 @@ public class Eyesis_Correction implements PlugIn, ActionListener {
 				e.printStackTrace();
 			}
 //			ComboMatch.testReadTiff();
-		} else if (label.equals("Ortho Pairs") || label.equals("Extract Objects")) {
+		} else if (label.equals("Ortho Pairs") || label.equals("Extract Objects") || label.equals("Manual pair")) {
 			DEBUG_LEVEL = MASTER_DEBUG_LEVEL;
 			EYESIS_CORRECTIONS.setDebug(DEBUG_LEVEL);
 			if (GPU_TILE_PROCESSOR == null) {
@@ -5731,6 +5732,7 @@ public class Eyesis_Correction implements PlugIn, ActionListener {
 					CLT_PARAMETERS,     // CLTParameters    clt_parameters,
 					GPU_TILE_PROCESSOR,
 					label.equals("Extract Objects"), // boolean    extract_mines,
+					label.equals("Manual pair"), // boolean          manual_pair,
 					DEBUG_LEVEL);
 		} else if (label.equals("Test video")) {
 			ImagePlus imp_sel = WindowManager.getCurrentImage();

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

@@ -61,6 +61,7 @@ public class ComboMatch {
 			 CLTParameters    clt_parameters,
 			 GPUTileProcessor gpu_tile_processor, // initialized by the caller
 			 boolean          extract_objects,
+			 boolean          manual_pair,
 			 int              debugLevel) {
 		boolean create_kernels = debugLevel>1000;
 		if (create_kernels) {
@@ -70,7 +71,7 @@ public class ComboMatch {
 		GPU_TILE_PROCESSOR = gpu_tile_processor;
 		PairwiseOrthoMatch pairwiseOrthoMatch = null;
 		String [] pair_names = new String[2];
-		ImagePlus imp_sel = WindowManager.getCurrentImage();
+		ImagePlus imp_sel = manual_pair? WindowManager.getCurrentImage() : null;
 		String [] gpu_spair = null;
 		boolean use_marked_image =    false; // will be set if found
 		String [] all_scenes = null;

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

@@ -21,9 +21,11 @@ import java.time.format.DateTimeFormatter;
 import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.Calendar;
+import java.util.Collections;
 import java.util.HashMap;
 import java.util.HashSet;
 import java.util.List;
+import java.util.Set;
 import java.util.concurrent.atomic.AtomicBoolean;
 import java.util.concurrent.atomic.AtomicInteger;
 
@@ -5230,6 +5232,19 @@ public class OrthoMapsCollection  implements Serializable{
 		heur =             (int) gd.getNextNumber();
 		use_multi =              gd.getNextBoolean();
 		double max_rmse_reuse= max_rms_refine;
+		int [][] pairs_defined = filterPairs(
+				indices,          // int []  indices_in,
+				min_overlap_frac, // double  min_overlap_frac,
+				max_rmse_reuse,   // double  max_rmse,
+				true,             // boolean max_resolution,
+				null);            // int [][] remove_pairs
+		int [][] pairs_undefined = filterPairs(
+				indices,          // int []  indices_in,
+				min_overlap_frac, // double  min_overlap_frac,
+				0,                // max_rmse_reuse,   // double  max_rmse,
+				false,            // boolean max_resolution,
+				pairs_defined);   // int [][] remove_pairs
+		/*
 		PairsGraph  pairsGraph = new PairsGraph(
 				this,             // OrthoMapsCollection orthoMapsCollection,
 				indices,          // int []  indices,
@@ -5237,6 +5252,13 @@ public class OrthoMapsCollection  implements Serializable{
 				max_rmse_reuse,   // double  max_rmse_reuse,
 				use_multi,        // boolean multi,
 				debugLevel);      // int     debugLevel);
+		*/
+		PairsGraph  pairsGraph = new PairsGraph(
+				this,             // OrthoMapsCollection orthoMapsCollection,
+				pairs_undefined,  // int [][] undefined_pairs,
+				pairs_defined,    // int [][] defined_pairs,
+				use_multi,        // boolean multi,
+				debugLevel);      // int     debugLevel);
 		
 		if (dry_run) {
 			return pairsGraph.dryRun(
@@ -6184,4 +6206,118 @@ public class OrthoMapsCollection  implements Serializable{
 		ImageDtt.startAndJoin(threads);
 		return overlaps;
 	}
+	
+	public int [][] filterPairs(
+			int []   indices_in,
+			double   min_overlap_frac,
+			double   max_rmse,
+			boolean  max_resolution, // require defined and full resolution
+			int [][] remove_pairs) { 
+		if (indices_in == null) {
+			indices_in = new int [ortho_maps.length];
+			for (int i = 0; i < indices_in.length; i++) {
+				indices_in[i] = i;
+			}
+		}
+		boolean [] used_scenes = new boolean [ortho_maps.length];
+		for (int i:indices_in) {
+			used_scenes[i] = true;
+		}
+		HashSet <Point> donotuse_set = new HashSet<Point>();
+		if (remove_pairs != null) {
+			for (int [] p: remove_pairs) {
+				donotuse_set.add(new Point(p[0],p[1]));
+			}
+		}
+		ArrayList<Point> pairs_list = new ArrayList<Point>();
+		for (int scene0:indices_in) {
+			Set<String> match_names = ortho_maps[scene0].pairwise_matches.keySet();
+			ArrayList<String> names_list = new ArrayList<String>();
+			names_list.addAll(match_names);
+			Collections.sort(names_list);
+			for (String scene1_name:names_list) {
+				PairwiseOrthoMatch match = ortho_maps[scene0].getMatch(scene1_name, !max_resolution); // may be not defined only
+				if (match != null) {
+					int scene1 = getIndex(scene1_name);
+					if ( used_scenes[scene1] && (!max_resolution || match.isDefined()) &&
+							(match.getOverlap() >= min_overlap_frac) &&
+							((max_rmse <= 0) || (match.getRMS() <= max_rmse))
+							){
+						if (max_resolution) {
+							int min_zoom = Math.min(ortho_maps[scene0].getOriginalZoomLevel(), ortho_maps[scene1].getOriginalZoomLevel());
+							if (match.getZoomLevel() < min_zoom) {
+								continue;
+							}
+						}
+						Point p = new Point(scene0, scene1);
+						if (remove_pairs != null) {
+							if (donotuse_set.contains(p)) {
+								continue;
+							}
+						}
+						System.out.println(String.format("%5d: %3d-%3d, %7.4f, %7.4f",
+								pairs_list.size(), scene0, scene1, match.getOverlap(), match.getRMS()));
+						pairs_list.add(p);
+					}
+				}
+			}
+		}
+		int [][] pairs = new int [pairs_list.size()][2];
+		for (int i = 0; i < pairs.length; i++) {
+			Point p = pairs_list.get(i);
+			pairs[i][0] = p.x;
+			pairs[i][1] = p.y;
+		}
+		return pairs;
+	}
+	
+	public int [] getScenesFromPairs(
+			int [][] pairs,
+			int [] indices_in) { // preselected indices or null
+		boolean [] used_scenes = new boolean [ortho_maps.length];
+		if (indices_in != null) {
+			for (int i:indices_in) {
+				used_scenes[i] = true;
+			}
+		}
+		for (int [] p:pairs) {
+			used_scenes[p[0]] = true;
+			used_scenes[p[1]] = true;
+		}
+		int indx = 0;
+		for (int i = 0; i < used_scenes.length; i++) if (used_scenes[i]){
+			indx++;	
+		}
+		int [] indices = new int [indx];
+		indx = 0;
+		for (int i = 0; i < used_scenes.length; i++) if (used_scenes[i]){
+			indices[indx++] = i;	
+		}
+		return indices;
+	}
+	/**
+	 * Re-index pairs to exclude scenes not present in indices[] 
+	 * @param pairs   - array of start,end absolute scene numbers
+	 * @param indices - ascending array of used scenes (or null - all scenes)
+	 * @return  re-indexed pairs, indices exclude scenes that are not in indices[]
+	 */
+	public int [][] condensePairs(
+			int [][] pairs_all,
+			int [] indices) {
+		if (indices == null) {
+			return pairs_all;
+		}
+		int [] reindex = new int [ortho_maps.length];
+		int [][] pairs = new int [pairs_all.length][2];
+		Arrays.fill(reindex, -1);
+		for (int i = 0; i < indices.length; i++) {
+			reindex[indices[i]] = i;
+		}
+		for (int i = 0; i < pairs.length; i++) {
+			pairs[i][0] = reindex[pairs_all[i][0]];
+			pairs[i][1] = reindex[pairs_all[i][1]];
+		}
+		return pairs;
+	}
+	
 }

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

@@ -221,6 +221,8 @@ public class OrthoMultiLMA {
 			String              orthoMapsCollection_path
 			) {
 		boolean all_pairs =      true;
+		double  min_overlap_frac = clt_parameters.imp.pwise_overlap; // 0.25;
+		double  max_rms_refine =      clt_parameters.imp.pwise_max_rms;  // 0.35; //
 		boolean move_only =      clt_parameters.imp.pmap_move_only;      // false;
 		boolean ignore_affines = clt_parameters.imp.pmap_ignore_affines; // false;
         boolean use_inv =        clt_parameters.imp.pmap_use_inv;        // false;
@@ -236,6 +238,8 @@ public class OrthoMultiLMA {
 
 		GenericJTabbedDialog gd = new GenericJTabbedDialog("Pairwise Match Parameters",1200,400);
 		gd.addCheckbox    ("Use all available pairs",  all_pairs,  "Use all available pairs.");
+		gd.addNumericField("Minimal overlap fraction",    min_overlap_frac,  3,7,"",	    "Minimal overlap fraction.");
+		gd.addNumericField("Satisfactory RMSE, final",    max_rms_refine,3,7,"scaled pix",	"Maximal RMSE to consider match, in scaled pixels, during refine.");
 		gd.addCheckbox    ("Moves only",               move_only,  "Moves only, no affine transform.");
 		gd.addCheckbox    ("Ignore existing affines",  ignore_affines, "Start from unity matrices, ignore saved affines.");
 		gd.addCheckbox    ("Use reversed pairs",       use_inv,     "Use reversed (late-early timestamps) pairs.");
@@ -252,6 +256,8 @@ public class OrthoMultiLMA {
  		gd.showDialog();
 		if (gd.wasCanceled()) return -1;
 		all_pairs =           gd.getNextBoolean();
+		min_overlap_frac =    gd.getNextNumber(); 
+ 		max_rms_refine   =    gd.getNextNumber();
         move_only =		      gd.getNextBoolean();
         ignore_affines =      gd.getNextBoolean();
         use_inv =             gd.getNextBoolean();
@@ -270,6 +276,10 @@ public class OrthoMultiLMA {
 				maps_collection,          // OrthoMapsCollection maps_collection,
 				orthoMapsCollection_path, // String              orthoMapsCollection_path,
 				all_pairs,                // boolean             all_pairs,
+				// filtering of the pairs
+				min_overlap_frac,         // double              min_overlap_frac,
+				max_rms_refine,           // double              max_rms,
+
 				move_only,                // boolean             move_only,
 				ignore_affines,           // boolean             ignore_affines,
 				use_inv,                  // boolean             use_inv,
@@ -288,6 +298,9 @@ public class OrthoMultiLMA {
 				OrthoMapsCollection maps_collection,
 				String              orthoMapsCollection_path,
 				boolean             all_pairs,
+				double              min_overlap_frac,
+				double              max_rms,
+				
 				boolean             move_only,
 				boolean             ignore_affines,
 		        boolean             use_inv,
@@ -304,6 +317,7 @@ public class OrthoMultiLMA {
 		boolean             corr_avg= (skew_pull > 0) || (tilt_pull > 0) || (scale_pull > 0);
 		int [] indices = null;
 		if (all_pairs) {
+			/*
 			boolean [] used_scenes = new boolean [maps_collection.ortho_maps.length];
 			for (int scene0 = 0; scene0 < (used_scenes.length-1); scene0++) {
 				Set<String> match_names = maps_collection.ortho_maps[scene0].pairwise_matches.keySet();
@@ -328,11 +342,25 @@ public class OrthoMultiLMA {
 			if (debugLevel > -1) {
 				System.out.println("buildOrthoMap(): got "+indices.length+" scenes with pairs");
 			}
+			*/
 		} else {
 			indices = maps_collection.getScenesSelection(
 					null, // boolean select_all,
 					" to build a map with LMA from pair-wise matches"); // String purpose)
 		}
+		
+		int [][] pairs_defined_abs = maps_collection.filterPairs(  // absolute indices
+				indices,          // int []  indices_in,
+				min_overlap_frac, // double  min_overlap_frac,
+				max_rms,          // double  max_rmse,
+				true,             // boolean max_resolution,
+				null);            // int [][] remove_pairs
+		indices= maps_collection.getScenesFromPairs(
+				pairs_defined_abs,// int [][] pairs,
+				null);            // int [] indices_in)  // preselected indices or null
+		int [][] defined_pairs =   maps_collection.condensePairs (pairs_defined_abs,indices);
+
+		
 		OrthoMultiLMA oml = new OrthoMultiLMA(
 				corr_avg,
 				move_only);
@@ -345,6 +373,7 @@ public class OrthoMultiLMA {
 				clt_parameters,   // CLTParameters       clt_parameters,
 				maps_collection,  // OrthoMapsCollection maps_collection,
 				indices,          // int []              indices,
+				defined_pairs, // int [][]            pairs, // or null? condensed
 				ignore_affines,   // boolean             ignore_affines,
 				val_coord,        // double []           val_coord, // 1 - valid, 0 - invalid, minimize coordinates errors
 				position_pull,    // double              position_pull,
@@ -442,6 +471,7 @@ public class OrthoMultiLMA {
 			CLTParameters       clt_parameters,
 			OrthoMapsCollection maps_collection,
 			int []              indices,
+			int [][]            pairs_pre, // or null?
 			boolean             ignore_affines,
 			double []           val_coord, // 1 - valid, 0 - invalid, minimize coordinates errors
 			double              position_pull,
@@ -456,6 +486,16 @@ public class OrthoMultiLMA {
 		matches = new PairwiseOrthoMatch[indices.length][indices.length];
 		ArrayList<Point> pairs_list = new ArrayList<Point>();
 //		ArrayList<Double> offset_list = new ArrayList<Double>();
+		if (pairs_pre != null) {
+			for (int [] pair:pairs_pre) {
+				int i = pair[0], j = pair[1];
+				int scene0=indices[i],scene1=indices[j];
+				PairwiseOrthoMatch match = maps_collection.ortho_maps[scene0].getMatch(maps_collection.ortho_maps[scene1].getName());
+				matches[i][j] = match;
+//				matches[j][i] = inv_match;
+				pairs_list.add(new Point(i,j)); // only once?
+			}
+		} else {
 			for (int i = 0; i < num_scenes-1; i++) {
 				int scene0 = indices[i]; 
 				for (int j = i+1; j < num_scenes; j++){
@@ -482,6 +522,7 @@ public class OrthoMultiLMA {
 					}
 				}
 			}
+		}
 		num_pairs = pairs_list.size();
 		offsets = new double [num_pairs][2];
 		pairs =   new int[num_pairs][2];

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

@@ -54,6 +54,7 @@ public class PairsGraph {
 	private final int         debugLevel;
 	private boolean           multi; // use single-threaded in debug mode?
 
+	
 	public PairsGraph (
 			OrthoMapsCollection orthoMapsCollection,
 			int []  indices,
@@ -121,6 +122,50 @@ public class PairsGraph {
 		}
 	}
 	
+	
+	public PairsGraph (
+			OrthoMapsCollection orthoMapsCollection,
+			int [][] undefined_pairs_all, // indices in orthoMapsCollection.ortho_maps[] (all scenes, not just selected)
+			int [][] defined_pairs_all,   // indices in orthoMapsCollection.ortho_maps[] (all scenes, not just selected)
+			boolean multi,
+			int     debugLevel) {
+		this.orthoMapsCollection = orthoMapsCollection;
+		int [] indices0 =          orthoMapsCollection.getScenesFromPairs(undefined_pairs_all, null);
+		this.indices =             orthoMapsCollection.getScenesFromPairs(defined_pairs_all, indices0);
+		int [][] undefined_pairs = orthoMapsCollection.condensePairs (undefined_pairs_all,indices);
+		int [][] defined_pairs =   orthoMapsCollection.condensePairs (defined_pairs_all,indices);
+		this.debugLevel =          debugLevel;
+		this.multi =               multi;
+		pair_state =               new int [indices.length][indices.length];
+		overlaps =                 new double [indices.length][indices.length];
+		timestamps =               new double [indices.length];
+		groups =                   new int [indices.length];
+		dist =                     new int [indices.length][indices.length];
+		OrthoMap []                ortho_maps=orthoMapsCollection.getMaps();
+		for (int i = 0; i < indices.length; i++) {
+			groups[i] = i;
+			timestamps[i] = ortho_maps[indices[i]].getTimeStamp();
+		}
+		
+		for (int [] u_pair: undefined_pairs) {
+			pair_state[u_pair[0]][u_pair[0]] = PAIR_UNDEFINED;
+		}
+		for (int [] d_pair: defined_pairs) {
+			pair_state[d_pair[0]][d_pair[0]] = PAIR_DEFINED;
+			recordPair(
+					d_pair, // int []   pair,
+					true,             // boolean  success,
+					multi);
+		}
+		pairs = multi? getPairsIndicesMulti():getPairsIndicesSingle();
+		if (debugLevel > -1) {
+			System.out.println("Number of scenes - "+indices.length);
+			System.out.println("Number of defined pairs - "+defined_pairs.length);
+			System.out.println("Number of undefined pairs - "+undefined_pairs.length);
+			System.out.println("Number of disconnected groups - "+getNumberOfGroups());
+		}
+	}
+	
 	public int getNumberOfGroups() {
 		HashSet<Integer> hs = new HashSet<Integer>();
 		for (int i:groups) {

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

@@ -228,6 +228,10 @@ public class PairwiseOrthoMatch implements Serializable {
 		return affine1;
 	}	
 	
+	public int getZoomLevel() {
+		return zoom_lev;
+	}
+	
 	public double [][] getAffine(){
 		if (affine == null) {
 			return new double [][] {{1,0,0},{0,1,0}};