before implementing interscene ERS correction

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

@@ -5010,6 +5010,9 @@ private Panel panel1,
     } else if (label.equals("LIST extrinsics")) {
         DEBUG_LEVEL=MASTER_DEBUG_LEVEL;
     	EYESIS_CORRECTIONS.setDebug(DEBUG_LEVEL);
+    	if (EYESIS_CORRECTIONS_AUX == null) {
+    		EYESIS_CORRECTIONS_AUX = new EyesisCorrections(SYNC_COMMAND.stopRequested,CORRECTION_PARAMETERS.getAux());
+    	}
     	listExtrinsics();
     	return;
 /* ======================================================================== */
@@ -6531,7 +6534,10 @@ private Panel panel1,
 		if (dir!=null) {
 			System.out.println("top directory = "+dir);
 		}
-		return MLStats.listExtrinsics(dir); // , mask);
+		return MLStats.listExtrinsics(
+				dir, // ); // , mask);
+				EYESIS_CORRECTIONS,
+				EYESIS_CORRECTIONS_AUX);
 	}
 
 	public boolean mlRecalc() {

src/main/java/com/elphel/imagej/tileprocessor/Corr2dLMA.java

@@ -1461,7 +1461,7 @@ public class Corr2dLMA {
 	}
 
 	
-	public double [][] lmaDisparityStrength( // restored from git
+	public double [][] lmaDisparityStrength1( // restored from git
 			double  lma_max_rel_rms,  // maximal relative (to average max/min amplitude LMA RMS) // May be up to 0.3)
 			double  lma_min_strength, // minimal composite strength (sqrt(average amp squared over absolute RMS)
 			double  lma_min_ac,       // minimal of A and C coefficients maximum (measures sharpest point/line)
@@ -1510,7 +1510,7 @@ public class Corr2dLMA {
 
 
 	
-	public double [][] lmaDisparityStrength0(
+	public double [][] lmaDisparityStrength(
 			double  lma_max_rel_rms,  // maximal relative (to average max/min amplitude LMA RMS) // May be up to 0.3)
 			double  lma_min_strength, // minimal composite strength (sqrt(average amp squared over absolute RMS)
 			double  lma_min_max_ac,   // minimal of A and C coefficients maximum (measures sharpest point/line)
@@ -1554,7 +1554,7 @@ public class Corr2dLMA {
 			if ((strength < lma_min_strength) || Double.isNaN(disparity)) {
 				continue;
 			}
-//			strength = Math.sqrt(strength * Math.sqrt(abc[tile][0] * abc[tile][2])); // / area ); // new strength
+			strength = Math.sqrt(strength * Math.sqrt(abc[tile][0] * abc[tile][2])); // / area ); // new strength
 			ds[tile][0] = disparity;
 			ds[tile][1] = (strength * lma_str_scale) + lma_str_offset;
 		}

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

@@ -386,14 +386,60 @@ public class TileNeibs{
 	}
 
 
+	public int [] distanceFromEdge(
+			boolean [] tiles) {
+		int [] dfe = new int [tiles.length];
+		for (int i = 0; i < tiles.length; i++) dfe[i] = tiles[i] ? -1 : 0;
+		ArrayList<Integer> front = new ArrayList<Integer>();
+		int dist = 0;
+		for (boolean has_empty = true; has_empty;) {
+			has_empty = false;
+			for (int start_indx = 0; start_indx < tiles.length; start_indx++) if (dfe[start_indx] < 0){
+				has_empty = true;
+				// see if it has wave front around
+				boolean has_front_near = false;
+				for (int d = 0; (d < dirs) && !has_front_near; d++){
+					int ipx1 = 	getNeibIndex(start_indx, d);
+					if ((ipx1 >= 0) && (dfe[ipx1] == dist)) {
+						has_front_near = true;
+					}
+				}
+				if (has_front_near) {
+					dfe[start_indx] = dist+1;
+					front.add(start_indx);
+					// build wave front (may be several)
+					while (!front.isEmpty()) {
+						int ipx = front.remove(0);// get oldest element
+						for (int d = 0; (d < dirs) && !has_front_near; d++){
+							int ipx1 = 	getNeibIndex(ipx, d);
+							if ((ipx1 >= 0) && (dfe[ipx1] < 0)) { // fresh cell
+								// does it has front neighbor?
+
+								for (int d1 = 0; (d1 < dirs) && !has_front_near; d1++){
+									int ipx2 = 	getNeibIndex(ipx1, d1);
+									if ((ipx2 >= 0) && (dfe[ipx2] == dist)) { // old front cell
+										dfe[ipx1] = dist+1;
+										front.add(ipx1);
+										break;
+									}
+								}
+							}
+						}
+					}		
+
+				}
+			}
+			dist++; 
+		}
+		return dfe;
+	}
+	
 	/**
 	 * Enumerate clusters on rectangular area
 	 * @param tiles   selected tiles, size should be sizeX * sizeY
 	 * @param ordered if true, order tiles from largest to smallest5
 	 * @return integer array, where 0 is unused, 1+ cluster it belongs to
 	 */
-
-
 	public int [] enumerateClusters(
 			boolean [] tiles,
 			boolean ordered)

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

@@ -8325,11 +8325,14 @@ if (debugLevel > -100) return true; // temporarily !
 								"pre-adjust-extrinsic-scan-"+s); //String title)
 					}
 				}
-			    double inf_min = -1.0;
-			    double inf_max =  1.0;
-			    if (num_adjust_main >= (adjust_main/2)) {
-			        inf_min = -0.2;
-			        inf_max = 0.05;
+			    double inf_min = clt_parameters.ly_inf_min_broad; // -0.5;
+			    double inf_max = clt_parameters.ly_inf_max_broad; // 0.5;
+			    if (clt_parameters.ly_inf_force_fine || (num_adjust_main >= (adjust_main/2))) {
+			        inf_min = clt_parameters.ly_inf_min_narrow; // -0.2;
+			        inf_max = clt_parameters.ly_inf_max_narrow; // 0.05;
+			        System.out.println("Late adjustment, using narrow band infinity detection, inf_min="+inf_min+", inf_max="+inf_max);
+			    } else {
+			        System.out.println("Early adjustment, using wide band infinity detection, inf_min="+inf_min+", inf_max="+inf_max);
 			    }
 				boolean ok = quadCLT_main.extrinsicsCLT(
 						clt_parameters, // EyesisCorrectionParameters.CLTParameters           clt_parameters,
@@ -8407,7 +8410,7 @@ if (debugLevel > -100) return true; // temporarily !
 						quadCLT_main.tp.clt_3d_passes.get( quadCLT_main.tp.clt_3d_passes.size() -1),
 						false); // boolean force_final);
 
-				  if (debugLevel > -5){
+				  if (debugLevel > -1) { //-5){
 					  int scan_index =  quadCLT_main.tp.clt_3d_passes.size() -1;
 					  quadCLT_main.tp.showScan(
 							  quadCLT_main.tp.clt_3d_passes.get(scan_index),   // CLTPass3d   scan,
@@ -8508,6 +8511,18 @@ if (debugLevel > -100) return true; // temporarily !
 				}
 				if (num_restored < 2) {
 					System.out.println("No DSI from the main camera is available. Please re-run with 'clt_batch_explore' enabled to generate it");
+					if (quadCLT_main.correctionsParameters.clt_batch_save_extrinsics) {
+						saveProperties(
+								null,        // String path,                // full name with extension or w/o path to use x3d directory
+								null,        // Properties properties,      // if null - will only save extrinsics)
+								debugLevel);
+					}
+					if (quadCLT_main.correctionsParameters.clt_batch_save_all) {
+						saveProperties(
+								null,        // String path,                // full name with extension or w/o path to use x3d directory
+								properties,  // Properties properties,    // if null - will only save extrinsics)
+								debugLevel);
+					}
 					continue; // skipping to the next file
 				}
 			}
@@ -8681,6 +8696,8 @@ if (debugLevel > -100) return true; // temporarily !
 						updateStatus,   // final boolean                            updateStatus,
 						debugLevel);    // final int                                debugLevel)
 			}
+			
+			
 
 			if (quadCLT_main.correctionsParameters.clt_batch_save_extrinsics) {
 				saveProperties(