debugging illustrations

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

@@ -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);
 		
 		
@@ -9434,22 +9437,29 @@ if (MORE_BUTTONS) {
 					LENS_DISTORTIONS,            // Distortions       distortions,
 					SYNC_COMMAND.stopRequested,  // 	AtomicInteger                  stopRequested,
 					MASTER_DEBUG_LEVEL);         // 		int                            debug_level);
-			/*
-			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,
-				SYNC_COMMAND.stopRequested, // 	AtomicInteger                  stopRequested,
-				MASTER_DEBUG_LEVEL); // 		int                            debug_level);
-				*/
 		}
-//		CALIBRATION_ILLUSTRATION.selectUsefulGrids();
 		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(
+					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.removeBadGrids();
+		return;
+	}
 	
 /* ======================================================================== */
 	if       (label.equals("Manual hint")) {

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

 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,
+			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){
@@ -103,15 +123,52 @@ 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)) {
-							ip.setColor(color_grid);
+							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]);
-						line.drawPixels(ip);
+						/*
+						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] + 0.5*dx, pXY0[1] + 0.5*dy, pXY1[0] + 0.5*dx,pXY1[1] + 0.5*dy);
+								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);
+						}
+						*/
 					}
 				}
 			}
@@ -119,160 +176,280 @@ public class CalibrationIllustration {
 	}
 	
 	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]) {
-			// 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
-					// construct source file name
-					String srcPath = null;
-					int numImg = -1;
-					if (dcd.gIS[nSet].imageSet[nChn] != null) {
-						srcPath = dcd.gIS[nSet].imageSet[nChn].source_path;
-						numImg = dcd.gIS[nSet].imageSet[nChn].getImageNumber();
-					} else {
-						// find other non-null
-						for (int i = 0; i < dcd.gIS[nSet].imageSet.length; i++) {
-							if (dcd.gIS[nSet].imageSet[i] != null) {
-								String other_path = dcd.gIS[nSet].imageSet[i].source_path;
-								String set_path = other_path.substring(0,other_path.lastIndexOf(Prefs.getFileSeparator()));
-		        				File set_dir = new File(set_path);
-		        				String [] sfiles = set_dir.list(sourceFilter);
-		        				for (String spath:sfiles) {
-		            				int chn = DistortionCalibrationData.pathToChannel(spath);
-		            				if (chn == nChn) {
-		            					srcPath = (new File(set_dir,spath)).getPath();
-		            					break;
-		            				}
-		        				}
-		        				break;
+		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 = 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;
+								if (dcd.gIS[nSet].imageSet[nChn] != null) {
+									srcPath = dcd.gIS[nSet].imageSet[nChn].source_path;
+									numImg = dcd.gIS[nSet].imageSet[nChn].getImageNumber();
+								} else {
+									// find other non-null
+									for (int i = 0; i < dcd.gIS[nSet].imageSet.length; i++) {
+										if (dcd.gIS[nSet].imageSet[i] != null) {
+											String other_path = dcd.gIS[nSet].imageSet[i].source_path;
+											String set_path = other_path.substring(0,other_path.lastIndexOf(Prefs.getFileSeparator()));
+											File set_dir = new File(set_path);
+											String [] sfiles = set_dir.list(sourceFilter);
+											for (String spath:sfiles) {
+												int chn = DistortionCalibrationData.pathToChannel(spath);
+												if (chn == nChn) {
+													srcPath = (new File(set_dir,spath)).getPath();
+													break;
+												}
+											}
+											break;
+										}
+									}
+								}
+								// open 32-bit image
+								if (srcPath == null) {
+									System.out.println ("Source image for set "+nSet+", channel "+nChn+" does not exist");
+									continue;
+								}
+								ImagePlus imp = new ImagePlus(srcPath);
+								// convert to 8-bit color?
+								int width = imp.getWidth();
+								int height = imp.getHeight();
+								float [] pixels = (float[]) imp.getProcessor().getPixels();
+								String title = imp.getTitle();
+								if (title.lastIndexOf(".") > 0) {
+									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] > illustrationParameters.getThresholdContrast()) num_above++;
+									}
+									if (num_above < illustrationParameters.getThresholdNumber()) {
+										title_annot += "-BAD";
+									}
+								} 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],
+											illustrationParameters.getLwirRange(nChn- lwir0)[1],
+											255.0);
+									for (int i = 0; i < pixels.length; i++) {
+										double [] rgb = tc.getRGB((double) pixels[i]);
+										pseudo_pixels[0][i] = rgb[0]; // red
+										pseudo_pixels[1][i] = rgb[1]; // green
+										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"};
+								stack = (new  ShowDoubleFloatArrays()).makeStack(
+										pseudo_pixels, // iclt_data,
+										width,         // (tilesX + 0) * clt_parameters.transform_size,
+										height,        // (tilesY + 0) * clt_parameters.transform_size,
+										rgb_titles,    // or use null to get chn-nn slice names
+										true);         // replace NaN with 0.0
+								ImagePlus imp_annot =  EyesisCorrections.convertRGBAFloatToRGBA32(
+										stack,   // ImageStack stackFloat, //r,g,b,a
+										//						name+"ARGB"+suffix, // String title,
+										title_annot, // String title,
+										0.0,   // double r_min,
+										255.0, // double r_max,
+										0.0,   // double g_min,
+										255.0, // double g_max,
+										0.0,   // double b_min,
+										255.0, // double b_max,
+										0.0,   // double alpha_min,
+										1.0);  // double alpha_max)
+								if (numImg >=0) {
+									plotGrid(numImg,
+											line_width,
+											imp_annot,
+											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()
+											);
+								}
+
+								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()){ // Should be created before threads !
+									if (!destDir.mkdirs()) {
+										IJ.showMessage("Error","Failed to create results directory "+chn_ill_dir+". *** It should be already created! ***");
+										continue;
+									}
+								}
+								EyesisCorrections.saveAndShow(
+										imp_annot,
+										chn_ill_dir,
+										illustrationParameters.save_png,
+										false, // show
+										illustrationParameters.JPEG_quality, //  <0 - keep current, 0 - force Tiff, >0 use for JPEG
+										0); // debug_level); 
 							}
 						}
 					}
-					// open 32-bit image
-					if (srcPath == null) {
-						System.out.println ("Source image for set "+nSet+", channel "+nChn+" does not exist");
-						continue;
-					}
-					ImagePlus imp = new ImagePlus(srcPath);
-					// convert to 8-bit color?
-					int width = imp.getWidth();
-					int height = imp.getHeight();
-					float [] pixels = (float[]) imp.getProcessor().getPixels();
-					String title = imp.getTitle();
-					if (title.lastIndexOf(".") > 0) {
-						title = title.substring(0, title.lastIndexOf("."));
-					}
-					String title_annot = 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";
-						}
-					}
-					double [][]  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],
-							illustrationParameters.getLwirRange(nChn- lwir0)[1],
-							255.0);
-					for (int i = 0; i < pixels.length; i++) {
-						double [] rgb = tc.getRGB((double) pixels[i]);
-						pseudo_pixels[0][i] = rgb[0]; // red
-						pseudo_pixels[1][i] = rgb[1]; // green
-						pseudo_pixels[2][i] = rgb[2]; // blue
-						pseudo_pixels[3][i] = 1.0; // alpha
-					}
-					String [] rgb_titles =  {"red","green","blue","alpha"};
-					ImageStack stack = (new  ShowDoubleFloatArrays()).makeStack(
-							pseudo_pixels, // iclt_data,
-							width,         // (tilesX + 0) * clt_parameters.transform_size,
-							height,        // (tilesY + 0) * clt_parameters.transform_size,
-							rgb_titles,    // or use null to get chn-nn slice names
-							true);         // replace NaN with 0.0
-					ImagePlus imp_annot =  EyesisCorrections.convertRGBAFloatToRGBA32(
-							stack,   // ImageStack stackFloat, //r,g,b,a
-							//						name+"ARGB"+suffix, // String title,
-							title_annot, // String title,
-							0.0,   // double r_min,
-							255.0, // double r_max,
-							0.0,   // double g_min,
-							255.0, // double g_max,
-							0.0,   // double b_min,
-							255.0, // double b_max,
-							0.0,   // double alpha_min,
-							1.0);  // double alpha_max)
-					if (numImg >=0) {
-						plotGrid(numImg,
-								imp_annot,
-								new Color(250, 0,  0), //  color_grid,
-								new Color(200, 200,0) // null // //at least one end points to extra (unreliable) nodes
-								);
-					}
-					
-//					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);
-					// 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;
+				};
+			}
+			startAndJoin(threads);
+		}
+		System.out.println("All done in "+ IJ.d2s(0.000000001*(System.nanoTime()-startTime),3)+" sec.");
+		return true;
+	}
+
+	
+	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();
+									}
+								}
+							}
 						}
 					}
-					EyesisCorrections.saveAndShow(
-							imp_annot,
-							chn_ill_dir,
-							illustrationParameters.save_png,
-							false, // show
-							illustrationParameters.JPEG_quality, //  <0 - keep current, 0 - force Tiff, >0 use for JPEG
-							0); // debug_level); 
-				}
+				};
 			}
+			startAndJoin(threads);
 		}
+		System.out.println("Remoded "+(numRemoved.get())+" bad grid files 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;
+	
+	
+	/* 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);
+		}
+	}
 	
 }

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

 package com.elphel.imagej.calibration;
 
+import java.awt.Color;
+import java.net.MalformedURLException;
 import java.util.Properties;
 
+import com.elphel.imagej.cameras.EyesisCameraParameters;
 import com.elphel.imagej.common.GenericJTabbedDialog;
 import com.elphel.imagej.lwir.LwirReaderParameters;
 
 public class CalibrationIllustrationParameters {
-	double               dflt_lwir_lo = 22500.0;
-	double               dflt_lwir_hi = 23500.0;
-	LwirReaderParameters lwirReaderParameters;
-	double [][]          lwir_ranges; //  = new double [lwirReaderParameters.getLwirChannels(false).length][2];
-	int                  palette = 0; // 0 - white - hot, 1 - black - hot, 2+ - colored
-	String               src_chn_prefix="src_chn-";
-	boolean              save_png = true;
-	int                  JPEG_quality = 90;
-	String               channel_dir_prefix = "chn_";
+	static double          DFLT_LWIR_LO = 22500.0;
+	static double          DFLT_LWIR_HI = 23500.0;
+	static double          DFLT_EO_R2G =  1.03;  // gain red relative to green
+	static double          DFLT_EO_B2G =  1.03;  // gain blue relative to green
+	static double          DFLT_EO_HI =   255.0; // range to map to 255.0
+	LwirReaderParameters   lwirReaderParameters;
+	EyesisCameraParameters eyesisCameraParameters;
 	
-	public CalibrationIllustrationParameters (LwirReaderParameters lwirReaderParameters) {
+	double [][]            lwir_ranges; //  = new double [lwirReaderParameters.getLwirChannels(false).length][2];
+	int                    palette = 0; // 0 - white - hot, 1 - black - hot, 2+ - colored
+	String                 src_chn_prefix="src_chn-";
+	boolean                save_png = true;
+	int                    JPEG_quality = 90;
+	String                 channel_dir_prefix = "chn_";
+	double [][]            eo_rb2g_hi; // []{r2g,b2g,rgb_hi}
+	double                 eo_gamma = 0.57;
+	double                 eo_minlin_gamma = 20.0;
+	double                 eo_saturation = 1.5; // color saturation
+	double                 threshold_contrast = 10.0;
+	int                    threshold_number =   10;// grid should have this number of nodes with above-threshold contrast
+	int                    station_sel =        0xf; // bitmask: 0 - station 0; 1 - station 1, ...
+	boolean                station_in_filenames = true;
+    Color                  color_grid =         new Color(250, 0,  0, 255);
+    Color                  color_grid_weak =    new Color(200, 100,  0, 128);
+	Color                  color_grid_extra =   new Color(150, 150,0, 255); // at least one end points to extra (unreliable) nodes (may be null)
+	int                    line_width_eo =      3;
+	int                    line_width_lwir =    1;
+	
+	public CalibrationIllustrationParameters (
+			LwirReaderParameters lwirReaderParameters,
+			EyesisCameraParameters eyesisCameraParameters) {
 		this.lwirReaderParameters = lwirReaderParameters;
+		this.eyesisCameraParameters = eyesisCameraParameters;
+	}
+	
+	public static long getLongColor(Color color) {
+		return ((long) color.getRGB()) & 0xffffffffL;
 	}
+	public static Color setLongColor(long lcolor) {
+		if (lcolor < (1 << 24)) { // no alpha
+			return new Color((int) lcolor);
+		} else { // has alpha, may or may not fit into int
+			if (lcolor > Integer.MAX_VALUE) {
+				lcolor -= (1L << 32);
+			}
+			return new Color((int) lcolor, true);
+		}
+	}
+	
+	
+	
 	public void setProperties(String prefix,Properties properties){
 //		properties.setProperty(prefix+"camera_name",         this.camera_name+"");
 		set_parameters();
@@ -30,8 +71,32 @@ public class CalibrationIllustrationParameters {
 		properties.setProperty(prefix+"save_png",           this.save_png+"");
 		properties.setProperty(prefix+"JPEG_quality",       this.JPEG_quality+"");
 		properties.setProperty(prefix+"channel_dir_prefix", this.channel_dir_prefix);
+		for (int i = 0; i < eo_rb2g_hi.length; i++) {
+			properties.setProperty(prefix+"eo_r2g_"+i,      this.eo_rb2g_hi[i][0]+"");
+			properties.setProperty(prefix+"eo_b2g_"+i,      this.eo_rb2g_hi[i][1]+"");
+			properties.setProperty(prefix+"eo_hi_"+i,       this.eo_rb2g_hi[i][2]+"");
+		}		
+		properties.setProperty(prefix+"eo_gamma",           this.eo_gamma+"");
+		properties.setProperty(prefix+"eo_minlin_gamma",    this.eo_minlin_gamma+"");
+		properties.setProperty(prefix+"eo_saturation",      this.eo_saturation+"");
+		properties.setProperty(prefix+"threshold_contrast", this.threshold_contrast+"");
+		properties.setProperty(prefix+"threshold_number",   this.threshold_number+"");
+		properties.setProperty(prefix+"station_sel",        this.station_sel+"");
+		properties.setProperty(prefix+"station_in_filenames", this.station_in_filenames+"");
+		long lcolor_grid =       (color_grid == null) ? -1 : getLongColor(color_grid);
+		long lcolor_grid_weak =  (color_grid_weak == null) ? -1 : getLongColor(color_grid_weak);
+		long lcolor_grid_extra = (color_grid_extra == null) ? -1 : getLongColor(color_grid_extra);
+		properties.setProperty(prefix+"color_grid",         lcolor_grid+"");
+		properties.setProperty(prefix+"color_grid_weak",    lcolor_grid_weak+"");
+		properties.setProperty(prefix+"color_grid_extra",   lcolor_grid_extra+"");
+
+		properties.setProperty(prefix+"line_width_eo",      this.line_width_eo+"");
+		properties.setProperty(prefix+"line_width_lwir",    this.line_width_lwir+"");
+	
 	}
 
+	
+	
 	public void getProperties(String prefix,Properties properties){
 		set_parameters();
 		for (int i = 0; i < lwir_ranges.length; i++) {
@@ -47,27 +112,144 @@ public class CalibrationIllustrationParameters {
 		if (properties.getProperty(prefix+"JPEG_quality")!=null) this.JPEG_quality = Integer.parseInt(properties.getProperty(prefix+"JPEG_quality"));
 		if (properties.getProperty(prefix+"channel_dir_prefix")!=null) this.channel_dir_prefix = (String) properties.getProperty(prefix+"channel_dir_prefix");
 
+		for (int i = 0; i < eo_rb2g_hi.length; i++) {
+			if (properties.getProperty(prefix+"eo_r2g_"+i)!=null) {
+				this.eo_rb2g_hi[i][0] = Double.parseDouble(properties.getProperty(prefix+"eo_r2g_"+i));
+			}
+			if (properties.getProperty(prefix+"eo_b2g_"+i)!=null) {
+				this.eo_rb2g_hi[i][1] = Double.parseDouble(properties.getProperty(prefix+"eo_b2g_"+i));
+			}
+			if (properties.getProperty(prefix+"eo_hi_"+i)!=null) {
+				this.eo_rb2g_hi[i][2] = Double.parseDouble(properties.getProperty(prefix+"eo_hi_"+i));
+			}
+		}		
+		if (properties.getProperty(prefix+"eo_gamma")!=null)           this.eo_gamma = Double.parseDouble(properties.getProperty(prefix+"eo_gamma"));
+		if (properties.getProperty(prefix+"eo_minlin_gamma")!=null)    this.eo_minlin_gamma = Double.parseDouble(properties.getProperty(prefix+"eo_minlin_gamma"));
+		if (properties.getProperty(prefix+"eo_saturation")!=null)      this.eo_saturation = Double.parseDouble(properties.getProperty(prefix+"eo_saturation"));
+		if (properties.getProperty(prefix+"threshold_contrast")!=null) this.threshold_contrast = Double.parseDouble(properties.getProperty(prefix+"threshold_contrast"));
+		if (properties.getProperty(prefix+"threshold_number")!=null)   this.threshold_number = Integer.parseInt(properties.getProperty(prefix+"threshold_number"));
+		if (properties.getProperty(prefix+"station_sel")!=null)        this.station_sel = Integer.parseInt(properties.getProperty(prefix+"station_sel"));
+		if (properties.getProperty(prefix+"station_in_filenames")!=null)        this.station_in_filenames = Boolean.parseBoolean(properties.getProperty(prefix+"station_in_filenames"));
+		if  (properties.getProperty(prefix+"color_grid")!=null) {
+			long lcolor_grid = Long.parseLong(properties.getProperty(prefix+"color_grid"));
+			if (lcolor_grid < 0) this.color_grid = null;
+			else this.color_grid = setLongColor(lcolor_grid);
+		}
+		if  (properties.getProperty(prefix+"color_grid_weak")!=null) {
+			long lcolor_grid_weak = Long.parseLong(properties.getProperty(prefix+"color_grid_weak"));
+			if (lcolor_grid_weak < 0) this.color_grid_weak = null;
+			else this.color_grid_weak = setLongColor(lcolor_grid_weak);
+		}
+		if  (properties.getProperty(prefix+"color_grid_extra")!=null) {
+			long lcolor_grid_extra = Long.parseLong(properties.getProperty(prefix+"color_grid_extra"));
+			if (lcolor_grid_extra < 0) this.color_grid = null;
+			else this.color_grid_extra = setLongColor(lcolor_grid_extra);
+		}
+		if (properties.getProperty(prefix+"line_width_eo")!=null)      this.line_width_eo = Integer.parseInt(properties.getProperty(prefix+"line_width_eo"));
+		if (properties.getProperty(prefix+"line_width_lwir")!=null)    this.line_width_lwir = Integer.parseInt(properties.getProperty(prefix+"line_width_lwir"));
 	}
 	public void dialogQuestions(GenericJTabbedDialog gd) {
+		final int lwir0 = getLwirReaderParameters().getLwirChn0();
+		final int eo0 =   getLwirReaderParameters().getEoChn0();
+		final int numStations = eyesisCameraParameters.getNumStations();
+        gd.addTab("LWIR","LWIR photometric parameters");
+		gd.addNumericField("Thermal color palette", this.palette,  0,3,"","0 - white-hot, 1 - black-hot, 2+ - colored");
 		for (int i = 0; i < lwir_ranges.length; i++) {
-			gd.addNumericField("LWIR chn:"+i+" low range", this.lwir_ranges[i][0],  0,8,"","LWIR sensor range low level ");
-			gd.addNumericField("LWIR chn:"+i+" high range", this.lwir_ranges[i][1],  0,8,"","LWIR sensor range high level ");
+			gd.addNumericField("LWIR chn:"+(i+lwir0)+" center", 0.5*(this.lwir_ranges[i][1]+this.lwir_ranges[i][0]),  1,8,"","LWIR sensor range center");
+			gd.addNumericField("LWIR chn:"+(i+lwir0)+" range", this.lwir_ranges[i][1]-this.lwir_ranges[i][0],  1,8,"","LWIR sensor range");
 		}
-		gd.addNumericField("Thermal color palette", this.palette,  0,3,"","0 - white-hot, 1 - black-hot, 2+ - colored");
+        gd.addTab("EO","EO photometric parameters");
+		for (int i = 0; i < eo_rb2g_hi.length; i++) {
+			gd.addNumericField("EO chn:"+(i+eo0)+" r2g", this.eo_rb2g_hi[i][0],  4,8,"","gain ratio red to green");
+			gd.addNumericField("EO chn:"+(i+eo0)+" b2g", this.eo_rb2g_hi[i][1],  4,8,"","gain ratio red to green");
+			gd.addNumericField("EO chn:"+(i+eo0)+" full range", this.eo_rb2g_hi[i][2],  1,8,"","Full intensity range to map to 255 in the output");
+		}
+		gd.addNumericField("Gamma correction",  this.eo_gamma,        3,6,"","Gamma correction: 1.0 - linear, lower increases dynamic range.");
+		gd.addNumericField("Linear range",      this.eo_minlin_gamma, 1,6,"","Apply gamma only to higher input values");
+		gd.addNumericField("Color saturation",  this.eo_saturation,   3,6,"","Boost color saturation from the linear representation");
+		
+        gd.addTab("Grid lines","Grid lines parameters");
+		gd.addNumericField("Line width for LWIR images", this.line_width_lwir,  0,3,"pix","line width for the grid in LWIR images");
+		gd.addNumericField("Line width for LWIR images", this.line_width_eo,  0,3,"pix","line width for the grid in EO images");
+		String scolor = (this.color_grid==null)?"none":String.format("%08x", getLongColor(this.color_grid));
+		gd.addStringField ("Line color for the grid lines (actual grid)",scolor, 8, "Any invalid hex number disables drawing lines");
+		String scolor_weak = (this.color_grid_weak==null)?"none":String.format("%08x", getLongColor(this.color_grid_weak));
+		gd.addStringField ("Line color for the weak grid lines (below threshold)",scolor_weak, 8, "Any invalid hex number disables drawing lines");
+		String scolor_extra = (this.color_grid_extra==null)?"none":String.format("%08x", getLongColor(this.color_grid_extra));
+		gd.addStringField ("Line color for the extended grid lines (extra grid)",scolor_extra, 8, "Any invalid hex number disables drawing lines");
+        
+        gd.addTab("General","Output format and other parameters");
+    	gd.addStringField ("Channel directory prefix",this.channel_dir_prefix, 15,"Prefix to a directory name to save channel annotated files");
+        gd.addMessage("Stations to include");
+        for (int i = 0; i < numStations;i++) {
+        	gd.addCheckbox("Use station "+i, ((this.station_sel >> i) & 1) != 0, "Include Station "+i+" in generated files.");
+        }
+    	gd.addCheckbox("Include station number in result file names", this.station_in_filenames, "Use station number as a part of the result file names.");
 		gd.addCheckbox("Save as PNG instead of JPEG", save_png);
-		gd.addNumericField("JPEG quality", this.JPEG_quality,  0,3,"","Jpeg quality, 0 - use Tiff");
-    	gd.addStringField ("Channel directory prefix",this.channel_dir_prefix, 15,"prefix to a directory name to save channel annotated files");
+		gd.addNumericField("JPEG quality", this.JPEG_quality,  0,3,"","JPEG quality, 0 - use Tiff");
+		gd.addNumericField("Threshold contrast",  this.threshold_contrast,   3,6,"","Consider grid nodes with higher contrast to determine bad grids.");
+		gd.addNumericField("Minimal number of high-contrast nodes", this.threshold_number,  0,3,"","Consider a failed grid if the number of strong nodes is below this.");
 	}
 	
+	
 	public void dialogAnswers(GenericJTabbedDialog gd) {
+// --- LWIR ---		
+		this.palette =          (int) gd.getNextNumber();
 		for (int i = 0; i < lwir_ranges.length; i++) {
-			this.lwir_ranges[i][0] = gd.getNextNumber();
-			this.lwir_ranges[i][1] = gd.getNextNumber();
+			double center = gd.getNextNumber();
+			double range =  gd.getNextNumber();
+			this.lwir_ranges[i][0] =  center - 0.5*range;
+			this.lwir_ranges[i][1] =  center + 0.5*range;
+		}
+// --- EO ---		
+		for (int i = 0; i < eo_rb2g_hi.length; i++) {
+			this.eo_rb2g_hi[i][0] =  gd.getNextNumber();
+			this.eo_rb2g_hi[i][1] =  gd.getNextNumber();
+			this.eo_rb2g_hi[i][2] =  gd.getNextNumber();
+		}
+		this.eo_gamma =              gd.getNextNumber();
+		this.eo_minlin_gamma =       gd.getNextNumber();
+		this.eo_saturation =         gd.getNextNumber();		
+// --- Grid lines ---
+		this.line_width_lwir = (int) gd.getNextNumber();
+		this.line_width_eo =   (int) gd.getNextNumber();
+		String scolor =              gd.getNextString();
+		long lcolor = -1;
+		try {
+			lcolor = Long.parseLong(scolor,16);
+			this.color_grid = setLongColor(lcolor);
+		} catch(NumberFormatException e){
+			this.color_grid = null;
 		}
-		this.palette =      (int) gd.getNextNumber();
-		this.save_png =           gd.getNextBoolean();
-		this.JPEG_quality = (int) gd.getNextNumber();
-		this.channel_dir_prefix = gd.getNextString();
+		scolor =                     gd.getNextString();
+		try {
+			lcolor = Long.parseLong(scolor,16);
+			this.color_grid_weak = setLongColor(lcolor);
+		} catch(NumberFormatException e){
+			this.color_grid_weak = null;
+		}	
+
+		scolor =                     gd.getNextString();
+		try {
+			lcolor = Long.parseLong(scolor,16);
+			this.color_grid_extra = setLongColor(lcolor);
+		} catch(NumberFormatException e){
+			this.color_grid_extra = null;
+		}	
+		
+// --- General ---		
+		this.channel_dir_prefix =    gd.getNextString();
+		this.station_sel = 0;
+		for (int i = 0; i < eyesisCameraParameters.getNumStations();i++) {
+			if (gd.getNextBoolean()) {
+				this.station_sel |=  1 << i;
+			}
+		}
+		this.station_in_filenames =  gd.getNextBoolean();
+		this.save_png =              gd.getNextBoolean();
+		this.JPEG_quality =    (int) gd.getNextNumber();
+		this.threshold_contrast =    gd.getNextNumber();
+		this.threshold_number= (int) gd.getNextNumber();
 	}
 	public boolean showJDialog() {
 		set_parameters();
@@ -83,12 +265,71 @@ public class CalibrationIllustrationParameters {
 		if ((lwir_ranges == null) || (lwir_ranges.length != lwirReaderParameters.getLwirChannels(false).length)){
 			lwir_ranges = new double [lwirReaderParameters.getLwirChannels(false).length][2];
 			for (int i = 0; i < lwir_ranges.length; i++) {
-				this.lwir_ranges[i][0] = dflt_lwir_lo;
-				this.lwir_ranges[i][1] = dflt_lwir_hi;
+				this.lwir_ranges[i][0] = DFLT_LWIR_LO;
+				this.lwir_ranges[i][1] = DFLT_LWIR_HI;
 			}
 		}
+		if ((eo_rb2g_hi == null) || (eo_rb2g_hi.length != lwirReaderParameters.getEoChannels(false).length)) {
+			eo_rb2g_hi = new double [lwirReaderParameters.getEoChannels(false).length][3];
+			for (int i = 0; i < lwir_ranges.length; i++) {
+				eo_rb2g_hi[i][0] = DFLT_EO_R2G;  // gain red relative to green
+				eo_rb2g_hi[i][1] = DFLT_EO_B2G;  // gain blue relative to green
+				eo_rb2g_hi[i][2] = DFLT_EO_HI;   // range to map to 255.0
+			}
+		}
+	}
+
+	public double getGamma() {
+		return this.eo_gamma;
 	}
 	
+	public double getMinLin() {
+		return this.eo_minlin_gamma;
+	}
+	public double getSaturation() {
+		return this.eo_saturation;
+	}
+
+	public int getLineWidthLwir() {
+		return this.line_width_lwir;
+	}
+
+	public int getLineWidthEo() {
+		return this.line_width_eo;
+	}
+	public Color getGridColor() {
+		return this.color_grid;
+	}
+	public Color getGridWeakColor() {
+		return this.color_grid_weak;
+	}
+	public Color getGridExtraColor() {
+		return this.color_grid_extra;
+	}
+	public String getChannelPrefix() {
+		return this.channel_dir_prefix;
+	}
+	public boolean useStation(int st_num) {
+		return (this.station_sel & (1 << st_num)) != 0;
+	}
+	public boolean useStationInFilenames() {
+		return this.station_in_filenames;
+	}
+	public boolean usePNG() {
+		return this.save_png;
+	}
+	public int getJPEG_quality() {
+		return this.JPEG_quality;
+	}
+	
+	public double getThresholdContrast() {
+		return this.threshold_contrast;
+	}
+
+	public int getThresholdNumber() {
+		return this.threshold_number;
+	}
+
 	public int getPalette() {
 		return this.palette;
 	}

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

@@ -3346,7 +3346,7 @@ public class MatchSimulatedPattern {
 	}
 
 	/* ======================================================================== */
-	private double[] combineDiagonalGreens(double[] green0, double[] green3, int half_width, int half_height) {
+	private static double[] combineDiagonalGreens(double[] green0, double[] green3, int half_width, int half_height) {
 		int y, x, base;
 		int base_b = 0;
 		double[] result = new double[green0.length];
@@ -3568,18 +3568,27 @@ public class MatchSimulatedPattern {
 	 * Wave vector 2 x component [2][1] - Wave vector 2 y component [2][2] - Wave
 	 * vector 2 phase (not used here)
 	 */
-	public double[][] tryPattern(LwirReaderParameters lwirReaderParameters, // null is OK
-			DoubleFHT doubleFHT, double[] point, // xy to try
+	public double[][] tryPattern(
+			LwirReaderParameters lwirReaderParameters, // null is OK
+			DoubleFHT doubleFHT,
+			double[] point, // xy to try
 			final DistortionParameters distortionParameters, //
-			final MatchSimulatedPattern.PatternDetectParameters patternDetectParameters, final double min_half_period,
-			final double max_half_period, final SimulationPattern.SimulParameters thisSimulParameters,
-			final MatchSimulatedPattern matchSimulatedPattern, final MatchSimulatedPattern matchSimulatedPatternCorr,
-			final SimulationPattern simulationPattern, final boolean equalizeGreens, final ImagePlus imp, // image to
-																											// process
-			double[] bPattern, double[] windowFunction, double[] windowFunctionCorr, double[] windowFunctionCorr2,
-			double[] windowFunctionCorr4, double[][] locsNeib, // which neibors to try (here - just the center)
+			final MatchSimulatedPattern.PatternDetectParameters patternDetectParameters,
+			final double min_half_period,
+			final double max_half_period,
+			final SimulationPattern.SimulParameters thisSimulParameters,
+			final MatchSimulatedPattern matchSimulatedPattern,
+			final MatchSimulatedPattern matchSimulatedPatternCorr,
+			final SimulationPattern simulationPattern,
+			final boolean equalizeGreens,
+			final ImagePlus imp, // image to process
+			double[] bPattern,
+			double[] windowFunction,
+			double[] windowFunctionCorr,
+			double[] windowFunctionCorr2,
+			double[] windowFunctionCorr4,
+			double[][] locsNeib, // which neibors to try (here - just the center)
 			String dbgStr) {
-
 //		this.debugLevel = 3;
 		if (this.debugLevel == 3) {
 			System.out.println("tryPattern(): this.debugLevel = 3");
@@ -3590,7 +3599,7 @@ public class MatchSimulatedPattern {
 				System.out.println(dbgStr + " imp==null");
 			return null;
 		}
-		boolean is_lwir = ((lwirReaderParameters != null) && lwirReaderParameters.is_LWIR(imp));
+		boolean is_lwir = ((lwirReaderParameters != null) && LwirReaderParameters.is_LWIR(imp));
 		int fft_size = is_lwir ? distortionParameters.FFTSize_lwir : distortionParameters.FFTSize;
 
 		int xc = (int) (2 * Math.round(0.5 * point[0]));
@@ -3906,33 +3915,27 @@ public class MatchSimulatedPattern {
 	// it now can start with non-empty Grid
 	public int distortions( // returns number of grid cells
 			final LwirReaderParameters lwirReaderParameters, // null is OK
-			final boolean[] triedIndices, final DistortionParameters distortionParameters, //
-			final MatchSimulatedPattern.PatternDetectParameters patternDetectParameters, final double min_half_period,
-			final double max_half_period, final SimulationPattern.SimulParameters simulParameters,
-			final boolean equalizeGreens, final ImagePlus imp, // image to process
-			final int threadsMax, final boolean updateStatus, final int debug_level, // debug level used inside loops
+			final boolean[] triedIndices,
+			final DistortionParameters distortionParameters, //
+			final MatchSimulatedPattern.PatternDetectParameters patternDetectParameters,
+			final double min_half_period,
+			final double max_half_period,
+			final SimulationPattern.SimulParameters simulParameters,
+			final boolean equalizeGreens,
+			final ImagePlus imp, // image to process
+			final int threadsMax,
+			final boolean updateStatus,
+			final int debug_level, // debug level used inside loops
 			final int global_debug_level) {
 		if (imp == null)
 			return 0;
 		final int debugThreshold = 1;
-//		final boolean is_lwir = ((lwirReaderParameters != null) && lwirReaderParameters.is_LWIR(imp));
-//		final int fft_size = is_lwir ? distortionParameters.FFTSize_lwir : distortionParameters.FFTSize;
-//		final int correlation_size = is_lwir ? distortionParameters.correlationSizeLwir
-//				: distortionParameters.correlationSize;
-//		final int max_correlation_size = is_lwir ? distortionParameters.maximalCorrelationSizeLwir
-//				: distortionParameters.maximalCorrelationSize;
-//		final int minimal_pattern_cluster = is_lwir ? distortionParameters.minimalPatternClusterLwir
-//				: distortionParameters.minimalPatternCluster;
 		
 		final int sensor_type = LwirReaderParameters.sensorType(imp);
 		final int fft_size =                distortionParameters.getFFTSize(sensor_type);
 		final int correlation_size =        distortionParameters.getCorrelationSize(sensor_type);
-//		final int max_correlation_size =    distortionParameters.getMaximalCorrelationSize(sensor_type);
 		final int minimal_pattern_cluster = distortionParameters.getMinimalPatternCluster(sensor_type);
-		
-		
 		final int[][] directionsUV = { { 1, 0 }, { 0, 1 }, { -1, 0 }, { 0, -1 } }; // should have opposite direction
-																					// shifted by half
 		final int[][] directionsUV8 = { { 1, 0 }, { 0, 1 }, { -1, 0 }, { 0, -1 }, { 1, 1 }, { -1, 1 }, { -1, -1 },
 				{ 1, -1 } }; // first 8 should be the same as in directionsUV
 		final int[] directionsBits8 = { 1, 4, 1, 4, 2, 8, 2, 8 }; // should match directionsUV8
@@ -4103,19 +4106,33 @@ public class MatchSimulatedPattern {
 					System.out.println("distortions(): startScanIndex=" + startScanIndex + " > 3 ####");
 
 				if (startScanIndex < numTries) {
-					nodeQueue = findPatternCandidates(lwirReaderParameters, // LwirReaderParameters
-																			// lwirReaderParameters, // null is OK
-							triedIndices, startScanIndex, // [0] will be updated
-							tryHor, tryVert,
+					nodeQueue = findPatternCandidates(
+							lwirReaderParameters, // LwirReaderParameters
+							triedIndices,
+							startScanIndex, // [0] will be updated
+							tryHor,
+							tryVert,
 							// numTries,
-							selection, thisDistortionParameters, // no control of the displacement
-							patternDetectParameters, min_half_period, max_half_period, thisSimulParameters,
-							matchSimulatedPattern, matchSimulatedPatternCorr, simulationPattern, equalizeGreens, imp, // image
-																														// to
-																														// process
-							bPattern, windowFunction, windowFunctionCorr, windowFunctionCorr2, windowFunctionCorr4,
+							selection,
+							thisDistortionParameters, // no control of the displacement
+							patternDetectParameters,
+							min_half_period,
+							max_half_period,
+							thisSimulParameters,
+							matchSimulatedPattern,
+							matchSimulatedPatternCorr,
+							simulationPattern,
+							equalizeGreens,
+							imp, // image to process
+							bPattern,
+							windowFunction,
+							windowFunctionCorr,
+							windowFunctionCorr2,
+							windowFunctionCorr4,
 							locsNeib, // which neighbors to try (here - just the center)
-							threadsMax, updateStatus, this.debugLevel);
+							threadsMax,
+							updateStatus,
+							this.debugLevel);
 					if (nodeQueue.isEmpty()) { // nodes==null){
 						// if (debugLevel>1) System.out.println("All start points tried");
 						if (global_debug_level > (debugThreshold + 1)) {
@@ -4932,26 +4949,32 @@ public class MatchSimulatedPattern {
 		}
 	}
 
-	private Queue<GridNode> findPatternCandidates(final LwirReaderParameters lwirReaderParameters, // null is OK
+	private Queue<GridNode> findPatternCandidates(
+			final LwirReaderParameters lwirReaderParameters, // null is OK
 			final boolean[] triedIndices, // which indices are already tried
-			final int startScanIndex, final int tryHor, final int tryVert, final Rectangle selection,
+			final int startScanIndex,
+			final int tryHor,
+			final int tryVert,
+			final Rectangle selection,
 			final DistortionParameters distortionParameters, //
-			final MatchSimulatedPattern.PatternDetectParameters patternDetectParameters, final double min_half_period,
-			final double max_half_period, final SimulationPattern.SimulParameters thisSimulParameters,
-			final MatchSimulatedPattern matchSimulatedPattern, final MatchSimulatedPattern matchSimulatedPatternCorr,
-			final SimulationPattern simulationPattern, final boolean equalizeGreens, final ImagePlus imp, // image to
-																											// process
-			final double[] bPattern, final double[] windowFunction, final double[] windowFunctionCorr,
-			final double[] windowFunctionCorr2, final double[] windowFunctionCorr4, final double[][] locsNeib, // which
-																												// neibors
-																												// to
-																												// try
-																												// (here
-																												// -
-																												// just
-																												// the
-																												// center)
-			final int threadsMax, final boolean updateStatus, final int debugLevel) {
+			final MatchSimulatedPattern.PatternDetectParameters patternDetectParameters,
+			final double min_half_period,
+			final double max_half_period,
+			final SimulationPattern.SimulParameters thisSimulParameters,
+			final MatchSimulatedPattern matchSimulatedPattern,
+			final MatchSimulatedPattern matchSimulatedPatternCorr,
+			final SimulationPattern simulationPattern,
+			final boolean equalizeGreens,
+			final ImagePlus imp, // image to process
+			final double[] bPattern,
+			final double[] windowFunction,
+			final double[] windowFunctionCorr,
+			final double[] windowFunctionCorr2,
+			final double[] windowFunctionCorr4,
+			final double[][] locsNeib, // which  neibors  to try  (here  -  just  the  center)
+			final int threadsMax,
+			final boolean updateStatus,
+			final int debugLevel) {
 		final int debugThreshold = 2; // -1; // 1; ** Restore 1
 		if ((debugThreshold < 0) || (debugLevel < -10000)) {
 			System.out.println("findPatternCandidates(): debugThreshold < 0 - restore when done");
@@ -5013,17 +5036,26 @@ public class MatchSimulatedPattern {
 											+ ", nh=" + nh + ")");
 								if (debugLevel > 2)
 									System.out.println(debugNumThread + ":" + n + " >> ");
-								double[][] node = tryPattern(lwirReaderParameters, // LwirReaderParameters
-																					// lwirReaderParameters, // null is
-																					// OK
-										doubleFHT, point, // xy to try
+								double[][] node = tryPattern(
+										lwirReaderParameters, // LwirReaderParameters lwirReaderParameters, null is OK
+										doubleFHT,
+										point, // xy to try
 										distortionParameters, // no control of the displacement
-										patternDetectParameters, min_half_period, max_half_period, thisSimulParameters,
-										matchSimulatedPattern, matchSimulatedPatternCorr, simulationPattern,
-										equalizeGreens, imp, // image to process
-										bPattern, windowFunction, windowFunctionCorr, windowFunctionCorr2,
-										windowFunctionCorr4, locsNeib, // which neighbors to try (here - just the
-																		// center)
+										patternDetectParameters,
+										min_half_period,
+										max_half_period,
+										thisSimulParameters,
+										matchSimulatedPattern,
+										matchSimulatedPatternCorr,
+										simulationPattern,
+										equalizeGreens,
+										imp, // image to process
+										bPattern,
+										windowFunction,
+										windowFunctionCorr,
+										windowFunctionCorr2,
+										windowFunctionCorr4,
+										locsNeib, // which neighbors to try (here - just the  center)
 										(debugLevel > debugThreshold)
 												? ("" + debugNumThread + ":" + n + ", nv=" + nv + ", nh=" + nh + ", nb="
 														+ nb + " " + point[0] + "/" + point[1])
@@ -6590,6 +6622,7 @@ public class MatchSimulatedPattern {
 				&& (grid[uv[1]][uv[0]] != null) && (grid[uv[1]][uv[0]][0] != null));
 	}
 
+	
 	private boolean isCellDefined(double[][][][] grid, int u, int v) {
 		return ((v >= 0) && (u >= 0) && (v < grid.length) && (u < grid[v].length) && (grid[v][u] != null)
 				&& (grid[v][u][0] != null));
@@ -6679,16 +6712,31 @@ public class MatchSimulatedPattern {
 		return numDefinedCells(this.PATTERN_GRID);
 	}
 
-	public int numDefinedCells(double[][][][] grid) { // calulate/print number of defined nodes in a grid
+	public int numDefinedCells(double[][][][] grid) { // calculate/print number of defined nodes in a grid
 		int[] iUV = new int[2];
-		int numDefinedCells = 0;
+		int numCells = 0;
 		for (iUV[1] = 0; iUV[1] < grid.length; iUV[1]++)
 			for (iUV[0] = 0; iUV[0] < grid[0].length; iUV[0]++)
 				if (this.isCellDefined(grid, iUV))
-					numDefinedCells++;
-		return numDefinedCells;
+					numCells++;
+		return numCells;
 	}
 
+	public int numStrongCells(double min_contrast) {
+		return numStrongCells(this.PATTERN_GRID, min_contrast);
+	}
+	
+	public int numStrongCells(double[][][][] grid, double min_contrast) { // calculate/print number of defined high-contrast nodes in a grid
+		int[] iUV = new int[2];
+		int numCells = 0;
+		for (iUV[1] = 0; iUV[1] < grid.length; iUV[1]++)
+			for (iUV[0] = 0; iUV[0] < grid[0].length; iUV[0]++)
+				if (this.getCellContrast(grid, iUV) > min_contrast) {
+					numCells++;
+				}
+		return numCells;
+	}
+	
 	public int gridUVWidth() {
 		return ((this.PATTERN_GRID == null) || (this.PATTERN_GRID.length == 0l) || (this.PATTERN_GRID[0] == null)) ? 0
 				: this.PATTERN_GRID[0].length;
@@ -6704,20 +6752,20 @@ public class MatchSimulatedPattern {
 	 * returns number of laser pointers matched (or negative error) if
 	 * (this.flatFieldForGrid!=null) it should already be applied !!
 	 */
-	public int calculateDistortions(LwirReaderParameters lwirReaderParameters, // null is OK
+	public int calculateDistortions(
+			LwirReaderParameters lwirReaderParameters, // null is OK
 			MatchSimulatedPattern.DistortionParameters distortionParameters, //
 			MatchSimulatedPattern.PatternDetectParameters patternDetectParameters,
-			SimulationPattern.SimulParameters simulParameters, boolean equalizeGreens, ImagePlus imp, // image to
-																										// process //
-																										// has WOI_TOP
-																										// and possibly
-																										// -
-																										// WOI_COMPENSATED
+			SimulationPattern.SimulParameters simulParameters,
+			boolean equalizeGreens,
+			ImagePlus imp, // image to process has WOI_TOP and possibly WOI_COMPENSATED
 			LaserPointer laserPointer, // LaserPointer object or null
 			boolean removeOutOfGridPointers, //
 			double[][][] hintGrid, // predicted grid array (or null)
 			double hintGridTolerance, // allowed mismatch (fraction of period) or 0 - orientation only
-			int threadsMax, boolean updateStatus, int global_debug_level, // DEBUG_LEVEL
+			int threadsMax,
+			boolean updateStatus,
+			int global_debug_level, // DEBUG_LEVEL
 			int debug_level, // debug level used inside loops
 			boolean noMessageBoxes) {
 		
@@ -6726,13 +6774,16 @@ public class MatchSimulatedPattern {
 			return 0;
 		}
 		final int debugThreshold = 1;
-		boolean is_lwir = ((lwirReaderParameters != null) && lwirReaderParameters.is_LWIR(imp));
+		boolean is_lwir = ((lwirReaderParameters != null) && LwirReaderParameters.is_LWIR(imp));
 		double min_half_period = (is_lwir ? patternDetectParameters.minGridPeriodLwir
 				: patternDetectParameters.minGridPeriod) / 2;
 		double max_half_period = (is_lwir ? patternDetectParameters.maxGridPeriodLwir
 				: patternDetectParameters.maxGridPeriod) / 2;
 		int minimal_pattern_cluster = is_lwir ? distortionParameters.minimalPatternClusterLwir
 				: distortionParameters.minimalPatternCluster;
+		double threshold_contrast = distortionParameters.threshold_contrast;
+		int threshold_number = distortionParameters.threshold_number;
+		
 
 		boolean invert = false; // is_lwir;
 
@@ -6802,126 +6853,153 @@ public class MatchSimulatedPattern {
 		boolean[] triedIndices = new boolean[numTries + 1]; // last set - all used
 		for (int i = 0; i < triedIndices.length; i++)
 			triedIndices[i] = (i < 3); // mark first 3 as if they are already used
+		while (reTries > 0) { // outer loop, including refines
+			while (reTries-- > 0) {
+				this.PATTERN_GRID = null;
+				invalidateCalibration();
+
+				patternCells = distortions( // calculates matchSimulatedPattern.DIST_ARRAY // invalidates calibration,
+						// flatFieldForGrid, resets this.PATTERN_GRID
+						lwirReaderParameters, // null is OK
+						triedIndices,
+						distortionParameters, //
+						patternDetectParameters,
+						min_half_period,
+						max_half_period,
+						simulParameters,
+						equalizeGreens,
+						imp,
+						threadsMax, updateStatus, debug_level, global_debug_level); // debug level
+				if (global_debug_level > 0)
+					System.out.println(
+							"Pattern correlation done at " + IJ.d2s(0.000000001 * (System.nanoTime() - startTime), 3)
+							+ " found " + patternCells + " cells, reTries left: " + reTries);
+				if (patternCells > 0) {
+					foundGoodCluster = true;
+					break; // new distortions() code - returns non-zero only if passed other tests
+				}
 
-		while (reTries-- > 0) {
-			this.PATTERN_GRID = null;
-			invalidateCalibration();
-
-			patternCells = distortions( // calculates matchSimulatedPattern.DIST_ARRAY // invalidates calibration,
-										// flatFieldForGrid, resets this.PATTERN_GRID
-					lwirReaderParameters, // null is OK
-					triedIndices, distortionParameters, //
-					patternDetectParameters, min_half_period, max_half_period, simulParameters, equalizeGreens, imp,
-					threadsMax, updateStatus, debug_level, global_debug_level); // debug level
-			if (global_debug_level > 0)
-				System.out.println(
-						"Pattern correlation done at " + IJ.d2s(0.000000001 * (System.nanoTime() - startTime), 3)
-								+ " found " + patternCells + " cells, reTries left: " + reTries);
-			if (patternCells > 0) {
-				foundGoodCluster = true;
-				break; // new distortions() code - returns non-zero only if passed other tests
-			}
-
-			boolean someLeft = false;
-			int startScanIndex = 0;
-			for (startScanIndex = 3; startScanIndex < triedIndices.length; startScanIndex++)
-				if (!triedIndices[startScanIndex]) {
-					someLeft = true;
+				boolean someLeft = false;
+				int startScanIndex = 0;
+				for (startScanIndex = 3; startScanIndex < triedIndices.length; startScanIndex++)
+					if (!triedIndices[startScanIndex]) {
+						someLeft = true;
+						break;
+					}
+
+				if (someLeft) {
+					if (global_debug_level > 0) {
+						System.out.println("Initial pattern cluster is too small (" + patternCells
+								+ "), continuing scanning from index " + startScanIndex);
+					}
+				} else { // all tried
+					if (global_debug_level > 0)
+						System.out.println("--- Tried all - nothing found --- at "
+								+ IJ.d2s(0.000000001 * (System.nanoTime() - startTime), 3));
 					break;
 				}
+			}
 
-			if (someLeft) {
-				if (global_debug_level > 0) {
-					System.out.println("Initial pattern cluster is too small (" + patternCells
-							+ "), continuing scanning from index " + startScanIndex);
-				}
+			// restore initial distortionParameters.correlationMinInitialContrast
+			distortionParameters.correlationMinInitialContrast = savedCorrelationMinInitialContrast;
+			if (!foundGoodCluster) {
+				if (global_debug_level > (debugThreshold + 1))
+					System.out.println(
+							"calculateDistortions(): Pattern too small, initial cluster had " + patternCells + " cells");
+				if (global_debug_level > (debugThreshold + 2))
+					IJ.showMessage("Error", "Pattern too small: " + patternCells);
+				return distortionParameters.errPatternNotFound;
+			}
+			if (!patternOK()) {
+				if (global_debug_level > (debugThreshold + 1))
+					System.out.println("Pattern not found");
+				if (global_debug_level > (debugThreshold + 2))
+					IJ.showMessage("Error", "Pattern not found");
+				return distortionParameters.errPatternNotFound;
 			} else {
-				if (global_debug_level > 0)
-					System.out.println("--- Tried all - nothing found --- at "
-							+ IJ.d2s(0.000000001 * (System.nanoTime() - startTime), 3));
-				break;
+				if (global_debug_level > 0) // (debugThreshold + 1))
+					System.out.println("Initial pattern cluster has " + patternCells + " cells");
 			}
-		}
-
-		// restore initial distortionParameters.correlationMinInitialContrast
-		distortionParameters.correlationMinInitialContrast = savedCorrelationMinInitialContrast;
-		if (!foundGoodCluster) {
 			if (global_debug_level > (debugThreshold + 1))
 				System.out.println(
-						"calculateDistortions(): Pattern too small, initial cluster had " + patternCells + " cells");
-			if (global_debug_level > (debugThreshold + 2))
-				IJ.showMessage("Error", "Pattern too small: " + patternCells);
-			return distortionParameters.errPatternNotFound;
-		}
-		if (!patternOK()) {
-			if (global_debug_level > (debugThreshold + 1))
-				System.out.println("Pattern not found");
-			if (global_debug_level > (debugThreshold + 2))
-				IJ.showMessage("Error", "Pattern not found");
-			return distortionParameters.errPatternNotFound;
-		} else {
-			if (global_debug_level > 0) // (debugThreshold + 1))
-				System.out.println("Initial pattern cluster has " + patternCells + " cells");
-		}
-		if (global_debug_level > (debugThreshold + 1))
-			System.out.println(
-					"Wave vectors recalculated at " + IJ.d2s(0.000000001 * (System.nanoTime() - startTime), 3));
-		recalculateWaveVectors(updateStatus, debug_level);// debug level used inside loops
-		ImagePlus imp_eq;
-		if (distortionParameters.flatFieldCorrection && (this.flatFieldForGrid == null)) // if it is not null it is
-																							// already supposed to be
-																							// applied!
-			imp_eq = equalizeGridIntensity(
-					imp,
-					this.PATTERN_GRID,
-					distortionParameters, // // makes no sense for LWIR as it normalizes absolute data - actually it does! 
-					equalizeGreens,
-					global_debug_level,
-					updateStatus,
-					threadsMax);
-		else
-			imp_eq = imp;
-
-		if (distortionParameters.refineCorrelations) {
-			double maxActualCorr = refineDistortionCorrelation(
-					lwirReaderParameters, // LwirReaderParameters lwirReaderParameters, // null is OK
-					distortionParameters, //
-					patternDetectParameters,
-					simulParameters,
-					equalizeGreens,
-					imp_eq,
-					0.0, // final double maxCorr, maximal allowed correction, in pixels (0.0) - any
-					threadsMax,
-					updateStatus,
-					debug_level); // debug level
-			System.out.println(".... maxActualCorr="+maxActualCorr);
-			if (maxActualCorr <= 0.0) {
-				return distortionParameters.errRefineFailed; // 2021
-			}
-			recalculateWaveVectors(
-					updateStatus,
-					debug_level);// debug level used inside loops
-			if (global_debug_level > (debugThreshold + 1))
-				System.out.println("Second pass over at " + IJ.d2s(0.000000001 * (System.nanoTime() - startTime), 3));
-		}
-		// hack gridSize
-		if ((distortionParameters.gridSize & 1) != 0) {
-			refineDistortionCorrelation(lwirReaderParameters, // LwirReaderParameters lwirReaderParameters, // null is OK
-					distortionParameters, //
-					patternDetectParameters,
-					simulParameters,
-					equalizeGreens,
-					imp_eq,
-					0.0, // final double maxCorr, maximal allowed correction, in pixels (0.0) - any
-					threadsMax,
-					updateStatus,
-					debug_level); // debug level
-
+						"Wave vectors recalculated at " + IJ.d2s(0.000000001 * (System.nanoTime() - startTime), 3));
 			recalculateWaveVectors(updateStatus, debug_level);// debug level used inside loops
-			if (global_debug_level > 0)
-				System.out.println("Third pass over at " + IJ.d2s(0.000000001 * (System.nanoTime() - startTime), 3));
+			ImagePlus imp_eq;
+			if (distortionParameters.flatFieldCorrection && (this.flatFieldForGrid == null)) // if it is not null it is
+				// already supposed to be
+				// applied!
+				imp_eq = equalizeGridIntensity(
+						imp,
+						this.PATTERN_GRID,
+						distortionParameters, // // makes no sense for LWIR as it normalizes absolute data - actually it does! 
+						equalizeGreens,
+						global_debug_level,
+						updateStatus,
+						threadsMax);
+			else
+				imp_eq = imp;
+
+			if (distortionParameters.refineCorrelations) {
+				double maxActualCorr = refineDistortionCorrelation(
+						lwirReaderParameters, // LwirReaderParameters lwirReaderParameters, // null is OK
+						distortionParameters, //
+						patternDetectParameters,
+						simulParameters,
+						equalizeGreens,
+						imp_eq,
+						0.0, // final double maxCorr, maximal allowed correction, in pixels (0.0) - any
+						threadsMax,
+						updateStatus,
+						debug_level); // debug level
+				System.out.println(".... maxActualCorr="+maxActualCorr);
+				if (maxActualCorr <= 0.0) {
+					return distortionParameters.errRefineFailed; // 2021
+				}
+				recalculateWaveVectors(
+						updateStatus,
+						debug_level);// debug level used inside loops
+				if (global_debug_level > (debugThreshold + 1))
+					System.out.println("Second pass over at " + IJ.d2s(0.000000001 * (System.nanoTime() - startTime), 3));
+			}
 			// hack gridSize
-		}
+			if ((distortionParameters.gridSize & 1) != 0) {
+				refineDistortionCorrelation(lwirReaderParameters, // LwirReaderParameters lwirReaderParameters, // null is OK
+						distortionParameters, //
+						patternDetectParameters,
+						simulParameters,
+						equalizeGreens,
+						imp_eq,
+						0.0, // final double maxCorr, maximal allowed correction, in pixels (0.0) - any
+						threadsMax,
+						updateStatus,
+						debug_level); // debug level
+
+				recalculateWaveVectors(updateStatus, debug_level);// debug level used inside loops
+				if (global_debug_level > 0)
+					System.out.println("Third pass over at " + IJ.d2s(0.000000001 * (System.nanoTime() - startTime), 3));
+				// hack gridSize
+			}
+			// Test number of cells with contrast > (~10.0) and fail if number Of over threshold is below minimal_pattern_cluster?
+			patternCells = numDefinedCells();
+			if ((roi != null) && (patternCells < minimal_pattern_cluster) && !(roi instanceof PointRoi)) {
+				if (global_debug_level > (debugThreshold + 0))
+					System.out.println("Detected pattern is too small: " + patternCells + ", minimum is set to "
+							+ minimal_pattern_cluster+". Will try again search for a new start point.");
+				//return distortionParameters.errTooFewCells; // -10
+				continue;
+			}
+			patternCells = numStrongCells(threshold_contrast);
+			if ((roi != null) && (patternCells < threshold_number) && !(roi instanceof PointRoi)) {
+				if (global_debug_level > (debugThreshold + 0))
+					System.out.println("Detected pattern has too few strong cells (with contrast > "+ threshold_contrast+
+							"): " + patternCells + ", minimum number is set to "
+							+ threshold_number+". Will try again search for a new start point.");
+				//return distortionParameters.errTooFewCells; // -10
+				continue;
+			}
+			break; // enough cells?
+		} // end of outer loop that includes refines
+		
 		patternCells = numDefinedCells();
 		if ((roi != null) && (patternCells < minimal_pattern_cluster) && !(roi instanceof PointRoi)) {
 			if (global_debug_level > (debugThreshold + 0))
@@ -6929,6 +7007,15 @@ public class MatchSimulatedPattern {
 						+ minimal_pattern_cluster);
 			return distortionParameters.errTooFewCells; // -10
 		}
+		patternCells = numStrongCells(threshold_contrast);
+		if ((roi != null) && (patternCells < threshold_number) && !(roi instanceof PointRoi)) {
+			if (global_debug_level > (debugThreshold + 0))
+				System.out.println("Detected pattern has too few strong cells (with contrast > "+ threshold_contrast+
+						"): " + patternCells + ", minimum number is set to "
+						+ threshold_number+".");
+			//return distortionParameters.errTooFewCells; // -10
+			return distortionParameters.errTooFewCells; // -10
+		}
 
 		double[] xy0 = { simulParameters.offsetX, simulParameters.offsetY }; // debug
 		createUV_INDEX(imp, // or null - just to determine WOI (when getWOI matches image size)
@@ -12554,6 +12641,10 @@ public class MatchSimulatedPattern {
 	/* ======================================================================== */
 
 	public static class DistortionParameters {
+		// TODO: make configurable
+		public double threshold_contrast = 10.0;
+		public int    threshold_number =  10; // grid should have this number of nodes with above-threshold contrast
+		
 		private int correlationSize; // FFTSize/4
 		private int correlationSizeLwir;
 		private int maximalCorrelationSize; // FFTSize/2
@@ -12746,6 +12837,10 @@ public class MatchSimulatedPattern {
 
 			gd.addNumericField("Minimal initial pattern cluster size (0 - disable retries)", distortionParameters.minimalPatternCluster, 0); // 40
 			gd.addNumericField("Minimal initial LWIR pattern cluster size (0 - disable retries)", distortionParameters.minimalPatternClusterLwir, 0); // 10
+			
+			gd.addMessage("thresholdContrast=" + threshold_contrast);
+			gd.addMessage("threshold_number=" + threshold_number);
+
 			gd.addNumericField("Scale minimal contrast if the initial cluster is nonzero but smaller", distortionParameters.scaleMinimalInitialContrast, 3);
 			gd.addNumericField("Overlap of FFT areas when searching for pattern", distortionParameters.searchOverlap, 3);
 
@@ -13506,6 +13601,276 @@ public class MatchSimulatedPattern {
 		return bayer_pixels;
 	}
 
+	
+	public static double[][] splitBayer(ImagePlus imp, int sliceNumber, Rectangle r, boolean equalize_greens, int debug_level) {
+		if (imp == null)
+			return null;
+		ImageProcessor ip = null;
+		float[] pixels;
+		if (imp.getStackSize() > 1) {
+			ip = imp.getStack().getProcessor(sliceNumber);
+		} else {
+			ip = imp.getProcessor();
+		}
+		pixels = (float[]) ip.getPixels(); // null pointer
+		int full_width = imp.getWidth(); // full image width
+		int full_height = imp.getHeight(); // full image height
+		if (r == null)
+			r = new Rectangle(0, 0, full_width, full_height);
+		if (debug_level > 10)
+			IJ.showMessage("splitBayer", "r.width=" + r.width + "\nr.height=" + r.height + "\nr.x=" + r.x + "\nr.y="
+					+ r.y + "\nlength=" + pixels.length);
+		if ((debug_level > 2)
+				&& ((r.x < 0) || (r.y < 0) || ((r.x + r.width) >= full_width) || ((r.y + r.height) >= full_height)))
+			System.out.println("r.width=" + r.width + " r.height=" + r.height + " r.x=" + r.x + " r.y=" + r.y);
+		int x, y, base, base_b, bv, i, j;
+		int half_height = (r.height >> 1);
+		int half_width = (r.width >> 1);
+		// make them all 0 if not a single pixel falls into the image
+		int numColors = (half_height == half_width) ? 5 : 4;
+		int pixX, pixY;
+		double[][] bayer_pixels = new double[numColors][half_height * half_width];
+		if ((r.x >= full_width) || (r.y >= full_height) || ((r.x + r.width) < 0) || ((r.y + r.height) < 0)) {
+			for (i = 0; i < bayer_pixels.length; i++)
+				for (j = 0; j < bayer_pixels[i].length; j++)
+					bayer_pixels[i][j] = 0.0;
+			return bayer_pixels;
+		}
+		// base=r.width*((y<<1)+bv);
+		for (y = 0; y < half_height; y++)
+			for (bv = 0; bv < 2; bv++) {
+				pixY = (y * 2) + bv + r.y;
+				base_b = half_width * y;
+				// if ((pixY>=0)
+
+				if (pixY < 0) {
+					pixY = bv;
+				} else if (pixY >= full_height) {
+					pixY = full_height - 2 + bv;
+				}
+				base = full_width * pixY + ((r.x > 0) ? r.x : 0);
+				// base=full_width*((y*2)+bv+r.y)+r.x;
+				pixX = r.x;
+				if (bv == 0)
+					for (x = 0; x < half_width; x++) {
+						if ((pixX < 0) || (pixX >= (full_width - 2))) {
+							bayer_pixels[0][base_b] = pixels[base];
+							bayer_pixels[1][base_b] = pixels[base + 1];
+						} else {
+							bayer_pixels[0][base_b] = pixels[base++];
+							bayer_pixels[1][base_b] = pixels[base++];
+						}
+						base_b++;
+						pixX += 2;
+					}
+				else
+					for (x = 0; x < half_width; x++) {
+						if ((pixX < 0) || (pixX >= (full_width - 2))) {
+							bayer_pixels[2][base_b] = pixels[base];
+							bayer_pixels[3][base_b] = pixels[base + 1];
+						} else {
+							bayer_pixels[2][base_b] = pixels[base++];
+							bayer_pixels[3][base_b] = pixels[base++];
+						}
+						base_b++;
+						pixX += 2;
+					}
+			}
+		if (equalize_greens) {
+			double g0 = 0.0, g3 = 0.0, g02 = 0.0, g32 = 0.0, a0, a3, b0, b3;
+			int n = bayer_pixels[0].length;
+			for (i = 0; i < bayer_pixels[0].length; i++) {
+				g0 += bayer_pixels[0][i];
+				g02 += bayer_pixels[0][i] * bayer_pixels[0][i];
+				g3 += bayer_pixels[3][i];
+				g32 += bayer_pixels[3][i] * bayer_pixels[3][i];
+			}
+			g0 /= n; // mean value
+			g3 /= n; // meran value
+			g02 = g02 / n - g0 * g0;
+			g32 = g32 / n - g3 * g3;
+			b0 = Math.sqrt(Math.sqrt(g32 / g02));
+			b3 = 1.0 / b0;
+			a0 = (g0 + g3) / 2 - b0 * g0;
+			a3 = (g0 + g3) / 2 - b3 * g3;
+			if (debug_level > 2) {
+				System.out.println("g0= " + g0 + ", g3= " + g3);
+				System.out.println("g02=" + g02 + ", g32=" + g32);
+				System.out.println("a0=" + a0 + ", b0=" + b0);
+				System.out.println("a3=" + a3 + ", b3=" + b3);
+			}
+			for (i = 0; i < bayer_pixels[0].length; i++) {
+				bayer_pixels[0][i] = a0 + bayer_pixels[0][i] * b0;
+				bayer_pixels[3][i] = a3 + bayer_pixels[3][i] * b3;
+			}
+		}
+		if (numColors > 4)
+			bayer_pixels[4] = combineDiagonalGreens(bayer_pixels[0], bayer_pixels[3], half_width, half_height);
+		return bayer_pixels;
+	}
+	//Assuming gr/bg
+	public static double [][] simpleDemosaic(
+			ImagePlus imp,
+			double r2g,
+			double b2g,
+			double saturation,
+			double gamma,
+			double minlin_gamma, // do not apply gamma to lower values
+			double hi            // map to 255, gamma will preserve 
+			) {
+		boolean debug_this = false;
+		double kr= 0.299;
+		double kb = 0.114;
+		double kg = 1.0 - kr - kb;
+		ImageProcessor ip = null;
+		float[] pixels;
+		ip = imp.getProcessor();
+		pixels = (float[]) ip.getPixels(); // null pointer
+		int width = imp.getWidth(); // full image width
+		int height = imp.getHeight(); // full image height
+		double [][] rgb = new double [3][width*height];
+		double [] sg= {0.0,0.0};
+		for (int y = 0; y < height; y+=2) {
+			for (int x = 0; x < width; x+=2) {
+				int indx0 = width*y+x;
+				int indx3 = indx0+width+1;
+				sg[0]+=pixels[indx0];
+				sg[1]+=pixels[indx3];
+			}
+		}
+		double g_av = Math.sqrt(sg[0] * sg[1]); 
+		double g2g0 = g_av/sg[0];
+		double g2g3 = g_av/sg[1];
+		for (int y = 0; y < height; y+=2) {
+			for (int x = 0; x < width; x+=2) {
+				int indx0 = width*y+x;
+				int indx1 = indx0+1;
+				int indx2 = indx0+width;
+				int indx3 = indx2+1;
+				sg[0]+=pixels[indx0];
+				sg[1]+=pixels[indx3];
+				rgb[1][indx0] = pixels[indx0] * g2g0;
+				rgb[1][indx3] = pixels[indx3] * g2g3;
+				rgb[0][indx1] = pixels[indx1] * r2g;
+				rgb[2][indx2] = pixels[indx2] * b2g;
+			}
+		}
+		if (debug_this) {
+			(new ShowDoubleFloatArrays()).showArrays(rgb, width, height, true,imp.getTitle()+"split");
+		}
+		if (debug_this) { // remove
+			System.out.println("sg="+sg[0]+", "+sg[1]+", g_av="+g_av);
+		}
+		// bi-linear interpolation
+		for (int y = 0; y < height; y+=2) {
+			for (int x = 0; x < width; x+=2) {
+				int [][] ind = new int[4][4];
+				int base = (y-1)*width+(x-1);
+				for (int i = 0; i < 4;i++) {
+					int ie = i;
+					if ((i==0) && (y==0)) {
+						ie = 2;
+					} else if ((i==3) && (y==(height - 2))) {
+						ie = 1;
+					}	
+					for (int j = 0; j < 4; j++) {
+						int je = j;
+						if ((j==0) && (x==0)) {
+							je = 2;
+						} else if ((j==3) && (x==(width - 2))) {
+							je = 1;
+						}
+						ind[i][j] = base+ie*width+je;
+					}
+				}
+				// red in top left
+				rgb[0][ind[1][1]] = 0.5* (
+						rgb[0][ind[1][0]] +
+						rgb[0][ind[1][2]]);
+				// blue in top left
+				rgb[2][ind[1][1]] = 0.5* (
+						rgb[2][ind[0][1]] +
+						rgb[2][ind[2][1]]);
+				// green in top right
+				rgb[1][ind[1][2]] = 0.25*(
+						rgb[1][ind[0][2]] +
+						rgb[1][ind[1][1]] +
+						rgb[1][ind[1][3]] +
+						rgb[1][ind[2][2]]);
+				// blue in top right
+				rgb[2][ind[1][2]] = 0.25*(
+						rgb[2][ind[0][1]] +
+						rgb[2][ind[0][3]] +
+						rgb[2][ind[2][1]] +
+						rgb[2][ind[2][3]]);
+				// red in bottom left
+				rgb[0][ind[2][1]] = 0.25*(
+						rgb[0][ind[1][0]] +
+						rgb[0][ind[1][2]] +
+						rgb[0][ind[3][0]] +
+						rgb[0][ind[3][2]]);
+				// green in bottom left
+				rgb[1][ind[2][1]] = 0.25*(
+						rgb[1][ind[1][1]] +
+						rgb[1][ind[2][0]] +
+						rgb[1][ind[2][2]] +
+						rgb[1][ind[3][1]]);
+				// red in bottom right
+				rgb[0][ind[2][2]] = 0.5* (
+						rgb[0][ind[1][2]] +
+						rgb[0][ind[3][2]]);
+				// blue in bottom right
+				rgb[2][ind[2][2]] = 0.5* (
+						rgb[2][ind[2][1]] +
+						rgb[2][ind[2][3]]);
+			}
+		}
+		if (debug_this) {
+			(new ShowDoubleFloatArrays()).showArrays(rgb, width, height, true,imp.getTitle()+"bilinear");
+		}
+		if (saturation != 1.0) {
+			for (int i = 0; i < rgb[0].length; i++) {
+				rgb[0][i] = rgb[1][i] * Math.pow(rgb[0][i]/rgb[1][i], saturation); 
+				rgb[2][i] = rgb[1][i] * Math.pow(rgb[2][i]/rgb[1][i], saturation); 
+			}
+		}
+		
+		// gamma-correction
+/*
+			double gamma,
+			double minlin_gamma, // do not apply gamma to lower values
+			double hi            // map to 255, gamma will preserve 
+		
+ */	   
+		boolean nogamma = (gamma == 1.0); 
+		double out_range = 255.0;
+		double lin_scale =  out_range/hi;
+		if (nogamma) {
+			minlin_gamma = hi;
+		}
+		double scale_out = out_range / (Math.pow(hi,  gamma) - Math.pow(minlin_gamma, gamma)*(1.0 - gamma));
+//		double Y0 = scale_out * Math.pow(minlin_gamma, gamma)*(1.0 - gamma);
+		double rY0 = Math.pow(minlin_gamma, gamma)*(1.0 - gamma);
+		if (!nogamma) {
+			lin_scale = scale_out* gamma*Math.pow(minlin_gamma, gamma - 1); 
+		}
+		for (int indx = 0; indx < rgb[0].length; indx++) {
+			double Y = rgb[0][indx]*kr+rgb[1][indx]*kg+rgb[2][indx]*kb; // intensity to apply gamma
+			double s = lin_scale;
+			if (!nogamma && (Y > minlin_gamma)) {
+				s = scale_out * (Math.pow(Y, gamma) - rY0)/Y;
+			}
+			for (int i = 0; i < 3; i++) {
+				rgb[i][indx] *= s;
+			}
+		}
+		if (debug_this) {
+			(new ShowDoubleFloatArrays()).showArrays(rgb, width, height, true,imp.getTitle()+"gamma");
+		}
+		
+		return rgb;
+	}
+	
 	public double[][] splitBayerOne(ImagePlus imp, Rectangle r, boolean equalize_greens) {
 		ImageProcessor ip = imp.getProcessor();
 		float[] pixels;

src/main/java/com/elphel/imagej/lwir/LwirReader.java

@@ -748,7 +748,7 @@ public class LwirReader {
 	 * 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 Thread[] newThreadArray(int maxCPUs) {
+	private static Thread[] newThreadArray(int maxCPUs) {
 		int n_cpus = Runtime.getRuntime().availableProcessors();
 		if (n_cpus>maxCPUs)n_cpus=maxCPUs;
 		return new Thread[n_cpus];

src/main/java/com/elphel/imagej/lwir/LwirReaderParameters.java

@@ -111,7 +111,7 @@ public class LwirReaderParameters {
 		return absolute_chn;
 	}
 
-	public int [] getAbsoluteEoChannels(boolean absolote) {
+	public int [] getEoChannels(boolean absolote) {
 		int [] absolute_chn = new int [eo_channels.length];
 		for (int i = 0; i < absolute_chn.length; i++) {
 			absolute_chn[i] = eo_channels[i] +  + (absolote? getEoChn0():0);