DATI and pattern matching

src/main/java/com/elphel/imagej/common/DoubleFHT.java

@@ -418,7 +418,54 @@ public class DoubleFHT  {
     	 return first;
      }
 
+     /**
+      * Transform pattern once, and then use FD of the pattern for each overlapping image tile
+      * @param second pattern to be transform
+      * @return transformed pattern ( the original is also modified)
+      */
+     public double [] transformPattern ( // new
+    		 double [] second ){  //null-OK
+    	 updateMaxN(second);
+    	 swapQuadrants(second);
+    	 if (!transform(second,false)) return null; // direct FHT
+    	 return second;
+     }
+
+     /**
+      * Phase correlate with pattern, that is transformed separately with transformPattern()
+      * @param first square array to be phase-correlated, modified but not with result!
+      * @param secondFD   pattern already transformed to FD 
+      * @param phaseCoeff 0 - regular correlation, 1.0 - pure phase correlation
+      * @param filter     frequency filter or null
+      * @param first_save null or array to accommodate FD of the first array before updating it with correlation
+      * @return phase correlation, first still contains original transformed! 
+      */
+     public double [] phaseCorrelatePattern ( // new
+    		 double [] first,
+    		 double [] secondFD,
+    		 double    phaseCoeff,
+    		 double [] filter,       //  high/low pass filtering
+    		 double [] first_save ){  //null-OK
+    	 if (first.length!=secondFD.length) {
+    		 IJ.showMessage("Error","Correlation arrays should be the same size");
+    		 return null;
+    	 }
+    	 updateMaxN(first);
+    	 swapQuadrants(first);
+    	 if (!transform(first,false))  return null; // direct FHT
+    	 if (first_save != null) System.arraycopy(first, 0, first_save, 0, first.length);
+
+    	 first= phaseMultiplyNorm(first, secondFD, phaseCoeff); // correlation, not convolution
+    	 if (filter!=null) multiplyByReal(first, filter);
+    	 transform(first,true) ; // inverse transform
+    	 swapQuadrants(first);
+    	 return first;
+     }
 
+     
+     
+     
+     
 
 //
      public double [] applyFreqFilter(

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

@@ -847,9 +847,12 @@ public class Eyesis_Correction implements PlugIn, ActionListener {
 			addButton("Set pair",  panelLWIRWorld, color_process);
 			addButton("Warp pair",  panelLWIRWorld, color_process);
 			addButton("Read Tiff",  panelLWIRWorld, color_process);
-			addButton("Set pair GPS",  panelLWIRWorld, color_process);
 			addButton("Test video",  panelLWIRWorld, color_process);
-			addButton("Deconvolve Slices",  panelLWIRWorld, color_process);
+			addButton("Ortho Pairs",  panelLWIRWorld, color_process);
+			addButton("Mismatched resolutions",  panelLWIRWorld, color_process);
+			addButton("Generate DATI",  panelLWIRWorld, color_process);
+			addButton("Create mine",  panelLWIRWorld, color_process);
+			addButton("Pattern correlate",  panelLWIRWorld, color_process);
 			plugInFrame.add(panelLWIRWorld);
 			
 		}
@@ -5705,7 +5708,7 @@ public class Eyesis_Correction implements PlugIn, ActionListener {
 				e.printStackTrace();
 			}
 //			ComboMatch.testReadTiff();
-		} else if (label.equals("Set pair GPS")) {
+		} else if (label.equals("Ortho Pairs")) {
 			DEBUG_LEVEL = MASTER_DEBUG_LEVEL;
 			EYESIS_CORRECTIONS.setDebug(DEBUG_LEVEL);
 			if (GPU_TILE_PROCESSOR == null) {
@@ -5734,24 +5737,44 @@ public class Eyesis_Correction implements PlugIn, ActionListener {
 				return;
 			}
 			OrthoMap.testVideo(imp_sel);
-		} else if (label.equals("Deconvolve Slices")) {
+		} else if (label.equals("Mismatched resolutions")) {
 			ImagePlus imp_sel = WindowManager.getCurrentImage();
 			if (imp_sel == null) {
 				IJ.showMessage("Error", "No images selected");
 				return;
 			}
-			OrthoMap.testDeconvolveSlices(
+			OrthoMap.createMismatchedResolutionKernel(
 					imp_sel,          // ImagePlus imp,
 					512,              // int [] slices,
 					new int [] {1,2}, // int [] slices, deconvolve slice 2 with slice1
-					4,                // int kernel_radius,
+					6, // 4,                // int kernel_radius,
 					true,             // boolean hor_sym,
 					true,             // boolean vert_sym,
 					true, // false,            // boolean all_sym,
 					DEBUG_LEVEL);     // int debugLevel) { // >0
+		} else if (label.equals("Generate DATI")) {
+			ImagePlus imp_sel = WindowManager.getCurrentImage();
+			if (imp_sel == null) {
+				IJ.showMessage("Error", "No images selected");
+				return;
+			}
+			OrthoMap.generateDATI(
+					imp_sel,          // ImagePlus imp,
+					512,              // int [] slices,
+					new int [] {1,2}, // int [] slices, deconvolve slice 2 with slice1
+					DEBUG_LEVEL);     // int debugLevel) { // >0
+		} else if (label.equals("Create mine")) {
+			OrthoMap.testPatternGenerate();
+		} else if (label.equals("Pattern correlate")) {
+			ImagePlus imp_sel = WindowManager.getCurrentImage();
+			if (imp_sel == null) {
+				IJ.showMessage("Error", "No images selected");
+				return;
+			}
+			OrthoMap.testPatternCorrelate(imp_sel);
 		}
 	}
-
+// 
 	public boolean debugInitOneScene() {
 		DEBUG_LEVEL = MASTER_DEBUG_LEVEL;
 		if (EYESIS_CORRECTIONS_AUX == null) {

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

@@ -82,8 +82,15 @@ public class ComboMatch {
 //		String orthoMapsCollection_path = "/media/elphel/SSD3-4GB/lwir16-proc/ortho_videos/maps_08_november.data";
 //		String files_list_path =          "/media/elphel/SSD3-4GB/lwir16-proc/ortho_videos/maps_10_short.list";
 //		String orthoMapsCollection_path = "/media/elphel/SSD3-4GB/lwir16-proc/ortho_videos/maps_10_short.data";
-		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_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_19_sep13_25-50-75-100m",
+				"/media/elphel/SSD3-4GB/lwir16-proc/ortho_videos/maps_nov3_50-75"};
+		
+		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
 //maps_08_november.list		
@@ -129,26 +136,20 @@ public class ComboMatch {
 		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
 		if (!use_marked_image) {
-			process_correlation=false; // use already adjusted by defualt
+			process_correlation=false; // use already adjusted by default
 		}
 		
 		
 		GenericJTabbedDialog gd = new GenericJTabbedDialog("Set image pair",1200,900);
-		gd.addStringField ("Image list full path",  files_list_path, 180, "Image list full path.");
-		gd.addStringField ("Maps collection save path",  orthoMapsCollection_path, 180, "Save path for serialized map collection data.");
+		gd.addChoice      ("Files list/data path (w/o extension):", files_lists_paths, files_lists_paths[files_lists_paths.length-1]);
 		gd.addCheckbox    ("Use saved maps collection", use_saved_collection, "If false - use files list.");
 		gd.addCheckbox    ("Save maps collection", save_collection, "Save maps collection to be able to restore.");
 		gd.addCheckbox    ("Process correlations", process_correlation, "false to skip to just regenerate new save file.");
 		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.");
-		
-		//
-//		for (int n = 0; n < image_paths_pre.length; n++) {
-//			gd.addStringField ("Image path "+n,  image_paths_pre[n], 180, "Image "+n+" full path w/o ext");		
-//		}
-//		gd.addStringField ("First image path",  image_paths_pre[0], 180, "First image full path w/o ext");		
-//		gd.addStringField ("Second image path", image_paths_pre[1], 180, "Second image full path w/o ext");		
+		/*
 		for (int n = 0; n < image_enuatr.length; n++) {
 			gd.addMessage("image["+n+"] pose");
 			gd.addNumericField("East",   image_enuatr[n][0][0],  3,7,"m",	"Move image "+n+" East.");
@@ -158,6 +159,7 @@ public class ComboMatch {
 			gd.addNumericField("Tilt",   image_enuatr[n][1][1],  3,7,"deg",	"Rotate image "+n+" around East.");
 			gd.addNumericField("Roll",   image_enuatr[n][1][2],  3,7,"deg",	"Rotate image "+n+" around North.");
 		}
+		*/
 		gd.addNumericField("Zoom level",              zoom_lev,  0,4,"",
 				"Zoom level: +1 - zoom in twice, -1 - zoom out twice");
 		gd.addNumericField("GPU image width",              gpu_width,  0,4,"",
@@ -167,23 +169,24 @@ public class ComboMatch {
 		gd.addCheckbox    ("Show transformation centers", show_centers, "Mark verticals from the UAS on the ground.");
 		gd.addCheckbox    ("Show combo image map",      show_combo_map, "Load and process altitude maps.");
 		gd.addCheckbox    ("Show altitude combo image", use_alt, "Load and process altitude maps.");
-//		gd.addStringField ("First matching timestamp",  gpu_spair[0], 20, "First GPU-matching timestamp with '_' for decimal point.");
-//		gd.addStringField ("Second matching timestamp", gpu_spair[1], 20, "First GPU-matching timestamp with '_' for decimal point.");
 		gd.addNumericField("Remove fraction of worst matches",   frac_remove,  3,7,"",	"When fitting scenes remove this fraction of worst match.");
 		gd.addNumericField("Maximal metric error",      metric_error,  3,7,"m",	"Maximal tolerable fitting error caused by elevation variations.");
 		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.showDialog();
 		if (gd.wasCanceled()) return false;
-		files_list_path = gd.getNextString();
-		
-		orthoMapsCollection_path = gd.getNextString();
+		int choice_index = gd.getNextChoiceIndex();
+		files_list_path =         files_lists_paths[choice_index]+".list";
+		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();
+		/*
 		for (int n = 0; n < image_enuatr.length; n++) {
 			image_enuatr[n][0][0] = gd.getNextNumber();
 			image_enuatr[n][0][1] = gd.getNextNumber();
@@ -192,6 +195,7 @@ public class ComboMatch {
 			image_enuatr[n][1][1] = gd.getNextNumber();
 			image_enuatr[n][1][2] = gd.getNextNumber();
 		}
+		*/
 		zoom_lev =            (int) gd.getNextNumber();
 		gpu_width =           (int) gd.getNextNumber();
 		gpu_height =          (int) gd.getNextNumber();
@@ -209,6 +213,7 @@ public class ComboMatch {
 		if (use_marked_image ) { // will only be used if found and asked
 			use_marked_image=       gd.getNextBoolean();
 		}
+		update_lla=                 gd.getNextBoolean();
 		OrthoMapsCollection maps_collection=null;
 		if (use_saved_collection) {
 			try {
@@ -245,8 +250,11 @@ public class ComboMatch {
 		
 		//getTemperature()
 		// get all temperatures
-		maps_collection. getAllTemperatures();
-		
+		maps_collection.getAllTemperatures();
+		if (update_lla) {
+			System.out.println("Updating map files metadata");
+			maps_collection.updateLLa();
+		}
 		
         // which pair to compare
 //		String [] gpu_spair = {names[gpu_ipair[0]],names[gpu_ipair[1]]}; 
@@ -310,7 +318,7 @@ public class ComboMatch {
         	int max_zoom_lev = Math.max(
         			maps_collection.ortho_maps[gpu_pair[0]].getOriginalZoomLevel(),
         			maps_collection.ortho_maps[gpu_pair[1]].getOriginalZoomLevel());
-        	int initial_zoom = max_zoom_lev - 3;  // another algorithm?
+        	int initial_zoom = max_zoom_lev - 4;  // another algorithm?
 
         	
         	System.out.println("Setting up GPU");

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

@@ -60,8 +60,8 @@ public class OrthoMapsCollection  implements Serializable{
 			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);
+//				String scene_path = getSceneDir(scenes_path, name);
+				ortho_maps[n] = new OrthoMap(paths[n]); // , scene_path);
 				ortho_maps[n].setAffine(affine);
 			}
 		}
@@ -117,9 +117,15 @@ public class OrthoMapsCollection  implements Serializable{
 	public void getAllTemperatures() {
 		for (int n = 0; n < ortho_maps.length; n++) {
 			ortho_maps[n].getTemperature();
+			ortho_maps[n].getTemperatureAndTelemetry();
 		}
 	}
 	
+	public void updateLLa() { // make automatic by saving/testing file modification stamp?
+		for (int n = 0; n < ortho_maps.length; n++) {
+			ortho_maps[n].updateLLA();
+		}		
+	}
 	
 	public static String[] getPathsFromSorceList(
 			String files_list) {
@@ -683,6 +689,12 @@ public class OrthoMapsCollection  implements Serializable{
 			}
 			gpu_pair_img[n] = ortho_maps[gpu_pair[n]].getPaddedGPU (zoom_lev); // int zoom_level,
 		}
+		boolean invert_second = (debugLevel > 1000);
+		if (invert_second) {
+			for (int i = 0; i < gpu_pair_img[1].length; i++) {
+				gpu_pair_img[1][i]= -gpu_pair_img[1][i];
+			}
+		}
 		if (show_gpu_img) {
 			String [] dbg_titles = {ortho_maps[gpu_pair[0]].getName(),ortho_maps[gpu_pair[1]].getName()};
     		ShowDoubleFloatArrays.showArrays(
@@ -1271,7 +1283,7 @@ public class OrthoMapsCollection  implements Serializable{
     				num_passes,           // int       num_passes,
     				max_diff,             // double    max_diff,
     				ImageDtt.THREADS_MAX, // int       threadsMax,
-    				debugLevel);          // int       debug_level)
+    				debugLevel-1);        // int       debug_level)
     	}		
 		if (debugLevel > 0) {
 			String [] dbg_titles = {"x-raw","x_filled","y-raw","y_filled"};

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

+package com.elphel.imagej.orthomosaic;
+
+import java.io.IOException;
+import java.io.ObjectInputStream;
+import java.io.ObjectOutputStream;
+import java.io.Serializable;
+
+public class SensorTemperatureData  implements Serializable  {
+	private static final long serialVersionUID = 1L;	
+	double averagePixelValue;
+	double TLM_FPA_KELV;
+	double TLM_FFC_KELV;
+	double TLM_CORE_TEMP;
+	int    TLM_FRAME_FFC;
+	int    TLM_FRAME;
+	
+	private void writeObject(ObjectOutputStream oos) throws IOException {
+		oos.defaultWriteObject();
+	}
+	private void readObject(ObjectInputStream ois) throws ClassNotFoundException, IOException {
+		ois.defaultReadObject();
+	}
+	
+}

src/main/java/com/elphel/imagej/tileprocessor/TileNeibs.java

@@ -100,10 +100,10 @@ public class TileNeibs{
 	
 	int getY(int indx) {return indx / sizeX;};
 	
-	int getSizeX() {
+	public int getSizeX() {
 		return sizeX;
 	}
-	int getSizeY() {
+	public int getSizeY() {
 		return sizeY;
 	}