Object matching in different flights

src/main/java/com/elphel/imagej/correction/Eyesis_Correction.java

@@ -849,6 +849,7 @@ public class Eyesis_Correction implements PlugIn, ActionListener {
 			addButton("Read Tiff",  panelLWIRWorld, color_process);
 			addButton("Test video",  panelLWIRWorld, color_process);
 			addButton("Ortho Pairs",  panelLWIRWorld, color_process);
+			addButton("Extract Objects",  panelLWIRWorld, color_process);
 			addButton("Mismatched resolutions",  panelLWIRWorld, color_process);
 			addButton("Generate DATI",  panelLWIRWorld, color_process);
 			addButton("Create mine",  panelLWIRWorld, color_process);
@@ -5708,7 +5709,7 @@ public class Eyesis_Correction implements PlugIn, ActionListener {
 				e.printStackTrace();
 			}
 //			ComboMatch.testReadTiff();
-		} else if (label.equals("Ortho Pairs")) {
+		} else if (label.equals("Ortho Pairs") || label.equals("Extract Objects")) {
 			DEBUG_LEVEL = MASTER_DEBUG_LEVEL;
 			EYESIS_CORRECTIONS.setDebug(DEBUG_LEVEL);
 			if (GPU_TILE_PROCESSOR == null) {
@@ -5729,6 +5730,7 @@ public class Eyesis_Correction implements PlugIn, ActionListener {
 			ComboMatch.openTestPairGps(
 					CLT_PARAMETERS,     // CLTParameters    clt_parameters,
 					GPU_TILE_PROCESSOR,
+					label.equals("Extract Objects"), // boolean    extract_mines,
 					DEBUG_LEVEL);
 		} else if (label.equals("Test video")) {
 			ImagePlus imp_sel = WindowManager.getCurrentImage();

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

+package com.elphel.imagej.orthomosaic;
+
+import java.io.IOException;
+import java.io.ObjectInputStream;
+import java.io.ObjectOutputStream;
+import java.io.Serializable;
+import java.util.ArrayList;
+
+import ij.Prefs;
+
+public class AltitudeMismatchKernel implements Serializable{
+	private static final long serialVersionUID = 1L;	
+	public static String kernels_directory;
+	public int    zoom_level;
+	public double agl_from;
+	public double agl_to;
+	public String filename;
+	public AltitudeMismatchKernel (
+			String filename,
+			int zoom_level,
+			double agl_from,
+			double agl_to) {
+		this.filename =   filename;
+		this.zoom_level = zoom_level;
+		this.agl_from =   agl_from;
+		this.agl_to =     agl_to;
+	}
+	private void writeObject(ObjectOutputStream oos) throws IOException {
+		oos.defaultWriteObject();
+	}
+	private void readObject(ObjectInputStream ois) throws ClassNotFoundException, IOException {
+		ois.defaultReadObject();
+	}
+
+	public static void setKernelsDirectory(
+			String directory) {
+		while (directory.endsWith(Prefs.getFileSeparator())){
+			directory=directory.substring(0, directory.length()-1);
+		}
+		kernels_directory = directory;
+	}
+	public static String getKernelsDirectory() {
+		return kernels_directory;
+	}
+	
+	public String getKernelPath() {
+		return kernels_directory+Prefs.getFileSeparator()+filename;
+	}
+	
+	public static AltitudeMismatchKernel getKernel(
+			int                               zoom_level,
+			double                            agl_from,
+			double                            agl_to,
+			ArrayList<AltitudeMismatchKernel> kernels) {
+		double tolerance = 0.15;
+		double agl_from_min = agl_from * (1.0 - tolerance);
+		double agl_from_max = agl_from * (1.0 + tolerance);
+		double agl_to_min = agl_to * (1.0 - tolerance);
+		double agl_to_max = agl_to * (1.0 + tolerance);
+		for (AltitudeMismatchKernel kernel:kernels) {
+			if (zoom_level == kernel.zoom_level) {
+				if (    (kernel.agl_from >= agl_from_min) &&
+						(kernel.agl_from <= agl_from_max) &&
+						(kernel.agl_to >= agl_to_min) &&
+						(kernel.agl_to <= agl_to_max))
+				return kernel;
+			}
+		}
+		return null;
+	}
+
+}

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

@@ -46,6 +46,7 @@ public class ComboMatch {
 	public static boolean openTestPairGps(
 			 CLTParameters    clt_parameters,
 			 GPUTileProcessor gpu_tile_processor, // initialized by the caller
+			 boolean    extract_mines,
 			 int        debugLevel) {
 		GPU_TILE_PROCESSOR = gpu_tile_processor;
 		PairwiseOrthoMatch pairwiseOrthoMatch = null;
@@ -85,11 +86,13 @@ public class ComboMatch {
 //		String files_list_path =          "/media/elphel/SSD3-4GB/lwir16-proc/ortho_videos/maps_19_sep13_25-50-75-100m.list";
 //		String orthoMapsCollection_path = "/media/elphel/SSD3-4GB/lwir16-proc/ortho_videos/maps_19_sep13_25-50-75-100m.data";
 		String [] files_lists_paths = {
+				"/media/elphel/SSD3-4GB/lwir16-proc/ortho_videos/maps_sep12-13_50-25-50-75-100m",
 				"/media/elphel/SSD3-4GB/lwir16-proc/ortho_videos/maps_19_sep13_25-50-75-100m",
-				"/media/elphel/SSD3-4GB/lwir16-proc/ortho_videos/maps_nov3_50-75"};
+				"/media/elphel/SSD3-4GB/lwir16-proc/ortho_videos/maps_nov3_50-75",
+				"/media/elphel/SSD3-4GB/lwir16-proc/ortho_videos/maps_sep12-50m"};
 		
-		String files_list_path =          "/media/elphel/SSD3-4GB/lwir16-proc/ortho_videos/maps_nov3_50-75.list";
-		String orthoMapsCollection_path = "/media/elphel/SSD3-4GB/lwir16-proc/ortho_videos/maps_nov3_50-75.data";
+//		String files_list_path =          "/media/elphel/SSD3-4GB/lwir16-proc/ortho_videos/maps_nov3_50-75.list";
+//		String orthoMapsCollection_path = "/media/elphel/SSD3-4GB/lwir16-proc/ortho_videos/maps_nov3_50-75.data";
 //maps_nov3_50-75		
 //maps_19_sep13.list		
 		//maps_09_short.list
@@ -133,10 +136,16 @@ public class ComboMatch {
 		boolean process_correlation = true; // use false to save new version of data
 		boolean update_match =        true; // use false to save new version of data
 		boolean render_match =        true;
+
+		boolean pattern_match =       false;
+		
+		boolean bounds_to_indices =   true;
+		int     temp_mode =           1;
 		boolean restore_temp =        true;
 		double  frac_remove  =        0.15;
 		double  metric_error =        0.05; // 0.02;//  2 cm
 		boolean update_lla =          false; // re-read file metadata
+		boolean update_kernel_patterns = false;
 		if (!use_marked_image) {
 			process_correlation=false; // use already adjusted by default
 		}
@@ -149,6 +158,13 @@ public class ComboMatch {
 		gd.addCheckbox    ("Process correlations", process_correlation, "false to skip to just regenerate new save file.");
 		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    ("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.");
+		gd.addNumericField("Temp mode",          temp_mode,  0,4,"",
+				"O - do not modify average pixels, 1 - equalize second image to first, 2 - try to account for raw average");
+		//temp_mode
 		/*
 		for (int n = 0; n < image_enuatr.length; n++) {
 			gd.addMessage("image["+n+"] pose");
@@ -174,18 +190,24 @@ public class ComboMatch {
 		if (use_marked_image ) {
 			gd.addCheckbox    ("Use marked image data",   true, "Use markes from the selected image");
 		}
-		gd.addCheckbox    ("Update files metadata",   update_lla, "Re-read files metadata (ifd it was modified)");
-
+		gd.addCheckbox    ("Update files metadata",   update_lla, "Re-read files metadata (if it was modified)");
+		gd.addCheckbox    ("Update kernels/patterns",   update_kernel_patterns, "Re-read kernels and patterns from *.list file");
+//		update_kernel_patterns
 		gd.showDialog();
 		if (gd.wasCanceled()) return false;
 		int choice_index = gd.getNextChoiceIndex();
-		files_list_path =         files_lists_paths[choice_index]+".list";
-		orthoMapsCollection_path =files_lists_paths[choice_index]+".data";
+		String files_list_path =         files_lists_paths[choice_index]+".list";
+		String orthoMapsCollection_path =files_lists_paths[choice_index]+".data";
 		use_saved_collection =     gd.getNextBoolean();
 		save_collection =          gd.getNextBoolean();
 		process_correlation=       gd.getNextBoolean();
 		update_match=              gd.getNextBoolean();
 		render_match=              gd.getNextBoolean();
+		
+		pattern_match=             gd.getNextBoolean();
+		
+		bounds_to_indices=         gd.getNextBoolean();
+		temp_mode =          (int) gd.getNextNumber();
 		/*
 		for (int n = 0; n < image_enuatr.length; n++) {
 			image_enuatr[n][0][0] = gd.getNextNumber();
@@ -214,6 +236,7 @@ public class ComboMatch {
 			use_marked_image=       gd.getNextBoolean();
 		}
 		update_lla=                 gd.getNextBoolean();
+		update_kernel_patterns=     gd.getNextBoolean();
 		OrthoMapsCollection maps_collection=null;
 		if (use_saved_collection) {
 			try {
@@ -222,6 +245,11 @@ public class ComboMatch {
 				// TODO Auto-generated catch block
 				e.printStackTrace();
 			}
+			//files_list_path
+			if (update_kernel_patterns) {
+				maps_collection.updateKernels(files_list_path);
+				maps_collection.updatePatterns(files_list_path);
+			}
 		} else {
 			maps_collection = new OrthoMapsCollection(files_list_path); // should have ".list" extension
 		}
@@ -266,6 +294,7 @@ public class ComboMatch {
 					false,             // boolean     use_alt,
 					show_centers,      // boolean     show_centers,
 					zoom_lev,          // int         zoom_level,
+					temp_mode,         // int         temp_mode, // 0 - do nothing, 1 - equalize average,2 - try to correct
 					origin);           // int []      origin){
 			imp_img.show();
 		}
@@ -276,10 +305,11 @@ public class ComboMatch {
 					true,              // boolean     use_alt,
 					show_centers,      // boolean     show_centers,
 					zoom_lev,          // int         zoom_level,
+					0,                 // int         temp_mode, // 0 - do nothing, 1 - equalize average,2 - try to correct
 					origin);           // int []      origin){
 			imp_alt.show();
 		}
-        if (process_correlation || render_match ) {
+        if (process_correlation || render_match || pattern_match) {
 //        	int [] gpu_pair;
         	if (gpu_spair == null) {
         		ArrayList<Point> pairs_list = new ArrayList<Point>(); 
@@ -409,40 +439,26 @@ public class ComboMatch {
 							System.out.println();
 						}
 					}
-					if (render_match) {
-						ImagePlus imp_img_pair = 	maps_collection.renderMulti (
-								"multi_"+gpu_spair[0]+"-"+gpu_spair[1]+"-zoom_"+min_zoom_lev+"_"+zoom_lev, // String      title,
-								false,             // boolean     use_alt,
+					if (pattern_match) {
+						ImagePlus imp_pat_match = maps_collection.patterMatchDualWrap (
 								gpu_pair, // int []        indices, // null or which indices to use (normally just 2 for pairwise comparison)
 								affines,  // double [][][] affines, // null or [indices.length][2][3] 
-								warp,              // FineXYCorr    warp,
-								show_centers,      // boolean     show_centers,
-								min_zoom_lev,      // int         zoom_level,
-								origin);           // int []      origin){
-						imp_img_pair.show();
-
-						/*
-						
-						int gpu_tilesX = gpu_width/GPUTileProcessor.DTT_SIZE; 
-						Rectangle tile_woi = OrthoMapsCollection.scaleRectangle (woi, GPUTileProcessor.DTT_SIZE);
-						double [][] vector_field_interpolated = interpolateVectorField(
-								vector_field, // final double [][] vector_field, // sparse {vx,vy,strength}
-								gpu_tilesX,   // final int gpu_tilesX, // 512
-								tile_woi,     // final Rectangle tile_woi, // only width, height are used top-left corners are the same
-								scale,        // final double scale,
-								1);           // final int debugLevel);
-						
-						
+								warp);    // FineXYCorr    warp)
+//						imp_pat_match.show();
+					}
+					if (render_match) {
 						ImagePlus imp_img_pair = 	maps_collection.renderMulti (
 								"multi_"+gpu_spair[0]+"-"+gpu_spair[1]+"-zoom_"+min_zoom_lev+"_"+zoom_lev, // String      title,
 								false,             // boolean     use_alt,
 								gpu_pair,          // int []        indices, // null or which indices to use (normally just 2 for pairwise comparison)
+								bounds_to_indices, // boolean       bounds_to_indices,
+								temp_mode,         // int           temp_mode, // 0 - do nothing, 1 - equalize average,2 - try to correct
 								affines,           // double [][][] affines, // null or [indices.length][2][3]
+								warp,              // FineXYCorr    warp,
 								show_centers,      // boolean     show_centers,
 								min_zoom_lev,      // int         zoom_level,
 								origin);           // int []      origin){
  						imp_img_pair.show();
-						*/
 					}
 				}
 			}

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

@@ -5,6 +5,7 @@ import java.awt.Rectangle;
 import com.elphel.imagej.gpu.GPUTileProcessor;
 
 public class FineXYCorr {
+	public double      scale_warp = 1.0;
 	public double []   top_left_metric; // relative to the reference image vertical point, normally negative
 	public int         width_tiles;
 	public int         height_tiles;
@@ -60,7 +61,7 @@ public class FineXYCorr {
 	 * Apply warping to the x,y pair
 	 * @param xy {X,Y} before and after warping
 	 */
-	public void warpXY(// in render pixels
+	public void warpXY(// in render pixels NOT_USED
 			double [] xy) { // no interpolation - using nearest
 		int ix = (int) Math.round((xy[0] - render_tl[0]) * render_div_tile);
 		int iy = (int) Math.round((xy[1] - render_tl[1]) * render_div_tile);
@@ -82,8 +83,8 @@ public class FineXYCorr {
 			double [] dxdy = warp_xy[ix + width_tiles * iy];
 			if (dxdy != null) {
 				return new double [] {
-						dxdy[0]*pix_div_render,
-						dxdy[1]*pix_div_render};
+						dxdy[0]*pix_div_render*scale_warp,
+						dxdy[1]*pix_div_render*scale_warp};
 			}
 		}
 		return new double [2];

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

+package com.elphel.imagej.orthomosaic;
+
+import java.io.IOException;
+import java.io.ObjectInputStream;
+import java.io.ObjectOutputStream;
+import java.io.Serializable;
+import java.time.LocalDateTime;
+import java.util.ArrayList;
+
+import ij.Prefs;
+
+public class GroundObjectPattern implements Serializable {
+	private static final long serialVersionUID = 1L;	
+	public static long UTC_EAST_HRS = 3;
+	public static String  patterns_directory;
+	//public LocalDateTime plusHours(long hours) 	
+	public int     zoom_level;     // 1 for 5mm/pix 
+	public String  object_type;    // like "TM62"
+//	public String  object_version; // just change config 
+	LocalDateTime  utcDateTime;    // UTC
+	public String  filename;       // should be square
+	
+	public GroundObjectPattern(
+			String        filename,
+			int           zoom_level,
+			String        object_type,
+			LocalDateTime utcDateTime) {
+		this.filename =    filename;
+		this.zoom_level =  zoom_level;
+		this.object_type = object_type;
+		this.utcDateTime = utcDateTime;
+	}
+	private void writeObject(ObjectOutputStream oos) throws IOException {
+		oos.defaultWriteObject();
+	}
+	private void readObject(ObjectInputStream ois) throws ClassNotFoundException, IOException {
+		ois.defaultReadObject();
+	}
+	
+	public static void setPatternsDirectory(
+			String directory) {
+		while (directory.endsWith(Prefs.getFileSeparator())){
+			directory=directory.substring(0, directory.length()-1);
+		}
+		patterns_directory = directory;
+	}
+	
+	public String getPatternPath() {
+		return patterns_directory+Prefs.getFileSeparator()+filename;
+	}
+	
+	public static String getPatternsDirectory() {
+		return patterns_directory;
+	}
+	
+	public static GroundObjectPattern getPattern(
+			String        object_type,
+			LocalDateTime utcDateTime,
+			ArrayList<GroundObjectPattern> patterns) {
+		GroundObjectPattern best_gop = null;
+		long best_hrs_diff = 24;
+		for (GroundObjectPattern gop:patterns) {
+			if ((object_type == null) || object_type.equals(gop.object_type)) {
+				if (utcDateTime != null) {
+					long hrs_diff = Math.abs(utcDateTime.getHour()-gop.utcDateTime.getHour());
+					if (hrs_diff > 12) {
+						hrs_diff = 24 -hrs_diff;
+					}
+					if (hrs_diff < best_hrs_diff) {
+						best_gop = gop; 
+						best_hrs_diff = hrs_diff;
+					}
+				} else {
+					best_gop = gop; // use latest
+				}
+			}
+		}
+		return best_gop;
+	}
+	
+	public LocalDateTime getUTC() {
+		return utcDateTime;
+	}
+	public LocalDateTime getLocalDT() {
+		return utcDateTime.plusHours(UTC_EAST_HRS);
+	}
+	public boolean isEvening() {
+		return getLocalDT().getHour() >= 12;
+	}
+	
+	public double getAGL() {
+		double agl = 50; // zoom 0 for 50m AGL
+		for (int z = zoom_level; z > 0; z--) {
+			agl /=2;
+		}
+		for (int z = zoom_level; z < 0; z++) {
+			agl *=2;
+		}
+		return agl;
+	}
+	
+	public int getZoomLevel() {
+		return zoom_level;
+	}
+}

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

+package com.elphel.imagej.orthomosaic;
+
+public class ObjectLocation {
+	String name;
+	double [] xy_meters;
+}

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

@@ -57,8 +57,9 @@ public class OrthoMap implements Comparable <OrthoMap>, Serializable{
 	public static boolean FIX_VERT_Y = false; // true; // temporarily fix vertical Y coordinate bug (use -GCORR in the filename?)
 	public static int gpu_width =  4096;
 	public static int gpu_height =  4096;
-	public static final String [] KEY_DIRS= {"rootDirectory", // from EyesisCorrectionParameters
-			"sourceDirectory","linkedModels","videoDirectory","x3dDirectory","resultsDirectory"};
+//	public static final String [] KEY_DIRS= {"rootDirectory", // from EyesisCorrectionParameters
+//			"sourceDirectory","linkedModels","videoDirectory","x3dDirectory","resultsDirectory",
+//			"kernelsDirectory", "patternsDirectory"};
 	public static final String [] kernel_paths = {
 			"--- no convolution (same altitude) ---",
 			"/media/elphel/NVME/lwir16-proc/ortho_videos/kernel_25_50.tiff", 
@@ -94,7 +95,7 @@ public class OrthoMap implements Comparable <OrthoMap>, Serializable{
 	transient HashMap <Integer, FloatImageData> images;
 	HashMap <String, PairwiseOrthoMatch>        pairwise_matches;
 	public transient SensorTemperatureData[]    temp_data;
-	
+	public transient double                     agl = Double.NaN; 
 	private void writeObject(ObjectOutputStream oos) throws IOException {
 		oos.defaultWriteObject();
 		oos.writeObject(path);
@@ -114,6 +115,7 @@ public class OrthoMap implements Comparable <OrthoMap>, Serializable{
 		// images is not saved
 		// pairwise_matches is not transient
 		oos.writeObject(temp_data); // temporary, while transient
+		oos.writeObject(agl);
 	}
 
 	private void readObject(ObjectInputStream ois) throws ClassNotFoundException, IOException {
@@ -132,6 +134,9 @@ public class OrthoMap implements Comparable <OrthoMap>, Serializable{
 		// orig_image was not saved
 		// alt_image was not saved
 		temp_data = (SensorTemperatureData[]) ois.readObject();
+		agl = (double)  ois.readObject();
+		
+		
 		images = new HashMap <Integer, FloatImageData>(); // field images was not saved
 		averageImagePixel = Double.NaN; // average image pixel value (to combine with raw)
 		
@@ -482,6 +487,26 @@ public class OrthoMap implements Comparable <OrthoMap>, Serializable{
 		return true;
 	}
 	
+	/**
+	 * Get average altitude above ground (AGL)
+	 * @return AGL or NaN
+	 */
+	public double getAGL() {
+		if (Double.isNaN(agl)) {
+			final FloatImageData src_elev = getAltData();
+			if (src_elev == null) {
+				System.out.println("getTileElevations(): No elevation data available for "+name);
+				return Double.NaN;
+			}
+			double average_asl = getMaskedAverage (
+					src_elev.data, // final double [] data,
+					null); // final boolean [] mask) 
+			agl= lla[2] - average_asl;
+		}
+		return agl;
+	}
+	
+	
 	public ImagePlus getOriginalImage(boolean show_markers) {
 		FloatImageData orig_image = getImageData();
 		if (orig_image != null) {
@@ -764,10 +789,6 @@ public class OrthoMap implements Comparable <OrthoMap>, Serializable{
 		final double [] elev = new double [tilesX*tilesY];
 		Arrays.fill(elev, Double.NaN);
 		final int diff_zoom_lev = zoom_level-orig_zoom_level;
-//   	double s = 1.0;
-//		int zl = diff_zoom_lev;
-//		for (; zl< 0; zl++) s *= 2.0;
-//		for (; zl> 0; zl--) s *= 0.5; // normally will not happen
 		final double scale = 1.0/getScale (diff_zoom_lev); //	int zoom_lev);
 		
 		final Thread[] threads = ImageDtt.newThreadArray();
@@ -1070,7 +1091,7 @@ public class OrthoMap implements Comparable <OrthoMap>, Serializable{
 	}
 
 	/**
-	 * Read one of the convolution kernels (or nun if no convolution is needed)
+	 * Read one of the convolution kernels (or null if no convolution is needed)
 	 * @return square kernel as a 1-d double array or null
 	 */
 	public static double [] getConvolutionKernel() {
@@ -2500,6 +2521,42 @@ public class OrthoMap implements Comparable <OrthoMap>, Serializable{
 		return avg/num;
 	}
 
+	/**
+	 * Calculate average of a float array, ignore masked out (!mask[i] and NaNs in the data)
+	 * @param data double data array
+	 * @param mask optional (may be null) boolean mask - ignore data items that have corresponding mask element false
+	 * @return average value of the non-NaN and not disabled by mask elements of data[] 
+	 */
+
+	private static double getMaskedAverage (
+			final float []   data,
+			final boolean [] mask) {
+		final Thread[] threads = ImageDtt.newThreadArray();
+		final AtomicInteger ai = new AtomicInteger(0);
+		final AtomicInteger ati = new AtomicInteger(0);
+		final double [] avg_arr = new double [threads.length];
+		final double [] npix_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 iPix = ai.getAndIncrement(); iPix < data.length; iPix = ai.getAndIncrement()) if (!Double.isNaN(data[iPix]) && ((mask == null) || (mask[iPix]))){
+						avg_arr[thread_num] += data[iPix];
+						npix_arr[thread_num] += 1.0;
+					}
+				}
+			};
+		}		      
+		ImageDtt.startAndJoin(threads);
+		double avg=0, num=0;
+		for (int i = 0; i < avg_arr.length; i++) {
+			avg+=avg_arr[i];
+			num+=npix_arr[i];
+		}
+		return avg/num;
+	}
+	
+	
 	/**
 	 * Remove double [] data elements that are lower than threshold_low or greater than threshold_high, ignore masked out and NaN elements
 	 * @param data double [] input data
@@ -3136,37 +3193,77 @@ 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";
-		int       zoomout =     1;
-		int       corr_size = 256;
+//		String pattern_file= "patterns_50m_zoom1_200x200.tiff";
+		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"};
+		int       zoomout =     2; // 1;
+		int       corr_size = 128; // 256;
 		double    phaseCoeff = 0.5;
 		int       debugLevel = 1;
-		double    min_corr  = 0.0025; // real max >0.005 with scale -500000;
+		double    min_corr  =          0.01; // 0.0025; // real max >0.005 with scale -500000;
+		double    min_corr_full_rel  = 0.75; // minimal correlation with full pattern
+		double    full_preference =    1.4;  // prefer full pattern if its strength is slightly lower than for partial
+		double    max_min_ratio =      3.0;  // ratio of halves best/worst to use half-pattern     
+		boolean   combine_full = true;
 		double    adv_radius = 60.0; // pixels
-		int       corr_radius = 30; // may use same as adv_radius; but not more
+		int       corr_radius = (int) (Math.sqrt(0.5)* adv_radius) -1 ; // 30; // may use same as adv_radius; but not more
+		double [][] src_marks = null;
+		PointRoi pRoi = (PointRoi) imp_src.getRoi();
+		if (pRoi != null) {
+			FloatPolygon fp = pRoi.getContainedFloatPoints();
+			src_marks = new double[fp.npoints][2];
+			for (int i = 0; i < src_marks.length; i++) {
+				src_marks[i][0] = fp.xpoints[i];
+				src_marks[i][1] = fp.ypoints[i];
+			}
+		}
+		
 		
 		GenericJTabbedDialog gd = new GenericJTabbedDialog("Correlate image with pattern",1200,500);
 		gd.addStringField ("Pattern directory",  pattern_dir, 180, 	"Absolute path including trailing \"/\".");
-		gd.addStringField ("Pattern filename",   pattern_file,180, 	"Pattern filename.");
+//		gd.addStringField ("Pattern filename",   pattern_file,180, 	"Pattern filename.");
+		gd.addChoice("Pattern filename:", pattern_files, pattern_files[pattern_files.length-1]);
+		
 		gd.addNumericField("Zoom-out factor",            zoomout,  0,4,"x", "Reduce pattern resolution to match image.");
 		gd.addNumericField("Phase correlation coefficient",  phaseCoeff,  3,7,"","1.0 - pure phase correlation, 0.0 - regular correlation.");
-		gd.addNumericField("Minimal correlation",  min_corr,  3,7,"","Minimal correlation value to keep.");
+		gd.addNumericField("Minimal correlation",        min_corr,  5,7,"","Minimal correlation value to keep.");
+		gd.addNumericField("Minimal relative full correlation",   min_corr_full_rel,  5,7,"","Minimal relative correlation value with full circular pattern to keep.");
+		gd.addNumericField("Prefer full pattern",        full_preference,  3,7,"","Prefer full pattern to partial; scale by this value.");
+		gd.addNumericField("Max/min halves ratio",       max_min_ratio,  3,7,"","Ratio of halves best/worst to use half-pattern.");
+		gd.addCheckbox    ("Combine with full pattern",  combine_full, "Multiply by normalized full pattern correlation maximum.");
 		gd.addNumericField("Adversarial distance",       adv_radius,  1,6,"pix", "Suppress weaker if they have closer strong ones.");
-		gd.addNumericField("Correlation peak max radius", corr_radius,  0,4,"pix", "Limit correlation peak radius. Should be <= adversarial");
+		gd.addNumericField("Correlation peak max radius",corr_radius,  0,4,"pix", "Limit correlation peak radius. Should be <= adversarial");
 		gd.addNumericField("Correlation size",           corr_size,  0,4,"pix", "Should be power of 2.");
 		gd.addNumericField("Debug level",                debugLevel,  0,4,"", "Debug level.");
 		gd.showDialog();
 		if (gd.wasCanceled()) return;
 		pattern_dir=        gd.getNextString();		
-		pattern_file=       gd.getNextString();
+//		pattern_file=       gd.getNextString();
+		String pattern_file = pattern_files[gd.getNextChoiceIndex()];
 		zoomout=        (int) gd.getNextNumber();
 		phaseCoeff=           gd.getNextNumber();
 		min_corr=             gd.getNextNumber();
+		min_corr_full_rel=    gd.getNextNumber();
+		full_preference=      gd.getNextNumber();
+		max_min_ratio=        gd.getNextNumber();		
+		combine_full =        gd.getNextBoolean();
 		adv_radius=           gd.getNextNumber();
 		corr_radius=    (int) gd.getNextNumber();
 		corr_size=      (int) gd.getNextNumber();
 		debugLevel=     (int) gd.getNextNumber();
 		
+		if (corr_radius > ( (int) (Math.sqrt(0.5)* adv_radius) -1)){
+			corr_radius  =  (int) (Math.sqrt(0.5)* adv_radius) -1;
+			System.out.println("testPatternCorrelate(): Reducing corr_radius to "+corr_radius+" to avoid thread races");
+		}
+		
+		double min_corr_full = min_corr*min_corr_full_rel;
 		float [] fpixels = (float[]) imp_src.getProcessor().getPixels();
 		int      width = imp_src.getWidth();
 		int      height = imp_src.getHeight();
@@ -3200,7 +3297,7 @@ 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 [][] 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(
@@ -3224,47 +3321,83 @@ public class OrthoMap implements Comparable <OrthoMap>, Serializable{
 					phaseCoeff,       // final double    phaseCoeff,
 					debugLevel);      // final int       debugLevel) {
 		}
-		ShowDoubleFloatArrays.showArrays(
+		String [] patt_titles = new String[corrs_out.length];
+		for (int i = 0; i < patt_titles.length; i++) {
+			patt_titles[i] = "patt_"+i;
+		}
+		ImagePlus imp_corrs = ShowDoubleFloatArrays.makeArrays(
 				corrs_out,
 				width,
 				height,
-				true,
-				removeKnownExtension(imp_src.getTitle())+"-PATTERN_CORR-0");
-
-		
+				removeKnownExtension(imp_src.getTitle())+"-PATTERN_CORRS",				
+				patt_titles); // test_titles,
+		if (src_marks != null) {
+			PointRoi roi = new PointRoi();
+			roi.setOptions("label");
+			for (int i = 0; i < src_marks.length; i++) {
+				roi.addPoint(src_marks[i][0],src_marks[i][1]); // ,1);
+			}
+			imp_corrs.setRoi(roi);
+		}
+		imp_corrs.show();
 		
 //data
 		double []   bestcorr = new double [data.length];
+		double []   fullcorr = new double [data.length];
 		int []      bestpatt = new int [bestcorr.length];
 		ArrayList<Point> object_list =  combineDirCorrs (
 				corrs_out,       // final double [][] corrs,
 				width,           // final int         width,
-				bestcorr,     // final double []   bestcorr
+				fullcorr,        // final double []   fullcorr_in,
+				bestcorr,        // final double []   bestcorr_in
 				bestpatt,        // final int []      bestpatt_in,
 				min_corr,        // final double      min_corr,
+				min_corr_full,   // final double      min_corr_full,
+				full_preference, // final double      full_preference,
+				max_min_ratio,   // final double      max_min_ratio,
+				combine_full,    // final boolean     combine_full,    // multiply by normalized full pattern correlation maximum
 				adv_radius,      // final double      adv_radius,
 				corr_radius);    // final int         corr_radius)
+		
+		
+		
+		
 		System.out.println("testPatternCorrelate(): Found "+object_list.size()+" candidates");
-		ShowDoubleFloatArrays.showArrays(
+		ImagePlus imp_best = ShowDoubleFloatArrays.makeArrays(
 				bestcorr,
 				width,
 				height,
 				removeKnownExtension(imp_src.getTitle())+"-BEST_CORR");				
+		double [] dbg_bestpatt = new double [bestpatt.length];
+		Arrays.fill(dbg_bestpatt, Double.NaN);
+		for (int i = 0; i <bestpatt.length; i++) {
+			if (bestpatt[i] >=0) {
+				dbg_bestpatt[i] = bestpatt[i];
+			}
+		}
+		ImagePlus imp_bestpatt = ShowDoubleFloatArrays.makeArrays(
+				dbg_bestpatt,
+				width,
+				height,
+				removeKnownExtension(imp_src.getTitle())+"-BEST_PATT");				
+		if (src_marks != null) {
+			PointRoi roi = new PointRoi();
+			roi.setOptions("label");
+			for (int i = 0; i < src_marks.length; i++) {
+				roi.addPoint(src_marks[i][0],src_marks[i][1]); // ,1);
+			}
+			imp_best.setRoi(roi);
+			imp_bestpatt.setRoi(roi);
+		}
+		imp_best.show();
+		imp_bestpatt.show();
+		
+		
 		double [][] filtered_corrs = splitPattenCorrelations(
 				patterns.length, // final int         num_patterns,
 				bestcorr,        // final double []   bestcorr,
 				bestpatt);       // final int []      bestpatt)		
 		
-		/*
-		for (int n = 0; n < patterns.length; n++) {
-			lim_corr[n] = corrs_out[n].clone();
-			for (int i = 0; i < lim_corr.length; i++) {
-				if (lim_corr[n][i] < min_corr) {
-					lim_corr[n][i] = 0;
-				}
-			}
-		}
-		*/
 		for (int n = 0; n < patterns.length; n++) {
 			convolve_out[n]= correlateWithPattern(
 					filtered_corrs[n],// corrs_out[n], // final double [] data,
@@ -3278,7 +3411,6 @@ public class OrthoMap implements Comparable <OrthoMap>, Serializable{
 		double [] convolved_merged = mergePattenConvolutions(
 				convolve_out); // final double [][] convs)
 		
-		
 		String [] rslt_titles =new String [patterns.length+2]; 
 		double [][] rslt = new double [patterns.length + 2][]; // ]{data, corr_out};
 		double [][] conv_rslt = new double [patterns.length + 2][]; // ]{data, corr_out};
@@ -3295,20 +3427,39 @@ public class OrthoMap implements Comparable <OrthoMap>, Serializable{
 			conv_rslt[i+2] = convolve_out[i];
 			rslt_titles[i+2] = "corr_"+pattern_labels[i];
 		}
-		ShowDoubleFloatArrays.showArrays(
+		
+		ImagePlus imp_patt_corrs = ShowDoubleFloatArrays.makeArrays(
 				rslt,
 				width,
 				height,
-				true,
 				removeKnownExtension(imp_src.getTitle())+"-PATTERN_CORR",
 				rslt_titles);
-		ShowDoubleFloatArrays.showArrays(
+		if (src_marks != null) {
+			PointRoi roi = new PointRoi();
+			roi.setOptions("label");
+			for (int i = 0; i < src_marks.length; i++) {
+				roi.addPoint(src_marks[i][0],src_marks[i][1]); // ,1);
+			}
+			imp_patt_corrs.setRoi(roi);
+		}
+		imp_patt_corrs.show();
+		
+		
+		ImagePlus imp_patt_conv = ShowDoubleFloatArrays.makeArrays(
 				conv_rslt,
 				width,
 				height,
-				true,
 				removeKnownExtension(imp_src.getTitle())+"-PATTERN_CORR_CONVOLVE_min_corr"+min_corr,
 				rslt_titles);
+		if (src_marks != null) {
+			PointRoi roi = new PointRoi();
+			roi.setOptions("label");
+			for (int i = 0; i < src_marks.length; i++) {
+				roi.addPoint(src_marks[i][0],src_marks[i][1]); // ,1);
+			}
+			imp_patt_conv.setRoi(roi);
+		}
+		imp_patt_conv.show();
 		System.out.println("testPatternCorrelate(): correlation done");
 	}
 	
@@ -3320,7 +3471,7 @@ public class OrthoMap implements Comparable <OrthoMap>, Serializable{
 	 * @param width width of the correlation array
 	 * @param bestcorr_in null or double array  [corrs[0].length] will contain
 	 *        best correlation value from multiple patterns of corrs[][].
-	 * @param bestbatt_in null or integer array  [corrs[0].length] will contain
+	 * @param bestpatt_in null or integer array  [corrs[0].length] will contain
 	 *        number of the best pattern 
 	 * @param min_corr - minimal correlation value to use (lower - replace with 0)
 	 * @param adv_radius - suppress weaker local maximums near the stronger one 
@@ -3336,7 +3487,6 @@ public class OrthoMap implements Comparable <OrthoMap>, Serializable{
 			final double      min_corr,
 			final double      adv_radius,
 			final int         corr_radius) { 
-//		final int num_patt =       corrs.length;
 		final int height = corrs[0].length/width;
 		final double [] bestcorr = (bestcorr_in != null) ? bestcorr_in: (new double [corrs[0].length]);
 		final int []    bestpatt = (bestpatt_in != null) ? bestpatt_in: (new int    [corrs[0].length]);
@@ -3345,7 +3495,6 @@ public class OrthoMap implements Comparable <OrthoMap>, Serializable{
 		final int []    bestpatt0 =  new int    [corrs[0].length];
 		Arrays.fill(bestpatt, -1);
 		Arrays.fill(bestpatt0, -1); // maybe not needed
-//		final boolean [] local_max = new boolean [bestcorr.length];
 		final Thread[] threads = ImageDtt.newThreadArray();
 		final AtomicInteger ai = new AtomicInteger(0);
 		final TileNeibs tn =  new TileNeibs(width, height);
@@ -3390,7 +3539,7 @@ public class OrthoMap implements Comparable <OrthoMap>, Serializable{
 							System.out.println("combineDirCorrs(): ipix="+ipix);
 						}
 						is_max: {
-							for (int dir = 0; dir > TileNeibs.DIRS; dir++) {
+							for (int dir = 0; dir < TileNeibs.DIRS; dir++) {
 								int ipix1 = tn.getNeibIndex(ipix, dir);
 								if ((ipix1 >= 0) && (bestcorr0[ipix1] > bestcorr0[ipix])){
 									break is_max;
@@ -3468,6 +3617,217 @@ public class OrthoMap implements Comparable <OrthoMap>, Serializable{
 		}
 		return list;
 	}
+	
+	/**
+	 * Combine results of the phase correlations with different patters
+	 * (now with semi-obscured half-circles), using the best (highest value match),
+	 * filter by correlation value and suppress weaker maximums by stronger neighbors
+	 * @param corrs            array of 2D correlation results [num_pattern][pixel]
+	 * @param width            width of the correlation array
+	 * @param fullcorr_in      null or double array  [corrs[0].length] will contain
+	 *                         full pattern (corrs[0][]) correlation value.
+	 * @param bestcorr_in      null or double array  [corrs[0].length] will contain
+	 *                         best correlation value from multiple patterns of corrs[][].
+	 * @param bestpatt_in      null or integer array  [corrs[0].length] will contain
+	 *                         number of the best pattern. 
+	 * @param min_corr minimal correlation value to use (lower - replace with 0)
+	 * @param min_corr_full    correlation with full pattern still needs to exceed this
+	 *                         even if correlation with partial (obscured) pattern will
+	 *                         be used
+	 * @param full_preference  when looking for the best pattern to match, increase correlation
+	 *                         with full pattern
+	 * @param max_min_ratio    ratio of halves best/worst to use half-pattern                         
+	 * @param combine_full     multiply best pattern correlation by relative (to the center pixel)
+	 *                         correlation by the full pattern correlation 
+	 * @param adv_radius       suppress weaker local maximums near the stronger one 
+	 * @param corr_radius      maximal correlation peak radius (zero out outside).
+	 *                         Should be <= adv_radius to avoid thread races 
+	 * @return ArrayList of integer pairs - pixel index (x+y*width) and the pattern index
+	 */
+	public static ArrayList<Point> combineDirCorrs (
+			final double [][] corrs,
+			final int         width,
+			final double []   fullcorr_in,
+			final double []   bestcorr_in,
+			final int []      bestpatt_in,
+			final double      min_corr,
+			final double      min_corr_full,
+			final double      full_preference,
+			final double      max_min_ratio, // ratio of halves best/worst to use half-pattern
+			final boolean     combine_full,    // multiply by normalized full pattern correlation maximum
+			final double      adv_radius,
+			final int         corr_radius) { 
+		final int height = corrs[0].length/width;
+		final int full_patt_indx = 0; 
+		final double [] fullcorr = (fullcorr_in != null) ? fullcorr_in: (new double [corrs[0].length]); 
+		// before adversarial filtering
+		final Thread[] threads = ImageDtt.newThreadArray();
+		final AtomicInteger ai = new AtomicInteger(0);
+		final TileNeibs tn =  new TileNeibs(width, height);
+		final AtomicInteger ati = new AtomicInteger(0);
+		ArrayList<ArrayList<Point>> lists = new ArrayList<ArrayList<Point>>();
+		for (int i = 0; i < threads.length; i++) {
+			lists.add(new ArrayList<Point>());
+		}
+		// create fullcorr and list using only full correlation. Later will deal with obscured patterns
+		final int iradius = (int) Math.ceil(adv_radius);
+		final double adv_radius2 = adv_radius * adv_radius;
+		final double corr_radius2 = corr_radius*corr_radius;
+		
+		final double [] bestcorr = (bestcorr_in != null) ? bestcorr_in: (new double [corrs[0].length]);
+		final int []    bestpatt = (bestpatt_in != null) ? bestpatt_in: (new int    [corrs[0].length]);
+		Arrays.fill(bestpatt, -1);
+		final int dbg_pix =  -2827823; // 3649679;// #3 
+		final int dbg_pix1 = -3649679;// #3 
+		final int dbg_pix0=  1439210; // -2827822; // 3649679;// #3 
+		final int dbg_pix2 = 1442449; // -2831060; 
+		final int dbg_pix3 = 1439211; // 2827822; 
+		
+		for (int ithread = 0; ithread < threads.length; ithread++) {
+			threads[ithread] = new Thread() {
+				public void run() {
+					int thread_num = ati.getAndIncrement();
+					final TileNeibs tn =  new TileNeibs(width, height);
+					int corr_diameter = 2*corr_radius+1;
+					TileNeibs tnl =  new TileNeibs(corr_diameter,corr_diameter);
+					int local_center = (2 * corr_radius + 2) * corr_radius;
+					boolean [] mask = new boolean [corr_diameter*corr_diameter];
+
+					for (int ipix = ai.getAndIncrement(); ipix < fullcorr.length; ipix = ai.getAndIncrement()) if (corrs[full_patt_indx][ipix] >= min_corr_full) {
+						boolean dbg= (ipix==dbg_pix) || (ipix==dbg_pix1) || (ipix==dbg_pix2) || (ipix==dbg_pix3);
+						if (dbg) {
+							System.out.println("combineDirCorrs(): ipix="+ipix);
+						}
+						is_max: {
+							for (int dir = 0; dir < TileNeibs.DIRS; dir++) {
+								int ipix1 = tn.getNeibIndex(ipix, dir);
+								if ((ipix1 >= 0) && (corrs[full_patt_indx][ipix1] > corrs[full_patt_indx][ipix])){
+									break is_max;
+								}
+							}
+							// compare with others in adversarial radius, if equal - use higher index ipix
+							for (int dy = -iradius; dy <= iradius; dy++) {
+								for (int dx = -iradius; dx <= iradius; dx++) {
+									double r2 = dx*dx + dy*dy;
+									if ((r2 < adv_radius2) && (r2 > 2.1)) {
+										int ipix1 = tn.getNeibIndex(ipix, dx, dy);
+										if (ipix1 >= 0) {
+											if (corrs[full_patt_indx][ipix1] > corrs[full_patt_indx][ipix]) {
+												break is_max;
+											} else if ((corrs[full_patt_indx][ipix1] == corrs[full_patt_indx][ipix]) && (ipix1 < ipix)) {
+												break is_max;
+											}
+										}
+									}
+								}								
+							}
+							//corrs[full_patt_indx]
+							// find best patter here, using full_preference;
+							//max_min_ratio, // ratio of halves best/worst to use half-pattern
+							int patt = full_patt_indx;
+							double best_val = full_preference*corrs[full_patt_indx][ipix];
+							double max_val = corrs[1][ipix];
+							double min_val = max_val;
+							int max_indx = 1;
+							for (int i = 1; i < corrs.length; i++) {
+								if (corrs[i][ipix] > best_val) {
+									best_val = corrs[i][ipix];
+									patt = i;
+								}
+								if (corrs[i][ipix] > max_val) {
+									max_val = corrs[i][ipix];
+									max_indx = i;
+								}
+								if (corrs[i][ipix] < min_val) {
+									min_val = corrs[i][ipix]; 
+								}
+							}
+							if ((min_val == 0) ||(max_val/min_val > max_min_ratio)) {
+								patt = max_indx;
+							}
+							if (corrs[patt][ipix] < min_corr) {
+								break is_max; // too weak maximum
+							}
+//							int patt = bestpatt0[ipix];
+							lists.get(thread_num).add(new Point(ipix,patt));
+							// Below should be no conflicts as no intersect
+							Arrays.fill(mask, false);
+							for (int dy = -corr_radius; dy <= corr_radius; dy++) {
+								for (int dx = -corr_radius; dx <= corr_radius; dx++) {
+									double r2 = dx*dx + dy*dy;
+									if (r2 < corr_radius2) {
+										int ipix1 = tn.getNeibIndex(ipix, dx, dy);
+										// TODO: mark mask with continuous pixels
+										if (ipix1 >= 0) {
+											int li =  tnl.getNeibIndex(local_center, dx, dy); // should be always
+											if (li < 0) {
+												System.out.println("combineDirCorrs(): BUG1 li<0");
+											} else {
+												mask[li] = (corrs[patt][ipix1] >= min_corr) && // only consider the same pattern
+														 (corrs[full_patt_indx][ipix1] >= min_corr_full);
+											}
+										}										
+									}
+								}
+							}
+							int [] clusters = tnl.enumerateClusters(
+									mask, // boolean [] tiles,
+									null,   // int []     num_clusters,
+									false); // boolean ordered)
+							if (dbg) {
+								String[] dbg_titles={"mask","cluster"};
+								double [][] dbg_img = new double [2][mask.length];
+								for (int i = 0; i < mask.length; i++) {
+									dbg_img[0][i] = mask[i]? corrs.length:0;
+									dbg_img[1][i] = clusters[i];
+								}
+								ShowDoubleFloatArrays.showArrays(
+										dbg_img,
+										corr_diameter,
+										corr_diameter,
+										true,
+										"clusters_"+ipix,
+										dbg_titles);
+							}
+
+							int center_cluster = clusters[local_center];
+							// Copy continuous pixels from the selected pattern
+							for (int dy = -corr_radius; dy <= corr_radius; dy++) {
+								for (int dx = -corr_radius; dx <= corr_radius; dx++) {
+									int li =  tnl.getNeibIndex(local_center, dx, dy); // should be always
+									if (li < 0) {
+										System.out.println("combineDirCorrs(): BUG2 li<0");
+									} else {
+										if (clusters[li] == center_cluster) {
+											int ipix1 = tn.getNeibIndex(ipix, dx, dy);
+											if (ipix1 == dbg_pix0) {
+												System.out.println("ipix1="+ipix1);
+											}
+											if (ipix1 >= 0) {
+												bestcorr[ipix1] = corrs[patt][ipix1];
+												if (combine_full) {
+													bestcorr[ipix1] *= corrs[full_patt_indx][ipix1]/corrs[full_patt_indx][ipix];
+												}
+												bestpatt[ipix1] = patt;
+											}
+										}
+									}
+								}
+							}
+						}
+					}
+				}
+			};
+		}		      
+		ImageDtt.startAndJoin(threads);
+		// combine all lists
+		ArrayList<Point> list = new ArrayList<Point>();
+		for (int i = 0; i < lists.size(); i++) {
+			list.addAll(lists.get(i));
+		}
+		return list;
+	}
+	
 	/**
 	 * Split correlation filter results into per-pattern ones before convolution.
 	 * Temporary solution as convolution is needed only for a few found maximums
@@ -3521,28 +3881,88 @@ 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;
 		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    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
 		double    cut_frac =  0.6; // half-cut width fraction of diameter 
 		
 		int       corr_size = 128;
 		int       zoomout =   2;
-		boolean   out_normalize = true;
-		
-		GenericJTabbedDialog gd = new GenericJTabbedDialog("Create circulat pattern",1200,600);
+		boolean   out_normalize = false; // true;
+		
+		GenericJTabbedDialog gd0 = new GenericJTabbedDialog("Create circular pattern",1200,600);
+		gd0.addCheckbox    ("Evening mode",         evening_mode, "True - evening (cooling down), false - morning (warming up).");
+		gd0.showDialog();
+		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;
+			radius_in= 10; // if 0 - skip
+			edge_in =   8;
+			scale_in = -0.1; // 7;
+			scale =   -40; // black 200
+		} else {
+			radius_out= 42;
+			edge_out =  6;
+			scale_out =.08;
+			radius =   30; // 32; // 32;
+			edge=      10; //  4;
+			radius_in= 15; // if 0 - skip
+			edge_in =   8;
+			scale_in = -0.05;
+			scale =  -170; // black 200
+		}
+		
+		GenericJTabbedDialog gd = new GenericJTabbedDialog("Create circular pattern",1200,600);
 		gd.addNumericField("Half pattern size",    half_size,  0,4,"pix", "Pattern will be square, twice this side.");
 		gd.addCheckbox    ("Pattern center between pixels",      half_pix, "If false - center will be at integer pixel X/Y.");
+//		gd.addCheckbox    ("Evening mode",         evening_mode, "True - evening (cooling down), false - morning (warming up).");
 		gd.addNumericField("Radius at half height",  radius,  3,7,"pix",	".");
 		gd.addNumericField("Edge width",  edge,  3,7,"pix",	"Transition from full on to zero.");
 		gd.addNumericField("Optional inner feature radius",  radius_in,  3,7,"pix",	"Put 0 if not needed.");
 		gd.addNumericField("Inner feature edge",   edge_in,  3,7,"pix",	"Transition for the inner feature.");
-		gd.addNumericField("Inner feature scale",  scale_in,  3,7,"",	"Negative OK.");
+		gd.addNumericField("Inner feature scale",  scale_in,  3,7,"",	"Relative to the main feature.");
+		gd.addNumericField("Optional outer feature radius",  radius_out, 3,7,"pix",	"Put 0 if not needed.");
+		gd.addNumericField("Outer feature edge",   edge_out,  3,7,"pix","Transition for the outer feature.");
+		gd.addNumericField("Outer feature scale",  scale_out,  3,7,"",	"Relative to the main feature.");
 		gd.addNumericField("Overall pattern scale",  scale,  3,7,"",	"Multiply pattern by this number.");
 		gd.addCheckbox    ("Normalize",      normalize, "Make sum of all pixel equal to 1.0");
 		gd.addMessage("--- obscured round objects, trying halves ---");
@@ -3560,11 +3980,15 @@ public class OrthoMap implements Comparable <OrthoMap>, Serializable{
 		if (gd.wasCanceled()) return;
 		half_size=     (int) gd.getNextNumber();
 		half_pix=            gd.getNextBoolean();
+//		evening_mode=        gd.getNextBoolean();
 		radius=              gd.getNextNumber();
 		edge=                gd.getNextNumber();
 		radius_in=           gd.getNextNumber();
 		edge_in=             gd.getNextNumber();
 		scale_in=            gd.getNextNumber();
+		radius_out=          gd.getNextNumber();
+		edge_out=            gd.getNextNumber();
+		scale_out=           gd.getNextNumber();
 		scale=               gd.getNextNumber();
 		normalize=           gd.getNextBoolean();
 		
@@ -3577,14 +4001,17 @@ public class OrthoMap implements Comparable <OrthoMap>, Serializable{
 		
 		double [] kernel =  getConvolutionKernel();
 		int size = 2*half_size;
-		double [] pattern = generateDoubleCircularPattern (
+		double [] pattern = generateTrippleCircularPattern( // generateDoubleCircularPattern (
 				half_size,  // int       half_size,
 				half_pix,   // boolean   half_pix, // center between pixels
 				radius,     // double    radius,
 				edge,       // double    edge,
 				radius_in,  // double    radius_in, // if 0 - skip
 				edge_in,    // double    edge_in,
-				scale_in); // double    scale_in)
+				scale_in,   // double    scale_in)
+				radius_out, // double    radius_out, // if 0 - skip
+				edge_out,   // double    edge_out,
+				scale_out); // double    scale_out)
 		
 		if (normalize) {
 			double sum_pix = 0;
@@ -3620,8 +4047,10 @@ public class OrthoMap implements Comparable <OrthoMap>, Serializable{
 			}
 		}
 		
-		String pattern_name = "patterns_r"+radius+"_e"+edge+"_ir"+radius_in+
-				"ie"+edge_in+"_is"+scale_in+"_h"+halves_number+"_w"+cut_frac+
+		String pattern_name = "patterns_r"+radius+"_e"+edge+
+				"_ir"+radius_in+ "_ie"+edge_in+ "_is"+scale_in+
+				"_or"+radius_out+"_oe"+edge_out+"_os"+scale_out+
+				"_h"+halves_number+"_w"+cut_frac+
 				"_s"+scale+	"_"+size+"x"+size;
 		String [] pattern_titles = new String [patterns.length];
 		pattern_titles[0] = "full";
@@ -3726,6 +4155,44 @@ public class OrthoMap implements Comparable <OrthoMap>, Serializable{
 		return pattern;
 	}
 	
+	public static double [] generateTrippleCircularPattern (
+			int       half_size,
+			boolean   half_pix, // center between pixels
+			double    radius,
+			double    edge,
+			double    radius_in, // if 0 - skip
+			double    edge_in,
+			double    scale_in,
+			double    radius_out, // if 0 - skip
+			double    edge_out,
+			double    scale_out) {
+		double [] pattern = generateCircularPattern (
+				half_size, // int       half_size,
+				half_pix,  // boolean   half_pix, // center between pixels
+				radius,    // double    radius,
+				edge);     // double    edge) 
+		if (radius_in > 0) {
+			double [] pattern1 = generateCircularPattern (
+					half_size, // int       half_size,
+					half_pix,  // boolean   half_pix, // center between pixels
+					radius_in, // double    radius,
+					edge_in);  // double    edge)
+			for (int i = 0; i < pattern.length; i++) {
+				pattern[i] += scale_in*pattern1[i];
+			}
+		}
+		if (radius_out > 0) {
+			double [] pattern2 = generateCircularPattern (
+					half_size, // int       half_size,
+					half_pix,  // boolean   half_pix, // center between pixels
+					radius_out, // double    radius,
+					edge_out);  // double    edge)
+			for (int i = 0; i < pattern.length; i++) {
+				pattern[i] += scale_out*pattern2[i];
+			}
+		}
+		return pattern;
+	}
 	
 	public static double [] generateCircularPattern (
 			int       half_size,

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

 package com.elphel.imagej.orthomosaic;
 
+import java.awt.Point;
 import java.awt.Rectangle;
 import java.io.File;
 import java.io.FileInputStream;
@@ -12,6 +13,7 @@ import java.nio.charset.StandardCharsets;
 import java.nio.file.Files;
 import java.nio.file.Path;
 import java.nio.file.Paths;
+import java.time.LocalDateTime;
 import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.HashMap;
@@ -19,6 +21,7 @@ import java.util.List;
 import java.util.concurrent.atomic.AtomicInteger;
 
 import com.elphel.imagej.cameras.CLTParameters;
+import com.elphel.imagej.common.GenericJTabbedDialog;
 import com.elphel.imagej.common.ShowDoubleFloatArrays;
 import com.elphel.imagej.gpu.GPUTileProcessor;
 import com.elphel.imagej.gpu.TpTask;
@@ -29,23 +32,39 @@ import com.elphel.imagej.tileprocessor.TDCorrTile;
 import ij.ImagePlus;
 import ij.ImageStack;
 import ij.gui.PointRoi;
+import ij.process.FloatPolygon;
 
 
 public class OrthoMapsCollection  implements Serializable{
 	private static final long serialVersionUID = 1L;
 	public static final String [] KEY_DIRS= {"rootDirectory", // from EyesisCorrectionParameters
-			"sourceDirectory","linkedModels","videoDirectory","x3dDirectory","resultsDirectory","scenesDirectory"};
+			"sourceDirectory","linkedModels","videoDirectory","x3dDirectory","resultsDirectory","scenesDirectory",
+			"kernelsDirectory", "patternsDirectory"};
+	
 	OrthoMap []                                 ortho_maps;
 	transient HashMap<Double,Integer>           map_index;
 	transient HashMap<String,Integer>           map_index_string;
+	transient ArrayList<AltitudeMismatchKernel> kernels;
+	transient ArrayList<GroundObjectPattern>    patterns;
+	
 	
 	private void writeObject(ObjectOutputStream oos) throws IOException { // ?
 		oos.defaultWriteObject();
+		oos.writeObject(AltitudeMismatchKernel.getKernelsDirectory());
+		oos.writeObject(kernels);
+		oos.writeObject(GroundObjectPattern.getPatternsDirectory());		
+		oos.writeObject(patterns);
 //		oos.writeObject(path);
 		// ortho_maps is not transient
 	}
+	@SuppressWarnings("unchecked")
 	private void readObject(ObjectInputStream ois) throws ClassNotFoundException, IOException {
 		ois.defaultReadObject();
+		AltitudeMismatchKernel.setKernelsDirectory((String) ois.readObject());
+		kernels = (ArrayList<AltitudeMismatchKernel>) ois.readObject();
+		GroundObjectPattern.setPatternsDirectory((String) ois.readObject());
+		patterns = (ArrayList<GroundObjectPattern>)   ois.readObject();
+		
 		reindex(); // will recreate map_index, map_index_string
 		// lla is not transient
 	}
@@ -54,20 +73,59 @@ public class OrthoMapsCollection  implements Serializable{
 			String path) {
 		if (path.endsWith(".list")) {
 			String[] scenes0 = new String[1];
-			String[] paths = getPathsAndScenesFromSourceList(path, scenes0);
+			kernels = new ArrayList<AltitudeMismatchKernel>(); 
+			patterns = new ArrayList<GroundObjectPattern>();
+			
+			String[] paths = getPathsAndScenesFromSourceList(
+					path,
+					scenes0,
+					kernels,   // ArrayList<AltitudeMismatchKernel> kernels,
+					patterns); // ArrayList<GroundObjectPattern>    patterns);
+			
 			String scenes_path = scenes0[0];
 			double [][] affine = {{1,0,0},{0,1,0}}; // maybe later calculate from mage_enuatr
 			ortho_maps = new OrthoMap[paths.length];
+			
 			for (int n = 0; n < ortho_maps.length; n++) {
 				String name = OrthoMap.getNameFromPath(paths[n]);
-//				String scene_path = getSceneDir(scenes_path, name);
 				ortho_maps[n] = new OrthoMap(paths[n]); // , scene_path);
 				ortho_maps[n].setAffine(affine);
 			}
+		} else {
+			System.out.println("OrthoMapsCollection(): path should end with \".list\"");
 		}
 		Arrays.sort(ortho_maps);
 		reindex();
 	}
+	// add update kernels, update patterns
+	public void updateKernels (
+			String path) {
+		if (path.endsWith(".list")) {
+			kernels = new ArrayList<AltitudeMismatchKernel>(); 
+			getPathsAndScenesFromSourceList(
+					path,
+					null,
+					kernels, // ArrayList<AltitudeMismatchKernel> kernels,
+					null);   // ArrayList<GroundObjectPattern>    patterns);
+		} else {
+			System.out.println("updateKernels(): path should end with \".list\"");
+		}
+	}
+	
+	public void updatePatterns (
+			String path) {
+		if (path.endsWith(".list")) {
+			patterns = new ArrayList<GroundObjectPattern>();
+			getPathsAndScenesFromSourceList(
+					path,
+					null,
+					null, // ArrayList<AltitudeMismatchKernel> kernels,
+					patterns);   // ArrayList<GroundObjectPattern>    patterns);
+		} else {
+			System.out.println("updatePatterns(): path should end with \".list\"");
+		}
+	}
+	
 	
 	static String getSceneDir(String scenes_path, String name) {
 		File [] scene_dirs = (new File(scenes_path)).listFiles(); // may contain non-directories, will be filtered by filterScenes
@@ -125,16 +183,27 @@ public class OrthoMapsCollection  implements Serializable{
 		for (int n = 0; n < ortho_maps.length; n++) {
 			ortho_maps[n].updateLLA();
 		}
+		updateAGL();
+	}
+	
+	public void updateAGL() {
+		for (int n = 0; n < ortho_maps.length; n++) {
+			ortho_maps[n].agl = Double.NaN;
+			ortho_maps[n].agl = ortho_maps[n].getAGL();
+		}		
 	}
 	
+	/*
 	public static String[] getPathsFromSorceList(
 			String files_list) {
 		return getPathsAndScenesFromSourceList(files_list, null);
 	}
-
+    */
 	public static String[] getPathsAndScenesFromSourceList(
 			String files_list,
-			String[] scenes0) {
+			String[] scenes0,
+			ArrayList<AltitudeMismatchKernel> kernels,
+			ArrayList<GroundObjectPattern>    patterns) {
 		List<String> lines;
 		List<String> rel_files = new ArrayList<String>(); 
 		Path seq_path = Paths.get(files_list);
@@ -160,6 +229,22 @@ public class OrthoMapsCollection  implements Serializable{
 						}
 						System.out.println("*********** Unknown SET: "+tokens[1]+" in line: "+line);
 					}
+				} else if ((tokens.length > 0) && (tokens[0].toUpperCase().equals("KERNEL"))) {
+					if ((kernels != null) && (tokens.length > 4)) {
+						kernels.add(new AltitudeMismatchKernel(
+								tokens[1],
+								Integer.parseInt(tokens[2]),
+								Double.parseDouble(tokens[3]),
+								Double.parseDouble(tokens[4])));
+					}
+				} else if ((tokens.length > 0) && (tokens[0].toUpperCase().equals("PATTERN"))) {
+					if ((patterns != null) && (tokens.length > 4)) {
+						patterns.add(new GroundObjectPattern(
+								tokens[1],
+								Integer.parseInt(tokens[2]),
+								tokens[3],
+								LocalDateTime.parse(tokens[4])));
+					}
 				} else if ((tokens.length == 1) && (tokens[0].length() > 0)) {
 					rel_files.add(tokens[0]);
 				}
@@ -185,6 +270,21 @@ public class OrthoMapsCollection  implements Serializable{
 				scenes0[0]=(base_path.resolve(Paths.get(dir_map.get("scenesDirectory")))).toString();
 			}
 		}
+		
+		String kernelsDirectory = base_path.toString();
+		// set sourceDirectory: 
+		if (dir_map.containsKey("kernelsDirectory")) {
+			kernelsDirectory=(base_path.resolve(Paths.get(dir_map.get("kernelsDirectory")))).toString();
+		}
+		AltitudeMismatchKernel.setKernelsDirectory(kernelsDirectory);
+		
+		String patternsDirectory = base_path.toString();
+		// set sourceDirectory: 
+		if (dir_map.containsKey("patternsDirectory")) {
+			patternsDirectory=(base_path.resolve(Paths.get(dir_map.get("patternsDirectory")))).toString();
+		}
+		GroundObjectPattern.setPatternsDirectory(patternsDirectory);
+		
 		return paths;
 	}
 	
@@ -197,8 +297,9 @@ public class OrthoMapsCollection  implements Serializable{
 	 * @return {{min_x,max_x},{min_y, max_y}} relative to the origin of the first image
 	 */
 	public int [][] getBoundsPixels(
-			int zoom_level){ // maps[0] as a reference
-		double [][] bounds_meters = getBoundsMeters();
+			int zoom_level, // maps[0] as a reference
+			int [] indices) {
+		double [][] bounds_meters = getBoundsMeters(indices);
 		double pix_size = OrthoMap.getPixelSizeMeters (zoom_level);
 		int [][] bounds_pix = new int[2][2];
 		for (int n = 0; n < bounds_pix.length; n++) {
@@ -207,13 +308,17 @@ public class OrthoMapsCollection  implements Serializable{
 		}
 		return bounds_pix;
 	}
-	
+	public int [][] getBoundsPixels(
+			int zoom_level) { // maps[0] as a reference
+		return getBoundsPixels(zoom_level, null);
+	}
 	/**
 	 * Get rectified bounds of all provided ortho images relative to the origin (vertical
 	 * point) of the first one in meters
 	 * @return {{min_x,max_x},{min_y,max_y}} bounds that include all provided maps
 	 *         relative to the origin (vertical point) of the first image
 	 */
+	/*
 	public double [][] getBoundsMeters(){ // maps[0] as a reference
 		double [][] bounds = ortho_maps[0].getBoundsMeters(true);
 		for (int nmap = 1; nmap < ortho_maps.length; nmap++) {
@@ -227,6 +332,39 @@ public class OrthoMapsCollection  implements Serializable{
 		}
 		return bounds;
 	}
+	*/
+	public double [][] getBoundsMeters(){ // maps[0] as a reference
+		return getBoundsMeters(null);
+	}
+	/**
+	 * Get rectified bounds of all (if indices==null) or selected by indices[] 
+	 * provided ortho images relative to the origin (vertical
+	 * point) of the first one in meters
+	 * @param indices - image indices to process or null to process all images
+	 * @return {{min_x,max_x},{min_y,max_y}} bounds that include all provided maps
+	 *         relative to the origin (vertical point) of the first image
+	 */
+
+	public double [][] getBoundsMeters(int [] indices){ // maps[0] as a reference
+		if (indices == null) {
+			indices = new int [ortho_maps.length];
+			for (int i = 0; i < indices.length; i++) {
+				indices[i] = i;
+			}
+		}
+		double [][] bounds = ortho_maps[indices[0]].getBoundsMeters(true);
+		for (int imap = 1; imap < indices.length; imap++) {
+			int nmap = indices[imap];
+			double [][] bounds_other = ortho_maps[nmap].getBoundsMeters(true);
+			double [] enuOffset = ortho_maps[indices[0]].enuOffsetTo(ortho_maps[nmap]);
+			double [] rd = {enuOffset[0], -enuOffset[1]}; // {right,down} of the image 
+			for (int n = 0; n < bounds.length; n++) {
+				bounds[n][0] = Math.min(bounds[n][0],bounds_other[n][0]+ rd[n]);
+				bounds[n][1] = Math.max(bounds[n][1],bounds_other[n][1]+ rd[n]);
+			}
+		}
+		return bounds;
+	}
 
 	/**
 	 * Get rectified overlap bounds of two provided ortho images relative to the origin (vertical
@@ -265,11 +403,14 @@ public class OrthoMapsCollection  implements Serializable{
 			boolean     use_alt,
 			boolean     show_centers,
 			int         zoom_level,
+			int         temp_mode, // 0 - do nothing, 1 - equalize average,2 - try to correct
 			int []      origin){
 		return renderMulti (
 				title,        // String        title,
-				use_alt, //boolean       use_alt,
+				use_alt,      // boolean       use_alt,
 				null,         // int []        indices, // null or which indices to use (normally just 2 for pairwise comparison)
+				false,        // bounds_to_indices, // boolean       bounds_to_indices,
+				temp_mode,    // int           temp_mode, // 0 - do nothing, 1 - equalize average,2 - try to correct
 				null,         // double [][][] affines, // null or [indices.length][2][3]
 				null,         // FineXYCorr    warp,
 				show_centers, // boolean       show_centers,
@@ -281,16 +422,20 @@ public class OrthoMapsCollection  implements Serializable{
 			String        title,
 			boolean       use_alt,
 			int []        indices, // null or which indices to use (normally just 2 for pairwise comparison)
+			boolean       bounds_to_indices,
+			int           temp_mode, // 0 - do nothing, 1 - equalize average,2 - try to correct
 			double [][][] affines, // null or [indices.length][2][3] 
 			FineXYCorr    warp,    // use for a single pair only
 			boolean       show_centers,
 			int           zoom_level,
 			int []        origin){
 		int []     wh = new int[2];
+//		boolean       bounds_to_indices = true;
 		double [][] centers = new double [(indices !=null)? indices.length: ortho_maps.length][];
 		float [][] multi = renderMulti (
 				use_alt,    // boolean     use_alt,
 				indices,    // int []        indices, // null or which indices to use (normally just 2 for pairwise comparison)
+				bounds_to_indices, // boolean       bounds_to_indices,
 				affines,    // double [][][] affines, // null or [indices.length][2][3]
 				warp,       // FineXYCorr    warp,,
 				zoom_level, // int         zoom_level,
@@ -312,9 +457,18 @@ public class OrthoMapsCollection  implements Serializable{
 			int map0= (indices != null)? indices[0] : 0;
 			if (!use_alt) {
 				for (int n = 1; n < num_images; n++) {
+                    //temp_mode, // 0 - do nothing, 1 - equalize average,2 - try to correct
 					int mapn= (indices != null)? indices[n] : n;
-					double offs = ortho_maps[mapn].getTemperature()-ortho_maps[mapn].getAveragePixel()
+					double offs = 0;
+					switch (temp_mode) {
+					case 1:
+						offs = ortho_maps[map0].getAveragePixel()-ortho_maps[mapn].getAveragePixel();
+						break;
+					case 2:
+						offs = ortho_maps[mapn].getTemperature()-ortho_maps[mapn].getAveragePixel()
 								-(ortho_maps[map0].getTemperature()-ortho_maps[map0].getAveragePixel());
+						break;
+					}
 					float foffs= (float) offs;
 					for (int i = 0; i < extra_multi[n].length; i++) if (!Float.isNaN(extra_multi[n][i])) {
 						extra_multi[n][i]+= foffs;
@@ -342,7 +496,9 @@ public class OrthoMapsCollection  implements Serializable{
         	roi.setOptions("label");
         	imp.setRoi(roi);
         }
+        imp.show(); // debugging
         return imp;
+        
 	}
 	
 	
@@ -367,6 +523,7 @@ public class OrthoMapsCollection  implements Serializable{
 		return renderMulti (
 				use_alt,    // boolean       use_alt,
 				null,       // int []        indices,
+				false,      // boolean       bounds_to_indices,
 				null,       // double [][][] affines,
 				null,       // FineXYCorr    warp,
 				zoom_level, // int           zoom_level,
@@ -374,9 +531,11 @@ public class OrthoMapsCollection  implements Serializable{
 				origin,     // int []        origin, // maps[0] as a reference
 				centers);   // double [][]   centers)
 	}
+	
 	public float [][] renderMulti (
 			boolean       use_alt,
 			int []        indices, // null or which indices to use (normally just 2 for pairwise comparison)
+			boolean       bounds_to_indices,
 			double [][][] affines, // null or [indices.length][2][3] 
 			FineXYCorr    warp,
 			int           zoom_level,
@@ -385,7 +544,8 @@ public class OrthoMapsCollection  implements Serializable{
 			double [][]   centers){
 		final int dbg_x=2783, dbg_y=-5228;
 		int [][] bounds = getBoundsPixels( // should be for rectified, {-bounds[0][0], -bounds[0][1]} - exact center
-				zoom_level);
+				zoom_level,
+				bounds_to_indices? indices: null); 
 		int width =  bounds[0][1] - bounds[0][0]; // bounds[x][0] - negative 
 		int height = bounds[1][1] - bounds[1][0];
 		if (wh != null) {
@@ -416,7 +576,7 @@ public class OrthoMapsCollection  implements Serializable{
 //					ortho_maps[nmap].getBoundsMeters(true, affines[indx]): // use provided affine
 //						ortho_maps[nmap].getBoundsMeters(true);
 			double [][] mbounds = ortho_maps[nmap].getBoundsMeters(true); // keep original bounds
-			double [] enu_offset = ortho_maps[0].enuOffsetTo(ortho_maps[nmap]);
+			double [] enu_offset = ortho_maps[indices[0]].enuOffsetTo(ortho_maps[nmap]);
 			final double [] scaled_out_center = { // xy center to apply affine to
 					-bounds[0][0] + scale * enu_offset[0],
 					-bounds[1][0] - scale * enu_offset[1]};
@@ -496,6 +656,125 @@ public class OrthoMapsCollection  implements Serializable{
 		return fpixels;
 	}
 	
+	
+	public double [][] renderMultiDouble (
+			boolean       use_alt,
+			int []        indices, // null or which indices to use (normally just 2 for pairwise comparison)
+			boolean       bounds_to_indices,
+			double [][][] affines, // null or [indices.length][2][3] 
+			FineXYCorr    warp,
+			int           zoom_level,
+			int []        wh,
+			int []        origin, // maps[0] as a reference
+			double [][]   centers){
+		final int dbg_x=2783, dbg_y=-5228;
+		int [][] bounds = getBoundsPixels( // should be for rectified, {-bounds[0][0], -bounds[0][1]} - exact center
+				zoom_level,
+				bounds_to_indices? indices: null); 
+		int width =  bounds[0][1] - bounds[0][0]; // bounds[x][0] - negative 
+		int height = bounds[1][1] - bounds[1][0];
+		if (wh != null) {
+			wh[0] = width;
+			wh[1] = height;
+		}
+		if (origin != null) {
+			origin[0] = -bounds[0][0];
+			origin[1] = -bounds[1][0];
+		}
+		if (indices == null) {
+			indices = new int [ortho_maps.length];
+			for (int i = 0; i < indices.length; i++) {
+				indices[i] = i;
+			}
+		}
+		
+		final double [][] dpixels = new double [indices.length][width * height];
+		for (int indx = 0; indx < indices.length; indx++) { //:indices) { // = 0; nmap< ortho_maps.length; nmap++) {
+			final int findx= indx;
+			final int nmap = indices[indx]; // nmap;
+			Arrays.fill(dpixels[findx], Float.NaN);
+			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
+		// metric bounds of the rectified image relative to its origin
+			double [][] mbounds = ortho_maps[nmap].getBoundsMeters(true); // keep original bounds
+			double [] enu_offset = ortho_maps[indices[0]].enuOffsetTo(ortho_maps[nmap]);
+			final double [] scaled_out_center = { // xy center to apply affine to
+					-bounds[0][0] + scale * enu_offset[0],
+					-bounds[1][0] - scale * enu_offset[1]};
+			if (centers != null) {
+				centers[findx] = scaled_out_center;
+			}
+			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 = (affines !=null) ? affines[indx]: ortho_maps[nmap].affine; // only here use provided
+			final int src_width = use_alt? ortho_maps[nmap].getAltData().width: ortho_maps[nmap].getImageData().width;
+			final int src_height = use_alt? ortho_maps[nmap].getAltData().height : ortho_maps[nmap].getImageData().height;
+			final float [] src_img = use_alt? ortho_maps[nmap].getAltData().data : ortho_maps[nmap].getImageData().data;
+			if ((indx==0) && (warp != null)) { // set center from the first image
+				warp.setRender(
+						zoom_level, // int zoom_lev,
+						scaled_out_center[0], // double px0, // in render pixels
+						scaled_out_center[1]); // // double py0);
+			}
+			final Rectangle warp_woi =((indx==1) && (warp != null))? warp.getRenderWOI():null; 
+			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 nPix = ai.getAndIncrement(); nPix < ownd_len; nPix = ai.getAndIncrement()) {
+							int opX = nPix % ownd_width + obounds[0][0]; // absolute output pX, pY
+							int opY = nPix / ownd_width + obounds[1][0];
+							double dX = (opX - scaled_out_center[0]) /scale; // in original image scale 
+							double dY = (opY - scaled_out_center[1]) /scale;
+							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])};
+							// limit to the source image
+							if ((warp_woi != null) && (warp_woi.contains(opX,opY))) {
+								if ((opX==dbg_x) && (opY==dbg_y)) {
+									System.out.println("opX="+opX+", opy="+opY);
+								}
+								double [] dxy = warp.getWarp(opX,opY);
+								xy_src[0] += dxy[0];
+								xy_src[1] += dxy[1];
+							}
+							if  ((xy_src[0] >= 0) && (xy_src[0] < (src_width-1)) &&
+									(xy_src[1] >= 0) && (xy_src[1] < (src_height-1))) { 
+								int [] ixy_src = {(int) Math.floor(xy_src[0]), (int)Math.floor(xy_src[1]) };
+								double [] kxy = {xy_src[0]-ixy_src[0], xy_src[1]-ixy_src[1]}; 
+								int indx00 = ixy_src[0] + ixy_src[1] * src_width; 
+								double d00 = src_img[indx00];
+								if (!Double.isNaN(d00)) {
+									double d01 = src_img[indx00 + 1];
+									double d10 = src_img[indx00 + src_width];
+									double d11 = src_img[indx00 + src_width + 1];
+									double d = d00*(1.0 - kxy[0])*(1.0 - kxy[1])+
+											d01*       kxy[0] *(1.0 - kxy[1])+
+											d10*(1.0 - kxy[0])*       kxy[1]+
+											d11*       kxy[0] *       kxy[1];
+									dpixels[findx][opX + opY*width] = (float) d;
+								}
+							}
+						}
+					}
+				};
+			}		      
+			ImageDtt.startAndJoin(threads);
+		}
+		return dpixels;
+	}
+
+	
 	public int getIndex(String sindx) {
 		return map_index_string.get(sindx);
 	}
@@ -1313,5 +1592,361 @@ public class OrthoMapsCollection  implements Serializable{
 		return vf_out;
 	}
 	
+	public ImagePlus patterMatchDualWrap (
+			int []        indices, // null or which indices to use (normally just 2 for pairwise comparison)
+			double [][][] affines, // null or [indices.length][2][3] 
+			FineXYCorr    warp) {    // use for a single pair only
+		
+		double []     min_corrs = {0.01,0.005}; // morning/evening
+		double        phaseCoeff =        0.5;
+		double        min_corr_full_rel = 0.75;
+		double        full_preference  =  1.4;
+		double        max_min_ratio =     3.0;
+		boolean       combine_full =      true; 
+		int           corr_size =       128; // pix
+		double        adv_radius =       30.0; // cm 
+		String        object_type =      "TM62";
+		double        scale_warp =        1.0; // use 4?
+		int           debugLevel =        1;
+		
+		GenericJTabbedDialog gd = new GenericJTabbedDialog("Correlate two images with patterns",1200,500);
+		gd.addNumericField("Minimal correlation, first",        min_corrs[0],  5,7,"","Minimal correlation value to keep, first scene.");
+		gd.addNumericField("Minimal correlation, second",       min_corrs[1],  5,7,"","Minimal correlation value to keep, secondscene.");
+		gd.addNumericField("Phase correlation coefficient",     phaseCoeff,  3,7,"","1.0 - pure phase correlation, 0.0 - regular correlation.");
+		gd.addNumericField("Minimal relative full correlation", min_corr_full_rel,  5,7,"","Minimal relative correlation value with full circular pattern to keep.");
+		gd.addNumericField("Prefer full pattern",               full_preference,  3,7,"","Prefer full pattern to partial; scale by this value.");
+		gd.addNumericField("Max/min halves ratio",              max_min_ratio,  3,7,"","Ratio of halves best/worst to use half-pattern.");
+		gd.addCheckbox    ("Combine with full pattern",         combine_full, "Multiply by normalized full pattern correlation maximum.");
+		gd.addNumericField("Correlation size",                  corr_size,  0,4,"pix", "Should be power of 2.");
+		gd.addNumericField("Adversarial distance",              adv_radius,  1,6,"pix", "Suppress weaker if they have closer strong ones.");
+		gd.addStringField ("Object type",                       object_type, 20,"Object type/name.");
+		gd.addNumericField("Scale warp",                        scale_warp,  1,6,"x", "Scale second image warping.");
+		gd.addNumericField("Debug level",                       debugLevel,  0,4,"", "Debug level.");
+		gd.showDialog();
+		if (gd.wasCanceled()) return null;
+		min_corrs[0]=         gd.getNextNumber();
+		min_corrs[1]=         gd.getNextNumber();
+		phaseCoeff=           gd.getNextNumber();
+		min_corr_full_rel=    gd.getNextNumber();
+		full_preference=      gd.getNextNumber();
+		max_min_ratio=        gd.getNextNumber();		
+		combine_full =        gd.getNextBoolean();
+		corr_size=      (int) gd.getNextNumber();
+		adv_radius=           gd.getNextNumber();
+		object_type=          gd.getNextString();		
+		scale_warp =          gd.getNextNumber();
+		debugLevel=     (int) gd.getNextNumber();
+
+		return patternMatchDual (
+				indices,           // int []        indices, // null or which indices to use (normally just 2 for pairwise comparison)
+				affines,           // double [][][] affines, // null or [indices.length][2][3] 
+				warp,              // FineXYCorr    warp);
+				min_corrs,         // double []     min_corrs, // one per
+				phaseCoeff,        // double        phaseCoeff,
+				min_corr_full_rel, // double        min_corr_full_rel,
+				full_preference,   // double        full_preference,
+				max_min_ratio,     // double        max_min_ratio,
+				combine_full,      // boolean       combine_full,
+				corr_size,         // int           corr_size,
+				adv_radius,        // double        adv_radius, // 
+				object_type,       // String        object_type,
+				scale_warp,        // double        scale_warp,
+				debugLevel);       // int           debugLevel)			
+	}
+
+	public ImagePlus patternMatchDual (
+			int []        indices, // null or which indices to use (normally just 2 for pairwise comparison)
+			double [][][] affines, // null or [indices.length][2][3] 
+			FineXYCorr    warp,    // use for a single pair only
+			double []     min_corrs, // one per
+			double        phaseCoeff,
+			double        min_corr_full_rel,
+			double        full_preference,
+			double        max_min_ratio,
+			boolean       combine_full,
+			int           corr_size,
+			double        adv_radius, // 
+			String        object_type,
+			double        scale_warp,
+			int           debugLevel) {
+		warp.scale_warp = scale_warp; 
+		int       corr_radius = (int) (Math.sqrt(0.5)* adv_radius) -1 ;
+		//						String  title_match = OrthoMap.removeKnownExtension(imp_src.getTitle())+"-PATTERN_CORRS"
+    	int min_zoom_lev = Math.min(
+    			ortho_maps[indices[0]].getOriginalZoomLevel(),
+    			ortho_maps[indices[1]].getOriginalZoomLevel());
+    	int max_zoom_lev = Math.max(
+    			ortho_maps[indices[0]].getOriginalZoomLevel(),
+    			ortho_maps[indices[1]].getOriginalZoomLevel());
+		int     zoom_level = min_zoom_lev;
+		int []  wh = new int[2];
+		int []  origin = new int[2];
+		double [][] centers = new double [indices.length][];
+		double [][] dmulti = renderMultiDouble (
+				false,    // boolean     use_alt,
+				indices,    // int []        indices, // null or which indices to use (normally just 2 for pairwise comparison)
+				true, // boolean       bounds_to_indices,
+				affines,    // double [][][] affines, // null or [indices.length][2][3]
+				warp,       // FineXYCorr    warp,,
+				zoom_level, // int         zoom_level,
+				wh,         // int []      wh,
+				origin,     // int []      origin){ // maps[0] as a reference
+				centers);   // double [][] centers)
+		int width =  wh[0];
+		int height = wh[1];
+		double [][] src_marks = null;
+		/*
+		PointRoi pRoi = (PointRoi) imp_src.getRoi();
+		FloatPolygon fp = pRoi.getContainedFloatPoints();
+		if (fp != null) {
+			src_marks = new double[fp.npoints][2];
+			for (int i = 0; i < src_marks.length; i++) {
+				src_marks[i][0] = fp.xpoints[i];
+				src_marks[i][1] = fp.ypoints[i];
+			}
+		}
+		*/
+		
+//		double [] agls =       new double[indices.length];
+//		LocalDateTime [] dts = new LocalDateTime[indices.length];
+		/*
+		int [] zoom_levs =     new int[indices.length];
+		for (int scene_num = 0; scene_num < indices.length; scene_num++) {
+//			agls[n] =     ortho_maps[indices[n]].getAGL();
+//			dts[n] =      ortho_maps[indices[n]].getLocalDateTime();
+			zoom_levs[scene_num]= ortho_maps[indices[scene_num]].getOriginalZoomLevel();
+		}
+		*/
+		double [][][] patterns_all = new double [indices.length][][];
+		double [][] kernels_all = new double [indices.length][];
+		
+		GroundObjectPattern [] gops = new GroundObjectPattern[indices.length];
+		AltitudeMismatchKernel[] ak = new AltitudeMismatchKernel[indices.length]; 
+		int [] pattern_sizes = new int[indices.length];
+		String [][]  pattern_labels = new String[indices.length][];
+		double [][][] corrs_out =     new double[indices.length][][]; 
+		double [][][] convolve_out =  new double[indices.length][][]; 
+		double [][][] corr_patterns = new double[indices.length][][];
+		double [][][] filtered_corrs = new double[indices.length][][];		
+		int [] zoomout = new int[indices.length];
+		ImagePlus [] imp_corrs = new ImagePlus[indices.length];
+		double [][]   bestcorr = new double[indices.length][];
+		double [][]   fullcorr = new double[indices.length][];
+		int [][]      bestpatt = new int   [indices.length][];
+		double [] min_corrs_full = new double[indices.length];
+		ArrayList<ArrayList<Point>> object_lists = new ArrayList<ArrayList<Point>>();
+		ImagePlus [] imps_best = new ImagePlus[indices.length];
+		ImagePlus [] imps_bestpatt = new ImagePlus[indices.length];
+		double [][] convolved_merged = new double[indices.length][];
+		ImagePlus [] imps_patt_corrs = new ImagePlus[indices.length];
+		ImagePlus [] imps_patt_conv = new ImagePlus[indices.length];
+		for (int scene_num = 0; scene_num < indices.length; scene_num++) {
+			gops[scene_num] = GroundObjectPattern.getPattern(
+					object_type, // String        object_type,
+					ortho_maps[indices[scene_num]].getLocalDateTime(), // LocalDateTime utcDateTime,
+					patterns); // ArrayList<GroundObjectPattern> patterns)
+			ImagePlus imp_pattern = new ImagePlus(gops[scene_num].getPatternPath());
+			pattern_sizes[scene_num] =  imp_pattern.getWidth();
+			if (pattern_sizes[scene_num] == 0) {
+				System.out.println("testPatternCorrelate(): pattern \""+gops[scene_num].getPatternPath()+"\" is not found.");
+				return null;
+			}
+			ImageStack stack_pattern = imp_pattern.getStack();
+			int nSlices =       stack_pattern.getSize();
+			patterns_all[scene_num] =   new double[nSlices][];
+			pattern_labels[scene_num] = new String[nSlices];
+			for (int k = 0; k < patterns_all[scene_num].length; k++) {
+				pattern_labels[scene_num][k]=stack_pattern.getShortSliceLabel(k+1);
+				float [] fpixels_pattern = (float[]) stack_pattern.getPixels(k+1);
+				patterns_all[scene_num][k]=new double[fpixels_pattern.length];
+				for (int i = 0; i < fpixels_pattern.length; i++) {
+					patterns_all[scene_num][k][i] = fpixels_pattern[i];
+				}
+			}
+			ak[scene_num] = AltitudeMismatchKernel.getKernel(
+					gops[scene_num].getZoomLevel(), // zoom_level,       // int                               zoom_level,
+					gops[scene_num].getAGL(), // double                            agl_from,
+					ortho_maps[indices[scene_num]].getAGL(), // double                            agl_to,
+					kernels); // ArrayList<AltitudeMismatchKernel> kernels)
+			if (ak[scene_num] != null) {
+				String kernel_path = ak[scene_num].getKernelPath();
+				ImagePlus imp_kernel = new ImagePlus(kernel_path);
+				if (imp_kernel.getWidth() > 0) {
+					float [] kernel_pixels = (float[]) imp_kernel.getProcessor().getPixels();
+					kernels_all[scene_num] = new double[kernel_pixels.length];
+					for (int i = 0; i < kernel_pixels.length; i++) {
+						kernels_all[scene_num][i] = kernel_pixels[i];
+					}
+				}
+			}
+			corrs_out[scene_num] =     new double[patterns_all[scene_num].length][]; 
+			convolve_out[scene_num] =  new double[patterns_all[scene_num].length][]; 
+			corr_patterns[scene_num] = new double[patterns_all[scene_num].length][];
+			
+			zoomout[scene_num] = 1;
+			for (int i = zoom_level; i < gops[scene_num].getZoomLevel();i++) {
+				zoomout[scene_num] *= 2;
+			}
+			
+			for (int n = 0; n < patterns_all[scene_num].length; n++) {
+				corr_patterns[scene_num][n] = OrthoMap.patternZoomCropPad(
+						patterns_all[scene_num][n],      // double [] pattern,
+						pattern_sizes[scene_num],        // int       pattern_size,
+						corr_size,                       // int       size,
+						zoomout[scene_num],              // int       zoomout,
+						false);                          // out_normalize); // boolean   normalize) 
+				if (kernels_all[scene_num] != null) {
+					corr_patterns[scene_num][n] = OrthoMap.convolveWithKernel(
+							corr_patterns[scene_num][n], // final double [] data,
+							kernels_all[scene_num],      // final double [] kernel,
+							corr_size);                  // final int width)
+				}
+				corrs_out[scene_num][n]= OrthoMap.correlateWithPattern(
+						dmulti[scene_num],           // final double [] data,
+						width,                       // final int       width,
+						corr_size,                   // final int       psize,      // power of 2, such as 64
+						corr_patterns[scene_num][n], // final double [] pattern,    // [psize*psize]
+						false,                       // final boolean   convolve,   // convolve, not correlate
+						phaseCoeff,                  // final double    phaseCoeff,
+						debugLevel);                 // final int       debugLevel) {
+			}
+			String [] patt_titles = new String[corrs_out[scene_num].length];
+			for (int i = 0; i < patt_titles.length; i++) {
+				patt_titles[i] = "patt_"+i;
+			}
+			imp_corrs[scene_num] = ShowDoubleFloatArrays.makeArrays(
+					corrs_out[scene_num],
+					width,
+					height,
+					ortho_maps[indices[scene_num]].getName()+"-PATTERN_CORRS",				
+					patt_titles); // test_titles,
+			if (src_marks != null) {
+				PointRoi roi = new PointRoi();
+				roi.setOptions("label");
+				for (int i = 0; i < src_marks.length; i++) {
+					roi.addPoint(src_marks[i][0],src_marks[i][1]); // ,1);
+				}
+				imp_corrs[scene_num].setRoi(roi);
+			}
+			imp_corrs[scene_num].show();
+			bestcorr[scene_num] = new double [dmulti[scene_num].length];
+			fullcorr[scene_num] = new double [dmulti[scene_num].length];
+			bestpatt[scene_num] = new int [bestcorr[scene_num].length];
+			min_corrs_full[scene_num] = min_corrs[scene_num] * min_corr_full_rel;
+			
+			// TODO: scale adv_radius, corr_radius
+			object_lists.add(OrthoMap.combineDirCorrs (
+				corrs_out[scene_num],      // final double [][] corrs,
+				width,                     // final int         width,
+				fullcorr[scene_num],       // final double []   fullcorr_in,
+				bestcorr[scene_num],       // final double []   bestcorr_in
+				bestpatt[scene_num],       // final int []      bestpatt_in,
+				min_corrs[scene_num],      // final double      min_corr,
+				min_corrs_full[scene_num], // final double      min_corr_full,
+				full_preference,           // final double      full_preference,
+				max_min_ratio,             // final double      max_min_ratio,
+				combine_full,              // final boolean     combine_full,    // multiply by normalized full pattern correlation maximum
+				adv_radius,                // final double      adv_radius,
+				corr_radius));             // final int         corr_radius)
+			System.out.println("patternMatchDual(): Found "+object_lists.get(scene_num).size()+" candidates for scene #"+scene_num);
+			imps_best[scene_num] = ShowDoubleFloatArrays.makeArrays(
+					bestcorr[scene_num],
+					width,
+					height,
+					ortho_maps[indices[scene_num]].getName()+"-BEST_CORR");				
+			double [] dbg_bestpatt = new double [bestpatt[scene_num].length];
+			Arrays.fill(dbg_bestpatt, Double.NaN);
+			for (int i = 0; i <bestpatt[scene_num].length; i++) {
+				if (bestpatt[scene_num][i] >=0) {
+					dbg_bestpatt[i] = bestpatt[scene_num][i];
+				}
+			}
+			imps_bestpatt[scene_num] = ShowDoubleFloatArrays.makeArrays(
+					dbg_bestpatt,
+					width,
+					height,
+					ortho_maps[indices[scene_num]].getName()+"-BEST_PATT");				
+			if (src_marks != null) {
+				PointRoi roi = new PointRoi();
+				roi.setOptions("label");
+				for (int i = 0; i < src_marks.length; i++) {
+					roi.addPoint(src_marks[i][0],src_marks[i][1]); // ,1);
+				}
+				imps_best[scene_num].setRoi(roi);
+				imps_bestpatt[scene_num].setRoi(roi);
+			}
+			imps_best[scene_num].show();
+			imps_bestpatt[scene_num].show();
+			filtered_corrs[scene_num]= OrthoMap.splitPattenCorrelations(
+					corr_patterns[scene_num].length, // final int         num_patterns,
+					bestcorr[scene_num],        // final double []   bestcorr,
+					bestpatt[scene_num]);       // final int []      bestpatt)		
+
+			for (int n = 0; n < corr_patterns[scene_num].length; n++) {
+				convolve_out[scene_num][n]= OrthoMap.correlateWithPattern(
+						filtered_corrs[scene_num][n],// corrs_out[n], // final double [] data,
+						width,            // final int       width,
+						corr_size,        // final int       psize,      // power of 2, such as 64
+						corr_patterns[scene_num][n], // final double [] pattern,    // [psize*psize]
+						true,             // final boolean   convolve,   // convolve, not correlate
+						phaseCoeff,       // final double    phaseCoeff,
+						debugLevel);      // final int       debugLevel) {
+			}
+			convolved_merged[scene_num] = OrthoMap.mergePattenConvolutions(
+					convolve_out[scene_num]); // final double [][] convs)
+			String [] rslt_titles =new String [corr_patterns[scene_num].length+2]; 
+			double [][] rslt = new double [corr_patterns[scene_num].length + 2][]; // ]{data, corr_out};
+			double [][] conv_rslt = new double [corr_patterns[scene_num].length + 2][]; // ]{data, corr_out};
+			rslt[0] = dmulti[scene_num];
+			conv_rslt[0] = dmulti[scene_num];
+			rslt_titles[0] = "original";
+			rslt[1] = bestcorr[scene_num];
+			conv_rslt[1] = convolved_merged[scene_num];
+			rslt_titles[1] = "combined";
+			for (int i = 0; i < corr_patterns[scene_num].length; i++) {
+				rslt[i+2] = filtered_corrs[scene_num][i];
+				conv_rslt[i+2] = convolve_out[scene_num][i];
+				rslt_titles[i+2] = "corr_"+pattern_labels[scene_num][i];
+			}
+			imps_patt_corrs[scene_num] = ShowDoubleFloatArrays.makeArrays(
+					rslt,
+					width,
+					height,
+					ortho_maps[indices[scene_num]].getName()+"-PATTERN_CORR",
+					rslt_titles);
+			if (src_marks != null) {
+				PointRoi roi = new PointRoi();
+				roi.setOptions("label");
+				for (int i = 0; i < src_marks.length; i++) {
+					roi.addPoint(src_marks[i][0],src_marks[i][1]); // ,1);
+				}
+				imps_patt_corrs[scene_num].setRoi(roi);
+			}
+			imps_patt_corrs[scene_num].show();
+			
+			imps_patt_conv[scene_num] = ShowDoubleFloatArrays.makeArrays(
+					conv_rslt,
+					width,
+					height,
+					ortho_maps[indices[scene_num]].getName()+"-PATTERN_CORR_CONVOLVE_min_corr"+min_corrs[scene_num],
+					rslt_titles);
+			if (src_marks != null) {
+				PointRoi roi = new PointRoi();
+				roi.setOptions("label");
+				for (int i = 0; i < src_marks.length; i++) {
+					roi.addPoint(src_marks[i][0],src_marks[i][1]); // ,1);
+				}
+				imps_patt_conv[scene_num].setRoi(roi);
+			}
+			imps_patt_conv[scene_num].show();
+			System.out.println("patternMatchDual(): correlation done for scene "+scene_num);
+			
+		}
+		System.out.println("patternMatchDual(): all correlations DONE");
+	
+		return null;
+	}
+	
+	
 	
 }