Debugging LY adjustment, tested semi-manual OK

src/main/java/com/elphel/imagej/cameras/CLTParameters.java

@@ -292,6 +292,8 @@ public class CLTParameters {
 	public double     ly_norm_disp =    5.0;     // Reduce weight of higher disparity tiles
 
 	// Lazy eye multi-step fitting
+	public String     lym_dbg_path =   "";      // read saved extrinsics_bgnd_combo.tif to bypass long preparation
+	
 	public double     lym_overexp     = 0.0001;  // Any (near) saturated pixels - discard tile (see sat_level also)
 	public boolean    lym_update_disp = true;    // Update target disparity after each step
 	public int        lym_iter =        25;      // Maximal number of iterations
@@ -1188,6 +1190,9 @@ public class CLTParameters {
 		properties.setProperty(prefix+"ly_disp_rvar_gt",            this.ly_disp_rvar_gt +"");
 		properties.setProperty(prefix+"ly_norm_disp",               this.ly_norm_disp +"");
 		properties.setProperty(prefix+"lym_overexp",                this.lym_overexp +"");
+
+		properties.setProperty(prefix+"lym_dbg_path",                this.lym_dbg_path +"");
+		
 		properties.setProperty(prefix+"lym_update_disp",            this.lym_update_disp+"");
 		properties.setProperty(prefix+"lym_iter",                   this.lym_iter+"");
 		properties.setProperty(prefix+"lym_change",                 this.lym_change +"");
@@ -1997,6 +2002,7 @@ public class CLTParameters {
 		if (properties.getProperty(prefix+"ly_disp_rvar_gt")!=null)               this.ly_disp_rvar_gt=Double.parseDouble(properties.getProperty(prefix+"ly_disp_rvar_gt"));
 		if (properties.getProperty(prefix+"ly_norm_disp")!=null)                  this.ly_norm_disp=Double.parseDouble(properties.getProperty(prefix+"ly_norm_disp"));
 		if (properties.getProperty(prefix+"lym_overexp")!=null)                   this.lym_overexp=Double.parseDouble(properties.getProperty(prefix+"lym_overexp"));
+		if (properties.getProperty(prefix+"lym_dbg_path")!=null)                  this.lym_dbg_path= (String) properties.getProperty(prefix+"lym_dbg_path");
 		if (properties.getProperty(prefix+"lym_update_disp")!=null)               this.lym_update_disp=Boolean.parseBoolean(properties.getProperty(prefix+"lym_update_disp"));
 		if (properties.getProperty(prefix+"lym_iter")!=null)                      this.lym_iter=Integer.parseInt(properties.getProperty(prefix+"lym_iter"));
 		if (properties.getProperty(prefix+"lym_change")!=null)                    this.lym_change=Double.parseDouble(properties.getProperty(prefix+"lym_change"));
@@ -2895,6 +2901,8 @@ public class CLTParameters {
 				"Full allowed mismatch is a sum of absolute and disparity times relative (relaxed when ground truth is available)");
 		gd.addNumericField("Reduce weight of higher disparity tiles",                                           this.ly_norm_disp, 5,8,"");
 		gd.addMessage     ("--- Lazy eye multi-step fitting ---");
+
+		gd.addStringField ("Read extrinsics_bgnd_combo instead of building it",                                 this.lym_dbg_path, 80);
 		gd.addNumericField("Any (near) saturated pixels - discard tile (see sat_level also)",                   this.lym_overexp,  10,12,"");
 		gd.addCheckbox    ("Update target disparity after each step",                                           this.lym_update_disp);
 		gd.addNumericField("Maximal number of iterations",                                                      this.lym_iter,  0);
@@ -3833,6 +3841,8 @@ public class CLTParameters {
 		this.ly_disp_var_gt=        gd.getNextNumber();
 		this.ly_disp_rvar_gt=       gd.getNextNumber();
 		this.ly_norm_disp=          gd.getNextNumber();
+		
+		this.lym_dbg_path =         gd.getNextString();
 		this.lym_overexp=           gd.getNextNumber();
 		this.lym_update_disp=       gd.getNextBoolean();
 		this.lym_iter=        (int) gd.getNextNumber();

src/main/java/com/elphel/imagej/tileprocessor/CLTPass3d.java

@@ -902,7 +902,9 @@ public class CLTPass3d{
 		 */
 		public void updateDisparity()
 		{
-			setTileOpDisparity(null, getDisparity(0));
+			if (disparity_map != null) {
+				setTileOpDisparity(null, getDisparity(0));
+			}
 		}
 
 

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

@@ -1101,8 +1101,12 @@ matrix([[-0.125, -0.125,  0.125,  0.125, -0.125,  0.125, -0.   , -0.   ,   -0.
 				}
 			}
 			if (par_list.size() < par_mask.length) {
-				int[] sub_pars = par_list.stream().mapToInt(i -> i).toArray(); // Java8
-				from_sym = from_sym.getMatrix(0, par_mask.length,sub_pars); // remove masked columns
+				int[] sub_pars = new int [par_list.size()];
+				for (int i = 0; i < sub_pars.length; i++) {
+					sub_pars[i] = par_list.get(i); 
+				}
+//				int[] sub_pars = par_list.stream().mapToInt(i -> i).toArray(); // Java8
+				from_sym = from_sym.getMatrix(0, par_mask.length-1,sub_pars); // remove masked columns
 			}
 		}
 		Matrix pcd = new Matrix (port_coord_deriv); // rows: px0,py0,... px[n-1], py[n-1], columns: tar
@@ -1187,7 +1191,7 @@ matrix([[-0.125, -0.125,  0.125,  0.125, -0.125,  0.125, -0.   , -0.   ,   -0.
 			}
 			if (par_list.size() < par_mask.length) {
 				int[] sub_pars = par_list.stream().mapToInt(i -> i).toArray(); // Java8
-				to_sym = to_sym.getMatrix(sub_pars, 0, par_mask.length); // remove masked rows
+				to_sym = to_sym.getMatrix(sub_pars, 0, par_mask.length-1); // remove masked rows
 			}
 		}
 		Matrix tar = new Matrix(tar_array,tar_array.length);
@@ -1209,7 +1213,7 @@ matrix([[-0.125, -0.125,  0.125,  0.125, -0.125,  0.125, -0.   , -0.   ,   -0.
 			}
 			if (par_list.size() < par_mask.length) {
 				int[] sub_pars = par_list.stream().mapToInt(i -> i).toArray(); // Java8
-				from_sym = from_sym.getMatrix(0, par_mask.length,sub_pars); // remove masked columns
+				from_sym = from_sym.getMatrix(0, par_mask.length-1,sub_pars); // remove masked columns
 			}
 		}
 		Matrix sym = new Matrix(sym_array,sym_array.length);

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

@@ -2806,7 +2806,36 @@ public class GeometryCorrection {
 		return jt;
 	}
 
+	public double [][] getPortsXYDerivativesNew( // USED in lwir
+			GeometryCorrection gc_main,
+			boolean     use_rig_offsets,
+			Matrix []   rots,
+			Matrix [][] deriv_rots,
+			double []   py_offset,  // array of per-port average pY offset from the center (to correct ERS) or null (for no ERS)
+			double []   imu, // may be null
+			double []   xyz, // world XYZ for ERS correction
+			double      px,
+			double      py,
+			double      disparity)
+	{
+		// make sure initPrePostMatrices(true) already ran (in constructor). (true) means that minus sign is already incorporated
+		double [][] pXYNDderiv = new double [2*numSensors][]; // CorrVector.LENGTH][];
+		getPortsNonDistortedCoordinatesAndDerivativesNew( // USED in lwir
+				gc_main,
+				use_rig_offsets,
+				rots,
+				deriv_rots,
+				pXYNDderiv, // if not null, should be double[8][]
+				py_offset,   //  // array of per-port average pY offset from the center (to correct ERS) or null (for no ERS)
+				imu,
+				xyz,
+				px,
+				py,
+				disparity);
+		return(new Matrix(pXYNDderiv)).getArray();
+	}
 
+	
 
 
 

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

@@ -4042,6 +4042,28 @@ public class ImageDttCPU {
 										disparity_map[DISPARITY_INDEX_POLY+1][tIndex] = ds[0][1];
 										if (debugTile0) {
 											lma2.printStats(ds,1);
+											double [][] ddnd = lma2.getDdNd();
+											if (ddnd != null) {
+												double [][] dxy= new double [ddnd.length][2];
+												for (int i = 0; i < dxy.length; i++) {
+													dxy[i][0] = ddnd[i][0] * rXY[i][0] - ddnd[i][1] * rXY[i][1];
+													dxy[i][1] = ddnd[i][0] * rXY[i][1] + ddnd[i][1] * rXY[i][0];
+												}
+												System.out.print("       Port:  ");
+												for (int i = 0; i < dxy.length; i++) System.out.print(String.format("   %2d   ", i)); System.out.println();
+												System.out.print("Radial_in =  [");
+												for (int i = 0; i < dxy.length; i++) System.out.print(String.format(" %6.3f,", ddnd[i][0])); System.out.println("]");
+												System.out.print("Tangent_CW = [");
+												for (int i = 0; i < dxy.length; i++) System.out.print(String.format(" %6.3f,", ddnd[i][1])); System.out.println("]");
+												System.out.print("X =          [");
+												for (int i = 0; i < dxy.length; i++) System.out.print(String.format(" %6.3f,", dxy[i][0])); System.out.println("]");
+												System.out.print("Y =          [");
+												for (int i = 0; i < dxy.length; i++) System.out.print(String.format(" %6.3f,", dxy[i][1])); System.out.println("]");
+												System.out.println();
+											}
+											
+											
+											
 										}
 									}
 								}

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

@@ -103,7 +103,7 @@ public class SymmVector {
 				full_type2,
 				debug_level);
 		rvs.xy =     sv.exportXY();
-		rvs.rt =     sv.exportRT();
+		rvs.rt =     sv.exportRT(); // radius/tangential (out, cw, out, cw
 		rvs.dir_rt = sv.exportDirRT();
 		rvs.rots =   sv.exportRZ(false); // include common roll
 		rvs.zooms =  sv.exportRZ(true);  // no common zoom
@@ -1152,8 +1152,9 @@ public class SymmVector {
 		for (int i = 0; i < N - 1; i++) {
 			xy2ta.set(    i, 2* i + 1, TILT_SIGN);
 			xy2ta.set(N-1+i, 2 *i + 0, AZIMUTH_SIGN);
-		}		
-		return xy2ta.times(sym2xy);
+		}
+		Matrix sym2ta = xy2ta.times(sym2xy);
+		return sym2ta;
 	}
 	
 	/**
@@ -1195,6 +1196,7 @@ public class SymmVector {
 		to_sym.setMatrix(i1,i2-1,i1,i2-1, sym2roll.inverse());
 		to_sym.setMatrix(i2,i3-1,i2,i3-1, sym2zoom.inverse());
 		to_sym.setMatrix(i3,i4-1,i3,i4-1, sym2ers.inverse());
+//		Matrix dbg = from_sym.times(to_sym);
 		return new Matrix[] {from_sym,to_sym};
 	}
 	//getColumnDimension

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

@@ -9495,41 +9495,49 @@ if (debugLevel > -100) return true; // temporarily !
 					System.out.println("Building basic  DSI for the AUX camera image set "+quadCLT_main.image_name+
 							" using main camera DSI, pass "+(num_adjust_aux+1)+" of "+adjust_aux);
 				}
-				quadCLT_aux.preExpandCLTQuad3d( // returns ImagePlus, but it already should be saved/shown
-						imp_srcs_aux, // [srcChannel], // should have properties "name"(base for saving results), "channel","path"
-						saturation_imp_aux, // boolean [][] saturation_imp, // (near) saturated pixels or null
-						clt_parameters,
-						debayerParameters,
-						colorProcParameters_aux,
-						rgbParameters,
-						threadsMax,  // maximal number of threads to launch
-						updateStatus,
-						debugLevelInner);
-				// adjust extrinsics here
-				System.out.println("Adjust AUX extrinsics here");
-				if (updateStatus) IJ.showStatus("Adjusting AUX camera image set for "+quadCLT_aux.image_name+
-						", pass "+(num_adjust_aux+1)+" of "+adjust_aux);
-				if (debugLevel > -5) {
-					System.out.println("Adjusting AUX camera image set for "+quadCLT_aux.image_name+
-							", pass "+(num_adjust_aux+1)+" of "+adjust_aux);
-				}
+			    String dbg_path = clt_parameters.lym_dbg_path; // /home/elphel/lwir16-proc/proc1/results_cuda/25/extrinsics_bgnd_combo.tif
+			    if (dbg_path.length()==0) {
+			    	dbg_path = null;
+			    }
+//			    dbg_path = "/home/elphel/lwir16-proc/proc1/results_cuda/25/extrinsics_bgnd_combo.tif";
+			    if (dbg_path == null) {
+			    	quadCLT_aux.preExpandCLTQuad3d( // returns ImagePlus, but it already should be saved/shown
+			    			imp_srcs_aux, // [srcChannel], // should have properties "name"(base for saving results), "channel","path"
+			    			saturation_imp_aux, // boolean [][] saturation_imp, // (near) saturated pixels or null
+			    			clt_parameters,
+			    			debayerParameters,
+			    			colorProcParameters_aux,
+			    			rgbParameters,
+			    			threadsMax,  // maximal number of threads to launch
+			    			updateStatus,
+			    			debugLevelInner);
+			    	// adjust extrinsics here
+			    	System.out.println("Adjust AUX extrinsics here");
+			    	if (updateStatus) IJ.showStatus("Adjusting AUX camera image set for "+quadCLT_aux.image_name+
+			    			", pass "+(num_adjust_aux+1)+" of "+adjust_aux);
+			    	if (debugLevel > -5) {
+			    		System.out.println("Adjusting AUX camera image set for "+quadCLT_aux.image_name+
+			    				", pass "+(num_adjust_aux+1)+" of "+adjust_aux);
+			    	}
+			    }
 				if (quadCLT_aux.ds_from_main == null) {
 					System.out.println("BUG: quadCLT_aux.ds_from_main should be not null here!");
 				    double inf_min = -1.0;
 				    double inf_max =  1.0;
 				    if (num_adjust_aux >= (adjust_aux/2)) {
 				        inf_min = -0.2;
-				        inf_max = 0.05;
+				        inf_max = 0.2;  // 0.05; Changed for LWIR16
 				    }
 					// adjust w/o main camera - maybe will be used in the future
 					boolean ok = quadCLT_aux.extrinsicsCLT(
 							clt_parameters, // EyesisCorrectionParameters.CLTParameters           clt_parameters,
+							dbg_path,
 							false, // adjust_poly,
 				            inf_min, // double inf_min,
 				            inf_max,  // double inf_max,
 							threadsMax,  //final int        threadsMax,  // maximal number of threads to launch
 							updateStatus,// final boolean    updateStatus,
-							debugLevelInner); // final int        debugLevel)
+							1); // debugLevelInner); // final int        debugLevel)
 					if (!ok) break;
 				} else {
 					boolean ok = quadCLT_aux.extrinsicsCLTfromGT(