Testing DATI (24a92f5c) · Commits · Elphel / imagej-elphel

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

+133 −18

Original line number	Diff line number	Diff line
		@@ -42,12 +42,43 @@ public class ComboMatch {
		public static boolean openTestPairGps(
		CLTParameters clt_parameters,
		GPUTileProcessor gpu_tile_processor, // initialized by the caller
		final int debugLevel) {
		int debugLevel) {
		GPU_TILE_PROCESSOR = gpu_tile_processor;
		// find -L /media/elphel/SSD3-4GB/lwir16-proc/berdich3/linked/linked_1697875868-1697879449-b/ -type f -name "*-GCORR-GEO.tiff" \| sort > GCORR-GEO.list

		String files_list_path = "/media/elphel/SSD3-4GB/lwir16-proc/ortho_videos/maps_03_short.list";
		String orthoMapsCollection_path = "/media/elphel/SSD3-4GB/lwir16-proc/ortho_videos/ortho_maps_collection.data";
		// String files_list_path = "/media/elphel/SSD3-4GB/lwir16-proc/ortho_videos/maps_03_short.list";
		// String orthoMapsCollection_path = "/media/elphel/SSD3-4GB/lwir16-proc/ortho_videos/ortho_maps_collection.data";

		// String files_list_path = "/media/elphel/SSD3-4GB/lwir16-proc/ortho_videos/maps_04_short_20min.list";
		// String orthoMapsCollection_path = "/media/elphel/SSD3-4GB/lwir16-proc/ortho_videos/maps_04_short_20min.data";
		// String files_list_path = "/media/elphel/SSD3-4GB/lwir16-proc/ortho_videos/maps_05_short_27.list";
		// String orthoMapsCollection_path = "/media/elphel/SSD3-4GB/lwir16-proc/ortho_videos/maps_05_short_27.data";
		// String files_list_path = "/media/elphel/SSD3-4GB/lwir16-proc/ortho_videos/maps_07_short_27.list";
		// String orthoMapsCollection_path = "/media/elphel/SSD3-4GB/lwir16-proc/ortho_videos/maps_07_short_27.data";
		// String files_list_path = "/media/elphel/SSD3-4GB/lwir16-proc/ortho_videos/maps_08_november.list";
		// 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.list";
		String orthoMapsCollection_path = "/media/elphel/SSD3-4GB/lwir16-proc/ortho_videos/maps_19_sep13.data";
		//maps_19_sep13.list
		//maps_09_short.list
		//maps_08_november.list
		// int [] gpu_ipair = {1,2};
		// int [] gpu_ipair = {4,9}; //-> {4,24}
		// int [] gpu_ipair = {4,18};
		// String [] gpu_spair = {"1697877420_556997", "1697877527_942766"}; // 1697877564_888405"}; //58, 220
		// String [] gpu_spair = {"1697877419_940125", "1697877527_942766"}; // 1697877564_888405"}; //58, 220
		// String [] gpu_spair = {"1697877412_004148", "1697877522_274211"}; // 1697877564_888405"}; //58, 220
		// String [] gpu_spair = {"1697877409_353265", "1697877518_773045"};
		// String [] gpu_spair = {"1697877465_672024", "1697877563_587972"};
		// String [] gpu_spair = {"1697877465_672024", "1697878995_797332"};
		// String [] gpu_spair = {"1697877465_672024", "1697877528_776377"};
		// String [] gpu_spair = {"1694564245_111645", "1694564701_230240"}; // Morning Sep, 13
		// String [] gpu_spair = {"1694564245_111645", "1694564822_637346"}; // Morning Sep, 13
		String [] gpu_spair = {"1694564248_145989", "1694564819_336247"}; // Morning Sep, 13

		//

		double [][][] image_enuatr = {{{0,0,0},{0,0,0}},{{0,0,0},{0,0,0}}};
		int gpu_width= clt_parameters.imp.rln_gpu_width; // 3008;
		@@ -58,6 +89,7 @@ public class ComboMatch {
		boolean use_saved_collection = true; // false;
		boolean save_collection = true;
		boolean process_correlation = true; // use false to save new version of data
		boolean restore_temp = true;
		GenericJTabbedDialog gd = new GenericJTabbedDialog("Set image pair",1200,800);
		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.");
		@@ -87,6 +119,8 @@ public class ComboMatch {
		"GPU image height");
		gd.addCheckbox ("Show transformation centers", show_centers, "Mark verticals from the UAS on the ground.");
		gd.addCheckbox ("Process altitude images", 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.showDialog();
		if (gd.wasCanceled()) return false;
		@@ -113,6 +147,10 @@ public class ComboMatch {

		show_centers = gd.getNextBoolean();
		use_alt = gd.getNextBoolean();

		gpu_spair[0] = gd.getNextString();
		gpu_spair[1] = gd.getNextString();

		OrthoMapsCollection maps_collection=null;
		if (use_saved_collection) {
		try {
		@@ -125,9 +163,14 @@ public class ComboMatch {
		maps_collection = new OrthoMapsCollection(files_list_path); // should have ".list" extensiohn
		}
		String [] names = maps_collection.getNames();

		//getTemperature()
		// get all temperatures
		maps_collection. getAllTemperatures();


		// which pair to compare
		int [] gpu_pair = {1,2};
		String [] gpu_spair = {names[gpu_pair[0]],names[gpu_pair[1]]};
		// String [] gpu_spair = {names[gpu_ipair[0]],names[gpu_ipair[1]]};
		int [] origin = new int[2];
		ImagePlus imp_img = maps_collection.renderMulti (
		"multi_"+zoom_lev, // String title,
		@@ -165,14 +208,73 @@ public class ComboMatch {
		}

		double [][] affine0 = {{1,0,0},{0,1,0}}; // will always stay the same
		double [][] affine1 = {{1,0,0},{0,1,0}}; // will be variable // here in meters, relative to vertical point
		// double [][] affine1 = {
		// {1,0,-1.47336},
		// {0,1,-3.46664}}; // will be variable // here in meters, relative to vertical point
		//1697877414_404948 - 4 (0)
		//1697879062_336162 - 9 (1)
		// double [][] affine1 = {
		// {1.0002226408872814, -0.007965644488589378, -1.512310157498787},
		// {0.006494702666097521, 1.0002691922354188, -3.4553628872407023}};
		// double [][] affine1 = {{1,0,0},{0,1,0}}; // will always stay the same
		// [[1.0001698416441531, 0.0035703780078751575, 1.3965061354976767],
		// [0.005158652079706154, 1.0014361052510927, 1.204551528740014]]]
		// double [][] affine1 = {{1,0,1.33},
		// {0,1,1.227}};

		double [][] affine1 = {
		{1,0,0},
		{0,1,0}};

		// affine1[0][2] = 0.64; affine1[1][2] = 1.253; // {"1697877412_004148", "1697877522_274211"}; //
		// (346.250-348.000)/12.5,(277.000-269.250)/12.5 = (-0.14, 0.62)
		// affine1[0][2] = -0.14; affine1[1][2] = 0.62; // {"1697877409_353265", "1697877518_773045"}; //
		// affine1[0][2] = -1.44; affine1[1][2] = 1.653; //"1697877465_672024", "1697877563_587972"
		// affine1[0][2] = -0.25; affine1[1][2] = -1.627; //{"1697877465_672024", "1697878995_797332"};
		// affine1[0][2] = -1.08; affine1[1][2] = 3.267; //{"1697877465_672024", "1697877528_776377"};
		// affine1[0][2] = -1.2; affine1[1][2] = -0.9066; //{"1694564245_111645", "1694564701_230240"};
		// affine1[0][2] = 0.933; affine1[1][2] = -2.2667; //{"1694564245_111645", "1694564822_637346"};
		affine1[0][2] = 2.08; affine1[1][2] = -0.093; //{"1694564248_145989", "1694564819_336247"};
		double [][][] affines = {affine0,affine1};
		int [] gpu_pair = new int[gpu_spair.length];
		for (int i = 0; i < gpu_pair.length; i++) {
		gpu_pair[i] = maps_collection.getIndex(gpu_spair[i]);
		}
		int [] zooms = {-3,-1,1000,1000};
		debugLevel = 0;
		boolean batch_mode = true;
		for (int zi = 0; zi < zooms.length; zi++) {
		zoom_lev = zooms[zi];
		if (zoom_lev >=1000) {
		break;
		}
		// will modify affines[1], later add jtj, weight, smth. else?
		double [][] corr_pair_rslt = maps_collection.correlateOrthoPair(
		clt_parameters, // CLTParameters clt_parameters,
		gpu_spair, // String [] gpu_spair,
		batch_mode, // boolean batch_mode,
		gpu_pair, // String [] gpu_spair,
		affines, // double [][][] affines, // on top of GPS offsets
		zoom_lev, // int zoom_lev,
		debugLevel); // final int debugLevel)
		int render_zoom_lev = maps_collection.ortho_maps[gpu_pair[0]].getOriginalZoomLevel();
		ImagePlus imp_img_pair = maps_collection.renderMulti (
		"multi_"+gpu_spair[0]+"-"+gpu_spair[1]+"-zoom_"+render_zoom_lev+"_"+zoom_lev, // String title,
		false, // boolean use_alt,
		gpu_pair, // int [] indices, // null or which indices to use (normally just 2 for pairwise comparison)
		affines, // double [][][] affines, // null or [indices.length][2][3]
		show_centers, // boolean show_centers,
		render_zoom_lev, // int zoom_level,
		origin); // int [] origin){
		imp_img_pair.show();
		System.out.println("Done");
		if (debugLevel>-4) {
		System.out.println("adjusted affines[1] for a pair: "+gpu_spair[0]+"/"+gpu_spair[1]);
		System.out.println("[["+affines[1][0][0]+","+affines[1][0][1]+","+affines[1][0][2]+"],");
		System.out.println(" ["+affines[1][1][0]+","+affines[1][1][1]+","+affines[1][1][2]+"]]");
		System.out.println();
		}
		}

		}
		if (save_collection) {
		try {
		@@ -188,6 +290,20 @@ public class ComboMatch {
		return true;
		}
		/*
		adjusted affines[1] for a pair: 1697877465_672024/1697877563_587972 RMS= 0.14511264718699468 (0.14577676900752629)
		[[1.0065661054211072,0.009234141675959222,-1.4706666954418992],
		[-0.004304610680434175,1.0012437786888277,1.6394608778426498]]

		adjusted affines[1] for a pair: 1694564245_111645/1694564701_230240
		[[1.021246208683918,0.006667337255903127,-1.0137566435443375],
		[-0.010035351748801541,1.0294363088409202,-0.8395952637299295]]

		adjusted affines[1] for a pair: 1694564245_111645/1694564822_637346
		[[1.0148318094351692,0.01611699521114023,1.1534804399270817],
		[-0.025584298199020607,1.0182605131307008,-2.157143969635918]]

		*
		*
		double [] offset_xy_second = {0,0};
		double [][] corr_pair_rslt = maps_collection. correlateOrthoPair(
		clt_parameters, // CLTParameters clt_parameters,
		@@ -438,10 +554,10 @@ public class ComboMatch {
		clt_parameters.gpu_sigma_b, // final double gpu_sigma_b, // 0.9, 1.1
		clt_parameters.gpu_sigma_g, // final double gpu_sigma_g, // 0.6, 0.7
		clt_parameters.gpu_sigma_m, // final double gpu_sigma_m, // = 0.4; // 0.7;
		debugLevel); // final int globalDebugLevel)
		batch_mode? -3: debugLevel); // final int globalDebugLevel)
		int tilesX = img_width/GPUTileProcessor.DTT_SIZE;
		int tilesY = wh[1]/GPUTileProcessor.DTT_SIZE;
		if (debugLevel > 1) {
		if (!batch_mode && (debugLevel > 1)) {
		renderFromTD (
		true, // boolean use_reference,
		"ref"); //String suffix
		@@ -453,6 +569,7 @@ public class ComboMatch {
		final double gpu_sigma_log_corr = clt_parameters.getGpuCorrLoGSigma(image_dtt.isMonochrome());
		image_dtt.interRectilinearCorrTD(
		clt_parameters.img_dtt, //final ImageDttParameters imgdtt_params, // Now just extra correlation parameters, later will include, most others
		batch_mode, // final boolean batch_mode,
		erase_clt, // final int erase_clt,
		fpixels[1], // final float [] fpixels,
		wh, // final int [] wh, // null (use sensor dimensions) or pair {width, height} in pixels
		@@ -518,10 +635,8 @@ public class ComboMatch {
		rln_cent_radius, // final double centroid_radius, // 0 - all same weight, > 0 cosine(PI/2*sqrt(dx^2+dy^2)/rad)
		rln_n_recenter); // final int n_recenter); // re-center window around new maximum. 0 -no refines (single-pass)
		}

		boolean show_vector_field = true;

		boolean show_2d_correlations = true;
		boolean show_vector_field = (debugLevel>100); // true;
		boolean show_2d_correlations = (debugLevel>0); // true;
		final int corr_size = 2 * GPUTileProcessor.DTT_SIZE -1;
		if (show_2d_correlations) {
		double [][] dbg_2d_corrs = ImageDtt.corr_partial_dbg( // not used in lwir

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

+112 −2

Original line number	Diff line number	Diff line
		@@ -27,6 +27,7 @@ import com.elphel.imagej.common.ShowDoubleFloatArrays;
		import com.elphel.imagej.gpu.TpTask;
		import com.elphel.imagej.ims.Imx5;
		import com.elphel.imagej.readers.ElphelTiffReader;
		import com.elphel.imagej.readers.ImagejJp4Tiff;
		import com.elphel.imagej.tileprocessor.ImageDtt;
		import com.elphel.imagej.tileprocessor.IntersceneMatchParameters;
		import com.elphel.imagej.tileprocessor.QuadCLT;
		@@ -41,6 +42,7 @@ import ij.plugin.filter.GaussianBlur;
		import ij.process.FloatProcessor;
		import ij.process.ImageConverter;
		import ij.process.ImageProcessor;
		import loci.formats.FormatException;

		public class OrthoMap implements Comparable <OrthoMap>, Serializable{
		private static final long serialVersionUID = 1L;
		@@ -55,6 +57,7 @@ public class OrthoMap implements Comparable <OrthoMap>, Serializable{
		public transient String name; // timestamp
		public transient double ts;
		public transient String path; // full path to the model directory (including /vXX?)
		public transient String scenes_path; // full path to the model directory (including /vXX?)
		public double [] lla; // lat/long/alt
		public LocalDateTime dt;
		// affine convert (input) rectified coordinates (meters) relative to vert_meters to source image
		@@ -69,6 +72,8 @@ public class OrthoMap implements Comparable <OrthoMap>, Serializable{
		public int orig_zoom_level;
		public boolean orig_zoom_valid;
		public double need_extra_zoom;
		public double averageRawPixel = Double.NaN; // measure of scene temperature
		public transient double averageImagePixel = Double.NaN; // average image pixel value (to combine with raw)
		transient HashMap <Integer, FloatImageData> images;
		HashMap <Double, PairwiseOrthoMatch> pairwise_matches;

		@@ -76,6 +81,7 @@ public class OrthoMap implements Comparable <OrthoMap>, Serializable{
		private void writeObject(ObjectOutputStream oos) throws IOException {
		oos.defaultWriteObject();
		oos.writeObject(path);
		oos.writeObject(scenes_path);
		// lla is not transient
		// dt is not transient
		// affine is not transient
		@@ -97,6 +103,7 @@ public class OrthoMap implements Comparable <OrthoMap>, Serializable{
		path = (String) ois.readObject();
		name = getNameFromPath(path);
		ts= Double.parseDouble(name.replace("_", "."));
		scenes_path= (String) ois.readObject();
		// lla is not transient
		// dt is not transient
		// affine is not transient
		@@ -107,6 +114,8 @@ public class OrthoMap implements Comparable <OrthoMap>, Serializable{
		// orig_image was not saved
		// alt_image was not saved
		images = new HashMap <Integer, FloatImageData>(); // field images was not saved
		averageImagePixel = Double.NaN; // average image pixel value (to combine with raw)

		// pairwise_matches is not transient
		// pairwise_matches = new HashMap<Double, PairwiseOrthoMatch>();
		}
		@@ -129,11 +138,14 @@ public class OrthoMap implements Comparable <OrthoMap>, Serializable{
		public int getHeight() {
		return orig_height;
		}

		public int getOriginalZoomLevel() {
		return orig_zoom_level;
		}
		// Generate ALT image path from the GEO
		public static String getAltPath(String path) {
		int p1 = path.lastIndexOf(".");
		return path.substring(0,p1)+ALT_SUFFIX+".tiff";

		}
		public static String getNameFromPath(String path) {
		int p1 = path.lastIndexOf(Prefs.getFileSeparator());
		@@ -143,8 +155,65 @@ public class OrthoMap implements Comparable <OrthoMap>, Serializable{
		return path.substring(p1+1, p2);
		}

		public OrthoMap (String path) {
		/**
		* Gets average pixel value of all sensors of the reference scene
		* @return
		*/
		public double getTemperature() {
		if (Double.isNaN(averageRawPixel)) {
		final String TIFF_EXT=".tiff";
		final File [] raw_files = (new File(scenes_path)).listFiles();
		final Thread[] threads = ImageDtt.newThreadArray();
		final AtomicInteger ai = new AtomicInteger(0);
		final AtomicInteger ati = new AtomicInteger(0);
		final double [] avg_arr = new double [threads.length];
		final double [] npix_arr = new double [threads.length];
		for (int ithread = 0; ithread < threads.length; ithread++) {
		threads[ithread] = new Thread() {
		public void run() {
		int thread_num = ati.getAndIncrement();
		ImagejJp4Tiff imagejJp4Tiff = new ImagejJp4Tiff();
		for (int iFile = ai.getAndIncrement(); iFile < raw_files.length; iFile = ai.getAndIncrement()) {
		if (raw_files[iFile].getName().endsWith(TIFF_EXT)) {
		ImagePlus imp = null;
		String spath = raw_files[iFile].toString();
		try {
		imp= imagejJp4Tiff.readTiffJp4(spath);
		} catch (IOException e) {
		System.out.println("getImagesMultithreaded IOException " + spath);
		} catch (FormatException e) {
		System.out.println("getImagesMultithreaded FormatException " + spath);
		}
		if (imp != null) {
		npix_arr[thread_num] = imp.getWidth()*imp.getHeight();
		float [] fpixels = (float[]) imp.getProcessor().getPixels();
		for (int i = 0; i < fpixels.length; i++) {
		avg_arr[thread_num] += fpixels[i];
		}
		avg_arr[thread_num] /= npix_arr[thread_num];
		}
		}
		}
		}
		};
		}
		ImageDtt.startAndJoin(threads);
		double avg=0, num=0;
		for (int i = 0; i < avg_arr.length; i++) {
		avg+=avg_arr[i]*npix_arr[i];
		num+=npix_arr[i];
		}
		averageRawPixel = avg/num;
		}
		return averageRawPixel;
		}


		public OrthoMap (
		String path,
		String scenes_path) {
		this.path = path;
		this.scenes_path = scenes_path;
		name = getNameFromPath(path);
		ts= Double.parseDouble(name.replace("_", "."));
		Properties imp_prop = null;
		@@ -171,6 +240,8 @@ public class OrthoMap implements Comparable <OrthoMap>, Serializable{
		need_extra_zoom = FloatImageData.needZoomIn(orig_pix_meters);
		images = new HashMap <Integer, FloatImageData>();
		pairwise_matches = new HashMap<Double, PairwiseOrthoMatch>();
		averageRawPixel = Double.NaN; // measure of scene temperature
		averageImagePixel = Double.NaN; // average image pixel value (to combine with raw)
		}


		@@ -221,6 +292,7 @@ public class OrthoMap implements Comparable <OrthoMap>, Serializable{
		if (orig_image == null) {
		readImageData();
		}
		getAveragePixel();
		return orig_image;
		}
		public FloatImageData getAltData() {
		@@ -246,9 +318,47 @@ public class OrthoMap implements Comparable <OrthoMap>, Serializable{
		if (orig_zoom_valid) {
		images.put(orig_zoom_level, orig_image);
		}
		averageImagePixel = Double.NaN;
		return true;
		}

		public double getAveragePixel() {
		if (Double.isNaN(averageImagePixel)) {
		if (orig_image == null) {
		readImageData();
		}
		final float [] pixels = orig_image.data;
		final Thread[] threads = ImageDtt.newThreadArray();
		final AtomicInteger ai = new AtomicInteger(0);
		final AtomicInteger ati = new AtomicInteger(0);
		final double [] avg_arr = new double [threads.length];
		final double [] npix_arr = new double [threads.length];
		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 < pixels.length; ipix = ai.getAndIncrement()) {
		float p = pixels[ipix];
		if (!Float.isNaN(p)) {
		avg_arr[thread_num] += p;
		npix_arr[thread_num] +=1;
		}
		}
		}
		};
		}
		ImageDtt.startAndJoin(threads);
		double avg=0, num=0;
		for (int i = 0; i < avg_arr.length; i++) {
		avg+=avg_arr[i]; // *npix_arr[i];
		num+=npix_arr[i];
		}
		averageImagePixel = avg/num;
		}
		return averageImagePixel;
		}


		private boolean readAltData() { // assuming the same scale as main image
		ImagePlus imp = new ImagePlus(getAltPath(path));
		int width = imp.getWidth();

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