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

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

+16 −0

Original line number	Original line	Diff line number	Diff line
	@@ -268,6 +268,22 @@ import ij.process.ImageProcessor;
	return array_stack;		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) {		public static ImagePlus [] makeArrays(double[][] pixels, int width, int height, String title) {
	int i,j;		int i,j;

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

+49 −19

Original line number	Original line	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_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_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_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;		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 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";		// 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_width= clt_parameters.imp.rln_gpu_width; // 3008;
	int gpu_height= clt_parameters.imp.rln_gpu_height; // 3008;		int gpu_height= clt_parameters.imp.rln_gpu_height; // 3008;
	int zoom_lev = -3; // 0; // +1 - zoom in twice, -1 - zoom out twice		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_map = false; // true;
			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;
	boolean use_saved_collection = true; // false;		boolean use_saved_collection = true; // false;
	@@ -164,6 +167,10 @@ public class ComboMatch {
	if (!use_marked_image) {		if (!use_marked_image) {
	process_correlation=false; // use already adjusted by default		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);		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,"",		gd.addNumericField("GPU image height", gpu_height, 0,4,"",
	"GPU image height");		"GPU image height");
	gd.addCheckbox ("Show transformation centers", show_centers, "Mark verticals from the UAS on the ground.");		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 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.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.");
	gd.addNumericField("Maximal metric error", metric_error, 3,7,"m", "Maximal tolerable fitting error caused by elevation variations.");		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);		OrthoMap.setGPUWidthHeight(gpu_width,gpu_height);

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

	// gpu_spair[0] = gd.getNextString();		// gpu_spair[0] = gd.getNextString();
	@@ -271,8 +282,10 @@ public class ComboMatch {
	}		}
	} else {		} else {
	maps_collection = new OrthoMapsCollection(files_list_path); // should have ".list" extension		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) {		if (object_list != null) {
	int corr_size = 128;		int corr_size = 128;
	int extr_size = 200; // 256;		int extr_size = 200; // 256;
	@@ -300,7 +313,6 @@ public class ComboMatch {
	double inv_blur_rate = 0.2; // blur increase outside of blur_radius		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/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_dir= "/media/elphel/NVME/lwir16-proc/ortho_videos/mines_extract/evening_50m_sept12/debug_cross/new_synth/";
	String [] pattern_files={		String [] pattern_files={
	@@ -392,8 +404,6 @@ public class ComboMatch {
	if (gdo.wasCanceled()) return false;		if (gdo.wasCanceled()) return false;
	corr_size = (int) gdo.getNextNumber();		corr_size = (int) gdo.getNextNumber();
	extr_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();		pattern_dir= gdo.getNextString();
	String pattern_file = pattern_files[gdo.getNextChoiceIndex()];		String pattern_file = pattern_files[gdo.getNextChoiceIndex()];
	zoomout= (int) gdo.getNextNumber();		zoomout= (int) gdo.getNextNumber();
	@@ -718,16 +728,27 @@ public class ComboMatch {
	if (update_lla) {		if (update_lla) {
	System.out.println("Updating map files metadata");		System.out.println("Updating map files metadata");
	maps_collection.updateLLa();		maps_collection.updateLLa();
			maps_collection.updateNumberScenes();
			maps_collection.updateSfmGain();
	}		}

	// which pair to compare		// which pair to compare
	// String [] gpu_spair = {names[gpu_ipair[0]],names[gpu_ipair[1]]};		// String [] gpu_spair = {names[gpu_ipair[0]],names[gpu_ipair[1]]};
	int [] origin = new int[2];		int [] origin = new int[2];
	ImagePlus imp_img = null;		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) {		if (show_combo_map) {
	imp_img = maps_collection.renderMulti (		imp_img = maps_collection.renderMulti (
	"multi_zoom"+zoom_lev, // String title,		"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,		show_centers, // boolean show_centers,
	zoom_lev, // int zoom_level,		zoom_lev, // int zoom_level,
	temp_mode, // int temp_mode, // 0 - do nothing, 1 - equalize average,2 - try to correct		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) {		if (use_alt) {
	imp_alt =maps_collection.renderMulti (		imp_alt =maps_collection.renderMulti (
	"multi_alt_zoom"+zoom_lev, // String title,		"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,		show_centers, // boolean show_centers,
	zoom_lev, // int zoom_level,		zoom_lev, // int zoom_level,
	0, // int temp_mode, // 0 - do nothing, 1 - equalize average,2 - try to correct		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 (		ImagePlus imp_img_pair = maps_collection.renderMulti (
	//_zoom<integer> is needed for opening with "Extract Objects" command		//_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,		"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)		gpu_pair, // 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,
	temp_mode, // int temp_mode, // 0 - do nothing, 1 - equalize average,2 - try to correct		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);		System.out.println("Saved data to "+ orthoMapsCollection_path);
	}		}
	return true;		return true;
	}

	public void printSceneStats() {

	}		}

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

+119 −6

Original line number	Original line	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.readers.ImagejJp4Tiff;
	import com.elphel.imagej.tileprocessor.ImageDtt;		import com.elphel.imagej.tileprocessor.ImageDtt;
	import com.elphel.imagej.tileprocessor.IntersceneMatchParameters;		import com.elphel.imagej.tileprocessor.IntersceneMatchParameters;
			import com.elphel.imagej.tileprocessor.OpticalFlow;
	import com.elphel.imagej.tileprocessor.QuadCLT;		import com.elphel.imagej.tileprocessor.QuadCLT;
	import com.elphel.imagej.tileprocessor.TileNeibs;		import com.elphel.imagej.tileprocessor.TileNeibs;

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

	public class OrthoMap implements Comparable <OrthoMap>, Serializable{		public class OrthoMap implements Comparable <OrthoMap>, Serializable{
	private static final long serialVersionUID = 1L;		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 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_width = 4096;
	public static int gpu_height = 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 static final String ALT_SUFFIX = "-ALT";
	// public transient final String name; // timestamp
	// public transient final double ts;
	public transient String name; // timestamp		public transient String name; // timestamp
	public transient double ts;		public transient double ts;
	public transient String path; // full path to the model directory (including /vXX?)		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 double [] lla; // lat/long/alt
	public LocalDateTime dt;		public LocalDateTime dt;
	// affine convert (input) rectified coordinates (meters) relative to vert_meters to source image		// 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;		HashMap <String, PairwiseOrthoMatch> pairwise_matches;
	public transient SensorTemperatureData[] temp_data;		public transient SensorTemperatureData[] temp_data;
	public transient double agl = Double.NaN;		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 {		private void writeObject(ObjectOutputStream oos) throws IOException {
	oos.defaultWriteObject();		oos.defaultWriteObject();
	oos.writeObject(path);		oos.writeObject(path);
	@@ -130,9 +132,13 @@ public class OrthoMap implements Comparable <OrthoMap>, Serializable{
	// pairwise_matches is not transient		// pairwise_matches is not transient
	oos.writeObject(temp_data); // temporary, while transient		oos.writeObject(temp_data); // temporary, while transient
	oos.writeObject(agl);		oos.writeObject(agl);
			oos.writeObject(num_scenes);
			oos.writeObject(sfm_gain);
	}		}

	private void readObject(ObjectInputStream ois) throws ClassNotFoundException, IOException {		private void readObject(ObjectInputStream ois) throws ClassNotFoundException, IOException {
			// sfm_gain = Double.NaN;
			// num_scenes = -1;
	ois.defaultReadObject();		ois.defaultReadObject();
	path = (String) ois.readObject();		path = (String) ois.readObject();
	name = getNameFromPath(path);		name = getNameFromPath(path);
	@@ -149,8 +155,8 @@ public class OrthoMap implements Comparable <OrthoMap>, Serializable{
	// alt_image was not saved		// alt_image was not saved
	temp_data = (SensorTemperatureData[]) ois.readObject();		temp_data = (SensorTemperatureData[]) ois.readObject();
	agl = (double) 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		images = new HashMap <Integer, FloatImageData>(); // field images was not saved
	averageImagePixel = Double.NaN; // average image pixel value (to combine with raw)		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";		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() {		public void updateLLA() {
	Properties imp_prop = null;		Properties imp_prop = null;
	try {		try {
	@@ -520,6 +598,41 @@ public class OrthoMap implements Comparable <OrthoMap>, Serializable{
	return agl;		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) {		public ImagePlus getOriginalImage(boolean show_markers) {
	FloatImageData orig_image = getImageData();		FloatImageData orig_image = getImageData();

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

+151 −15

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