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/MLStats.java

@@ -45,6 +45,7 @@ import com.elphel.imagej.cameras.ColorProcParameters;
 import com.elphel.imagej.cameras.EyesisCorrectionParameters;
 import com.elphel.imagej.common.DoubleGaussianBlur;
 import com.elphel.imagej.common.ShowDoubleFloatArrays;
+import com.elphel.imagej.correction.EyesisCorrections;
 import com.elphel.imagej.jp4.JP46_Reader_camera;
 
 import ij.IJ;
@@ -555,18 +556,23 @@ public class MLStats {
 	}
 
 
-	public static boolean listExtrinsics(String dir) // , String mask)
+	public static boolean listExtrinsics(
+			String dir, //) // , String mask)
+			EyesisCorrections eyesis_corrections_main,
+			EyesisCorrections eyesis_corrections_aux)
 	{
 		Path path= Paths.get(dir);
 		boolean inPixels =        true;
 		boolean inMrad =          false;
 		boolean showATR =         true;
 		boolean showZooms =       true;
+		boolean showERS =         true;
 		boolean showSym =         true;
 		boolean showRigATR =      true;
 		boolean showRigZoom =     true;
 		boolean showRigAngle =    true;
 		boolean showRigBaseline = false;
+		boolean showAux =         true;
 		String mask = ".*EXTRINSICS\\.corr-xml";
 
 		GenericDialog gd = new GenericDialog("Select file mask and output format");
@@ -575,11 +581,13 @@ public class MLStats {
 		gd.addCheckbox("Show results in mrad (false in arcseconds)",     inMrad);
 		gd.addCheckbox("Show azimuths, tilts, rolls",                    showATR);
 		gd.addCheckbox("Show zooms",                                     showZooms);
+		gd.addCheckbox("Show ERS",                                       showERS);
 		gd.addCheckbox("Show symmetric angles",                          showSym);
 		gd.addCheckbox("Show rig azimuth, tilt, roll",                   showRigATR);
 		gd.addCheckbox("Show rig zoom",                                  showRigZoom);
 		gd.addCheckbox("Show rig angle",                                 showRigAngle);
 		gd.addCheckbox("Show rig baseline",                              showRigBaseline);
+		gd.addCheckbox("Show aux camera and rig",                        showAux);
 		gd.showDialog ();
 		if (gd.wasCanceled()) return false;
 		mask =             gd.getNextString();
@@ -587,19 +595,30 @@ public class MLStats {
 		inMrad =           gd.getNextBoolean();
 		showATR =          gd.getNextBoolean();
 		showZooms =        gd.getNextBoolean();
+		showERS =          gd.getNextBoolean();
 		showSym =          gd.getNextBoolean();
 		showRigATR =       gd.getNextBoolean();
 		showRigZoom =      gd.getNextBoolean();
 		showRigAngle =     gd.getNextBoolean();
 		showRigBaseline =  gd.getNextBoolean();
+		showAux =          gd.getNextBoolean();
+		if (!showAux) {
+			showRigATR =      false;
+			showRigZoom =     false;
+			showRigAngle =    false;
+			showRigBaseline = false;
+		}
 
 		String units =  inPixels ? "pix":(inMrad?"mil":"\"");
 		String zunits = inPixels ? "pix":(inMrad?"mil":"\"");
+		String ers_lin_units = inPixels ? "mm/s":"m/s";
 		double scale = inPixels ? 1.0 : (inMrad?1000.0:(180.0/Math.PI*60*60)); //leave pixels as is, convert radians to arc-sec
 		String fmt =  "\t"+(inPixels ? "%8.4f":(inMrad?"%8.4f":"%8.2f"));
 		String fmt_angle =  "\t%8.3f";
 		String fmt_len =    "\t%8.3f";
-		int num_sym = showZooms? GeometryCorrection.CorrVector.LENGTH:GeometryCorrection.CorrVector.ZOOM_INDEX;
+		int num_sym = showZooms? GeometryCorrection.CorrVector.IMU_INDEX:GeometryCorrection.CorrVector.ZOOM_INDEX; // update
+		if (showERS) num_sym =  GeometryCorrection.CorrVector.LENGTH;
+		
 		class ModVerString{
 			String model;
 			String version;
@@ -632,6 +651,12 @@ public class MLStats {
 			num_col+=4;
 		}
 
+		if (showERS) {
+			header+=String.format("\ters tilt (%s/s)\ters az (%s/s)\ters roll (%s/s)", units, units, units);
+			header+=String.format("\ters Vx (%s)\ters Vy (%s)\ters Vz (%s)", ers_lin_units, ers_lin_units, ers_lin_units);
+			num_col+=6;
+		}
+		
 		if (showSym) {
 			for (int i = 0; i < num_sym; i++) {
 				header+=String.format("\tsym%02d-m", i);
@@ -639,7 +664,7 @@ public class MLStats {
 			num_col+=num_sym;
 
 		}
-
+		if (showAux) {
 			if (showATR) {
 				header+=String.format("\taz a0 (%s)\taz a1 (%s)\taz a2 (%s)\taz a3 (%s)"+
 						"\ttl a0 (%s)\ttl  a1 (%s) \ttl a2 (%s)\ttl a3 (%s)"+
@@ -651,12 +676,18 @@ public class MLStats {
 				header+=String.format("\tzm a0 (%s)\tzm a1 (%s)\tzm a2 (%s)\tzm a3 (%s)", zunits, zunits, zunits, zunits);
 				num_col+=4;
 			}
+			if (showERS) {
+				header+=String.format("\ters tilt (%s/s) a\ters az (%s/s) a\ters roll (%s/s) a", units, units, units);
+				header+=String.format("\ters Vx (%s)\ters Vy (%s)\ters Vz (%s)", ers_lin_units, ers_lin_units, ers_lin_units);
+				num_col+=6;
+			}
 			if (showSym) {
 				for (int i = 0; i < num_sym; i++) {
 					header+=String.format("\tsym%02d-a", i);
 				}
 				num_col+=num_sym;
 			}
+		}
 		if (showRigATR) {
 			header+=String.format("\trig azmth (%s)\trig tilt(%s)\trig roll (%s)", units, units, units);
 			num_col+=3;
@@ -712,13 +743,13 @@ public class MLStats {
 				QuadCLT qcm = new QuadCLT(
 						QuadCLT.PREFIX, // String                                          prefix,
 						properties, // Properties                                      properties,
-						null, // EyesisCorrections                               eyesisCorrections,
+						eyesis_corrections_main, // null, // EyesisCorrections                               eyesisCorrections,
 						null // EyesisCorrectionParameters.CorrectionParameters correctionsParameters
 						);
 				QuadCLT qca = new QuadCLT(
 						QuadCLT.PREFIX_AUX, // String                                          prefix,
 						properties, // Properties                                      properties,
-						null, // EyesisCorrections                               eyesisCorrections,
+						eyesis_corrections_aux, //null, // EyesisCorrections                               eyesisCorrections,
 						null // EyesisCorrectionParameters.CorrectionParameters correctionsParameters
 						);
 				System.out.println(indx+": model:"+model+", version:"+version+", name: "+name);
@@ -778,6 +809,17 @@ public class MLStats {
 					}
 				}
 
+				if (showERS) { // main camera
+					double [] v = new double[6];
+					for (int i = 0; i < v.length ; i++) {
+						v[i] =  scale * cvm.getExtrinsicParameterValue(i+GeometryCorrection.CorrVector.IMU_INDEX, inPixels);
+						sb.append(String.format(fmt,v[i])); // zooms
+						fmts [ncol] = fmt;
+						stats[ncol  ][0]+=v[i];
+						stats[ncol++][1]+=v[i]*v[i];
+					}
+				}
+				
 				if (showSym) {
 					for (int i = 0; i < num_sym; i++) {
 						double v =  scale * cvm.getExtrinsicSymParameterValue(i, inPixels);
@@ -788,7 +830,7 @@ public class MLStats {
 					}
 				}
 
-
+				if (showAux) {
 					if (showATR) { // aux camera
 						double [] v = new double[4];
 						for (int i = 0; i <4; i++) {
@@ -837,6 +879,17 @@ public class MLStats {
 							stats[ncol++][1]+=v[i]*v[i];
 						}
 					}
+					if (showERS) { // main camera
+						double [] v = new double[6];
+						for (int i = 0; i < v.length ; i++) {
+							v[i] =  scale * cva.getExtrinsicParameterValue(i+GeometryCorrection.CorrVector.IMU_INDEX, inPixels);
+							sb.append(String.format(fmt,v[i])); // zooms
+							fmts [ncol] = fmt;
+							stats[ncol  ][0]+=v[i];
+							stats[ncol++][1]+=v[i]*v[i];
+						}
+					}
+
 					if (showSym) {
 						for (int i = 0; i < num_sym; i++) {
 							double v =  scale * cva.getExtrinsicSymParameterValue(i, inPixels);
@@ -846,6 +899,7 @@ public class MLStats {
 							stats[ncol++][1]+=v*v;
 						}
 					}
+				}
 				if (showRigATR) {
 					int [] indices = {
 							GeometryCorrection.RigOffset.AUX_AZIMUTH_INDEX,

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
 				}
 			}
@@ -8682,6 +8697,8 @@ if (debugLevel > -100) return true; // temporarily !
 						debugLevel);    // final int                                debugLevel)
 			}
 			
+			
+
 			if (quadCLT_main.correctionsParameters.clt_batch_save_extrinsics) {
 				saveProperties(
 						null,        // String path,                // full name with extension or w/o path to use x3d directory