Working snapshot,single-connected pairs

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

@@ -1303,6 +1303,8 @@ public class ComboMatch {
 				System.out.println("This can happen if files have different resolution for new run.");
 				System.out.println("Verify path, then modify filenames[i], break at line above: 'maps_collection.ortho_maps[i].setFileName(filenames[i])'.");
 				System.out.println("Reduce i by 1 and continue");
+			} else {
+				maps_collection.ortho_maps[i] = new OrthoMap(path);
 			}
 		}		
 		return true;

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

@@ -913,6 +913,10 @@ public class OrthoMap implements Comparable <OrthoMap>, Serializable{
 		int swidth =  getWidth();
 		int sheight = getHeight();
 		final float [] spix = orig_image.data;
+		if (swidth*sheight != spix.length) {
+			System.out.println ("downScaleForGPU(): swidth="+ swidth+", sheight="+sheight+", swidth*sheight="+(swidth*sheight)+", spix.length="+spix.length);
+			System.out.println ();
+		}
 		final int width = (swidth+frscale-1)/frscale;
 		final int height = (sheight+frscale-1)/frscale;
 		final int tiles = width * height;
@@ -939,17 +943,28 @@ public class OrthoMap implements Comparable <OrthoMap>, Serializable{
                     	for (int py = 0; py < tileH; py++) {
                     		int ls = (tileY*frscale + py)*swidth;
                     		for (int px = 0; px < tileW; px++) {
-                    			double d = spix[ls + tileX*frscale+px];
+                    			int indx = ls + tileX*frscale+px;
+                    			if ((indx >=0) && (indx < spix.length)) {
+                    				double d = spix[ls + tileX*frscale+px]; //java.lang.ArrayIndexOutOfBoundsException: Index 3892800 out of bounds for length 3892680
                     				if (!Double.isNaN(d)) {
                     					double w = wnd[py][px];
                     					sw += w;
                     					swd += w*d;
                     				}
-                    			if (sw > 0) {
-                    				opix[tileY * width + tileX] = (float) (swd/sw);
+                    			} else {
+                    				System.out.println("downScaleForGPU(): indx = "+indx+" ("+spix.length+"), tileX= "+
+                    						tileX+", tileY="+tileY+", px="+px+", py="+py+", ls="+ls);	
+                    			}
+//                    			if (sw > 0) {
+//                    				opix[tileY * width + tileX] = (float) (swd/sw);
+//                    			}
                     		}
                     	}
+            			if (sw > 0) {
+            				opix[tileY * width + tileX] = (float) (swd/sw);
             			}
+
+                    	
                     }
                 }
             };

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

@@ -29,6 +29,8 @@ import java.awt.Point;
 import java.io.IOException;
 import java.util.ArrayList;
 import java.util.Arrays;
+import java.util.HashMap;
+import java.util.Set;
 import java.util.concurrent.atomic.AtomicInteger;
 
 import com.elphel.imagej.cameras.CLTParameters;
@@ -218,6 +220,7 @@ public class OrthoMultiLMA {
 			OrthoMapsCollection maps_collection,
 			String              orthoMapsCollection_path
 			) {
+		boolean all_pairs =      true;
 		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;
@@ -232,22 +235,23 @@ public class OrthoMultiLMA {
 		int     debugLevel =     clt_parameters.imp.pmap_debugLevel;     // 2;
 
 		GenericJTabbedDialog gd = new GenericJTabbedDialog("Pairwise Match Parameters",1200,400);
+		gd.addCheckbox    ("Use all available pairs",  all_pairs,  "Use all available pairs.");
 		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.");
-		gd.addNumericField("Skew pull",                skew_pull,    7,10,"",	"Intention to have axes perpendicular.");
-		gd.addNumericField("Tilt pull",                tilt_pull,    7,10,"",	"Intention to have axes same length.");
-		gd.addNumericField("Scale pull",               scale_pull,   7,10,"",	"Intention to have average scale of images = 1.0.");
-		gd.addNumericField("Position pull",            position_pull,7,10,"",	"Intension to match IMS (GNSS) coordinates.");
+		gd.addNumericField("Skew pull",                skew_pull,    7,11,"",	"Intention to have axes perpendicular.");
+		gd.addNumericField("Tilt pull",                tilt_pull,    7,11,"",	"Intention to have axes same length.");
+		gd.addNumericField("Scale pull",               scale_pull,   7,11,"",	"Intention to have average scale of images = 1.0.");
+		gd.addNumericField("Position pull",            position_pull,7,11,"",	"Intension to match IMS (GNSS) coordinates.");
 		gd.addNumericField("Overlap inportance",       overlap_pow,  3,7,"",	"Raise overlap fraction (of the smaller image) to this power before using as weight.");
-		gd.addNumericField("RMSE relative improvement",rms_diff,     8,10,"",	"Relative RMSE improvement to exit LMA.");
+		gd.addNumericField("RMSE relative improvement",rms_diff,     8,11,"",	"Relative RMSE improvement to exit LMA.");
 		gd.addNumericField("LMA iterations",           num_iter, 0,3,"",".Maximal number of the LMA iterations.");
 		gd.addCheckbox    ("Show result image",        show_result, ".");
 		gd.addNumericField("Debug level for maps",     debugLevel, 0,3,"","Debug building for LMA building maps.");
 
  		gd.showDialog();
 		if (gd.wasCanceled()) return -1;
-
+		all_pairs =           gd.getNextBoolean();
         move_only =		      gd.getNextBoolean();
         ignore_affines =      gd.getNextBoolean();
         use_inv =             gd.getNextBoolean();
@@ -265,6 +269,7 @@ public class OrthoMultiLMA {
 				clt_parameters,           // CLTParameters       clt_parameters,
 				maps_collection,          // OrthoMapsCollection maps_collection,
 				orthoMapsCollection_path, // String              orthoMapsCollection_path,
+				all_pairs,                // boolean             all_pairs,
 				move_only,                // boolean             move_only,
 				ignore_affines,           // boolean             ignore_affines,
 				use_inv,                  // boolean             use_inv,
@@ -282,6 +287,7 @@ public class OrthoMultiLMA {
 				CLTParameters       clt_parameters,
 				OrthoMapsCollection maps_collection,
 				String              orthoMapsCollection_path,
+				boolean             all_pairs,
 				boolean             move_only,
 				boolean             ignore_affines,
 		        boolean             use_inv,
@@ -296,9 +302,37 @@ public class OrthoMultiLMA {
 				int                 debugLevel) {
 		double []           val_coord =      null; // 1 - valid, 0 - invalid, minimize coordinates errors
 		boolean             corr_avg= (skew_pull > 0) || (tilt_pull > 0) || (scale_pull > 0);
-		int [] indices = maps_collection.getScenesSelection(
+		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();
+				for (String scene1_name:match_names) {
+					PairwiseOrthoMatch match = maps_collection.ortho_maps[scene0].getMatch(scene1_name); // defined only
+					if (match != null) {
+						int scene1 = maps_collection.getIndex(scene1_name);
+						used_scenes[scene0] = true;
+						used_scenes[scene1] = true;
+					}
+				}
+			}
+			int num_scenes = 0;
+			for (int i = 0; i < used_scenes.length; i++) if (used_scenes[i]){
+				num_scenes++;
+			}
+			indices = new int [num_scenes];
+			int indx = 0;
+			for (int i = 0; i < used_scenes.length; i++) if (used_scenes[i]){
+				indices[indx++] = i;
+			}
+			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"); // String purpose)
+					" to build a map with LMA from pair-wise matches"); // String purpose)
+		}
 		OrthoMultiLMA oml = new OrthoMultiLMA(
 				corr_avg,
 				move_only);

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

@@ -57,6 +57,8 @@ public class PairsGraph {
 	public PairsGraph (
 			OrthoMapsCollection orthoMapsCollection,
 			int []  indices,
+			double  min_overlap_frac,
+			double  max_rmse_reuse,
 			boolean multi,
 			int     debugLevel) {
 		this.orthoMapsCollection = orthoMapsCollection;
@@ -75,19 +77,30 @@ public class PairsGraph {
 		}
 		int num_defined = 0;
 		int num_undefined = 0;
-		
+		int num_bad = 0;
+		int num_low_overlap = 0;
 		for (int i = 0; i < indices.length-1; i++) {
 			for (int j = i+1; j < indices.length; j++){
 				String name2 = ortho_maps[indices[j]].getName();
 				PairwiseOrthoMatch match = ortho_maps[indices[i]].getMatch(name2,true);
 				if (match != null) {
+					if (match.getOverlap() < min_overlap_frac){
+						num_low_overlap++;			
+					} else {
 						if (match.isDefined()) {
+							if ((match.getOverlap() < min_overlap_frac) || ((max_rmse_reuse > 0) && !(match.getRMS() <= max_rmse_reuse))) {
+								pair_state[i][j] = PAIR_UNDEFINED;
+								num_undefined++;
+								num_bad++;
+							} else {
 								pair_state[i][j] = PAIR_DEFINED;
 								num_defined++;
 								recordPair(
 										new int [] {i,j}, // int []   pair,
 										true,             // boolean  success,
 										multi);
+							}
+
 						} else {
 							pair_state[i][j] = PAIR_UNDEFINED;
 							num_undefined++;
@@ -96,19 +109,38 @@ public class PairsGraph {
 					}
 				}
 			}
-		HashSet<Integer> hs = new HashSet<Integer>();
-		for (int i:groups) {
-			hs.add(i);
 		}
 		pairs = multi? getPairsIndicesMulti():getPairsIndicesSingle();
-		if (debugLevel > 0) {
+		if (debugLevel > -1) {
 			System.out.println("Number of scenes - "+indices.length);
 			System.out.println("Number of defined pairs - "+num_defined);
 			System.out.println("Number of undefined pairs - "+num_undefined);
-			System.out.println("Number of disconnected groups - "+hs.size());
+			System.out.println("Number of low overlap pairs ("+min_overlap_frac+") - "+num_low_overlap);
+			System.out.println("Number of bad rms pairs ("+max_rmse_reuse+") - "+num_bad);
+			System.out.println("Number of disconnected groups - "+getNumberOfGroups());
 		}
 	}
 	
+	public int getNumberOfGroups() {
+		HashSet<Integer> hs = new HashSet<Integer>();
+		for (int i:groups) {
+			hs.add(i);
+		}
+		return hs.size();
+	}
+	
+	public int [] getIndices() {
+		return indices;
+	}
+
+	public boolean useMultiThreaded() {
+		return multi;
+	}
+	
+	public double getOverlap(
+			int [] pair) {
+		return overlaps[Math.min(pair[0],pair[1])][Math.max(pair[0],pair[1])];
+	}
 	public boolean dryRun(
 			int heur,
 			int debugLevel) {

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

@@ -37,6 +37,9 @@ public class PairwiseOrthoMatch implements Serializable {
 		this.rms =     rms;
 		this.overlap = overlap;
 	}
+	public double getRMS() {
+		return this.rms;
+	}
 	
 	public boolean isDefined() {
 		return affine != null;

src/main/java/com/elphel/imagej/tileprocessor/IntersceneMatchParameters.java

@@ -143,6 +143,7 @@ public class IntersceneMatchParameters {
     // pairwise match parameters
 	public int      pwise_zoom =         -5;
 	public double   pwise_overlap =      0.25;
+    public double   pwise_max_rms =      0.6;    // maximal acceptable LMA RMS - best during refine 
 	public boolean  pwise_skip_exist =   true;
 	public boolean  pwise_refine_exist = true;  // if false, start from scratch, true - start from previous
 	public boolean  pwise_delete_fail =  true;  // delete existing match if now failed 
@@ -795,7 +796,7 @@ public class IntersceneMatchParameters {
 		gd.addNumericField("Spiral search radius",        this.ospir_range, 3,7,"scaled pix",	"Maximal radius of the spiral search, in scaled pixels.");
 		gd.addNumericField("Mitigate small overlap",      this.ospir_double, 3,7,"","For small overlaps increase zoom by 1 and range - twice.");
 		gd.addNumericField("RMSE to end search",          this.ospir_good_rms,  3,7,"scaled pix",	"Maximal RMSE to consider match, in scaled pixels.");
-		gd.addNumericField("Satisfactory RMSE",           this.ospir_max_rms,  3,7,"scaled pix",	"Maximal RMSE to consider match, in scaled pixels.");
+		gd.addNumericField("Satisfactory RMSE, spiral",           this.ospir_max_rms,  3,7,"scaled pix",	"Maximal RMSE to consider match, in scaled pixels, during spiral.");
 		gd.addNumericField("Minimal overlap",             this.ospir_overlap,  0,4,"scaled pix ^ 2","Minimal overlap area in square scaled pixels.");
 		gd.addNumericField("LMA iterations",              this.ospir_num_iter, 0,2,"",              "Number of LMA iterations during spiral search.");
 		gd.addNumericField("RMSE at first iteration",     this.ospir_rms_iter[0],  3,7,"scaled pix","Maximal RMSE at first iteration.");
@@ -806,6 +807,7 @@ public class IntersceneMatchParameters {
 		gd.addMessage  ("Pairwise image matching");
 		gd.addNumericField("Zoom level",                  this.pwise_zoom, 0,3,"","Low-res images to determine overlaps.");
 		gd.addNumericField("Minimal overlap fraction",    this.pwise_overlap,  3,7,"",	"Minimal overlap area as a fraction of the smaller of the two images.");
+		gd.addNumericField("Satisfactory RMSE, refine",   this.pwise_max_rms,  3,7,"scaled pix",	"Maximal RMSE to consider match, in scaled pixels, during refine (high res).");
 		gd.addCheckbox    ("Skip existing",               this.pwise_skip_exist, "Do not regenerate if match with same or higher resolution exists.");
 		gd.addCheckbox    ("Refine existing",             this.pwise_refine_exist, "Refine existing matches (false - start from scratch with spiral search).");
 		gd.addCheckbox    ("Delete failed",               this.pwise_delete_fail, "Delete previous matches if it failed now.");
@@ -819,12 +821,12 @@ public class IntersceneMatchParameters {
 		gd.addCheckbox    ("Moves only",                  this.pmap_move_only,  "Moves only, no affine transform.");
 		gd.addCheckbox    ("Ignore existing affines",     this.pmap_ignore_affines, "Start from unity matrices, ignore saved affines.");
 		gd.addCheckbox    ("Use reversed pairs",          this.pmap_use_inv,     "Use reversed (late-early timestamps) pairs.");
-		gd.addNumericField("Skew pull",                   this.pmap_skew_pull,    3,7,"",	"Intention to have axes perpendicular.");
-		gd.addNumericField("Tilt pull",                   this.pmap_tilt_pull,    3,7,"",	"Intention to have axes same length.");
-		gd.addNumericField("Scale pull",                  this.pmap_scale_pull,   3,7,"",	"Intention to have average scale of images = 1.0.");
-		gd.addNumericField("Position pull",               this.pmap_position_pull,  3,7,"",	"Intension to match IMS (GNSS) coordinates.");
+		gd.addNumericField("Skew pull",                   this.pmap_skew_pull,    7,11,"",	"Intention to have axes perpendicular.");
+		gd.addNumericField("Tilt pull",                   this.pmap_tilt_pull,    7,11,"",	"Intention to have axes same length.");
+		gd.addNumericField("Scale pull",                  this.pmap_scale_pull,   7,11,"",	"Intention to have average scale of images = 1.0.");
+		gd.addNumericField("Position pull",               this.pmap_position_pull,7,11,"",	"Intension to match IMS (GNSS) coordinates.");
 		gd.addNumericField("Overlap inportance",          this.pmap_overlap_pow,  3,7,"",	"Raise overlap fraction (of the smaller image) to this power before using as weight.");
-		gd.addNumericField("RMSE relative improvement",   this.pmap_rms_diff,     3,7,"",	"Relative RMSE improvement to exit LMA.");
+		gd.addNumericField("RMSE relative improvement",   this.pmap_rms_diff,     8,11,"",	"Relative RMSE improvement to exit LMA.");
 		gd.addNumericField("LMA iterations",              this.pmap_num_iter,      0,3,"",".Maximal number of the LMA iterations.");
 		gd.addCheckbox    ("Show result image",           this.pmap_show_result, ".");
 		gd.addNumericField("Debug level for maps",        this.pmap_debugLevel, 0,3,"","Debug building for LMA building maps.");
@@ -1721,6 +1723,7 @@ public class IntersceneMatchParameters {
         
         this.pwise_zoom =               (int) gd.getNextNumber();
         this.pwise_overlap =                  gd.getNextNumber();
+        this.pwise_max_rms =                  gd.getNextNumber();
         this.pwise_skip_exist =               gd.getNextBoolean();
         this.pwise_refine_exist =             gd.getNextBoolean();
         this.pwise_delete_fail =              gd.getNextBoolean();
@@ -2249,6 +2252,8 @@ public class IntersceneMatchParameters {
 		
 		properties.setProperty(prefix+"pwise_zoom",                    this.pwise_zoom + "");                  // int
 		properties.setProperty(prefix+"pwise_overlap",                 this.pwise_overlap + "");               // double
+		properties.setProperty(prefix+"pwise_max_rms",                 this.pwise_max_rms + "");               // double
+				
 		properties.setProperty(prefix+"pwise_skip_exist",              this.pwise_skip_exist + "");            // boolean
 		properties.setProperty(prefix+"pwise_refine_exist",            this.pwise_refine_exist + "");          // boolean
 		properties.setProperty(prefix+"pwise_delete_fail",             this.pwise_delete_fail + "");           // boolean
@@ -2740,6 +2745,8 @@ public class IntersceneMatchParameters {
 
 		if (properties.getProperty(prefix+"pwise_zoom")!=null)         this.pwise_zoom=Integer.parseInt(properties.getProperty(prefix+            "pwise_zoom"));
 		if (properties.getProperty(prefix+"pwise_overlap")!=null)      this.pwise_overlap=Double.parseDouble(properties.getProperty(prefix+       "pwise_overlap"));
+		if (properties.getProperty(prefix+"pwise_max_rms")!=null)      this.pwise_max_rms=Double.parseDouble(properties.getProperty(prefix+       "pwise_max_rms"));
+		
 		if (properties.getProperty(prefix+"pwise_skip_exist")!=null)   this.pwise_skip_exist=Boolean.parseBoolean(properties.getProperty(prefix+  "pwise_skip_exist"));		
 		if (properties.getProperty(prefix+"pwise_refine_exist")!=null) this.pwise_refine_exist=Boolean.parseBoolean(properties.getProperty(prefix+"pwise_refine_exist"));		
 		if (properties.getProperty(prefix+"pwise_delete_fail")!=null)  this.pwise_delete_fail=Boolean.parseBoolean(properties.getProperty(prefix+ "pwise_delete_fail"));		
@@ -3257,6 +3264,7 @@ public class IntersceneMatchParameters {
 
         imp.pwise_zoom                    = this.pwise_zoom;
         imp.pwise_overlap                 = this.pwise_overlap;
+        imp.pwise_max_rms                 = this.pwise_max_rms;
         imp.pwise_skip_exist              = this.pwise_skip_exist;
         imp.pwise_refine_exist            = this.pwise_refine_exist;
         imp.pwise_delete_fail             = this.pwise_delete_fail;