Started LMA S/N measurements to compare contrast enhancement (b66e802e) · Commits · Elphel / imagej-elphel

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

+115 −1

Original line number	Diff line number	Diff line
		@@ -112,7 +112,121 @@ public class ThermalColor {
		0xfff8c4, 0xfff9c7, 0xfff9ca, 0xfff9cd, 0xfffad1, 0xfffad4, 0xfffbd8, 0xfffcdb,
		0xfffcdf, 0xfffde2, 0xfffde5, 0xfffde8, 0xfffeeb, 0xfffeee, 0xfffef1, 0xfffef4,
		0xffffff};
		int [][] palettes = {white_hot_palette, black_hot_palette, iron_palette};
		int [] pal01_palette = {0x1f77b4,0xff7f0e,
		0x2ca02c,
		0xd62728,
		0x9467bd,
		0x8c564b,
		0xe377c2,
		0x7f7f7f,
		0xbcbd22,
		0x17becf};
		int [] viridis_palette = {
		0x46317e,
		0x365b8c,
		0x277e8e,
		0x1fa187,
		0x49c16d,
		0x9fd938};

		int [] viridis_mod_palette = {
		0x401080,
		0x46317e,
		0x365b8c,
		0x277e8e,
		0x1fa187,
		0x49c16d,
		0x9fd938,
		0xcc9000,
		0xff6000
		};

		int [] coolwarm_palette = {
		0x6788ed ,
		0x99bafe ,
		0xc8d7ef ,
		0xedd0c1 ,
		0xf6a789 ,
		0xe16852};
		int [] cubehelix_palette = {
		0x1a2341 ,
		0x1b6144 ,
		0x687a30 ,
		0xc77a7c ,
		0xcda2e0 ,
		0xc6e1f1};
		int [] hsv_palette = {
		0xffd400 ,
		0x4eff00 ,
		0xff85 ,
		0x9dff ,
		0x3600ff ,
		0xff00ec};
		int [] hsv2_palette = {
		0xffd400 ,
		0x4eff00 ,
		0xff85 ,
		0x9dff ,
		0x3600ff ,
		0xff00ec,
		0xffd400 ,
		0x4eff00 ,
		0xff85 ,
		0x9dff ,
		0x3600ff ,
		0xff00ec};
		int [] hsv3_palette = {
		0xffd400 ,
		0x4eff00 ,
		0xff85 ,
		0x9dff ,
		0x3600ff ,
		0xff00ec,
		0xffd400 ,
		0x4eff00 ,
		0xff85 ,
		0x9dff ,
		0x3600ff ,
		0xff00ec ,
		0xffd400 ,
		0x4eff00 ,
		0xff85 ,
		0x9dff ,
		0x3600ff ,
		0xff00ec};

		int [] spectral_palette = {
		0xe1514a ,
		0xfba55c ,
		0xfee899 ,
		0xecf7a2 ,
		0xa1d9a4 ,
		0x479fb3};

		int [] spectral_r_palette = {
		0x479fb3 ,
		0xa1d9a4 ,
		0xecf7a2 ,
		0xfee899 ,
		0xfba55c ,
		0xe1514a};


		int [][] palettes = {
		white_hot_palette,
		black_hot_palette,
		iron_palette,
		pal01_palette,
		viridis_palette,
		coolwarm_palette,
		cubehelix_palette,
		hsv_palette,
		hsv2_palette,
		hsv3_palette,
		viridis_mod_palette,
		spectral_palette,
		spectral_r_palette
		};
		if (indx <0) indx = 0;
		else if (indx >= palettes.length) indx = palettes.length - 1;
		return palettes[indx];

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

+37 −16

Original line number	Diff line number	Diff line
		@@ -7374,36 +7374,57 @@ private Panel panel1,
		IJ.showMessage("Error","No images selected");
		return false;
		}
		double disparity0 = 0.75;
		double disparity_max = 75.0; // pix
		String sky_mask = "/home/elphel/lwir16-proc/results-cuda/ERS-debug1/models3/1626032208_613623/v01/1626032208_613623-sky_mask.tiff";
		double disp_inf = -0.2; // -1.0; // 0.0;
		double disparity0 = 0.75; // 2; // 0.75;
		double disparity_max = 23; // 75.0; // pix
		boolean show_dialog2 = false;
		boolean linear_disparity = false;
		int palette = 4;

		int legend_width = 0;
		int legend_gap = 5;

		int legend_width = 2; // 0;
		int legend_gap = 2; // 5;
		GenericJTabbedDialog gd0 = new GenericJTabbedDialog("Ln mode");
		gd0.addNumericField("disparity0", disparity0, 5,8,"pix", "Disparity to swict from linear to log. ) - skip log mode");
		gd0.addStringField ("File path of the sky mask", sky_mask, 80,"optional file with 0.0 - keep, >0.0 - replace with NaN");
		gd0.addNumericField("Disparity at infinity", disp_inf, 5,8,"pix", "Disparity at infinity ");
		gd0.addNumericField("disparity0", disparity0, 5,8,"pix", "Disparity to switch from linear to log. ) - skip log mode");
		gd0.addNumericField("Maximal disparity", disparity_max, 5,8,"pix", "Fixed maximal disparity (0 - auto");
		gd0.addCheckbox("Linear disparity legend", linear_disparity);
		gd0.addNumericField("Legend width", legend_width, 0,3,"", "Optional disparity legend vertical bar width");
		gd0.addNumericField("Legend gap", legend_gap, 0,3,"", "Optional disparity legend vertical bar gap");
		gd0.addNumericField("palette", palette, 0,3,"", "Palette index");
		gd0.addCheckbox("Show second dialog", show_dialog2);

		gd0.showDialog();
		if (gd0.wasCanceled()) return false;
		sky_mask = gd0.getNextString();
		disp_inf = gd0.getNextNumber();
		disparity0= gd0.getNextNumber();
		disparity_max= gd0.getNextNumber();
		linear_disparity = gd0.getNextBoolean();
		legend_width= (int) gd0.getNextNumber();
		legend_gap= (int) gd0.getNextNumber();
		palette= (int) gd0.getNextNumber();
		show_dialog2 = gd0.getNextBoolean();

		boolean log_mode = disparity0 > 0.0;


		boolean log_mode = disparity0 > 0.00;
		float [] fsky_mask = null;
		if (sky_mask.length() > 0) {
		ImagePlus imp_sky_mask = new ImagePlus(sky_mask);
		fsky_mask = (float[]) imp_sky_mask.getProcessor().getPixels();
		}
		// float [] pixels=(float []) imp_srcs[srcChannel].getProcessor().getPixels();
		int current_slice = imp_sel.getCurrentSlice();
		ImageStack imageStack = imp_sel.getStack();
		float [] fpixels = (float[]) imageStack.getPixels(current_slice);
		float [] fpixels0 = (float[]) imageStack.getPixels(current_slice);
		float [] fpixels = fpixels0.clone();
		for (int i = 0; i <fpixels.length; i++) {
		fpixels[i] -= (float) disp_inf;
		if ((fsky_mask != null) && (fsky_mask[i] > 0.0f)) {
		fpixels[i] = Float.NaN;
		}
		}
		int width = imp_sel.getWidth();
		int height = imp_sel.getHeight();
		String title = imp_sel.getShortTitle(); // getTitle();
		@@ -7441,11 +7462,10 @@ private Panel panel1,
		}
		}
		}
		double mn = fpixels[0];
		double mn = dpixels[0];
		double mx = mn;
		double pwr = 1.0;
		int palette = 2;
		for (int i = 0; i < fpixels.length; i++) {
		for (int i = 0; i < dpixels.length; i++) {
		double d = dpixels[i];
		if (log_mode) {
		if (!Double.isNaN(d)) {
		@@ -7458,7 +7478,8 @@ private Panel panel1,
		}
		}
		}
		if (!Double.isNaN(d)) {
		int px = i % width;
		if ((px < width0) && !Double.isNaN(d)) { // do not use legend
		if (!(d <= mx)) mx = d;
		if (!(d >= mn)) mn = d;
		}
		@@ -7483,13 +7504,11 @@ private Panel panel1,
		gd.addNumericField("min", mn, 5,8,"", "Minimal value to map");
		gd.addNumericField("max", mx, 5,8,"", "Maximal value to map");
		gd.addNumericField("pwr", pwr, 5,8,"", "Exponent power");
		gd.addNumericField("palette", palette, 0,3,"", "Palette index");
		gd.showDialog();
		if (gd.wasCanceled()) return false;
		mn= gd.getNextNumber();
		mx= gd.getNextNumber();
		pwr= gd.getNextNumber();
		palette= (int)gd.getNextNumber();
		}
		if (pwr != 1.0) {
		if (mn < 0) {
		@@ -7516,6 +7535,8 @@ private Panel panel1,
		}
		}

		System.out.println("mn="+mn+", mx="+mx);
		// (new ShowDoubleFloatArrays()) .showArrays(dpixels, width, height, "test_depth_mn="+mn+"_mx="+mx);

		double [][] pseudo_pixels = new double [3] [dpixels.length];
		ThermalColor tc = new ThermalColor(

src/main/java/com/elphel/imagej/tileprocessor/Correlation2d.java

+57 −1

Original line number	Diff line number	Diff line
		@@ -209,6 +209,12 @@ public class Correlation2d {

		private static int SUB_SAMPLE = 16; // subsample source pixel in each direction when generating
		public static int THREADS_MAX = 100;
		public int getPairLength(int pair) {
		return pair_length[pair];
		}
		public int [] getPairLengths() {
		return pair_length;
		}

		// All used pairs (but the diameters) are clockwise (end is clockwise of start)
		// Orientation calculations are valid for clockwise only
		@@ -429,7 +435,7 @@ public class Correlation2d {
		* Add 2D correlation for a pair to the combined correlation tile, applying rotation/scaling
		* @param accum_tile tile for accumulation in line-scan order, same dimension as during generateResample()
		* @param corr_tile correlation tile (currently 15x15)
		* @param num_pair number of correlation pair for which resamplind data exists
		* @param num_pair number of correlation pair for which resampling data exists
		* @param weight multiply added tile data by this coefficient before accumulation
		*/
		public void accummulatePair(
		@@ -472,6 +478,26 @@ public class Correlation2d {
		return sumw;
		}

		public double accummulatePairs(
		double [] accum_tile,
		double [][] corr_tiles,
		double [] weights) {
		double sumw = 0.0;
		for (int num_pair = 0; num_pair < weights.length; num_pair++) {
		if ((weights[num_pair]>0.0) && (corr_tiles[num_pair] != null)) {
		accummulatePair(
		accum_tile,
		corr_tiles[num_pair],
		num_pair,
		weights[num_pair]);
		sumw+=weights[num_pair];
		}
		}
		return sumw;
		}



		public void normalizeAccumulatedPairs(
		double [] accum_tile,
		double sumw) {
		@@ -483,6 +509,36 @@ public class Correlation2d {
		}
		}

		/**
		* Calculate correlation pair width in the disparity direction to boost weights of the most
		* informative (for disparity) pairs
		* @param corr_tile for selected pair
		* @param num_pair selected pair number
		* @return pair width (in pixels) in the disparity direction after applying rotation and scaling
		*/
		public double getPairWidth(
		double [] corr_tile,
		int num_pair){ // Center line only
		if ((resample_indices == null) \|\| (resample_indices[num_pair] == null)) {
		throw new IllegalArgumentException ("getPairWidth(): No resample data for num_pair = "+num_pair);
		}
		double s0 = 0.0, s1 = 0.0, s2 = 0.0;
		int indx = mcorr_comb_width * (mcorr_comb_offset + ((mcorr_comb_height - 1) / 2));
		for (int ix = 0; ix < mcorr_comb_width; ix ++ ) if (resample_indices[num_pair][indx] != null){
		for (int j = 0; j < resample_indices[num_pair][indx].length; j++) {
		double d = corr_tile[resample_indices[num_pair][indx][j]] * resample_weights[num_pair][indx][j];
		if (d < 0) {
		d = 0.0; // was get5ting negative (s0s2- s1s1) !
		}
		s0 += d;
		s1 += d * ix;
		s2 += d * ix * ix;
		}
		indx++;
		}
		return Math.sqrt(s0s2- s1s1)/s0;
		}


		public double [] accumulateInit() {return new double [mcorr_comb_width * mcorr_comb_height]; }
		public int getCombWidth() {return mcorr_comb_width;}

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

+3 −2

Original line number	Diff line number	Diff line
		@@ -917,7 +917,7 @@ public class ErsCorrection extends GeometryCorrection {
		* @param camera_xyz camera lens position during centerline acquisition in world coordinates, null - use instance global
		* @param camera_atr camera orientation during centerline acquisition in world frame, null - use instance global
		* @param line_err iterate until the line (pY) correction is below this value
		* @return {px, py, disparity } (right, down) or null if behind the camera
		* @return {px, py, disparity } (right, down) or null if behind the camera of the other camera
		*/

		public double [] getImageCoordinatesERS(
		@@ -1064,7 +1064,8 @@ public class ErsCorrection extends GeometryCorrection {
		* @param line_err iterate until the line (pY) correction is below this value
		* @return {px, py, disparity } (right, down)
		*/
		public double [] getImageCoordinatesERS( // USED in lwir
		@Deprecated
		public double [] getImageCoordinatesERS( // not used?
		double [] xyzw,
		boolean correctDistortions, // correct distortion (will need corrected background too !)
		double line_err) // threshold error in scan lines (1.0)

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

+54 −6

Original line number	Diff line number	Diff line
		@@ -16193,7 +16193,11 @@ public class ImageDttCPU {
		}
		}
		}
		boolean debugTile0 =(tileX == debug_tileX) && (tileY == debug_tileY) && (globalDebugLevel > -3);
		boolean debugTile0 =(tileX == debug_tileX) && (tileY == debug_tileY) && (globalDebugLevel > -6);
		if (debugTile0) {
		System.out.println("clt_process_tl_correlations(): tileX="+tileX+", tileY="+tileY);
		}

		// TODO: move port coordinates out of color channel loop
		// double [][] centersXY = tp_tasks[iTile].getDoubleXY(); // isAux());
		double [][] disp_dist = tp_tasks[iTile].getDoubleDispDist();
		@@ -16225,11 +16229,55 @@ public class ImageDttCPU {
		double [] disp_str = {0.0, 0.0}; // diaprity = 0 will be initial approximation for LMA if no averaging
		if (combine_corrs) {
		double [] corr_combo_tile = correlation2d.accumulateInit(); // combine all available pairs
		double sumw = correlation2d.accummulatePairs(
		double sumw = 0.0;

		if (imgdtt_params.mcorr_static_weights \|\| imgdtt_params.mcorr_dynamic_weights) {
		double [] weights = new double [correlation2d.getNumPairs()];
		if (imgdtt_params.mcorr_static_weights) {
		int [] pair_lengths = correlation2d.getPairLengths();
		for (int npair = 0; npair< weights.length; npair++) if (corrs[npair] != null) {
		weights[npair] = imgdtt_params.mcorr_weights[pair_lengths[npair] - 1];
		}
		} else {
		for (int npair = 0; npair< weights.length; npair++) if (corrs[npair] != null) {
		weights[npair] = 1.0;
		}
		// Arrays.fill(weights, 1.0);
		}
		if (imgdtt_params.mcorr_dynamic_weights) {
		for (int npair = 0; npair< weights.length; npair++) if (corrs[npair] != null) {
		double pair_width = correlation2d. getPairWidth(
		corrs[npair] , //double [] corr_tile,
		npair); // int num_pair)
		if (pair_width < 0.1) {
		System.out.println("pair_width["+npair+"]="+pair_width);
		} else {
		weights[npair] /= Math.pow(pair_width, imgdtt_params.mcorr_weights_power);
		}
		}

		}
		if (debugTile0) {
		System.out.println("clt_process_tl_correlations(): per-pair weights:");
		for (int npair = 0; npair< weights.length; npair++) if (weights[npair] > 0.0) {
		int [] pair = correlation2d.getPair(npair);
		int pair_length = correlation2d.getPairLength(npair);
		System.out.println(String.format("%3d: %2d -> %2d [%2d]: %8.5f",npair,pair[0],pair[1],pair_length,weights[npair]));
		}
		}
		sumw = correlation2d.accummulatePairs(
		corr_combo_tile, // double [] accum_tile,
		corrs, // double [][] corr_tiles, may be longer than selection, extra will be ignored
		weights); // double [] weights);
		} else { // old way, same weight for all pairs
		sumw = correlation2d.accummulatePairs(
		corr_combo_tile, // double [] accum_tile,
		corrs, // double [][] corr_tiles, may be longer than selection, extra will be ignored
		correlation2d.selectAll(), // boolean [] selection,
		1.0); // double weight);
		}


		correlation2d.normalizeAccumulatedPairs(
		corr_combo_tile,
		sumw);

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