semi-working terrain elevation (f2072077) · Commits · Elphel / imagej-elphel

src/main/java/com/elphel/imagej/tileprocessor/IntersceneMatchParameters.java

+26 −13

Original line number	Diff line number	Diff line
		@@ -762,13 +762,12 @@ min_str_neib_fpn 0.35
		public boolean terr_fit_alpha = true; // adjust vegetation alpha pixels
		public boolean terr_fit_scenes = true; // adjust scene offsets (start from 0 always?)
		public boolean terr_fit_elevations = false; // adjust elevation pixels (not yet implemented)
		// public boolean [][] terr_fits = {{true},{true},{true},{false},{true}};
		// public boolean [] terr_fit_disable = new boolean [VegetationLMA.TVAO_TYPES];
		// public boolean [][] terr_fits_disable = new boolean [VegetationLMA.TVAO_TYPES][1];
		public boolean [][] terr_fits_disable = {{false},{false},{false},{true,false,true},{false}};
		public boolean terr_fit_terr_elev = false; // adjust terrain elevation (common, maybe add per-pixel later)
		public boolean [][] terr_fits_disable = {{false},{false},{false},{true,false,true},{false},{false}};

		public double terr_max_warp = 1.8;
		public int terr_max_elevation = 22; // maximal offset to consider when looking for vegetation influence
		public int terr_max_elev_terr = 2; // maximal offset to consider when looking for terrain of variable elevation


		@Deprecated
		@@ -2119,15 +2118,18 @@ min_str_neib_fpn 0.35
		gd.addCheckbox ("Adjust terrain", terr_fit_terr, "Adjust terrain pixels.");
		gd.addCheckbox ("Adjust vegetation", terr_fit_veget, "Adjust vegetation pixels.");
		gd.addCheckbox ("Adjust alpha", terr_fit_alpha, "Adjust vegetation alpha pixels.");
		gd.addCheckbox ("Adjust scene offsets", terr_fit_scenes, "Adjust scene offsets (start from 0 always?).");
		gd.addCheckbox ("Adjust elevation", terr_fit_elevations,"Adjust elevation pixels.");
		gd.addCheckbox ("Adjust terrain elevation",terr_fit_terr_elev,"Adjust terrain elevation common.");
		gd.addCheckbox ("Adjust scene offsets", terr_fit_scenes, "Adjust scene offsets (start from 0 always?).");


		for (int i = 0; i < terr_fits_disable.length; i++) {
		gd.addStringField ("Skip "+VegetationLMA.TVAO_NAMES[i], booleansToString(terr_fits_disable[i],2), 40,
		"Skip adjustment of "+VegetationLMA.TVAO_NAMES[i]+". Use comma/space separated list of true/false, 1/0 or +/-." );
		}
		gd.addNumericField("Maximal warp", terr_max_warp, 5,7,"pix", "(1.8) Do not use scenes where distance between vegetation projection exceeds this.");
		gd.addNumericField("Min elevation/offset", terr_max_elevation, 0,3,"pix","Maximal offset to consider when looking for vegetation influence.");
		gd.addNumericField("Max elevation/offset", terr_max_elevation, 0,3,"pix","Maximal offset to consider when looking for vegetation influence.");
		gd.addNumericField("Max terrain elevation",terr_max_elev_terr, 0,3,"pix","Maximal terrain offset to consider when looking for variable-elevation terrain.");

		gd.addNumericField("(Min influenced scenes)",terr_min_scenes, 0,3, "", "Deprecated: Minimal number of scenes (inside woi) vegetation pixel must influence.");
		gd.addNumericField("Minimal samples/scene",terr_min_samples_scene, 0,3,"","Minimal samples per scene used for fitting (skip scene if less).");
		@@ -2908,13 +2910,15 @@ min_str_neib_fpn 0.35
		terr_fit_terr = gd.getNextBoolean();// boolean
		terr_fit_veget = gd.getNextBoolean();// boolean
		terr_fit_alpha = gd.getNextBoolean();// boolean
		terr_fit_scenes = gd.getNextBoolean();// boolean
		terr_fit_elevations = gd.getNextBoolean();// boolean
		terr_fit_terr_elev = gd.getNextBoolean();// boolean
		terr_fit_scenes = gd.getNextBoolean();// boolean
		for (int i = 0; i < terr_fits_disable.length; i++) {
		terr_fits_disable[i] = StringToBooleans(gd.getNextString());// booleans
		}
		terr_max_warp = gd.getNextNumber();// double
		terr_max_elevation = (int) gd.getNextNumber();// int
		terr_max_elev_terr = (int) gd.getNextNumber();// int

		terr_min_scenes = (int) gd.getNextNumber();// int
		terr_min_samples_scene=(int) gd.getNextNumber();// int
		@@ -3653,14 +3657,17 @@ min_str_neib_fpn 0.35
		properties.setProperty(prefix+"terr_fit_terr", terr_fit_terr+""); // boolean
		properties.setProperty(prefix+"terr_fit_veget", terr_fit_veget+""); // boolean
		properties.setProperty(prefix+"terr_fit_alpha", terr_fit_alpha+""); // boolean
		properties.setProperty(prefix+"terr_fit_scenes", terr_fit_scenes+""); // boolean
		properties.setProperty(prefix+"terr_fit_elevations", terr_fit_elevations+""); // boolean
		properties.setProperty(prefix+"terr_fit_terr_elev", terr_fit_terr_elev+""); // boolean
		properties.setProperty(prefix+"terr_fit_scenes", terr_fit_scenes+""); // boolean

		for (int i = 0; i < terr_fits_disable.length; i++) {
		String prop_name = prefix+"terr_fits_disable_"+VegetationLMA.TVAO_NAMES[i];
		properties.setProperty(prop_name, booleansToString(terr_fits_disable[i],2)); // boolean
		}
		properties.setProperty(prefix+"terr_max_warp", terr_max_warp+""); // double
		properties.setProperty(prefix+"terr_max_elevation", terr_max_elevation+""); // int
		properties.setProperty(prefix+"terr_max_elev_terr", terr_max_elev_terr+""); // int
		properties.setProperty(prefix+"terr_min_scenes", terr_min_scenes+""); // int
		properties.setProperty(prefix+"terr_min_samples_scene", terr_min_samples_scene+""); // int
		properties.setProperty(prefix+"terr_min_total_scenes", terr_min_total_scenes+""); // int
		@@ -4416,8 +4423,9 @@ min_str_neib_fpn 0.35
		if (properties.getProperty(prefix+"terr_fit_terr")!= null) terr_fit_terr=Boolean.parseBoolean(properties.getProperty(prefix+"terr_fit_terr"));
		if (properties.getProperty(prefix+"terr_fit_veget")!= null) terr_fit_veget=Boolean.parseBoolean(properties.getProperty(prefix+"terr_fit_veget"));
		if (properties.getProperty(prefix+"terr_fit_alpha")!= null) terr_fit_alpha=Boolean.parseBoolean(properties.getProperty(prefix+"terr_fit_alpha"));
		if (properties.getProperty(prefix+"terr_fit_scenes")!= null) terr_fit_scenes=Boolean.parseBoolean(properties.getProperty(prefix+"terr_fit_scenes"));
		if (properties.getProperty(prefix+"terr_fit_elevations")!= null) terr_fit_elevations=Boolean.parseBoolean(properties.getProperty(prefix+"terr_fit_elevations"));
		if (properties.getProperty(prefix+"terr_fit_terr_elev")!= null) terr_fit_terr_elev=Boolean.parseBoolean(properties.getProperty(prefix+"terr_fit_terr_elev"));
		if (properties.getProperty(prefix+"terr_fit_scenes")!= null) terr_fit_scenes=Boolean.parseBoolean(properties.getProperty(prefix+"terr_fit_scenes"));
		for (int i = 0; i < terr_fits_disable.length; i++) {
		String prop_name_old = prefix+"terr_fit_disable_"+VegetationLMA.TVAO_NAMES[i];
		if (properties.getProperty(prop_name_old)!=null) terr_fits_disable[i]= StringToBooleans(properties.getProperty(prop_name_old));// booleans
		@@ -4426,6 +4434,7 @@ min_str_neib_fpn 0.35
		}
		if (properties.getProperty(prefix+"terr_max_warp")!= null) terr_max_warp=Double.parseDouble(properties.getProperty(prefix+"terr_max_warp"));
		if (properties.getProperty(prefix+"terr_max_elevation")!= null) terr_max_elevation=Integer.parseInt(properties.getProperty(prefix+"terr_max_elevation"));
		if (properties.getProperty(prefix+"terr_max_elev_terr")!= null) terr_max_elev_terr=Integer.parseInt(properties.getProperty(prefix+"terr_max_elev_terr"));
		if (properties.getProperty(prefix+"terr_min_scenes")!= null) terr_min_scenes=Integer.parseInt(properties.getProperty(prefix+"terr_min_scenes"));
		if (properties.getProperty(prefix+"terr_min_samples_scene")!= null) terr_min_samples_scene=Integer.parseInt(properties.getProperty(prefix+"terr_min_samples_scene"));
		if (properties.getProperty(prefix+"terr_min_total_scenes")!= null) terr_min_total_scenes=Integer.parseInt(properties.getProperty(prefix+"terr_min_total_scenes"));
		@@ -5153,13 +5162,15 @@ min_str_neib_fpn 0.35
		imp.terr_fit_terr = this.terr_fit_terr;
		imp.terr_fit_veget = this.terr_fit_veget;
		imp.terr_fit_alpha = this.terr_fit_alpha;
		imp.terr_fit_scenes = this.terr_fit_scenes;
		imp.terr_fit_elevations = this.terr_fit_elevations;
		imp.terr_fit_terr_elev = this.terr_fit_terr_elev;
		imp.terr_fit_scenes = this.terr_fit_scenes;
		for (int i = 0; i < terr_fits_disable.length; i++) {
		imp.terr_fits_disable[i] = this.terr_fits_disable[i].clone();
		}
		imp.terr_max_warp = this.terr_max_warp;
		imp.terr_max_elevation = this.terr_max_elevation;
		imp.terr_max_elev_terr = this.terr_max_elev_terr;
		imp.terr_min_scenes = this.terr_min_scenes;
		imp.terr_min_samples_scene = this.terr_min_samples_scene;
		imp.terr_min_total_scenes = this.terr_min_total_scenes;
		@@ -5363,7 +5374,9 @@ min_str_neib_fpn 0.35
		}
		}

		public static String booleansToString (boolean [] data, int mode) { // 0 : true/false, 1: 0/1, 2: +/-
		public static String booleansToString (boolean [] data, int mode) { // 0 : true/false, 1: 0/1, 2: +/-, negative - skip separators (", ")
		boolean use_sep = mode >= 0;
		mode = Math.abs(mode);
		String s = "";
		for (int i = 0; i < data.length; i++) {
		switch (mode) {
		@@ -5372,7 +5385,7 @@ min_str_neib_fpn 0.35
		case 2: s += data[i] ? "+":"-"; break;
		default: s += data[i];// true/false
		}
		if (i < (data.length - 1)) {
		if (use_sep && (i < (data.length - 1))) {
		s+= ", ";
		}
		}

src/main/java/com/elphel/imagej/vegetation/VegetationLMA.java

+1226 −465

File changed.

Preview size limit exceeded, changes collapsed.

src/main/java/com/elphel/imagej/vegetation/VegetationModel.java

+13 −4

Original line number	Diff line number	Diff line
		@@ -1488,7 +1488,8 @@ public class VegetationModel {
		boolean skip_existing_woi = clt_parameters.imp.terr_skip_exist; // skip existing woi/parameters, already saved.
		boolean continue_woi = clt_parameters.imp.terr_continue; // false;
		double max_warp = clt_parameters.imp.terr_max_warp; // 1.8 - do not use scenes where distance between vegetation projection exceeds this
		int max_offset = clt_parameters.imp.terr_max_elevation; // maximal "elevation" to consider
		int max_elevation = clt_parameters.imp.terr_max_elevation; // maximal "elevation" to consider
		int max_elev_terr = clt_parameters.imp.terr_max_elev_terr; // maximal "elevation" to consider

		// int min_scenes = clt_parameters.imp.terr_min_scenes; // 1;
		// int min_samples_scene = clt_parameters.imp.terr_min_samples_scene; //10;
		@@ -1570,6 +1571,7 @@ public class VegetationModel {
		boolean fit_alpha = clt_parameters.imp.terr_fit_alpha; // true; // adjust vegetation alpha pixels
		boolean fit_scenes = clt_parameters.imp.terr_fit_scenes; // true; // adjust scene offsets (start from 0 always?)
		boolean fit_elevations = clt_parameters.imp.terr_fit_elevations; // false; // adjust elevation pixels (not yet implemented)
		boolean fit_terr_elev = clt_parameters.imp.terr_fit_terr_elev; // false; // adjust terrain elevation (common, maybe add per-pixel later)

		// boolean [] fit_disable = clt_parameters.imp.terr_fit_disable.clone();
		boolean [][] fits_disable = new boolean[clt_parameters.imp.terr_fits_disable.length][];
		@@ -2084,8 +2086,10 @@ public class VegetationModel {
		false, // final boolean keep_parameters,
		woi, // final Rectangle woi,
		null, // final Rectangle woi_veg_in, // used when loading from file (may be different)
		null, // final Rectangle woi_terr_in, // used when loading from file (may be different)
		max_warp, // final double max_warp, // 1.8 - do not use scenes where distance between vegetation projection exceeds this
		max_offset, // final int max_offset, // maximal "elevation" to consider
		max_elevation, // final int max_offset, // maximal "elevation" to consider
		max_elev_terr, // final int max_elev_terr, // maximal terrain "elevation" to consider
		elevation_radius, // final double elevation_radius, // Radius of elevation/vegetation influence.
		null, // final boolean [] valid_scene_pix,
		hifreq_weight, //final double hifreq_weight, // 22.5 0 - do not use high-freq. Relative weight of laplacian components
		@@ -2095,6 +2099,7 @@ public class VegetationModel {
		fit_alpha, // final boolean adjust_alpha,
		fit_scenes, // final boolean adjust_scenes,
		fit_elevations, // final boolean adjust_elevations,
		fit_terr_elev, // final boolean fit_terr_elev,
		thisOrLast(step_restore, fits_disable), // fits_disables[0], // final boolean [] fit_disable,
		reg_weights, // final double reg_weights, // fraction of the total weight used for regularization
		alpha_loss, // final double alpha_loss, // alpha quadratic growing loss for when out of [0,1] range
		@@ -2189,7 +2194,7 @@ public class VegetationModel {
		vegetationLMA.restoreParametersFile( //FIXME: Not finished for real import !
		par_path, // String path,
		true, // boolean keep_settings,
		null, // Rectangle [] file_wois); // if not null, should be Rectangle[2] {woi_veg,woi} - will return woi data and not input parameters to this instance
		/// null, // Rectangle [] file_wois); // if not null, should be Rectangle[2] {woi_veg,woi} - will return woi data and not input parameters to this instance
		null); // double [] other_pars)
		if (thisOrLast(step_restore,recalc_weights)) {
		System.out.println ("---- Recalculating weights from transparency after loading parameters");
		@@ -2230,6 +2235,7 @@ public class VegetationModel {
		vegetationLMA.showYfX(
		null, // double [] vector,
		"reconstructed_model-x"+woi.x+"-y"+woi.y+"-w"+woi.width+"-h"+woi.height); // String title)
		/*
		vegetationLMA.showResults(
		"terr_split-x"+woi.x+"-y"+woi.y+"-w"+woi.width+"-h"+woi.height, // String title,
		vegetationLMA.getParametersVector(), // double [] vector,
		@@ -2237,6 +2243,8 @@ public class VegetationModel {
		min_max_terrain, // double min_max_terrain, //0.1
		min_terrain, //double min_terrain, //0.001
		min_vegetation); // double min_vegetation) { // 0.5
		*/

		}
		/// next_run = true;
		vegetationLMA.debug_index = 0;
		@@ -2270,6 +2278,7 @@ public class VegetationModel {
		for (; step_restore <= last_series; step_restore++) {
		// vegetationLMA.fits_disable[VegetationLMA.TVAO_ELEVATION] = fits_disable[step_restore][VegetationLMA.TVAO_ELEVATION];
		vegetationLMA.fits_disable[VegetationLMA.TVAO_ELEVATION] =thisOrLast(step_restore,fits_disable)[VegetationLMA.TVAO_ELEVATION];
		vegetationLMA.fits_disable[VegetationLMA.TVAO_TERR_ELEV] =thisOrLast(step_restore,fits_disable)[VegetationLMA.TVAO_TERR_ELEV];
		if (thisOrLast(step_restore,recalc_weights)) {
		System.out.println ("---- Recalculating weights from transparency");
		String dbg_title= (!tile_woi && (debugLevel > -2)) ? ("transparency_"+step_restore) : null;

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