done refactoring, starting debugging (7f9773fb) · Commits · Elphel / imagej-elphel

src/main/java/com/elphel/imagej/orthomosaic/Affine2Import.java

0 → 100644

+29 −0

Original line number	Diff line number	Diff line
		package com.elphel.imagej.orthomosaic;

		public class Affine2Import {
		public static final String AFFINE2_TAG = "AFFINE2";
		public static final int AFFINE2_LEN = 10;
		public String name1;
		public String name2;
		public double overlap;
		public double [][] affine;
		public static boolean matches(String [] tokens) {
		return ((tokens.length == AFFINE2_LEN) && AFFINE2_TAG.equals(tokens[0]));
		}
		public Affine2Import(
		String [] tokens) {
		if (!matches(tokens)) {
		throw new IllegalArgumentException ("Not Affine2Import tokens");
		}
		int indx = 1;
		name1 = tokens[indx++];
		name2 = tokens[indx++];
		overlap = Double.parseDouble(tokens[indx++]);
		affine = new double [2][3];
		for (int i = 0; i < affine.length; i++) {
		for (int j = 0; j < affine[i].length; j++) {
		affine[i][j] = Double.parseDouble(tokens[indx++]);
		}
		}
		}
		}

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

0 → 100644

+27 −0

Original line number	Diff line number	Diff line
		package com.elphel.imagej.orthomosaic;

		public class AffineImport {
		public static final String AFFINE_TAG = "AFFINE";
		public static final int AFFINE_LEN = 8;
		public String name;
		public double [][] affine;
		public static boolean matches(String [] tokens) {
		return ((tokens.length == AFFINE_LEN) && AFFINE_TAG.equals(tokens[0]));
		}
		public AffineImport(
		String [] tokens) {
		if (!matches(tokens)) {
		throw new IllegalArgumentException ("Not AffineImport tokens");
		}
		int indx = 1;
		name = tokens[indx++];
		affine = new double [2][3];
		for (int i = 0; i < affine.length; i++) {
		for (int j = 0; j < affine[i].length; j++) {
		affine[i][j] = Double.parseDouble(tokens[indx++]);
		}
		}
		}

		// String[] tokens
		}

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

+381 −166

Original line number	Diff line number	Diff line
		@@ -43,6 +43,7 @@ import ij.gui.PointRoi;
		import ij.process.FloatPolygon;

		public class ComboMatch {
		public static final String [] SUFFIXES_BL_BC= {"","-BL","-BC"};
		public static GPUTileProcessor GPU_TILE_PROCESSOR = null;
		public static GpuQuad GPU_QUAD_AFFINE = null;
		public static ImagePlus imp_src1 = null;
		@@ -174,9 +175,6 @@ public class ComboMatch {
		boolean display_pairs = false;
		boolean create_map = false;
		boolean create_equalize = false;



		boolean use_saved_collection = false; // true; // false;
		boolean save_collection = false; // true;
		boolean process_correlation = true; // use false to save new version of data
		@@ -191,23 +189,24 @@ public class ComboMatch {
		boolean restore_temp = true;
		double frac_remove = clt_parameters.imp.pmtch_frac_remove; // 0.15;
		double metric_error = clt_parameters.imp.pmtch_metric_err; // 0.05; // 0.02;// 2 cm
		boolean update_files = false;
		boolean update_lla = false; // re-read file metadata
		boolean update_kernel_patterns = false;
		boolean update_bl_bc = false;
		boolean export_affine = false; // export per-scene affines
		boolean export_affine2 = false; // export per-pair affines

		boolean import_export = false;
		// boolean update_files = false;
		// boolean update_lla = false; // re-read file metadata
		// boolean update_kernel_patterns = false;
		// boolean update_bl_bc = false;
		// boolean export_affine = false; // export per-scene affines
		// boolean export_affine2 = false; // export per-pair affines


		boolean fix_duplicates = false;
		String [] suffixes_bl_bc= {"","-BL","-BC"};
		boolean log_append = clt_parameters.imp.pwise_log_append;
		String log_path = clt_parameters.imp.pwise_log_path;
		String omtch_img_set = clt_parameters.imp.omtch_img_set;

		// boolean READ_NO_ALT = false; // to read older format data file where pairs do not have alt_data[]

		int suffix_bc_bl_indx = 2;
		// int suffix_bc_bl_indx = 2;
		if (!use_marked_image) {
		process_correlation=false; // use already adjusted by default
		}
		@@ -217,12 +216,10 @@ public class ComboMatch {
		}

		GenericJTabbedDialog gd = new GenericJTabbedDialog("Set image pair",1200,900);
		// gd.addChoice ("Files list/data path (w/o extension):", FILES_LISTS_PATHS, FILES_LISTS_PATHS[default_list_choice]);
		gd.addChoice ("Files list/data path (w/o extension):", FILES_LISTS_PATHS, omtch_img_set);
		gd.addCheckbox ("Use saved maps collection ", use_saved_collection, " (if available). 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.");
		// int num_tries_fit = 10;
		gd.addNumericField("Num tries fit", num_tries_fit, 0,4,"", "Try matching images this number of times");

		gd.addCheckbox ("Update match if calculated", update_match, "Will update correlation match for a pair if found.");
		@@ -254,20 +251,21 @@ public class ComboMatch {
		if (use_marked_image ) {
		gd.addCheckbox ("Use marked image data", true, "Use markes from the selected image");
		}
		gd.addCheckbox ("Update scene files", update_files, "Re-read files as specified in .list file, possibly changing versions");
		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");
		gd.addCheckbox ("Import/Export operations", import_export, "Import/export and update operations");
		// gd.addCheckbox ("Update scene files", update_files, "Re-read files as specified in .list file, possibly changing versions");
		// 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");
		gd.addCheckbox ("Remove duplicate scenes", fix_duplicates, "Remove scenes with the same timestamp");

		gd.addCheckbox ("Update BC/BL suffix", update_bl_bc,
		"Change source filenames to use -BC for bicubic, -BL - for bilinear, or empty - for old bilinear files");
		gd.addChoice("BL/BC suffix:",
		suffixes_bl_bc,
		suffixes_bl_bc[suffix_bc_bl_indx],
		"Select interpolation mode of the source files: old bilinear (empty), bilinear (-BL), or bicubic (-BC)", 0);
		// gd.addCheckbox ("Update BC/BL suffix", update_bl_bc,
		// "Change source filenames to use -BC for bicubic, -BL - for bilinear, or empty - for old bilinear files");
		// gd.addChoice("BL/BC suffix:",
		// SUFFIXES_BL_BC,
		// SUFFIXES_BL_BC[suffix_bc_bl_indx],
		// "Select interpolation mode of the source files: old bilinear (empty), bilinear (-BL), or bicubic (-BC)", 0);

		gd.addCheckbox ("Export scene affines", export_affine, "Export per-scene affines in text format for migration.");
		gd.addCheckbox ("Export pairs affines", export_affine2, "Export per-pair affines in text format for migration.");
		// gd.addCheckbox ("Export scene affines", export_affine, "Export per-scene affines in text format for migration.");
		// gd.addCheckbox ("Export pairs affines", export_affine2, "Export per-pair affines in text format for migration.");

		gd.addCheckbox ("Write log file", log_append, "Enable writing log file with matching results.");
		gd.addStringField ("Log file full path", log_path, 150, "Path of the log file to be appended.");
		@@ -285,6 +283,7 @@ public class ComboMatch {
		String orthoMapsCollection_path =omtch_img_set+".data";
		String affines_path = omtch_img_set+".affines"; // for export per-scene affines
		String affines2_path = omtch_img_set+".affines2"; // for export per-pair affines

		use_saved_collection = gd.getNextBoolean();
		save_collection = gd.getNextBoolean();
		String orthoMapsCollection_savepath = save_collection?orthoMapsCollection_path:null;
		@@ -317,15 +316,16 @@ public class ComboMatch {
		if (use_marked_image ) { // will only be used if found and asked
		use_marked_image= gd.getNextBoolean();
		}
		update_files= gd.getNextBoolean();
		update_lla= gd.getNextBoolean();
		update_kernel_patterns= gd.getNextBoolean();
		import_export = gd.getNextBoolean();
		// update_files= gd.getNextBoolean();
		// update_lla= gd.getNextBoolean();
		// update_kernel_patterns= gd.getNextBoolean();
		fix_duplicates= gd.getNextBoolean();
		update_bl_bc= gd.getNextBoolean();
		suffix_bc_bl_indx = gd.getNextChoiceIndex();
		// update_bl_bc= gd.getNextBoolean();
		// suffix_bc_bl_indx = gd.getNextChoiceIndex();

		export_affine = gd.getNextBoolean();
		export_affine2 = gd.getNextBoolean();
		// export_affine = gd.getNextBoolean();
		// export_affine2 = gd.getNextBoolean();


		log_append = gd.getNextBoolean();
		@@ -343,13 +343,13 @@ public class ComboMatch {
		}
		//files_list_path
		if (!use_files_list) {
		if (update_kernel_patterns) {
		maps_collection.updateKernels(files_list_path);
		maps_collection.updatePatterns(files_list_path);
		}
		if (update_files) {
		maps_collection.updateFiles(files_list_path);
		}
		// if (update_kernel_patterns) {
		// maps_collection.updateKernels(files_list_path);
		// maps_collection.updatePatterns(files_list_path);
		// }
		// if (update_files) {
		// maps_collection.updateFiles(files_list_path);
		// }
		}
		} else {
		use_files_list = true;
		@@ -360,6 +360,15 @@ public class ComboMatch {
		maps_collection.updateSfmGain();
		}

		if (import_export) {
		return updateImportExport(
		omtch_img_set, // String files_base
		maps_collection); // OrthoMapsCollection maps_collection

		}


		/*
		if (export_affine) {
		StringBuffer sb = new StringBuffer();
		for (OrthoMap omap : maps_collection.ortho_maps) {
		@@ -415,22 +424,23 @@ public class ComboMatch {
		if (export_affine \|\| export_affine2) {
		return true; // do not save
		}

		*/

		if (fix_duplicates) {
		removeDuplicateScenes (maps_collection);
		}

		/*
		if (update_bl_bc) {
		boolean OK = updateBlBcFileNames(
		suffixes_bl_bc[suffix_bc_bl_indx], // String suffix,
		SUFFIXES_BL_BC[suffix_bc_bl_indx], // String suffix,
		"-FLAT",// String before,
		maps_collection); // OrthoMapsCollection maps_collection)
		if (!OK) {
		System.out.println("Failed to update filenames for different interpolation mode");
		}
		}

		*/


		String [] names = maps_collection.getNames(); // null
		@@ -608,7 +618,7 @@ public class ComboMatch {
		}
		}

		maps_collection.reverseRender(
		maps_collection.reverseRender( // assuming image, not alt
		object_list, // ArrayList<ObjectLocation> objects,
		zool_lev_objects, // int zoom_level){
		indices); // int [] indices){ // null or selected image indices
		@@ -843,12 +853,12 @@ public class ComboMatch {
		//getTemperature()
		// get all temperatures
		maps_collection.getAllTemperatures();
		if (update_lla) {
		System.out.println("Updating map files metadata");
		maps_collection.updateLLa();
		maps_collection.updateNumberScenes();
		maps_collection.updateSfmGain();
		}
		// if (update_lla) {
		// System.out.println("Updating map files metadata");
		// maps_collection.updateLLA();
		// maps_collection.updateNumberScenes();
		// maps_collection.updateSfmGain();
		// }

		// which pair to compare
		// String [] gpu_spair = {names[gpu_ipair[0]],names[gpu_ipair[1]]};
		@@ -2652,5 +2662,210 @@ adjusted affines[1] for a pair: 1694564291_293695/1694564778_589341
		}
		}

		public static boolean updateImportExport(
		String files_base,
		OrthoMapsCollection maps_collection) {
		if (maps_collection == null) {
		throw new IllegalArgumentException ("maps_collection is not initialized!");
		}
		int suffix_bc_bl_indx = 2;
		boolean update_files = false;
		boolean update_lla = false; // re-read file metadata
		boolean update_kernel_patterns = false;
		boolean update_bl_bc = false;
		boolean export_affine = false; // export per-scene affines
		boolean export_affine2 = false; // export per-pair affines
		boolean overwrite_affine = false;
		boolean import_affine = false; // export per-scene affines
		boolean import_affine2 = false; // export per-pair affines
		String files_list_path = files_base+".list";
		// String orthoMapsCollection_path =omtch_img_set+".data";
		String affines_path = files_base+".affines"; // for export per-scene affines
		String affines2_path = files_base+".affines2"; // for export per-pair affines


		GenericJTabbedDialog gd = new GenericJTabbedDialog("Select Update, Import or Export operations",1200,900);
		gd.addStringField ("List file full path", files_list_path, 150, "Path to read/update directories and GEO files.");
		gd.addStringField ("Scene affines full path", affines_path, 150, "Path to import/export scenes affines.");
		gd.addStringField ("Pairwise affines full path", affines2_path, 150, "Path to import/export scenes pairs affines.");
		gd.addCheckbox ("Update scene files", update_files, "Re-read files as specified in .list file, possibly changing versions");
		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");
		gd.addCheckbox ("Export scene affines", export_affine, "Export per-scene affines in text format for migration.");
		gd.addCheckbox ("Export pairs affines", export_affine2, "Export per-pair affines in text format for migration.");

		gd.addCheckbox ("Overwrite affines on import",overwrite_affine, "Overwrite existing non-trivial affines on import.");
		gd.addCheckbox ("Import scene affines", import_affine, "Export per-scene affines in text format for migration.");
		gd.addCheckbox ("Import pairs affines", import_affine2, "Export per-pair affines in text format for migration.");
		gd.addCheckbox ("Update BC/BL suffix", update_bl_bc,
		"Change source filenames to use -BC for bicubic, -BL - for bilinear, or empty - for old bilinear files");
		gd.addChoice("BL/BC suffix:",
		SUFFIXES_BL_BC,
		SUFFIXES_BL_BC[suffix_bc_bl_indx],
		"Select interpolation mode of the source files: old bilinear (empty), bilinear (-BL), or bicubic (-BC)", 0);
		gd.showDialog();
		if (gd.wasCanceled()) return false;
		files_list_path = gd.getNextString();
		affines_path = gd.getNextString();
		affines2_path = gd.getNextString();
		update_files= gd.getNextBoolean();
		update_lla= gd.getNextBoolean();
		update_kernel_patterns= gd.getNextBoolean();
		export_affine = gd.getNextBoolean();
		export_affine2 = gd.getNextBoolean();
		overwrite_affine = gd.getNextBoolean();
		import_affine = gd.getNextBoolean();
		import_affine2 = gd.getNextBoolean();
		update_bl_bc= gd.getNextBoolean();
		suffix_bc_bl_indx = gd.getNextChoiceIndex();

		if (update_files) {
		maps_collection.updateFiles(files_list_path);
		maps_collection.updateNumberScenes(); // number of scenes in each sequence
		}
		if (update_lla) {
		System.out.println("Updating map files metadata");
		maps_collection.updateLLA();
		maps_collection.updateNumberScenes();
		maps_collection.updateSfmGain();
		}
		if (update_kernel_patterns) {
		maps_collection.updateKernels(files_list_path);
		maps_collection.updatePatterns(files_list_path);
		}

		if (export_affine) {
		StringBuffer sb = new StringBuffer();
		for (OrthoMap omap : maps_collection.ortho_maps) {
		String name = omap.getName();
		double [][] affine = omap.getAffine();
		if (affine != null) {
		sb.append(String.format("AFFINE %s %11.8f %11.8f %11.8f %11.8f %11.8f %11.8f\n",
		name, affine[0][0], affine[0][1], affine[0][2], affine[1][0], affine[1][1], affine[1][2]));
		}
		}
		CalibrationFileManagement.saveStringToFile (
		affines_path, //String path,
		sb.toString(), // data,
		false); // boolean append)
		}

		if (export_affine2) {
		StringBuffer sb = new StringBuffer();
		ArrayList<Point> pairs_list = new ArrayList<Point>();
		for (OrthoMap map : maps_collection.ortho_maps) {
		for (String other_name: map.pairwise_matches.keySet()) {
		pairs_list.add(new Point(
		maps_collection.getIndex(map.getName()),
		maps_collection.getIndex(other_name)));
		}
		}
		Collections.sort(pairs_list, new Comparator<Point>() {
		@Override
		public int compare(Point lhs, Point rhs) {
		return (rhs.x > lhs.x) ? -1 : (rhs.x < lhs.x) ? 1 :
		((rhs.y > lhs.y) ? -1 : (rhs.y < lhs.y) ? 1 : 0); // increasing
		}
		});
		for (Point pair: pairs_list) {
		PairwiseOrthoMatch pom = maps_collection.ortho_maps[pair.x].getMatch(
		maps_collection.ortho_maps[pair.y].getName(), false); // undef_only \|\| nan_rms);
		if ((pom !=null) && pom.isDefined()) {
		double overlap = pom.overlap;
		double [][] affine = pom.getAffine();
		sb.append(String.format("AFFINE2 %s %s %11.8f %11.8f %11.8f %11.8f %11.8f %11.8f %11.8f\n",
		maps_collection.ortho_maps[pair.x].getName(),
		maps_collection.ortho_maps[pair.y].getName(),
		overlap,
		affine[0][0], affine[0][1], affine[0][2], affine[1][0], affine[1][1], affine[1][2]));
		}
		}
		CalibrationFileManagement.saveStringToFile (
		affines2_path, //String path,
		sb.toString(), // data,
		false); // boolean append)
		}

		if (import_affine) {
		ArrayList<AffineImport> affine_import = new ArrayList<AffineImport>();
		OrthoMapsCollection.getPathsAndScenesFromSourceList(
		affines_path,
		null, // scenes0,
		null, // ArrayList<AltitudeMismatchKernel> kernels,
		null, // ArrayList<GroundObjectPattern> patterns);
		null, // ArrayList<ModelRegex> model_regexes,
		null, // String [] regex_use) {
		affine_import, // ArrayList<AffineImport> affine_import,
		null); // ArrayList<Affine2Import> affine2_import) {
		int num_updated_affines = 0;
		for (AffineImport affineImport: affine_import) {
		OrthoMap map = maps_collection.getMap(affineImport.name);
		if (map != null) {
		if (overwrite_affine \|\| !map.isAffineNonTrivial()) {
		map.setAffine(affineImport.affine);
		num_updated_affines++;
		}
		}
		}
		maps_collection.updateNumberScenes();
		System.out.println("Updated "+num_updated_affines+" affines of "+affine_import.size()+" specified. There are "+
		maps_collection.ortho_maps.length+" maps in the system.");
		}
		if (import_affine2) {
		ArrayList<Affine2Import> affine2_import = new ArrayList<Affine2Import>();
		OrthoMapsCollection.getPathsAndScenesFromSourceList(
		affines_path,
		null, // scenes0,
		null, // ArrayList<AltitudeMismatchKernel> kernels,
		null, // ArrayList<GroundObjectPattern> patterns);
		null, // ArrayList<ModelRegex> model_regexes,
		null, // String [] regex_use) {
		null, // ArrayList<AffineImport> affine_import,
		affine2_import); // ArrayList<Affine2Import> affine2_import) {
		int num_updated_affines = 0;
		for (Affine2Import affine2Import: affine2_import) {
		OrthoMap map = maps_collection.getMap(affine2Import.name1);
		if (map != null) {
		PairwiseOrthoMatch pom = map.getMatch(affine2Import.name2,true);
		if (pom != null) {
		if (overwrite_affine \|\| !pom.isAffineNonTrivial()) {
		pom.setOverlap(affine2Import.overlap);
		pom.setAffine(affine2Import.affine); // does not clone - OK
		}
		} else {
		OrthoMap map2 = maps_collection.getMap(affine2Import.name2);
		int zoom_lev = Math.min(map.getOriginalZoomLevel(), map2.getOriginalZoomLevel());
		pom= new PairwiseOrthoMatch(
		affine2Import.affine, // double [][] affine,
		null, // double [][] jtj,
		Double.NaN, // double rms,
		zoom_lev, // int zoom_lev,
		affine2Import.overlap); // double overlap)
		}


		}




		}
		}

		if (update_bl_bc) {
		boolean OK = updateBlBcFileNames(
		SUFFIXES_BL_BC[suffix_bc_bl_indx], // String suffix,
		"-FLAT",// String before,
		maps_collection); // OrthoMapsCollection maps_collection)
		if (!OK) {
		System.out.println("Failed to update filenames for different interpolation mode");
		}
		}

		return true;
		}




		}

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

+4 −0

Original line number	Diff line number	Diff line
		@@ -238,6 +238,10 @@ public class FloatImageData implements Serializable {
		return extra_zoom[0];
		}

		public double needZoomIn() {
		return needZoomIn(pix_meters);
		}

		public int getZoomLevel() {
		return zoom_lev;
		}

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