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;
+}