modifying parameters input (7c77ddba) · Commits · Elphel / imagej-elphel

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

+15 −4

Original line number	Diff line number	Diff line
		@@ -729,6 +729,7 @@ min_str_neib_fpn 0.35
		public String terr_model_path = "/media/elphel/SSD3-4GB/lwir16-proc/berdich3/models/models_1697875868-1697879449-b/1697877487_245877/v35";
		public String terr_model_state = "1697877487_245877-TERR-VEG-STATE";
		public String terr_segments_dir = "sections";
		public String terr_segments_suffix = "-new";
		public String terr_par_dir = ""; // directory path to intermediate parameters
		public String terr_par_file = ""; // file name of the intermediate parameters
		public boolean terr_par_restore = false; // restore parameters from file
		@@ -815,6 +816,7 @@ min_str_neib_fpn 0.35
		public double terr_elev_lpf = 50.0; // pull elevation to average of 4 neighbors
		public double terr_terr_pull0 = 0.1; // pull terrain to initial (pre-adjustment) values
		public double terr_terr_pull_up= 0.25; // pull terrain to initial when it is colder
		public double terr_terr_pull_avg= 0.1; // Pull terrain to the initial offset by the average offset of all terrain pixels
		public double terr_veget_pull0 = 5.0; // pull vegetation initial (pre-adjustment) values
		public double terr_elev_pull0 = 1.0; // pull elevation to initial (pre-adjustment) values
		public boolean terr_elev_alpha_en = false;// Enable loss for low vegetation with high opacity
		@@ -2054,6 +2056,7 @@ min_str_neib_fpn 0.35
		gd.addStringField ("Model path", terr_model_path, 120, "Model directory path with version.");
		gd.addStringField ("Model state file", terr_model_state, 50, "Model vegetation source data (w/o extension).");
		gd.addStringField ("Segments subdir", terr_segments_dir, 50,"Model vegetation source data (w/o extension).");
		gd.addStringField ("Segments suffix", terr_segments_suffix, 50,"suffix to select from multiple versions (w/o \".par-tiff\".");

		gd.addStringField ("Restore directory", terr_par_dir, 120, "Directory to resore initial parameters from.");
		gd.addStringField ("Restore file", terr_par_file, 120, "Filename to resore initial parameters from.");
		@@ -2138,7 +2141,8 @@ min_str_neib_fpn 0.35
		gd.addNumericField("Vegetation diffusion", terr_veget_lpf, 5,7,"", "LPF for vegetation pixels (diffusion to 4 neighbors).");
		gd.addNumericField("Elevation diffusion", terr_elev_lpf, 5,7,"", "LPF for elevation pixels (diffusion to 4 neighbors).");
		gd.addNumericField("Terrain pull", terr_terr_pull0, 5,7,"", "Terrain pixels pull to initial (pre-adjustment) values.");
		gd.addNumericField("Terrain pull up", terr_terr_pull_up, 5,7,"", "Terrain pixels pull to initial (pre-adjustment) values when it is colder than initial.");
		gd.addNumericField("Terrain pull up", terr_terr_pull_up, 5,7,"", "Terrain pixels pull to initial (pre-adjustment) values when it is colder than initial (<0 - sqme as above).");
		gd.addNumericField("Terrain pull to average",terr_terr_pull_avg, 5,7,"","Pull terrain to the initial offset by the average offset of all terrain pixels.");
		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.");

		@@ -2824,7 +2828,7 @@ min_str_neib_fpn 0.35
		terr_model_path = gd.getNextString();
		terr_model_state = gd.getNextString();
		terr_segments_dir = gd.getNextString();

		terr_segments_suffix = gd.getNextString();
		terr_par_dir = gd.getNextString();
		terr_par_file = gd.getNextString();
		terr_par_restore = gd.getNextBoolean(); // boolean
		@@ -2898,6 +2902,7 @@ min_str_neib_fpn 0.35
		terr_elev_lpf = gd.getNextNumber();// double
		terr_terr_pull0 = gd.getNextNumber();// double
		terr_terr_pull_up = gd.getNextNumber();// double
		terr_terr_pull_avg = gd.getNextNumber();// double
		terr_veget_pull0 = gd.getNextNumber();// double
		terr_elev_pull0 = gd.getNextNumber();// double
		terr_elev_alpha_en = gd.getNextBoolean();// boolean
		@@ -3541,6 +3546,7 @@ min_str_neib_fpn 0.35
		properties.setProperty(prefix+"terr_model_path", terr_model_path+""); // String
		properties.setProperty(prefix+"terr_model_state", terr_model_state+""); // String
		properties.setProperty(prefix+"terr_segments_dir", terr_segments_dir+""); // String
		properties.setProperty(prefix+"terr_segments_suffix", terr_segments_suffix+""); // String

		properties.setProperty(prefix+"terr_par_dir", terr_par_dir+""); // String
		properties.setProperty(prefix+"terr_par_file", terr_par_file+""); // String
		@@ -3616,6 +3622,7 @@ min_str_neib_fpn 0.35
		properties.setProperty(prefix+"terr_elev_lpf", terr_elev_lpf+""); // double
		properties.setProperty(prefix+"terr_terr_pull0", terr_terr_pull0+""); // double
		properties.setProperty(prefix+"terr_terr_pull_up", terr_terr_pull_up+""); // double
		properties.setProperty(prefix+"terr_terr_pull_avg", terr_terr_pull_avg+""); // 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
		@@ -4282,6 +4289,7 @@ min_str_neib_fpn 0.35
		if (properties.getProperty(prefix+"terr_model_path")!= null) terr_model_path=(String) properties.getProperty(prefix+"terr_model_path");
		if (properties.getProperty(prefix+"terr_model_state")!= null) terr_model_state=(String) properties.getProperty(prefix+"terr_model_state");
		if (properties.getProperty(prefix+"terr_segments_dir")!= null) terr_segments_dir=(String) properties.getProperty(prefix+"terr_segments_dir");
		if (properties.getProperty(prefix+"terr_segments_suffix")!= null) terr_segments_suffix=(String) properties.getProperty(prefix+"terr_segments_suffix");

		if (properties.getProperty(prefix+"terr_par_dir")!= null) terr_par_dir=(String) properties.getProperty(prefix+"terr_par_dir");
		if (properties.getProperty(prefix+"terr_par_file")!= null) terr_par_file=(String) properties.getProperty(prefix+"terr_par_file");
		@@ -4355,6 +4363,7 @@ min_str_neib_fpn 0.35
		if (properties.getProperty(prefix+"terr_elev_lpf")!= null) terr_elev_lpf=Double.parseDouble(properties.getProperty(prefix+"terr_elev_lpf"));
		if (properties.getProperty(prefix+"terr_terr_pull0")!= null) terr_terr_pull0=Double.parseDouble(properties.getProperty(prefix+"terr_terr_pull0"));
		if (properties.getProperty(prefix+"terr_terr_pull_up")!= null) terr_terr_pull_up=Double.parseDouble(properties.getProperty(prefix+"terr_terr_pull_up"));
		if (properties.getProperty(prefix+"terr_terr_pull_avg")!= null) terr_terr_pull_avg=Double.parseDouble(properties.getProperty(prefix+"terr_terr_pull_avg"));
		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"));
		@@ -4993,6 +5002,7 @@ min_str_neib_fpn 0.35
		imp.terr_model_path = this. terr_model_path;
		imp.terr_model_state = this. terr_model_state;
		imp.terr_segments_dir = this. terr_segments_dir;
		imp.terr_segments_suffix = this.terr_segments_suffix;

		imp.terr_par_dir = this. terr_par_dir;
		imp.terr_par_file = this. terr_par_file;
		@@ -5064,6 +5074,7 @@ min_str_neib_fpn 0.35
		imp.terr_elev_lpf = this.terr_elev_lpf;
		imp.terr_terr_pull0 = this.terr_terr_pull0;
		imp.terr_terr_pull_up = this.terr_terr_pull_up;
		imp.terr_terr_pull_avg = this.terr_terr_pull_avg;
		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;

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

+111 −30

Original line number	Diff line number	Diff line
		@@ -7,7 +7,6 @@ import java.text.SimpleDateFormat;
		import java.util.ArrayList;
		import java.util.Arrays;
		import java.util.Calendar;
		import java.util.Collections;
		import java.util.Comparator;
		import java.util.HashSet;
		import java.util.concurrent.atomic.AtomicBoolean;
		@@ -186,7 +185,8 @@ public class VegetationLMA {

		// when unsharp mask is applied , pulling to 0 (when alpha is 0 (for vegetation) or 1.0 (for terrain) makes sense
		private double terr_pull0 = 0; // (+) now - pull to filled terrain - terrain_average
		private double terr_pull_up = 0; // Terrain pixels pull to initial (pre-adjustment) values when it is colder than initial
		private double terr_pull_up = 0; // (+) Terrain pixels pull to initial (pre-adjustment) values when it is colder than initial
		private double terr_pull_avg = 0; // (+) pull terrain to the initial offset by the average offset of all terrain pixels
		private double veget_pull0 = 0; // (+) now - pull to vegetation_pull (extended vegetation)
		public double elevation_pull0 = 0; // (*) now - pull to initial elevation

		@@ -231,6 +231,7 @@ public class VegetationLMA {
		private double [] initial_rms = null; // {rms, rms_pure}, first-calcualted rms
		private double [] last_ymfx = null;
		private double [][] last_jt = null;
		public double terrain_offset = Double.NaN; // average offset from the initial

		public VegetationLMA (
		int width,
		@@ -518,6 +519,7 @@ public class VegetationLMA {
		final double elevation_lpf,
		final double terr_pull0, // pull terrain to initial (pre-adjustment) values
		final double terr_pull_up, // Terrain pixels pull to initial (pre-adjustment) values when it is colder than initial.
		final double terr_pull_avg, // pull terrain to the initial offset by the average offset of all terrain pixels
		final double veget_pull0, // pull vegetation to initial (pre-adjustment) values
		final double elev_pull0, // pull elevation to initial (pre-adjustment) values
		final boolean elev_alpha_en, // false; // Enable loss for low vegetation with high opacity
		@@ -561,6 +563,7 @@ public class VegetationLMA {
		this.elevation_lpf = elevation_lpf;
		this.terr_pull0 = terr_pull0;
		this.terr_pull_up= (terr_pull_up > 0) ? terr_pull_up : terr_pull0;
		this.terr_pull_avg = terr_pull_avg;
		this.veget_pull0 = veget_pull0;
		this.elevation_pull0 = elev_pull0;
		this.elev_alpha_en = elev_alpha_en;
		@@ -583,7 +586,7 @@ public class VegetationLMA {
		scales_xy, // final double [][][] scales_xy,
		full.width); // final int width)

		if (debugLevel > -2) {
		if (!vegetationModel.tile_woi && (debugLevel > -2)) {
		// not enough memory to allocate 468000MB (640x327580x585) stack
		// vegetationModel.reference_scene
		showWarps(
		@@ -638,7 +641,7 @@ public class VegetationLMA {



		if (debugLevel > -2) { // 3) {
		if (!vegetationModel.tile_woi && (debugLevel > -2)) { // 3) {
		int first_scene = num_scenes;
		int last_scene = -1;
		for (int i = 0; i < num_scenes; i++) if (valid_scenes[i]){
		@@ -1166,6 +1169,7 @@ public class VegetationLMA {
		boolean show_all = debug_level > 4;
		debugImageSaveShow(
		parameters_vector, // double [] vector
		last_rms, // double [] rms,
		save_dir, // String save_dir, // save if not null
		debug_title, // String title, // not null
		save_all, // boolean save_all,
		@@ -1344,6 +1348,7 @@ public class VegetationLMA {
		boolean show_all = debug_level > 4;
		debugImageSaveShow(
		new_vector, // double [] vector
		rms, // double [] rms,
		save_dir, // String save_dir, // save if not null
		debug_title, // String title, // not null
		save_all, // boolean save_all,
		@@ -1404,7 +1409,7 @@ public class VegetationLMA {
		debug_title += "-hf"+hifreq_weight+"-tc"+terrain_correction;
		debug_title += "-al"+alpha_loss+"-alo"+alpha_offset+"-amv"+alpha_min_veg+"-alp"+alpha_lpf+"-als"+alpha_scale_avg+(alpha_piece_linear?"-alin":"-acos");
		debug_title += "-ap"+alpha_push+"-apn"+alpha_push_neutral+"-apc"+alpha_push_center+(alpha_en_holes?("-amm"+alpha_mm_hole):"");
		debug_title += "-tl"+terr_lpf+"-vl"+veget_lpf+"-el"+elevation_lpf+"-tp"+terr_pull0+"-vp"+veget_pull0+"-ep"+elevation_pull0;
		debug_title += "-tl"+terr_lpf+"-vl"+veget_lpf+"-el"+elevation_lpf+"-tp"+terr_pull0+"-tu"+terr_pull_up+"-ta"+terr_pull_avg+"-vp"+veget_pull0+"-ep"+elevation_pull0;
		if (elev_alpha_en) {
		debug_title += "-ea"+elev_alpha+"-ep"+elev_alpha_pwr+"-lv"+low_veget;
		}
		@@ -1416,6 +1421,7 @@ public class VegetationLMA {

		public void debugImageSaveShow(
		double [] vector,
		double [] rms,
		String save_dir, // save if not null
		String title, // not null
		boolean save_all,
		@@ -1448,9 +1454,9 @@ public class VegetationLMA {

		debug_iters[debug_index] = debug_iter;
		debug_series[debug_index] = (vegetationModel != null) ? vegetationModel.step_restore : -1;
		debug_rms[debug_index] = last_rms.clone();
		debug_rms[debug_index] = rms.clone();
		debug_improvements[debug_index] = debug_improved;
		title += "-"+debug_iter+ "_"+debug_index+String.format("_rms%8.5f_rms-pure%8.5f", last_rms[0],last_rms[1]);
		title += "-"+debug_iter+ "_"+debug_index+String.format("_rms%8.5f_rms-pure%8.5f", rms[0],rms[1]);
		if (!debug_improved) {
		title+="-WORSE";
		}
		@@ -3102,7 +3108,39 @@ public class VegetationLMA {
		} // if (alpha_lpf >= 0) {

		if (samples_pointers[SAMPLES_TERRAIN_PULL][1]>0) { // fits[TVAO_TERRAIN] && (terr_lpf >= 0)) {
		// final int ind_y_terr = samples_pointers[SAMPLES_TERRAIN_PULL][0]; // ind_next;
		final double [] offsets_sum_threaded = new double [threads.length];
		final AtomicInteger anum=new AtomicInteger(0);
		double offsets_sum = 0;
		if (terr_pull_avg > 0) { // TODO: need to join all terrain samples
		// calculate average offset between current and initial terrain pixels
		ai.set(0);
		ati.set(0);
		for (int ithread = 0; ithread < threads.length; ithread++) {
		threads[ithread] = new Thread() {
		public void run() {
		int nthread = ati.getAndIncrement();
		for (int n = ai.getAndIncrement(); n < num_pars[TVAO_TERRAIN]; n = ai.getAndIncrement()) {
		int np = n + samples_pointers[SAMPLES_TERRAIN_PULL][2];
		int nx = n + samples_pointers[SAMPLES_TERRAIN_PULL][0];
		int findx = par_rindex[np][1];
		double terr_pull = terrain_average[findx]; // maybe use tvao[TVAO_TERRAIN][findx] ?
		if (Double.isNaN(terr_pull)) {
		terr_pull= 0; // should not happen
		}
		offsets_sum_threaded[nthread] += vector[np] - terr_pull;
		anum.getAndIncrement();
		}
		}
		};
		}
		ImageDtt.startAndJoin(threads);
		for (double d :offsets_sum_threaded) {
		offsets_sum += d;
		}
		}
		final int num = anum.get();
		// final double offset_avg;
		terrain_offset = (num > 0)? (offsets_sum/num) : 0;
		ai.set(0);
		for (int ithread = 0; ithread < threads.length; ithread++) {
		threads[ithread] = new Thread() {
		@@ -3110,20 +3148,33 @@ public class VegetationLMA {
		for (int n = ai.getAndIncrement(); n < num_pars[TVAO_TERRAIN]; n = ai.getAndIncrement()) {
		int np = n + samples_pointers[SAMPLES_TERRAIN_PULL][2];
		int nx = n + samples_pointers[SAMPLES_TERRAIN_PULL][0];
		double d = 0;
		boolean pull_up = false;
		if ((terr_pull0 > 0) \|\| (terr_pull_up > 0)) {
		int findx = par_rindex[np][1];
		double terr_pull = terrain_average[findx]; // maybe use tvao[TVAO_TERRAIN][findx] ?
		if (Double.isNaN(terr_pull)) {
		terr_pull= 0; // should not happen
		}
		if ((terr_pull0 > 0) \|\| (terr_pull_up > 0)) {
		double diff = vector[np] - terr_pull;
		pull_up = vector[np] < terr_pull;
		fX[nx] += (pull_up ? terr_pull_up : terr_pull0) * (vector[np] - terr_pull);
		fX[nx] += (pull_up ? terr_pull_up : terr_pull0) * diff;
		}
		if (jt != null) {
		jt[np][nx] += pull_up ? terr_pull_up : terr_pull0; // terr_pull0;
		}
		if (terr_pull_avg >0) { // TODO: maybe apply sign of difference here?
		double diff = vector[np] - (terr_pull + terrain_offset);
		fX[nx] += terr_pull_avg * diff;
		if (jt != null) {
		jt[np][nx] += terr_pull_avg; // terr_pull0;
		// now apply to all (others and this) derivative form offset_avg
		double dd = terr_pull_avg / num;
		for (int n_other = 0; n_other < num_pars[TVAO_TERRAIN]; n_other++) {
		int np_other = n_other + samples_pointers[SAMPLES_TERRAIN_PULL][2];
		jt[np_other][nx] -= dd; // terr_pull0;
		}
		}
		}
		}
		}
		};
		@@ -3538,6 +3589,26 @@ public class VegetationLMA {

		param_pivot = listsToPivot(
		param_lists); // final int [][] par_lists)

		if ((samples_pointers[SAMPLES_TERRAIN_PULL][1]>0) && (terr_pull_avg > 0)) {
		// make all terrain pixels to depend on each other
		ai.set(0);
		for (int ithread = 0; ithread < threads.length; ithread++) {
		threads[ithread] = new Thread() {
		public void run() {
		for (int n = ai.getAndIncrement(); n < num_pars[TVAO_TERRAIN]; n = ai.getAndIncrement()) {
		int np = n + samples_pointers[SAMPLES_TERRAIN_PULL][2];
		for (int n_other = n+1; n_other < num_pars[TVAO_TERRAIN]; n_other++) {
		int np_other = n_other + samples_pointers[SAMPLES_TERRAIN_PULL][2];
		param_pivot[np][np_other] = true;
		param_pivot[np_other][np] = true;
		}
		}
		}
		};
		}
		ImageDtt.startAndJoin(threads);
		}
		if (debug_level>4) showPivot(param_pivot, "pivot-all");
		}
		return fX;
		@@ -4145,6 +4216,8 @@ public class VegetationLMA {
		imp.setProperty("LPF_FIXED_ELEVATION", ""+lpf_fixed[TVAO_ELEVATION]);
		imp.setProperty("LPF_FIXED_SCENE_OFFSET", ""+lpf_fixed[TVAO_SCENE_OFFSET]);
		imp.setProperty("TERR_PULL0", ""+terr_pull0);
		imp.setProperty("TERR_PULL_UP", ""+terr_pull_up);
		imp.setProperty("TERR_PULL_AVG", ""+terr_pull_avg);
		imp.setProperty("VEGET_PULL0", ""+veget_pull0);
		imp.setProperty("ELEVATION_PULL0", ""+elevation_pull0);
		imp.setProperty("ELEV_ALPHA_EN", ""+elev_alpha_en);
		@@ -4165,6 +4238,7 @@ public class VegetationLMA {
		imp.setProperty("IND_PARS_ALPHA", ""+ind_pars[TVAO_ALPHA]);
		imp.setProperty("IND_PARS_ELEVATION", ""+ind_pars[TVAO_ELEVATION]);
		imp.setProperty("IND_PARS_SCENES", ""+ind_pars[TVAO_SCENE_OFFSET]);
		imp.setProperty("TERRAIN_OFFSET", ""+terrain_offset);

		// samples_pointers
		for (int nsp = 0; nsp < SAMPLES_SIZE; nsp++) {
		@@ -4195,7 +4269,8 @@ public class VegetationLMA {
		public double [][] restoreParametersFile( //FIXME: Not finished for real import !
		String path,
		boolean keep_settings,
		Rectangle [] file_wois){ // if not null, should be Rectangle[2] {woi_veg,woi} - will return woi data and not input parameters to this instance
		Rectangle [] file_wois, // if not null, should be Rectangle[2] {woi_veg,woi} - will return woi data and not input parameters to this instance
		double [] other_pars){
		ImagePlus imp_pars = new ImagePlus (path);
		if (imp_pars.getWidth()==0) {
		throw new IllegalArgumentException("Could not read "+path);
		@@ -4276,6 +4351,9 @@ public class VegetationLMA {
		}
		}
		data[TVAO_SCENE_OFFSET] = scene_offsets;
		if ((other_pars != null) && (other_pars.length >0)){
		if (imp_pars.getProperty("TERRAIN_OFFSET") != null) other_pars[0] = Double.parseDouble((String) imp_pars.getProperty("TERRAIN_OFFSET"));
		}
		} else {
		this.woi_veg = woi_veg;
		this.woi = woi;
		@@ -4312,6 +4390,8 @@ public class VegetationLMA {
		lpf_fixed[TVAO_ELEVATION] = Boolean.parseBoolean((String) imp_pars.getProperty("LPF_FIXED_ELEVATION"));
		lpf_fixed[TVAO_SCENE_OFFSET]=Boolean.parseBoolean((String)imp_pars.getProperty("LPF_FIXED_SCENE_OFFSET"));
		terr_pull0 = Double.parseDouble((String) imp_pars.getProperty("TERR_PULL0"));
		terr_pull_up = Double.parseDouble((String) imp_pars.getProperty("TERR_PULL_UP"));
		terr_pull_avg = Double.parseDouble((String) imp_pars.getProperty("TERR_PULL_AVG"));
		veget_pull0 = Double.parseDouble((String) imp_pars.getProperty("VEGET_PULL0"));
		elevation_pull0 = Double.parseDouble((String) imp_pars.getProperty("ELEVATION_PULL0"));
		if (imp_pars.getProperty("ELEV_ALPHA_EN") != null) elev_alpha_en = Boolean.parseBoolean((String) imp_pars.getProperty("ELEV_ALPHA_EN"));
		@@ -4321,6 +4401,7 @@ public class VegetationLMA {
		scenes_pull0 = Double.parseDouble((String) imp_pars.getProperty("SCENES_PULL0"));
		scale_scenes_pull = Double.parseDouble((String) imp_pars.getProperty("SCALE_SCENES_PULL"));
		boost_parallax = Double.parseDouble((String) imp_pars.getProperty("BOOST_PARALLAX"));
		if (imp_pars.getProperty("TERRAIN_OFFSET") != null) terrain_offset = Double.parseDouble((String) imp_pars.getProperty("TERRAIN_OFFSET"));
		}
		num_pars[TVAO_TERRAIN] = Integer.parseInt((String) imp_pars.getProperty("NUM_PARS_TERRAIN"));
		num_pars[TVAO_VEGETATION] = Integer.parseInt((String) imp_pars.getProperty("NUM_PARS_VEGETATION"));
		@@ -4878,7 +4959,8 @@ public class VegetationLMA {


		public VegetationSegment [] readAllSegments(
		String dir_path) {
		String dir_path,
		String suffix) {

		FileFilter parFileFilter = new FileFilter()
		{
		@@ -4886,7 +4968,7 @@ public class VegetationLMA {
		public boolean accept(File file) {

		//if the file extension is .log return true, else false
		if (file.isFile() && file.getName().endsWith(PAR_EXT)) {
		if (file.isFile() && file.getName().endsWith(suffix+PAR_EXT)) {
		return true;
		}
		return false;
		@@ -4895,21 +4977,24 @@ public class VegetationLMA {
		File dir = new File(dir_path);
		File [] par_files = dir.listFiles(parFileFilter);
		VegetationSegment [] segments = new VegetationSegment [par_files.length];
		double [] other_pars = new double [1];
		for (int n = 0; n < par_files.length; n++) {

		Rectangle [] wois = new Rectangle[2];
		double [][] tvao = restoreParametersFile( // already trimmed to actual lengths FIXME: Not finished for real import !
		par_files[n].getPath(), // String path,
		false, // boolean keep_settings,
		wois); // Rectangle file_woi)
		wois, // Rectangle file_woi)
		other_pars); //double [] other_pars)
		Rectangle woi_veg = wois[0];
		Rectangle woi = wois[1];


		segments[n] = new VegetationSegment(
		par_files[n].getPath(), // String path,
		woi_veg, // Rectangle woi_veg,
		woi, // Rectangle woi,
		tvao[TVAO_SCENE_OFFSET], // datadouble [] scene_offsets,
		new double [][] {tvao[0],tvao[1],tvao[2]}); // double [][] tva) {} {}
		other_pars[0], // terrain_offset,
		tvao[TVAO_SCENE_OFFSET], // double [] scene_offsets,
		new double [][] {tvao[0],tvao[1],tvao[2],tvao[2]}); // double [][] tva) {} {}
		}
		// sort in line-scan order
		Arrays.sort(segments, new Comparator<VegetationSegment>() {
		@@ -4919,10 +5004,6 @@ public class VegetationLMA {
		((rhs.woi_veg.x > lhs.woi_veg.x) ? -1 : (rhs.woi_veg.x < lhs.woi_veg.x) ? 1 : 0); // increasing
		}
		});




		return segments;
		}

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

+34 −34

File changed.

Preview size limit exceeded, changes collapsed.

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

+7 −0

Original line number	Diff line number	Diff line
		@@ -7,13 +7,20 @@ public class VegetationSegment {
		public Rectangle woi;
		public double [] scene_offsets;
		public double [][] tva;
		public double terrain_offset;
		public String path;
		public VegetationSegment(
		String path,
		Rectangle woi_veg,
		Rectangle woi,
		double terrain_offset,
		double [] scene_offsets, // has NaNs
		double [][] tva) {
		this.path = path;
		this.woi = woi;
		this.woi_veg = woi_veg;
		this.scene_offsets = scene_offsets;
		this.tva = tva;
		this.terrain_offset = terrain_offset;
		}
		}

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