More debugging (5fb0ddfb) · Commits · Elphel / imagej-elphel

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

+4 −0

Original line number	Diff line number	Diff line
		@@ -129,6 +129,7 @@ import com.elphel.imagej.tileprocessor.SymmVector;
		import com.elphel.imagej.tileprocessor.TwoQuadCLT;
		import com.elphel.imagej.tileprocessor.lwoc.LwirWorld;
		import com.elphel.imagej.vegetation.VegetationModel;
		import com.elphel.imagej.vegetation.VegetationSegment;

		import ij.CompositeImage;
		import ij.IJ;
		@@ -863,6 +864,7 @@ public class Eyesis_Correction implements PlugIn, ActionListener {
		addButton("Process Merged", panelOrange, color_process);
		addButton("Vegetation LMA", panelOrange, color_process);
		addButton("Combine LMA Segments", panelOrange, color_process);
		addButton("Generate LWIR target", panelOrange, color_process);
		plugInFrame.add(panelOrange);
		}
		plugInFrame.pack();
		@@ -5805,6 +5807,8 @@ public class Eyesis_Correction implements PlugIn, ActionListener {
		SYNC_COMMAND, // // SyncCommand SYNC_COMMAND,
		CLT_PARAMETERS, //CLTParameters clt_parameters,
		true); //boolean combine_segments);
		} else if (label.equals("Generate LWIR target")) {
		VegetationSegment.generateSineTarget();
		}
		//
		}

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

+12 −12

Original line number	Diff line number	Diff line
		@@ -871,8 +871,8 @@ min_str_neib_fpn 0.35
		public double terr_rms_diff = 1e-8; // 0.0001; virtually forever
		public int terr_last_series = -1; // Last LMA adjustment series (<0 - to the terr_num_iters.length -1)
		public int [] terr_num_iters = {30}; //sequence on numbers of iterations
		public boolean terr_only_special = true; // special sequences for terrain-only tiles
		public boolean terr_only_pix = true; // force per-pixel terrain elevation in terrain-only mode, overwrite fits_disable[TVAO_TERR_ELEV_PIX]
		/// public boolean terr_only_special = true; // special sequences for terrain-only tiles
		/// public boolean terr_only_pix = true; // force per-pixel terrain elevation in terrain-only mode, overwrite fits_disable[TVAO_TERR_ELEV_PIX]
		public int terr_only_series = -1; // similar to terr_last_series but for terrain-only mode (<0 - length of terr_only_num_iters)
		public int [] terr_only_num_iters = {25}; // number of iterations

		@@ -2246,8 +2246,8 @@ min_str_neib_fpn 0.35
		gd.addStringField ("Maximal iterations", intsToString(terr_num_iters), 40, "Maximal number of LMA iterations per series, 1 or several values.");

		gd.addMessage ("Terrain-only LMA");
		gd.addCheckbox ("Terrain-only mode", terr_only_special, "Treat terrain-only tiles differently (below).");
		gd.addCheckbox ("Adjust pixel elevation",terr_only_pix, "Force per-pixel terrain elevation adjustment in terrain-only mode.");
		/// gd.addCheckbox ("Terrain-only mode", terr_only_special, "Treat terrain-only tiles differently (below).");
		/// gd.addCheckbox ("Adjust pixel elevation",terr_only_pix, "Force per-pixel terrain elevation adjustment in terrain-only mode.");
		gd.addNumericField("Terrain-only iterations",terr_only_series, 0,3,"", "Last LMA series in terrain-only mode, -1 - to last available in the sequence below.");
		gd.addStringField ("Maximal iterations", intsToString(terr_only_num_iters), 40, "Maximal number of LMA iterations per series, 1 or several values.");

		@@ -3041,8 +3041,8 @@ min_str_neib_fpn 0.35
		terr_last_series = (int) gd.getNextNumber();// int
		terr_num_iters = StringToInts(gd.getNextString());

		terr_only_special = gd.getNextBoolean();// boolean
		terr_only_pix = gd.getNextBoolean();// boolean
		/// terr_only_special = gd.getNextBoolean();// boolean
		/// terr_only_pix = gd.getNextBoolean();// boolean
		terr_only_series = (int) gd.getNextNumber();// int
		terr_only_num_iters = StringToInts(gd.getNextString());

		@@ -3811,8 +3811,8 @@ min_str_neib_fpn 0.35
		properties.setProperty(prefix+"terr_last_series", terr_last_series+""); // int
		properties.setProperty(prefix+"terr_num_iters", intsToString(terr_num_iters)+""); // int []

		properties.setProperty(prefix+"terr_only_special", terr_only_special+""); // boolean
		properties.setProperty(prefix+"terr_only_pix", terr_only_pix+""); // boolean
		/// properties.setProperty(prefix+"terr_only_special", terr_only_special+""); // boolean
		/// properties.setProperty(prefix+"terr_only_pix", terr_only_pix+""); // boolean
		properties.setProperty(prefix+"terr_only_series", terr_only_series+""); // int
		properties.setProperty(prefix+"terr_only_num_iters", intsToString(terr_only_num_iters)+""); // int []

		@@ -4596,8 +4596,8 @@ min_str_neib_fpn 0.35
		if (properties.getProperty(prefix+"terr_num_iter")!= null) terr_num_iters=new int[] {Integer.parseInt(properties.getProperty(prefix+"terr_num_iter"))};
		if (properties.getProperty(prefix+"terr_num_iters")!= null) terr_num_iters=StringToInts((String) properties.getProperty(prefix+"terr_num_iters"));

		if (properties.getProperty(prefix+"terr_only_special")!= null) terr_only_special=Boolean.parseBoolean(properties.getProperty(prefix+"terr_only_special"));
		if (properties.getProperty(prefix+"terr_only_pix")!= null) terr_only_pix=Boolean.parseBoolean(properties.getProperty(prefix+"terr_only_pix"));
		/// if (properties.getProperty(prefix+"terr_only_special")!= null) terr_only_special=Boolean.parseBoolean(properties.getProperty(prefix+"terr_only_special"));
		/// if (properties.getProperty(prefix+"terr_only_pix")!= null) terr_only_pix=Boolean.parseBoolean(properties.getProperty(prefix+"terr_only_pix"));
		if (properties.getProperty(prefix+"terr_only_series")!= null) terr_only_series=Integer.parseInt(properties.getProperty(prefix+"terr_only_series"));
		if (properties.getProperty(prefix+"terr_only_num_iters")!= null) terr_only_num_iters=StringToInts((String) properties.getProperty(prefix+"terr_only_num_iters"));

		@@ -5344,8 +5344,8 @@ min_str_neib_fpn 0.35
		imp.terr_last_series = this.terr_last_series;
		imp.terr_num_iters = this.terr_num_iters.clone();

		imp.terr_only_special = this.terr_only_special;
		imp.terr_only_pix = this.terr_only_pix;
		/// imp.terr_only_special = this.terr_only_special;
		/// imp.terr_only_pix = this.terr_only_pix;
		imp.terr_only_series = this.terr_only_series;
		imp.terr_only_num_iters = this.terr_only_num_iters.clone();

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

+77 −33

Original line number	Diff line number	Diff line
		@@ -165,6 +165,7 @@ public class VegetationLMA {
		private double [] weights; // normalized so sum is 1.0 for all - samples and extra regularization

		boolean [] fits_disable = new boolean[TVAO_TYPES]; // (+)
		boolean [] fits_disable_terronly = new boolean[TVAO_TYPES]; // (+)
		private double terrain_correction = 0.02; // (+) weight of y_wavg

		// Parameters saved/resored in a file
		@@ -234,8 +235,8 @@ public class VegetationLMA {
		public double ttop_rel_rad = 0.25; // (+) Relative (to the top height) sample ring radius
		public double ttop_frac = 0.5; // (+) Minimal fraction of the ring pixels below sample level
		public double ttop_rem_rad = 0.25; // (+) Relative (to the top height) remove transparency radius
		public boolean terr_only_special = true; // (+) special sequences for terrain-only tiles
		public boolean terr_only_pix = true; // (+) force per-pixel terrain elevation in terrain-only mode, overwrite fits_disable[TVAO_TERR_ELEV_PIX]
		// public boolean terr_only_special = true; // (+) special sequences for terrain-only tiles
		// public boolean terr_only_pix = true; // (+) force per-pixel terrain elevation in terrain-only mode, overwrite fits_disable[TVAO_TERR_ELEV_PIX]

		public double boost_parallax = 1; // (+)
		public double max_parallax = 10; // (+)
		@@ -868,6 +869,7 @@ public class VegetationLMA {
		final boolean fit_terr_elev,
		final boolean fit_terr_elev_pix,
		final boolean [] fits_disable,
		final boolean [] fits_disable_terronly,
		final double reg_weights, // fraction of the total weight used for regularization
		final double alpha_loss, // alpha quadratic growing loss for when out of [0,1] range
		final double alpha_loss_lin, // alpha linear growing loss for when out of [0,1] range and below minimal vegetation alpha
		@@ -912,8 +914,8 @@ public class VegetationLMA {
		final double ttop_rel_rad, // 0.25; // Relative (to the top height) sample ring radius
		final double ttop_frac, // 0.5; // Minimal fraction of the ring pixels below sample level
		final double ttop_rem_rad, // 0.25; // Relative (to the top height) remove transparency radius
		final boolean terr_only_special,//true; // special sequences for terrain-only tiles
		final boolean terr_only_pix, //true; // force per-pixel terrain elevation in terrain-only mode, overwrite fits_disable[TVAO_TERR_ELEV_PIX]
		/// final boolean terr_only_special,//true; // special sequences for terrain-only tiles
		/// final boolean terr_only_pix, //true; // force per-pixel terrain elevation in terrain-only mode, overwrite fits_disable[TVAO_TERR_ELEV_PIX]
		final double boost_parallax, // increase weight of scene with maximal parallax relative to the reference scene
		final double max_parallax, // do not consider maximal parallax above this (consider it a glitch)
		final int debugLevel,
		@@ -932,8 +934,12 @@ public class VegetationLMA {
		fits[TVAO_TERR_ELEV] = fit_terr_elev \|\| fit_terr_elev_pix; // always both
		fits[TVAO_TERR_ELEV_PIX] = fit_terr_elev \|\| fit_terr_elev_pix;
		this.fits_disable = fits_disable.clone();
		this.fits_disable_terronly = (fits_disable_terronly != null)? fits_disable_terronly.clone() : null;
		// TODO: modify fits_disable with setter only ?
		this.fits_disable[TVAO_TERR_ELEV] \|= !(this.fits_disable[TVAO_TERR_ELEV_PIX] && fits[TVAO_TERR_ELEV_PIX]); // can not be enabled simultaneously
		if (this.fits_disable_terronly!= null) {
		this.fits_disable_terronly[TVAO_TERR_ELEV] \|= !(this.fits_disable_terronly[TVAO_TERR_ELEV_PIX] && fits[TVAO_TERR_ELEV_PIX]); // can not be enabled simultaneously
		}
		this.reg_weights = reg_weights; // fraction of the total weight used for regularization
		this.alpha_loss = alpha_loss;
		this.alpha_loss_lin = alpha_loss_lin;
		@@ -978,8 +984,8 @@ public class VegetationLMA {
		this.ttop_rel_rad = ttop_rel_rad;
		this.ttop_frac = ttop_frac;
		this.ttop_rem_rad = ttop_rem_rad;
		this.terr_only_special = terr_only_special;
		this.terr_only_pix = terr_only_pix;
		/// this.terr_only_special = terr_only_special;
		/// this.terr_only_pix = terr_only_pix;
		this.boost_parallax = boost_parallax;
		this.max_parallax = max_parallax; // parallax limit when evaluating boost parallax
		this.max_warp = max_warp;
		@@ -1109,10 +1115,21 @@ public class VegetationLMA {
		fits[TVAO_ALPHA] = false;
		fits[TVAO_ELEVATION] = false;
		}
		if (fits_disable_terronly!= null) {
		for (int i = 0; i < this.fits_disable.length; i++) {
		this.fits_disable[i] = fits_disable_terronly[i];
		}
		if (debugLevel > -3) {
		System.out.println("Using fits="+IntersceneMatchParameters.booleansToString(this.fits,2)+
		" fits_disable = "+IntersceneMatchParameters.booleansToString(this.fits_disable,2));
		}
		}
		/*
		if (terr_only_special) {
		fits_disable[TVAO_TERR_ELEV] = terr_only_pix;
		fits_disable[TVAO_TERR_ELEV_PIX] = !terr_only_pix;
		}
		*/
		}


		@@ -1877,7 +1894,7 @@ public class VegetationLMA {
		max_elev_terr_chg, // double max_diff,
		debug_level + 2); // int debugLevel)
		if ((debug_level > -3) && (num_terr_elev_mods > 0)) {
		System.out.println("lmaStep(): modified "+num_terr_elev_mods+" terrain elevation values to fit limuts.");
		System.out.println("lmaStep(): modified "+num_terr_elev_mods+" terrain elevation values to fit limits.");
		}
		/*
		if (par_indx_terr_elev >= 0) {
		@@ -3341,22 +3358,47 @@ public class VegetationLMA {
		vector, // final double [] vector,
		(jt != null), // final boolean calc_derivatives,
		debug_level); // final int debugLevel) {
		final boolean use_terr_elev_pix = (getIndxTerrElevPix() >=0) &&
		(!fits_disable[TVAO_TERR_ELEV_PIX] \|\| fits_disable[TVAO_TERR_ELEV]); // when both are disabled
		final boolean use_terr_elev = (getIndxTerrElev() >=0) && !use_terr_elev_pix;
		// only one of terr_elev_parameters, terr_elpix_parameters may be true simultaneously
		final boolean terr_elev_parameters = use_terr_elev; // (num_pars[TVAO_TERR_ELEV] > 0) && !fits_disable[TVAO_TERR_ELEV];
		final boolean terr_elpix_parameters = use_terr_elev_pix; // (num_pars[TVAO_TERR_ELEV_PIX]> 0) && !fits_disable[TVAO_TERR_ELEV_PIX];

		if (use_terr_elev_pix) { // (getIndxTerrElevPix() >=0) && !fits_disable[TVAO_TERR_ELEV_PIX]) {
		setupTerrainElevationPixLMA(
		vector, // final double [] vector,
		terr_elev_radius, // final double radius,
		(jt != null), // final boolean calc_derivatives,
		debug_level); // final int debugLevel)
		} else {
		terr_elpix_woi4 = null;
		if (use_terr_elev) { //(getIndxTerrElev() >=0) && !fits_disable[TVAO_TERR_ELEV]) {
		setupTerrainElevationLMA(
		vector, // final double [] vector,
		terr_elev_radius, // final double radius,
		(jt != null), // final boolean calc_derivatives,
		debug_level); // final int debugLevel) {
		} else {
		terr_elev_woi4 = null;
		}
		}
		/*
		// FIXME: probably wrong - as soon as per-pixel are different, has to always use them
		if ((getIndxTerrElev() >=0) && !fits_disable[TVAO_TERR_ELEV]) {
		if (use_terr_elev) { //(getIndxTerrElev() >=0) && !fits_disable[TVAO_TERR_ELEV]) {
		setupTerrainElevationLMA(
		vector, // final double [] vector,
		terr_elev_radius, // final double radius,
		(jt != null), // final boolean calc_derivatives,
		debug_level); // final int debugLevel) {
		} else if ((getIndxTerrElevPix() >=0) && !fits_disable[TVAO_TERR_ELEV_PIX]) {
		} else if (use_terr_elev_pix) { // (getIndxTerrElevPix() >=0) && !fits_disable[TVAO_TERR_ELEV_PIX]) {
		setupTerrainElevationPixLMA(
		vector, // final double [] vector,
		terr_elev_radius, // final double radius,
		(jt != null), // final boolean calc_derivatives,
		debug_level); // final int debugLevel) {
		}

		*/
		/// final boolean offset_terrain = !Double.isNaN(terr_elev_last) && (terr_elev_last != 0); // if 0, use terrain pixels directly

		final int woi_length = woi.width * woi.height;
		@@ -3369,9 +3411,6 @@ public class VegetationLMA {
		final boolean vegetation_parameters = (num_pars[TVAO_VEGETATION] > 0); // 0 when woi_veg==null
		final boolean alpha_parameters = (num_pars[TVAO_ALPHA] > 0); // 0 when woi_veg==null
		final boolean terrain_parameters = (num_pars[TVAO_TERRAIN] > 0);
		// only one of terr_elev_parameters, terr_elpix_parameters may be true simultaneously
		final boolean terr_elev_parameters = (num_pars[TVAO_TERR_ELEV] > 0) && !fits_disable[TVAO_TERR_ELEV];
		final boolean terr_elpix_parameters = (num_pars[TVAO_TERR_ELEV_PIX]> 0) && !fits_disable[TVAO_TERR_ELEV_PIX];
		final boolean scenes_parameters = (num_pars[TVAO_SCENE_OFFSET] > 0);
		final AtomicInteger anum_elev_err = new AtomicInteger(0);
		// final boolean use_hf = samples_pointers[SAMPLES_Y_HF][1]>0;
		@@ -3429,7 +3468,7 @@ public class VegetationLMA {
		double [][] dveget_woi = null;
		double [][] dterrain_woi_dterrain = null; // derivatives of terrain in image [woi] per terrain [woi_terr]
		double [] dterrain_woi_dtelev = null; // derivatives of terrain in image [woi] per terrain elevation [1]
		double [][] dterrain_woi_dtelpix = null; // derivatives of terrain in image [woi] per terrain elevation [woi_terr]
		//// double [][] dterrain_woi_dtelpix = null; // derivatives of terrain in image [woi] per terrain elevation [woi_terr]
		int nthread = ati.getAndIncrement();
		ArrayList<HashSet<Integer>> contrib_thread = null;
		if (need_derivs) {
		@@ -3445,9 +3484,9 @@ public class VegetationLMA {
		if (terr_elev_parameters) {
		dterrain_woi_dtelev = new double [woi_length];
		}
		if (terr_elpix_parameters) {
		dterrain_woi_dtelpix = new double [num_pars[TVAO_TERR_ELEV_PIX]][woi_length];
		}
		//// if (terr_elpix_parameters) {
		//// dterrain_woi_dtelpix = new double [num_pars[TVAO_TERR_ELEV_PIX]][woi_length];
		//// }
		}
		for (int nScene = ai.getAndIncrement(); nScene < num_scenes; nScene = ai.getAndIncrement()) if (valid_scenes[nScene]){
		Arrays.fill(alpha_woi,0);
		@@ -3602,7 +3641,6 @@ public class VegetationLMA {
		}
		} // if (terr_elev_woi4 != null) {


		if (terr_elpix_woi4 != null) { // per-pixel terrain elevation. Make mutually-exclusive with terr_elev_woi4
		for (int wtindex = 0; wtindex < woi_terr_length; wtindex++) if (terr_elpix_woi4[nScene][wtindex] != null) {
		int wtx = wtindex % woi_terr.width; // relative to woi_terr
		@@ -3664,7 +3702,7 @@ public class VegetationLMA {
		}
		}
		}
		} // if (terr_elev_woi4 != null) {
		} // if (terr_elpix_woi4 != null) {


		for (int windx = 0; windx < woi_length; windx++) if (valid_terr_proj[windx]) {
		@@ -3681,7 +3719,7 @@ public class VegetationLMA {
		}
		double terrain = 0;
		double stw = 0;
		if (terr_elpix_parameters) {
		if (terr_elpix_parameters) { // almost always
		stw = terr_elpix_sum_weights[nScene][windx];
		} else if (terr_elev_parameters) {
		stw = terr_elev_sum_weights[nScene][windx];
		@@ -3857,7 +3895,7 @@ public class VegetationLMA {
		jt[ind_pars[TVAO_TERR_ELEV]][y_indx] += dterrain_woi_dtelev[windx] * (1 - k);// sum_a; // d/dterrain
		} // if (terr_elev_parameters) {

		if (terr_elpix_parameters) {
		if (terr_elpix_parameters && !fits_disable[TVAO_TERR_ELEV_PIX]) { // skip if derivatives not needed
		/// here - just derivatives as direct influence of elevations is already processed
		/// we have dsw_delevations (for all elevation parameters) - ,
		HashSet<Integer> tepars_set = terr_elpix_contribs.get(windx);
		@@ -3936,7 +3974,7 @@ public class VegetationLMA {
		contrib_thread.get(windx).add(ind_pars[TVAO_TERR_ELEV]); // full parameter index - this result pixel depends on this terrain parameter
		jt[ind_pars[TVAO_TERR_ELEV]][y_indx] += dterrain_woi_dtelev[windx];// sum_a; // d/dterrain
		}
		if (terr_elpix_parameters) {
		if (terr_elpix_parameters && !fits_disable[TVAO_TERR_ELEV_PIX]) { // skip if derivatives are not needed
		HashSet<Integer> tepars_set = terr_elpix_contribs.get(windx);
		for (int npar: tepars_set) { // elevation parameters - full
		int ntepar = npar-ind_pars[TVAO_TERR_ELEV_PIX];
		@@ -5567,6 +5605,7 @@ public class VegetationLMA {
		imp.setProperty("FIT_DISABLE_ALPHA", ""+fits_disable[TVAO_ALPHA]);
		imp.setProperty("FIT_DISABLE_ELEVATION", ""+fits_disable[TVAO_ELEVATION]);
		imp.setProperty("FIT_DISABLE_TERR_ELEV", ""+fits_disable[TVAO_TERR_ELEV]);
		imp.setProperty("FIT_DISABLE_TERR_ELEV_PIX", ""+fits_disable[TVAO_TERR_ELEV_PIX]);
		imp.setProperty("FIT_DISABLE_SCENE_OFFSET", ""+fits_disable[TVAO_SCENE_OFFSET]);
		// imp.setProperty("TERR_ELEVATION_FULL", ""+terr_elevation_full);
		imp.setProperty("ALPHA_LOSS", ""+alpha_loss);
		@@ -5629,8 +5668,8 @@ public class VegetationLMA {
		imp.setProperty("TTOP_REL_RAD", ""+ttop_rel_rad);
		imp.setProperty("TTOP_FRAC", ""+ttop_frac);
		imp.setProperty("TTOP_REM_RAD", ""+ttop_rem_rad);
		imp.setProperty("TERR_ONLY_SPECIAL", ""+terr_only_special);
		imp.setProperty("TERR_ONLY_PIX", ""+terr_only_pix);
		/// imp.setProperty("TERR_ONLY_SPECIAL", ""+terr_only_special);
		/// imp.setProperty("TERR_ONLY_PIX", ""+terr_only_pix);
		imp.setProperty("BOOST_PARALLAX", ""+boost_parallax);
		imp.setProperty("MAX_PARALLAX", ""+max_parallax);
		imp.setProperty("MAX_WARP", ""+max_warp);
		@@ -5758,12 +5797,16 @@ public class VegetationLMA {
		fits[TVAO_VEGETATION] = Boolean.parseBoolean((String) imp_pars.getProperty("FIT_VEGETATION"));
		fits[TVAO_ALPHA] = Boolean.parseBoolean((String) imp_pars.getProperty("FIT_ALPHA"));
		fits[TVAO_ELEVATION] = Boolean.parseBoolean((String) imp_pars.getProperty("FIT_ELEVATION"));
		fits[TVAO_TERR_ELEV] = getProperty(imp_pars,"FIT_TERR_ELEV", fits[TVAO_TERR_ELEV]);
		fits[TVAO_TERR_ELEV_PIX] = getProperty(imp_pars,"FIT_TERR_ELEV_PIX", fits[TVAO_TERR_ELEV_PIX]);
		fits[TVAO_SCENE_OFFSET] = Boolean.parseBoolean((String) imp_pars.getProperty("FIT_SCENE_OFFSET"));

		fits_disable[TVAO_TERRAIN] = getProperty(imp_pars,"FIT_DISABLE_TERRAIN", fits_disable[TVAO_TERRAIN]);
		fits_disable[TVAO_VEGETATION] = getProperty(imp_pars,"FIT_DISABLE_VEGETATION", fits_disable[TVAO_VEGETATION]);
		fits_disable[TVAO_ALPHA] = getProperty(imp_pars,"FIT_DISABLE_ALPHA", fits_disable[TVAO_ALPHA]);
		fits_disable[TVAO_ELEVATION] = getProperty(imp_pars,"FIT_DISABLE_ELEVATION", fits_disable[TVAO_ELEVATION]);
		fits_disable[TVAO_TERR_ELEV] = getProperty(imp_pars,"FIT_DISABLE_TERR_ELEV", fits_disable[TVAO_TERR_ELEV]);
		fits_disable[TVAO_TERR_ELEV_PIX] =getProperty(imp_pars,"FIT_DISABLE_TERR_ELEV_PIX",fits_disable[TVAO_TERR_ELEV_PIX]);
		fits_disable[TVAO_SCENE_OFFSET] = getProperty(imp_pars,"FIT_DISABLE_SCENE_OFFSET", fits_disable[TVAO_SCENE_OFFSET]);

		// terr_elevation_full = getProperty(imp_pars,"TERR_ELEVATION_FULL", terr_elevation_full);
		@@ -5826,8 +5869,8 @@ public class VegetationLMA {
		ttop_rel_rad = getProperty(imp_pars,"TTOP_REL_RAD", ttop_rel_rad);
		ttop_frac = getProperty(imp_pars,"TTOP_FRAC", ttop_frac);
		ttop_rem_rad = getProperty(imp_pars,"TTOP_REM_RAD", ttop_rem_rad);
		terr_only_special = getProperty(imp_pars,"TERR_ONLY_SPECIAL", terr_only_special);
		terr_only_pix = getProperty(imp_pars,"TERR_ONLY_PIX", terr_only_pix);
		/// terr_only_special = getProperty(imp_pars,"TERR_ONLY_SPECIAL", terr_only_special);
		/// terr_only_pix = getProperty(imp_pars,"TERR_ONLY_PIX", terr_only_pix);
		boost_parallax = getProperty(imp_pars,"BOOST_PARALLAX", boost_parallax);
		max_parallax = getProperty(imp_pars,"MAX_PARALLAX", max_parallax);
		max_warp = getProperty(imp_pars,"MAX_WARP", max_warp);
		@@ -6098,6 +6141,7 @@ public class VegetationLMA {
		getProperty(imp_pars, "FIT_TERR_ELEV_PIX", fits[TVAO_TERR_ELEV_PIX]),// final boolean adjust_terr_elev_pix,
		// getProperty(imp_pars,"TERR_ELEVATION_FULL", terr_elevation_full),
		getProperty(imp_pars, disable_names, fits_disable), // final boolean [] fit_disable,
		null, // fits_disable_terronly,// final boolean [] fits_disable_terronly,
		getProperty(imp_pars, "REG_WEIGHTS", reg_weights), // final double reg_weights, // fraction of the total weight used for regularization
		getProperty(imp_pars, "ALPHA_LOSS", alpha_loss), // final double alpha_loss, // alpha quadratic growing loss for when out of [0,1] range
		getProperty(imp_pars, "ALPHA_LOSS_LIN", alpha_loss_lin), // final double alpha_loss_lin, // alpha linear growing loss for when out of [0,1] range and below minimal vegetation alpha
		@@ -6143,8 +6187,8 @@ public class VegetationLMA {
		getProperty(imp_pars, "TTOP_REL_RAD", ttop_rel_rad), // final double ttop_rel_rad,
		getProperty(imp_pars, "TTOP_FRAC", ttop_frac), // final double ttop_frac,
		getProperty(imp_pars, "TTOP_REM_RAD", ttop_rem_rad), // final double ttop_rem_rad,
		getProperty(imp_pars, "TERR_ONLY_SPECIAL", terr_only_special), // final boolean terr_only_special,//true; // special sequences for terrain-only tiles
		getProperty(imp_pars, "TERR_ONLY_PIX", terr_only_pix), // final boolean terr_only_pix, //true; // force per-pixel terrain elevation in terrain-only mode, overwrite fits_disable[TVAO_TERR_ELEV_PIX]
		/// getProperty(imp_pars, "TERR_ONLY_SPECIAL", terr_only_special), // final boolean terr_only_special,//true; // special sequences for terrain-only tiles
		/// getProperty(imp_pars, "TERR_ONLY_PIX", terr_only_pix), // final boolean terr_only_pix, //true; // force per-pixel terrain elevation in terrain-only mode, overwrite fits_disable[TVAO_TERR_ELEV_PIX]
		getProperty(imp_pars, "BOOST_PARALLAX", boost_parallax), // final double boost_parallax, // increase weight of scene with maximal parallax relative to the reference scene
		getProperty(imp_pars, "MAX_PARALLAX", max_parallax), // final double max_parallax, // do not consider maximal parallax above this (consider it a glitch)

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

+17 −12

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

+66 −172

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