Extracting radial pattern (86efce83) · Commits · Elphel / imagej-elphel

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

+301 −25

Original line number	Diff line number	Diff line
		@@ -46,7 +46,7 @@ public class ComboMatch {
		public static boolean openTestPairGps(
		CLTParameters clt_parameters,
		GPUTileProcessor gpu_tile_processor, // initialized by the caller
		boolean extract_mines,
		boolean extract_objects,
		int debugLevel) {
		GPU_TILE_PROCESSOR = gpu_tile_processor;
		PairwiseOrthoMatch pairwiseOrthoMatch = null;
		@@ -55,6 +55,19 @@ public class ComboMatch {
		String [] gpu_spair = null;
		boolean use_marked_image = false; // will be set if found
		String [] all_scenes = null;
		ArrayList<ObjectLocation> object_list = null;
		int zool_lev_objects = 0;
		if (extract_objects) {
		if (imp_sel == null) {
		System.out.println("Need multi-sliced image with marked objects as points");
		return false;
		}
		int [] zoom_lev_objectsp = new int [1];
		object_list = getObjectsFromSelectedImage(
		imp_sel,
		zoom_lev_objectsp); // ImagePlus imp)
		zool_lev_objects = zoom_lev_objectsp[0];
		} else {
		if (imp_sel != null) {
		pair_names = new String[2];
		String [][] all_scenes1=new String[1][];
		@@ -68,6 +81,7 @@ public class ComboMatch {
		all_scenes = all_scenes1[0];
		}
		}
		}
		// find -L /media/elphel/SSD3-4GB/lwir16-proc/berdich3/linked/linked_1697875868-1697879449-b/ -type f -name "*-GCORR-GEO.tiff" \| sort > GCORR-GEO.list

		// String files_list_path = "/media/elphel/SSD3-4GB/lwir16-proc/ortho_videos/maps_03_short.list";
		@@ -254,6 +268,236 @@ public class ComboMatch {
		maps_collection = new OrthoMapsCollection(files_list_path); // should have ".list" extension
		}
		String [] names = maps_collection.getNames();
		if (object_list != null) {
		int corr_size = 128;
		int extr_size = 200; // 256;
		int zoomout = 2; // 1; //2; // 1; 2 for simulated,1 - for extracted
		int patt_choice = 3;
		double phaseCoeff = 0.98;
		double min_corr = 0.01; // 0.0025; // real max >0.005 with scale -500000;
		int radius_search = 32;
		int radius_centroid = 4;
		double lim_rad = 80; // 60; // 40; // 50.0;
		double trans_width = 60; // 40; // 20.0;
		double reversal_rad = 0; // 26;// 22; // cut at first direction reversal after
		double frac_outliers = 0.4;
		int default_kernel = 1; // 0; // 1; // default kernel choice 25-> 50// 1 for simulated, 0 - for extracted
		boolean only_correlate = true;
		int sub_pattern_index = 0;

		// String pattern_dir= "/media/elphel/SSD3-4GB/lwir16-proc/ortho_videos/debug/mines/pattern_25m_zoom1/synthetic/";
		String pattern_dir= "/media/elphel/NVME/lwir16-proc/ortho_videos/mines_extract/evening_50m_sept12/debug_cross/new_synth/";
		String [] pattern_files={
		"patterns_r30.0_e8.0_ir10.0_ie8.0_is-0.1_or45.0_oe30.0_os-1.5_h8_w0.6_s-40.0_200x200.tif",
		"old_02.tiff",
		"patterns_r30.0_e24.0_ir10.0_ie8.0_is-0.1_or62.0_oe40.0_os-1.0_h8_w0.6_s-60.0_200x200.tif",
		"patterns_r30.0_e8.0_ir10.0_ie8.0_is-0.1_or45.0_oe30.0_os-1.0_h8_w0.6_s-60.0_200x200.tif",
		"patterns_r30.0_e8.0_ir10.0_ie8.0_is0.0_or45.0_oe30.0_os-1.0_h8_w0.6_s-60.0_200x200.tif",
		"patterns_r30.0_e6.0_ir10.0_ie8.0_is0.0_or45.0_oe30.0_os-1.0_h8_w0.6_s-60.0_200x200.tif",
		"patterns_r30.0_e6.0_ir10.0_ie6.0_is-1.0_or45.0_oe30.0_os-1.0_h8_w0.6_s-60.0_200x200.tif",
		"patterns_r30.0_e6.0_ir10.0_ie6.0_is-0.8_or45.0_oe30.0_os-1.0_h8_w0.6_s-60.0_200x200.tif",
		"patterns_r30.0_e4.0_ir10.0_ie4.0_is-1.0_or45.0_oe30.0_os-1.0_h8_w0.6_s-60.0_200x200.tif",
		"patterns_r30.0_e5.0_ir12.0_ie5.0_is-1.0_or45.0_oe30.0_os-1.0_h8_w0.6_s-60.0_200x200.tif",
		"patterns_r30.0_e5.0_ir12.0_ie5.0_is-1.0_or45.0_oe20.0_os-1.0_h8_w0.6_s-60.0_200x200.tif",
		"patterns_r30.0_e5.0_ir12.0_ie5.0_is-1.0_or50.0_oe40.0_os-1.0_h8_w0.6_s-60.0_200x200.tif", // best
		"patterns_r30.0_e5.0_ir12.0_ie5.0_is-1.0_or55.0_oe50.0_os-1.0_h8_w0.6_s-60.0_200x200.tif",
		"patterns_r30.0_e5.0_ir12.0_ie5.0_is0.0_or50.0_oe40.0_os-1.0_h8_w0.6_s-60.0_200x200.tif"
		};


		GenericJTabbedDialog gdo = new GenericJTabbedDialog("Set image pair",1200,900);
		gdo.addNumericField("Correlation size", corr_size, 0,4,"",
		"Correlation size, power of 2");
		gdo.addNumericField("Extracted size", extr_size, 0,4,"",
		"size of a square output size");
		// gdo.addStringField ("Pattern directory", OrthoMap.pattern_dir, 180, "Absolute path including trailing \"/\".");
		// gdo.addChoice ("Pattern filename:", OrthoMap.pattern_files, OrthoMap.pattern_files[patt_choice]);
		gdo.addStringField ("Pattern directory", pattern_dir, 180, "Absolute path including trailing \"/\".");
		gdo.addChoice ("Pattern filename:", pattern_files, OrthoMap.pattern_files[patt_choice]);
		gdo.addNumericField("Zoom-out factor", zoomout, 0,4,"x", "Reduce pattern resolution to match image.");
		gdo.addNumericField("Phase correlation coefficient", phaseCoeff, 3,7,"","1.0 - pure phase correlation, 0.0 - regular correlation.");
		gdo.addNumericField("Minimal correlation", min_corr, 5,7,"","Minimal correlation value to keep.");
		gdo.addNumericField("Search radius", radius_search, 0,4,"pix", "Radius to search for the object center.");
		gdo.addNumericField("Centroid radius", radius_centroid, 0,4,"pix", "Limit centroid radius.");
		gdo.addMessage("Clean-up circular pattern:");

		gdo.addNumericField("Limit output patter radius", lim_rad, 0,4,"pix", "All zero outside this radius.");
		gdo.addNumericField("Transition width", trans_width, 0,4,"pix", "cosine transition width.");
		gdo.addNumericField("Last reversal radius", reversal_rad, 0,4,"pix", "Cut at first derivative reversal after this.");
		gdo.addNumericField("Outlier fraction", frac_outliers, 3,7,"", "Remove outliers when averaging different directions.");
		gdo.addCheckbox ("Only correlate", only_correlate, "do not generate circular kernel.");
		gdo.addNumericField("subpattern index", sub_pattern_index,0,4,"", "0 - full pattern, 1-8 - half-pattern.");

		//only_correlate
		gdo.showDialog();
		if (gdo.wasCanceled()) return false;
		corr_size = (int) gdo.getNextNumber();
		extr_size = (int) gdo.getNextNumber();
		// OrthoMap.pattern_dir= gdo.getNextString();
		// String pattern_file = OrthoMap.pattern_files[gdo.getNextChoiceIndex()];
		pattern_dir= gdo.getNextString();
		String pattern_file = pattern_files[gdo.getNextChoiceIndex()];
		zoomout= (int) gdo.getNextNumber();
		phaseCoeff= gdo.getNextNumber();
		min_corr= gdo.getNextNumber();
		radius_search= (int) gdo.getNextNumber();
		radius_centroid= (int) gdo.getNextNumber();
		lim_rad= gdo.getNextNumber();
		trans_width= gdo.getNextNumber();
		reversal_rad= gdo.getNextNumber();
		frac_outliers= gdo.getNextNumber();
		only_correlate = gdo.getNextBoolean();
		sub_pattern_index= (int) gdo.getNextNumber();

		System.out.println("Will extract objects here, image zoom_level="+zool_lev_objects);
		for (ObjectLocation ol: object_list) {
		System.out.println(ol.name+": "+ol.xy_meters[0]+"/"+ol.xy_meters[1]);
		}
		maps_collection.reverseRender(
		object_list, // ArrayList<ObjectLocation> objects,
		zool_lev_objects); // int zoom_level){
		System.out.println("Object coordinates in source images: ");
		for (ObjectLocation ol: object_list) {
		System.out.println(ol.name+": "+ol.getPixels()[0]+"/"+ol.getPixels()[1]);
		}
		double [][] object_stack = new double [object_list.size()][];
		String [] object_titles = new String [object_stack.length];
		for (int i = 0; i < object_stack.length; i++) {
		ObjectLocation ol = object_list.get(i);
		object_titles[i] = ol.getName();
		object_stack[i] = ol.extractObjectImage(
		maps_collection,
		extr_size);

		}
		ImagePlus imp_obj = ShowDoubleFloatArrays.makeArrays(
		object_stack,
		extr_size,
		extr_size,
		OrthoMap.removeKnownExtension(imp_sel.getTitle())+"-OBJECT_"+extr_size+"x"+extr_size+".tiff",
		object_titles); // test_titles,
		imp_obj.show();

		// get pattern(s)
		// String pattern_path=OrthoMap.pattern_dir+pattern_file;
		String pattern_path=pattern_dir+pattern_file;
		ImagePlus imp_pattern = new ImagePlus(pattern_path);
		int pattern_size = imp_pattern.getWidth();
		if (pattern_size == 0) {
		System.out.println("testPatternCorrelate(): pattern \""+pattern_path+"\" is not found.");
		return false;
		}
		System.out.println("Using pattern file: "+pattern_path+", subpattern="+sub_pattern_index);
		ImageStack stack_pattern = imp_pattern.getStack();
		int nSlices = stack_pattern.getSize();
		double [][] patterns = new double[nSlices][];
		String [] pattern_labels = new String[nSlices];
		for (int n = 0; n < patterns.length; n++) {
		pattern_labels[n]=stack_pattern.getShortSliceLabel(n+1);
		float [] fpixels_pattern = (float[]) stack_pattern.getPixels(n+1);
		patterns[n]=new double[fpixels_pattern.length];
		for (int i = 0; i < fpixels_pattern.length; i++) {
		patterns[n][i] = fpixels_pattern[i];
		}
		}
		double [] kernel = OrthoMap.getConvolutionKernel(default_kernel);
		double [][] centers = new double [object_stack.length][];
		for (int i = 0; i < object_stack.length; i++) {
		String dbg_prefix = "corr_patt_"+i;
		ObjectLocation ol = object_list.get(i);
		centers[i] = ObjectLocation.getPatternCenter(
		object_stack[i], // double [] data,
		patterns[sub_pattern_index], // double [] pattern,
		kernel, // double [] kernel,
		zoomout, // int zoomout,
		phaseCoeff, // double phaseCoeff,
		min_corr, // double min_corr,
		radius_search, // int radius_search,
		radius_centroid, // int radius_centroid,
		dbg_prefix, // String dbg_prefix,
		debugLevel); // int debugLevel)
		System.out.println(i+": center at "+centers[i][0]+"/"+centers[i][1]+", strength="+centers[i][2]);
		}
		PointRoi roi = new PointRoi();
		roi.setOptions("label");
		for (int i = 0; i < centers.length; i++) {
		roi.addPoint(centers[i][0]+extr_size/2, centers[i][1]+extr_size/2, i+1); // ,1);
		}
		imp_obj.setRoi(roi);
		if (only_correlate) {
		System.out.println("testPatternCorrelate(): correlation DONE, only_correlate is set to true, exiting");
		return true;
		}

		// imp_obj.show();
		// First process each captured object separately, then compare and average?
		// TODO: use finer grid, deconvolve with altitude kernel, calculate effective width of the pattern
		double [][] output_patterns = new double [object_stack.length+1][];
		String [] output_patt_titles = new String[output_patterns.length];
		output_patt_titles[output_patt_titles.length-1]= "average";
		output_patterns[object_stack.length] = new double [corr_size*corr_size];
		//object_titles
		boolean debug_good = debugLevel > -4;
		boolean [][] good_pix = debug_good ? (new boolean[object_stack.length][extr_size*extr_size]) : null; // debugging
		String settings_str = "_fo"+frac_outliers+"_lr"+lim_rad+"_tw"+trans_width+"_rr"+reversal_rad;
		for (int i = 0; i < object_stack.length; i++) {
		output_patterns[i] = ObjectLocation.getRadialPattern(
		object_stack[i], // double [] data,
		centers[i], // double [] xy_offs,
		corr_size, // int corr_size,
		lim_rad, // double lim_rad, // outside all 0
		trans_width, //double trans_width, // lim_rad-trans_width - start reducing
		frac_outliers, // double frac_outliers,
		reversal_rad, // double reversal_rad,
		((good_pix != null)? good_pix[i] : null), // boolean [] good, // null or same size as data
		debugLevel); // int debugLevel)
		output_patt_titles[i] = object_titles[i];
		for (int j = 0; j < output_patterns[i].length; j++) {
		output_patterns[object_stack.length][j] += output_patterns[i][j];
		}
		}
		for (int j = 0; j < output_patterns[0].length; j++) {
		output_patterns[object_stack.length][j] /= object_stack.length;
		}
		ImagePlus imp_out_patt = ShowDoubleFloatArrays.makeArrays(
		output_patterns,
		corr_size,
		corr_size,
		OrthoMap.removeKnownExtension(imp_sel.getTitle())+"-PATTERN"+settings_str+"_"+corr_size+"x"+corr_size+".tiff",
		output_patt_titles); // test_titles,
		imp_out_patt.show();
		if (good_pix != null) {
		double [][] object_stack_masked = new double [2 * object_stack.length][];
		String [] object_titles_masked = new String [2 * object_stack.length];
		PointRoi roi_masked = new PointRoi();
		roi_masked.setOptions("label");
		for (int i = 0; i < centers.length; i++) {
		roi_masked.addPoint(centers[i][0]+extr_size/2, centers[i][1]+extr_size/2, 2*i+1); // ,1);
		roi_masked.addPoint(centers[i][0]+extr_size/2, centers[i][1]+extr_size/2, 2*i+2); // ,1);
		}

		for (int i = 0; i < object_stack.length; i++) {
		object_stack_masked[2*i + 0] = object_stack[i];
		object_stack_masked[2*i + 1] = object_stack[i].clone();
		for (int j = 0; j < object_stack[i].length; j++) {
		if (!good_pix[i][j]) {
		object_stack_masked[2*i + 1][j] = Double.NaN;
		}
		}
		}
		ImagePlus imp_obj_masked = ShowDoubleFloatArrays.makeArrays(
		object_stack_masked,
		extr_size,
		extr_size,
		OrthoMap.removeKnownExtension(imp_sel.getTitle())+"-OBJECT_MASKED"+settings_str+"_"+extr_size+"x"+extr_size+".tiff",
		object_titles_masked); // test_titles,
		imp_obj_masked.setRoi(roi_masked);
		imp_obj_masked.show();
		}
		return true;
		}


		if (use_marked_image) {
		// verify matching names
		//all_scenes
		@@ -691,6 +935,50 @@ adjusted affines[1] for a pair: 1694564291_293695/1694564778_589341
		return null;
		}

		public static ArrayList<ObjectLocation> getObjectsFromSelectedImage(
		ImagePlus imp,
		int [] zoom_levp) {
		// get zoom from the name and list of the slice names prefixes (before second "_"
		String title = imp.getTitle();
		String[] tokens = title.replace(".","_").split("_");
		for (int i = 0; i < tokens.length; i++) {
		if (tokens[i].startsWith("zoom")) {
		int zoom_level = Integer.parseInt(tokens[i].substring(4));
		System.out.println("zoom level = "+zoom_level);
		double pix_size = OrthoMap.getPixelSizeMeters (zoom_level); // meters
		ImageStack stack_scenes = imp.getStack();
		int nSlices = stack_scenes.getSize();
		String [] scene_names = new String [nSlices];
		for (int n = 0; n < scene_names.length; n++) {
		scene_names[n] = stack_scenes.getSliceLabel(n+1).substring(0,17);
		}
		PointRoi pRoi = (PointRoi) imp.getRoi();
		FloatPolygon fp = pRoi.getContainedFloatPoints();
		// Use only 2 last markers
		if (fp == null) {
		System.out.println("getPairFromSelectedImage(): no markers found");
		return null;
		}
		ArrayList<ObjectLocation> list = new ArrayList<ObjectLocation>();
		for (int np = 0; np < fp.npoints; np++) {
		String name = scene_names[pRoi.getPointPosition(np) -1];
		double [] xy_meters = {
		fp.xpoints[np] * pix_size,
		fp.ypoints[np] * pix_size};
		list.add(new ObjectLocation (
		name, // String name,
		xy_meters)); // double [] xy_meters)
		}
		if (zoom_levp != null) {
		zoom_levp[0] = zoom_level;
		}
		return list;
		}
		}
		return null;
		}


		public static String [] getPairChoices(
		int [][] pairs,
		String [] names) {
		@@ -703,18 +991,6 @@ adjusted affines[1] for a pair: 1694564291_293695/1694564778_589341



		/*
		public static TDCorrTile [] rectilinearCorrelate_TD( // scene0/scene1
		final CLTParameters clt_parameters,
		final float [][] fpixels, // to check for empty
		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
		final boolean batch_mode,
		final int debugLevel) {
		*/


		public static double [][][] rectilinearVectorField( // scene0/scene1
		final CLTParameters clt_parameters,
		final float [][] fpixels, // to check for empty

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

+388 −0

File changed.

Preview size limit exceeded, changes collapsed.

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

+39 −40

Original line number	Diff line number	Diff line
		@@ -67,6 +67,20 @@ public class OrthoMap implements Comparable <OrthoMap>, Serializable{
		"/media/elphel/NVME/lwir16-proc/ortho_videos/kernel_50_100.tiff"
		};

		public static String pattern_dir= "/media/elphel/SSD3-4GB/lwir16-proc/ortho_videos/debug/mines/pattern_25m_zoom1/synthetic/";
		public static String [] pattern_files=
		{"patterns_50m_zoom1_200x200.tiff",
		"patterns_50m_evening_zoom1_200x200.tiff",
		"patterns_50m_evening_01_zoom1_200x200_00.tiff",
		"patterns_50m_evening_02_zoom1_200x200_00.tiff",
		"patterns_50m_evening_03_zoom1_200x200_00.tiff",
		"patterns_50m_evening_04_zoom1_200x200_00.tiff",
		"patterns_50m_evening_05_zoom1_200x200_00.tiff",
		"mine1_zoom0.tiff",
		"mine2_zoom0.tiff",
		"mine3_zoom0.tiff",
		"mine4_zoom0.tiff",
		"mine6_zoom0.tiff"};


		public static final String ALT_SUFFIX = "-ALT";
		@@ -1095,9 +1109,12 @@ public class OrthoMap implements Comparable <OrthoMap>, Serializable{
		* @return square kernel as a 1-d double array or null
		*/
		public static double [] getConvolutionKernel() {
		return getConvolutionKernel(kernel_paths.length-1);
		}
		public static double [] getConvolutionKernel(int choice) {
		String kernel_path = null;
		GenericJTabbedDialog gds = new GenericJTabbedDialog("Select kernel path",1200,400);
		gds.addChoice("Kernel path:", kernel_paths, kernel_paths[kernel_paths.length-1]);
		gds.addChoice("Kernel path:", kernel_paths, kernel_paths[choice]);
		gds.showDialog();
		if (gds.wasCanceled()) return null;
		int kernel_index = gds.getNextChoiceIndex();
		@@ -3038,6 +3055,7 @@ public class OrthoMap implements Comparable <OrthoMap>, Serializable{
		double [] wnd_in,
		double phaseCoeff) {
		// phaseCoeff = 0.5;
		boolean dbg=false;
		double [] data = data_in.clone();
		double [] pattern = pattern_in.clone();
		double [] wnd = wnd_in.clone();
		@@ -3047,7 +3065,7 @@ public class OrthoMap implements Comparable <OrthoMap>, Serializable{
		for (int i = 0; i < data.length; i++) {
		data[i] *= wnd[i];
		}
		{
		if (dbg) {
		String [] rslt_titles= {"original","window","windowed","pattern"};
		ShowDoubleFloatArrays.showArrays(
		new double[][] {data_orig, wnd, data, pattern},
		@@ -3096,7 +3114,7 @@ public class OrthoMap implements Comparable <OrthoMap>, Serializable{
		}
		}

		{
		if (dbg) {
		String [] rslt_titles= {"corr", "original","window","windowed","pattern"};
		ShowDoubleFloatArrays.showArrays(
		new double[][] {corr_out, data_orig, wnd, data_orig2, pattern_orig},
		@@ -3106,7 +3124,7 @@ public class OrthoMap implements Comparable <OrthoMap>, Serializable{
		convolve?"output_conv":("output_corr"+phaseCoeff),
		rslt_titles);
		}
		System.out.println("testPhaseCorr() done");
		if (dbg) System.out.println("testPhaseCorr() done");
		return corr_out;
		}

		@@ -3192,8 +3210,8 @@ public class OrthoMap implements Comparable <OrthoMap>, Serializable{

		public static void testPatternCorrelate(
		ImagePlus imp_src) {
		/*
		String pattern_dir= "/media/elphel/SSD3-4GB/lwir16-proc/ortho_videos/debug/mines/pattern_25m_zoom1/synthetic/";
		// String pattern_file= "patterns_50m_zoom1_200x200.tiff";
		String [] pattern_files=
		{"patterns_50m_zoom1_200x200.tiff",
		"patterns_50m_evening_zoom1_200x200.tiff",
		@@ -3202,6 +3220,7 @@ public class OrthoMap implements Comparable <OrthoMap>, Serializable{
		"patterns_50m_evening_03_zoom1_200x200_00.tiff",
		"patterns_50m_evening_04_zoom1_200x200_00.tiff",
		"patterns_50m_evening_05_zoom1_200x200_00.tiff"};
		*/
		int zoomout = 2; // 1;
		int corr_size = 128; // 256;
		double phaseCoeff = 0.5;
		@@ -3297,7 +3316,6 @@ public class OrthoMap implements Comparable <OrthoMap>, Serializable{

		double [][] corrs_out = new double[patterns.length][];
		double [][] convolve_out = new double[patterns.length][];
		// double [][] lim_corr = new double[patterns.length][];
		double [][] corr_patterns = new double[patterns.length][];
		for (int n = 0; n < patterns.length; n++) {
		corr_patterns[n] = patternZoomCropPad(
		@@ -3331,6 +3349,11 @@ public class OrthoMap implements Comparable <OrthoMap>, Serializable{
		height,
		removeKnownExtension(imp_src.getTitle())+"-PATTERN_CORRS",
		patt_titles); // test_titles,





		if (src_marks != null) {
		PointRoi roi = new PointRoi();
		roi.setOptions("label");
		@@ -3881,40 +3904,16 @@ public class OrthoMap implements Comparable <OrthoMap>, Serializable{
		public static void testPatternGenerate() {
		int half_size = 100;
		boolean half_pix = false; // center between pixels
		boolean evening_mode = false; // glare around object, use radius
		double radius_out= 42;
		double edge_out = 6;
		double scale_out = 1.5;
		boolean evening_mode = true; // false; // glare around object, use radius
		double radius = 30; // 32; // 32;
		double edge= 15; // 4;
		double radius_in= 15; // if 0 - skip
		double edge_in = 8;
		double scale_in = -0.05;
		double radius_out= 42;
		double edge_out = 6;
		double scale_out = 1.5;
		double scale = -200; // black 200
		if (evening_mode) {
		radius_out= 42;
		edge_out = 8;
		scale_out =-1.5; // relative to scale
		radius = 30; // 32; // 32;
		edge= 15; // 4;
		radius_in= 10; // if 0 - skip
		edge_in = 8;
		scale_in = -0.7;
		scale = -40; // black 200

		} else {
		radius_out= 42;
		edge_out = 6;
		scale_out =.08;
		radius = 30; // 32; // 32;
		edge= 15; // 4;
		radius_in= 15; // if 0 - skip
		edge_in = 8;
		scale_in = -0.05;
		scale = -170; // black 200
		}



		boolean normalize = false;
		int halves_number = 8; // hidden mines - number of diameter cuts
		@@ -3930,15 +3929,15 @@ public class OrthoMap implements Comparable <OrthoMap>, Serializable{
		if (gd0.wasCanceled()) return;
		evening_mode= gd0.getNextBoolean();
		if (evening_mode) {
		radius_out= 62; // 42;
		edge_out = 40; // 8;
		scale_out =-1.5; // relative to scale
		radius = 30; // 32; // 32;
		edge= 24; // 8; // 4;
		edge= 8; // 8; // 4;
		radius_in= 10; // if 0 - skip
		edge_in = 8;
		scale_in = -0.1; // 7;
		scale = -40; // black 200
		scale_in = 0; // -0.1; // 7;
		radius_out= 45; // 42;
		edge_out = 30; // 8;
		scale_out =-1.0; // relative to scale
		scale = -60; // black 200
		} else {
		radius_out= 42;
		edge_out = 6;

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

+58 −0

Original line number	Diff line number	Diff line
		@@ -396,6 +396,64 @@ public class OrthoMapsCollection implements Serializable{
		return bounds;
		}

		/**
		* Use object coordinates (now metric) on the composite image to
		* determine corresponding pixel coordinates of the source images
		* @param objects ArrayList of objects with the scene name and xy coordinates
		* in the composite image. Will fill in pixel coordinates of the objects
		* @param zoom_level zoom level of the composite image
		*/
		public void reverseRender(
		ArrayList<ObjectLocation> objects,
		int zoom_level){
		int [][] bounds = getBoundsPixels( // should be for rectified, {-bounds[0][0], -bounds[0][1]} - exact center
		zoom_level,
		null);
		int width = bounds[0][1] - bounds[0][0]; // bounds[x][0] - negative
		int height = bounds[1][1] - bounds[1][0];
		/*
		int [] indices = new int [ortho_maps.length]; //maybe will get rid of
		for (int i = 0; i < indices.length; i++) {
		indices[i] = i;
		}
		*/
		final int reference_index = 0;
		for (ObjectLocation ol: objects) {
		int nmap =getIndex(ol.getName());
		final double scale = 1.0/OrthoMap.getPixelSizeMeters(zoom_level);
		final double src_scale = 1.0/OrthoMap.getPixelSizeMeters(ortho_maps[nmap].orig_zoom_level); // pix per meter
		double [][] mbounds = ortho_maps[nmap].getBoundsMeters(true); // keep original bounds
		double [] enu_offset = ortho_maps[reference_index].enuOffsetTo(ortho_maps[nmap]);
		double [] scaled_out_center = { // xy center to apply affine to
		-bounds[0][0] + scale * enu_offset[0],
		-bounds[1][0] - scale * enu_offset[1]};
		double [] metric_center = { // back to meters to match objects
		scaled_out_center[0]/scale,
		scaled_out_center[1]/scale};
		double dX = ol.getMetric()[0]-metric_center[0]; // matching dX, dY in renderMulti()
		double dY = ol.getMetric()[1]-metric_center[1];

		// final int [][] obounds = new int [2][2]; // output (rectified, combined) image bounds, relative to thje top-left
		// for (int n = 0; n< 2; n++) {
		// obounds[n][0] = (int) Math.floor(scaled_out_center[n] + scale*mbounds[n][0]);
		// obounds[n][1] = (int) Math.ceil (scaled_out_center[n] + scale*mbounds[n][1]);
		// }
		// Output window size (keep original affine - OK if will not exactly fit)
		// final int ownd_width = obounds[0][1] - obounds[0][0];
		// final int ownd_height = obounds[1][1] - obounds[1][0];
		// final int ownd_len = ownd_width * ownd_height;
		double [][] src_bounds=ortho_maps[nmap].getBoundsMeters (true); // using original affines
		final double [] src_center = {-src_bounds[0][0],-src_bounds[1][0]}; // x,y center offset in the source image
		final double [][] affine = ortho_maps[nmap].affine; // only here use provided
		// final int src_width = ortho_maps[nmap].getImageData().width;
		// final int src_height = ortho_maps[nmap].getImageData().height;
		// final float [] src_img = ortho_maps[nmap].getImageData().data; // FIXME: will not use
		double [] xy_src = { // pixels of the source image
		src_scale * (affine[0][0]dX + affine[0][1]dY + affine[0][2] + src_center[0]),
		src_scale * (affine[1][0]dX + affine[1][1]dY + affine[1][2] + src_center[1])};
		ol.setPixels(xy_src);
		}
		}


		public ImagePlus renderMulti (

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