Matching altitudes (7ad0875e) · Commits · Elphel / imagej-elphel

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

+1 −0

Original line number	Diff line number	Diff line
		@@ -114,6 +114,7 @@ public class DoubleGaussianBlur {
		* @param extraLines Number of lines (parallel to the blurring direction)
		* below and above the roi bounds that should be processed.
		*/
		// TODO: Make threaded!
		public void blur1Direction(double [] pixels,
		int width,
		int height,

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

+127 −3

Original line number	Diff line number	Diff line
		@@ -11,6 +11,8 @@ import java.util.Arrays;
		import java.util.Calendar;
		import java.util.Collections;
		import java.util.Comparator;
		import java.util.HashMap;
		import java.util.HashSet;
		import java.util.Properties;
		import java.util.Random;
		import java.util.concurrent.atomic.AtomicInteger;
		@@ -27,6 +29,7 @@ import com.elphel.imagej.gpu.TpTask;
		import com.elphel.imagej.ims.Imx5;
		import com.elphel.imagej.readers.ElphelTiffReader;
		import com.elphel.imagej.tileprocessor.ImageDtt;
		import com.elphel.imagej.tileprocessor.IntersceneMatchParameters;
		import com.elphel.imagej.tileprocessor.OpticalFlow;
		import com.elphel.imagej.tileprocessor.QuadCLT;
		import com.elphel.imagej.tileprocessor.TDCorrTile;
		@@ -166,10 +169,13 @@ public class ComboMatch {
		boolean create_pairwise_affines = false;
		boolean augment_pairwise_affines = false; // needs to repeat create_pairwise_matches to update overlaps
		boolean equalize_overlaps = false;
		boolean altitude_match_pairs = false;
		boolean display_pairs = false;
		boolean create_map = false;
		boolean create_equalize = false;



		boolean use_saved_collection = true; // false;
		boolean save_collection = true;
		boolean process_correlation = true; // use false to save new version of data
		@@ -187,6 +193,7 @@ public class ComboMatch {
		boolean update_lla = false; // re-read file metadata
		boolean update_kernel_patterns = false;
		boolean update_bl_bc = false;
		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;
		@@ -232,6 +239,8 @@ public class ComboMatch {
		gd.addCheckbox ("Create pairwise affines", create_pairwise_affines, "Create affines for scene pairs.");
		gd.addCheckbox ("Augment pairwise affines", augment_pairwise_affines, "Augment pairwise affines after building initial map and re-running create_pairwise_matches.");
		gd.addCheckbox ("Equalize overlap pairs", equalize_overlaps, "Equalize intensities in overlaps.");
		gd.addCheckbox ("Altitude match pairs", altitude_match_pairs, "Pairwise match scenes altitude.");
		gd.addCheckbox ("Display pairs", display_pairs, "Display pairwise match data.");
		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.addNumericField("Remove fraction of worst matches", frac_remove, 3,7,"", "When fitting scenes remove this fraction of worst match.");
		@@ -241,6 +250,8 @@ public class ComboMatch {
		}
		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:",
		@@ -284,6 +295,8 @@ public class ComboMatch {
		create_pairwise_affines = gd.getNextBoolean();
		augment_pairwise_affines = gd.getNextBoolean();
		equalize_overlaps = gd.getNextBoolean();
		altitude_match_pairs = gd.getNextBoolean();
		display_pairs = gd.getNextBoolean();
		create_map = gd.getNextBoolean();
		create_equalize = gd.getNextBoolean();
		frac_remove = gd.getNextNumber();
		@@ -293,6 +306,7 @@ public class ComboMatch {
		}
		update_lla= gd.getNextBoolean();
		update_kernel_patterns= gd.getNextBoolean();
		fix_duplicates= gd.getNextBoolean();
		update_bl_bc= gd.getNextBoolean();
		suffix_bc_bl_indx = gd.getNextChoiceIndex();
		log_append = gd.getNextBoolean();
		@@ -325,6 +339,9 @@ public class ComboMatch {
		maps_collection.updateNumberScenes();
		maps_collection.updateSfmGain();
		}
		if (fix_duplicates) {
		removeDuplicateScenes (maps_collection);
		}

		if (update_bl_bc) {
		boolean OK = updateBlBcFileNames(
		@@ -826,6 +843,19 @@ public class ComboMatch {
		return ok; // Just exit, do not try other commands. if (!ok) return false;
		}

		if (altitude_match_pairs) {
		boolean ok =maps_collection.altutudeMatchPairs(
		clt_parameters, // CLTParameters clt_parameters,
		orthoMapsCollection_savepath); // String orthoMapsCollection_path);
		return ok; // Just exit, do not try other commands. if (!ok) return false;
		}

		if (display_pairs) {
		boolean ok =maps_collection.displayScenePairs(
		clt_parameters, // CLTParameters clt_parameters,
		orthoMapsCollection_savepath); // String orthoMapsCollection_path);
		return ok; // Just exit, do not try other commands. if (!ok) return false;
		}
		if (process_correlation \|\| render_match \|\| pattern_match \|\| test_multi_lma) {
		// int [] gpu_pair;
		if (gpu_spair == null) {
		@@ -864,11 +894,15 @@ public class ComboMatch {
		boolean flt_filt_zoom = clt_parameters.imp.flt_filt_zoom; // true;
		int flt_min_zoom = clt_parameters.imp.flt_min_zoom; // -2;
		int flt_max_zoom = clt_parameters.imp.flt_max_zoom; // 10;
		double flt_min_sfm = clt_parameters.imp.flt_min_sfm; // 0.0;
		double flt_max_sfm = clt_parameters.imp.flt_max_sfm; //1000.0;
		int flt_alt = clt_parameters.imp.flt_alt; // 0;

		boolean flt_show_names = clt_parameters.imp.flt_show_names; // true;
		boolean flt_show_overlaps = clt_parameters.imp.flt_show_overlaps; // true;
		boolean flt_show_rms = clt_parameters.imp.flt_show_rms; // true;
		boolean flt_show_zoom = clt_parameters.imp.flt_show_zoom; // true;
		boolean flt_show_alt = clt_parameters.imp.flt_show_alt; // true;
		boolean flt_update_config = false;
		String flt_extra_line = "--- select a single image ---";
		GenericJTabbedDialog gdf = new GenericJTabbedDialog("Select pairs filter/display",800,500);
		@@ -882,11 +916,16 @@ public class ComboMatch {
		gdf.addCheckbox ("Filter by zoom level" , flt_filt_zoom, "Filter by the zoom level used for matching.");
		gdf.addNumericField("Minimal zoom", flt_min_zoom, 0,3,"","Minimal zoom level used for matching.");
		gdf.addNumericField("Maximal zoom", flt_max_zoom, 0,3,"","Maximal zoom level used for matching.");
		gdf.addNumericField("Minimal SfM gain", flt_min_sfm, 3,7,"","Minimal SfM gain of the minimum in the scene pair.");
		gdf.addNumericField("Maximal SfM gain", flt_max_sfm, 3,7,"","Maximal SfM gain of the minimum in the scene pair.");
		gdf. addChoice("Filter by pairwise ALT availability",IntersceneMatchParameters.FLT_ALT_MODES, IntersceneMatchParameters.FLT_ALT_MODES[flt_alt],
		"Filter by pairwise ALT availability.");

		gdf.addCheckbox ("Show scene names", flt_show_names, "Show scene full names (timestamps) in selection drop-down list.");
		gdf.addCheckbox ("Show scene overlaps", flt_show_overlaps, "Show scene overlaps (in percents) in selection drop-down list.");
		gdf.addCheckbox ("Show pairs RMSE", flt_show_rms, "Show scene match RMSE in selection drop-down list.");
		gdf.addCheckbox ("Show zoom level", flt_show_zoom, "Show zoom level.");
		gdf.addCheckbox ("Show ALT", flt_show_alt, "Show altitude data availability.");

		gdf.addCheckbox ("Update configuration", flt_update_config, "Update matching configuration parameters to be saved as defaults.");
		gdf.showDialog();
		@@ -901,11 +940,15 @@ public class ComboMatch {
		flt_filt_zoom = gdf.getNextBoolean();
		flt_min_zoom =(int) gdf.getNextNumber();
		flt_max_zoom =(int) gdf.getNextNumber();
		flt_min_sfm = gdf.getNextNumber();
		flt_max_sfm = gdf.getNextNumber();
		flt_alt = gdf.getNextChoiceIndex();

		flt_show_names = gdf.getNextBoolean();
		flt_show_overlaps = gdf.getNextBoolean();
		flt_show_rms = gdf.getNextBoolean();
		flt_show_zoom = gdf.getNextBoolean();
		flt_show_alt = gdf.getNextBoolean();
		flt_update_config = gdf.getNextBoolean();
		if (flt_update_config) {
		clt_parameters.imp.flt_list = flt_list;
		@@ -918,10 +961,14 @@ public class ComboMatch {
		clt_parameters.imp.flt_filt_zoom = flt_filt_zoom;
		clt_parameters.imp.flt_min_zoom = flt_min_zoom;
		clt_parameters.imp.flt_max_zoom = flt_max_zoom;
		clt_parameters.imp.flt_min_sfm = flt_min_sfm;
		clt_parameters.imp.flt_max_sfm = flt_max_sfm;
		clt_parameters.imp.flt_alt = flt_alt;
		clt_parameters.imp.flt_show_names = flt_show_names;
		clt_parameters.imp.flt_show_overlaps = flt_show_overlaps;
		clt_parameters.imp.flt_show_rms = flt_show_rms;
		clt_parameters.imp.flt_show_zoom = flt_show_zoom;
		clt_parameters.imp.flt_show_alt = flt_show_alt;
		}

		if (flt_list) {
		@@ -935,7 +982,11 @@ public class ComboMatch {
		flt_nan_rms, // boolean nan_rms)
		flt_filt_zoom, // boolean filt_zoom,
		flt_min_zoom, // int min_zoom,
		flt_max_zoom); // int max_zoom)
		flt_max_zoom, // int max_zoom)
		flt_min_sfm, // double min_sfm,
		flt_max_sfm, // double max_sfm,
		flt_alt); // int flt_alt)

		}

		String [] choices_all = maps_collection.textPairs (
		@@ -944,6 +995,8 @@ public class ComboMatch {
		flt_show_overlaps, // boolean show_overlap,
		flt_show_rms, // boolean show_rms,
		flt_show_zoom, // boolean show_zoom,
		flt_show_alt, // boolean show_alt,
		false, // boolean use_tab,
		flt_extra_line); // String extra_line)

		GenericJTabbedDialog gdc = new GenericJTabbedDialog("Select image pair",1200,100);
		@@ -1399,6 +1452,77 @@ public class ComboMatch {
		return pairwiseOrthoMatch;
		}

		public static boolean removeDuplicateScenes(
		OrthoMapsCollection maps_collection) {
		String duplicate_name=null;
		do {
		HashSet<String> scene_names = new HashSet<String>();
		duplicate_name=null;
		for (int i = 0; i < maps_collection.ortho_maps.length; i++) {
		String name = maps_collection.ortho_maps[i].getName();
		if (scene_names.contains(name)) {
		duplicate_name=name;
		break;
		}
		scene_names.add(name);
		}
		if (duplicate_name != null) {
		long latest_modified = -1;
		int latest_index = -1;
		ArrayList<Integer> duplicates = new ArrayList<Integer>();
		for (int i = 0; i < maps_collection.ortho_maps.length; i++) {
		if (maps_collection.ortho_maps[i].getName().equals(duplicate_name)) {
		duplicates.add(i);
		long mod_ts = (new File(maps_collection.ortho_maps[i].getPath())).lastModified();
		if (mod_ts > latest_modified) {
		latest_index = i;
		}
		}
		}
		if (duplicates.size()> 1) {
		System.out.println("removeDuplicateScenes(): found " +duplicates.size()+ " duplicates for scene "+duplicate_name+":");
		for (int i :duplicates) {
		System.out.println(((i==latest_index)?" KEEP ":"REMOVE ")+maps_collection.ortho_maps[i].getPath());
		}

		// combine pairwise matches, remove self-paired
		HashMap <String, PairwiseOrthoMatch> combo_pairwise_matches = new HashMap <String, PairwiseOrthoMatch>();
		OrthoMap [] new_maps = new OrthoMap[maps_collection.ortho_maps.length-duplicates.size()+1];
		int indx = 0;
		int new_indx = -1;
		for (int i = 0; i < maps_collection.ortho_maps.length; i++) {
		if (duplicates.contains(i)) {
		for (String key:maps_collection.ortho_maps[i].pairwise_matches.keySet()) {
		if (!key.equals(duplicate_name) && !combo_pairwise_matches.containsKey(key)) {
		combo_pairwise_matches.put(key, maps_collection.ortho_maps[i].pairwise_matches.get(key));
		}
		}
		}
		if (!duplicates.contains(i) \|\| (i == latest_index)) {

		if (i == latest_index) {
		new_indx = indx;
		}
		new_maps[indx++] = maps_collection.ortho_maps[i];
		}
		}
		maps_collection.ortho_maps = new_maps;
		maps_collection.ortho_maps[new_indx].pairwise_matches = combo_pairwise_matches;
		// remove pairs with (now) itself
		} else {
		System.out.println("removeDuplicateScenes(): BUG - number of duplicates = "+duplicates.size()+", aborting.");
		return false;
		}
		// find latest file
		}

		} while (duplicate_name != null);
		maps_collection.reindex();
		return true;
		}



		public static boolean updateBlBcFileNames(
		String suffix,
		String before,

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

0 → 100644

+308 −0

File added.

Preview size limit exceeded, changes collapsed.

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

+292 −2

Original line number	Diff line number	Diff line
		@@ -27,6 +27,7 @@ import java.util.concurrent.atomic.AtomicInteger;

		import com.elphel.imagej.cameras.CLTParameters;
		import com.elphel.imagej.common.DoubleFHT;
		import com.elphel.imagej.common.DoubleGaussianBlur;
		import com.elphel.imagej.common.GenericJTabbedDialog;
		import com.elphel.imagej.common.PolynomialApproximation;
		import com.elphel.imagej.common.ShowDoubleFloatArrays;
		@@ -3468,6 +3469,141 @@ public class OrthoMap implements Comparable <OrthoMap>, Serializable{
		return mask;
		}

		/**
		* Remove specified fractions (0 <= (rlow+rhigh) <= 1.0) of too low and too high values
		* @param data double [] input data
		* @param mask_in optional (may be null) mask for the data array. Will be modified if provided.
		* @param abs_dif high limit of the histogram (reasonably higher than useful range of the data[])
		* @param rel_frac fraction of the highest data[] elements to remove
		* @param ground_plane null or {tilt_x, tilt_y, offs, x0,y0}, where tilt_x and tilt_y are per pixel.
		* x0, y0 are also in pixels (not meters)
		* @param width - width of the data[] array. Only used if ground_plane != null
		* @param num_bins number of the histogram bins
		* @return boolean array of the remaining data elements. Input mask_in array (if not null) is modified too.
		*/
		public static boolean [] removeRelativeLowHigh (
		final double [] data,
		final boolean [] mask_in,
		final double abs_diff,
		final double rel_frac,
		final double [] ground_plane, // tiltx,tilty, offs, x0(pix), y0(pix) or null
		final int width, // only used with ground_plane != null;
		final int num_bins) {
		final boolean [] mask = (mask_in == null) ? new boolean [data.length] : mask_in;
		if (mask_in == null) {
		Arrays.fill(mask, true);
		}
		final Thread[] threads = ImageDtt.newThreadArray();
		final AtomicInteger ai = new AtomicInteger(0);
		final AtomicInteger ati = new AtomicInteger(0);
		final double [][] hist2 = new double [threads.length][num_bins];
		final double scale = num_bins/abs_diff;
		for (int ithread = 0; ithread < threads.length; ithread++) {
		threads[ithread] = new Thread() {
		public void run() {
		int thread_num = ati.getAndIncrement();
		for (int nPix = ai.getAndIncrement(); nPix < data.length; nPix = ai.getAndIncrement()) if (mask[nPix]){
		double d = data[nPix];
		if (!Double.isNaN(d)) {
		if (ground_plane != null) {
		double x = nPix % width - ground_plane[3];
		double y = nPix/width - ground_plane[4];
		double tilt_x = ground_plane[0];
		double tilt_y = ground_plane[1];
		double offs = ground_plane[2];
		d -= x * tilt_x + y * tilt_y + offs;
		}
		int bin = Math.min(Math.max(((int) Math.round(Math.abs(d)*scale)), 0), num_bins-1);
		hist2[thread_num][bin] += 1.0;
		}
		}
		}
		};
		}
		ImageDtt.startAndJoin(threads);
		ai.set(0);
		final double [] hist = new double [num_bins];
		for (int ithread = 0; ithread < threads.length; ithread++) {
		threads[ithread] = new Thread() {
		public void run() {
		for (int bin = ai.getAndIncrement(); bin < num_bins; bin = ai.getAndIncrement()) {
		for (int i = 0; i < hist2.length; i++) {
		hist[bin]+= hist2[i][bin];
		}
		}
		}
		};
		}
		ImageDtt.startAndJoin(threads);
		double sw = 0;
		for (int bin = 0; bin < num_bins; bin++) {
		sw += hist[bin];
		}
		// double trlow = sw * rlow;
		double trhigh = sw * rel_frac; // rhigh;
		double sh = 0, shp = 0;
		double threshold_high = abs_diff; // abs_high;
		for (int bin = num_bins-1; bin>=0; bin--) {
		shp = sh;
		sh += hist[bin];
		if (sh > trhigh) {
		double r = (sh-trhigh)/(sh-shp);
		threshold_high = (bin + r)/scale; // abs_low + (bin + r)/scale;
		break;
		}
		}
		sh = 0;
		shp = 0;
		/*
		double threshold_low = abs_low;
		for (int bin = 0; bin < num_bins; bin++) {
		shp = sh;
		sh += hist[bin];
		if (sh > trlow) {
		double r = (trlow-shp)/(sh-shp);
		threshold_low = abs_low + (bin + r)/scale;
		break;
		}
		}
		final double fthreshold_low = threshold_low;
		*/
		final double fthreshold_high = threshold_high;
		if (ground_plane == null) {
		return removeAbsoluteLowHigh (
		data, // final double [] data,
		mask, // final boolean [] mask,
		fthreshold_high, // final double threshold_high,
		-fthreshold_high); // fthreshold_low); // final double threshold_low)
		}
		ai.set(0);
		for (int ithread = 0; ithread < threads.length; ithread++) {
		threads[ithread] = new Thread() {
		public void run() {
		// int thread_num = ati.getAndIncrement();
		for (int nPix = ai.getAndIncrement(); nPix < data.length; nPix = ai.getAndIncrement()) if (mask[nPix]){
		double d = data[nPix];
		if (!Double.isNaN(d)) {
		double x = nPix % width - ground_plane[3];
		double y = nPix/width - ground_plane[4];
		double tilt_x = ground_plane[0];
		double tilt_y = ground_plane[1];
		double offs = ground_plane[2];
		d -= x * tilt_x + y * tilt_y + offs;
		// if (!((d >= fthreshold_low) && (d <= fthreshold_high))) {
		if (!((d >= -fthreshold_high) && (d <= fthreshold_high))) {
		mask[nPix] = false;
		}
		}
		}
		}
		};
		}
		ImageDtt.startAndJoin(threads);
		return mask;
		}



		/**
		* Remove (mask out) tiles that have high product of distance (in pixels) from the vertical point
		* by the metric difference between the elevation and an approximation plane
		@@ -3523,6 +3659,50 @@ public class OrthoMap implements Comparable <OrthoMap>, Serializable{
		return mask;
		}

		public static double [] getBorderWeights(
		final double [] data,
		final double sigma,
		int width) {
		double [] weights = new double [data.length];
		final Thread[] threads = ImageDtt.newThreadArray();
		final AtomicInteger ai = new AtomicInteger(0);
		for (int ithread = 0; ithread < threads.length; ithread++) {
		threads[ithread] = new Thread() {
		public void run() {
		for (int nPix = ai.getAndIncrement(); nPix < data.length; nPix = ai.getAndIncrement()){
		weights[nPix] = Double.isNaN(data[nPix])? -1:1;
		}
		}
		};
		}
		ImageDtt.startAndJoin(threads);

		// TODO: Make threaded !
		(new DoubleGaussianBlur()).blurDouble(
		weights, // double[] pixels,
		width, // int width,
		weights.length/width, // int height,
		sigma, // double sigmaX,
		sigma, // double sigmaY,
		0.01); // double accuracy);
		ai.set(0);
		for (int ithread = 0; ithread < threads.length; ithread++) {
		threads[ithread] = new Thread() {
		public void run() {
		for (int nPix = ai.getAndIncrement(); nPix < data.length; nPix = ai.getAndIncrement()){
		if (weights[nPix] < 0) {
		weights[nPix] = 0;
		}
		}
		}
		};
		}
		ImageDtt.startAndJoin(threads);
		return weights;
		}





		/**
		@@ -3534,12 +3714,13 @@ public class OrthoMap implements Comparable <OrthoMap>, Serializable{
		* @param xy0 a pair of x0, y0 - origin where the plane is referenced too
		* @return double array of {tiltx, tilty, offset, xy0[0] and xy0[1]).
		*/
		private static double [] getPlane(
		public static double [] getPlane(
		final double [] data,
		final boolean [] mask,
		final double [] weight,
		final int width,
		final double [] xy0) {
		int debug = -1;
		final double [][][] mdatai = new double [data.length][][];
		AtomicInteger anum_good = new AtomicInteger(0);
		final Thread[] threads = ImageDtt.newThreadArray();
		@@ -3547,7 +3728,7 @@ public class OrthoMap implements Comparable <OrthoMap>, Serializable{
		for (int ithread = 0; ithread < threads.length; ithread++) {
		threads[ithread] = new Thread() {
		public void run() {
		for (int nPix = ai.getAndIncrement(); nPix < data.length; nPix = ai.getAndIncrement()) if (mask[nPix]){
		for (int nPix = ai.getAndIncrement(); nPix < data.length; nPix = ai.getAndIncrement()) if ((mask == null) \|\| mask[nPix]){
		double d = data[nPix];
		if (!Double.isNaN(d)) {
		int x = nPix % width;
		@@ -3577,11 +3758,40 @@ public class OrthoMap implements Comparable <OrthoMap>, Serializable{
		null, // damping, // double [] damping, null OK
		-1); // debug level
		if (approx2d != null) {
		if (debug > 0) {
		double [] plane=new double[data.length];
		double [] diff=new double[data.length];
		double [] dweight = (weight != null) ? weight: new double[data.length];
		double [] dmask = new double[data.length];
		double [] masked = new double[data.length];
		Arrays.fill(masked, Double.NaN);
		for (int nPix = 0; nPix < plane.length; nPix++) {
		int x = nPix % width;
		int y = nPix / width;
		double dx = x-xy0[0];
		double dy = y-xy0[1];
		plane[nPix] = approx2d[0][2]+approx2d[0][0]dx+approx2d[0][1]dy;
		diff[nPix] = data[nPix]-plane[nPix];
		dmask[nPix] = ((mask == null) \|\| Double.isNaN(data[nPix]))? Double.NaN : (mask[nPix]?2:1);
		if ((mask == null) \|\| mask[nPix]) {
		masked[nPix] = diff[nPix];
		}
		}
		ShowDoubleFloatArrays.showArrays(
		new double[][] {data,plane,diff,masked,dweight,dmask},
		width,
		data.length/width,
		true,
		"plane_approximation",
		new String[] {"data","approx","diff","masked","weight","mask"});
		}

		return new double[] {approx2d[0][0], approx2d[0][1], approx2d[0][2], xy0[0], xy0[1]}; // tiltX, tiltY, offset
		}
		return null;
		}


		/**
		* Trying to estimate image OTF to modify correlation results. Some images are better, some - worse
		* (blurred because of elevation errors)? For all image or parts of it? So on some images all
		@@ -5359,6 +5569,86 @@ public class OrthoMap implements Comparable <OrthoMap>, Serializable{
		return new double [] {beta, s,t, g_p_b};
		}

		public static Rectangle getDefinedBounds(
		final double [][] data_slices,
		final int width) { // null or same length as data_slices[i]
		final int height = data_slices[0].length/width;
		final Thread[] threads = ImageDtt.newThreadArray();
		final AtomicInteger ai = new AtomicInteger(0);
		final AtomicInteger ati = new AtomicInteger(0);
		final int [][][] bounds = new int [threads.length][2][2]; // [thread][x/y][min/max]
		for (int i = 0; i < bounds.length; i++) {
		bounds[i][0][0] = width; // min x
		bounds[i][1][0] = height;// min y
		bounds[i][0][1] = -1; // max x
		bounds[i][1][1] = -1; // max y
		}
		for (int ithread = 0; ithread < threads.length; ithread++) {
		threads[ithread] = new Thread() {
		public void run() {
		int thread_num = ati.getAndIncrement();
		for (int ipix = ai.getAndIncrement(); ipix < data_slices[0].length; ipix = ai.getAndIncrement()) {
		pix_loop: {
		for (int i = 0; i < data_slices.length; i++) {
		if (Double.isNaN(data_slices[i][ipix])) {
		break pix_loop;
		}
		}
		int px = ipix % width;
		int py = ipix / width;
		if (px < bounds[thread_num][0][0]) bounds[thread_num][0][0] = px;
		if (px > bounds[thread_num][0][1]) bounds[thread_num][0][1] = px;
		if (py < bounds[thread_num][1][0]) bounds[thread_num][1][0] = py;
		if (py > bounds[thread_num][1][1]) bounds[thread_num][1][1] = py;
		}
		}
		}
		};
		}
		ImageDtt.startAndJoin(threads);
		for (int i = 1; i < bounds.length; i++) {
		for (int j = 0; j < 2; j++) {
		bounds [0][j][0] = Math.min(bounds [0][j][0], bounds [i][j][0]);
		bounds [0][j][1] = Math.max(bounds [0][j][1], bounds [i][j][1]);
		}
		}
		Rectangle rbounds = new Rectangle(
		bounds[0][0][0],
		bounds [0][1][0],
		bounds[0][0][1]-bounds[0][0][0]+1,
		bounds[0][1][1]-bounds[0][1][0]+1);
		return rbounds;
		}

		public static double [] subtractWoi(
		final double [] data0,
		final double [] data1,
		final int width,
		Rectangle woi_in) {
		final int height = data0.length/width;
		if (woi_in == null) {
		woi_in =new Rectangle(0,0,width,height);
		}
		final Rectangle woi = new Rectangle(woi_in);
		final int woi_len = woi.width*woi.height;
		final double [] data_out =new double [woi_len];
		final Thread[] threads = ImageDtt.newThreadArray();
		final AtomicInteger ai = new AtomicInteger(0);
		for (int ithread = 0; ithread < threads.length; ithread++) {
		threads[ithread] = new Thread() {
		public void run() {
		for (int iPix = ai.getAndIncrement(); iPix < woi_len; iPix = ai.getAndIncrement()) {
		int x = woi.x + (iPix % woi.width);
		int y = woi.y + (iPix / woi.width);
		int nPix = y * width + x;
		data_out[iPix] = data1[nPix] - data0[nPix];
		}
		}
		};
		}
		ImageDtt.startAndJoin(threads);
		return data_out;

		}

		}

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

+505 −80

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