Minor changes here and there during program use/debugging (151ea276) · Commits · Elphel / imagej-elphel

src/main/java/com/elphel/imagej/cameras/ThermalColor.java

+2 −2

Original line number	Diff line number	Diff line
		@@ -28,8 +28,8 @@ public class ThermalColor {
		double k = out_range/PALETTE_RANGE;
		double value = (v-min)/(max-min) * (this.palette.length - 1);
		int ivalue = (int) (value);
		if (ivalue < 0) return this.palette[0];
		if (ivalue >= (this.palette.length -1)) return this.palette[this.palette.length -1];
		if (value < 0) return this.palette[0];
		if (value >= (this.palette.length -1)) return this.palette[this.palette.length -1];
		double a = (value-ivalue); // 0..1
		double [] rslt = {
		k((1 - a) this.palette[ivalue][0] + a * this.palette[ivalue+1][0]),

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

+1 −1

Original line number	Diff line number	Diff line
		@@ -116,7 +116,7 @@ public class IntersceneLmaParameters {
		gd.addMessage("Interframe LMA parameters selection");
		gd.addCheckbox ("3D mode (use disparity)", this.ilma_3d,
		"Use disparity for interscene matching (as for UAS imagery)" );
		gd.addNumericField("Disp[arity weight", this.ilma_disparity_weight, 6,8,"",
		gd.addNumericField("Disparity weight", this.ilma_disparity_weight, 6,8,"",
		"Disparity component weight compared to dX and dY");
		gd.addCheckbox ("LMA in 3D mode", this.ilma_3d_lma,
		"Use LMA disparity for interscene matching (as for UAS imagery)" );

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

+94 −57

Original line number	Diff line number	Diff line
		@@ -4538,6 +4538,10 @@ public class OpticalFlow {
		int min_num_scenes = clt_parameters.imp.min_num_scenes; // abandon series if there are less than this number of scenes in it
		int max_num_scenes = clt_parameters.imp.max_num_scenes; // cut longer series

		double boost_max_short = 2.0; //



		double [] lma_rms = new double[2];
		double [] use_atr = null;

		@@ -4689,6 +4693,26 @@ public class OpticalFlow {
		scenes_xyzatr[scene_index][1].clone()};
		boolean rot_to_transl = after_spiral && clt_parameters.ilp.ilma_translation_priority;
		double [] reg_weights = rot_to_transl? clt_parameters.ilp.ilma_regularization_weights0 : clt_parameters.ilp.ilma_regularization_weights;
		min_max[1] = max_offset;
		if ((ref_index - scene_index) < min_num_scenes) {
		min_max[1] = boost_max_short * max_offset;
		if (debugLevel > -3) {
		System.out.println("As the current series ("+(ref_index - scene_index)+
		" scenes) is shorter than minimal ("+min_num_scenes+"), the maximal shift is scaled by "+
		boost_max_short + " to " + (boost_max_short * max_offset)+
		" pixels");
		}
		}
		if ((scene_index - earliest_scene) < min_num_scenes) {
		min_max[1] = boost_max_short * max_offset;
		if (debugLevel > -3) {
		System.out.println("As the remaining number of scenes to process ("+(scene_index - earliest_scene + 1)+
		") is less than minimal ("+min_num_scenes+"), the maximal shift is scaled by "+
		boost_max_short + " to " + (boost_max_short * max_offset)+
		" pixels");
		}
		}

		scenes_xyzatr[scene_index] = adjustPairsLMAInterscene(
		clt_parameters, // CLTParameters clt_parameters,
		use_lma_dsi, // clt_parameters.imp.use_lma_dsi,
		@@ -5107,7 +5131,7 @@ public class OpticalFlow {

		if (!force_initial_orientations) {
		if ((quadCLTs[ref_index].getNumOrient() == 0) \|\|(!quadCLTs[ref_index].propertiesContainString (".scenes_"))) {
		if (debugLevel >-2) {
		if (debugLevel >-3) {
		System.out.println("Egomotion data for scene "+set_channels[ref_index].set_name+" does not exist, forcing its calculation.");
		}
		force_initial_orientations = true;
		@@ -5794,12 +5818,64 @@ public class OpticalFlow {
		} // for (int ibase = 0; ibase < baselines.length; ibase++) {
		}// for (int mode3d = 0; mode3d<generate_modes3d.length; mode3d++) if (generate_modes3d[mode3d]) {
		} // if (generate_mapped) {
		if (export_dsi_image \|\| show_dsi_image) {
		if (combo_dsn_final == null) {
		/// combo_dsn_final =quadCLTs[ref_index].readDoubleArrayFromModelDirectory(
		/// "-INTER-INTRA-LMA", // String suffix,
		/// 0, // int num_slices, // (0 - all)
		/// null); // int [] wh);
		combo_dsn_final =quadCLTs[ref_index].restoreComboDSI(true); // also sets quadCLTs[ref_index].dsi and blue sky

		}

		// re-load , should create quadCLTs[ref_index].dsi
		double [][] dls = {
		combo_dsn_final[COMBO_DSN_INDX_DISP],
		combo_dsn_final[COMBO_DSN_INDX_LMA],
		combo_dsn_final[COMBO_DSN_INDX_STRENGTH]
		};
		int dbg_condition = debug_ranges ? Math.max(1, debugLevel) : debugLevel;
		double [][] ds = conditionInitialDS( // Add debug szxy by providing debugLevel=1
		true, // boolean use_conf, // use configuration parameters, false - use following
		clt_parameters, // CLTParameters clt_parameters,
		dls, // double [][] dls
		quadCLTs[ref_index], // QuadCLT scene,
		dbg_condition); // int debug_level)
		double [] disparity = ds[0];
		double [] strength = ds[1];
		double [][]szxy = getSceneSZXY(
		quadCLTs[ref_index], // QuadCLT scene,
		range_disparity_offset, // double disparity_offset,
		range_min_strength, // double min_strength,
		range_max, // double max_range,
		disparity, // double [] disparity,
		strength); // double [] strength)
		String [] szxy_titles = {"strength", "Z(m)", "X(m)", "Y(m)"};
		TileProcessor tp = quadCLTs[ref_index].getTileProcessor();
		int tilesX = tp.getTilesX();
		int tilesY = tp.getTilesY();
		ImagePlus impSZXY = ShowDoubleFloatArrays.makeArrays(
		szxy,
		tilesX,
		tilesY,
		quadCLTs[ref_index].getImageName()+"_SZXY",
		szxy_titles);
		if (export_dsi_image) {
		quadCLTs[ref_index].saveImagePlusInModelDirectory(
		null, // "GPU-SHIFTED-BACKGROUND", // String suffix,
		impSZXY); // ImagePlus imp)
		}
		if (show_dsi_image) {
		impSZXY.show();

		}
		}

		// debugging 3D model
		int [] whs = new int[3];
		double [] x0y0 = new double[2];
		if (export3d) { //combo_dsn_final had strength 1.0e-4 where it should not? Reset it?
		/* */
		/*
		boolean use_lma = true; // ;
		double discard_low = 0.01; // fraction of all pixels
		double discard_high = 0.5; // fraction of all pixels
		@@ -5817,6 +5893,7 @@ public class OpticalFlow {
		double [] hdr_x0y0 = new double[2];
		double [][] to_ground_xyxatr = quadCLTs[ref_index].getGround(
		use_lma, // boolean use_lma,
		clt_parameters.imp.range_disparity_offset,// double range_disparity_offset
		discard_low, // double discard_low, // fraction of all pixels
		discard_high, // double discard_high, // fraction of all pixels
		discard_adisp, // double discard_adisp, // discard above/below this fraction of average height
		@@ -5827,7 +5904,7 @@ public class OpticalFlow {
		hdr_whs, // int [] whs, // initialize to int[3] to return {width, height, scale reduction}
		debugLevel); // int debug_level

		/**/
		*/

		boolean ok_3d = TexturedModel.output3d( // quadCLTs have same image name, and everything else
		clt_parameters, // CLTParameters clt_parameters,
		@@ -6085,58 +6162,6 @@ public class OpticalFlow {
		}
		}

		if (export_dsi_image \|\| show_dsi_image) {
		if (combo_dsn_final == null) {
		/// combo_dsn_final =quadCLTs[ref_index].readDoubleArrayFromModelDirectory(
		/// "-INTER-INTRA-LMA", // String suffix,
		/// 0, // int num_slices, // (0 - all)
		/// null); // int [] wh);
		combo_dsn_final =quadCLTs[ref_index].restoreComboDSI(true); // also sets quadCLTs[ref_index].dsi and blue sky

		}

		// re-load , should create quadCLTs[ref_index].dsi
		double [][] dls = {
		combo_dsn_final[COMBO_DSN_INDX_DISP],
		combo_dsn_final[COMBO_DSN_INDX_LMA],
		combo_dsn_final[COMBO_DSN_INDX_STRENGTH]
		};
		int dbg_condition = debug_ranges ? Math.max(1, debugLevel) : debugLevel;
		double [][] ds = conditionInitialDS( // Add debug szxy by providing debugLevel=1
		true, // boolean use_conf, // use configuration parameters, false - use following
		clt_parameters, // CLTParameters clt_parameters,
		dls, // double [][] dls
		quadCLTs[ref_index], // QuadCLT scene,
		dbg_condition); // int debug_level)
		double [] disparity = ds[0];
		double [] strength = ds[1];
		double [][]szxy = getSceneSZXY(
		quadCLTs[ref_index], // QuadCLT scene,
		range_disparity_offset, // double disparity_offset,
		range_min_strength, // double min_strength,
		range_max, // double max_range,
		disparity, // double [] disparity,
		strength); // double [] strength)
		String [] szxy_titles = {"strength", "Z(m)", "X(m)", "Y(m)"};
		TileProcessor tp = quadCLTs[ref_index].getTileProcessor();
		int tilesX = tp.getTilesX();
		int tilesY = tp.getTilesY();
		ImagePlus impSZXY = ShowDoubleFloatArrays.makeArrays(
		szxy,
		tilesX,
		tilesY,
		quadCLTs[ref_index].getImageName()+"_SZXY",
		szxy_titles);
		if (export_dsi_image) {
		quadCLTs[ref_index].saveImagePlusInModelDirectory(
		null, // "GPU-SHIFTED-BACKGROUND", // String suffix,
		impSZXY); // ImagePlus imp)
		}
		if (show_dsi_image) {
		impSZXY.show();

		}
		}

		if (export_ml_files) {
		if (combo_dsn_final == null) { // always re-read?
		@@ -13112,11 +13137,22 @@ public class OpticalFlow {
		}
		return null;
		}

		if (avg_offs > min_max[1]) {// NaN - do not check;
		if (fail_reason != null) {
		fail_reason[0]=FAIL_REASON_MAX;
		}
		if (debug_level > -3){
		System.out.println ("interCorrPair(): avg_offs = "+avg_offs+
		" > "+min_max[1]+", sw = "+sw);
		}

		return null;
		} else {
		if (debug_level > -3){
		System.out.println ("interCorrPair(): avg_offs = "+avg_offs+
		" <= "+min_max[1]+", sw = "+sw);
		}
		}
		}
		double half_disparity = near_important ? 0.0 : clt_parameters.imp.half_disparity;
		@@ -14242,6 +14278,7 @@ public class OpticalFlow {
		// double mb_max_gain = clt_parameters.imp.mb_max_gain_inter; // 5.0; // motion blur maximal gain (if more - move second point more than a pixel
		int margin = clt_parameters.imp.margin;
		double second_margin = 1.1; // allow slightly larger offset for readjsutments (to be limited by the first pass)
		double boost_max_short = 5.0; // 2.0; // Some bug?
		int earliest_scene = 0;
		boolean use_combo_dsi = clt_parameters.imp.use_combo_dsi;
		boolean use_lma_dsi = clt_parameters.imp.use_lma_dsi;
		@@ -14250,14 +14287,14 @@ public class OpticalFlow {
		int tilesY = quadCLTs[ref_index].getTileProcessor().getTilesY();
		int tile_size = quadCLTs[ref_index].getTileProcessor().getTileSize();
		double min_offset = clt_parameters.imp.min_offset;
		double max_offset = second_marginclt_parameters.imp.max_rel_offset tilesX * tile_size;
		double max_offset = boost_max_shortsecond_marginclt_parameters.imp.max_rel_offset * tilesX * tile_size;
		double max_roll = second_marginclt_parameters.imp.max_roll_degMath.PI/180.0;
		double max_zoom_diff = second_margin*clt_parameters.imp.max_zoom_diff;
		boolean fpn_skip = clt_parameters.imp.fpn_skip; // if false - fail as before
		boolean fpn_rematch = clt_parameters.imp.fpn_rematch; // if false - keep previous
		double [] min_max = {min_offset, max_offset, 0.0} ; // {min, max, actual rms)
		int [] fail_reason = new int[1]; // null or int[1]: 0 - OK, 2 - LMA, 3 - min, 4 - max

		System.out.println("reAdjustPairsLMAInterscene(): min_offset="+min_max[0]+", max_offset="+min_max[1]);
		double [] disparity_raw = new double [tilesX * tilesY];
		Arrays.fill(disparity_raw,clt_parameters.disparity);
		/// double [][] combo_dsn_final = quadCLTs[ref_index].readDoubleArrayFromModelDirectory(

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

+44 −14

Original line number	Diff line number	Diff line
		@@ -223,6 +223,7 @@ public class QuadCLTCPU {
		// cac
		public double [][] getGround(
		boolean use_lma,
		double disparity_offset,
		double discard_low, // fraction of all pixels
		double discard_high, // fraction of all pixels
		double discard_adisp, // discard above/below this fraction of average height
		@@ -234,22 +235,24 @@ public class QuadCLTCPU {
		int debug_level
		) {
		double [] z_tilts = null;
		final int tilesX=getTileProcessor().getTilesX();
		final int tilesY=getTileProcessor().getTilesY();
		double hist_rlow = 0.4;
		double normal_damping = 0.001; // pull to horizontal if not enough data
		// final int tilesX=getTileProcessor().getTilesX();
		// final int tilesY=getTileProcessor().getTilesY();
		double hist_rlow = 0.5;
		double hist_rhigh = 2.0;
		int min_good = 20; //number of good tiles
		int min_good_quad = 20; // number of good tiles per quadrantto calculate tilts
		int gap_frac2= 20;
		/// int min_good_quad = 20; // number of good tiles per quadrant to calculate tilts
		/// int gap_frac2= 20;
		double rel_hight = 0.2; // when calculating scale, ignore objects far from plane
		int num_bins = 1000;
		double [][] dls = getDLS();
		if (dls==null) {
		return null;
		}
		double [][] ds = new double [][] {dls[use_lma?1:0], dls[2]};
		double [][] ds = new double [][] {dls[use_lma?1:0].clone(), dls[2]};
		double sw=0, swd=0;
		for (int i = 0; i < ds[0].length; i++) if (!Double.isNaN(ds[0][i])){
		ds[0][i] -= disparity_offset;
		sw += ds[1][i];
		swd += ds[0][i] * ds[1][i];
		}
		@@ -318,7 +321,9 @@ public class QuadCLTCPU {
		}
		return null; // too few good
		}
		double z_avg= getGeometryCorrection().getZFromDisparity(swd/sw);

		// double z_avg= getGeometryCorrection().getZFromDisparity(swd/sw);
		/*
		int gap_x_0 = tilesX/2 - tilesX/gap_frac2;
		int gap_x_1 = tilesX/2 + tilesX/gap_frac2;
		int gap_y_0 = tilesY/2 - tilesY/gap_frac2;
		@@ -348,9 +353,11 @@ public class QuadCLTCPU {
		System.out.println("There are less than 3 quadrants ("+num_good_quads+") having more than "+min_good_quad+" tiles");
		System.out.println("Using only level "+z_avg+", ignoring tilt.");
		}
		z_tilts = new double[] {z_avg, 0.0, 0.0}; // no tilts
		z_tilts = new double[] {-z_avg, 0.0, 0.0}; // no tilts
		// return new double[] {z_avg, 0.0, 0.0}; // no tilts
		} else {

		*/
		// fit plane
		double [] ref_disparity = ds[0].clone();
		for (int i = 0; i < ref_disparity.length; i++) {
		@@ -381,17 +388,18 @@ public class QuadCLTCPU {
		mindx++;
		}
		PolynomialApproximation pa = new PolynomialApproximation();
		double [] damping = new double [] {normal_damping, normal_damping};
		double[][] approx2d = pa.quadraticApproximation(
		mdata,
		true, // boolean forceLinear, // use linear approximation
		null, // double [] damping, null OK
		damping, // double [] damping, null OK
		-1); // debug level
		z_tilts= new double [] { approx2d[0][2], approx2d[0][0], approx2d[0][1]};
		if (debug_level > -3) {
		System.out.println("Found ground plane: level="+z_tilts[0]+", tiltX="+z_tilts[1]+", tiltY="+z_tilts[2]);
		}

		}
		/* } */
		// ground - negative Z. picture right - positive X, picture up - positive Y
		// positive tiltX - to the right higher ground (lower altitude above it) or camera tilted left
		// positive tiltY - picture up - higher ground (or camera tilted back)
		@@ -402,11 +410,16 @@ public class QuadCLTCPU {
		// It is approximate for small angles. OK for now
		double [][] to_ground_xyxatr = ErsCorrection.invertXYZATR(ground_xyxatr);
		// recalculate coordinates for all pixels including weak ones
		double [] ref_disparity = dls[0].clone();
		// double []
		ref_disparity = dls[0].clone();
		for (int i = 0; i < ref_disparity.length; i++) {
		if (Double.isNaN(ref_disparity[i])) ref_disparity[i] = 0.0;
		else {
		ref_disparity[i] -= disparity_offset;
		}
		double [][] wxyz = OpticalFlow.transformToWorldXYZ(
		}
		// double [][]
		wxyz = OpticalFlow.transformToWorldXYZ(
		ref_disparity, // final double [] disparity_ref, // invalid tiles - NaN in disparity
		(QuadCLT) this, // final QuadCLT quadClt, // now - may be null - for testing if scene is rotated ref
		THREADS_MAX); // int threadsMax)
		@@ -432,8 +445,11 @@ public class QuadCLTCPU {
		if (y < y_min_max[0]) y_min_max[0] = y;
		else if (y > y_min_max[1]) y_min_max[1] = y;
		}
		if ((x_min_max == null) \|\| (y_min_max == null)) {
		return null; // no points at all?
		}
		if (x0y0!=null) {
		x0y0[0] = x_min_max[0];
		x0y0[0] = x_min_max[0]; // null
		x0y0[1] = y_min_max[0];
		}
		int scale = 0;
		@@ -8387,6 +8403,9 @@ public class QuadCLTCPU {
		double [][] rgba = new double [num_slices][];
		for (int i = 0; i < 3; i++) rgba[i] = new double [texture_data[main_color_index].length];
		for (int i = 0; i < rbg_in[main_color_index].length; i++) {
		if (i==160000) {
		System.out.println ("i="+i);
		}
		double [] rgb = tc.getRGB(texture_data[main_color_index][i]);
		rgba[0][i] = rgb[0]; // red
		rgba[1][i] = rgb[1]; // green
		@@ -15421,6 +15440,7 @@ public class QuadCLTCPU {
		public boolean writeLwirPreview(
		final CLTParameters clt_parameters,
		double [] data,
		double [] minmax, // null for auto
		QuadCLT scene,
		int tex_palette,
		String suffix,
		@@ -15429,6 +15449,7 @@ public class QuadCLTCPU {
		clt_parameters,
		data,
		getTileProcessor().getTilesX() *getTileProcessor().getTileSize(),
		minmax, // double [] minmax, // null for auto
		scene,
		tex_palette,
		suffix,
		@@ -15438,6 +15459,7 @@ public class QuadCLTCPU {
		final CLTParameters clt_parameters,
		double [] data,
		int width,
		double [] minmax, // null for auto
		QuadCLT scene,
		int tex_palette,
		String suffix,
		@@ -15449,7 +15471,15 @@ public class QuadCLTCPU {
		for (int i = 0; i < rendered_texture[0].length; i++) {
		rendered_texture[1][i] = Double.isNaN(rendered_texture[0][i])? 0.0: 1.0;
		}
		double [] minmax = scene.getColdHot(); // used in linearStackToColor (from this current scene)
		// double [] minmax = scene.getColdHot(); // used in linearStackToColor (from this current scene)
		if (!suffix.equals("")) {
		if (minmax == null) { // to replace standard preview file name
		minmax = scene.getColdHot(); // used in linearStackToColor (from this current scene)
		suffix +="-AUTORANGE";
		} else {
		suffix +="-RANGE"+(minmax[1]-minmax[0]);
		}
		}
		// int width = getTileProcessor().getTilesX() *getTileProcessor().getTileSize();
		int height = data.length/width;
		String set_name = getImageName();

Admin message