Tuning classifier (c1e50a2a) · Commits · Elphel / imagej-elphel

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

+16 −0

Original line number	Diff line number	Diff line
		@@ -268,6 +268,22 @@ import ij.process.ImageProcessor;
		return array_stack;
		}

		public static ImageStack makeStack(byte[][] pixels, int width, int height, String [] titles) {
		ImageStack array_stack=new ImageStack(width,height);
		for (int i=0;i<pixels.length;i++) if (pixels[i]!=null) {
		if (pixels[i].length!=(width*height)){
		System.out.println("showArrays(): pixels["+i+"].length="+pixels[i].length+" != width (+"+width+") * height("+height+")="+(width*height));
		return null;
		}
		if (titles!=null){
		array_stack.addSlice(titles[i], pixels[i]);
		} else {
		array_stack.addSlice("chn-"+i, pixels[i]);
		}
		}
		return array_stack;
		}


		public static ImagePlus [] makeArrays(double[][] pixels, int width, int height, String title) {
		int i,j;

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

+49 −19

Original line number	Diff line number	Diff line
		@@ -103,7 +103,8 @@ public class ComboMatch {
		"/media/elphel/SSD3-4GB/lwir16-proc/ortho_videos/maps_sep12-13_50-25-50-75-100m",
		"/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",
		"/media/elphel/SSD3-4GB/lwir16-proc/ortho_videos/maps_sep12-50m"};
		"/media/elphel/SSD3-4GB/lwir16-proc/ortho_videos/maps_sep12-50m",
		"/media/elphel/SSD3-4GB/lwir16-proc/ortho_videos/maps_sep12-13_50-25-50-75-100m-SUBSET"};
		int default_list_choice = 0; // files_lists_paths.length-1;
		// 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";
		@@ -142,7 +143,9 @@ public class ComboMatch {
		int gpu_width= clt_parameters.imp.rln_gpu_width; // 3008;
		int gpu_height= clt_parameters.imp.rln_gpu_height; // 3008;
		int zoom_lev = -3; // 0; // +1 - zoom in twice, -1 - zoom out twice
		boolean show_map_stats = false;
		boolean show_combo_map = false; // true;
		boolean show_combo_mask = false; // generate image mas (where it is defined)_
		boolean use_alt = false;
		boolean show_centers = true;
		boolean use_saved_collection = true; // false;
		@@ -164,6 +167,10 @@ public class ComboMatch {
		if (!use_marked_image) {
		process_correlation=false; // use already adjusted by default
		}
		if (process_correlation) {
		render_match = true; // default
		pattern_match = false;
		}


		GenericJTabbedDialog gd = new GenericJTabbedDialog("Set image pair",1200,900);
		@@ -201,7 +208,9 @@ public class ComboMatch {
		gd.addNumericField("GPU image height", gpu_height, 0,4,"",
		"GPU image height");
		gd.addCheckbox ("Show transformation centers", show_centers, "Mark verticals from the UAS on the ground.");
		gd.addCheckbox ("Show statistics for ortho images", show_map_stats, "Generate and show statistics for ortho maps.");
		gd.addCheckbox ("Show combo image map", show_combo_map, "Load and process altitude maps.");
		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.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.");
		@@ -244,7 +253,9 @@ public class ComboMatch {
		OrthoMap.setGPUWidthHeight(gpu_width,gpu_height);

		show_centers = gd.getNextBoolean();
		show_map_stats = gd.getNextBoolean();
		show_combo_map = gd.getNextBoolean();
		show_combo_mask = gd.getNextBoolean();
		use_alt = gd.getNextBoolean();

		// gpu_spair[0] = gd.getNextString();
		@@ -271,8 +282,10 @@ public class ComboMatch {
		}
		} else {
		maps_collection = new OrthoMapsCollection(files_list_path); // should have ".list" extension
		maps_collection.updateNumberScenes();
		maps_collection.updateSfmGain();
		}
		String [] names = maps_collection.getNames();
		String [] names = maps_collection.getNames(); // null
		if (object_list != null) {
		int corr_size = 128;
		int extr_size = 200; // 256;
		@@ -300,7 +313,6 @@ public class ComboMatch {
		double inv_blur_rate = 0.2; // blur increase outside of blur_radius



		// String pattern_dir= "/media/elphel/SSD3-4GB/lwir16-proc/ortho_videos/debug/mines/pattern_25m_zoom1/synthetic/";
		String pattern_dir= "/media/elphel/NVME/lwir16-proc/ortho_videos/mines_extract/evening_50m_sept12/debug_cross/new_synth/";
		String [] pattern_files={
		@@ -392,8 +404,6 @@ public class ComboMatch {
		if (gdo.wasCanceled()) return false;
		corr_size = (int) gdo.getNextNumber();
		extr_size = (int) gdo.getNextNumber();
		// OrthoMap.pattern_dir= gdo.getNextString();
		// String pattern_file = OrthoMap.pattern_files[gdo.getNextChoiceIndex()];
		pattern_dir= gdo.getNextString();
		String pattern_file = pattern_files[gdo.getNextChoiceIndex()];
		zoomout= (int) gdo.getNextNumber();
		@@ -718,16 +728,27 @@ public class ComboMatch {
		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]]};
		int [] origin = new int[2];
		ImagePlus imp_img = null;
		if (show_map_stats) {
		boolean ok = maps_collection.showScenesStats(false); // boolean select_all)
		if (!ok) {
		return false;
		}

		// System.out.println("Exiting after generating stats");
		// return true; // do not process anything else
		}
		if (show_combo_map) {
		imp_img = maps_collection.renderMulti (
		"multi_zoom"+zoom_lev, // String title,
		false, // boolean use_alt,
		OrthoMapsCollection.MODE_IMAGE, // int mode, // 0 - regular image, 1 - altitudes, 2 - black/white mask // boolean use_alt,
		show_centers, // boolean show_centers,
		zoom_lev, // int zoom_level,
		temp_mode, // int temp_mode, // 0 - do nothing, 1 - equalize average,2 - try to correct
		@@ -738,7 +759,19 @@ public class ComboMatch {
		if (use_alt) {
		imp_alt =maps_collection.renderMulti (
		"multi_alt_zoom"+zoom_lev, // String title,
		true, // boolean use_alt,
		// true, // boolean use_alt,
		OrthoMapsCollection.MODE_ALT, // int mode, // 0 - regular image, 1 - altitudes, 2 - black/white mask // boolean use_alt,
		show_centers, // boolean show_centers,
		zoom_lev, // int zoom_level,
		0, // int temp_mode, // 0 - do nothing, 1 - equalize average,2 - try to correct
		origin); // int [] origin){
		imp_alt.show();
		}
		if (show_combo_mask) {
		imp_alt =maps_collection.renderMulti (
		"multi_alt_zoom"+zoom_lev, // String title,
		// true, // boolean use_alt,
		OrthoMapsCollection.MODE_MASK, // int mode, // 0 - regular image, 1 - altitudes, 2 - black/white mask // boolean use_alt,
		show_centers, // boolean show_centers,
		zoom_lev, // int zoom_level,
		0, // int temp_mode, // 0 - do nothing, 1 - equalize average,2 - try to correct
		@@ -886,7 +919,8 @@ public class ComboMatch {
		ImagePlus imp_img_pair = maps_collection.renderMulti (
		//_zoom<integer> is needed for opening with "Extract Objects" command
		"multi_"+gpu_spair[0]+"-"+gpu_spair[1]+"_zoom"+min_zoom_lev+"_"+zoom_lev, // String title,
		false, // boolean use_alt,
		// false, // boolean use_alt,
		OrthoMapsCollection.MODE_IMAGE, // int mode, // 0 - regular image, 1 - altitudes, 2 - black/white mask // boolean use_alt,
		gpu_pair, // int [] indices, // null or which indices to use (normally just 2 for pairwise comparison)
		bounds_to_indices, // boolean bounds_to_indices,
		temp_mode, // int temp_mode, // 0 - do nothing, 1 - equalize average,2 - try to correct
		@@ -910,10 +944,6 @@ public class ComboMatch {
		System.out.println("Saved data to "+ orthoMapsCollection_path);
		}
		return true;
		}

		public void printSceneStats() {

		}

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

+119 −6

Original line number	Diff line number	Diff line
		@@ -34,6 +34,7 @@ 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.OpticalFlow;
		import com.elphel.imagej.tileprocessor.QuadCLT;
		import com.elphel.imagej.tileprocessor.TileNeibs;

		@@ -54,6 +55,8 @@ import loci.formats.FormatException;

		public class OrthoMap implements Comparable <OrthoMap>, Serializable{
		private static final long serialVersionUID = 1L;
		public static final String DSI_SUFFIX = "-INTER-INTRA-LMA.tiff";
		public static final String MERGED_SUFFIX = "-MERGED.tiff";
		public static boolean FIX_VERT_Y = false; // true; // temporarily fix vertical Y coordinate bug (use -GCORR in the filename?)
		public static int gpu_width = 4096;
		public static int gpu_height = 4096;
		@@ -84,12 +87,9 @@ public class OrthoMap implements Comparable <OrthoMap>, Serializable{


		public static final String ALT_SUFFIX = "-ALT";
		// public transient final String name; // timestamp
		// public transient final double ts;
		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
		@@ -110,6 +110,8 @@ public class OrthoMap implements Comparable <OrthoMap>, Serializable{
		HashMap <String, PairwiseOrthoMatch> pairwise_matches;
		public transient SensorTemperatureData[] temp_data;
		public transient double agl = Double.NaN;
		public transient int num_scenes = -1;; // number of scenes that made up this image
		public transient double sfm_gain = Double.NaN; // maximal SfM gain of this map
		private void writeObject(ObjectOutputStream oos) throws IOException {
		oos.defaultWriteObject();
		oos.writeObject(path);
		@@ -130,9 +132,13 @@ public class OrthoMap implements Comparable <OrthoMap>, Serializable{
		// pairwise_matches is not transient
		oos.writeObject(temp_data); // temporary, while transient
		oos.writeObject(agl);
		oos.writeObject(num_scenes);
		oos.writeObject(sfm_gain);
		}

		private void readObject(ObjectInputStream ois) throws ClassNotFoundException, IOException {
		// sfm_gain = Double.NaN;
		// num_scenes = -1;
		ois.defaultReadObject();
		path = (String) ois.readObject();
		name = getNameFromPath(path);
		@@ -149,8 +155,8 @@ public class OrthoMap implements Comparable <OrthoMap>, Serializable{
		// alt_image was not saved
		temp_data = (SensorTemperatureData[]) ois.readObject();
		agl = (double) ois.readObject();


		num_scenes = (int) ois.readObject();
		sfm_gain = (double) ois.readObject();
		images = new HashMap <Integer, FloatImageData>(); // field images was not saved
		averageImagePixel = Double.NaN; // average image pixel value (to combine with raw)

		@@ -211,6 +217,78 @@ public class OrthoMap implements Comparable <OrthoMap>, Serializable{
		return getModelPathFromPath(this.path)+"/jp4";
		}

		/**
		* Get number of scenes used to generate this ortho image. Looks in subdirectories of the directory
		* where the image file is stored (currently they are v01, vo2, ...) and in subdirectories finds the
		* latest *-MERGED.tiff file. Each scene has a slice in this file
		* @return number of scenes that made this ortho image, also sets the num_scenes (saved in database)
		* so next time reading files will not be needed
		*/
		public int getNumberScenes() {
		if (num_scenes < 0) {
		String merged_path = getLatestFilePath(MERGED_SUFFIX);
		if (merged_path != null) {
		ImagePlus imp_merged = new ImagePlus(merged_path);
		if (imp_merged.getWidth() > 0) {
		num_scenes = imp_merged.getImageStack().getSize();
		}
		}
		}
		return num_scenes;
		}

		/**
		* Get maximal "SfM gain" - ratio between used interscene offset and the camera baseline.
		* Looks in subdirectories of the directory where the image file is stored (currently they are
		* v01, vo2, ...) and in subdirectories finds the latest *-INTER-INTRA-LMA.tiff file.
		* Those files have a slice (OpticalFlow.COMBO_DSN_INDX_SFM_GAIN + 1 as slices a numbered from 1)
		* that contains per-tile SfM gain.
		* @return Maximal SfM gain
		*/

		public double getSfmGain() {
		if (Double.isNaN(sfm_gain)) {
		String dsi_path = getLatestFilePath(DSI_SUFFIX);
		if (dsi_path != null) {
		ImagePlus imp_dsi = new ImagePlus(dsi_path);
		if (imp_dsi.getWidth() > 0) {
		float [] pixels = (float[]) imp_dsi.getImageStack().getPixels(OpticalFlow.COMBO_DSN_INDX_SFM_GAIN + 1);
		sfm_gain = 0;
		for (int i = 0; i < pixels.length; i++) {
		if (pixels[i] > sfm_gain) {
		sfm_gain = pixels[i];
		}
		}
		}
		}
		}
		return sfm_gain;
		}



		public String getLatestFilePath(String suffix) {
		String model_dir = getModelPathFromPath(this.path);
		File [] subdirs = (new File(model_dir)).listFiles();
		long latest_ms = 0;
		File latest_file = null;
		for (File subdir:subdirs) if (subdir.isDirectory()) {
		File [] file_vers = subdir.listFiles();
		for (File file:file_vers) if (file.isFile() && file.toString().endsWith(suffix)){
		long modified = file.lastModified();
		if (modified > latest_ms) {
		latest_ms = modified;
		latest_file = file;
		}
		}
		}
		if (latest_file != null) {
		return latest_file.getPath();
		}
		return null;
		}


		public void updateLLA() {
		Properties imp_prop = null;
		try {
		@@ -520,6 +598,41 @@ public class OrthoMap implements Comparable <OrthoMap>, Serializable{
		return agl;
		}

		/**
		* Get coordinates and altitude
		* @return {latitude(deg), longitude(deg), altitude(m)}
		*/
		public double [] getLLA() {
		return lla;
		}

		/**
		* Get original image resolution as pixel size in meters
		* @return image pixel size in meters
		*/
		public double getOrigPixMeters() {
		return orig_pix_meters;
		}

		/**
		* Get vertical point offset from the top-left corner of the original orthoimage in meters
		* @return vertical point X,Y offset in meters from the top-left image corner
		*/
		public double [] getVertMeters() {
		return vert_meters;
		}

		/**
		* Get vertical point offset from the top-left corner of the original orthoimage in pixels
		* of the original resolution
		* @return vertical point X,Y offset in pixels from the top-left image corner in original resolution
		*/
		public int [] getVertPixels() {
		return new int [] {
		(int) Math.round(vert_meters[0]/orig_pix_meters),
		(int) Math.round(vert_meters[0]/orig_pix_meters)};
		}


		public ImagePlus getOriginalImage(boolean show_markers) {
		FloatImageData orig_image = getImageData();

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