addin illustration generation

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

@@ -112,7 +112,7 @@ public class Aberration_Calibration extends PlugInFrame implements ActionListene
 	private Panel panelGoniometer;
 	private Panel panelPixelMapping, panelStereo,panelStereo1;
 	private Panel panelLWIR;
-//	private Panel panelLWIR16;
+	private Panel panelIllustrations;
 
 	private ShowDoubleFloatArrays SDFA_INSTANCE; // just for debugging?
 	JP46_Reader_camera JP4_INSTANCE;
@@ -597,6 +597,7 @@ public static MatchSimulatedPattern.DistortionParameters DISTORTION =new MatchSi
     	1         // public int    debugLevel=1;
     );
 
+    public static CalibrationIllustration CALIBRATION_ILLUSTRATION = null;
     public static RefineParameters REFINE_PARAMETERS = new RefineParameters();
     public static DistortionCalibrationData DISTORTION_CALIBRATION_DATA=null;
 //    public static FittingStrategy FITTING_STRATEGY=null;
@@ -666,7 +667,7 @@ 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);
 //	new CalibrationHardwareInterface.LaserPointers();
 	public class SyncCommand{
 	    public boolean isRunning=      false;
@@ -687,7 +688,7 @@ public static MatchSimulatedPattern.DistortionParameters DISTORTION =new MatchSi
 		addKeyListener(IJ.getInstance());
 //		setLayout(new GridLayout(ADVANCED_MODE?8:5, 1));
 //		setLayout(new GridLayout(ADVANCED_MODE?9:6, 1));
-		setLayout(new GridLayout(ADVANCED_MODE?21:21, 1));
+		setLayout(new GridLayout(ADVANCED_MODE?22:22, 1));
 		Color color_configure=     new Color(200, 200,160);
 		Color color_process=       new Color(180, 180, 240);
 		Color color_conf_process=  new Color(180, 240, 240);
@@ -1064,6 +1065,13 @@ if (MORE_BUTTONS) {
 		addButton("Manual hint",                panelLWIR,color_configure);
 		add(panelLWIR);
 		
+		panelIllustrations= new Panel();
+		panelIllustrations.setLayout(new GridLayout(1, 0, 5, 5)); // rows, columns, vgap, hgap
+		addButton("Illustrations Configure",    panelIllustrations,color_configure);
+		addButton("Illustrations",              panelIllustrations,color_bundle);
+		add(panelIllustrations);
+		
+		
 		pack();
 		GUI.center(this);
 		setVisible(true);
@@ -9372,6 +9380,77 @@ if (MORE_BUTTONS) {
 		selectLwirGrids(LWIR_PARAMETERS);
         return;
 	}
+/* ======================================================================== */
+	if (label.equals("Illustrations Configure")) {
+		CALIBRATION_ILLUSTRATION_PARAMETERS.showJDialog();
+		return;
+	}
+/* ======================================================================== */
+	if       (label.equals("Illustrations")) {
+		if (LENS_DISTORTIONS==null) {
+			IJ.showMessage("LENS_DISTORTION is not set"); // to use all grids imported
+			return;
+		}
+		EYESIS_ABERRATIONS.setDistortions(LENS_DISTORTIONS);
+		
+		if (EYESIS_ABERRATIONS.aberrationParameters.illustrationsDirectory.length()>0){
+			File dFile=new File(EYESIS_ABERRATIONS.aberrationParameters.illustrationsDirectory);
+			if (!dFile.isDirectory() &&  !dFile.mkdirs()) {
+				String msg="Failed to create directory "+EYESIS_ABERRATIONS.aberrationParameters.illustrationsDirectory;
+				IJ.showMessage("Warning",msg);
+	    		System.out.println("Warning: "+msg);
+	    		EYESIS_ABERRATIONS.aberrationParameters.illustrationsDirectory=""; // start over with selecting directory
+			}
+		}
+		String configPath=EYESIS_ABERRATIONS.aberrationParameters.selectIllustrationsDirectory(
+				true,
+				EYESIS_ABERRATIONS.aberrationParameters.illustrationsDirectory,
+				true);
+		if (configPath==null){
+    		String msg="No illustrations directory selected, command aborted";
+    		System.out.println("Warning: "+msg);
+    		IJ.showMessage("Warning",msg);
+    		return;
+		}
+		configPath+=Prefs.getFileSeparator()+"config-illustrations";
+		try {
+			saveTimestampedProperties(
+					configPath,      // full path or null
+					null, // use as default directory if path==null
+					true,
+					PROPERTIES);
+
+		} catch (Exception e){
+    		String msg="Failed to save configuration to "+configPath+", command aborted";
+    		System.out.println("Error: "+msg);
+    		IJ.showMessage("Error",msg);
+    		return;
+		}
+		
+		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 = 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("Manual hint")) {
 		DEBUG_LEVEL=MASTER_DEBUG_LEVEL;
@@ -10214,7 +10293,6 @@ if (MORE_BUTTONS) {
 		DEBUG_LEVEL=MASTER_DEBUG_LEVEL;
 		LENS_DISTORTIONS=new Distortions(LENS_DISTORTION_PARAMETERS,PATTERN_PARAMETERS,REFINE_PARAMETERS,this.SYNC_COMMAND.stopRequested);
 		// Maybe wrong ! Use folders that have at least all EO channels? 
-//		int min_files =    lwirReaderParameters.getNumChannels();// 8; // use folders that have all 8 files
 		int [] type_map = lwirReaderParameters.getTypeMap(); // 0 - eo, 1 -0 lwir
 		
 		int lwir_chn0 = lwirReaderParameters.getLwirChn0();
@@ -10242,8 +10320,6 @@ if (MORE_BUTTONS) {
 		allornone_eo =   gd.getNextBoolean();
 		allornone_lwir = gd.getNextBoolean();
 	    
-//		String [] grid_extensions={".tif",".tiff"};
-//		String [] src_extensions={".tif",".tiff"};
 		String [] grid_extensions={".tiff"};
 		String [] src_extensions={".tiff"};
 		MultipleExtensionsFileFilter gridFilter =
@@ -10251,11 +10327,8 @@ if (MORE_BUTTONS) {
 		MultipleExtensionsFileFilter sourceFilter =
 				new MultipleExtensionsFileFilter("",src_extensions,"Source calibration images");
 
-//		CalibrationFileManagement.DirectoryContentsFilter gridDirFilter =
-//				new CalibrationFileManagement.DirectoryContentsFilter (gridFilter, min_files, 0, null);
 
     	String [][] gridFileDirs=       new String [numStations][];
-//    	int [][]    gridUseTypes =      new int [numStations][]; // +1 - use eo channels,+2 - use lwir channels (in pointed set) 
     	boolean [][][] gridUseChn =     new boolean [numStations][][]; // channels to use in each scene  
 		String []   sourceStationDirs = new String [numStations];      // directories of the source files per station
 
@@ -11002,7 +11075,11 @@ if (MORE_BUTTONS) {
     	ABERRATIONS_PARAMETERS.autoRestore=false;
 //    	String confPath=loadProperties(null,PROCESS_PARAMETERS.kernelsDirectory, PROCESS_PARAMETERS.useXML, PROPERTIES);
     	String confPath = 	readPropertiesPath(null, PROCESS_PARAMETERS.kernelsDirectory,PROCESS_PARAMETERS.useXML);
-		PROPERTIES = readProperties( confPath, true, PROPERTIES);
+    	Properties properties = readProperties( confPath, true, PROPERTIES);
+    	if (properties == null) {
+    		return;
+    	}
+		PROPERTIES = properties; // readProperties( confPath, true, PROPERTIES);
 		getAllProperties(PROPERTIES);
 		if (DEBUG_LEVEL>0) System.out.println("Configuration parameters are restored from " + confPath);
 		DEBUG_LEVEL=MASTER_DEBUG_LEVEL;
@@ -16016,6 +16093,9 @@ private double [][] jacobianByJacobian(double [][] jacobian, boolean [] mask) {
 		} else {
 			properties = new Properties();
 		}
+		if (path == null) {
+			return null;
+		}
 	    InputStream is;
 		try {
 			is = new FileInputStream(path);
@@ -16151,6 +16231,7 @@ private double [][] jacobianByJacobian(double [][] jacobian, boolean [] mask) {
     	boolean select_FOCUSING_FIELD=!select;
     	boolean select_POWER_CONTROL=!select;
     	boolean select_LWIR=!select;
+    	boolean select_ILLUSTRATIONS=!select;
     	if (select) {
     		GenericDialog gd = new GenericDialog("Select parameters to save");
     		gd.addMessage("===== Individual parameters ======");
@@ -16193,6 +16274,7 @@ private double [][] jacobianByJacobian(double [][] jacobian, boolean [] mask) {
         	gd.addCheckbox("FOCUSING_FIELD",select_FOCUSING_FIELD);
         	gd.addCheckbox("POWER_CONTROL",select_POWER_CONTROL);
         	gd.addCheckbox("LWIR",select_LWIR);
+        	gd.addCheckbox("Illustrations",select_ILLUSTRATIONS);
 
             WindowTools.addScrollBars(gd);
             gd.showDialog();
@@ -16236,6 +16318,7 @@ private double [][] jacobianByJacobian(double [][] jacobian, boolean [] mask) {
         	select_FOCUSING_FIELD=gd.getNextBoolean();
         	select_POWER_CONTROL=gd.getNextBoolean();
         	select_LWIR=gd.getNextBoolean();
+        	select_ILLUSTRATIONS=gd.getNextBoolean();
     	}
 
        	if (select_MASTER_DEBUG_LEVEL) properties.setProperty("MASTER_DEBUG_LEVEL", MASTER_DEBUG_LEVEL+"");
@@ -16277,6 +16360,7 @@ private double [][] jacobianByJacobian(double [][] jacobian, boolean [] mask) {
         if ((select_FOCUSING_FIELD) && (FOCUSING_FIELD!=null)) FOCUSING_FIELD.setProperties("FOCUSING_FIELD.", properties);
         if (select_POWER_CONTROL) POWER_CONTROL.setProperties("POWER_CONTROL.", properties);
         if (select_LWIR) LWIR_PARAMETERS.setProperties("LWIR.", properties);
+        if (select_ILLUSTRATIONS) CALIBRATION_ILLUSTRATION_PARAMETERS.setProperties("ILLUSTRATIONS.", properties);
 
     	if (select) properties.remove("selected");
     }
@@ -16321,6 +16405,7 @@ private double [][] jacobianByJacobian(double [][] jacobian, boolean [] mask) {
        if (FOCUSING_FIELD!=null) FOCUSING_FIELD.getProperties("FOCUSING_FIELD.", properties,false); // false -> overwrite distortions center
        POWER_CONTROL.getProperties("POWER_CONTROL.", properties);
        LWIR_PARAMETERS.getProperties("LWIR.", properties);
+       CALIBRATION_ILLUSTRATION_PARAMETERS.getProperties("ILLUSTRATIONS.", properties);
     }
 
 	  private String selectSourceDirectory(String defaultPath) {

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

+package com.elphel.imagej.calibration;
+
+import java.awt.Color;
+import java.awt.Rectangle;
+import java.io.File;
+import java.util.Arrays;
+import java.util.concurrent.atomic.AtomicInteger;
+
+import com.elphel.imagej.calibration.DistortionCalibrationData.GridImageParameters;
+import com.elphel.imagej.cameras.ThermalColor;
+import com.elphel.imagej.common.ShowDoubleFloatArrays;
+import com.elphel.imagej.correction.EyesisCorrections;
+import com.elphel.imagej.lwir.LwirReaderParameters;
+
+import ij.IJ;
+import ij.ImagePlus;
+import ij.ImageStack;
+import ij.Prefs;
+import ij.gui.Line;
+import ij.process.ImageProcessor;
+
+public class CalibrationIllustration {
+	EyesisAberrations              eyesisAberrations;
+	Distortions                    distortions;
+	CalibrationIllustrationParameters illustrationParameters;	
+	LwirReaderParameters           lwirReaderParameters;
+	AtomicInteger                  stopRequested;
+	int                            debug_level;
+	int                            numStations;
+	int                            numSubCameras;
+	String [][]                    gridFileDirs; // =       new String [numStations][];
+	boolean [][][]                 gridUseChn; //  =     new boolean [numStations][][]; // channels to use in each scene  
+	String []                      sourceStationDirs; // = new String [numStations];      // directories of the source files per station
+	String []                      grid_extensions={".tiff"};
+	String []                      src_extensions={".tiff"};
+	
+	public CalibrationIllustration (
+			CalibrationIllustrationParameters illustrationParameters,			
+			EyesisAberrations              eyesisAberrations,
+			Distortions                    distortions,
+			AtomicInteger                  stopRequested,
+			int                            debug_level) {
+		this.illustrationParameters =      illustrationParameters;
+		this.eyesisAberrations =           eyesisAberrations;
+		this.distortions =                 distortions;
+		this.stopRequested =               stopRequested;
+		this.debug_level =                 debug_level;
+	}			
+
+	public void plotGrid(
+			int       numImg,
+			ImagePlus imp,
+			Color color_grid,
+			Color color_grid_extra // at least one end points to extra (unreliable) nodes (may be null)
+			) {
+		int line_width =  1; //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;
+		
+		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];
+			else if (pUV[i][0] > maxU) maxU = pUV[i][0];
+			if      (pUV[i][1] < minV) minV = pUV[i][1];
+			else if (pUV[i][1] > maxV) maxV = pUV[i][1];
+		}
+		if (color_grid_extra != null) {
+			for (int i = 0; i < pUV_extra.length; i++) {
+				if      (pUV_extra[i][0] < minU) minU = pUV_extra[i][0];
+				else if (pUV_extra[i][0] > maxU) maxU = pUV_extra[i][0];
+				if      (pUV_extra[i][1] < minV) minV = pUV_extra[i][1];
+				else if (pUV_extra[i][1] > maxV) maxV = pUV_extra[i][1];
+			}
+		}
+		
+		Rectangle dimsUV= new Rectangle(minU-1, minV-1, maxU-minU+2, maxV-minV+2);
+		int [] grid = new int [dimsUV.height * dimsUV.width];
+		Arrays.fill(grid,  -1);
+		int main_len = pUV.length;
+		for (int i = 0; i < main_len; i++) {
+			int indx = (pUV[i][0]-dimsUV.x) + (pUV[i][1]-dimsUV.y)* dimsUV.width;
+			grid[indx] = i;
+		}
+		if (color_grid_extra != null) {
+			for (int i = 0; i < pUV_extra.length; i++) {
+				int indx = (pUV_extra[i][0]-dimsUV.x) + (pUV_extra[i][1]-dimsUV.y)* dimsUV.width;
+				grid[indx] = i + main_len;
+			}
+		}
+		ImageProcessor ip = imp.getProcessor();
+		ip.setLineWidth(line_width);
+//		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){
+			// try to the right and down
+			int g0 = grid[indx];
+			for (int dir = 0; dir <2; dir++) { // 90 - right, 1 - down
+				int indx1 = indx + ((dir > 0) ? dimsUV.width : 1);
+				if (indx1 < grid.length) {
+					int g1 = grid[indx1];
+					if (g1 >= 0) {
+						if ((g0 < main_len) && (g1 < main_len)) {
+							ip.setColor(color_grid);
+						} else {
+							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);
+					}
+				}
+			}
+		}
+	}
+	
+	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 =
+				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;
+							}
+						}
+					}
+					// 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;
+						}
+					}
+					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); 
+				}
+			}
+		}
+		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;
+	}
+*/	
+
+	
+}

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

+package com.elphel.imagej.calibration;
+
+import java.util.Properties;
+
+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_";
+	
+	public CalibrationIllustrationParameters (LwirReaderParameters lwirReaderParameters) {
+		this.lwirReaderParameters = lwirReaderParameters;
+	}
+	public void setProperties(String prefix,Properties properties){
+//		properties.setProperty(prefix+"camera_name",         this.camera_name+"");
+		set_parameters();
+		for (int i = 0; i < lwir_ranges.length; i++) {
+			properties.setProperty(prefix+"lwir_range_lo_"+i,         this.lwir_ranges[i][0]+"");
+			properties.setProperty(prefix+"lwir_range_hi_"+i,         this.lwir_ranges[i][1]+"");
+		}		
+		properties.setProperty(prefix+"palette",            this.palette+"");
+		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);
+	}
+
+	public void getProperties(String prefix,Properties properties){
+		set_parameters();
+		for (int i = 0; i < lwir_ranges.length; i++) {
+			if (properties.getProperty(prefix+"lwir_range_lo_"+i)!=null) {
+				this.lwir_ranges[i][0] = Double.parseDouble(properties.getProperty(prefix+"lwir_range_lo_"+i));
+			}
+			if (properties.getProperty(prefix+"lwir_range_hi_"+i)!=null) {
+				this.lwir_ranges[i][1] = Double.parseDouble(properties.getProperty(prefix+"lwir_range_hi_"+i));
+			}
+		}
+		if (properties.getProperty(prefix+"palette")!=null)      this.palette = Integer.parseInt(properties.getProperty(prefix+"palette"));
+		if (properties.getProperty(prefix+"save_png")!=null)     this.save_png = Boolean.parseBoolean(properties.getProperty(prefix+"save_png"));
+		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");
+
+	}
+	public void dialogQuestions(GenericJTabbedDialog gd) {
+		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("Thermal color palette", this.palette,  0,3,"","0 - white-hot, 1 - black-hot, 2+ - colored");
+		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");
+	}
+	
+	public void dialogAnswers(GenericJTabbedDialog gd) {
+		for (int i = 0; i < lwir_ranges.length; i++) {
+			this.lwir_ranges[i][0] = gd.getNextNumber();
+			this.lwir_ranges[i][1] = gd.getNextNumber();
+		}
+		this.palette =      (int) gd.getNextNumber();
+		this.save_png =           gd.getNextBoolean();
+		this.JPEG_quality = (int) gd.getNextNumber();
+		this.channel_dir_prefix = gd.getNextString();
+	}
+	public boolean showJDialog() {
+		set_parameters();
+		GenericJTabbedDialog gd = new GenericJTabbedDialog("Set illustration parameters",800,900);
+		dialogQuestions(gd);
+		gd.showDialog();
+		if (gd.wasCanceled()) return false;
+		dialogAnswers(gd);
+		return true;
+	}
+	public void set_parameters () {
+		//		this.lwirReaderParameters = lwirReaderParameters;
+		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;
+			}
+		}
+	}
+	
+	public int getPalette() {
+		return this.palette;
+	}
+	public double [] getLwirRange(int lwir_index) {
+		return lwir_ranges[lwir_index];
+	}
+	public LwirReaderParameters getLwirReaderParameters() {
+		return lwirReaderParameters;
+	}
+}

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

@@ -1039,16 +1039,6 @@ import ij.text.TextWindow;
         					System.out.println("sfiles == null");
         				}
         				for (String spath:sfiles) {
-        					/*
-        					int last_dash = spath.lastIndexOf('-');
-        					int last =      spath.lastIndexOf('_');
-        					if (last_dash >last) last = last_dash;
-        					int last_dot = spath.lastIndexOf('.');
-        					if (last_dot < 0) {
-        						last_dot = spath.length();
-        					}
-        					int chn = Integer.parseInt(spath.substring(last+1, last_dot));
-        					*/
             				int chn = pathToChannel(spath);
         					spaths[chn] = (new File(set_dir,spath)).getPath();
         				}

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

@@ -4784,6 +4784,7 @@ public class EyesisAberrations {
     public static class AberrationParameters{
     	public String sourceDirectory="";
     	public String partialKernelDirectory="";
+    	public String illustrationsDirectory="";
     	public String psfKernelDirectory="";
     	public String aberrationsKernelDirectory="";
     	public String calibrationDirectory="";
@@ -4821,6 +4822,7 @@ public class EyesisAberrations {
 		public void setProperties(String prefix,Properties properties){
 			properties.setProperty(prefix+"sourceDirectory",this.sourceDirectory);
 			properties.setProperty(prefix+"partialKernelDirectory",this.partialKernelDirectory);
+			properties.setProperty(prefix+"illustrationsDirectory",this.illustrationsDirectory);
 			properties.setProperty(prefix+"psfKernelDirectory",this.psfKernelDirectory);
 			properties.setProperty(prefix+"aberrationsKernelDirectory",this.aberrationsKernelDirectory);
 			properties.setProperty(prefix+"calibrationDirectory",this.calibrationDirectory);
@@ -4866,6 +4868,7 @@ public class EyesisAberrations {
 		public void getProperties(String prefix,Properties properties){
 			if (properties.getProperty(prefix+"sourceDirectory")!=null)	           this.sourceDirectory=properties.getProperty(prefix+"sourceDirectory");
 			if (properties.getProperty(prefix+"partialKernelDirectory")!=null)     this.partialKernelDirectory=properties.getProperty(prefix+"partialKernelDirectory");
+			if (properties.getProperty(prefix+"illustrationsDirectory")!=null)     this.illustrationsDirectory=properties.getProperty(prefix+"illustrationsDirectory");
 			if (properties.getProperty(prefix+"psfKernelDirectory")!=null)         this.psfKernelDirectory=properties.getProperty(prefix+"psfKernelDirectory");
 			if (properties.getProperty(prefix+"aberrationsKernelDirectory")!=null) this.aberrationsKernelDirectory=properties.getProperty(prefix+"aberrationsKernelDirectory");
 			if (properties.getProperty(prefix+"calibrationDirectory")!=null)       this.calibrationDirectory=properties.getProperty(prefix+"calibrationDirectory");
@@ -5018,6 +5021,8 @@ public class EyesisAberrations {
     		gd.addCheckbox("Select source directory", false);
     		gd.addStringField("Partial kernels directory", this.partialKernelDirectory, 60);
     		gd.addCheckbox("Select partial kernels directory", false);
+    		gd.addStringField("Illustrations directory", this.illustrationsDirectory, 60);
+    		gd.addCheckbox("Select illustrations directory", false);
     		gd.addStringField("Combined kernels directory", this.psfKernelDirectory, 60);
     		gd.addCheckbox("Select combined kernsls directory", false);
     		gd.addStringField("Aberrations kernels directory", this.aberrationsKernelDirectory, 60);
@@ -5071,6 +5076,8 @@ public class EyesisAberrations {
     		if (gd.getNextBoolean()) selectSourceDirectory(false, this.sourceDirectory, false);
     		this.partialKernelDirectory=gd.getNextString();
     		if (gd.getNextBoolean()) selectPartialKernelDirectory(false, this.partialKernelDirectory, false);
+    		this.illustrationsDirectory=gd.getNextString();
+    		if (gd.getNextBoolean()) selectIllustrationsDirectory(false, this.illustrationsDirectory, false);
     		this.psfKernelDirectory=gd.getNextString();
     		if (gd.getNextBoolean()) selectPSFKernelDirectory(false, this.psfKernelDirectory, false);
     		this.aberrationsKernelDirectory=gd.getNextString();
@@ -5133,6 +5140,19 @@ public class EyesisAberrations {
     		if (dir!=null) this.partialKernelDirectory=dir;
     		return dir;
     	}
+
+    	public String selectIllustrationsDirectory(boolean smart, String defaultPath, boolean newAllowed) {
+    		String dir= CalibrationFileManagement.selectDirectory(
+    				smart,
+    				newAllowed, // save
+    				"Illustrations directory", // title
+    				"Select illustrations directory", // button
+    				null, // filter
+    				defaultPath); //this.sourceDirectory);
+    		if (dir!=null) this.illustrationsDirectory=dir;
+    		return dir;
+    	}
+    	
     	public String selectPSFKernelDirectory(boolean smart, String defaultPath, boolean newAllowed) {
     		String dir= CalibrationFileManagement.selectDirectory(
     				smart,

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

@@ -2696,7 +2696,7 @@ public class EyesisCorrections {
 	}
 
 
-	public void saveAndShow(
+	public static void saveAndShow(
 			ImagePlus             imp,
 			String                path,
 			boolean               png,
@@ -2716,12 +2716,12 @@ public class EyesisCorrections {
 				}
 			}
 
-			if (hasAlphaHighByte && (jpegQuality <= 0)){
+			if (hasAlphaHighByte && ((jpegQuality <= 0) || png)){
 				if (png){
 					if (debugLevel > 0) System.out.println("Saving RGBA result to "+path+".png");
 					(new EyesisTiff()).savePNG_ARGB32(
 							imp,
-							path+".png"
+							path +".png"
 							);
 
 				} else {
@@ -2729,7 +2729,7 @@ public class EyesisCorrections {
 					try {
 						(new EyesisTiff()).saveTiffARGB32(
 								imp,
-								path+".tiff",
+								path, // +".tiff",
 								false, // correctionsParameters.imageJTags,
 								debugLevel);
 					} catch (IOException e) {

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

@@ -102,6 +102,26 @@ public class LwirReaderParameters {
 	public LwirReaderParameters() {
 		
 	}
+	
+	public int [] getLwirChannels(boolean absolote) {
+		int [] absolute_chn = new int [lwir_channels.length];
+		for (int i = 0; i < absolute_chn.length; i++) {
+			absolute_chn[i] = lwir_channels[i] + (absolote? getLwirChn0() : 0);
+		}
+		return absolute_chn;
+	}
+
+	public int [] getAbsoluteEoChannels(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);
+		}
+		return absolute_chn;
+	}
+//	protected int []  lwir_channels =        {0, 1, 2 ,3};
+//	protected int []  eo_channels =          {0, 1, 2 ,3};
+	
+	
 	public LwirReaderParameters(String name) {
 		if (NAME_TALON.equals(name)) camera_name = NAME_TALON;
 		else if (NAME_LWIR16.equals(name)) camera_name = NAME_LWIR16;
@@ -133,11 +153,11 @@ public class LwirReaderParameters {
 	public int getNumFrames() {
 		return num_frames;
 	}
-	public int getLwirChn0 () {
+	public int getLwirChn0() {
 		return lwir_chn0;
 	}
 
-	public int getEoChn0 () {
+	public int getEoChn0() {
 		return isLwir16() ? 16:4;// eo_chn0;
 	}
 	

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

@@ -2191,7 +2191,7 @@ public class QuadCLT extends QuadCLTCPU {
 					true,  // smart,
 					true);  //newAllowed, // save
 			for (int sub_img = 0; sub_img < imps_RGB.length; sub_img++){
-				eyesisCorrections.saveAndShow(
+				EyesisCorrections.saveAndShow(
 						imps_RGB[sub_img],
 						x3d_path,
 						correctionsParameters.png && !clt_parameters.black_back,
@@ -2720,7 +2720,7 @@ public class QuadCLT extends QuadCLTCPU {
 					true,  // smart,
 					true);  //newAllowed, // save
 			for (int sub_img = 0; sub_img < imps_RGB.length; sub_img++){
-				quadCLT_main.eyesisCorrections.saveAndShow(
+				EyesisCorrections.saveAndShow(
 						imps_RGB[sub_img],
 						x3d_path,
 						quadCLT_main.correctionsParameters.png && !clt_parameters.black_back,

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

@@ -5159,7 +5159,7 @@ public class QuadCLTCPU {
 						  true,  // smart,
 						  true);  //newAllowed, // save
 				  for (int sub_img = 0; sub_img < 4; sub_img++){
-					  eyesisCorrections.saveAndShow(
+					  EyesisCorrections.saveAndShow(
 							  imps_RGB[sub_img],
 							  x3d_path,
 							  correctionsParameters.png && !clt_parameters.black_back,
@@ -12185,7 +12185,7 @@ public class QuadCLTCPU {
 
 		  }
 		  ImagePlus ip_thumb = new ImagePlus(name,ip);
-		  eyesisCorrections.saveAndShow(
+		  EyesisCorrections.saveAndShow(
 				  ip_thumb,
 				  dir,
 				  false,

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

@@ -50,6 +50,7 @@ import com.elphel.imagej.cameras.EyesisCorrectionParameters;
 import com.elphel.imagej.common.GenericJTabbedDialog;
 import com.elphel.imagej.common.ShowDoubleFloatArrays;
 import com.elphel.imagej.correction.CorrectionColorProc;
+import com.elphel.imagej.correction.EyesisCorrections;
 import com.elphel.imagej.gpu.GPUTileProcessor;
 import com.elphel.imagej.jp4.JP46_Reader_camera;
 
@@ -1030,7 +1031,7 @@ public class TwoQuadCLT {
 						true,  // smart,
 						true);  //newAllowed, // save
 				for (int sub_img = 0; sub_img < imps_RGB.length; sub_img++){
-					quadCLT_main.eyesisCorrections.saveAndShow(
+					EyesisCorrections.saveAndShow(
 							imps_RGB[sub_img],
 							x3d_path,
 							quadCLT_main.correctionsParameters.png && !clt_parameters.black_back,
@@ -1916,7 +1917,7 @@ public class TwoQuadCLT {
 						true,  // smart,
 						true);  //newAllowed, // save
 				for (int sub_img = 0; sub_img < imps_RGB.length; sub_img++){
-					quadCLT_main.eyesisCorrections.saveAndShow(
+					EyesisCorrections.saveAndShow(
 							imps_RGB[sub_img],
 							x3d_path,
 							quadCLT_main.correctionsParameters.png && !clt_parameters.black_back,