working on quaterions <-> affines (6a6d0c40) · Commits · Elphel / imagej-elphel

src/main/java/com/elphel/imagej/orthomosaic/OrthoAltitudeMatch.java

+212 −28

Original line number	Original line	Diff line number	Diff line
	@@ -54,6 +54,7 @@ public class OrthoAltitudeMatch {
	String log_path,		String log_path,
	String orthoMapsCollection_path,		String orthoMapsCollection_path,
	int debugLevel) {		int debugLevel) {
			boolean y_down_ccw = true;
	int [] indices = orthoMapsCollection.getScenesFromPairs( // may be shorter, each element - absolute scene number used in pairs		int [] indices = orthoMapsCollection.getScenesFromPairs( // may be shorter, each element - absolute scene number used in pairs
	available_pairs, // pairs_defined_abs,// int [][] pairs,		available_pairs, // pairs_defined_abs,// int [][] pairs,
	null); // int [] indices_in) // preselected indices or null		null); // int [] indices_in) // preselected indices or null
	@@ -128,30 +129,6 @@ public class OrthoAltitudeMatch {
	if (updateStatus) {		if (updateStatus) {
	IJ.showStatus("Processing pair "+npair+" of "+condensed_pairs.length+" "+ipair[0]+"->"+ipair[1]);		IJ.showStatus("Processing pair "+npair+" of "+condensed_pairs.length+" "+ipair[0]+"->"+ipair[1]);
	}		}
	/*

	PairwiseOrthoMatch pairwiseOrthoMatch = ortho_maps[ipair[0]].getMatch(ortho_maps[ipair[1]].getName(), true).clone(); // ?
	double [][] daffine = null;
	if (pairwiseOrthoMatch != null) {
	double [] enuOffset = ortho_maps[ipair[1]].enuOffsetTo(ortho_maps[ipair[0]]);
	double [] rd = {enuOffset[0], -enuOffset[1]}; // {right,down} of the image
	daffine = pairwiseOrthoMatch.getAffine();
	if ((daffine != null) && alt_pairwise) {
	} else { // combine differential affine from individual
	double [][] aff0 = ortho_maps[ipair[0]].getAffine();
	double [][] aff1 = ortho_maps[ipair[1]].getAffine();
	PairwiseOrthoMatch aff_match = new PairwiseOrthoMatch (
	aff0, // double [][] affine0,
	aff1, // double [][] affine1,
	rd); // double [] rd);
	daffine = aff_match.getAffine();
	pairwiseOrthoMatch.setAffine(daffine);
	}
	} else {
	System.out.println("BUG: Missing pair for ["+ipair[0]+", "+ipair[1]+"] ");
	continue;
	}
	*/
	PairwiseOrthoMatch pairwiseOrthoMatch = ortho_maps[ipair[0]].getMatch(ortho_maps[ipair[1]].getName(), true); // ?		PairwiseOrthoMatch pairwiseOrthoMatch = ortho_maps[ipair[0]].getMatch(ortho_maps[ipair[1]].getName(), true); // ?
	if (pairwiseOrthoMatch == null) {		if (pairwiseOrthoMatch == null) {
	System.out.println("BUG: Missing pair for ["+ipair[0]+", "+ipair[1]+"] ");		System.out.println("BUG: Missing pair for ["+ipair[0]+", "+ipair[1]+"] ");
	@@ -217,11 +194,218 @@ public class OrthoAltitudeMatch {
	break;		break;
	}		}
	}		}
			double [] alt_data = {alt_data5[0]/pix_size_meters, alt_data5[1]/pix_size_meters,alt_data5[2]};

			boolean test_quat = true;
			if (test_quat) {
			System.out.println(">>>>>>>>>>>>>>>>> npair="+npair+": "+ipair[0]+" -> "+ipair[1]);
			boolean [][] masks = new boolean[2][];
			double [][] alt_data5s = new double[2][];
			double [][] data_overlap = new double[2][];
			double [][] alt_datas = new double[3][];
			double [] quat_diff = QuatUtils.tiltToQuaternion(
			alt_data,
			y_down_ccw); // boolean y_down_ccw)
			double [][] quats01 = new double [alt_datas.length][];
			for (int ns = 0; ns < cpair.length; ns++) {
			data_overlap[ns] = OrthoMap.extractWoi(
			alt_multi[cpair[ns]], // final double [] data0,
			width, // final int width,
			woi_overlap); // Rectangle woi_in);

			for (int ntry = 0; ntry <= alt_refine; ntry++) {
			alt_data5s[ns] = OrthoMap.getPlane(
			data_overlap[ns], // final double [] data,
			masks[ns], // final boolean [] mask,
			weight, // final double [] weight,
			woi_overlap.width, // final int width,
			xy0); // final double [] xy0) {
			if ((alt_outliers > 0) && (ntry < alt_refine)){ // not the last pass
			masks[ns] = OrthoMap.removeRelativeLowHigh (
			data_overlap[ns], // final double [] data,
			null, // mask, // final boolean [] mask_in, // new mask for all data and latest plane
			alt_abs_outliers, // final double abs_diff,
			alt_outliers, // final double rel_frac,
			alt_data5s[ns], // final double [] ground_plane, // tiltx,tilty, offs, x0(pix), y0(pix) or null
			woi_overlap.width,// final int width, // only used with ground_plane != null;
			num_bins); // final int num_bins)
			} else {
			break;
			}
			}
			alt_datas[ns] = new double [] {alt_data5s[ns][0]/pix_size_meters, alt_data5s[ns][1]/pix_size_meters,alt_data5s[ns][2]};
			}
			alt_datas[2] = new double [3];
			for (int i = 0; i < alt_datas[2].length; i++) {
			alt_datas[2][i] = alt_datas[0][i]+alt_data[i];
			}
			for (int ns = 0; ns < quats01.length; ns++) {
			quats01[ns] = QuatUtils.tiltToQuaternion(
			alt_datas[ns],
			y_down_ccw); // boolean y_down_ccw)
			}
			double [] quat_rdiff = QuatUtils.invert(quat_diff);

			double [] quat2a = QuatUtils.multiply(quats01[0], quat_diff);
			double [] quat2b = QuatUtils.multiply(quat_diff, quats01[0]);
			double [] quat2ap = QuatUtils.pureTilt(quat2a);
			double [] quat2bp = QuatUtils.pureTilt(quat2b);
			double [] quat2an = QuatUtils.normalize(quat2a);
			double [] quat2bn = QuatUtils.normalize(quat2b);
			double [] quat2apn = QuatUtils.normalize(quat2ap);
			double [] quat2bpn = QuatUtils.normalize(quat2bp);


			double [] quat1ar = QuatUtils.multiply(quats01[1], quat_rdiff);
			double [] quat1br = QuatUtils.multiply(quat_rdiff, quats01[1]);
			double [] quat1cr = QuatUtils.multiply(quats01[2], quat_rdiff);
			double [] quat1dr = QuatUtils.multiply(quat_rdiff, quats01[2]);

			double [] quat1apr = QuatUtils.pureTilt(quat1ar);
			double [] quat1bpr = QuatUtils.pureTilt(quat1br);
			double [] quat1cpr = QuatUtils.pureTilt(quat1cr);
			double [] quat1dpr = QuatUtils.pureTilt(quat1dr);
			double [] quat1aprn = QuatUtils.normalize(quat1apr);
			double [] quat1bprn = QuatUtils.normalize(quat1bpr);
			double [] quat1cprn = QuatUtils.normalize(quat1cpr);
			double [] quat1dprn = QuatUtils.normalize(quat1dpr);
			double [] quat1arn = QuatUtils.normalize(quat1ar);
			double [] quat1brn = QuatUtils.normalize(quat1br);
			double [] quat1crn = QuatUtils.normalize(quat1cr);
			double [] quat1drn = QuatUtils.normalize(quat1dr);
			//pureTilt
			System.out.println("alt_data= ["+alt_data[0]+","+alt_data[1]+","+alt_data[2]+"]");
			System.out.println("alt_datas[0]=["+alt_datas[0][0]+","+alt_datas[0][1]+","+alt_datas[0][2]+"]");
			System.out.println("alt_datas[1]=["+alt_datas[1][0]+","+alt_datas[1][1]+","+alt_datas[1][2]+"]");
			System.out.println("alt_datas[2]=["+alt_datas[2][0]+","+alt_datas[2][1]+","+alt_datas[2][2]+"]");
			/*
			System.out.println("quat_diff= ["+quat_diff[0]+","+quat_diff[1]+","+quat_diff[2]+","+quat_diff[3]+"] "+QuatUtils.norm(quat_diff));
			System.out.println("quats01[0]= ["+quats01[0][0]+","+quats01[0][1]+","+quats01[0][2]+","+quats01[0][3]+"] "+QuatUtils.norm(quats01[0]));
			System.out.println("quats01[1]= ["+quats01[1][0]+","+quats01[1][1]+","+quats01[1][2]+","+quats01[1][3]+"] "+QuatUtils.norm(quats01[1]));
			System.out.println("quats01[2]= ["+quats01[2][0]+","+quats01[2][1]+","+quats01[2][2]+","+quats01[2][3]+"] "+QuatUtils.norm(quats01[2]));
			*/
			System.out.println("quat2a= ["+quat2a[0]+","+quat2a[1]+","+quat2a[2]+","+quat2a[3]+"] "+QuatUtils.norm(quat2a));
			System.out.println("quat2b= ["+quat2b[0]+","+quat2b[1]+","+quat2b[2]+","+quat2b[3]+"] "+QuatUtils.norm(quat2b));
			System.out.println("quat2ap= ["+quat2ap[0]+","+quat2ap[1]+","+quat2ap[2]+","+quat2ap[3]+"] "+QuatUtils.norm(quat2ap));
			System.out.println("quat2bp= ["+quat2bp[0]+","+quat2bp[1]+","+quat2bp[2]+","+quat2bp[3]+"] "+QuatUtils.norm(quat2bp));
			/*
			System.out.println("quat2an= ["+quat2an[0]+","+quat2an[1]+","+quat2an[2]+","+quat2an[3]+"] "+QuatUtils.norm(quat2an));
			System.out.println("quat2bn= ["+quat2bn[0]+","+quat2bn[1]+","+quat2bn[2]+","+quat2bn[3]+"] "+QuatUtils.norm(quat2bn));
			System.out.println("quat2apn= ["+quat2apn[0]+","+quat2apn[1]+","+quat2apn[2]+","+quat2apn[3]+"] "+QuatUtils.norm(quat2apn));
			System.out.println("quat2bpn= ["+quat2bpn[0]+","+quat2bpn[1]+","+quat2bpn[2]+","+quat2bpn[3]+"] "+QuatUtils.norm(quat2bpn));
			System.out.println("quat1apr= ["+quat1apr[0]+","+quat1apr[1]+","+quat1apr[2]+","+quat1apr[3]+"] "+QuatUtils.norm(quat1apr)); // +
			System.out.println("quat1bpr= ["+quat1bpr[0]+","+quat1bpr[1]+","+quat1bpr[2]+","+quat1bpr[3]+"] "+QuatUtils.norm(quat1bpr)); // ++
			System.out.println("quat1cpr= ["+quat1cpr[0]+","+quat1cpr[1]+","+quat1cpr[2]+","+quat1cpr[3]+"] "+QuatUtils.norm(quat1cpr)); // +++
			System.out.println("quat1dpr= ["+quat1dpr[0]+","+quat1dpr[1]+","+quat1dpr[2]+","+quat1dpr[3]+"] "+QuatUtils.norm(quat1dpr)); // +++
			System.out.println("quat1aprn= ["+quat1aprn[0]+","+quat1aprn[1]+","+quat1aprn[2]+","+quat1aprn[3]+"] "+QuatUtils.norm(quat1aprn)); // +
			System.out.println("quat1bprn= ["+quat1bprn[0]+","+quat1bprn[1]+","+quat1bprn[2]+","+quat1bprn[3]+"] "+QuatUtils.norm(quat1bprn)); // ++
			System.out.println("quat1cprn= ["+quat1cprn[0]+","+quat1cprn[1]+","+quat1cprn[2]+","+quat1cprn[3]+"] "+QuatUtils.norm(quat1cprn)); // +++
			System.out.println("quat1dprn= ["+quat1dprn[0]+","+quat1dprn[1]+","+quat1dprn[2]+","+quat1dprn[3]+"] "+QuatUtils.norm(quat1dprn)); // +++
			System.out.println("quat1arn= ["+quat1arn[0]+","+quat1arn[1]+","+quat1arn[2]+","+quat1arn[3]+"] "+QuatUtils.norm(quat1arn)); // +
			System.out.println("quat1brn= ["+quat1brn[0]+","+quat1brn[1]+","+quat1brn[2]+","+quat1brn[3]+"] "+QuatUtils.norm(quat1brn)); // ++
			System.out.println("quat1crn= ["+quat1crn[0]+","+quat1crn[1]+","+quat1crn[2]+","+quat1crn[3]+"] "+QuatUtils.norm(quat1crn)); // +++
			System.out.println("quat1drn= ["+quat1drn[0]+","+quat1drn[1]+","+quat1drn[2]+","+quat1drn[3]+"] "+QuatUtils.norm(quat1drn)); // +++
			*/
			double [][] affine_pair = pairwiseOrthoMatch.getAffine();
			double [][][] affines = new double [][][] {ortho_maps[ipair[0]].getAffine(),ortho_maps[ipair[1]].getAffine()};
			boolean make__pure_tilt = false;
			double [][] aff1_stretch = QuatUtils.quatToAffine(
			quats01[0], // double [] quat,
			true, // boolean stretch,
			make__pure_tilt, // boolean make__pure_tilt)
			y_down_ccw); // boolean y_down_ccw);
			double [][] aff2_shrink = QuatUtils.quatToAffine(
			quats01[2], // double [] quat,
			false, // boolean stretch,
			make__pure_tilt, // boolean make__pure_tilt)
			y_down_ccw); // boolean y_down_ccw);
			double [][] aff2_stretch = QuatUtils.quatToAffine(
			quats01[2], // double [] quat,
			true, // boolean stretch,
			make__pure_tilt, // boolean make__pure_tilt)
			y_down_ccw); // boolean y_down_ccw);

			double [][] qaffd_pm = QuatUtils.affineToQuatScaled(affine_pair, y_down_ccw);
			double [] sqaffd_pm = {QuatUtils.normalizeInPlace(qaffd_pm[0]),QuatUtils.normalizeInPlace(qaffd_pm[1])}; // normalizes
			System.out.println("qaffd_pm[0]= ["+qaffd_pm[0][0]+ ","+qaffd_pm[0][1]+ ","+qaffd_pm[0][2]+ ","+qaffd_pm[0][3]+ "] scale="+sqaffd_pm[0]);
			System.out.println("qaffd_pm[1]= ["+qaffd_pm[1][0]+ ","+qaffd_pm[1][1]+ ","+qaffd_pm[1][2]+ ","+qaffd_pm[1][3]+ "] scale="+sqaffd_pm[1]);
			double [][] qaff1_pm = QuatUtils.affineToQuatScaled(aff1_stretch, y_down_ccw);
			double [] sqaff1_pm = {QuatUtils.normalizeInPlace(qaffd_pm[0]),QuatUtils.normalizeInPlace(qaff1_pm[1])}; // normalizes
			System.out.println("qaff1_pm[0]= ["+qaff1_pm[0][0]+ ","+qaff1_pm[0][1]+ ","+qaff1_pm[0][2]+ ","+qaff1_pm[0][3]+ "] scale="+sqaff1_pm[0]);
			System.out.println("qaff1_pm[1]= ["+qaff1_pm[1][0]+ ","+qaff1_pm[1][1]+ ","+qaff1_pm[1][2]+ ","+qaff1_pm[1][3]+ "] scale="+sqaff1_pm[1]);
			double [][] qaff2a_pm = QuatUtils.affineToQuatScaled(aff2_shrink, y_down_ccw);
			double [] sqaff2a_pm = {QuatUtils.normalizeInPlace(qaff2a_pm[0]),QuatUtils.normalizeInPlace(qaff2a_pm[1])}; // normalizes
			System.out.println("qaff2a_pm[0]= ["+qaff2a_pm[0][0]+","+qaff2a_pm[0][1]+","+qaff2a_pm[0][2]+","+qaff2a_pm[0][3]+"] scale="+sqaff2a_pm[0]);
			System.out.println("qaff2a_pm[1]= ["+qaff2a_pm[1][0]+","+qaff2a_pm[1][1]+","+qaff2a_pm[1][2]+","+qaff2a_pm[1][3]+"] scale="+sqaff2a_pm[1]);
			double [][] qaff2_pm = QuatUtils.affineToQuatScaled(aff2_stretch, y_down_ccw);
			double [] sqaff2_pm = {QuatUtils.normalizeInPlace(qaff2_pm[0]),QuatUtils.normalizeInPlace(qaff2_pm[1])}; // normalizes
			System.out.println("qaff2_pm[0]= ["+qaff2_pm[0][0]+ ","+qaff2_pm[0][1]+ ","+qaff2_pm[0][2]+ ","+qaff2_pm[0][3]+ "] scale="+sqaff2_pm[0]);
			System.out.println("qaff2_pm[1]= ["+qaff2_pm[1][0]+ ","+qaff2_pm[1][1]+ ","+qaff2_pm[1][2]+ ","+qaff2_pm[1][3]+ "] scale="+sqaff2_pm[1]);
			double [][] qaffine0_pm = QuatUtils.affineToQuatScaled(affines[0], y_down_ccw);
			double [] sqaffine0_pm ={QuatUtils.normalizeInPlace(qaffine0_pm[0]),QuatUtils.normalizeInPlace(qaffine0_pm[1])}; // normalizes
			System.out.println("qaffine0_pm[0]=["+qaffine0_pm[0][0]+ ","+qaffine0_pm[0][1]+ ","+qaffine0_pm[0][2]+ ","+qaffine0_pm[0][3]+ "] scale="+sqaffine0_pm[0]);
			System.out.println("qaffine0_pm[1]=["+qaffine0_pm[1][0]+ ","+qaffine0_pm[1][1]+ ","+qaffine0_pm[1][2]+ ","+qaffine0_pm[1][3]+ "] scale="+sqaffine0_pm[1]);
			double [][] qaffine1_pm = QuatUtils.affineToQuatScaled(affines[1], y_down_ccw);
			double [] sqaffine1_pm ={QuatUtils.normalizeInPlace(qaffine1_pm[0]),QuatUtils.normalizeInPlace(qaffine1_pm[1])}; // normalizes
			System.out.println("qaffine1_pm[0]=["+qaffine1_pm[0][0]+ ","+qaffine1_pm[0][1]+ ","+qaffine1_pm[0][2]+ ","+qaffine1_pm[0][3]+ "] scale="+sqaffine1_pm[0]);
			System.out.println("qaffine1_pm[1]=["+qaffine1_pm[1][0]+ ","+qaffine1_pm[1][1]+ ","+qaffine1_pm[1][2]+ ","+qaffine1_pm[1][3]+ "] scale="+sqaffine1_pm[1]);


			double [][] aff_combo = QuatUtils.matMult(aff2_shrink,aff1_stretch);
			System.out.println("affine_pair= [["+affine_pair[0][0]+","+affine_pair[0][1]+","+affine_pair[0][2]+"]");
			System.out.println(" ["+affine_pair[1][0]+","+affine_pair[1][1]+","+affine_pair[1][2]+"]]");
			System.out.println("affines[0]= [["+affines[0][0][0]+ ","+affines[0][0][1]+ ","+affines[0][0][2]+"]");
			System.out.println(" ["+affines[0][1][0]+ ","+affines[0][1][1]+ ","+affines[0][1][2]+"]]");
			System.out.println("affines[1]= [["+affines[1][0][0]+ ","+affines[1][0][1]+ ","+affines[1][0][2]+"]");
			System.out.println(" ["+affines[1][1][0]+ ","+affines[1][1][1]+ ","+affines[1][1][2]+"]]");
			System.out.println("aff1_stretch= [["+aff1_stretch[0][0]+ ","+aff1_stretch[0][1]+"]");
			System.out.println(" ["+aff1_stretch[1][0]+ ","+aff1_stretch[1][1]+"]]");
			System.out.println("aff2_shrink= [["+aff2_shrink[0][0]+ ","+aff2_shrink[0][1]+ "]");
			System.out.println(" ["+aff2_shrink[1][0]+ ","+aff2_shrink[1][1]+ "]]");
			System.out.println("aff2_stretch= [["+aff2_stretch[0][0]+ ","+aff2_stretch[0][1]+"]");
			System.out.println(" ["+aff2_stretch[1][0]+ ","+aff2_stretch[1][1]+"]]");
			System.out.println("aff_combo= [["+aff_combo[0][0]+ ","+aff_combo[0][1]+ "]");
			System.out.println(" ["+aff_combo[1][0]+ ","+aff_combo[1][1]+ "]]");
			/*
			double [] svd_affine_pair = OrthoMap.singularValueDecomposeScaleTilt(affine_pair, y_down_ccw); // boolean y_down_ccw)
			double [][] svd_affines = {OrthoMap.singularValueDecomposeScaleTilt(affines[0], y_down_ccw), OrthoMap.singularValueDecomposeScaleTilt(affines[1], y_down_ccw)};
			double [] svd_aff1_stretch = OrthoMap.singularValueDecomposeScaleTilt(aff1_stretch, y_down_ccw);
			double [] svd_aff2_shrink = OrthoMap.singularValueDecomposeScaleTilt(aff2_shrink, y_down_ccw);
			double [] svd_aff2_stretch = OrthoMap.singularValueDecomposeScaleTilt(aff2_stretch, y_down_ccw);
			double [] svd_aff_combo = OrthoMap.singularValueDecomposeScaleTilt(aff_combo, y_down_ccw);
			*/
			SingularValueDecomposition svd_affine_pair = SingularValueDecomposition.singularValueDecomposeScaleTiltGamma(affine_pair, y_down_ccw); // boolean y_down_ccw)
			SingularValueDecomposition[] svd_affines = {SingularValueDecomposition.singularValueDecomposeScaleTiltGamma(affines[0], y_down_ccw), SingularValueDecomposition.singularValueDecomposeScaleTiltGamma(affines[1], y_down_ccw)};
			SingularValueDecomposition svd_aff1_stretch = SingularValueDecomposition.singularValueDecomposeScaleTiltGamma(aff1_stretch, y_down_ccw);
			SingularValueDecomposition svd_aff2_shrink = SingularValueDecomposition.singularValueDecomposeScaleTiltGamma(aff2_shrink, y_down_ccw);
			SingularValueDecomposition svd_aff2_stretch = SingularValueDecomposition.singularValueDecomposeScaleTiltGamma(aff2_stretch, y_down_ccw);
			SingularValueDecomposition svd_aff_combo = SingularValueDecomposition.singularValueDecomposeScaleTiltGamma(aff_combo, y_down_ccw);
			System.out.println("scale,tilt_rad,gamma,rot");
			System.out.println("svd_affine_pair= ["+svd_affine_pair.scale+ ","+svd_affine_pair.getTiltAngle()+ ","+svd_affine_pair.gamma+ ","+svd_affine_pair.rot+ "] tilt="+(svd_affine_pair.getTiltAngle()180/Math.PI)+ "\u00B0, dir="+(svd_affine_pair.gamma180/Math.PI)+"\u00B0");
			System.out.println("svd_affines[0]= ["+svd_affines[0].scale+ ","+ svd_affines[0].getTiltAngle()+ ","+svd_affines[0].gamma+ ","+svd_affines[0].rot+ "] tilt="+(svd_affines[0].getTiltAngle()* 180/Math.PI)+ "\u00B0, dir="+(svd_affines[0].gamma*180/Math.PI)+"\u00B0");
			System.out.println("svd_affines[1]= ["+svd_affines[1].scale+ ","+ svd_affines[1].getTiltAngle()+ ","+svd_affines[1].gamma+ ","+svd_affines[1].rot+ "] tilt="+(svd_affines[1].getTiltAngle()* 180/Math.PI)+ "\u00B0, dir="+(svd_affines[1].gamma*180/Math.PI)+"\u00B0");
			System.out.println("svd_aff1_stretch= ["+svd_aff1_stretch.scale+","+ svd_aff1_stretch.getTiltAngle()+","+svd_aff1_stretch.gamma+","+svd_aff1_stretch.rot+"] tilt="+(svd_aff1_stretch.getTiltAngle()180/Math.PI)+ "\u00B0, dir="+(svd_aff1_stretch.gamma180/Math.PI)+"\u00B0");
			System.out.println("svd_aff2_shrink= ["+svd_aff2_shrink.scale+ ","+ svd_aff2_shrink.getTiltAngle()+ ","+svd_aff2_shrink.gamma+ ","+svd_aff2_shrink.rot+ "] tilt="+(svd_aff2_shrink.getTiltAngle()180/Math.PI)+ "\u00B0, dir="+(svd_aff2_shrink.gamma180/Math.PI)+"\u00B0");
			System.out.println("svd_aff2_stretch= ["+svd_aff2_stretch.scale+","+ svd_aff2_stretch.getTiltAngle()+","+svd_aff2_stretch.gamma+","+svd_aff2_stretch.rot+"] tilt="+(svd_aff2_stretch.getTiltAngle()180/Math.PI)+ "\u00B0, dir="+(svd_aff2_stretch.gamma180/Math.PI)+"\u00B0");
			System.out.println("svd_aff_combo= ["+svd_aff_combo.scale+ ","+ svd_aff_combo.getTiltAngle()+ ","+svd_aff_combo.gamma+ ","+svd_aff_combo.rot+ "] tilt="+(svd_aff_combo.getTiltAngle()180/Math.PI)+ "\u00B0, dir="+(svd_aff_combo.gamma180/Math.PI)+"\u00B0");


			System.out.println("quat_diff= ["+quat_diff[0]+ ","+quat_diff[1]+ ","+quat_diff[2]+ ","+quat_diff[3]+ "] tilt="+2Math.acos(quat_diff[0])+ " dir="+Math.atan2(quat_diff[2],quat_diff[1])+", tilt="+(2Math.acos(quat_diff[0])180/Math.PI)+ "\u00B0, dir="+(Math.atan2(quat_diff[2],quat_diff[1])180/Math.PI)+"\u00B0");
			System.out.println("quats01[0]= ["+quats01[0][0]+","+quats01[0][1]+","+quats01[0][2]+","+quats01[0][3]+"] tilt="+2Math.acos(quats01[0][0])+" dir="+Math.atan2(quats01[0][2],quats01[0][1])+", tilt="+(2Math.acos(quats01[0][0])180/Math.PI)+ "\u00B0, dir="+(Math.atan2(quats01[0][2],quats01[0][1])180/Math.PI)+"\u00B0");
			System.out.println("quats01[1]= ["+quats01[1][0]+","+quats01[1][1]+","+quats01[1][2]+","+quats01[1][3]+"] tilt="+2Math.acos(quats01[1][0])+" dir="+Math.atan2(quats01[1][2],quats01[1][1])+", tilt="+(2Math.acos(quats01[1][0])180/Math.PI)+ "\u00B0, dir="+(Math.atan2(quats01[1][2],quats01[1][1])180/Math.PI)+"\u00B0");
			System.out.println("quats01[2]= ["+quats01[2][0]+","+quats01[2][1]+","+quats01[2][2]+","+quats01[2][3]+"] tilt="+2Math.acos(quats01[2][0])+" dir="+Math.atan2(quats01[2][2],quats01[2][1])+", tilt="+(2Math.acos(quats01[2][0])180/Math.PI)+ "\u00B0, dir="+(Math.atan2(quats01[2][2],quats01[2][1])180/Math.PI)+"\u00B0");
			/*
			System.out.println("quat_diff_tilt= "+2*Math.acos(quat_diff[0]));
			System.out.println("quats01_0_tilt= "+2*Math.acos(quats01[0][0]));
			System.out.println("quats01_1_tilt= "+2*Math.acos(quats01[1][0]));
			System.out.println("quats01_2_tilt= "+2*Math.acos(quats01[2][0]));
			*/
			}



	// double [] alt_data = new double[3];		// double [] alt_data = new double[3];
	// System.arraycopy(alt_data5, 0, alt_data, 0, alt_data.length);		// System.arraycopy(alt_data5, 0, alt_data, 0, alt_data.length);
	double [] alt_data = {alt_data5[0]/pix_size_meters, alt_data5[1]/pix_size_meters,alt_data5[2]};
	pairwiseOrthoMatch.setAltData(alt_data);		pairwiseOrthoMatch.setAltData(alt_data);

	if (log_append && (log_path != null)) { // assuming directory exists		if (log_append && (log_path != null)) { // assuming directory exists

Admin message