tested derivative for the OrthoMultiLMA (352aa9e1) · Commits · Elphel / imagej-elphel

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

+20 −22

Original line number	Diff line number	Diff line
		@@ -166,7 +166,7 @@ public class ComboMatch {
		int num_tries_fit = 10;
		boolean update_match = true; // use false to save new version of data
		boolean render_match = false; // true;

		boolean test_multi_lma = false;
		boolean pattern_match = true; // false;

		boolean bounds_to_indices = true;
		@@ -202,7 +202,8 @@ public class ComboMatch {

		gd.addCheckbox ("Update match if calculated", update_match, "Will update correlation match for a pair if found.");
		gd.addCheckbox ("Render match", render_match, "Render a pair of matched images.");

		gd.addCheckbox ("Test multi LMA", test_multi_lma, "Temporary debug.");
		//
		gd.addCheckbox ("Pattern match", pattern_match, "Search for patterns for both images in a pair, first is primary.");

		gd.addCheckbox ("Bounds to selected images", bounds_to_indices, "Set combo image bounds to selected images only. False - all images.");
		@@ -262,7 +263,7 @@ public class ComboMatch {
		num_tries_fit = (int) gd.getNextNumber();
		update_match= gd.getNextBoolean();
		render_match= gd.getNextBoolean();

		test_multi_lma= gd.getNextBoolean();
		pattern_match= gd.getNextBoolean();

		bounds_to_indices= gd.getNextBoolean();
		@@ -774,7 +775,7 @@ public class ComboMatch {
		orthoMapsCollection_path); // String orthoMapsCollection_path);
		if (!ok) return false;
		}
		if (process_correlation \|\| render_match \|\| pattern_match) {
		if (process_correlation \|\| render_match \|\| pattern_match \|\| test_multi_lma) {
		// int [] gpu_pair;
		if (gpu_spair == null) {
		ArrayList<Point> pairs_list = new ArrayList<Point>();
		@@ -859,24 +860,8 @@ public class ComboMatch {
		double agl_ratio = max_agl/50.0;
		double metric_error_adj = metric_error * agl_ratio * agl_ratio; // metric_error settings is good for 50m. Increase for higher Maybe squared?
		int initial_zoom = max_zoom_lev - 4; // another algorithm?
		/*
		if (GPU_QUAD_AFFINE == null) {
		System.out.println("Setting up GPU");
		try {
		GPU_QUAD_AFFINE = new GpuQuad(//
		GPU_TILE_PROCESSOR, // GPUTileProcessor gpuTileProcessor,
		gpu_max_width, // final int max_width,
		gpu_max_height, // final int max_height,
		1, // final int num_colors, // normally 1?
		clt_parameters.gpu_debug_level);
		} catch (Exception e) {
		System.out.println("Failed to initialize GpuQuad class");
		// TODO Auto-generated catch block
		e.printStackTrace();
		return false;
		} // final int debugLevel);
		}
		*/

		// Here - always start with unity affine0 and affine1 from possibly matched pair
		double [][] affine0 = {{1,0,0},{0,1,0}}; // will always stay the same
		double [][] affine1 = null;

		@@ -893,6 +878,13 @@ public class ComboMatch {
		}

		} else {
		if (test_multi_lma) {
		OrthoMultiLMA.testMultiLMA(
		clt_parameters, // CLTParameters clt_parameters,
		maps_collection, // OrthoMapsCollection maps_collection,
		gpu_pair); // int [] indices)
		return true;
		}
		if (process_correlation && !use_marked_image) { // match may or may not exist
		// if match exists - ask if use it. If not - open dialog and start spiral
		pairwiseOrthoMatch = initialPairAdjust(
		@@ -1095,6 +1087,7 @@ public class ComboMatch {
		boolean log_append = clt_parameters.imp.pwise_log_append;
		String log_path = clt_parameters.imp.pwise_log_path;

		boolean pmtch_use_affine = clt_parameters.imp.pmtch_use_affine;
		double max_std = clt_parameters.imp.pmtch_max_std; // 1.5; // maximal standard deviation to limit center area
		double min_std_rad = clt_parameters.imp.pmtch_min_std_rad;// 2.0; // minimal radius of the central area (if less - fail)
		double rad_fraction = clt_parameters.imp.pmtch_cent_rad; // center circle radius fraction of 0.5* min(width, height) in tiles
		@@ -1126,6 +1119,7 @@ public class ComboMatch {
		gd.addNumericField("Spiral search debug level",spiral_debug, 0,3,"","Debug level during Spiral search.");

		gd.addMessage("Parameters, common to all matching, not only spiral");
		gd.addCheckbox ("Use scenes' affine", pmtch_use_affine, "Use known scenes' affine matrices, false - start from scratch (unity) ones.");
		gd.addNumericField("Central area standard deviation", max_std, 3,7,"", "Central area limit by the standard deviation.");
		gd.addNumericField("Central area minimal radius", min_std_rad, 3,7,"tile", "Minimal radius of the central area after all LMA passes.");
		gd.addNumericField("Central area radius as fraction", rad_fraction, 3,7,"", "Central area radius as fraction of half minimal WOI dimension.");
		@@ -1154,6 +1148,7 @@ public class ComboMatch {
		log_path = gd.getNextString();
		spiral_debug = (int) gd.getNextNumber();
		search_step= gd.getNextNumber();
		pmtch_use_affine= gd.getNextBoolean();
		max_std= gd.getNextNumber();
		min_std_rad= gd.getNextNumber();
		rad_fraction= gd.getNextNumber();
		@@ -1180,6 +1175,8 @@ public class ComboMatch {
		clt_parameters, // CLTParameters clt_parameters,
		frac_remove, // double frac_remove, // = 0.25
		metric_error, // double metric_error,
		pmtch_use_affine, // boolean pmtch_use_affine,

		max_std, // double max_std, // maximal standard deviation to limit center area
		min_std_rad, // double min_std_rad, // minimal radius of the central area (if less - fail)
		rad_fraction, // double rad_fraction,
		@@ -1198,6 +1195,7 @@ public class ComboMatch {
		min_overlap, // int min_overlap, // 3000
		ignore_rms, // boolean ignore_rms,
		null,//double [] max_rms_iter, // = {1.0, 0.6};//
		1.0, // double overlap,
		spiral_debug); // int debugLevel){
		if (log_append && (log_path != null)) { // assuming directory exists
		StringBuffer sb = new StringBuffer();

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

+2 −1

Original line number	Diff line number	Diff line
		@@ -829,6 +829,7 @@ public class OrthoMap implements Comparable <OrthoMap>, Serializable{
		* @param affine [2][3] array were the last column is made of the offsets (in meters)
		* @return [2][3] array that converts from the image metric coordinates relative to the
		* "vert_meters" point to the rectified metric coordinates relative to the same point.
		*
		*/
		public static double [][] invertAffine(double [][] affine){
		Matrix A = new Matrix (

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

+33 −13

Original line number	Diff line number	Diff line
		@@ -115,6 +115,11 @@ public class OrthoMapsCollection implements Serializable{
		Arrays.sort(ortho_maps);
		reindex();
		}

		public static double [][] unityAffine() {
		return new double [][] {{1,0,0},{0,1,0}};
		}

		// add update kernels, update patterns
		public void updateKernels (
		String path) {
		@@ -945,6 +950,7 @@ public class OrthoMapsCollection implements Serializable{
		CLTParameters clt_parameters,
		double frac_remove, // = 0.25
		double metric_error,
		boolean pmtch_use_affine,
		double max_std, // maximal standard deviation to limit center area
		double min_std_rad, // minimal radius of the central area (if less - fail)
		double rad_fraction,
		@@ -963,6 +969,7 @@ public class OrthoMapsCollection implements Serializable{
		int min_overlap, // = 5
		boolean ignore_rms,
		double [] max_rms_iter, // = {1.0, 0.6};//
		double overlap,
		int debugLevel){
		double [][] affine1 = new double [][] {affines_init[1][0].clone(),affines_init[1][1].clone()};
		double [][][] affines = new double [][][] {affines_init[0],affine1};
		@@ -976,7 +983,8 @@ public class OrthoMapsCollection implements Serializable{
		affines[1], // double [][] affine,
		null, // double [][] jtj,
		Double.NaN, // double rms,
		zoom_lev); // int zoom_lev);
		zoom_lev, // int zoom_lev);
		overlap); // double overlap);
		// double max_std = 0.5; // maximal standard deviation to limit center area
		// double min_std_rad = 2.0; // minimal radius of the central area (if less - fail)
		int best_nx = -1, best_ny = -1;
		@@ -1059,7 +1067,7 @@ public class OrthoMapsCollection implements Serializable{
		}



		/*
		public FineXYCorr correlateOrthoPair( // not used
		CLTParameters clt_parameters,
		PairwiseOrthoMatch pairwiseOrthoMatch, // will return statistics
		@@ -1113,7 +1121,7 @@ public class OrthoMapsCollection implements Serializable{
		max_rms_iter, // = {1.0, 0.6};// double [] max_rms_iter, // = {1.0, 0.6};//
		debugLevel); // final int debugLevel)
		}

		*/
		public FineXYCorr correlateOrthoPair(
		CLTParameters clt_parameters,
		PairwiseOrthoMatch pairwiseOrthoMatch, // will return statistics, may be null if not needed
		@@ -1711,6 +1719,7 @@ public class OrthoMapsCollection implements Serializable{
		if (pairwiseOrthoMatch != null) {
		pairwiseOrthoMatch.jtj = jtj;
		pairwiseOrthoMatch.rms= rms;
		pairwiseOrthoMatch.zoom_lev = zoom_lev;
		}

		double [] tlo_src_metric_other = new double[2]; // check affines[][][] here -
		@@ -4112,6 +4121,7 @@ public class OrthoMapsCollection implements Serializable{
		//Final pairwise scenes matching
		double frac_remove = clt_parameters.imp.pmtch_frac_remove;// 0.15;
		double metric_err = clt_parameters.imp.pmtch_metric_err;// 0.05; // 0.02;// 2 cm
		boolean pmtch_use_affine = clt_parameters.imp.pmtch_use_affine;
		double max_std = clt_parameters.imp.pmtch_max_std;// 1.5; // maximal standard deviation to limit center area
		double min_std_rad = clt_parameters.imp.pmtch_min_std_rad;// 2.0; // minimal radius of the central area (if less - fail)
		boolean ignore_prev_rms = clt_parameters.imp.pmtch_ignore_rms;// true;
		@@ -4154,6 +4164,7 @@ public class OrthoMapsCollection implements Serializable{
		gd.addMessage ("Final pairwise scenes matching");
		gd.addNumericField("Remove fraction of worst matches", frac_remove, 3,7,"", "When fitting scenes remove this fraction of worst match tiles.");
		gd.addNumericField("Maximal metric error", metric_err, 3,7,"m", "Maximal tolerable fitting error caused by elevation variations.");
		gd.addCheckbox ("Use scenes' affine", pmtch_use_affine, "Use known scenes' affine matrices, false - start from scratch (unity) ones.");
		gd.addNumericField("Central area standard deviation", max_std, 3,7,"", "Central area limit by the standard deviation.");
		gd.addNumericField("Central area minimal radius", min_std_rad, 3,7,"tile", "Minimal radius of the central area after all LMA passes.");
		gd.addCheckbox ("Ignore previous RMSE", ignore_prev_rms, "Do not exit full fitting cycles if the RMSE worsened/not improved.");
		@@ -4190,6 +4201,7 @@ public class OrthoMapsCollection implements Serializable{

		frac_remove = gd.getNextNumber();
		metric_err = gd.getNextNumber();
		pmtch_use_affine= gd.getNextBoolean();
		max_std = gd.getNextNumber();
		min_std_rad = gd.getNextNumber();
		ignore_prev_rms = gd.getNextBoolean();
		@@ -4224,6 +4236,7 @@ public class OrthoMapsCollection implements Serializable{
		spiral_debug, // int spiral_debug,
		frac_remove, // double frac_remove,
		metric_err, // double metric_error,
		pmtch_use_affine, // boolean pmtch_use_affine,
		max_std, // double max_std,
		min_std_rad, // double min_std_rad,
		ignore_prev_rms, // boolean ignore_prev_rms,
		@@ -4263,6 +4276,7 @@ public class OrthoMapsCollection implements Serializable{

		double frac_remove,
		double metric_error,
		boolean pmtch_use_affine,
		double max_std,
		double min_std_rad,
		boolean ignore_prev_rms,
		@@ -4305,7 +4319,7 @@ public class OrthoMapsCollection implements Serializable{
		sb.append("num_pairs\t"+ num_pairs+"\n");
		sb.append("num_new\t"+ num_new+"\n");
		sb.append(String.format("%4s\t%4s\t%17s\t%17s\t%6s\t%3s\t%4s,\t%4s\t%6s\t%6s\t%7s\n",
		"scn1","scn2","timestamp1","timestamp2","ovrlp","zl","nx","ny","RMS-sp","RMSfin","removed"));
		"scn1","scn2","timestamp1","timestamp2","ovrlp","zl","nx","ny","RMS-sp","RMSfin","fzl","removed"));
		CalibrationFileManagement.saveStringToFile (
		log_path, //String path,
		sb.toString(), // data,
		@@ -4361,11 +4375,12 @@ public class OrthoMapsCollection implements Serializable{
		if (skip) {
		if (log_append && (log_path != null)) { // assuming directory exists
		StringBuffer sb = new StringBuffer();
		sb.append(String.format("%4d\t%4d\t%s\t%s\t%6.4f\t%3d\tSKIP\t\t\t%6.4f\n",
		sb.append(String.format("%4d\t%4d\t%s\t%s\t%6.4f\t%3d\tSKIP\t\t\t%6.4f\t%3d\n",
		ipair[0], ipair[1],
		ortho_maps[ipair[0]].getName(), ortho_maps[ipair[1]].getName(),
		overlaps[overlap_indx], initial_zoom,
		direct_match.rms));
		direct_match.rms,
		direct_match.zoom_lev));
		CalibrationFileManagement.saveStringToFile (
		log_path, //String path,
		sb.toString(), // data,
		@@ -4374,8 +4389,11 @@ public class OrthoMapsCollection implements Serializable{
		continue;
		}
		PairwiseOrthoMatch pairwiseOrthoMatch = null;
		double [][] affine0 = ortho_maps[ipair[0]].getAffine(); // {{1,0,0},{0,1,0}}; // will always stay the same
		double [][] affine1 = ortho_maps[ipair[0]].getAffine(); // {{1,0,0},{0,1,0}}; // here (manual mode) start from the center, may use prediction in auto

		// unityAffine()

		double [][] affine0 = pmtch_use_affine?ortho_maps[ipair[0]].getAffine():unityAffine(); // {{1,0,0},{0,1,0}}; // will always stay the same
		double [][] affine1 = pmtch_use_affine?ortho_maps[ipair[0]].getAffine():unityAffine(); // {{1,0,0},{0,1,0}}; // here (manual mode) start from the center, may use prediction in auto
		double [][][] affines = new double[][][] {affine0,affine1};
		double spiral_rms = Double.NaN;
		if (use_direct) {
		@@ -4392,6 +4410,7 @@ public class OrthoMapsCollection implements Serializable{
		clt_parameters, // CLTParameters clt_parameters,
		frac_remove, // double frac_remove, // = 0.25
		metric_error_adj,// double metric_error,
		pmtch_use_affine, // boolean pmtch_use_affine,
		max_std, // double max_std, // maximal standard deviation to limit center area
		min_std_rad, // double min_std_rad, // minimal radius of the central area (if less - fail)
		rad_fraction, // double rad_fraction,
		@@ -4410,6 +4429,7 @@ public class OrthoMapsCollection implements Serializable{
		min_overlap, // int min_overlap, // 3000
		ignore_rms, // boolean ignore_rms,
		max_rms_iter, // double [] max_rms_iter, // = {1.0, 0.6};//
		overlaps[overlap_indx], // double overlap,
		spiral_debug); // int debugLevel)
		if ((pairwiseOrthoMatch == null) \|\| Double.isNaN(pairwiseOrthoMatch.rms)) {
		if (delete_failed) {
		@@ -4480,16 +4500,16 @@ public class OrthoMapsCollection implements Serializable{
		if (delete_failed) {
		ortho_maps[ipair[0]].unsetMatch(ortho_maps[ipair[1]].getName());
		}
		String str_failed = delete_failed?"\tFAILED\tREMOVED\n":"\tFAILED\n";
		String str_failed = delete_failed?"\tFAILED\t\tREMOVED\n":"\tFAILED\n";

		failed_pairs.add(pair);
		sb.append(String.format(str_failed));
		if (debugLevel > -4) System.out.print("Final adjustment"+str_failed);
		} else {
		sb.append(String.format("\t%6.4f\n",pairwiseOrthoMatch.rms));
		if (debugLevel > -4) System.out.println("Final adjustment RMSE="+pairwiseOrthoMatch.rms);
		// pairwiseOrthoMatch.zoom_lev = zoom_lev;
		// pairwiseOrthoMatch.affine = affines[1];
		pairwiseOrthoMatch.overlap = overlaps[overlap_indx]; // needed here if refining old/manual w/o overlap
		sb.append(String.format("\t%6.4f\t%3d\n",pairwiseOrthoMatch.rms,pairwiseOrthoMatch.zoom_lev));
		if (debugLevel > -4) System.out.println("Final adjustment RMSE="+pairwiseOrthoMatch.rms+
		", overlap = "+pairwiseOrthoMatch.overlap);
		ortho_maps[ipair[0]].setMatch(ortho_maps[ipair[1]].getName(),pairwiseOrthoMatch);
		if (save_each && (orthoMapsCollection_path != null)) {
		try {

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

0 → 100644

+337 −0

File added.

Preview size limit exceeded, changes collapsed.

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

+123 −13

Original line number	Diff line number	Diff line
		@@ -5,6 +5,8 @@ import java.io.ObjectInputStream;
		import java.io.ObjectOutputStream;
		import java.io.Serializable;

		import Jama.Matrix;

		public class PairwiseOrthoMatch implements Serializable {
		private static final long serialVersionUID = 1L;
		public double [][] affine = new double[2][3];
		@@ -12,6 +14,7 @@ public class PairwiseOrthoMatch implements Serializable {
		public int zoom_lev;
		public double rms = Double.NaN;
		public transient int [] nxy = null; // not saved, just to communicate for logging
		public transient double overlap = 0.0;
		public PairwiseOrthoMatch() {

		}
		@@ -19,11 +22,13 @@ public class PairwiseOrthoMatch implements Serializable {
		double [][] affine,
		double [][] jtj,
		double rms,
		int zoom_lev) {
		int zoom_lev,
		double overlap) {
		this.affine = affine;
		this.jtj = jtj;
		this.zoom_lev= zoom_lev;
		this.rms = rms;
		this.overlap = overlap;
		}
		public PairwiseOrthoMatch clone() {
		double [][] affine = {this.affine[0].clone(),this.affine[1].clone()};
		@@ -35,19 +40,63 @@ public class PairwiseOrthoMatch implements Serializable {
		affine,
		jtj,
		this.rms,
		this.zoom_lev);
		this.zoom_lev,
		this.overlap);
		if (nxy != null) {
		pom.nxy = nxy.clone();
		}
		return pom;
		}
		/**
		* If this match is calculated from scene0 to scene1, inverse one is from scene1 to scene0
		* @param rd displacement from scene0 reference (vertical) point to scene1 reference point
		* (GNSS-derived), referenced as -V in the notes below. (it is calculated as 0 from 1)
		* @return inverted 3x2 matrix
		*
		Xs0, Xs1 - metric coordinates (from top-left) in each of the source images
		V - image center offset of the second scene from the first in rectified space (GPS-derived)
		S0, S1 - vertical point offset from the top-left in image coordinates
		A0,A1 - affine transform matrices (sensor coordinates from rectified coordinates)
		B0, B1 centers offsets in image coordinates
		Xr - rectified coordinates. Xr1, Xr2 - just different points

		Xsi = Ai*(Xr - V) + Bi + Si

		1) A00 = E, A1, B1 - second image match when the first is unity:

		Xs0 = Xr1 + S0
		Xs1 = A1 * (Xr1 - V) + B1 + S1;

		2) calculate inverted A1,B1 of the first scene relative to the second one. In this case Xs0
		of the first scene should still correspond to Xs1
		Xs0 = A0 * (Xr2 + V) + B0 + S0;
		Xs1 = Xr2 + S1

		----
		Xs1 = A1 * (Xs0 - S0 - V) + B1 + S1;
		Xs1 - B1 - S1 = A1 * (Xs0 - S0 - V);
		A1inv*(Xs1 - B1 - S1) = Xs0 - S0 - V;
		Xs0 = A1inv*(Xs1 - B1 - S1) + S0 + V
		---
		Xr2 = Xs1 - S1
		Xs0 = A0 * (Xs1 - S1 + V) + B0 + S0;

		A1inv(Xs1 - B1 - S1) + S0 + V = A0 (Xs1 - S1 + V) + B0 + S0
		=> A0=A1inv
		A1inv(Xs1 - B1 - S1) + S0 + V = A1inv (Xs1 - S1 + V) + B0 + S0
		-A1inv( B1) + V = A1inv ( V) + B0
		A1inv * ( V) + B0 + A1inv*(B1) - V = 0
		B0 = -((A1inv-E)V + A1invB1)
		*/

		public PairwiseOrthoMatch getInverse(double [] rd) {
		double [][] affine = OrthoMap.invertAffine(getAffine());
		PairwiseOrthoMatch inverted_match = new PairwiseOrthoMatch(
		affine, // double [][] affine,
		null, // double [][] jtj,
		jtj, // double [][] jtj,
		rms, // double rms,
		zoom_lev); // int zoom_lev)
		zoom_lev, // int zoom_lev)
		overlap); //
		double [] corr = {
		rd[0] * (affine[0][0]-1.0)+ rd[1]*affine[0][1],
		rd[0] * affine[1][0]+ rd[1]*(affine[1][1]-1.0)};
		@@ -56,13 +105,72 @@ public class PairwiseOrthoMatch implements Serializable {
		return inverted_match;
		}

		public PairwiseOrthoMatch getInverse() {
		PairwiseOrthoMatch inverted_match = new PairwiseOrthoMatch(
		OrthoMap.invertAffine(getAffine()), // double [][] affine,
		null, // double [][] jtj,
		rms, // double rms,
		zoom_lev); // int zoom_lev)
		return inverted_match;
		/**
		* Create differential PairwiseOrthoMatch instance from 2 affines of the scenes and an offset vector
		* @param affine0
		* @param affine1
		* @param rd
		* Continued from getInverse notes:
		* =========================== V = -rd
		Xsi = Ai*(Xr - V) + Bi + Si

		Xs0 = A0*(Xr - 0) + B0 + S0
		Xs1 = A1*(Xr - V) + B1 + S1

		--- difference Ad, Bd
		Xs0 = Xr1 + S0
		Xs1 = Ad * (Xr1 - V) + Bd + S1;


		Xs0 = A0*(Xr - 0) + B0 + S0
		Xs0 - (B0 + S0) = A0*Xr
		Xr = A0inv*(Xs0 - (B0 + S0))
		Xs1 = A1((A0inv(Xs0 - (B0 + S0))) - V) + B1 + S1

		Xr1 = Xs0-S0

		Xs1 = Ad * ((Xs0-S0) - V) + Bd + S1;

		A1((A0inv(Xs0 - (B0 + S0))) - V) + B1 + S1 = Ad * ((Xs0-S0) - V) + Bd + S1

		A1((A0inv(Xs0 - (B0 + S0))) - V) + B1 = Ad * ((Xs0-S0) - V) + Bd

		A1((A0inv(Xs0 - (B0 + S0))) - V) + B1 = Ad * ((Xs0-S0) - V) + Bd
		A1 * A0inv * Xs0 - A1 * A0inv * (B0 + S0) - A1V + B1 - Ad Xs0 + Ad * S0 +Ad*V -Bd
		=> Ad = A1 * A0inv:
		- A1 * A0inv * (B0 + S0) - A1V + B1 + Ad S0 +Ad*V -Bd =
		- Ad * (B0 + S0) - A1V + B1 + Ad S0 + Ad*V - Bd =
		Ad * (S0 + V - B0 - S0) - A1*V + B1- Bd =
		Ad * (V - B0) - A1 * V + B1 - Bd
		Bd = Ad * (V - B0) - A1 * V + B1

		--- check if A0 = E, B0 = 0
		Ad = A1inv
		Bd = A1 * V - A1 *V + B1 = B1
		--- check if A1 = E, B1 = 0, V1= -V
		Bd = A0inv * (V1 - B0) - V1 =
		(A0inv-E)V1 -A0invB0 =
		-(A0inv-E)V -A0invB0 =
		*/
		public PairwiseOrthoMatch (
		double [][] affine0,
		double [][] affine1,
		double [] rd) {
		Matrix A0 = new Matrix (
		new double [][] {{affine0[0][0],affine0[0][1]},{affine0[1][0],affine0[1][1]}});
		Matrix B0 = new Matrix(new double [][] {{affine0[0][2]},{affine0[1][2]}});
		Matrix A1 = new Matrix (
		new double [][] {{affine1[0][0],affine1[0][1]},{affine1[1][0],affine1[1][1]}});
		Matrix B1 = new Matrix(new double [][] {{affine1[0][2]},{affine1[1][2]}});
		Matrix V = new Matrix(new double [][] {{-rd[0]},{-rd[1]}});
		Matrix A = A1.times(A0.inverse());
		Matrix B = A.times(V.minus(B0)).minus(A1.times(V)).plus(B1);
		affine = new double[][] {
		{A.get(0,0),A.get(0,1), B.get(0,0)},
		{A.get(1,0),A.get(1,1), B.get(1,0)}};
		// jtj = null;
		// rms = Double.NaN; // double rms,
		// zoom_lev = 0; // int zoom_lev)
		}

		public double [][] getAffine(){
		@@ -76,6 +184,7 @@ public class PairwiseOrthoMatch implements Serializable {
		oos.writeObject(jtj[i][j]);
		}
		}
		oos.writeObject(overlap);
		}
		private void readObject(ObjectInputStream ois) throws ClassNotFoundException, IOException {
		ois.defaultReadObject();
		@@ -88,6 +197,7 @@ public class PairwiseOrthoMatch implements Serializable {
		}
		}
		}
		overlap = (Double) ois.readObject();
		}
		//private void readObjectNoData() throws ObjectStreamException; // used to modify default values
		}

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