Initial testing of LMA for fitting pairs of ortho images

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

@@ -52,16 +52,19 @@ public class ComboMatch {
 		double [][][] image_enuatr = {{{0,0,0},{0,0,0}},{{0,0,0},{0,0,0}}};
 		int gpu_width=  clt_parameters.imp.rln_gpu_width; // 3008;
 		int gpu_height= clt_parameters.imp.rln_gpu_height; // 3008;
-		int zoom_lev = -4; // 0; // +1 - zoom in twice, -1 - zoom out twice
+		int zoom_lev = -3; // 0; // +1 - zoom in twice, -1 - zoom out twice
 		boolean use_alt = false;
 		boolean show_centers = true;
-		boolean use_saved_collection = false;
+		boolean use_saved_collection = true; // false;
 		boolean save_collection = true;
+		boolean process_correlation = true; // use false to save new version of data
 		GenericJTabbedDialog gd = new GenericJTabbedDialog("Set image pair",1200,800);
 		gd.addStringField ("Image list full path",  files_list_path, 180, "Image list full path.");
 		gd.addStringField ("Maps collection save path",  orthoMapsCollection_path, 180, "Save path for serialized map collection data.");
 		gd.addCheckbox    ("Use saved maps collection", use_saved_collection, "If false - use files list.");
-		gd.addCheckbox    ("Save maps collection", save_collection, "If false - use files list.");
+		gd.addCheckbox    ("Save maps collection", save_collection, "Save maps collection to be able to restore.");
+		gd.addCheckbox    ("Process correlations", process_correlation, "false to skip to just regenerate new save file.");
+		//
 //		for (int n = 0; n < image_paths_pre.length; n++) {
 //			gd.addStringField ("Image path "+n,  image_paths_pre[n], 180, "Image "+n+" full path w/o ext");		
 //		}
@@ -92,6 +95,7 @@ public class ComboMatch {
 		orthoMapsCollection_path = gd.getNextString();
 		use_saved_collection =     gd.getNextBoolean();
 		save_collection =          gd.getNextBoolean();
+		process_correlation=       gd.getNextBoolean();
 
 		for (int n = 0; n < image_enuatr.length; n++) {
 			image_enuatr[n][0][0] = gd.getNextNumber();
@@ -142,40 +146,41 @@ public class ComboMatch {
     				origin);           // int []      origin){
     		imp_alt.show();
         }
-        
-		System.out.println("Setting up GPU");
-		if (GPU_QUAD_AFFINE == null) {
-			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);
-		}
-        
-        double [][] affine0 = {{1,0,0},{0,1,0}}; // will always stay the same
-        double [][] affine1 = {{1,0,0},{0,1,0}}; // will be variable  // here in meters, relative to vertical point
-        double [][][] affines = {affine0,affine1};
-        double [][] corr_pair_rslt = maps_collection.correlateOrthoPair(
-        		clt_parameters, // CLTParameters    clt_parameters,
-        		gpu_spair,      // String []        gpu_spair,
-        		affines,        // double [][][]    affines, // on top of GPS offsets
-        		zoom_lev,       // int              zoom_lev,
-        		debugLevel);    // final int        debugLevel)       
+        if (process_correlation) {
+        	System.out.println("Setting up GPU");
+        	if (GPU_QUAD_AFFINE == null) {
+        		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);
+        	}
+
+        	double [][] affine0 = {{1,0,0},{0,1,0}}; // will always stay the same
+        	double [][] affine1 = {{1,0,0},{0,1,0}}; // will be variable  // here in meters, relative to vertical point
+        	double [][][] affines = {affine0,affine1};
+        	double [][] corr_pair_rslt = maps_collection.correlateOrthoPair(
+        			clt_parameters, // CLTParameters    clt_parameters,
+        			gpu_spair,      // String []        gpu_spair,
+        			affines,        // double [][][]    affines, // on top of GPS offsets
+        			zoom_lev,       // int              zoom_lev,
+        			debugLevel);    // final int        debugLevel)
+        }
         if (save_collection) {
         	try {
-				maps_collection.writeOrthoMapsCollection(orthoMapsCollection_path);
-			} catch (IOException e) {
-				// TODO Auto-generated catch block
-				e.printStackTrace();
-			}
+        		maps_collection.writeOrthoMapsCollection(orthoMapsCollection_path);
+        	} catch (IOException e) {
+        		// TODO Auto-generated catch block
+        		e.printStackTrace();
+        	}
         }
         
         
@@ -367,6 +372,7 @@ public class ComboMatch {
 				gpu_width,      // final int                    img_width,
 				null,           // Rectangle                    woi, // if null, use full GPU window
 				affine,         // final double [][][]          affine,  // [2][2][3] affine coefficients to translate common to 2 images
+				null,           // TpTask [][]                  tp_tasks_o,
 				false,          // final boolean                batch_mode,
 				debugLevel);    // final int                    debugLevel);
 //		renderFromTD (
@@ -395,6 +401,7 @@ public class ComboMatch {
 			final int                    img_width,
 			Rectangle                    woi, // if null, use full GPU window
 			final double [][][]          affine,  // [2][2][3] affine coefficients to translate common to 2 images
+			TpTask [][]                  tp_tasks_o,
 			final boolean                batch_mode,
 			final int                    debugLevel) {
 		int [] wh = {img_width, fpixels[0].length/img_width};
@@ -403,6 +410,9 @@ public class ComboMatch {
 				img_width, // final int           img_width,
 				woi,                     // Rectangle           woi,
 				affine); // final double [][][] affine  // [2][2][3] affine coefficients to translate common to 2 images
+		if (tp_tasks_o != null) {
+			for (int i = 0; i < tp_tasks_o.length; i++) tp_tasks_o[i] = tp_tasks[i];
+		}
 		boolean is_aux =  true;
 		boolean is_mono = true;
 		boolean is_lwir = true;

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

@@ -62,6 +62,8 @@ public class OrthoMap implements Comparable <OrthoMap>, Serializable{
 	public double [][]                          affine = new double[][] {{1,0,0},{0,1,0}}; // relative to vert_meters[]
 	public double                               orig_pix_meters;
 	public double []                            vert_meters;   // offset of the image vertical in meters (scale-invariant)
+	public int                                  orig_width;
+	public int                                  orig_height;
 	public transient FloatImageData             orig_image;
 	public transient FloatImageData             alt_image;
 	public int                                  orig_zoom_level;
@@ -79,6 +81,8 @@ public class OrthoMap implements Comparable <OrthoMap>, Serializable{
 		// affine is not transient
 		// orig_pix_meters is not transient
 		// vert_meters is not transient
+		// orig_width is not transient
+		// orig_height is not transient
 		// orig_image does not need to be saved
 		// alt_image does not need to be saved
 		// orig_zoom_level is not transient
@@ -98,6 +102,8 @@ public class OrthoMap implements Comparable <OrthoMap>, Serializable{
 		// affine is not transient
 		// orig_pix_meters is not transient
 		// vert_meters is not transient
+		// orig_width is not transient
+		// orig_height is not transient
 		// orig_image was not saved
 		// alt_image was not saved
 		images = new HashMap <Integer, FloatImageData>(); // field images was not saved
@@ -117,6 +123,12 @@ public class OrthoMap implements Comparable <OrthoMap>, Serializable{
 		gpu_height = height;		
 	}
 
+	public int getWidth() {
+		return orig_width;
+	}
+	public int getHeight() {
+		return orig_height;
+	}
 // Generate ALT image path from the GEO
 	public static String getAltPath(String path) {
 		int p1 = path.lastIndexOf(".");
@@ -151,6 +163,8 @@ public class OrthoMap implements Comparable <OrthoMap>, Serializable{
 			double height_meters = height_pix * orig_pix_meters;
 			vert_meters[1] = height_meters-vert_meters[1];
 		}
+		orig_width =  ElphelTiffReader.getWidth(imp_prop);
+		orig_height = ElphelTiffReader.getHeight(imp_prop);
 		
 		orig_zoom_level = FloatImageData.getZoomLevel(orig_pix_meters);
 		orig_zoom_valid = FloatImageData.isZoomValid(orig_pix_meters);
@@ -254,8 +268,8 @@ public class OrthoMap implements Comparable <OrthoMap>, Serializable{
 			String full_name = path.substring(path.lastIndexOf(Prefs.getFileSeparator()) + 1);
 			ImagePlus imp = ShowDoubleFloatArrays.makeArrays(
 					orig_image.data, // float[] pixels,
-					orig_image.width,
-					orig_image.height,
+					getWidth(),
+					getHeight(),
 					full_name);
 			if (show_markers) {
 				PointRoi roi = new PointRoi();
@@ -296,8 +310,8 @@ public class OrthoMap implements Comparable <OrthoMap>, Serializable{
 	 */
 	public double [][] get4SourceCornersMeters(){
 		FloatImageData orig_image = getImageData();
-		double width_meters = orig_image.width * orig_pix_meters;
-		double height_meters = orig_image.height * orig_pix_meters;
+		double width_meters = getWidth() * orig_pix_meters;
+		double height_meters = getHeight() * orig_pix_meters;
 		return new double[][] { // CW from TL
 			{             - vert_meters[0],               - vert_meters[1]},
 			{width_meters - vert_meters[0],               - vert_meters[1]},
@@ -440,8 +454,8 @@ public class OrthoMap implements Comparable <OrthoMap>, Serializable{
 			rscale *= 2;
 		}
 		final int frscale = rscale;
-		int swidth =  orig_image.width;
-		int sheight = orig_image.height;
+		int swidth =  getWidth();
+		int sheight = getHeight();
 		final float [] spix = orig_image.data;
 		final int width = (swidth+frscale-1)/frscale;
 		final int height = (sheight+frscale-1)/frscale;

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

@@ -20,6 +20,8 @@ import java.util.concurrent.atomic.AtomicInteger;
 
 import com.elphel.imagej.cameras.CLTParameters;
 import com.elphel.imagej.common.ShowDoubleFloatArrays;
+import com.elphel.imagej.gpu.GPUTileProcessor;
+import com.elphel.imagej.gpu.TpTask;
 import com.elphel.imagej.tileprocessor.ImageDtt;
 import com.elphel.imagej.tileprocessor.TDCorrTile;
 
@@ -441,6 +443,8 @@ public class OrthoMapsCollection  implements Serializable{
 			double [][][]    affines,  // here in meters, relative to vertical points
 			int              zoom_lev,
 			final int        debugLevel){
+		boolean show_gpu_img = true; // (debugLevel > 1);
+		boolean show_tile_centers = true; // (debugLevel > 1);
 		double [][] bounds_overlap_meters = getOverlapMeters(
 				gpu_pair[0],  // int ref_index,
 				gpu_pair[1],  // int other_index)
@@ -469,9 +473,9 @@ public class OrthoMapsCollection  implements Serializable{
 		tlo_rect_metric[0][0] = bounds_overlap_meters[0][0]; // relative to ref vert_meters
 		tlo_rect_metric[0][1] = bounds_overlap_meters[1][0]; // vert_meters
 		tlo_rect_metric[1][0] = bounds_overlap_meters[0][0]  // relative to other vert_meters
-				- rd[0] + ortho_maps[gpu_pair[1]].vert_meters[0]- ortho_maps[gpu_pair[0]].vert_meters[0];
+				- rd[0]; //  + ortho_maps[gpu_pair[1]].vert_meters[0]- ortho_maps[gpu_pair[0]].vert_meters[0];
 		tlo_rect_metric[1][1] = bounds_overlap_meters[1][0]
-				- rd[1] + ortho_maps[gpu_pair[1]].vert_meters[1]- ortho_maps[gpu_pair[0]].vert_meters[1];
+				- rd[1]; //  + ortho_maps[gpu_pair[1]].vert_meters[1]- ortho_maps[gpu_pair[0]].vert_meters[1];
 
 		double [][] tlo_src_metric = new double[tlo_rect_metric.length][2]; // relative to it's own vert_meters
 		for (int n=0; n <tlo_src_metric.length; n++) {
@@ -501,6 +505,17 @@ public class OrthoMapsCollection  implements Serializable{
 			}
 			gpu_pair_img[n] = ortho_maps[gpu_pair[n]].getPaddedGPU (zoom_lev); // int zoom_level,
 		}
+		if (show_gpu_img) {
+			String [] dbg_titles = {ortho_maps[gpu_pair[0]].getName(),ortho_maps[gpu_pair[1]].getName()};
+    		ShowDoubleFloatArrays.showArrays(
+    				gpu_pair_img,
+    				OrthoMap.gpu_width,
+    				OrthoMap.gpu_height,
+    				true,
+    				"gpu_img",
+    				dbg_titles);
+
+		}
 		Rectangle  woi = new Rectangle(0, 0, overlap_wh_pixel[0], overlap_wh_pixel[1]);
 		if (woi.width > OrthoMap.gpu_width) {
 			if (debugLevel > -3) {
@@ -517,6 +532,7 @@ public class OrthoMapsCollection  implements Serializable{
 		final int  gpu_width = OrthoMap.gpu_width; // static
 		// uses fixed_size gpu image size
 //		TDCorrTile [] td_corr_tiles =
+		TpTask [][] tp_tasks = new TpTask [2][];
 		double [][][] vector_field = 
 				ComboMatch.rectilinearVectorField(//rectilinearCorrelate_TD( // scene0/scene1
 				clt_parameters, // final CLTParameters          clt_parameters,
@@ -524,9 +540,69 @@ public class OrthoMapsCollection  implements Serializable{
 				gpu_width,      // final int                    img_width,
 				woi, // Rectangle                    woi, // if null, use full GPU window
 				affines_gpu,         // final double [][][]          affine,  // [2][2][3] affine coefficients to translate common to 2 images
+				tp_tasks, // TpTask [][]                  tp_tasks_o,
 				false,          // final boolean                batch_mode,
 				debugLevel);    // final int                    debugLevel);
 		// may use tl_rect_metric to remap to the original image
+		double [][] tile_centers = new double [vector_field[0].length][];
+		int tilesX = gpu_width/GPUTileProcessor.DTT_SIZE; 
+		for (TpTask task: tp_tasks[1]) {
+			int ti = task.getTileY() * tilesX + task.getTileX();
+			tile_centers[ti] = task.getDoubleCenterXY();
+		}
+		if (show_tile_centers){
+			double [][] dbg_img = new double [6][tile_centers.length];
+			String [] dbg_titles = {"cX","cY","px0","py0", "px1","py1"};
+			for (int i = 0; i< dbg_img.length;i++) Arrays.fill(dbg_img[i], Double.NaN);
+			for (int t = 0; t < tp_tasks[0].length; t++) {
+				TpTask task0 = tp_tasks[0][t];
+				TpTask task1 = tp_tasks[1][t];
+				int ti = task0.getTileY() * tilesX + task0.getTileX();
+				dbg_img[0][ti] = task0.getDoubleCenterXY()[0]; // same for task0, task1 
+				dbg_img[1][ti] = task1.getDoubleCenterXY()[1]; 
+				dbg_img[2][ti] = task0.getXY()[0][0];
+				dbg_img[3][ti] = task0.getXY()[0][1];
+				dbg_img[4][ti] = task1.getXY()[0][0];
+				dbg_img[5][ti] = task1.getXY()[0][1];
+			} // getXY()
+    		ShowDoubleFloatArrays.showArrays(
+    				dbg_img,
+    				tilesX,
+    				tile_centers.length/tilesX,
+    				true,
+    				"tile_centers",
+    				dbg_titles);
+		}
+		
+		
+		OrthoPairLMA orthoPairLMA = new OrthoPairLMA();
+		// vector_field[1] - neighbors
+		double lambda =            0.1;
+		double lambda_scale_good = 0.5;
+		double lambda_scale_bad =  8.0;
+		double lambda_max =      100;
+		double rms_diff =          0.001;
+		int    num_iter =         20;
+		boolean last_run =       false;
+		orthoPairLMA.prepareLMA(
+				// will always calculate relative affine, starting with unity
+				tilesX, // int           width,
+				vector_field[1], // double [][]   vector_XYS,    // optical flow X,Y, confidence obtained from the correlate2DIterate()
+				tile_centers, // double [][]   centers,       // tile centers (in pixels)
+				null, // double []     weights_extra, // optional, may be null 
+				true, // boolean       first_run,
+				debugLevel); // final int     debug_level)
+		int lma_rslt = orthoPairLMA.runLma( // <0 - failed, >=0 iteration number (1 - immediately)
+				lambda,             // double lambda,           // 0.1
+				lambda_scale_good,  // double lambda_scale_good,// 0.5
+				lambda_scale_bad,   // double lambda_scale_bad, // 8.0
+				lambda_max,         // double lambda_max,       // 100
+				rms_diff,           // double rms_diff,         // 0.001
+				num_iter,           // int    num_iter,         // 20
+				last_run,           // boolean last_run,
+				debugLevel);       // int    debug_level)
+		System.out.println("LMA result = "+lma_rslt);
+// analyze result, re-run correlation
 		
 /*
 		if (show_vector_field) {

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

+/**
+ **
+ ** OrthoPairLMA - Fit a pair of fixed-scale orthographic image by modifying
+ **                affine transform matrix of the second one using 2D phase 
+ **                correlation implemented in GPU
+ **
+ ** Copyright (C) 2024 Elphel, Inc.
+ **
+ ** -----------------------------------------------------------------------------**
+ **
+ **  OrthoPairLMA.java is free software: you can redistribute it and/or modify
+ **  it under the terms of the GNU General Public License as published by
+ **  the Free Software Foundation, either version 3 of the License, or
+ **  (at your option) any later version.
+ **
+ **  This program is distributed in the hope that it will be useful,
+ **  but WITHOUT ANY WARRANTY; without even the implied warranty of
+ **  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ **  GNU General Public License for more details.
+ **
+ **  You should have received a copy of the GNU General Public License
+ **  along with this program.  If not, see <http://www.gnu.org/licenses/>.
+ ** -----------------------------------------------------------------------------**
+ **
+ */
+
+package com.elphel.imagej.orthomosaic;
+
+import java.awt.Rectangle;
+import java.util.concurrent.atomic.AtomicInteger;
+
+import com.elphel.imagej.tileprocessor.ImageDtt;
+import com.elphel.imagej.tileprocessor.QuadCLT;
+
+import Jama.Matrix;
+
+public class OrthoPairLMA {
+	private boolean           thread_invariant= true;
+	private int               N =               0;
+	private Rectangle         woi =             null;
+	private int               width;
+	private double []         last_rms =        null; // {rms, rms_pure}, matching this.vector
+	private double []         good_or_bad_rms = null; // just for diagnostics, to read last (failed) rms
+	private double []         initial_rms =     null; // {rms, rms_pure}, first-calcualted rms
+	private double []         parameters_vector = null;
+//	private double []         x_vector =        null; // not used. Save total weight
+	private double []         y_vector =        null;
+	private double [][]       tile_centers =    null;
+	private double            weight = 0; // total weight
+	private double []         weights; // normalized so sum is 1.0 for all - samples and extra regularization
+//	private double            pure_weight; // weight of samples only	
+	private double []         last_ymfx =       null;
+	private double [][]       last_jt =         null;
+
+	public void prepareLMA(
+			// will always calculate relative affine, starting with unity
+			int           width, // tilesX
+			double [][]   vector_XYS,    // optical flow X,Y, confidence obtained from the correlate2DIterate()
+			double [][]   centers,       // tile centers (in pixels)
+			double []     weights_extra, // optional, may be null 
+			boolean       first_run,
+			final int     debug_level) {
+		tile_centers = centers;
+		this.width = width;
+		int height = vector_XYS.length / width;
+		int min_x = width, min_y=height, max_x = -1, max_y=-1;
+		for (int tile = 0; tile < vector_XYS.length; tile++) if ((vector_XYS[tile] !=null)) {
+			int tileX = tile % width;
+			int tileY = tile / width;
+			if (tileX < min_x) min_x = tileX;
+			if (tileX > max_x) max_x = tileX;
+			if (tileY < min_y) min_y = tileY;
+			if (tileY > max_y) max_y = tileY;
+		}
+		woi = new Rectangle (min_x, min_y, max_x - min_x + 1, max_y - min_y + 1);
+		N = woi.width*woi.height;
+		parameters_vector = new double [] {1,0,0,1,0,0};
+		setSamplesWeightsYCenters(
+				vector_XYS,
+				weights_extra, // null or additional weights (such as elevation-based)
+				centers);
+		last_jt = new double [parameters_vector.length][];
+		if (debug_level > 1) {
+			System.out.println("prepareLMA() 1");
+		}
+//		tile_centers = new double [N];
+		
+		last_rms = new double [2];
+//		double [] fx = getFxDerivs(
+//				parameters_vector, // double []         vector,
+//				last_jt,           // final double [][] jt, // should be null or initialized with [vector.length][]
+//				debug_level);      // final int         debug_level)
+		
+//		last_ymfx = getYminusFxWeighted(
+//				fx, // final double []   fx,
+//				last_rms); // final double []   rms_fp // null or [2]
+		initial_rms = last_rms.clone();
+		good_or_bad_rms = this.last_rms.clone();
+		
+	}
+	
+	private void setSamplesWeightsYCenters(
+			final double [][] vector_XYS,
+			final double []   weights_extra, // null or additional weights (such as elevation-based)
+			final double [][] centers)
+	{
+		//num_components 2 - old, 3 - with disparity
+		this.weights = new double [2*N]; // same for X and Y
+		y_vector = new double[2*N];
+		tile_centers = new double [N][];
+		final Thread[] threads = ImageDtt.newThreadArray();
+		final AtomicInteger ai = new AtomicInteger(0);
+		final AtomicInteger ati = new AtomicInteger(0);
+		final double [] sw_arr = new double [threads.length];
+//		double sum_weights;
+		for (int ithread = 0; ithread < threads.length; ithread++) {
+			threads[ithread] = new Thread() {
+				public void run() {
+					int thread_num = ati.getAndIncrement();
+					for (int iTile = ai.getAndIncrement(); iTile < N; iTile = ai.getAndIncrement()) {
+						int tileX = iTile % woi.width + woi.x;
+						int tileY = iTile / woi.width + woi.y;
+						int aTile = tileY * width + tileX;
+						if ((vector_XYS[aTile] != null) && (centers[aTile] != null)) {
+							double w = vector_XYS[aTile][2];
+							if (weights_extra != null) w *= weights_extra[aTile]; 
+							if (Double.isNaN(w)) w = 0;
+							sw_arr[thread_num] += 2*w;
+							weights [2*iTile + 0] = w;
+							weights [2*iTile + 1] = w;
+							y_vector[2*iTile + 0] = vector_XYS[aTile][0];
+							y_vector[2*iTile + 1] = vector_XYS[aTile][1];
+							tile_centers[iTile] = centers[aTile];
+						}
+					}
+				}
+			};
+		}		      
+		ImageDtt.startAndJoin(threads);
+		weight = 0.0;
+		for (double w:sw_arr) {
+			weight += w;
+		}
+		if (weight <= 1E-8) {
+			System.out.println("!!!!!! setSamplesWeights(): sum_weights="+weight+" <= 1E-8");
+		}
+		
+		ai.set(0);
+		final double s = 1.0/weight; // Was 0.5 - already taken care of
+		for (int ithread = 0; ithread < threads.length; ithread++) {
+			threads[ithread] = new Thread() {
+				public void run() {
+					for (int iTile = ai.getAndIncrement(); iTile < N; iTile = ai.getAndIncrement()) {
+						weights[2 * iTile    ] *= s;
+						weights[2 * iTile + 1] *= s;
+					}
+				}
+			};
+		}		      
+		ImageDtt.startAndJoin(threads);
+	}
+
+	public int runLma( // <0 - failed, >=0 iteration number (1 - immediately)
+			double lambda,           // 0.1
+			double lambda_scale_good,// 0.5
+			double lambda_scale_bad, // 8.0
+			double lambda_max,       // 100
+			double rms_diff,         // 0.001
+			int    num_iter,         // 20
+			boolean last_run,
+			int    debug_level)
+	{
+		boolean [] rslt = {false,false};
+		this.last_rms = null; // remove?
+		int iter = 0;
+		for (iter = 0; iter < num_iter; iter++) {
+			rslt =  lmaStep(
+					lambda,
+					rms_diff,
+					debug_level);
+			if (rslt == null) {
+				return -1; // false; // need to check
+			}
+			if (debug_level > 1) {
+				System.out.println("LMA step "+iter+": {"+rslt[0]+","+rslt[1]+"} full RMS= "+good_or_bad_rms[0]+
+						" ("+initial_rms[0]+"), pure RMS="+good_or_bad_rms[1]+" ("+initial_rms[1]+") + lambda="+lambda);
+			}
+			if (rslt[1]) {
+				break;
+			}
+			if (rslt[0]) { // good
+				lambda *= lambda_scale_good;
+			} else {
+				lambda *= lambda_scale_bad;
+				if (lambda > lambda_max) {
+					break; // not used in lwir
+				}
+			}
+		}
+		if (rslt[0]) { // better
+			if (iter >= num_iter) { // better, but num tries exceeded
+				if (debug_level > 1) System.out.println("Step "+iter+": Improved, but number of steps exceeded maximal");
+			} else {
+				if (debug_level > 1) System.out.println("Step "+iter+": LMA: Success");
+			}
+
+		} else { // improved over initial ?
+			if (last_rms[0] < initial_rms[0]) { // NaN
+				rslt[0] = true;
+				if (debug_level > 1) System.out.println("Step "+iter+": Failed to converge, but result improved over initial");
+			} else {
+				if (debug_level > 1) System.out.println("Step "+iter+": Failed to converge");
+			}
+		}
+		boolean show_intermediate = true;
+		if (show_intermediate && (debug_level > 0)) {
+			System.out.println("LMA: full RMS="+last_rms[0]+" ("+initial_rms[0]+"), pure RMS="+last_rms[1]+" ("+initial_rms[1]+") + lambda="+lambda);
+		}
+		if (debug_level > 2){ 
+			System.out.println("iteration="+iter);
+		}
+		if (debug_level > 0) {
+			if ((debug_level > 1) ||  last_run) { // (iter == 1) || last_run) {
+				if (!show_intermediate) {
+					System.out.println("LMA: iter="+iter+",   full RMS="+last_rms[0]+" ("+initial_rms[0]+"), pure RMS="+last_rms[1]+" ("+initial_rms[1]+") + lambda="+lambda);
+				}
+			}
+		}
+		if ((debug_level > -2) && !rslt[0]) { // failed
+			if ((debug_level > 1) || (iter == 1) || last_run) {
+				System.out.println("LMA failed on iteration = "+iter);
+			}
+			System.out.println();
+		}
+
+		return rslt[0]? iter : -1;
+	}
+	
+	
+	private boolean [] lmaStep(
+			double lambda,
+			double rms_diff,
+			int debug_level) {
+		boolean [] rslt = {false,false};
+		// maybe the following if() branch is not needed - already done in prepareLMA !
+		if (this.last_rms == null) { //first time, need to calculate all (vector is valid)
+			last_rms = new double[2];
+			if (debug_level > 1) {
+				System.out.println("lmaStep(): first step");
+			}
+			double [] fx = getFxDerivs(
+					parameters_vector, // double []         vector,
+					last_jt,           // final double [][] jt, // should be null or initialized with [vector.length][]
+					debug_level);      // final int         debug_level)
+			last_ymfx = getYminusFxWeighted(
+					fx, // final double []   fx,
+					last_rms); // final double []   rms_fp // null or [2]
+			this.initial_rms = this.last_rms.clone();
+			this.good_or_bad_rms = this.last_rms.clone();
+
+			if (debug_level > -1) { // temporary
+				/*
+				dbgYminusFxWeight(
+						this.last_ymfx,
+						this.weights,
+						"Initial_y-fX_after_moving_objects");
+                */
+			}
+			if (last_ymfx == null) {
+				return null; // need to re-init/restart LMA
+			}
+			// TODO: Restore/implement
+			if (debug_level > 3) {
+				/*
+				 dbgJacobians(
+							corr_vector, // GeometryCorrection.CorrVector corr_vector,
+							1E-5, // double delta,
+							true); //boolean graphic)
+				*/
+			}
+		}
+		Matrix y_minus_fx_weighted = new Matrix(this.last_ymfx, this.last_ymfx.length);
+
+		Matrix wjtjlambda = new Matrix(getWJtJlambda(
+				lambda, // *10, // temporary
+				this.last_jt)); // double [][] jt)
+		
+		if (debug_level>2) {
+			System.out.println("JtJ + lambda*diag(JtJ");
+			wjtjlambda.print(18, 6);
+		}
+		Matrix jtjl_inv = null;
+		try {
+			jtjl_inv = wjtjlambda.inverse(); // check for errors
+		} catch (RuntimeException e) {
+			rslt[1] = true;
+			if (debug_level > 0) {
+				System.out.println("Singular Matrix!");
+			}
+
+			return rslt;
+		}
+		if (debug_level>2) {
+			System.out.println("(JtJ + lambda*diag(JtJ).inv()");
+			jtjl_inv.print(18, 6);
+		}
+//last_jt has NaNs
+		Matrix jty = (new Matrix(this.last_jt)).times(y_minus_fx_weighted);
+		if (debug_level>2) {
+			System.out.println("Jt * (y-fx)");
+			jty.print(18, 6);
+		}
+		
+		
+		Matrix mdelta = jtjl_inv.times(jty);
+		if (debug_level>2) {
+			System.out.println("mdelta");
+			mdelta.print(18, 6);
+		}
+
+		double scale = 1.0;
+		double []  delta =      mdelta.getColumnPackedCopy();
+		double []  new_vector = parameters_vector.clone();
+		for (int i = 0; i < parameters_vector.length; i++) {
+			new_vector[i] += scale * delta[i];
+		}
+		
+		double [] fx = getFxDerivs(
+				new_vector, // double []         vector,
+				last_jt,           // final double [][] jt, // should be null or initialized with [vector.length][]
+				debug_level);      // final int         debug_level)
+		double [] rms = new double[2];
+		last_ymfx = getYminusFxWeighted(
+//				vector_XYS, // final double [][] vector_XYS,
+				fx, // final double []   fx,
+				rms); // final double []   rms_fp // null or [2]
+		if (debug_level > 2) {
+			/*
+			dbgYminusFx(this.last_ymfx, "next y-fX");
+			dbgXY(new_vector, "XY-correction");
+			*/
+		}
+
+		if (last_ymfx == null) {
+			return null; // need to re-init/restart LMA
+		}
+
+		this.good_or_bad_rms = rms.clone();
+		if (rms[0] < this.last_rms[0]) { // improved
+			rslt[0] = true;
+			rslt[1] = rms[0] >=(this.last_rms[0] * (1.0 - rms_diff));
+			this.last_rms = rms.clone();
+
+			this.parameters_vector = new_vector.clone();
+			if (debug_level > 2) {
+				// print vectors in some format
+				/*
+				System.out.print("delta: "+corr_delta.toString()+"\n");
+				System.out.print("New vector: "+new_vector.toString()+"\n");
+				System.out.println();
+				*/
+			}
+		} else { // worsened
+			rslt[0] = false;
+			rslt[1] = false; // do not know, caller will decide
+			// restore state
+			fx = getFxDerivs(
+					parameters_vector, // double []         vector,
+					last_jt,           // final double [][] jt, // should be null or initialized with [vector.length][]
+					debug_level);      // final int         debug_level)
+			last_ymfx = getYminusFxWeighted(
+					fx, // final double []   fx,
+					this.last_rms); // final double []   rms_fp // null or [2]
+			if (last_ymfx == null) {
+				return null; // need to re-init/restart LMA
+			}
+			if (debug_level > 2) {
+				/*
+				 dbgJacobians(
+							corr_vector, // GeometryCorrection.CorrVector corr_vector,
+							1E-5, // double delta,
+							true); //boolean graphic)
+							*/
+			}
+		}
+		return rslt;
+	}
+	
+	
+	private double [][] getWJtJlambda( // USED in lwir
+			final double      lambda,
+			final double [][] jt)
+	{
+		final int num_pars = jt.length;
+		final int num_pars2 = num_pars * num_pars;
+		final int nup_points = jt[0].length;
+		final double [][] wjtjl = new double [num_pars][num_pars];
+		final Thread[] threads = ImageDtt.newThreadArray();
+		final AtomicInteger ai = new AtomicInteger(0);
+		for (int ithread = 0; ithread < threads.length; ithread++) {
+			threads[ithread] = new Thread() {
+				public void run() {
+					for (int indx = ai.getAndIncrement(); indx < num_pars2; indx = ai.getAndIncrement()) {
+						int i = indx / num_pars;
+						int j = indx % num_pars;
+						if (j >= i) {
+							double d = 0.0;
+							for (int k = 0; k < nup_points; k++) {
+								if (jt[i][k] != 0) {
+									d+=0;
+								}
+								d += weights[k]*jt[i][k]*jt[j][k];
+							}
+							wjtjl[i][j] = d;
+							if (i == j) {
+								wjtjl[i][j] += d * lambda;
+							} else {
+								wjtjl[j][i] = d;
+							}
+						}
+					}
+				}
+			};
+		}		      
+		ImageDtt.startAndJoin(threads);
+		return wjtjl;
+	}
+	
+	
+	
+	private double [] getFxDerivs(
+			final double []         vector,
+			final double [][] jt, // should be null or initialized with [vector.length][]
+			final int         debug_level)
+	{
+//		final double [][] affine = {{vector[0],vector[1],vector[4]},{vector[2],vector[3],vector[5]}};
+		final double [] fx = new double [weights.length]; // weights.length]; : weights.length :
+		if (jt != null) {
+			for (int i = 0; i < jt.length; i++) {
+				jt[i] = new double [weights.length]; // weights.length];
+			}
+		}
+		final Thread[] threads = ImageDtt.newThreadArray();
+		final AtomicInteger ai = new AtomicInteger(0);
+		for (int ithread = 0; ithread < threads.length; ithread++) {
+			threads[ithread] = new Thread() {
+				public void run() {
+					for (int iTile = ai.getAndIncrement(); iTile < N; iTile = ai.getAndIncrement()) if (tile_centers[iTile] !=null) {
+						double x = tile_centers[iTile][0];
+						double y = tile_centers[iTile][1];
+						double vx = (vector[0] - 1.0) * x +  vector[1]        * y + vector[4];
+						double vy =  vector[2] *        x + (vector[3] - 1.0) * y + vector[5];
+						fx[2 * iTile + 0] = vx;
+						fx[2 * iTile + 1] = vy;
+						if (jt != null) {
+							jt[0][2 * iTile + 0] = x;
+							jt[1][2 * iTile + 0] = y;
+							jt[2][2 * iTile + 0] = 0.0;
+							jt[3][2 * iTile + 0] = 0.0;
+							jt[4][2 * iTile + 0] = 1.0;
+							jt[5][2 * iTile + 0] = 0.0;
+							jt[0][2 * iTile + 1] = 0.0;
+							jt[1][2 * iTile + 1] = 0.0;
+							jt[2][2 * iTile + 1] = x;
+							jt[3][2 * iTile + 1] = y;
+							jt[4][2 * iTile + 1] = 0.0;
+							jt[5][2 * iTile + 1] = 1.0;
+						}
+					}
+				}
+			};
+		}		      
+		ImageDtt.startAndJoin(threads);
+		return fx;
+	}	
+	
+	private double [] getYminusFxWeighted(
+			final double []   fx,
+			final double []   rms_fp // null or [2]
+			) {
+		if (thread_invariant) {
+			return getYminusFxWeightedInvariant(fx,rms_fp); // null or [>0]
+		} else {
+			return getYminusFxWeightedFast     (fx,rms_fp); // null or [>0]
+		}
+	}	
+	
+	private double [] getYminusFxWeightedInvariant(
+			final double []   fx,
+			final double []   rms_fp // null or [2]
+			) {
+		final Thread[]      threads =     ImageDtt.newThreadArray();
+		final AtomicInteger ai =          new AtomicInteger(0);
+		final double []     wymfw =       new double [fx.length];
+		double s_rms; 
+		final int num_samples = 2 * N;
+		final double [] l2_arr = new double [num_samples]; 
+		for (int ithread = 0; ithread < threads.length; ithread++) {
+			threads[ithread] = new Thread() {
+				public void run() {
+					for (int i = ai.getAndIncrement(); i < num_samples; i = ai.getAndIncrement()) if (weights[i] > 0) {
+						double d = y_vector[i] - fx[i];
+						double wd = d * weights[i];
+						if (Double.isNaN(wd)) {
+							System.out.println("getYminusFxWeighted(): weights["+i+"]="+weights[i]+", wd="+wd+
+									", y_vector[i]="+y_vector[i]+", fx[i]="+fx[i]);
+						}
+						//double l2 = d * wd;
+						l2_arr[i] = d * wd;
+						wymfw[i] = wd;
+					}
+				}
+			};
+		}		      
+		ImageDtt.startAndJoin(threads);
+		s_rms = 0.0;
+		for (double l2:l2_arr) {
+			s_rms += l2;
+		}
+		double rms = Math.sqrt(s_rms); // assuming sum_weights == 1.0; /pure_weight); shey should be re-normalized after adding regularization
+		if (rms_fp != null) {
+			rms_fp[0] = rms;
+		}
+		return wymfw;
+	}
+	private double [] getYminusFxWeightedFast(
+			final double []   fx,
+			final double []   rms_fp // null or [2]
+			) {
+		final int num_samples = 2 * N;
+		final Thread[]      threads =     ImageDtt.newThreadArray();
+		final AtomicInteger ai =          new AtomicInteger(0);
+		final double []     wymfw =       new double [fx.length];
+		final AtomicInteger ati = new AtomicInteger(0);
+		final double [] l2_arr = new double [threads.length];
+		for (int ithread = 0; ithread < threads.length; ithread++) {
+			threads[ithread] = new Thread() {
+				public void run() {
+					int thread_num = ati.getAndIncrement();
+					for (int i = ai.getAndIncrement(); i < num_samples; i = ai.getAndIncrement()) if (weights[i] > 0) {
+						double d = y_vector[i] - fx[i];
+						double wd = d * weights[i];
+						if (Double.isNaN(wd)) {
+							System.out.println("getYminusFxWeighted(): weights["+i+"]="+weights[i]+", wd="+wd+
+									", y_vector[i]="+y_vector[i]+", fx[i]="+fx[i]);
+						}
+						//double l2 = d * wd;
+						l2_arr[thread_num] += d * wd;
+						wymfw[i] = wd;
+					}
+				}
+			};
+		}		      
+		ImageDtt.startAndJoin(threads);
+		double s_rms = 0.0;
+		for (double l2:l2_arr) {
+			s_rms += l2;
+		}
+		double rms = Math.sqrt(s_rms); // assuming sum_weights == 1.0; /pure_weight); shey should be re-normalized after adding regularization
+		if (rms_fp != null) {
+			rms_fp[0] = rms;
+		}
+		return wymfw;
+	}
+	
+	
+	
+}