working snapshot (working on IMU-to-camera rotation calibration)

src/main/java/com/elphel/imagej/ims/Imx5.java

@@ -249,7 +249,7 @@ public class Imx5 {
 	 * Adjsut IMS orientation relative to the camera (or opposite?) by a correction quaternion
 	 * @param ims_atr original ATR of the IMS mount
 	 * @param corr_q correction quaternion
-	 * @return corrected ATR of teh IMU mount
+	 * @return corrected ATR of the IMU mount
 	 */
 	public static double [] adjustMountAtrByQuat(
 			double [] ims_atr,

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

@@ -5181,7 +5181,7 @@ public class Interscene {
 				debugLevel); // int            debugLevel
 		if (debugLevel > -3) {
         	Rotation rot = new Rotation(quatCorr[0],quatCorr[1],quatCorr[2],quatCorr[3], false); // no normalization - see if can be scaled
-			System.out.println("Applying correction ot the IMS to world orientation (rotating around IMS vertical):");
+			System.out.println("Applying correction to the IMS to world orientation (rotating around IMS vertical):");
 			double []  corr_angles = rot.getAngles(RotationOrder.YXZ, ErsCorrection.ROT_CONV);
 			double []  corr_degrees = new double[3];
 			for (int i = 0; i < 3; i++) corr_degrees[i]=corr_angles[i]*180/Math.PI;
@@ -5476,20 +5476,20 @@ public class Interscene {
 		double []     ims_mount_atr = clt_parameters.imp.getImsMountATR(); // converts to radians
 		QuadCLT       ref_scene = quadCLTs[ref_index];
 		ErsCorrection ers_reference = ref_scene.getErsCorrection();
-		double [][]   quat_lma_xyz =     new double [quadCLTs.length][3];
-		double [][]   quat_lma_enu_xyz = new double [quadCLTs.length][3];
+		double [][][]   quat_lma_xyzatr =     new double [quadCLTs.length][2][3];
+		double [][][]   quat_lma_enu_xyzatr = new double [quadCLTs.length][2][3];
 		Did_ins_2     d2_ref = quadCLTs[ref_index].did_ins_2;
 		for (int nscene = earliest_scene; nscene < quadCLTs.length; nscene++) {
 			QuadCLT scene = quadCLTs[nscene];
 			if (nscene == ref_index) {
-				quat_lma_xyz[nscene] =    new double[3];
+				quat_lma_xyzatr[nscene][0] =    new double[3];
 			} else {
 				String ts = scene.getImageName();
-				quat_lma_xyz[nscene] = ers_reference.getSceneXYZ(ts);
+				quat_lma_xyzatr[nscene][0] = ers_reference.getSceneXYZ(ts);
 			}
 			Did_ins_2   d2 = scene.did_ins_2;
 			double [] enu = Imx5.enuFromLla (d2.lla, d2_ref.lla);
-			quat_lma_enu_xyz[nscene] = Imx5.applyQuaternionTo(
+			quat_lma_enu_xyzatr[nscene][0] = Imx5.applyQuaternionTo(
 					Imx5.quaternionImsToCam(d2_ref.getQEnu(), // double[]  quat_enu,
 							ims_mount_atr,
 							ims_ortho),
@@ -5508,8 +5508,8 @@ public class Interscene {
 		int         debug_level = 1;
 		QuaternionLma quaternionLma = new QuaternionLma();
 		quaternionLma.prepareLMA(
-				quat_lma_enu_xyz, // quat_lma_xyz,     // double [][] vect_x,
-				quat_lma_xyz,     // double [][] vect_y,
+				quat_lma_enu_xyzatr, // quat_lma_xyz,     // double [][] vect_x,
+				quat_lma_xyzatr,     // double [][] vect_y,
 				null,             // double [][] vect_w, all same weight
 				reg_w,            // double      reg_w, // regularization weight [0..1) weight of q0^2+q1^2+q3^2 -1  
 				quat0,            // double []   quat0,

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

@@ -5425,68 +5425,13 @@ public class OpticalFlow {
 		}
 		// later move to the right place
 		if (adjust_imu_orient) { // (quadCLTs[ref_index].getNumOrient() >= clt_parameters.imp.mb_all_index)) {
-			double [][][] pimu_xyzatr = QuadCLT.integratePIMU(
-					clt_parameters, // final CLTParameters clt_parameters,
-					quadCLTs,       // final QuadCLT[]     quadCLTs,
-					ref_index,      // final int           ref_index,
-					null,           // double [][][]       dxyzatr,
-					earliest_scene, // final int           early_index,
-					last_index      //(quadCLTs.length -1) // int           last_index,
-		    		);
-			double [][][] xyzatr = new double [quadCLTs.length][][];
-			ErsCorrection ers_ref = quadCLTs[ref_index].getErsCorrection();
-	    	for (int nscene = earliest_scene; nscene <= last_index; nscene++) {
-	        	String ts = quadCLTs[nscene].getImageName();
-	        	xyzatr[nscene] = ers_ref.getSceneXYZATR(ts);
-	    	}
-	    	double [] rms = new double[5];
-	    	double [] quat = new double[4];
-	    	int quat_lma_mode = 03; // 4; // 3; //  2; // 1;
-	    	int debug_lev = debugLevel; // 3;
-	        double avg_z = quadCLTs[ref_index].getAverageZ(true); // in meters		
-	    	double  translation_weight =   1.0 / (avg_z + 1.0);
-	    	
-	    	double [][][] rotated_xyzatr = QuadCLT.rotateImsToCameraXYZ(
-	    			clt_parameters,     // CLTParameters clt_parameters,
-	    			quat_lma_mode,      // int quat_lma_mode,
-	    			avg_z,              // double        avg_height,
-	    			translation_weight, // double        translation_weight,
-	    			quadCLTs,           // QuadCLT[]     quadCLTs,
-	    			xyzatr,             // double [][][] xyzatr,
-	    			pimu_xyzatr,        // double [][][] ims_xyzatr,
-	    			ref_index,          // int           ref_index,
-	    			earliest_scene,     // int           early_index,
-	    			last_index,         // int           last_index,
-	    			rms,                //double []     rms, // null or double[5];
-	    			quat,               // double []     quaternion, // null or double[4]       
-	    			debug_lev); // int           debugLevel
-	    	if (rotated_xyzatr != null) {
-	        	Rotation rot = new Rotation(quat[0],quat[1],quat[2],quat[3], false); // no normalization - see if can be scaled
-	        	if (debugLevel > -3) {
-	        		System.out.println("Applying correction ot the IMS mount orientation:");
-					double []  corr_angles = rot.getAngles(RotationOrder.YXZ, ErsCorrection.ROT_CONV);
-					double []  corr_degrees = new double[3];
-					for (int i = 0; i < 3; i++) corr_degrees[i]=corr_angles[i]*180/Math.PI;
-		    		System.out.println("quat=["+quat[0]+", "+quat[1]+", "+quat[2]+", "+quat[3]+"]");
-		    		System.out.println("ATR(rad)=["+corr_angles[0]+", "+corr_angles[1]+", "+corr_angles[2]+"]");
-		    		System.out.println("ATR(deg)=["+corr_degrees[0]+", "+corr_degrees[1]+", "+corr_degrees[2]+"]");
-	        	}
-	        	double [] ims_mount_atr = clt_parameters.imp.getImsMountATR(); // converts to radians
-	        	double [] new_ims_mount_atr = Imx5.adjustMountAtrByQuat(
-	        			ims_mount_atr, // double [] ims_atr,
-	        			quat); // double [] corr_q)
-	        	clt_parameters.imp.setImsMountATR(new_ims_mount_atr);
-	        	if (debugLevel > -3) {
-	        		double [] new_atr = clt_parameters.imp.getImsMountATR(); // converts to radians
-					double [] degrees = new double[3];
-					for (int i = 0; i < 3; i++) degrees[i]=new_atr[i]*180/Math.PI;
-		    		System.out.println("New ATR(rad)=["+new_atr[0]+", "+new_atr[1]+", "+new_atr[2]+"]");
-		    		System.out.println("New ATR(deg)=["+degrees[0]+", "+degrees[1]+", "+degrees[2]+"]");
-		    		System.out.println ("*** Need to save the main configuration file ***");
-	        	}
-	    	} else {
-	    		System.out.println ("*** Failed to calculate IMS mount correction! ***");
-	    	}
+			   QuadCLT.adjustImuOrient(
+					   clt_parameters,     //CLTParameters clt_parameters,     // CLTParameters clt_parameters,
+					   quadCLTs, // QuadCLT[]     quadCLTs,
+					   ref_index, // int           ref_index,
+					   earliest_scene, // int           earliest_scene,
+					   last_index, // int           last_index,
+					   debugLevel); // 			    		int debugLevel
 		}
 		if (run_ly) {
 			if (debugLevel > -3) {
@@ -5602,7 +5547,7 @@ public class OpticalFlow {
 						debugLevel+1);
 				if (debugLevel > -3) {
 		        	Rotation rot = new Rotation(quatCorr[0],quatCorr[1],quatCorr[2],quatCorr[3], false); // no normalization - see if can be scaled
-					System.out.println("Applying correction ot the IMS to world orientation (rotating around IMS vertical):");
+					System.out.println("Applying correction to the IMS to world orientation (rotating around IMS vertical):");
 					double []  corr_angles = rot.getAngles(RotationOrder.YXZ, ErsCorrection.ROT_CONV);
 					double []  corr_degrees = new double[3];
 					for (int i = 0; i < 3; i++) corr_degrees[i]=corr_angles[i]*180/Math.PI;