DATI and pattern matching (81c431ad) · Commits · Elphel / imagej-elphel

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

+47 −0

Original line number	Original line	Diff line number	Diff line
	@@ -418,6 +418,53 @@ public class DoubleFHT {
	return first;		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;
			}






	//		//

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

+30 −7

Original line number	Original line	Diff line number	Diff line
	@@ -847,9 +847,12 @@ public class Eyesis_Correction implements PlugIn, ActionListener {
	addButton("Set pair", panelLWIRWorld, color_process);		addButton("Set pair", panelLWIRWorld, color_process);
	addButton("Warp pair", panelLWIRWorld, color_process);		addButton("Warp pair", panelLWIRWorld, color_process);
	addButton("Read Tiff", panelLWIRWorld, color_process);		addButton("Read Tiff", panelLWIRWorld, color_process);
	addButton("Set pair GPS", panelLWIRWorld, color_process);
	addButton("Test video", 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);		plugInFrame.add(panelLWIRWorld);

	}		}
	@@ -5705,7 +5708,7 @@ public class Eyesis_Correction implements PlugIn, ActionListener {
	e.printStackTrace();		e.printStackTrace();
	}		}
	// ComboMatch.testReadTiff();		// ComboMatch.testReadTiff();
	} else if (label.equals("Set pair GPS")) {		} else if (label.equals("Ortho Pairs")) {
	DEBUG_LEVEL = MASTER_DEBUG_LEVEL;		DEBUG_LEVEL = MASTER_DEBUG_LEVEL;
	EYESIS_CORRECTIONS.setDebug(DEBUG_LEVEL);		EYESIS_CORRECTIONS.setDebug(DEBUG_LEVEL);
	if (GPU_TILE_PROCESSOR == null) {		if (GPU_TILE_PROCESSOR == null) {
	@@ -5734,24 +5737,44 @@ public class Eyesis_Correction implements PlugIn, ActionListener {
	return;		return;
	}		}
	OrthoMap.testVideo(imp_sel);		OrthoMap.testVideo(imp_sel);
	} else if (label.equals("Deconvolve Slices")) {		} else if (label.equals("Mismatched resolutions")) {
	ImagePlus imp_sel = WindowManager.getCurrentImage();		ImagePlus imp_sel = WindowManager.getCurrentImage();
	if (imp_sel == null) {		if (imp_sel == null) {
	IJ.showMessage("Error", "No images selected");		IJ.showMessage("Error", "No images selected");
	return;		return;
	}		}
	OrthoMap.testDeconvolveSlices(		OrthoMap.createMismatchedResolutionKernel(
	imp_sel, // ImagePlus imp,		imp_sel, // ImagePlus imp,
	512, // int [] slices,		512, // int [] slices,
	new int [] {1,2}, // int [] slices, deconvolve slice 2 with slice1		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 hor_sym,
	true, // boolean vert_sym,		true, // boolean vert_sym,
	true, // false, // boolean all_sym,		true, // false, // boolean all_sym,
	DEBUG_LEVEL); // int debugLevel) { // >0		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() {		public boolean debugInitOneScene() {
	DEBUG_LEVEL = MASTER_DEBUG_LEVEL;		DEBUG_LEVEL = MASTER_DEBUG_LEVEL;
	if (EYESIS_CORRECTIONS_AUX == null) {		if (EYESIS_CORRECTIONS_AUX == null) {

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

+28 −20

Original line number	Original line	Diff line number	Diff line
	@@ -82,8 +82,15 @@ public class ComboMatch {
	// String orthoMapsCollection_path = "/media/elphel/SSD3-4GB/lwir16-proc/ortho_videos/maps_08_november.data";		// 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 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 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 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 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_19_sep13.list
	//maps_09_short.list		//maps_09_short.list
	//maps_08_november.list		//maps_08_november.list
	@@ -129,26 +136,20 @@ public class ComboMatch {
	boolean restore_temp = true;		boolean restore_temp = true;
	double frac_remove = 0.15;		double frac_remove = 0.15;
	double metric_error = 0.05; // 0.02;// 2 cm		double metric_error = 0.05; // 0.02;// 2 cm
			boolean update_lla = false; // re-read file metadata
	if (!use_marked_image) {		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);		GenericJTabbedDialog gd = new GenericJTabbedDialog("Set image pair",1200,900);
	gd.addStringField ("Image list full path", files_list_path, 180, "Image list full path.");		gd.addChoice ("Files list/data path (w/o extension):", files_lists_paths, files_lists_paths[files_lists_paths.length-1]);
	gd.addStringField ("Maps collection save path", orthoMapsCollection_path, 180, "Save path for serialized map collection data.");
	gd.addCheckbox ("Use saved maps collection", use_saved_collection, "If false - use files list.");		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 ("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 ("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 ("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 ("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++) {		for (int n = 0; n < image_enuatr.length; n++) {
	gd.addMessage("image["+n+"] pose");		gd.addMessage("image["+n+"] pose");
	gd.addNumericField("East", image_enuatr[n][0][0], 3,7,"m", "Move image "+n+" East.");		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("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("Roll", image_enuatr[n][1][2], 3,7,"deg", "Rotate image "+n+" around North.");
	}		}
			*/
	gd.addNumericField("Zoom level", zoom_lev, 0,4,"",		gd.addNumericField("Zoom level", zoom_lev, 0,4,"",
	"Zoom level: +1 - zoom in twice, -1 - zoom out twice");		"Zoom level: +1 - zoom in twice, -1 - zoom out twice");
	gd.addNumericField("GPU image width", gpu_width, 0,4,"",		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 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 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.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("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.");		gd.addNumericField("Maximal metric error", metric_error, 3,7,"m", "Maximal tolerable fitting error caused by elevation variations.");
	if (use_marked_image ) {		if (use_marked_image ) {
	gd.addCheckbox ("Use marked image data", true, "Use markes from the selected 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();		gd.showDialog();
	if (gd.wasCanceled()) return false;		if (gd.wasCanceled()) return false;
	files_list_path = gd.getNextString();		int choice_index = gd.getNextChoiceIndex();
			files_list_path = files_lists_paths[choice_index]+".list";
	orthoMapsCollection_path = gd.getNextString();		orthoMapsCollection_path =files_lists_paths[choice_index]+".data";
	use_saved_collection = gd.getNextBoolean();		use_saved_collection = gd.getNextBoolean();
	save_collection = gd.getNextBoolean();		save_collection = gd.getNextBoolean();
	process_correlation= gd.getNextBoolean();		process_correlation= gd.getNextBoolean();
	update_match= gd.getNextBoolean();		update_match= gd.getNextBoolean();
	render_match= gd.getNextBoolean();		render_match= gd.getNextBoolean();
			/*
	for (int n = 0; n < image_enuatr.length; n++) {		for (int n = 0; n < image_enuatr.length; n++) {
	image_enuatr[n][0][0] = gd.getNextNumber();		image_enuatr[n][0][0] = gd.getNextNumber();
	image_enuatr[n][0][1] = 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][1] = gd.getNextNumber();
	image_enuatr[n][1][2] = gd.getNextNumber();		image_enuatr[n][1][2] = gd.getNextNumber();
	}		}
			*/
	zoom_lev = (int) gd.getNextNumber();		zoom_lev = (int) gd.getNextNumber();
	gpu_width = (int) gd.getNextNumber();		gpu_width = (int) gd.getNextNumber();
	gpu_height = (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		if (use_marked_image ) { // will only be used if found and asked
	use_marked_image= gd.getNextBoolean();		use_marked_image= gd.getNextBoolean();
	}		}
			update_lla= gd.getNextBoolean();
	OrthoMapsCollection maps_collection=null;		OrthoMapsCollection maps_collection=null;
	if (use_saved_collection) {		if (use_saved_collection) {
	try {		try {
	@@ -246,7 +251,10 @@ public class ComboMatch {
	//getTemperature()		//getTemperature()
	// get all temperatures		// 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		// which pair to compare
	// String [] gpu_spair = {names[gpu_ipair[0]],names[gpu_ipair[1]]};		// String [] gpu_spair = {names[gpu_ipair[0]],names[gpu_ipair[1]]};
	@@ -310,7 +318,7 @@ public class ComboMatch {
	int max_zoom_lev = Math.max(		int max_zoom_lev = Math.max(
	maps_collection.ortho_maps[gpu_pair[0]].getOriginalZoomLevel(),		maps_collection.ortho_maps[gpu_pair[0]].getOriginalZoomLevel(),
	maps_collection.ortho_maps[gpu_pair[1]].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");		System.out.println("Setting up GPU");

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

+1487 −103

File changed.

Preview size limit exceeded, changes collapsed.

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

+15 −3

Original line number	Original line	Diff line number	Diff line
	@@ -60,8 +60,8 @@ public class OrthoMapsCollection implements Serializable{
	ortho_maps = new OrthoMap[paths.length];		ortho_maps = new OrthoMap[paths.length];
	for (int n = 0; n < ortho_maps.length; n++) {		for (int n = 0; n < ortho_maps.length; n++) {
	String name = OrthoMap.getNameFromPath(paths[n]);		String name = OrthoMap.getNameFromPath(paths[n]);
	String scene_path = getSceneDir(scenes_path, name);		// String scene_path = getSceneDir(scenes_path, name);
	ortho_maps[n] = new OrthoMap(paths[n], scene_path);		ortho_maps[n] = new OrthoMap(paths[n]); // , scene_path);
	ortho_maps[n].setAffine(affine);		ortho_maps[n].setAffine(affine);
	}		}
	}		}
	@@ -117,9 +117,15 @@ public class OrthoMapsCollection implements Serializable{
	public void getAllTemperatures() {		public void getAllTemperatures() {
	for (int n = 0; n < ortho_maps.length; n++) {		for (int n = 0; n < ortho_maps.length; n++) {
	ortho_maps[n].getTemperature();		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(		public static String[] getPathsFromSorceList(
	String files_list) {		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,		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) {		if (show_gpu_img) {
	String [] dbg_titles = {ortho_maps[gpu_pair[0]].getName(),ortho_maps[gpu_pair[1]].getName()};		String [] dbg_titles = {ortho_maps[gpu_pair[0]].getName(),ortho_maps[gpu_pair[1]].getName()};
	ShowDoubleFloatArrays.showArrays(		ShowDoubleFloatArrays.showArrays(
	@@ -1271,7 +1283,7 @@ public class OrthoMapsCollection implements Serializable{
	num_passes, // int num_passes,		num_passes, // int num_passes,
	max_diff, // double max_diff,		max_diff, // double max_diff,
	ImageDtt.THREADS_MAX, // int threadsMax,		ImageDtt.THREADS_MAX, // int threadsMax,
	debugLevel); // int debug_level)		debugLevel-1); // int debug_level)
	}		}
	if (debugLevel > 0) {		if (debugLevel > 0) {
	String [] dbg_titles = {"x-raw","x_filled","y-raw","y_filled"};		String [] dbg_titles = {"x-raw","x_filled","y-raw","y_filled"};