Tested LMA equalization, some bug fixes (75c570c2) · Commits · Elphel / imagej-elphel

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

+18 −5

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

0 → 100644

+659 −0

File added.

Preview size limit exceeded, changes collapsed.

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

+4 −1

Original line number	Original line	Diff line number	Diff line
	@@ -117,6 +117,9 @@ public class OrthoMap implements Comparable <OrthoMap>, Serializable{
	public transient double sfm_gain = Double.NaN; // maximal SfM gain of this map		public transient double sfm_gain = Double.NaN; // maximal SfM gain of this map
	public transient double [] equalize = {1,0}; // rectified value = equalize[0]*source_value+equalize[1]		public transient double [] equalize = {1,0}; // rectified value = equalize[0]*source_value+equalize[1]
	private void writeObject(ObjectOutputStream oos) throws IOException {		private void writeObject(ObjectOutputStream oos) throws IOException {
			// temporary fix:
			// double [][] affine_clone = {affine[0].clone(), affine[1].clone()};
			// affine = affine_clone;
	oos.defaultWriteObject();		oos.defaultWriteObject();
	oos.writeObject(path);		oos.writeObject(path);
	// oos.writeObject(scenes_path);		// oos.writeObject(scenes_path);
	@@ -511,7 +514,7 @@ public class OrthoMap implements Comparable <OrthoMap>, Serializable{
	}		}

	public void setAffine(double [][] affine) {		public void setAffine(double [][] affine) {
	this.affine = affine;		this.affine = new double[][] {affine[0].clone(),affine[1].clone()};
	}		}
	public double [][] getAffine(){		public double [][] getAffine(){
	return affine;		return affine;

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

+25 −8

Original line number	Original line	Diff line number	Diff line
	@@ -4893,7 +4893,7 @@ public class OrthoMapsCollection implements Serializable{
	int debugLevel) {		int debugLevel) {
	int [] indices = getScenesSelection(		int [] indices = getScenesSelection(
	null, // boolean select_all,		null, // boolean select_all,
	" to process"); // String purpose)		" to process/display"); // String purpose)
	if (indices == null) {		if (indices == null) {
	return false;		return false;
	}		}
	@@ -4907,7 +4907,7 @@ public class OrthoMapsCollection implements Serializable{
	int [] indices,		int [] indices,
	int debugLevel) {		int debugLevel) {
	boolean show_map_stats = false;		boolean show_map_stats = false;
	boolean show_combo_map = false; // true;		boolean show_combo_map = true; // false; // true;
	boolean show_alt_map = false;		boolean show_alt_map = false;
	boolean show_combo_mask = false; // generate image mas (where it is defined)		boolean show_combo_mask = false; // generate image mas (where it is defined)
	boolean show_frames = false;		boolean show_frames = false;
	@@ -4920,6 +4920,8 @@ public class OrthoMapsCollection implements Serializable{
	boolean show_centers = true;		boolean show_centers = true;
	boolean bounds_to_indices = true;		boolean bounds_to_indices = true;
	boolean merge_layers = false; // instead of individuals		boolean merge_layers = false; // instead of individuals
			boolean ignore_affines = false;
			boolean ignore_equalize = false;

	String save_top_dir = "/media/elphel/NVME/lwir16-proc/ortho_videos/debug/sept12-13/pattern_match/";		String save_top_dir = "/media/elphel/NVME/lwir16-proc/ortho_videos/debug/sept12-13/pattern_match/";
	String sub_dir = "combo_maps";		String sub_dir = "combo_maps";
	@@ -4946,6 +4948,11 @@ public class OrthoMapsCollection implements Serializable{
	gd.addCheckbox ("Bounds to selected images", bounds_to_indices, "Set combo image bounds to selected images only. False - all images.");		gd.addCheckbox ("Bounds to selected images", bounds_to_indices, "Set combo image bounds to selected images only. False - all images.");
	gd.addCheckbox ("Merge layers", merge_layers, "Generate composite binary image.");		gd.addCheckbox ("Merge layers", merge_layers, "Generate composite binary image.");

			gd.addCheckbox ("Ignore affines", ignore_affines, "Ignore available affines, use unity.");
			gd.addCheckbox ("Ignore equalization", ignore_equalize, "Ignore available intensity equalization, use unity.");



	gd.addStringField ("Pattern match save directory", save_top_dir, 120, "Top directory to save combo maps");		gd.addStringField ("Pattern match save directory", save_top_dir, 120, "Top directory to save combo maps");
	gd.addStringField ("Save subdirectory", sub_dir, 80, "Subdirectory for versions of the same scene/pair of scenes");		gd.addStringField ("Save subdirectory", sub_dir, 80, "Subdirectory for versions of the same scene/pair of scenes");
	gd.addCheckbox ("Show generated images", show_images, "Display generated images.");		gd.addCheckbox ("Show generated images", show_images, "Display generated images.");
	@@ -4968,7 +4975,8 @@ public class OrthoMapsCollection implements Serializable{
	show_centers = gd.getNextBoolean();		show_centers = gd.getNextBoolean();
	bounds_to_indices = gd.getNextBoolean();		bounds_to_indices = gd.getNextBoolean();
	merge_layers = gd.getNextBoolean();		merge_layers = gd.getNextBoolean();
			ignore_affines = gd.getNextBoolean();
			ignore_equalize = gd.getNextBoolean();
	save_top_dir= gd.getNextString();		save_top_dir= gd.getNextString();
	sub_dir= gd.getNextString();		sub_dir= gd.getNextString();
	show_images= gd.getNextBoolean();		show_images= gd.getNextBoolean();
	@@ -5015,13 +5023,22 @@ public class OrthoMapsCollection implements Serializable{
	int [] wh = new int[2];		int [] wh = new int[2];
	int [] origin = new int[2];		int [] origin = new int[2];
	double [][] centers = show_centers? (new double [indices.length][]): null;		double [][] centers = show_centers? (new double [indices.length][]): null;
			double [][][] affines = null;
			if (ignore_affines) {
			affines = new double [indices.length][2][3];
			for (int i = 0; i < indices.length; i++) {
			affines[i][0][0] = 1;
			affines[i][1][1] = 1;
			}
			}

	double [][] dmulti = renderMultiDouble (		double [][] dmulti = renderMultiDouble (
	null, // double [][] ground_planes, // null - images, non-null altitudes. use new double[2][3] for old way alt		null, // double [][] ground_planes, // null - images, non-null altitudes. use new double[2][3] for old way alt
	indices, // int [] indices, // null or which indices to use (normally just 2 for pairwise comparison)		indices, // int [] indices, // null or which indices to use (normally just 2 for pairwise comparison)
	bounds_to_indices, // boolean bounds_to_indices,		bounds_to_indices, // boolean bounds_to_indices,
	null, // affines, // double [][][] affines, // null or [indices.length][2][3]		affines, // null, // affines, // double [][][] affines, // null or [indices.length][2][3]
	null, // double [][] equalize,		null, // double [][] equalize,
	true, // boolean ignore_equalize,		ignore_equalize, // true, // boolean ignore_equalize,
	null, // warp, // FineXYCorr warp,,		null, // warp, // FineXYCorr warp,,
	zoom_lev, // int zoom_level,		zoom_lev, // int zoom_level,
	wh, // int [] wh,		wh, // int [] wh,

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

+61 −91

Original line number	Original line	Diff line number	Diff line
	/**		/**
	**		**
	** OrthoMultiLMA - Fit multiple scenes orthographic using pair-wise affine		** OrthoMultiLMA - Fit multiple scenes orthographic using pair-wise affine
	** tr4ansform matrices already calculated.		** transform matrices already calculated.
	**		**
	** Copyright (C) 2024 Elphel, Inc.		** Copyright (C) 2024 Elphel, Inc.
	**		**
	@@ -48,8 +48,6 @@ public class OrthoMultiLMA {
	private double [] parameters_vector = null;		private double [] parameters_vector = null;
	// private double [] x_vector = null; // not used. Save total weight		// private double [] x_vector = null; // not used. Save total weight
	private double [] y_vector = null;		private double [] y_vector = null;
	private double [][] tile_centers = null;
	private double weight = 0; // total weight
	private double pure_weight; // weight of samples only as a fraction of total weight		private double pure_weight; // weight of samples only as a fraction of total weight
	private double [] weights; // normalized so sum is 1.0 for all - samples and extra regularization		private double [] weights; // normalized so sum is 1.0 for all - samples and extra regularization
	// private double pure_weight; // weight of samples only		// private double pure_weight; // weight of samples only
	@@ -219,17 +217,18 @@ public class OrthoMultiLMA {
	OrthoMapsCollection maps_collection,		OrthoMapsCollection maps_collection,
	String orthoMapsCollection_path		String orthoMapsCollection_path
	) {		) {
	int debugLevel = 1;		int debugLevel = 2;
	boolean move_only = false;		boolean move_only = false;
	double [] val_coord = null; // 1 - valid, 0 - invalid, minimize coordinates errors		double [] val_coord = null; // 1 - valid, 0 - invalid, minimize coordinates errors
			boolean ignore_affines = false;
	boolean use_inv = false;		boolean use_inv = false;
	double overlap_pow = 2.0; // match weight as overlap fraction to this power		double overlap_pow = 2.0; // match weight as overlap fraction to this power

	double skew_pull = 1.0;		double skew_pull = 1.0;
	double tilt_pull = 1.0;		double tilt_pull = 1.0;
	double scale_pull = 0.1; // .0;		double scale_pull = 0.1; // .0;
	double position_pull = 0.0001;		double position_pull = 0.0001;
	boolean corr_avg= (skew_pull > 0) \|\| (tilt_pull > 0) \|\| (scale_pull > 0);		boolean corr_avg= (skew_pull > 0) \|\| (tilt_pull > 0) \|\| (scale_pull > 0);
			boolean show_result_image = false;
	int [] indices = maps_collection.getScenesSelection(		int [] indices = maps_collection.getScenesSelection(
	null, // boolean select_all,		null, // boolean select_all,
	" to build a map"); // String purpose)		" to build a map"); // String purpose)
	@@ -247,6 +246,7 @@ public class OrthoMultiLMA {
	clt_parameters, // CLTParameters clt_parameters,		clt_parameters, // CLTParameters clt_parameters,
	maps_collection, // OrthoMapsCollection maps_collection,		maps_collection, // OrthoMapsCollection maps_collection,
	indices, // int [] indices,		indices, // int [] indices,
			ignore_affines, // boolean ignore_affines,
	val_coord, // double [] val_coord, // 1 - valid, 0 - invalid, minimize coordinates errors		val_coord, // double [] val_coord, // 1 - valid, 0 - invalid, minimize coordinates errors
	position_pull, // double position_pull,		position_pull, // double position_pull,
	skew_pull, // double skew_pull,		skew_pull, // double skew_pull,
	@@ -273,26 +273,10 @@ public class OrthoMultiLMA {
	}		}

	//Get and apply affines		//Get and apply affines
	//oml.updateAffines(maps_collection);		oml.updateAffines(maps_collection);
			if (show_result_image) {
	double [][][] affines = oml.getAffines();		double [][][] affines = oml.getAffines();
	double [] fx = oml.getFx();		double [] fx = oml.getFx();
	// test
	/*
	PairwiseOrthoMatch match = maps_collection.ortho_maps[indices[0]].getMatch(maps_collection.ortho_maps[indices[1]].getName());
	double [][] match_affine = match.getAffine();

	double [] enuOffset = maps_collection.ortho_maps[indices[1]].enuOffsetTo(maps_collection.ortho_maps[indices[0]]);
	double [] rd = {enuOffset[0], -enuOffset[1]}; // {right,down} of the image

	double [][] affine1a = PairwiseOrthoMatch.combineAffines(
	affines[0], // double [][] affine0,
	match_affine, //double [][] affine, // differential
	rd); // double [] rd);
	PairwiseOrthoMatch test_match = new PairwiseOrthoMatch (
	affines[0], // double [][] affine0,
	affines[1], // double [][] affine1,
	rd); // double [] rd);
	*/

	int zoom_level = -2;		int zoom_level = -2;
	int [] wh = new int[2];		int [] wh = new int[2];
	@@ -328,21 +312,8 @@ public class OrthoMultiLMA {
	roi.setOptions("label");		roi.setOptions("label");
	imp_multi.setRoi(roi);		imp_multi.setRoi(roi);
	imp_multi.show();		imp_multi.show();
	/*		}
	double [][] affine = getAffineAndDerivatives(
	move_only, //boolean move_only,
	affines[0], // double [][] affine00,
	affines[1], // double [][] affine10,
	oml.offsets[0], // double [] rd,
	null); // double [][][] derivs)
	PairwiseOrthoMatch pom = new PairwiseOrthoMatch (
	affines[0],
	affines[1],
	oml.offsets[0]);
	*/


	/*
	if (orthoMapsCollection_path != null) {		if (orthoMapsCollection_path != null) {
	try {		try {
	maps_collection.writeOrthoMapsCollection(orthoMapsCollection_path);		maps_collection.writeOrthoMapsCollection(orthoMapsCollection_path);
	@@ -354,7 +325,6 @@ public class OrthoMultiLMA {
	System.out.println("Saved data to "+ orthoMapsCollection_path);		System.out.println("Saved data to "+ orthoMapsCollection_path);
	}		}
	}		}
	*/
	return 0;		return 0;
	}		}

	@@ -373,6 +343,7 @@ public class OrthoMultiLMA {
	CLTParameters clt_parameters,		CLTParameters clt_parameters,
	OrthoMapsCollection maps_collection,		OrthoMapsCollection maps_collection,
	int [] indices,		int [] indices,
			boolean ignore_affines,
	double [] val_coord, // 1 - valid, 0 - invalid, minimize coordinates errors		double [] val_coord, // 1 - valid, 0 - invalid, minimize coordinates errors
	double position_pull,		double position_pull,
	double skew_pull,		double skew_pull,
	@@ -434,7 +405,7 @@ public class OrthoMultiLMA {
	weights = new double [n62num_pairs + 2 num_scenes + (corr_avg ? 3:0)];		weights = new double [n62num_pairs + 2 num_scenes + (corr_avg ? 3:0)];
	parameters_vector = new double [n62*num_scenes]; // maybe will need move-only mode?		parameters_vector = new double [n62*num_scenes]; // maybe will need move-only mode?
	for (int n = 0; n < num_scenes; n++) {		for (int n = 0; n < num_scenes; n++) {
	double [][] affine = maps_collection.ortho_maps[indices[n]].getAffine();		double [][] affine = ignore_affines? (new double[][] {{1,0,0},{0,1,0}}):maps_collection.ortho_maps[indices[n]].getAffine();
	System.arraycopy(affine[0], 0, parameters_vector, n62*n, n13);		System.arraycopy(affine[0], 0, parameters_vector, n62*n, n13);
	System.arraycopy(affine[1], 0, parameters_vector, n62*n + n13, n13);		System.arraycopy(affine[1], 0, parameters_vector, n62*n + n13, n13);
	y_vector[n62num_pairs+2n + 0] = affine[0][2];		y_vector[n62num_pairs+2n + 0] = affine[0][2];
	@@ -760,7 +731,7 @@ public class OrthoMultiLMA {
	return affine; // _alt;		return affine; // _alt;
	}		}

	private static int [][] createNonIntersectingPairs(int [][] pairs) {		public static int [][] createNonIntersectingPairs(int [][] pairs) {
	ArrayList<Integer> pairs_list = new ArrayList<Integer>();		ArrayList<Integer> pairs_list = new ArrayList<Integer>();
	for (int i = 0; i < pairs.length; i++) {		for (int i = 0; i < pairs.length; i++) {
	pairs_list.add(i);		pairs_list.add(i);
	@@ -835,7 +806,7 @@ public class OrthoMultiLMA {
	System.out.println("LMA step "+iter+": {"+rslt[0]+","+rslt[1]+"} full RMS= "+good_or_bad_rms[0]+		System.out.println("LMA step "+iter+": {"+rslt[0]+","+rslt[1]+"} full RMS= "+good_or_bad_rms[0]+
	" ("+initial_rms[0]+"), pure RMS="+good_or_bad_rms[1]+" ("+initial_rms[1]+") + lambda="+lambda);		" ("+initial_rms[0]+"), pure RMS="+good_or_bad_rms[1]+" ("+initial_rms[1]+") + lambda="+lambda);
	}		}
	if (rslt[1]) {		if (rslt[1]) {// the place to put a breakpoint
	break;		break;
	}		}
	if (rslt[0]) { // good		if (rslt[0]) { // good
	@@ -1035,7 +1006,6 @@ public class OrthoMultiLMA {
	return rslt;		return rslt;
	}		}


	private double [][] getWJtJlambda(		private double [][] getWJtJlambda(
	final double lambda,		final double lambda,
	final double [][] jt)		final double [][] jt)
	@@ -1129,11 +1099,11 @@ public class OrthoMultiLMA {
	return last_rms;		return last_rms;

	}		}

	public double [] getInitialRms() {		public double [] getInitialRms() {
	return initial_rms;		return initial_rms;
	}		}


	private double [] getFxDerivs(		private double [] getFxDerivs(
	final double [] vector,		final double [] vector,
	final double [][] jt, // should be null or initialized with [vector.length][]		final double [][] jt, // should be null or initialized with [vector.length][]

Original line number	Original line	Diff line number	Diff line
	@@ -159,6 +159,8 @@ public class ComboMatch {
	boolean create_overlaps = false;		boolean create_overlaps = false;
	boolean equalize_overlaps = false;		boolean equalize_overlaps = false;
	boolean create_map = false;		boolean create_map = false;
			boolean create_equalize = false;

	// boolean show_combo_mask = false; // generate image mas (where it is defined)_		// boolean show_combo_mask = false; // generate image mas (where it is defined)_
	// boolean use_alt = false;		// boolean use_alt = false;
	// boolean show_centers = true;		// boolean show_centers = true;
	@@ -194,7 +196,7 @@ public class ComboMatch {
	}		}


	GenericJTabbedDialog gd = new GenericJTabbedDialog("Set image pair",1200,700);		GenericJTabbedDialog gd = new GenericJTabbedDialog("Set image pair",1200,800);
	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, files_lists_paths[default_list_choice]);
	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.");
	@@ -235,6 +237,7 @@ public class ComboMatch {
	gd.addCheckbox ("Create overlap pairs", create_overlaps, "Create scene pairs overlaps.");		gd.addCheckbox ("Create overlap pairs", create_overlaps, "Create scene pairs overlaps.");
	gd.addCheckbox ("Equalize overlap pairs", equalize_overlaps, "Equalize intensities in overlaps.");		gd.addCheckbox ("Equalize overlap pairs", equalize_overlaps, "Equalize intensities in overlaps.");
	gd.addCheckbox ("Create map", create_map, "Create combined map from pairwise matches.");		gd.addCheckbox ("Create map", create_map, "Create combined map from pairwise matches.");
			gd.addCheckbox ("Equalize intensities", create_equalize, "Create map intensities equalization from pairwise matches.");
	// gd.addCheckbox ("Show combo image mask", show_combo_mask, "Display combo binary image.");		// gd.addCheckbox ("Show combo image mask", show_combo_mask, "Display combo binary image.");
	// 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.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.");
	@@ -263,6 +266,7 @@ public class ComboMatch {
	String orthoMapsCollection_path =files_lists_paths[choice_index]+".data";		String 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();
			String orthoMapsCollection_savepath = save_collection?orthoMapsCollection_path:null;
	process_correlation= gd.getNextBoolean();		process_correlation= gd.getNextBoolean();
	num_tries_fit = (int) gd.getNextNumber();		num_tries_fit = (int) gd.getNextNumber();
	update_match= gd.getNextBoolean();		update_match= gd.getNextBoolean();
	@@ -292,6 +296,7 @@ public class ComboMatch {
	create_overlaps = gd.getNextBoolean();		create_overlaps = gd.getNextBoolean();
	equalize_overlaps = gd.getNextBoolean();		equalize_overlaps = gd.getNextBoolean();
	create_map = gd.getNextBoolean();		create_map = gd.getNextBoolean();
			create_equalize = gd.getNextBoolean();
	frac_remove = gd.getNextNumber();		frac_remove = gd.getNextNumber();
	metric_error= gd.getNextNumber();		metric_error= gd.getNextNumber();