Tested rig (2 quad cameras) matrices and manual adjustment

src/main/java/AlignmentCorrection.java

@@ -731,6 +731,7 @@ public class AlignmentCorrection {
 			double centerY = tileY * qc.tp.getTileSize() + qc.tp.getTileSize()/2;//- shiftY;
 
 			double [][] centersXY_disp = qc.geometryCorrection.getPortsCoordinatesAndDerivatives(
+					false,          // boolean use_rig_offsets,
 					corr_rots, // Matrix []   rots,
 					null,      //  Matrix [][] deriv_rots,
 					null,      // double [][] pXYderiv, // if not null, should be double[8][]
@@ -738,6 +739,7 @@ public class AlignmentCorrection {
 					centerY,
 					disp_strength[2 * s.series + 0][s.tile]/magic_coeff); // disparity
 			double [][] centersXY_inf = qc.geometryCorrection.getPortsCoordinatesAndDerivatives(
+					false,          // boolean use_rig_offsets,
 					corr_rots, // Matrix []   rots,
 					null,      //  Matrix [][] deriv_rots,
 					null,      // double [][] pXYderiv, // if not null, should be double[8][]
@@ -2434,6 +2436,7 @@ System.out.println("test1234");
 			double [][] deriv = new double [2 * NUM_SENSORS][];
 			int dbg_index =dbg_index (pXY, dbg_decimate);
 			geometryCorrection.getPortsCoordinatesAndDerivatives(
+					false,          // boolean use_rig_offsets,
 					corr_rots,   //  Matrix []   rots,
 					deriv_rots,  //  Matrix [][] deriv_rots,
 					deriv,       // 	boolean calc_deriv,
@@ -2458,6 +2461,7 @@ System.out.println("test1234");
 				double [][] deriv_dbg = new double [2 * NUM_SENSORS][];
 				double [] dbg_a_vector= null;
 				geometryCorrection.getPortsCoordinatesAndDerivatives(
+						false,          // boolean use_rig_offsets,
 						dbg_a_vector, // double [] dbg_a_vector, // replace actual radial distortion coefficients
 						1E-9, // 1E-8, //6,    // double delta, // 1e-6
 						corr_vector, // CorrVector corr_vector,
@@ -2596,6 +2600,7 @@ System.out.println("test1234");
 			Mismatch mm = mismatch_list.get(indx);
 			double [] pXY = mm.getPXY();
 			double [][] f = geometryCorrection.getPortsCoordinatesAndDerivatives( // 4x2
+					false,          // boolean use_rig_offsets,
 					corr_rots,    //  Matrix []   rots,
 					null, //  Matrix [][] deriv_rots,
 					null,        //	boolean calc_deriv,

src/main/java/EyesisCorrectionParameters.java

@@ -730,7 +730,7 @@ public class EyesisCorrectionParameters {
     		updateAuxFromMain();
 
 
-    		gd.addTab         ("File paths", "Select files and directories paths (common to main and optional auxilliary)");
+    		gd.addTab         ("File paths", "Select files and directories paths (common to main and optional auxiliary)");
 			gd.addMessage     ("============ Common to the main and optional auxiliary camera============");
 
     		gd.addCheckbox    ("Save current settings with results",               this.saveSettings);           // 1

src/main/java/Eyesis_Correction.java

@@ -578,6 +578,7 @@ private Panel panel1,
 			panelClt4.setLayout(new GridLayout(1, 0, 5, 5)); // rows, columns, vgap, hgap
 			addButton("Import Aux",                 panelClt4, color_restore);
 			addButton("Setup CLT Batch parameters", panelClt4, color_configure);
+			addButton("CLT rig edit",               panelClt4, color_configure);
 			addButton("CLT 2*4 images",             panelClt4, color_conf_process);
 			addButton("CLT 2*4 images - 2",         panelClt4, color_conf_process);
 			addButton("CLT 2*4 images - 3",         panelClt4, color_conf_process);
@@ -4490,11 +4491,28 @@ private Panel panel1,
         	}
         }
         QUAD_CLT_AUX.showExtrinsicCorr("aux");// show_fine_corr("aux");
-//        QuadCLT dbg_QUAD_CLT = QUAD_CLT;
-//        QuadCLT dbg_QUAD_CLT_AUX = QUAD_CLT_AUX;
+        QuadCLT dbg_QUAD_CLT = QUAD_CLT;
+        QuadCLT dbg_QUAD_CLT_AUX = QUAD_CLT_AUX;
 
         return;
-
+        /* ======================================================================== */
+    } else if (label.equals("CLT rig edit")) {
+        DEBUG_LEVEL=MASTER_DEBUG_LEVEL;
+        if (QUAD_CLT_AUX == null){
+        	if (EYESIS_CORRECTIONS_AUX == null) {
+        		EYESIS_CORRECTIONS_AUX = new EyesisCorrections(SYNC_COMMAND.stopRequested,CORRECTION_PARAMETERS.getAux());
+        	}
+        	QUAD_CLT_AUX = new  QuadCLT (
+        			QuadCLT.PREFIX_AUX,
+        			PROPERTIES,
+        			EYESIS_CORRECTIONS_AUX,
+        			CORRECTION_PARAMETERS.getAux());
+        	if (DEBUG_LEVEL > 0){
+        		System.out.println("Created new QuadCLT instance, will need to read CLT kernels for aux camera");
+        	}
+        }
+        QUAD_CLT_AUX.editRig();
+    	return;
 //JTabbedTest
 // End of buttons code
     }
@@ -4559,8 +4577,6 @@ private Panel panel1,
     			CHANNEL_GAINS_PARAMETERS_AUX = new CorrectionColorProc.ColorGainsParameters();
     		}
     		CHANNEL_GAINS_PARAMETERS_AUX.getProperties("CHANNEL_GAINS_PARAMETERS.", aux_properties);
-//    		QUAD_CLT_AUX.getProperties(QuadCLT.PREFIX);
-//    		QUAD_CLT_AUX.setProperties(QuadCLT.PREFIX_AUX);
 /*
  * 	public void copyPropertiesFrom(Properties other_properties, String other_prefix, String this_prefix){ // save
 
@@ -4834,6 +4850,9 @@ private Panel panel1,
         	TWO_QUAD_CLT = new TwoQuadCLT();
         }
         if (new_mode) {
+        	if (DEBUG_LEVEL > -2){
+        		System.out.println("++++++++++++++ Calculating combined correlations ++++++++++++++");
+        	}
         	try {
         		TWO_QUAD_CLT.processCLTQuadCorrPairs(
         				QUAD_CLT, // QuadCLT quadCLT_main,
@@ -4852,6 +4871,9 @@ private Panel panel1,
         		e.printStackTrace();
         	} //final int        debugLevel);
         } else {
+        	if (DEBUG_LEVEL > -2){
+        		System.out.println("++++++++++++++ Calculating per quad camera correlations ++++++++++++++");
+        	}
         	try {
         		TWO_QUAD_CLT.processCLTQuadCorrs(
         				QUAD_CLT, // QuadCLT quadCLT_main,

src/main/java/QuadCLT.java

@@ -67,6 +67,7 @@ public class QuadCLT {
 	String                                                 image_name = null;
 	double [][][]                                          image_data = null;
     boolean [][]                                           saturation_imp = null; // (near) saturated pixels or null
+    boolean                                                is_aux = false;
 
 
 // magic scale should be set before using  TileProcessor (calculated disparities depend on it)
@@ -96,6 +97,7 @@ public class QuadCLT {
 		this.eyesisCorrections=      eyesisCorrections;
 		this.correctionsParameters = correctionsParameters;
 		this.properties =            properties;
+		is_aux =                     prefix.equals(PREFIX_AUX);
 //		this.properties_prefix =     prefix;
 //		System.out.println("new QuadCLT(), prefix = "+prefix);
 		getProperties(prefix);
@@ -125,6 +127,9 @@ public class QuadCLT {
 			properties.setProperty(name,  gc.getCorrVector().toArray()[i]+"");
 //			System.out.println("setProperties():"+i+": setProperty("+name+","+gc.getCorrVector().toArray()[i]+"");
 		}
+		if (is_aux && (gc.rigOffset != null)) {
+			gc.rigOffset.setProperties(prefix,properties);
+		}
 	}
 
 
@@ -197,8 +202,17 @@ public class QuadCLT {
   				}
   			}
 		}
-	}
+//		if (is_aux && (geometryCorrection != null)) {
+//			geometryCorrection.setRigOffsetFromProperies(prefix, properties);
+//		}
+		if (geometryCorrection == null) {
+			geometryCorrection = new GeometryCorrection(this.extrinsic_corr);
+		}
 
+		if (is_aux) {
+			geometryCorrection.setRigOffsetFromProperies(prefix, properties);
+		}
+	}
 
 	public void setKernelImageFile(ImagePlus img_kernels){
 		eyesisKernelImage = img_kernels;
@@ -212,10 +226,13 @@ public class QuadCLT {
 		return clt_kernels != null;
 	}
 	public boolean geometryCorrectionAvailable(){
-		return geometryCorrection != null;
+		return (geometryCorrection != null) && geometryCorrection.isInitialized();
 	}
 	public boolean initGeometryCorrection(int debugLevel){
-		geometryCorrection = new GeometryCorrection(extrinsic_corr);
+		// keep rig offsets if edited
+		if (geometryCorrection == null) {
+			geometryCorrection = new GeometryCorrection(extrinsic_corr);
+		}
 		PixelMapping.SensorData [] sensors =  eyesisCorrections.pixelMapping.sensors;
 		// verify that all sensors have the same distortion parameters
 		int numSensors = sensors.length;
@@ -4527,6 +4544,32 @@ public class QuadCLT {
 			  System.out.println(geometryCorrection.getCorrVector().toString());
 		  }
 	  }
+
+	  public boolean editRig()
+	  {
+		  if (!is_aux) {
+			  System.out.println("Rig offsets can only be edited for the auxiliary camera, not for the amin one");
+			  return false;
+		  }
+//		  GeometryCorrection gc = this.geometryCorrection;
+		  if (this.geometryCorrection == null){
+			  System.out.println("geometryCorrection is not set, creating one");
+			  this.geometryCorrection = new GeometryCorrection(this.extrinsic_corr);
+		  }
+		  boolean edited = this.geometryCorrection.editRig();
+//		  if (edited) {
+//			  gc.rigOffset.setProperties(prefix,properties);
+//		  }
+		  return edited;
+	  }
+/*
+		if (is_aux && (gc.rigOffset != null)) {
+			gc.rigOffset.setProperties(prefix,properties);
+		}
+
+ */
+
+
 	  public void resetExtrinsicCorr(
 			  EyesisCorrectionParameters.CLTParameters           clt_parameters)
 	  {

src/main/java/TwoQuadCLT.java

@@ -381,7 +381,7 @@ public class TwoQuadCLT {
 						  quadCLT_main.getGeometryCorrection(), // final GeometryCorrection  geometryCorrection_main,
 						  quadCLT_aux.getGeometryCorrection(),  // final GeometryCorrection  geometryCorrection_aux,
 						  quadCLT_main.getCLTKernels(),         // final double [][][][][][] clt_kernels_main, // [channel_in_quad][color][tileY][tileX][band][pixel] , size should match image (have 1 tile around)
-						  quadCLT_main.getCLTKernels(),         // final double [][][][][][] clt_kernels_aux,  // [channel_in_quad][color][tileY][tileX][band][pixel] , size should match image (have 1 tile around)
+						  quadCLT_aux.getCLTKernels(),          // final double [][][][][][] clt_kernels_aux,  // [channel_in_quad][color][tileY][tileX][band][pixel] , size should match image (have 1 tile around)
 						  clt_parameters.corr_magic_scale,      // final double              corr_magic_scale, // still not understood coefficient that reduces reported disparity value.  Seems to be around 0.85
 						  true,                                 // 	final boolean             keep_clt_data,
 						  threadsMax,                           // final int                 threadsMax,  // maximal number of threads to launch
@@ -496,7 +496,7 @@ public class TwoQuadCLT {
 							  colorProcParameters,
 							  rgbParameters,
 							  name+"-texture", // String name,
-							  "-D"+clt_parameters.disparity, //String suffix, // such as disparity=...
+							  "-D"+clt_parameters.disparity+"-MAIN", //String suffix, // such as disparity=...
 							  toRGB,
 							  !quadCLT_main.correctionsParameters.jpeg, // boolean bpp16, // 16-bit per channel color mode for result
 							  true, // boolean saveShowIntermediate, // save/show if set globally
@@ -511,7 +511,7 @@ public class TwoQuadCLT {
 							  colorProcParameters,
 							  rgbParameters,
 							  name+"-texture", // String name,
-							  "-D"+clt_parameters.disparity, //String suffix, // such as disparity=...
+							  "-D"+clt_parameters.disparity+"-AUX", //String suffix, // such as disparity=...
 							  toRGB,
 							  !quadCLT_aux.correctionsParameters.jpeg, // boolean bpp16, // 16-bit per channel color mode for result
 							  true, // boolean saveShowIntermediate, // save/show if set globally