Extracting radial pattern

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

@@ -67,6 +67,20 @@ public class OrthoMap implements Comparable <OrthoMap>, Serializable{
 			"/media/elphel/NVME/lwir16-proc/ortho_videos/kernel_50_100.tiff"
 	};
 
+	public static String pattern_dir= "/media/elphel/SSD3-4GB/lwir16-proc/ortho_videos/debug/mines/pattern_25m_zoom1/synthetic/";
+	public static String [] pattern_files=
+		{"patterns_50m_zoom1_200x200.tiff",
+		"patterns_50m_evening_zoom1_200x200.tiff",
+		"patterns_50m_evening_01_zoom1_200x200_00.tiff",
+		"patterns_50m_evening_02_zoom1_200x200_00.tiff",
+		"patterns_50m_evening_03_zoom1_200x200_00.tiff",
+		"patterns_50m_evening_04_zoom1_200x200_00.tiff",
+		"patterns_50m_evening_05_zoom1_200x200_00.tiff",
+		"mine1_zoom0.tiff",
+		"mine2_zoom0.tiff",
+		"mine3_zoom0.tiff",
+		"mine4_zoom0.tiff",
+		"mine6_zoom0.tiff"};
 	
 	
 	public static final String ALT_SUFFIX = "-ALT";
@@ -1095,9 +1109,12 @@ public class OrthoMap implements Comparable <OrthoMap>, Serializable{
 	 * @return square kernel as a 1-d double array or null
 	 */
 	public static double [] getConvolutionKernel() {
+		return getConvolutionKernel(kernel_paths.length-1);
+	}
+	public static double [] getConvolutionKernel(int choice) {
 		String kernel_path = null;
 		GenericJTabbedDialog gds = new GenericJTabbedDialog("Select kernel path",1200,400);
-		gds.addChoice("Kernel path:", kernel_paths, kernel_paths[kernel_paths.length-1]);
+		gds.addChoice("Kernel path:", kernel_paths, kernel_paths[choice]);
 		gds.showDialog();
 		if (gds.wasCanceled()) return null;
 		int kernel_index = gds.getNextChoiceIndex();
@@ -3038,6 +3055,7 @@ public class OrthoMap implements Comparable <OrthoMap>, Serializable{
 			double [] wnd_in,
 			double    phaseCoeff) {
 //		phaseCoeff = 0.5;
+		boolean dbg=false;
 		double [] data = data_in.clone();
 		double [] pattern = pattern_in.clone();
 		double [] wnd = wnd_in.clone();
@@ -3047,7 +3065,7 @@ public class OrthoMap implements Comparable <OrthoMap>, Serializable{
 		for (int i = 0; i < data.length; i++) {
 			data[i] *= wnd[i];
 		}
-		{
+		if (dbg) {
 			String [] rslt_titles= {"original","window","windowed","pattern"};
 			ShowDoubleFloatArrays.showArrays(
 					new double[][] {data_orig, wnd, data, pattern},
@@ -3096,7 +3114,7 @@ public class OrthoMap implements Comparable <OrthoMap>, Serializable{
 			}
 		}
 		
-		{
+		if (dbg) {
 			String [] rslt_titles= {"corr", "original","window","windowed","pattern"};
 			ShowDoubleFloatArrays.showArrays(
 					new double[][] {corr_out, data_orig, wnd, data_orig2, pattern_orig},
@@ -3106,7 +3124,7 @@ public class OrthoMap implements Comparable <OrthoMap>, Serializable{
 					convolve?"output_conv":("output_corr"+phaseCoeff),
 					rslt_titles);
 		}
-		System.out.println("testPhaseCorr() done");
+		if (dbg) System.out.println("testPhaseCorr() done");
 		return corr_out;
 	}
 	
@@ -3192,8 +3210,8 @@ public class OrthoMap implements Comparable <OrthoMap>, Serializable{
 	
 	public static void testPatternCorrelate(
 			ImagePlus imp_src) {
+		/*
 		String pattern_dir= "/media/elphel/SSD3-4GB/lwir16-proc/ortho_videos/debug/mines/pattern_25m_zoom1/synthetic/";
-//		String pattern_file= "patterns_50m_zoom1_200x200.tiff";
 		String [] pattern_files=
 			{"patterns_50m_zoom1_200x200.tiff",
 			"patterns_50m_evening_zoom1_200x200.tiff",
@@ -3202,6 +3220,7 @@ public class OrthoMap implements Comparable <OrthoMap>, Serializable{
 			"patterns_50m_evening_03_zoom1_200x200_00.tiff",
 			"patterns_50m_evening_04_zoom1_200x200_00.tiff",
 			"patterns_50m_evening_05_zoom1_200x200_00.tiff"};
+      */			
 		int       zoomout =     2; // 1;
 		int       corr_size = 128; // 256;
 		double    phaseCoeff = 0.5;
@@ -3297,7 +3316,6 @@ public class OrthoMap implements Comparable <OrthoMap>, Serializable{
 
 		double [][] corrs_out =     new double[patterns.length][]; 
 		double [][] convolve_out =  new double[patterns.length][]; 
-//		double [][] lim_corr =      new double[patterns.length][];
 		double [][] corr_patterns = new double[patterns.length][];
 		for (int n = 0; n < patterns.length; n++) {
 			corr_patterns[n] = patternZoomCropPad(
@@ -3331,6 +3349,11 @@ public class OrthoMap implements Comparable <OrthoMap>, Serializable{
 				height,
 				removeKnownExtension(imp_src.getTitle())+"-PATTERN_CORRS",				
 				patt_titles); // test_titles,
+		
+		
+		
+		
+		
 		if (src_marks != null) {
 			PointRoi roi = new PointRoi();
 			roi.setOptions("label");
@@ -3881,40 +3904,16 @@ public class OrthoMap implements Comparable <OrthoMap>, Serializable{
 	public static void testPatternGenerate() {
 		int       half_size = 100;
 		boolean   half_pix = false; // center between pixels
-		boolean   evening_mode = false; // glare around object, use radius 
-		double    radius_out= 42;
-		double    edge_out =  6;
-		double    scale_out = 1.5;
+		boolean   evening_mode = true; // false; // glare around object, use radius 
 		double    radius =   30; // 32; // 32;
 		double    edge=      15; //  4;
 		double    radius_in= 15; // if 0 - skip
 		double    edge_in =   8;
 		double    scale_in = -0.05;
+		double    radius_out= 42;
+		double    edge_out =  6;
+		double    scale_out = 1.5;
 		double    scale =  -200; // black 200
-		if (evening_mode) {
-			radius_out= 42;
-			edge_out =  8;
-			scale_out =-1.5; // relative to scale
-			radius =   30; // 32; // 32;
-			edge=      15; //  4;
-			radius_in= 10; // if 0 - skip
-			edge_in =   8;
-			scale_in = -0.7;
-			scale =   -40; // black 200
-			
-		} else {
-			radius_out= 42;
-			edge_out =  6;
-			scale_out =.08;
-			radius =   30; // 32; // 32;
-			edge=      15; //  4;
-			radius_in= 15; // if 0 - skip
-			edge_in =   8;
-			scale_in = -0.05;
-			scale =  -170; // black 200
-		}
-		
-		
 		
 		boolean   normalize = false;
 		int       halves_number = 8; // hidden mines - number of diameter cuts
@@ -3930,15 +3929,15 @@ public class OrthoMap implements Comparable <OrthoMap>, Serializable{
 		if (gd0.wasCanceled()) return;
 		evening_mode=        gd0.getNextBoolean();
 		if (evening_mode) {
-			radius_out= 62; // 42;
-			edge_out =  40; // 8;
-			scale_out =-1.5; // relative to scale
 			radius =   30; // 32; // 32;
-			edge=       24; // 8; //  4;
+			edge=       8; // 8; //  4;
 			radius_in= 10; // if 0 - skip
 			edge_in =   8;
-			scale_in = -0.1; // 7;
-			scale =   -40; // black 200
+			scale_in = 0; // -0.1; // 7;
+			radius_out= 45; // 42;
+			edge_out =  30; // 8;
+			scale_out =-1.0; // relative to scale
+			scale =   -60; // black 200
 		} else {
 			radius_out= 42;
 			edge_out =  6;

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

@@ -396,6 +396,64 @@ public class OrthoMapsCollection  implements Serializable{
 		return bounds;
 	}
 	
+	/**
+	 * Use object coordinates (now metric) on the composite image to
+	 * determine corresponding pixel coordinates of the source images
+	 * @param objects ArrayList of objects with the scene name and xy coordinates
+	 *                in the composite image. Will fill in pixel coordinates of the objects 
+	 * @param zoom_level zoom level of the composite image
+	 */
+	public void reverseRender(
+			ArrayList<ObjectLocation> objects,
+			int         zoom_level){
+		int [][] bounds = getBoundsPixels( // should be for rectified, {-bounds[0][0], -bounds[0][1]} - exact center
+				zoom_level,
+				null); 
+		int width =  bounds[0][1] - bounds[0][0]; // bounds[x][0] - negative 
+		int height = bounds[1][1] - bounds[1][0];
+		/*
+		int [] indices = new int [ortho_maps.length]; //maybe will get rid of
+		for (int i = 0; i < indices.length; i++) {
+			indices[i] = i;
+		}
+		*/
+		final int reference_index = 0; 
+		for (ObjectLocation ol: objects) {
+			int nmap =getIndex(ol.getName());
+			final double scale = 1.0/OrthoMap.getPixelSizeMeters(zoom_level);
+			final double src_scale = 1.0/OrthoMap.getPixelSizeMeters(ortho_maps[nmap].orig_zoom_level); // pix per meter
+			double [][] mbounds = ortho_maps[nmap].getBoundsMeters(true); // keep original bounds
+			double [] enu_offset = ortho_maps[reference_index].enuOffsetTo(ortho_maps[nmap]);
+			double [] scaled_out_center = { // xy center to apply affine to
+					-bounds[0][0] + scale * enu_offset[0],
+					-bounds[1][0] - scale * enu_offset[1]};
+			double [] metric_center = { // back to meters to match objects
+					scaled_out_center[0]/scale,
+					scaled_out_center[1]/scale};
+			double dX = ol.getMetric()[0]-metric_center[0]; // matching dX, dY in renderMulti()
+			double dY = ol.getMetric()[1]-metric_center[1];
+			
+//			final int [][] obounds = new int [2][2]; // output (rectified, combined) image bounds, relative to thje top-left
+//			for (int n = 0; n< 2; n++) {
+//				obounds[n][0] = (int) Math.floor(scaled_out_center[n] + scale*mbounds[n][0]);
+//				obounds[n][1] = (int) Math.ceil (scaled_out_center[n] + scale*mbounds[n][1]);
+//			}
+			// Output window size (keep original affine - OK if will not exactly fit)
+//			final int ownd_width =  obounds[0][1] - obounds[0][0];
+//			final int ownd_height = obounds[1][1] - obounds[1][0];
+//			final int ownd_len = ownd_width * ownd_height;
+			double [][] src_bounds=ortho_maps[nmap].getBoundsMeters (true); // using original affines
+			final double [] src_center = {-src_bounds[0][0],-src_bounds[1][0]}; // x,y center offset in the source image
+			final double [][] affine = ortho_maps[nmap].affine; // only here use provided
+//			final int src_width =      ortho_maps[nmap].getImageData().width;
+//			final int src_height =     ortho_maps[nmap].getImageData().height;
+//			final float [] src_img =   ortho_maps[nmap].getImageData().data; // FIXME: will not use
+			double [] xy_src = { // pixels of the source image
+					src_scale * (affine[0][0]*dX + affine[0][1]*dY + affine[0][2] + src_center[0]),
+					src_scale * (affine[1][0]*dX + affine[1][1]*dY + affine[1][2] + src_center[1])};
+			ol.setPixels(xy_src);
+		}
+	}
 	
 	
 	public ImagePlus renderMulti (