Before implementing tree-top filter (cc900bac) · Commits · Elphel / imagej-elphel

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

+21 −4

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

+306 −391

File changed.

Preview size limit exceeded, changes collapsed.

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

+44 −12

Original line number	Original line	Diff line number	Diff line
	@@ -1597,12 +1597,19 @@ public class VegetationModel {
	double transparency_gb = clt_parameters.imp.terr_recalc_gb ; // 2.0; // Blur transparency-based confidence		double transparency_gb = clt_parameters.imp.terr_recalc_gb ; // 2.0; // Blur transparency-based confidence
	double transparency_boost = clt_parameters.imp.terr_recalc_boost ; // 5.0; // Maximal boost while increasing low-confidence pixel weights		double transparency_boost = clt_parameters.imp.terr_recalc_boost ; // 5.0; // Maximal boost while increasing low-confidence pixel weights
	boolean recalc_average = clt_parameters.imp.terr_recalc_average ; // false; // apply transparency to average mismatch		boolean recalc_average = clt_parameters.imp.terr_recalc_average ; // false; // apply transparency to average mismatch
			String debug_path = clt_parameters.imp.terr_debug_path; // Directory to save debug images
	boolean debug_save_improved = clt_parameters.imp.terr_debug_improved;		boolean debug_save_improved = clt_parameters.imp.terr_debug_improved;
	boolean debug_save_worsened = clt_parameters.imp.terr_debug_worsened;		boolean debug_save_worsened = clt_parameters.imp.terr_debug_worsened;
			int debug_length = clt_parameters.imp.terr_debug_length;




	// boolean restore_mode = false;		// boolean restore_mode = false;
	boolean save_par_files = true; // false;		boolean save_par_files = true; // false;
	String segments_dir = getSegmentsDir(segments_sub);		String segments_dir = getSegmentsDir(segments_sub);
	boolean read_pars = false; // true; /// false; /// true; // false; // true;		boolean read_pars = false; // true; /// false; /// true; // false; // true;
			boolean crop_combo = clt_parameters.imp.terr_crop; // Crop output image to the bounds of all segments

	// debug feature to read to continue - needs to be cleaned up/replaced		// 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";		// 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";
	@@ -2061,7 +2068,6 @@ public class VegetationModel {
	segments_dir, // String dir_path)		segments_dir, // String dir_path)
	segments_suffix); // String suffix);		segments_suffix); // String suffix);
	*/		*/
	boolean crop_combo = true;
	VegetationSegment [] segments = vegetationLMA.readAllSegments(		VegetationSegment [] segments = vegetationLMA.readAllSegments(
	segments_dir, // String dir_path)		segments_dir, // String dir_path)
	segments_suffix, // String suffix);		segments_suffix, // String suffix);
	@@ -2072,6 +2078,7 @@ public class VegetationModel {
	transparency_pow, // double transparency_pow,		transparency_pow, // double transparency_pow,
	transparency_gb, // double transparency_gb,		transparency_gb, // double transparency_gb,
	debugLevel, // int debugLevel,		debugLevel, // int debugLevel,
			debug_path, // String debug_path,
	debug_save_improved, // boolean debug_save_improved, // Save debug image after successful LMA step.");		debug_save_improved, // boolean debug_save_improved, // Save debug image after successful LMA step.");
	debug_save_worsened); // boolean debug_save_worsened) { // Save debug image after unsuccessful LMA step.");		debug_save_worsened); // boolean debug_save_worsened) { // Save debug image after unsuccessful LMA step.");
	VegetationSegment.combineSegments(		VegetationSegment.combineSegments(
	@@ -2116,9 +2123,11 @@ public class VegetationModel {
	int num_samples = vegetationLMA.prepareLMA(		int num_samples = vegetationLMA.prepareLMA(
	false, // final boolean keep_parameters,		false, // final boolean keep_parameters,
	woi, // final Rectangle woi,		woi, // final Rectangle woi,
			null, // final Rectangle woi_veg_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_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_offset, // final int max_offset, // maximal "elevation" to consider
	elevation_radius, // final double elevation_radius, // Radius of elevation/vegetation influence.		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		hifreq_weight, //final double hifreq_weight, // 22.5 0 - do not use high-freq. Relative weight of laplacian components
	terrain_correction,// final double terrain_correction,		terrain_correction,// final double terrain_correction,
	fit_terr, // final boolean adjust_terr,		fit_terr, // final boolean adjust_terr,
	@@ -2160,6 +2169,7 @@ public class VegetationModel {
	// (um_en? um_weight: 0.0), // final double um_weight,		// (um_en? um_weight: 0.0), // final double um_weight,
	// par_path, // final String parameters_read_path,		// par_path, // final String parameters_read_path,
	debugLevel, // final int debugLevel);		debugLevel, // final int debugLevel);
			debug_path, // final String debug_path,
	debug_save_improved, // final boolean debug_save_improved, // Save debug image after successful LMA step.");		debug_save_improved, // final boolean debug_save_improved, // Save debug image after successful LMA step.");
	debug_save_worsened);// final boolean debug_save_worsened) // Save debug image after unsuccessful LMA step.");		debug_save_worsened);// final boolean debug_save_worsened) // Save debug image after unsuccessful LMA step.");

	@@ -2168,12 +2178,32 @@ public class VegetationModel {
	continue;		continue;
	}		}

			// if (save_par_files && skip_existing_woi) { // check that segment already exists
	if (save_par_files && skip_existing_woi) { // check that segment already exists		if (save_par_files && skip_existing_woi) { // check that segment already exists
			// public boolean segmentFileExist(String dir_path) {
			/*
	String save_path = VegetationLMA.getSavePath(		String save_path = VegetationLMA.getSavePath(
	segments_dir, // String dir,		segments_dir, // String dir,
	vegetationLMA.getParametersDebugTitle()); // String title)		vegetationLMA.getParametersDebugTitle()); // String title)
	if (new File (save_path).exists()) {		if (new File (save_path).exists()) {
	System.out.println("File "+save_path+"\n already exists, skipping this woi");		*/
			File[] segment_files = vegetationLMA.getSegmentFiles(segments_dir);
			if (tile_woi) {
			if (segment_files.length > 0) {
			for (File f : segment_files) {
			System.out.println("File "+f+"\n with the same woi already exists, skipping this woi");
			}
			continue;
			}
			} else {
			String save_path = VegetationLMA.getSavePath(
			segments_dir, // String dir,
			vegetationLMA.getParametersDebugTitle()); // String title)
			if (new File (save_path).exists()) {
			System.out.println("File "+save_path+"\n (exactly) already exists, skipping this woi");
			// for (File f : segment_files) {
			// System.out.println("File "+f+"\n (exactly) already exists, skipping this woi");
			// }
	continue;		continue;
	}		}
	if (new File (save_path.replace("-new-","-file-")).exists()) {		if (new File (save_path.replace("-new-","-file-")).exists()) {
	@@ -2181,6 +2211,7 @@ public class VegetationModel {
	continue;		continue;
	}		}
	}		}
			}
	int num_iter = num_iters[step_restore]; //		int num_iter = num_iters[step_restore]; //
	if (par_restore) { // always use last number of iterations - not anymore		if (par_restore) { // always use last number of iterations - not anymore
	String par_path = parameters_dir;		String par_path = parameters_dir;
	@@ -2250,7 +2281,8 @@ public class VegetationModel {
	}		}
	/// next_run = true;		/// next_run = true;
	vegetationLMA.debug_index = 0;		vegetationLMA.debug_index = 0;
	vegetationLMA.debug_image = new double [100][]; // num_iter][];		vegetationLMA.debug_length = debug_length;
			vegetationLMA.debug_image = new double [vegetationLMA.debug_length][]; // num_iter][];

	int lma_rslt= vegetationLMA.runLma( // <0 - failed, >=0 iteration number (1 - immediately)		int lma_rslt= vegetationLMA.runLma( // <0 - failed, >=0 iteration number (1 - immediately)
	lambda, // double lambda, // 0.1		lambda, // double lambda, // 0.1

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

+102 −11

Original line number	Original line	Diff line number	Diff line
	@@ -15,6 +15,7 @@ public class VegetationSegment {
	public double [][] tva; // woi_veg		public double [][] tva; // woi_veg
	public double terrain_offset;		public double terrain_offset;
	public double [] confidence; // woi		public double [] confidence; // woi
			public boolean [] overlaid;
	public String path;		public String path;
	public VegetationSegment(		public VegetationSegment(
	String path,		String path,
	@@ -23,7 +24,8 @@ public class VegetationSegment {
	double terrain_offset,		double terrain_offset,
	double [] scene_offsets, // has NaNs		double [] scene_offsets, // has NaNs
	double [][] tva,		double [][] tva,
	double [] confidence) {		double [] confidence,
			boolean [] overlaid) {
	this.path = path;		this.path = path;
	this.woi = woi;		this.woi = woi;
	this.woi_veg = woi_veg;		this.woi_veg = woi_veg;
	@@ -31,6 +33,22 @@ public class VegetationSegment {
	this.tva = tva;		this.tva = tva;
	this.terrain_offset = terrain_offset;		this.terrain_offset = terrain_offset;
	this.confidence = confidence;		this.confidence = confidence;
			this.overlaid = overlaid;
			correctTerrainOffset();
			}

			public void correctTerrainOffset() {
			if (!Double.isNaN(terrain_offset) && (overlaid != null)) {
			int woi_length = woi.width * woi.height;
			for (int windx = 0; windx < woi_length; windx++) {
			int wx = windx % woi.width;
			int wy = windx / woi.height;
			int wvindx = (wx + woi.x - woi_veg.x) + (wy + woi.y - woi_veg.y) * woi_veg.width;
			if (overlaid[windx]) {
			tva[0][wvindx] += terrain_offset;
			}
			}
			}
	}		}

	public static Rectangle getBounds( // [0] - woi, [1] - woi_weg		public static Rectangle getBounds( // [0] - woi, [1] - woi_weg
	@@ -98,7 +116,7 @@ public class VegetationSegment {
	int x = wx + woi.x - out_woi.x;		int x = wx + woi.x - out_woi.x;
	int y = wy + woi.y - out_woi.y;		int y = wy + woi.y - out_woi.y;
	int indx = x + y * out_woi.width;		int indx = x + y * out_woi.width;
	preview_data[t][ns][indx] = woi_tva[t][wsrc];		preview_data[t][ns][indx] = woi_tva[t][wsrc]; // java.lang.ArrayIndexOutOfBoundsException: Index -43 out of bounds for length 550
	}		}
	break;		break;
	case 1: // vegetation		case 1: // vegetation
	@@ -156,10 +174,11 @@ public class VegetationSegment {
	}		}
	VegetationModel vegetationModel = vegetationLMA.getModel();		VegetationModel vegetationModel = vegetationLMA.getModel();
	String ref_scene = vegetationModel.reference_scene;		String ref_scene = vegetationModel.reference_scene;
			String pre_title = ref_scene+"-preview_segments-"+out_woi.x+"-"+out_woi.y+"-"+out_woi.width+"-"+out_woi.height;
	ShowDoubleFloatArrays.showArraysHyperstack(		ShowDoubleFloatArrays.showArraysHyperstack(
	preview_data, // double[][][] pixels,		preview_data, // double[][][] pixels,
	out_woi.width, // int width,		out_woi.width, // int width,
	ref_scene+"-preview_segments", // String title, "time_derivs-rt"+diff_time_rt+"-rxy"+diff_time_rxy,		pre_title, // String title, "time_derivs-rt"+diff_time_rt+"-rxy"+diff_time_rxy,
	titles, // String [] titles, // all slices*frames titles or just slice titles or null		titles, // String [] titles, // all slices*frames titles or just slice titles or null
	top_titles, // String [] frame_titles, // frame titles or null		top_titles, // String [] frame_titles, // frame titles or null
	true); // boolean show)		true); // boolean show)
	@@ -185,13 +204,23 @@ public class VegetationSegment {
	um_weight); // final double um_weight)		um_weight); // final double um_weight)
	String [] result_titles = {"ref_render", "terrain_accum",String.format("terrain_accum_UM%5.2f-%4.2f",um_sigma,um_weight),"terrain"};		String [] result_titles = {"ref_render", "terrain_accum",String.format("terrain_accum_UM%5.2f-%4.2f",um_sigma,um_weight),"terrain"};
	double [][] result_img = {terrain_reference,terrain_accumulated,terrain_um,preview_data[0][accum_indx]};		double [][] result_img = {terrain_reference,terrain_accumulated,terrain_um,preview_data[0][accum_indx]};
	// ref_scene+"-result-terrain"		boolean normalize = true;
			int norm_index = 1;
			if (normalize) {
			result_img = normalize (
			result_img, // final double [][] data,
			norm_index); // final int norm_index){
			}
			String res_title = ref_scene+"-result_terrain-"+out_woi.x+"-"+out_woi.y+"-"+out_woi.width+"-"+out_woi.height;
			if (normalize) {
			res_title+= "-normalized"+norm_index;
			}
	ShowDoubleFloatArrays.showArrays(		ShowDoubleFloatArrays.showArrays(
	result_img,		result_img,
	out_woi.width,		out_woi.width,
	out_woi.height,		out_woi.height,
	true,		true,
	ref_scene+"-result_terrain",		res_title,
	result_titles);		result_titles);


	@@ -439,6 +468,68 @@ public class VegetationSegment {
	}		}
	return cropped;		return cropped;
	}		}
			/**
			* Normalize slices to match the selected one by average and standard deviation
			* @param data array of image slices
			* @param norm_index index (0-based) of the reference slice
			* @return normalized image
			*/
			public static double [][] normalize (
			final double [][] data,
			final int norm_index){
			final int num_slices = data.length;
			final int num_pix = data[0].length;
			double [][] normalized = new double [num_slices][];
			for (int i = 0; i < num_slices; i++) {
			normalized[i] = data[i].clone();
			}
			final double [] mean = new double[num_slices];
			final double [] std = new double[num_slices];
			final Thread[] threads = ImageDtt.newThreadArray(QuadCLT.THREADS_MAX);
			final AtomicInteger ai = new AtomicInteger(0);
			for (int ithread = 0; ithread < threads.length; ithread++) { // first sum for pairs
			threads[ithread] = new Thread() {
			public void run() {
			for (int nSlice = ai.getAndIncrement(); nSlice < num_slices; nSlice = ai.getAndIncrement()) {
			double [] slice = normalized[nSlice];
			double s0=0, s1=0, s2=0;
			for (int i = 0; i < slice.length; i++) if (!Double.isNaN(slice[i])) {
			s0 += 1;
			s1 += slice[i];
			s2 += slice[i]*slice[i];
			}
			s1 /= s0;
			s2 /= s0;
			mean[nSlice] = s1;
			std[nSlice] = Math.sqrt(s2 - s1 * s1);
			}
			}
			};
			}
			ImageDtt.startAndJoin(threads);
			final double [] a = new double [num_slices], b = new double[num_slices];
			Arrays.fill(a, 1);
			for (int n = 0; n < num_slices; n++) if (n != norm_index){
			a[n] = std[norm_index]/std[n];
			b[n] = mean[norm_index] - a[n]*mean[n];
			}
			ai.set(0);
			for (int ithread = 0; ithread < threads.length; ithread++) { // first sum for pairs
			threads[ithread] = new Thread() {
			public void run() {
			for (int nPix = ai.getAndIncrement(); nPix < num_pix; nPix = ai.getAndIncrement()) {
			for (int n = 0; n < num_slices; n++) if (n != norm_index){
			double d = normalized[n][nPix];
			if (!Double.isNaN(d)) {
			normalized[n][nPix] = a[n]*d + b[n];
			}
			}
			}
			}
			};
			}
			ImageDtt.startAndJoin(threads);
			return normalized;
			}

	}		}

Original line number	Original line	Diff line number	Diff line
	@@ -859,6 +859,7 @@ min_str_neib_fpn 0.35


	// combine parameters		// combine parameters
			public boolean terr_crop = true; // Crop output image to the bounds of all segments
	public int terr_border_width = 6;		public int terr_border_width = 6;
	public boolean terr_render_open = true; // render open areas (no vegetation offset)		public boolean terr_render_open = true; // render open areas (no vegetation offset)
	public boolean terr_render_no_alpha = true; // render where no opacity is available		public boolean terr_render_no_alpha = true; // render where no opacity is available
	@@ -876,6 +877,8 @@ min_str_neib_fpn 0.35
	public double terr_min_terrain = 0.001;		public double terr_min_terrain = 0.001;
	public double terr_min_vegetation = 0.5;		public double terr_min_vegetation = 0.5;
	public int terr_debug = 0;		public int terr_debug = 0;
			public String terr_debug_path = "/media/elphel/SSD3-4GB/lwir16-proc/berdich3/debug/vegetation/lma_um/";
			public int terr_debug_length = 200;
	public boolean terr_debug_improved = true; // Save debug data if LMA step improved		public boolean terr_debug_improved = true; // Save debug data if LMA step improved
	public boolean terr_debug_worsened = true; // Save debug data if LMA step improved		public boolean terr_debug_worsened = true; // Save debug data if LMA step improved

	@@ -2191,6 +2194,7 @@ min_str_neib_fpn 0.35


	gd.addMessage ("Combining LMA results segments");		gd.addMessage ("Combining LMA results segments");
			gd.addCheckbox ("Crop result image", terr_crop, "Crop output image to the bounds of all segments.");
	gd.addNumericField("Overlap width", terr_border_width, 0,3,"","Width of the inter-tile oiverlap border.");		gd.addNumericField("Overlap width", terr_border_width, 0,3,"","Width of the inter-tile oiverlap border.");
	gd.addCheckbox ("Render open", terr_render_open, "");		gd.addCheckbox ("Render open", terr_render_open, "");
	gd.addCheckbox ("Render no alpha", terr_render_no_alpha, "");		gd.addCheckbox ("Render no alpha", terr_render_no_alpha, "");
	@@ -2206,7 +2210,9 @@ min_str_neib_fpn 0.35
	gd.addNumericField("Min max terrain", terr_min_max_terrain, 5,7,"", ".");		gd.addNumericField("Min max terrain", terr_min_max_terrain, 5,7,"", ".");
	gd.addNumericField("Minimal terrain", terr_min_terrain, 5,7,"", ".");		gd.addNumericField("Minimal terrain", terr_min_terrain, 5,7,"", ".");
	gd.addNumericField("Minimal vegetation", terr_min_vegetation, 5,7,"", ".");		gd.addNumericField("Minimal vegetation", terr_min_vegetation, 5,7,"", ".");
	gd.addNumericField("LMA debug level", terr_debug, 0,3,"", ".");		gd.addNumericField("LMA debug level", terr_debug, 0,3,"", "Debug level.");
			gd.addStringField ("Debug directory", terr_debug_path, 120,"Directory to save debug images.");
			gd.addNumericField("Debug length", terr_debug_length, 0,3,"","Maximal number of debug image slices.");
	gd.addCheckbox ("Debug improved", terr_debug_improved, "Save debug image after successful LMA step.");		gd.addCheckbox ("Debug improved", terr_debug_improved, "Save debug image after successful LMA step.");
	gd.addCheckbox ("Debug worsened", terr_debug_worsened, "Save debug image after unsuccessful LMA step.");		gd.addCheckbox ("Debug worsened", terr_debug_worsened, "Save debug image after unsuccessful LMA step.");

	@@ -2939,6 +2945,7 @@ min_str_neib_fpn 0.35
	terr_recalc_boost = gd.getNextNumber(); // double		terr_recalc_boost = gd.getNextNumber(); // double
	terr_recalc_average = gd.getNextBoolean();// boolean		terr_recalc_average = gd.getNextBoolean();// boolean

			terr_crop = gd.getNextBoolean();// boolean