debugging illustrations (3cb7b435) · Commits · Elphel / imagej-elphel

src/main/java/com/elphel/imagej/calibration/Aberration_Calibration.java

+23 −13

Original line number	Diff line number	Diff line
		@@ -667,7 +667,9 @@ public static MatchSimulatedPattern.DistortionParameters DISTORTION =new MatchSi
		public static Goniometer GONIOMETER=null;

		public static LwirReaderParameters LWIR_PARAMETERS = new LwirReaderParameters();
		public static CalibrationIllustrationParameters CALIBRATION_ILLUSTRATION_PARAMETERS = new CalibrationIllustrationParameters(LWIR_PARAMETERS);
		public static CalibrationIllustrationParameters CALIBRATION_ILLUSTRATION_PARAMETERS = new CalibrationIllustrationParameters(
		LWIR_PARAMETERS,
		EYESIS_CAMERA_PARAMETERS);
		// new CalibrationHardwareInterface.LaserPointers();
		public class SyncCommand{
		public boolean isRunning= false;
		@@ -1069,6 +1071,7 @@ if (MORE_BUTTONS) {
		panelIllustrations.setLayout(new GridLayout(1, 0, 5, 5)); // rows, columns, vgap, hgap
		addButton("Illustrations Configure", panelIllustrations,color_configure);
		addButton("Illustrations", panelIllustrations,color_bundle);
		addButton("Remove Bad grids", panelIllustrations,color_stop);
		add(panelIllustrations);


		@@ -9434,20 +9437,27 @@ if (MORE_BUTTONS) {
		LENS_DISTORTIONS, // Distortions distortions,
		SYNC_COMMAND.stopRequested, // AtomicInteger stopRequested,
		MASTER_DEBUG_LEVEL); // int debug_level);
		/*
		}
		CALIBRATION_ILLUSTRATION.convertSourceFiles();
		return;
		}
		/* ======================================================================== */
		if (label.equals("Remove Bad grids")) {
		if (LENS_DISTORTIONS==null) {
		IJ.showMessage("LENS_DISTORTION is not set"); // to use all grids imported
		return;
		}
		EYESIS_ABERRATIONS.setDistortions(LENS_DISTORTIONS);

		if (CALIBRATION_ILLUSTRATION == null) {
		CALIBRATION_ILLUSTRATION = new CalibrationIllustration(
		LWIR_PARAMETERS, // LwirReaderParameters lwirReaderParameters,
		LENS_DISTORTION_PARAMETERS, // LensDistortionParameters lensDistortionParameters,
		PATTERN_PARAMETERS, // PatternParameters patternParameters,
		REFINE_PARAMETERS, // RefineParameters refineParameters,
		DISTORTION_PROCESS_CONFIGURATION, // DistortionProcessConfiguration distortionProcessConfiguration,
		EYESIS_CAMERA_PARAMETERS, // EyesisCameraParameters eyesisCameraParameters,
		CALIBRATION_ILLUSTRATION_PARAMETERS, // CalibrationIllustrationParameters illustrationParameters,
		EYESIS_ABERRATIONS, // EyesisAberrations eyesisAberrations,
		LENS_DISTORTIONS, // Distortions distortions,
		SYNC_COMMAND.stopRequested, // AtomicInteger stopRequested,
		MASTER_DEBUG_LEVEL); // int debug_level);
		*/
		}
		// CALIBRATION_ILLUSTRATION.selectUsefulGrids();
		CALIBRATION_ILLUSTRATION.convertSourceFiles();
		CALIBRATION_ILLUSTRATION.removeBadGrids();
		return;
		}

src/main/java/com/elphel/imagej/calibration/CalibrationIllustration.java

+328 −151

Original line number	Diff line number	Diff line
		package com.elphel.imagej.calibration;

		import java.awt.BasicStroke;
		import java.awt.Color;
		import java.awt.Rectangle;
		import java.io.File;
		@@ -20,6 +21,9 @@ import ij.gui.Line;
		import ij.process.ImageProcessor;

		public class CalibrationIllustration {
		public static final int MAX_THREADS = 100; // combine from all classes?
		public static final int CONTRAST_INDEX = 2;

		EyesisAberrations eyesisAberrations;
		Distortions distortions;
		CalibrationIllustrationParameters illustrationParameters;
		@@ -49,18 +53,23 @@ public class CalibrationIllustration {

		public void plotGrid(
		int numImg,
		int line_width,
		ImagePlus imp,
		Color color_grid,
		Color color_grid_extra // at least one end points to extra (unreliable) nodes (may be null)
		Color color_grid_weak,
		Color color_grid_extra, // at least one end points to extra (unreliable) nodes (may be null)
		double weak_threshold
		) {
		int line_width = 1; //https://imagej.nih.gov/ij/developer/api/ij/ij/gui/Line.html#drawPixels(ij.process.ImageProcessor)
		// int line_width = 3; //https://imagej.nih.gov/ij/developer/api/ij/ij/gui/Line.html#drawPixels(ij.process.ImageProcessor)
		DistortionCalibrationData dcd = distortions.fittingStrategy.distortionCalibrationData;
		GridImageParameters gip = dcd.gIP[numImg];
		int [][] pUV = gip.pixelsUV;
		int [][] pUV_extra = gip.pixelsUV_extra;
		double [][] pXY = gip.pixelsXY;
		double [][] pXY_extra = gip.pixelsXY_extra;

		if ((pUV == null) \|\| (pUV.length==0)) {
		return;
		}
		int minU=pUV[0][0],maxU=minU,minV=pUV[0][1],maxV=minV;
		for (int i = 0; i < pUV.length; i++) {
		if (pUV[i][0] < minU) minU = pUV[i][0];
		@@ -93,6 +102,17 @@ public class CalibrationIllustration {
		}
		ImageProcessor ip = imp.getProcessor();
		ip.setLineWidth(line_width);
		// only use stroke for line_width>1
		/*
		BasicStroke stroke = null;
		if (line_width>1) {
		stroke = new BasicStroke(line_width, BasicStroke.CAP_ROUND, BasicStroke.JOIN_ROUND);
		}
		*/
		// BasicStroke stroke = new BasicStroke(line_width, BasicStroke.CAP_BUTT, BasicStroke.JOIN_ROUND);
		// BasicStroke stroke = new BasicStroke(line_width, BasicStroke.CAP_ROUND, BasicStroke.JOIN_ROUND);
		// roi.setStrokeColor(new Color(red, green, blue, alpha));
		// roi.setStroke(stroke);
		// int upper = dimsUV.width * (dimsUV.height-1);
		int upper = dimsUV.width * dimsUV.height;
		for (int indx = dimsUV.width + 1; indx < upper; indx++) if (grid[indx] >= 0){
		@@ -103,40 +123,92 @@ public class CalibrationIllustration {
		if (indx1 < grid.length) {
		int g1 = grid[indx1];
		if (g1 >= 0) {
		double [] pXY0 = (g0 < main_len) ? pXY[g0] : pXY_extra[g0 - main_len];
		double [] pXY1 = (g1 < main_len) ? pXY[g1] : pXY_extra[g1 - main_len];
		// Line line = new Line(pXY0[0], pXY0[1], pXY1[0],pXY1[1]);
		if ((g0 < main_len) && (g1 < main_len)) {
		if ((pXY0[CONTRAST_INDEX] >= weak_threshold) && (pXY1[CONTRAST_INDEX] >= weak_threshold)) {
		if (color_grid == null) {
		continue;
		}
		ip.setColor(color_grid);
		} else {
		if (color_grid_weak == null) {
		continue;
		}
		ip.setColor(color_grid_weak);
		}
		} else {
		if (color_grid_extra == null) {
		continue;
		}
		ip.setColor(color_grid_extra); // should not get here with color_grid_extra==null
		}
		double [] pXY0 = (g0 < main_len) ? pXY[g0] : pXY_extra[g0 - main_len];
		double [] pXY1 = (g1 < main_len) ? pXY[g1] : pXY_extra[g1 - main_len];
		Line line = new Line(pXY0[0], pXY0[1], pXY1[0],pXY1[1]);
		/*
		if (stroke != null) {
		if ((g0 < main_len) && (g1 < main_len)) {
		line.setStrokeColor(color_grid);
		} else {
		line.setStrokeColor(color_grid_extra); // should not get here with color_grid_extra==null
		}
		line.setStroke(stroke);
		}
		line.setStrokeWidth(1.0);
		*/
		for (int dy = -line_width+1; dy < line_width; dy+=2) {
		for (int dx = -line_width+1; dx < line_width; dx+=2) {
		Line line = new Line(pXY0[0] + 0.5dx, pXY0[1] + 0.5dy, pXY1[0] + 0.5dx,pXY1[1] + 0.5dy);
		line.drawPixels(ip);
		}
		}
		// Line line = new Line(pXY0[0], pXY0[1], pXY1[0],pXY1[1]);
		// line.drawPixels(ip);
		/*
		for (double lw = 0.5; lw <= line_width; lw+=0.5) {
		line.setStrokeWidth(lw);
		line.drawPixels(ip);
		}
		*/
		}
		}
		}
		}
		}

		public boolean convertSourceFiles() {
		double threshold_contrast = 10.0;
		int threshold_number = 10; // grid should have this number of nodes with above-threshold contrast
		int CONTRAST_INDEX = 2;
		//this.eyesisCameraParameters.numStations
		boolean [] selectedChannels = eyesisAberrations.aberrationParameters.getChannelSelection(distortions);
		DistortionCalibrationData dcd = distortions.fittingStrategy.distortionCalibrationData;
		int numStations = dcd.eyesisCameraParameters.getNumStations();
		boolean [] station_sel = new boolean[numStations];
		// Arrays.fill(station_sel, true);
		station_sel[0]= true; // only 06-L
		MultipleExtensionsFileFilter sourceFilter =
		long startTime=System.nanoTime(); // restart timer after possible interactive dialogs
		final boolean [] selectedChannels = eyesisAberrations.aberrationParameters.getChannelSelection(distortions);
		final DistortionCalibrationData dcd = distortions.fittingStrategy.distortionCalibrationData;
		final MultipleExtensionsFileFilter sourceFilter =
		new MultipleExtensionsFileFilter("",src_extensions,"Source calibration images");
		int lwir0 = illustrationParameters.getLwirReaderParameters().getLwirChn0();
		int eo0 = illustrationParameters.getLwirReaderParameters().getEoChn0();
		for (int nChn = 0; nChn < selectedChannels.length; nChn++) if (selectedChannels[nChn]) {
		final int lwir0 = illustrationParameters.getLwirReaderParameters().getLwirChn0();
		final int eo0 = illustrationParameters.getLwirReaderParameters().getEoChn0();
		final Thread[] threads = newThreadArray(MAX_THREADS);
		final AtomicInteger indxAtomic = new AtomicInteger(0);
		for (int iChn = 0; iChn < selectedChannels.length; iChn++) if (selectedChannels[iChn]) {
		final int nChn=iChn;
		indxAtomic.set(0);
		// Create directory before threads
		String illustrations_dir = eyesisAberrations.aberrationParameters.illustrationsDirectory;
		String chn_ill_dir = illustrations_dir+Prefs.getFileSeparator()+ illustrationParameters.getChannelPrefix()+String.format("%02d", nChn);
		// create directory if it does not exist
		File destDir= new File (chn_ill_dir);
		if (!destDir.exists()){
		if (!destDir.mkdirs()) {
		IJ.showMessage("Error","Failed to create results directory "+chn_ill_dir);
		continue;
		}
		}

		for (int ithread = 0; ithread < threads.length; ithread++) {
		threads[ithread] = new Thread() {
		@Override
		public void run() {
		// for (int nChn = indxAtomic.getAndIncrement(); nChn < selectedChannels.length; nChn = indxAtomic.getAndIncrement()) if (selectedChannels[nChn]) {
		// iterate through all image set (some grids may be missing)
		for (int nSet = 0; nSet < dcd.gIS.length; nSet++) {
		if (station_sel[dcd.gIS[nSet].getStationNumber()]) { // some stations only
		for (int nSet = indxAtomic.getAndIncrement(); nSet < dcd.gIS.length; nSet = indxAtomic.getAndIncrement()) {
		int station = dcd.gIS[nSet].getStationNumber();
		if (illustrationParameters.useStation(station)) { // some stations only
		// construct source file name
		String srcPath = null;
		int numImg = -1;
		@@ -177,18 +249,28 @@ public class CalibrationIllustration {
		title = title.substring(0, title.lastIndexOf("."));
		}
		String title_annot = title+"-annot";
		if (illustrationParameters.useStationInFilenames()) {
		title_annot = "station-"+station+"_"+title_annot;
		}
		if (numImg >=0) { // check if it is a bad image
		int num_above = 0;
		GridImageParameters gip = dcd.gIP[numImg];
		double [][] pXY = gip.pixelsXY;
		for (int i = 0; i < pXY.length; i++ ) {
		if (pXY[i][CONTRAST_INDEX] > threshold_contrast) num_above++;
		}
		if (num_above < threshold_number) {
		title_annot = title+"-annot"+"-BAD";
		if (pXY[i][CONTRAST_INDEX] > illustrationParameters.getThresholdContrast()) num_above++;
		}
		if (num_above < illustrationParameters.getThresholdNumber()) {
		title_annot += "-BAD";
		}
		double [][] pseudo_pixels = new double [4] [pixels.length];
		} else {
		title_annot += "-EMPTY";
		}
		int sensor_type = dcd.eyesisCameraParameters.getSensorType(nChn);
		ImageStack stack = null;
		double [][] pseudo_pixels;
		int line_width = 1;
		if (sensor_type == 1) {
		pseudo_pixels = new double [4] [pixels.length];
		ThermalColor tc = new ThermalColor(
		illustrationParameters.getPalette(), // public int lwir_palette = 0; // 0 - white - hot, 1 - black - hot, 2+ - colored
		illustrationParameters.getLwirRange(nChn- lwir0)[0],
		@@ -201,8 +283,27 @@ public class CalibrationIllustration {
		pseudo_pixels[2][i] = rgb[2]; // blue
		pseudo_pixels[3][i] = 1.0; // alpha
		}
		line_width = illustrationParameters.getLineWidthLwir();
		} else { // eo
		double [][] drgb = MatchSimulatedPattern.simpleDemosaic(
		imp,
		illustrationParameters.eo_rb2g_hi[nChn-eo0][0], // r2g,
		illustrationParameters.eo_rb2g_hi[nChn-eo0][1], // b2g,
		illustrationParameters.getSaturation(), // saturation,
		illustrationParameters.getGamma(), // gamma,
		illustrationParameters.getMinLin(), //minlin_gamma, // do not apply gamma to lower values
		illustrationParameters.eo_rb2g_hi[nChn-eo0][2]); // ,rgb_hi); // map to 255, gamma will preserve
		pseudo_pixels = new double [4][];
		for (int i = 0; i < drgb.length; i++) {
		pseudo_pixels[i] = drgb[i];
		}
		pseudo_pixels[3] = new double [pseudo_pixels[0].length];
		Arrays.fill(pseudo_pixels[3], 1.0);
		line_width = illustrationParameters.getLineWidthEo();
		}

		String [] rgb_titles = {"red","green","blue","alpha"};
		ImageStack stack = (new ShowDoubleFloatArrays()).makeStack(
		stack = (new ShowDoubleFloatArrays()).makeStack(
		pseudo_pixels, // iclt_data,
		width, // (tilesX + 0) * clt_parameters.transform_size,
		height, // (tilesY + 0) * clt_parameters.transform_size,
		@@ -222,21 +323,22 @@ public class CalibrationIllustration {
		1.0); // double alpha_max)
		if (numImg >=0) {
		plotGrid(numImg,
		line_width,
		imp_annot,
		new Color(250, 0, 0), // color_grid,
		new Color(200, 200,0) // null // //at least one end points to extra (unreliable) nodes
		illustrationParameters.getGridColor(), // new Color(250, 0, 0), // color_grid,
		illustrationParameters.getGridWeakColor(), // new Color(250, 0, 0), // color_grid,
		illustrationParameters.getGridExtraColor(), // new Color(200, 200,0) // null // //at least one end points to extra (unreliable) nodes
		illustrationParameters.getThresholdContrast()
		);
		}

		// imp_pseudo.getProcessor().resetMinAndMax();
		// imp_pseudo.show();
		String illustrations_dir = eyesisAberrations.aberrationParameters.illustrationsDirectory;
		String chn_ill_dir = illustrations_dir+Prefs.getFileSeparator()+ illustrationParameters.channel_dir_prefix+String.format("%02d", nChn);
		String chn_ill_dir = illustrations_dir+Prefs.getFileSeparator()+ illustrationParameters.getChannelPrefix()+String.format("%02d", nChn);
		// create directory if it does not exist
		File destDir= new File (chn_ill_dir);
		if (!destDir.exists()){
		if (!destDir.exists()){ // Should be created before threads !
		if (!destDir.mkdirs()) {
		IJ.showMessage("Error","Failed to create results directory "+chn_ill_dir);
		IJ.showMessage("Error","Failed to create results directory "+chn_ill_dir+". * It should be already created! *");
		continue;
		}
		}
		@@ -250,29 +352,104 @@ public class CalibrationIllustration {
		}
		}
		}
		};
		}
		startAndJoin(threads);
		}
		System.out.println("All done in "+ IJ.d2s(0.000000001*(System.nanoTime()-startTime),3)+" sec.");
		return true;
		}

		/*
		public CalibrationIllustration (
		LwirReaderParameters lwirReaderParameters,
		LensDistortionParameters lensDistortionParameters,
		PatternParameters patternParameters,
		RefineParameters refineParameters,
		DistortionProcessConfiguration distortionProcessConfiguration,
		EyesisCameraParameters eyesisCameraParameters,
		AtomicInteger stopRequested,
		int debug_level) {
		this.lwirReaderParameters = lwirReaderParameters;
		this.lensDistortionParameters = lensDistortionParameters;
		this.patternParameters = patternParameters;
		this.refineParameters = refineParameters;
		this.distortionProcessConfiguration = distortionProcessConfiguration;
		this.eyesisCameraParameters = eyesisCameraParameters;
		this.stopRequested = stopRequested;
		this.debug_level = debug_level;

		public boolean removeBadGrids() {
		long startTime=System.nanoTime(); // restart timer after possible interactive dialogs
		final boolean [] selectedChannels = eyesisAberrations.aberrationParameters.getChannelSelection(distortions);
		final DistortionCalibrationData dcd = distortions.fittingStrategy.distortionCalibrationData;
		final Thread[] threads = newThreadArray(MAX_THREADS);
		final AtomicInteger indxAtomic = new AtomicInteger(0);
		final AtomicInteger numRemoved = new AtomicInteger(0);
		for (int iChn = 0; iChn < selectedChannels.length; iChn++) if (selectedChannels[iChn]) {
		final int nChn=iChn;
		indxAtomic.set(0);
		// Create directory before threads
		String illustrations_dir = eyesisAberrations.aberrationParameters.illustrationsDirectory;
		String chn_ill_dir = illustrations_dir+Prefs.getFileSeparator()+ illustrationParameters.getChannelPrefix()+String.format("%02d", nChn);
		// create directory if it does not exist
		File destDir= new File (chn_ill_dir);
		if (!destDir.exists()){
		if (!destDir.mkdirs()) {
		IJ.showMessage("Error","Failed to create results directory "+chn_ill_dir);
		continue;
		}
		}
		for (int ithread = 0; ithread < threads.length; ithread++) {
		threads[ithread] = new Thread() {
		@Override
		public void run() {
		// for (int nChn = indxAtomic.getAndIncrement(); nChn < selectedChannels.length; nChn = indxAtomic.getAndIncrement()) if (selectedChannels[nChn]) {
		// iterate through all image set (some grids may be missing)
		for (int nSet = indxAtomic.getAndIncrement(); nSet < dcd.gIS.length; nSet = indxAtomic.getAndIncrement()) {
		int station = dcd.gIS[nSet].getStationNumber();
		if (illustrationParameters.useStation(station)) { // some stations only
		// construct source file name
		if (dcd.gIS[nSet].imageSet[nChn] != null) {
		int numImg = dcd.gIS[nSet].imageSet[nChn].getImageNumber();
		int num_above = 0;
		GridImageParameters gip = dcd.gIP[numImg];
		double [][] pXY = gip.pixelsXY;
		for (int i = 0; i < pXY.length; i++ ) {
		if (pXY[i][CONTRAST_INDEX] > illustrationParameters.getThresholdContrast()) num_above++;
		}
		if (num_above < illustrationParameters.getThresholdNumber()) {
		String grid_path = dcd.getImagePath(numImg);
		System.out.println("Removing bad grid file: "+grid_path);
		new File(dcd.getImagePath(numImg)).delete();
		numRemoved.getAndIncrement();
		}
		}
		}
		}
		}
		};
		}
		startAndJoin(threads);
		}
		System.out.println("Remoded "+(numRemoved.get())+" bad grid files in "+ IJ.d2s(0.000000001*(System.nanoTime()-startTime),3)+" sec.");
		return true;
		}




		/* Create a Thread[] array as large as the number of processors available.
		* From Stephan Preibisch's Multithreading.java class. See:
		* http://repo.or.cz/w/trakem2.git?a=blob;f=mpi/fruitfly/general/MultiThreading.java;hb=HEAD
		*/
		private static Thread[] newThreadArray(int maxCPUs) {
		int n_cpus = Runtime.getRuntime().availableProcessors();
		if (n_cpus>maxCPUs)n_cpus=maxCPUs;
		return new Thread[n_cpus];
		}
		/* Start all given threads and wait on each of them until all are done.
		* From Stephan Preibisch's Multithreading.java class. See:
		* http://repo.or.cz/w/trakem2.git?a=blob;f=mpi/fruitfly/general/MultiThreading.java;hb=HEAD
		*/
		private static void startAndJoin(Thread[] threads)
		{
		for (int ithread = 0; ithread < threads.length; ++ithread)
		{
		threads[ithread].setPriority(Thread.NORM_PRIORITY);
		threads[ithread].start();
		}

		try
		{
		for (int ithread = 0; ithread < threads.length; ++ithread)
		threads[ithread].join();
		} catch (InterruptedException ie)
		{
		throw new RuntimeException(ie);
		}
		}

		}

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