refactoring (d152fbaa) · Commits · Elphel / imagej-elphel

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

+74 −22

Original line number	Diff line number	Diff line
		@@ -720,10 +720,12 @@ min_str_neib_fpn 0.35
		public Color annotate_color_mono = new Color( 255, 180, 50); // reddish over grey
		public boolean annotate_transparent_mono = false; // // black if not transparent

		// terrain parameters
		// terrain/vegetation parameters
		public boolean terr_um_en = true;
		public double terr_um_sigma = 1.0;
		public double terr_um_weight = 0.8;
		public double terr_nan_tolerance = 0.001; // set undefined terrain (out of capture area) to nan, it is almost zero after UM
		public int terr_nan_grow = 20; // grow undefined terrain after detection

		public boolean terr_tile_woi = true; // if false - use woi50;
		public Rectangle terr_woi_enclos = new Rectangle(80, 210, 210, 230); // will be tiled, using width/height from woi_step;
		@@ -733,6 +735,10 @@ min_str_neib_fpn 0.35
		public boolean terr_continue= false; // start from last/single

		public int terr_min_scenes = 1; // minimal number of scenes (inside woi) vegetation pixel must influence
		public int terr_min_samples_scene = 10;
		public int terr_min_total_scenes = 2;
		public int terr_min_pixels = 10;

		public double terr_alpha_dflt = 0.5;
		public double terr_alpha_loss = 100.0;
		public double terr_alpha_offset = 0.0;
		@@ -750,6 +756,7 @@ min_str_neib_fpn 0.35

		// LMA parameters
		public double terr_boost_parallax = 3.0; //
		public double terr_max_parallax = 10.0; // parallax limit when evaluating boost parallax
		public double terr_reg_weights = 0.25; // fraction of the total weight used for regularization
		public double terr_lambda = 5.0; //
		public double terr_lambda_scale_good = 0.5;
		@@ -765,6 +772,9 @@ min_str_neib_fpn 0.35
		public double terr_alpha_min = 0.1; // below - completely transparent vegetation
		public double terr_alpha_max = 0.8; // above - completely opaque
		public double terr_weight_opaque = 0.02; // render through completely opaque vegetation
		public double terr_boost_render = 3.0; // boost parallax during render
		public double terr_max_render = 10.0; // maximal parallax during render

		public int terr_num_exaggerate = 3; // generate exagerrated rendering

		// Experimental reconstruction
		@@ -1944,6 +1954,8 @@ min_str_neib_fpn 0.35
		gd.addCheckbox ("Enable UM", terr_um_en, "Enable unsharp mask filter.");
		gd.addNumericField("UM sigma", terr_um_sigma, 5,7, "pix", "Unsharp mask sigma.");
		gd.addNumericField("UM weight", terr_um_weight, 5,7, "", "Unsharp mask weight.");
		gd.addNumericField("NaN tolerance", terr_nan_tolerance, 5,7,"", "Replace continuous almost zeros with NaN-s.");
		gd.addNumericField("NaN grow", terr_nan_grow, 0,3,"pix", "Grow \"almost\" zero areas after detection (+2 - 8 directions, +1 - only ortho).");

		gd.addMessage ("Scan WOI parameters");
		gd.addCheckbox ("Tiled WOI", terr_tile_woi, "Process tiled WOI (False - a single one).");
		@@ -1955,6 +1967,9 @@ min_str_neib_fpn 0.35

		gd.addMessage ("LMA losses and goals for alpha, terrain and vegetation pixels");
		gd.addNumericField("Min influenced scenes",terr_min_scenes, 0,3, "", "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).");
		gd.addNumericField("Minimum scenes used", terr_min_total_scenes, 0,3,"", "Minimal total number of scenes used (skip segment if less).");
		gd.addNumericField("Minimal pixels fitted",terr_min_pixels, 0,3,"", "Minimal number of terrain and vegetation pixels used for fitting in this segment(skip segment if less).");
		gd.addNumericField("Defalt alpha", terr_alpha_dflt, 5,7,"", "Default vegetation alpha.");
		gd.addNumericField("Alpha loss", terr_alpha_loss, 5,7,"", "Alpha quadratic growing loss for when out of [0,1] range");
		gd.addNumericField("Alpha offset", terr_alpha_offset, 5,7,"", "Start alpha losses above 0.0 and below 1.0 by this value.");
		@@ -1972,6 +1987,7 @@ min_str_neib_fpn 0.35

		gd.addMessage ("LMA parameters");
		gd.addNumericField("Boost parallax", terr_boost_parallax, 5,7,"", "Increase weight of scenes that have high parallax to the reference one.");
		gd.addNumericField("Limit parallax", terr_max_parallax, 5,7,"", "Parallax limit when evaluating boost parallax.");
		gd.addNumericField("Losses weight", terr_reg_weights, 5,7,"", "Fraction of other losses compared to the RMSE.");
		gd.addNumericField("Initial lambda", terr_lambda, 5,7,"", "Initial LMA lambda.");
		gd.addNumericField("Lambda scale on good", terr_lambda_scale_good, 5,7,"","Scale lambda if RMSE improved.");
		@@ -1987,6 +2003,8 @@ min_str_neib_fpn 0.35
		gd.addNumericField("Transparent alpha", terr_alpha_min, 5,7,"", ".");
		gd.addNumericField("Opaque alpha", terr_alpha_max, 5,7,"", ".");
		gd.addNumericField("Opaque weight", terr_weight_opaque, 5,7,"", ".");
		gd.addNumericField("Boost parallax render",terr_boost_render, 5,7,"", "Increase weight of scenes that have high parallax to the reference one (during render).");
		gd.addNumericField("Limit parallax render",terr_max_render, 5,7,"", "Parallax limit when evaluating boost parallax (during render).");
		gd.addNumericField("Exagerrate steps", terr_num_exaggerate, 0,3,"", ".");

		gd.addMessage ("Experimental");
		@@ -2616,6 +2634,9 @@ min_str_neib_fpn 0.35
		terr_um_en = gd.getNextBoolean();// boolean
		terr_um_sigma = gd.getNextNumber();// double
		terr_um_weight = gd.getNextNumber();// double
		terr_nan_tolerance = gd.getNextNumber();// double
		terr_nan_grow = (int) gd.getNextNumber();// int


		terr_tile_woi = gd.getNextBoolean();// boolean
		terr_continue = gd.getNextBoolean();// boolean
		@@ -2625,6 +2646,10 @@ min_str_neib_fpn 0.35
		terr_skip_exist = gd.getNextBoolean();// boolean

		terr_min_scenes = (int) gd.getNextNumber();// int
		terr_min_samples_scene=(int) gd.getNextNumber();// int
		terr_min_total_scenes=(int) gd.getNextNumber();// int
		terr_min_pixels = (int) gd.getNextNumber();// int

		terr_alpha_dflt = gd.getNextNumber();// double
		terr_alpha_loss = gd.getNextNumber();// double
		terr_alpha_offset = gd.getNextNumber();// double
		@@ -2641,6 +2666,7 @@ min_str_neib_fpn 0.35
		terr_veget_pull0 = gd.getNextNumber();// double

		terr_boost_parallax = gd.getNextNumber();// double
		terr_max_parallax = gd.getNextNumber();// double
		terr_reg_weights = gd.getNextNumber();// double
		terr_lambda = gd.getNextNumber();// double
		terr_lambda_scale_good = gd.getNextNumber();// double
		@@ -2655,6 +2681,8 @@ min_str_neib_fpn 0.35
		terr_alpha_min = gd.getNextNumber();// double
		terr_alpha_max = gd.getNextNumber();// double
		terr_weight_opaque = gd.getNextNumber();// double
		terr_boost_render = gd.getNextNumber();// double
		terr_max_render = gd.getNextNumber();// double
		terr_num_exaggerate = (int)gd.getNextNumber();// int

		terr_threshold_terrain = gd.getNextNumber();// double
		@@ -3254,6 +3282,8 @@ min_str_neib_fpn 0.35
		properties.setProperty(prefix+"terr_um_en", terr_um_en+""); // boolean
		properties.setProperty(prefix+"terr_um_sigma", terr_um_sigma+""); // double
		properties.setProperty(prefix+"terr_um_weight", terr_um_weight+""); // double
		properties.setProperty(prefix+"terr_nan_tolerance", terr_nan_tolerance+""); // double
		properties.setProperty(prefix+"terr_nan_grow", terr_nan_grow+""); // int

		properties.setProperty(prefix+"terr_tile_woi", terr_tile_woi+""); // boolean
		properties.setProperty(prefix+"terr_continue", terr_continue+""); // boolean
		@@ -3263,6 +3293,9 @@ min_str_neib_fpn 0.35
		properties.setProperty(prefix+"terr_skip_exist", terr_skip_exist+""); // boolean

		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
		properties.setProperty(prefix+"terr_min_pixels", terr_min_pixels+""); // int
		properties.setProperty(prefix+"terr_alpha_dflt", terr_alpha_dflt+""); // double
		properties.setProperty(prefix+"terr_alpha_loss", terr_alpha_loss+""); // double
		properties.setProperty(prefix+"terr_alpha_offset", terr_alpha_offset+""); // double
		@@ -3279,6 +3312,7 @@ min_str_neib_fpn 0.35
		properties.setProperty(prefix+"terr_veget_pull0", terr_veget_pull0+""); // double

		properties.setProperty(prefix+"terr_boost_parallax", terr_boost_parallax+""); // double
		properties.setProperty(prefix+"terr_max_parallax", terr_max_parallax+""); // double
		properties.setProperty(prefix+"terr_reg_weights", terr_reg_weights+""); // double
		properties.setProperty(prefix+"terr_lambda", terr_lambda+""); // double
		properties.setProperty(prefix+"terr_lambda_scale_good", terr_lambda_scale_good+""); // double
		@@ -3293,6 +3327,8 @@ min_str_neib_fpn 0.35
		properties.setProperty(prefix+"terr_alpha_min", terr_alpha_min+""); // double
		properties.setProperty(prefix+"terr_alpha_max", terr_alpha_max+""); // double
		properties.setProperty(prefix+"terr_weight_opaque", terr_weight_opaque+""); // double
		properties.setProperty(prefix+"terr_boost_render", terr_boost_render+""); // double
		properties.setProperty(prefix+"terr_max_render", terr_max_render+""); // double
		properties.setProperty(prefix+"terr_num_exaggerate", terr_num_exaggerate+""); // int

		properties.setProperty(prefix+"terr_threshold_terrain", terr_threshold_terrain+""); // double
		@@ -3915,6 +3951,8 @@ min_str_neib_fpn 0.35
		if (properties.getProperty(prefix+"terr_um_en")!= null) terr_um_en=Boolean.parseBoolean(properties.getProperty(prefix+"terr_um_en"));
		if (properties.getProperty(prefix+"terr_um_sigma")!= null) terr_um_sigma=Double.parseDouble(properties.getProperty(prefix+"terr_um_sigma"));
		if (properties.getProperty(prefix+"terr_um_weight")!= null) terr_um_weight=Double.parseDouble(properties.getProperty(prefix+"terr_um_weight"));
		if (properties.getProperty(prefix+"terr_nan_tolerance")!= null) terr_nan_tolerance=Double.parseDouble(properties.getProperty(prefix+"terr_nan_tolerance"));
		if (properties.getProperty(prefix+"terr_nan_grow")!= null) terr_nan_grow=Integer.parseInt(properties.getProperty(prefix+"terr_nan_grow"));

		if (properties.getProperty(prefix+"terr_tile_woi")!= null) terr_tile_woi=Boolean.parseBoolean(properties.getProperty(prefix+"terr_tile_woi"));
		if (properties.getProperty(prefix+"terr_continue")!= null) terr_continue=Boolean.parseBoolean(properties.getProperty(prefix+"terr_continue"));
		@@ -3924,6 +3962,9 @@ min_str_neib_fpn 0.35
		if (properties.getProperty(prefix+"terr_skip_exist")!= null) terr_skip_exist=Boolean.parseBoolean(properties.getProperty(prefix+"terr_skip_exist"));

		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"));
		if (properties.getProperty(prefix+"terr_min_pixels")!= null) terr_min_pixels=Integer.parseInt(properties.getProperty(prefix+"terr_min_pixels"));
		if (properties.getProperty(prefix+"terr_alpha_dflt")!= null) terr_alpha_dflt=Double.parseDouble(properties.getProperty(prefix+"terr_alpha_dflt"));
		if (properties.getProperty(prefix+"terr_alpha_loss")!= null) terr_alpha_loss=Double.parseDouble(properties.getProperty(prefix+"terr_alpha_loss"));
		if (properties.getProperty(prefix+"terr_alpha_offset")!= null) terr_alpha_offset=Double.parseDouble(properties.getProperty(prefix+"terr_alpha_offset"));
		@@ -3940,6 +3981,7 @@ min_str_neib_fpn 0.35
		if (properties.getProperty(prefix+"terr_veget_pull0")!= null) terr_veget_pull0=Double.parseDouble(properties.getProperty(prefix+"terr_veget_pull0"));

		if (properties.getProperty(prefix+"terr_boost_parallax")!= null) terr_boost_parallax=Double.parseDouble(properties.getProperty(prefix+"terr_boost_parallax"));
		if (properties.getProperty(prefix+"terr_max_parallax")!= null) terr_max_parallax=Double.parseDouble(properties.getProperty(prefix+"terr_max_parallax"));
		if (properties.getProperty(prefix+"terr_reg_weights")!= null) terr_reg_weights=Double.parseDouble(properties.getProperty(prefix+"terr_reg_weights"));
		if (properties.getProperty(prefix+"terr_lambda")!= null) terr_lambda=Double.parseDouble(properties.getProperty(prefix+"terr_lambda"));
		if (properties.getProperty(prefix+"terr_lambda_scale_good")!= null) terr_lambda_scale_good=Double.parseDouble(properties.getProperty(prefix+"terr_lambda_scale_good"));
		@@ -3954,6 +3996,8 @@ min_str_neib_fpn 0.35
		if (properties.getProperty(prefix+"terr_alpha_min")!= null) terr_alpha_min=Double.parseDouble(properties.getProperty(prefix+"terr_alpha_min"));
		if (properties.getProperty(prefix+"terr_alpha_max")!= null) terr_alpha_max=Double.parseDouble(properties.getProperty(prefix+"terr_alpha_max"));
		if (properties.getProperty(prefix+"terr_weight_opaque")!= null) terr_weight_opaque=Double.parseDouble(properties.getProperty(prefix+"terr_weight_opaque"));
		if (properties.getProperty(prefix+"terr_boost_render")!= null) terr_boost_render=Double.parseDouble(properties.getProperty(prefix+"terr_boost_render"));
		if (properties.getProperty(prefix+"terr_max_render")!= null) terr_max_render=Double.parseDouble(properties.getProperty(prefix+"terr_max_render"));
		if (properties.getProperty(prefix+"terr_num_exaggerate")!= null) terr_num_exaggerate=Integer.parseInt(properties.getProperty(prefix+"terr_num_exaggerate"));

		if (properties.getProperty(prefix+"terr_threshold_terrain")!= null) terr_threshold_terrain=Double.parseDouble(properties.getProperty(prefix+"terr_threshold_terrain"));
		@@ -4543,6 +4587,8 @@ min_str_neib_fpn 0.35
		imp.terr_um_en = this.terr_um_en;
		imp.terr_um_sigma = this.terr_um_sigma;
		imp.terr_um_weight = this.terr_um_weight;
		imp.terr_nan_tolerance = this.terr_nan_tolerance;
		imp.terr_nan_grow = this.terr_nan_grow;

		imp.terr_tile_woi = this.terr_tile_woi;
		imp.terr_continue = this.terr_continue;
		@@ -4552,6 +4598,9 @@ min_str_neib_fpn 0.35
		imp.terr_skip_exist = this.terr_skip_exist;

		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;
		imp.terr_min_pixels = this.terr_min_pixels;
		imp.terr_alpha_dflt = this.terr_alpha_dflt;
		imp.terr_alpha_loss = this.terr_alpha_loss;
		imp.terr_alpha_offset = this.terr_alpha_offset;
		@@ -4568,6 +4617,7 @@ min_str_neib_fpn 0.35
		imp.terr_veget_pull0 = this.terr_veget_pull0;

		imp.terr_boost_parallax = this.terr_boost_parallax;
		imp.terr_max_parallax = this.terr_max_parallax;
		imp.terr_reg_weights = this.terr_reg_weights;
		imp.terr_lambda = this.terr_lambda;
		imp.terr_lambda_scale_good = this.terr_lambda_scale_good;
		@@ -4582,6 +4632,8 @@ min_str_neib_fpn 0.35
		imp.terr_alpha_min = this.terr_alpha_min;
		imp.terr_alpha_max = this.terr_alpha_max;
		imp.terr_weight_opaque = this.terr_weight_opaque;
		imp.terr_boost_render = this.terr_boost_render;
		imp.terr_max_render = this.terr_max_render;
		imp.terr_num_exaggerate = this.terr_num_exaggerate;

		imp.terr_threshold_terrain = this.terr_threshold_terrain;

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

+18 −8

Original line number	Diff line number	Diff line
		@@ -1512,7 +1512,7 @@ public class VegetationLMA {
		for (int n = 0; n < 4; n++) {
		for (int i = 0; (i < indices[n].length) && (i < par_index[n].length); i++) {
		int indx = i;
		if (n < 3) {
		if (n < TVAO_SCENE_OFFSET) {
		int w = i % woi.width;
		int h = i / woi.width;
		indx = (h + woi.y) * full.width + (w + woi.x);
		@@ -1520,7 +1520,11 @@ public class VegetationLMA {
		int pindx = par_index[n][indx];
		indices[n][i] = pindx;
		if (pindx < 0) {
		if (n == TVAO_SCENE_OFFSET) {
		data[n][i] = Double.NaN;
		} else {
		data[n][i] = tvao[n][indx];
		}
		} else {
		data[n][i] = vector[pindx];
		}
		@@ -1644,9 +1648,17 @@ public class VegetationLMA {
		}
		}
		// Trim data to actiual
		int num_pars_scenes = Integer.parseInt((String) imp_pars.getProperty("NUM_PARS_SCENES"));
		double [] scene_offsets = new double [num_pars_scenes];
		System.arraycopy(data[3], 0, scene_offsets, 0, num_pars_scenes);
		// int num_pars_scenes = Integer.parseInt((String) imp_pars.getProperty("NUM_PARS_SCENES"));
		// double [] scene_offsets = new double [num_pars_scenes];
		double [] scene_offsets = new double [num_scenes];
		System.arraycopy(data[TVAO_SCENE_OFFSET], 0, scene_offsets, 0, scene_offsets.length);
		// temporary patch, later they will be NaNs already - Already done !
		for (int i = 0; i < scene_offsets.length; i++) {
		if (indices[TVAO_SCENE_OFFSET][i] < 0) {
		data[TVAO_SCENE_OFFSET][i] = Double.NaN;
		}
		}

		for (int n = 0; n < 3; n++) {
		if (woi.width * woi.height < data[n].length ) {
		double [] d = new double [woi.width * woi.height];
		@@ -1655,8 +1667,6 @@ public class VegetationLMA {
		}
		}
		data[3] = scene_offsets;


		} else {
		this.woi = woi;
		diff_offsets = Boolean.parseBoolean((String) imp_pars.getProperty("DIFF_OFFSETS"));
		@@ -2030,7 +2040,7 @@ public class VegetationLMA {
		woi); // Rectangle file_woi)
		segments[n] = new VegetationSegment(
		woi, // Rectangle woi,
		tvao[3], // datadouble [] scene_offsets,
		tvao[TVAO_SCENE_OFFSET], // datadouble [] scene_offsets,
		new double [][] {tvao[0],tvao[1],tvao[2]}); // double [][] tva) {} {}
		}
		// sort in line-scan order

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

+85 −61

File changed.

Preview size limit exceeded, changes collapsed.

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

+1 −1

Original line number	Diff line number	Diff line
		@@ -8,7 +8,7 @@ public class VegetationSegment {
		public double [][] tva;
		public VegetationSegment(
		Rectangle woi,
		double [] scene_offsets,
		double [] scene_offsets, // has NaNs
		double [][] tva) {
		this.woi = woi;
		this.scene_offsets = scene_offsets;