intermediate, before changing alpha pull (883c0212) · Commits · Elphel / imagej-elphel

src/main/java/com/elphel/imagej/correction/Eyesis_Correction.java

+2 −2

Original line number	Diff line number	Diff line
		@@ -5802,11 +5802,11 @@ public class Eyesis_Correction implements PlugIn, ActionListener {
		} else if (label.equals("Process Merged")) {
		OrangeTest.processMerged();
		} else if (label.equals("Vegetation LMA")) {
		VegetationModel.processVegetationLMA(
		VegetationModel.processVegetation(
		CLT_PARAMETERS, //CLTParameters clt_parameters,
		false); //boolean combine_segments);
		} else if (label.equals("Combine LMA Segments")) {
		VegetationModel.processVegetationLMA(
		VegetationModel.processVegetation(
		CLT_PARAMETERS, //CLTParameters clt_parameters,
		true); //boolean combine_segments);
		}

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

+66 −4

Original line number	Diff line number	Diff line
		@@ -786,6 +786,12 @@ min_str_neib_fpn 0.35
		public double terr_elevation_radius = 1.5; // Radius of elevation/vegetation influence
		public double terr_alpha_contrast = 1.0; // initial alpha contrast (>=1.0)
		public double terr_alpha_dflt = 0.5; // now unused

		public double terr_alpha_sigma = 8.0; // Initial alpha: Gaussian blur sigma to find local average for vegetation temperature.
		public double terr_alpha_init_min = 0.7; // Initial alpha: fraction for transparent
		public double terr_alpha_init_max = 0.95; // Initial alpha: fraction for opaque
		public double terr_alpha_init_offs = 0.01; // Initial alpha: opaque/transparent offset from 1.0/0.0

		public double terr_alpha_loss = 100.0;
		public double terr_alpha_offset = 0.0;
		public double terr_alpha_lpf = 2.5; // pull to average of 4 neighbors
		@@ -802,6 +808,10 @@ min_str_neib_fpn 0.35
		public double terr_terr_pull0 = 0.05; // pull terrain to initial (pre-adjustment) values
		public double terr_veget_pull0 = 0.05; // pull vegetation initial (pre-adjustment) values
		public double terr_elev_pull0 = 0.1; // pull elevation to initial (pre-adjustment) values
		public boolean terr_elev_alpha_en = false;// Enable loss for low vegetation with high opacity
		public double terr_elev_alpha = 1.0; // multiply alpha by under-low elevation for loss
		public double terr_elev_alpha_pwr = 2.0; // raise alpha to this power (when alpha > 0)
		public double terr_low_veget = 2.0; // (pix) Elevation considered low (lower loss for high alpha)
		public double terr_scenes_pull0 = 1.0; // pull average scene offset to zero

		// LMA parameters
		@@ -2083,6 +2093,12 @@ min_str_neib_fpn 0.35

		gd.addNumericField("Alpha initial contrast",terr_alpha_contrast, 5,7,"","Initial alpha contrast (>= 1.0).");
		gd.addNumericField("Defalt alpha", terr_alpha_dflt, 5,7,"", "Default vegetation alpha.");

		gd.addNumericField("Initial alpha sigma", terr_alpha_sigma, 5,7,"", "Initial alpha: Gaussian blur sigma to find local average for vegetation temperature..");
		gd.addNumericField("Initial alpha min frac",terr_alpha_init_min,5,7,"", "Initial alpha: fraction for transparent.");
		gd.addNumericField("Initial alpha max frac",terr_alpha_init_max,5,7,"", "Initial alpha: fraction for opaque.");
		gd.addNumericField("Initial alpha offset", terr_alpha_init_offs, 5,7,"","Initial alpha: opaque/transparent offset from 1.0/0.0.");

		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.");
		@@ -2100,6 +2116,12 @@ min_str_neib_fpn 0.35
		gd.addNumericField("Terrain pull", terr_terr_pull0, 5,7,"", "Terrain pixels pull to initial (pre-adjustment) values.");
		gd.addNumericField("Vegetation pull", terr_veget_pull0, 5,7,"", "Vegetation pixels pull initial (pre-adjustment) values.");
		gd.addNumericField("Elevation pull", terr_elev_pull0, 5,7,"", "Elevation pixels pull to initial (pre-adjustment) values.");

		gd.addCheckbox ("Enable low vegetation",terr_elev_alpha_en, "Enable loss for low vegetation with high opacity.");
		gd.addNumericField("Low vegetation loss", terr_elev_alpha, 5,7,"", "Multiply alpha by under-low elevation for loss.");
		gd.addNumericField("Low vegetation power", terr_elev_alpha_pwr, 5,7,"", "Raise alpha to this power for low vegetation loss.");
		gd.addNumericField("Low elevation", terr_low_veget, 5,7,"pix", "Elevation considered low (lower loss for high alpha.");

		gd.addNumericField("Pull scene offset", terr_scenes_pull0, 5,7,"", "Pull average scene offset to zero.");

		gd.addMessage ("LMA parameters");
		@@ -2817,6 +2839,12 @@ min_str_neib_fpn 0.35
		terr_elevation_radius = gd.getNextNumber();// double
		terr_alpha_contrast = gd.getNextNumber();// double
		terr_alpha_dflt = gd.getNextNumber();// double

		terr_alpha_sigma = gd.getNextNumber();// double
		terr_alpha_init_min = gd.getNextNumber();// double
		terr_alpha_init_max = gd.getNextNumber();// double
		terr_alpha_init_offs = gd.getNextNumber();// double

		terr_alpha_loss = gd.getNextNumber();// double
		terr_alpha_offset = gd.getNextNumber();// double
		terr_alpha_lpf = gd.getNextNumber();// double
		@@ -2834,6 +2862,10 @@ min_str_neib_fpn 0.35
		terr_terr_pull0 = gd.getNextNumber();// double
		terr_veget_pull0 = gd.getNextNumber();// double
		terr_elev_pull0 = gd.getNextNumber();// double
		terr_elev_alpha_en = gd.getNextBoolean();// boolean
		terr_elev_alpha = gd.getNextNumber();// double
		terr_elev_alpha_pwr = gd.getNextNumber();// double
		terr_low_veget = gd.getNextNumber();// double
		terr_scenes_pull0 = gd.getNextNumber();// double
		terr_boost_parallax = gd.getNextNumber();// double
		terr_max_parallax = gd.getNextNumber();// double
		@@ -3517,6 +3549,12 @@ min_str_neib_fpn 0.35
		properties.setProperty(prefix+"terr_elevation_radius", terr_elevation_radius+""); // double
		properties.setProperty(prefix+"terr_alpha_contrast", terr_alpha_contrast+""); // double
		properties.setProperty(prefix+"terr_alpha_dflt", terr_alpha_dflt+""); // double

		properties.setProperty(prefix+"terr_alpha_sigma", terr_alpha_sigma+""); // double
		properties.setProperty(prefix+"terr_alpha_init_min", terr_alpha_init_min+""); // double
		properties.setProperty(prefix+"terr_alpha_init_max", terr_alpha_init_max+""); // double
		properties.setProperty(prefix+"terr_alpha_init_offs", terr_alpha_init_offs+""); // double

		properties.setProperty(prefix+"terr_alpha_loss", terr_alpha_loss+""); // double
		properties.setProperty(prefix+"terr_alpha_offset", terr_alpha_offset+""); // double
		properties.setProperty(prefix+"terr_alpha_lpf", terr_alpha_lpf+""); // double
		@@ -3532,6 +3570,10 @@ min_str_neib_fpn 0.35
		properties.setProperty(prefix+"terr_terr_pull0", terr_terr_pull0+""); // double
		properties.setProperty(prefix+"terr_veget_pull0", terr_veget_pull0+""); // double
		properties.setProperty(prefix+"terr_elev_pull0", terr_elev_pull0+""); // double
		properties.setProperty(prefix+"terr_elev_alpha_en", terr_elev_alpha_en+""); // boolean
		properties.setProperty(prefix+"terr_elev_alpha", terr_elev_alpha+""); // double
		properties.setProperty(prefix+"terr_elev_alpha_pwr", terr_elev_alpha_pwr+""); // double
		properties.setProperty(prefix+"terr_low_veget", terr_low_veget+""); // double
		properties.setProperty(prefix+"terr_scenes_pull0", terr_scenes_pull0+""); // double

		properties.setProperty(prefix+"terr_boost_parallax", terr_boost_parallax+""); // double
		@@ -4234,6 +4276,12 @@ min_str_neib_fpn 0.35
		if (properties.getProperty(prefix+"terr_elevation_radius")!= null) terr_elevation_radius=Double.parseDouble(properties.getProperty(prefix+"terr_elevation_radius"));
		if (properties.getProperty(prefix+"terr_alpha_contrast")!= null) terr_alpha_contrast=Double.parseDouble(properties.getProperty(prefix+"terr_alpha_contrast"));
		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_sigma")!= null) terr_alpha_sigma=Double.parseDouble(properties.getProperty(prefix+"terr_alpha_sigma"));
		if (properties.getProperty(prefix+"terr_alpha_init_min")!= null) terr_alpha_init_min=Double.parseDouble(properties.getProperty(prefix+"terr_alpha_init_min"));
		if (properties.getProperty(prefix+"terr_alpha_init_max")!= null) terr_alpha_init_max=Double.parseDouble(properties.getProperty(prefix+"terr_alpha_init_max"));
		if (properties.getProperty(prefix+"terr_alpha_init_offs")!= null) terr_alpha_init_offs=Double.parseDouble(properties.getProperty(prefix+"terr_alpha_init_offs"));

		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"));
		if (properties.getProperty(prefix+"terr_alpha_lpf")!= null) terr_alpha_lpf=Double.parseDouble(properties.getProperty(prefix+"terr_alpha_lpf"));
		@@ -4250,6 +4298,10 @@ min_str_neib_fpn 0.35
		if (properties.getProperty(prefix+"terr_terr_pull0")!= null) terr_terr_pull0=Double.parseDouble(properties.getProperty(prefix+"terr_terr_pull0"));
		if (properties.getProperty(prefix+"terr_veget_pull0")!= null) terr_veget_pull0=Double.parseDouble(properties.getProperty(prefix+"terr_veget_pull0"));
		if (properties.getProperty(prefix+"terr_elev_pull0")!= null) terr_elev_pull0=Double.parseDouble(properties.getProperty(prefix+"terr_elev_pull0"));
		if (properties.getProperty(prefix+"terr_elev_alpha_en")!= null) terr_elev_alpha_en=Boolean.parseBoolean(properties.getProperty(prefix+"terr_elev_alpha_en"));
		if (properties.getProperty(prefix+"terr_elev_alpha")!= null) terr_elev_alpha=Double.parseDouble(properties.getProperty(prefix+"terr_elev_alpha"));
		if (properties.getProperty(prefix+"terr_elev_alpha_pwr")!= null) terr_elev_alpha_pwr=Double.parseDouble(properties.getProperty(prefix+"terr_elev_alpha_pwr"));
		if (properties.getProperty(prefix+"terr_low_veget")!= null) terr_low_veget=Double.parseDouble(properties.getProperty(prefix+"terr_low_veget"));
		if (properties.getProperty(prefix+"terr_scenes_pull0")!= null) terr_scenes_pull0=Double.parseDouble(properties.getProperty(prefix+"terr_scenes_pull0"));

		if (properties.getProperty(prefix+"terr_boost_parallax")!= null) terr_boost_parallax=Double.parseDouble(properties.getProperty(prefix+"terr_boost_parallax"));
		@@ -4917,6 +4969,12 @@ min_str_neib_fpn 0.35
		imp.terr_elevation_radius = this.terr_elevation_radius;
		imp.terr_alpha_contrast = this.terr_alpha_contrast;
		imp.terr_alpha_dflt = this.terr_alpha_dflt;

		imp.terr_alpha_sigma = this.terr_alpha_sigma;
		imp.terr_alpha_init_min = this.terr_alpha_init_min;
		imp.terr_alpha_init_max = this.terr_alpha_init_max;
		imp.terr_alpha_init_offs = this.terr_alpha_init_offs;

		imp.terr_alpha_loss = this.terr_alpha_loss;
		imp.terr_alpha_offset = this.terr_alpha_offset;
		imp.terr_alpha_lpf = this.terr_alpha_lpf;
		@@ -4933,6 +4991,10 @@ min_str_neib_fpn 0.35
		imp.terr_terr_pull0 = this.terr_terr_pull0;
		imp.terr_veget_pull0 = this.terr_veget_pull0;
		imp.terr_elev_pull0 = this.terr_elev_pull0;
		imp.terr_elev_alpha_en = this.terr_elev_alpha_en;
		imp.terr_elev_alpha = this.terr_elev_alpha;
		imp.terr_elev_alpha_pwr = this.terr_elev_alpha_pwr;
		imp.terr_low_veget = this.terr_low_veget;
		imp.terr_scenes_pull0 = this.terr_scenes_pull0;

		imp.terr_boost_parallax = this.terr_boost_parallax;

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

+192 −26

File changed.

Preview size limit exceeded, changes collapsed.

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

+31 −36

Original line number	Diff line number	Diff line
		@@ -1277,7 +1277,7 @@ public class VegetationModel {



		public static void processVegetationLMA(
		public static void processVegetation(
		CLTParameters clt_parameters,
		boolean combine_segments)
		{
		@@ -1296,7 +1296,7 @@ public class VegetationModel {
		VegetationModel vegetationModel = new VegetationModel(
		model_directory, // String dir,
		model_state_file); // String title)
		vegetationModel.testVegetationLMA(
		vegetationModel.processVegetationLMA(
		combine_segments, // boolean combine_segments,
		clt_parameters, // CLTParameters clt_parameters,
		-1); // int debugLevel) {
		@@ -1369,7 +1369,7 @@ public class VegetationModel {
		}
		}

		public void testVegetationLMA(
		public void processVegetationLMA(
		boolean combine_segments,
		CLTParameters clt_parameters,
		int debugLevel) {
		@@ -1418,7 +1418,13 @@ public class VegetationModel {
		// double terr_difference = clt_parameters.imp.terr_difference; // Pull vegetation to be this warmer
		// double terr_pull_cold = clt_parameters.imp.terr_pull_cold; // pull vegetations to warm, terrain to cold
		double elevation_radius = clt_parameters.imp.terr_elevation_radius; // Radius of elevation/vegetation influence
		double alpha_initial_contrast = clt_parameters.imp.terr_alpha_contrast; // initial alpha contrast (>=1.0)
		// double alpha_initial_contrast = clt_parameters.imp.terr_alpha_contrast; // initial alpha contrast (>=1.0)

		double alpha_sigma = clt_parameters.imp.terr_alpha_sigma; // 8.0; // Initial alpha: Gaussian blur sigma to find local average for vegetation temperature.
		double alpha_init_min= clt_parameters.imp.terr_alpha_init_min; // 0.7; // Initial alpha: fraction for transparent
		double alpha_init_max= clt_parameters.imp.terr_alpha_init_max; // 0.9; // Initial alpha: fraction for opaque
		double alpha_init_offs= clt_parameters.imp.terr_alpha_init_offs; // 0.01; // Initial alpha: opaque/transparent offset from 1.0/0.0

		double default_alpha = clt_parameters.imp.terr_alpha_dflt; // 0.5; // 0.8;
		double alpha_loss = clt_parameters.imp.terr_alpha_loss; //100.0; // 10.0; /// 100.0; // 10.0; // 10000.0; // 1000.0; // 100.; // 10.0; // quadratic loss when alpha reaches -1.0 or 2.0
		double alpha_offset = clt_parameters.imp.terr_alpha_offset; // 0.0; // 0.02; // 0.03; // if >0, start losses above 0.0 and below 1.0;
		@@ -1436,6 +1442,10 @@ public class VegetationModel {
		double terr_pull0 = clt_parameters.imp.terr_terr_pull0; // 0.05; //0.03; ////// 0.05; ///// 0.1; //// 0.01; /// 0.2; /// 0.1; //pull terrain to zero (makes sense with UM
		double veget_pull0 = clt_parameters.imp.terr_veget_pull0; // 0.05; //0.1; // 0.03; ////// 0.05; ///// 0.1; //// 0.01; /// 0.1; // pull vegetation to zero (makes sense with UM
		double elev_pull0 = clt_parameters.imp.terr_elev_pull0;
		boolean elev_alpha_en= clt_parameters.imp.terr_elev_alpha_en; // false;// Enable loss for low vegetation with high opacity
		double elev_alpha = clt_parameters.imp.terr_elev_alpha; // 1.0; // multiply alpha by under-low elevation for loss
		double elev_alpha_pwr = clt_parameters.imp.terr_elev_alpha_pwr; // 1.0; // multiply alpha by under-low elevation for loss
		double low_veget = clt_parameters.imp.terr_low_veget; // 2.0; // (pix) Elevation considered low (lower loss for high alpha)
		double scenes_pull0 = clt_parameters.imp.terr_scenes_pull0; // 1.0

		// LMA parameters
		@@ -1488,29 +1498,11 @@ public class VegetationModel {
		double transparency_frac = clt_parameters.imp.terr_recalc_frac ; // 1.0; // increase weight for far pixels (double if scale differece == this)
		double transparency_dist = clt_parameters.imp.terr_recalc_dist ; // 0.05; // weight of opaque tiles
		boolean recalc_average = clt_parameters.imp.terr_recalc_average ; //false; // apply transparency to average mismatch

		//clt_parameters.imp.; //


		boolean restore_mode = false;
		boolean save_par_files = true; // false;
		// boolean diff_mode = true;

		// String segments_dir = "/media/elphel/SSD3-4GB/lwir16-proc/berdich3/debug/vegetation/segments_new/";
		String segments_dir = getSegmentsDir(segments_sub);

		// boolean next_run = false;
		boolean read_pars = false; // true; /// false; /// true; // false; // true;






		// combine parameters



		// debug feature to read to continue - needs to be cleaned up/replaced
		String parameters_path = "/media/elphel/SSD3-4GB/lwir16-proc/berdich3/debug/vegetation/essential/parameters_vector_data_x143-y317-w35-h35-al100.0-alo0.0-alp10.0-alin-tl0.2-vl0.01-tp0.01-vp0.01-bp5.0-um1.0_0.8.tiff";

		@@ -1552,7 +1544,6 @@ public class VegetationModel {
		titles_laplacian, // String [] titles, // all slices*frames titles or just slice titles or null
		new String[] {"source","laplacian"}, // String [] frame_titles, // frame titles or null
		true); // boolean show)

		}
		}

		@@ -1933,21 +1924,21 @@ public class VegetationModel {


		} // if ((elevations == null) \|\| (scale_dirs == null)){


		// directions should not be averaged over scenes as the flight direction may change

		// if (debugLevel < 1000) {
		// return; //
		// }


		// initial_transparent = initial_split;
		// initial_opaque = 1.0 - initial_split;

		/*
		VegetationLMA vegetationLMA = new VegetationLMA (
		this,
		alpha_initial_contrast); // double alpha_initial_contrast)
		alpha_initial_contrast, // double alpha_initial_contrast)
		debugLevel); // int debugLevel)
		*/
		VegetationLMA vegetationLMA = new VegetationLMA (
		this,
		alpha_init_offs, // 0.01; // double alpha_offs,
		alpha_init_min, // 0.7; // double alpha_min,
		alpha_init_max, // 0.9; // double alpha_max,
		alpha_sigma, // 8.0; // double alpha_sigma,
		debugLevel); // int debugLevel)


		if (debugLevel > -2) {
		double [][] dbg_img = {
		vegetationLMA.tvao[VegetationLMA.TVAO_TERRAIN],
		@@ -2030,6 +2021,10 @@ public class VegetationModel {
		terr_pull0, // final double terr_pull0, // pull terrain to initial (pre-adjustment) values
		veget_pull0, // final double veget_pull0, // pull vegetation to initial (pre-adjustment) values
		elev_pull0, // final double elev_pull0, // pull elevation to initial (pre-adjustment) values
		elev_alpha_en, // final boolean elev_alpha_en, // false; // Enable loss for low vegetation with high opacity
		elev_alpha, // final double elev_alpha, // 1.0; // multiply alpha by under-low elevation for loss
		elev_alpha_pwr, // final double elev_alpha_pwr, // 2.0; // raise alpha to this power (when alpha > 0)
		low_veget, // final double low_veget, // 2.0; // (pix) Elevation considered low (lower loss for high alpha)
		scenes_pull0, // final double scenes_pull0,
		boost_parallax,// final double boost_parallax, // increase weight of scene with maximal parallax relative to the reference scene
		max_parallax, //final double max_parallax, // do not consider maximal parallax above this (consider it a glitch)

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