pending commits while working on LWIR16 calibration

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

@@ -1041,6 +1041,8 @@ if (MORE_BUTTONS) {
 		addButton("Goniometer Move",            panelLWIR,color_debug);
 		addButton("LWIR Goniometer",            panelLWIR,color_conf_process);
 		addButton("LWIR grids",                 panelLWIR,color_process);
+		addButton("LWIR15 GEOM",                panelLWIR,color_configure);
+		
 		addButton("Import Subsystem",           panelLWIR,color_configure);
 		addButton("Select LWIR grids",          panelLWIR,color_configure);
 		addButton("Grid offset",                panelLWIR,color_process);
@@ -5822,7 +5824,7 @@ if (MORE_BUTTONS) {
 			double patternHeight=PATTERN_PARAMETERS.patternHeight;
 			double targetAngleHorizontal=360*Math.atan(patternWidth/2/distanceToTarget)/Math.PI;
 			double targetAngleVertical=  360*Math.atan(patternHeight/2/distanceToTarget)/Math.PI;
-			if (DEBUG_LEVEL>0) System.out.println(
+			if (DEBUG_LEVEL>-1) System.out.println(
 					"Using:\n"+
 					"Distance from target:          "+IJ.d2s(distanceToTarget,1)+" mm\n"+
 					"         Taget width:          "+IJ.d2s(patternWidth,1)+" mm\n"+
@@ -9387,6 +9389,7 @@ if (MORE_BUTTONS) {
 /* ======================================================================== */
     if (label.equals("LWIR_ACQUIRE")) {
         DEBUG_LEVEL=MASTER_DEBUG_LEVEL;
+        /*
 		ImagePlus [][] imps;
 		if (LWIR_PARAMETERS.isLwir16()) {
 			if (LWIR16_READER == null) {
@@ -9403,6 +9406,49 @@ if (MORE_BUTTONS) {
 			LWIR_READER.acquire(DISTORTION_PROCESS_CONFIGURATION.sourceDirectory); // directory to save
 //          ImagePlus [] imps = LWIR_READER.acquire("attic/lwir_test_images"); // directory to save
 		}
+		*/
+		if ((GONIOMETER==null) || (LWIR_PARAMETERS.isLwir16()?(GONIOMETER.lwir16Reader ==  null):(GONIOMETER.lwirReader ==  null))) {
+			if (LWIR_PARAMETERS.isLwir16()) {
+				if (LWIR16_READER == null) {
+					LWIR16_READER =  new Lwir16Reader(LWIR_PARAMETERS);
+				}
+				GONIOMETER= new Goniometer(
+						LWIR16_READER,
+						DISTORTION, //MatchSimulatedPattern.DistortionParameters distortion,
+						PATTERN_DETECT, //MatchSimulatedPattern.PatternDetectParameters patternDetectParameters,
+						EYESIS_CAMERA_PARAMETERS, //EyesisCameraParameters eyesisCameraParameters,
+						LASER_POINTERS, // MatchSimulatedPattern.LaserPointer laserPointers
+						SIMUL,                       //SimulationPattern.SimulParameters  simulParametersDefault,
+						GONIOMETER_PARAMETERS, //LensAdjustment.FocusMeasurementParameters focusMeasurementParameters,
+						DISTORTION_PROCESS_CONFIGURATION);
+				LWIR16_READER.setMotorsPosition(GONIOMETER_PARAMETERS.goniometerMotors.getCurrentPositions()); // getTargetPositions()); // Used target, not current to prevent minor variations				
+				
+			} else {
+				if (LWIR_READER == null) {
+					LWIR_READER =  new LwirReader(LWIR_PARAMETERS);
+				}
+				GONIOMETER= new Goniometer(
+						LWIR_READER,
+						DISTORTION, //MatchSimulatedPattern.DistortionParameters distortion,
+						PATTERN_DETECT, //MatchSimulatedPattern.PatternDetectParameters patternDetectParameters,
+						EYESIS_CAMERA_PARAMETERS, //EyesisCameraParameters eyesisCameraParameters,
+						LASER_POINTERS, // MatchSimulatedPattern.LaserPointer laserPointers
+						SIMUL,                       //SimulationPattern.SimulParameters  simulParametersDefault,
+						GONIOMETER_PARAMETERS, //LensAdjustment.FocusMeasurementParameters focusMeasurementParameters,
+						DISTORTION_PROCESS_CONFIGURATION);
+				LWIR_READER.setMotorsPosition(GONIOMETER_PARAMETERS.goniometerMotors.getCurrentPositions()); // getTargetPositions()); // Used target, not current to prevent minor variations				
+			}
+			if (DEBUG_LEVEL>1){
+				System.out.println("Initialized Goniometer class for "+LWIR_PARAMETERS.getCameraName());
+			}
+		} else if (DEBUG_LEVEL>1){
+			System.out.println("GONIOMETER was initialized for "+LWIR_PARAMETERS.getCameraName());
+		}
+		if (LWIR_PARAMETERS.isLwir16()) {
+			LWIR16_READER.acquire(DISTORTION_PROCESS_CONFIGURATION.sourceDirectory); // directory to save
+		} else {
+			LWIR_READER.acquire(DISTORTION_PROCESS_CONFIGURATION.sourceDirectory); // directory to save
+		}		
 		return;
 	}
 
@@ -9451,7 +9497,7 @@ if (MORE_BUTTONS) {
 		double patternHeight=PATTERN_PARAMETERS.patternHeight;
 		double targetAngleHorizontal=360*Math.atan(patternWidth/2/distanceToTarget)/Math.PI;
 		double targetAngleVertical=  360*Math.atan(patternHeight/2/distanceToTarget)/Math.PI;
-		if (DEBUG_LEVEL>0) System.out.println(
+		if (DEBUG_LEVEL>-1) System.out.println(
 				"Using:\n"+
 				"Distance from target:          "+IJ.d2s(distanceToTarget,1)+" mm\n"+
 				"         Taget width:          "+IJ.d2s(patternWidth,1)+" mm\n"+
@@ -9475,6 +9521,12 @@ if (MORE_BUTTONS) {
 	    calculateLwirGrids();
         return;
 	}
+/* ======================================================================== */
+	if       (label.equals("LWIR15 GEOM")) {
+		EYESIS_CAMERA_PARAMETERS.setLwir16Geometry();
+		return;
+	}
+	
 /* ======================================================================== */
 	if       (label.equals("Import Subsystem")) {
 		importSystem(null, "EYESIS_CAMERA_PARAMETERS.");
@@ -9978,7 +10030,8 @@ if (MORE_BUTTONS) {
 		//DistortionProcessConfiguration
 		DEBUG_LEVEL=MASTER_DEBUG_LEVEL;
 		LENS_DISTORTIONS=new Distortions(LENS_DISTORTION_PARAMETERS,PATTERN_PARAMETERS,REFINE_PARAMETERS,this.SYNC_COMMAND.stopRequested);
-		int min_files = 8; // use folders that have all 8 files
+		// 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 lwir_chn0 = lwirReaderParameters.getLwirChn0();
 		int eo_chn0 = lwirReaderParameters.getEoChn0();
 		int numStations = 3;
@@ -10011,7 +10064,7 @@ if (MORE_BUTTONS) {
 	    for (int numStation=0;numStation<numStations;numStation++){
 	    	DirectoryChoser dc = new DirectoryChoser(
 	    			gridFilter,
-	    			min_files,
+	    			min_files, // not actually used
 	    			0,
 	    			null);
 	    	dc.setFileSelectionMode(JFileChooser.DIRECTORIES_ONLY);
@@ -10215,8 +10268,8 @@ if (MORE_BUTTONS) {
 
         		matchSimulatedPattern.invalidateFlatFieldForGrid(); //Reset Flat Field calibration - different image.
         		matchSimulatedPattern.invalidateFocusMask();
-        		boolean is_lwir = LWIR_PARAMETERS.is_LWIR(imp_sel);
-        		int numAbsolutePoints=matchSimulatedPattern.calculateDistortions(
+        		boolean is_lwir = LWIR_PARAMETERS.is_LWIR(imp_sel); // Not used!
+        		int numAbsolutePoints=matchSimulatedPattern.calculateDistortions( // matchSimulatedPattern.PATTERN_GRID already set
         				LWIR_PARAMETERS, // LwirReaderParameters lwirReaderParameters,
         				DISTORTION, //
         				PATTERN_DETECT,
@@ -11543,7 +11596,7 @@ if (MORE_BUTTONS) {
 		} else {
 			System.out.println("No pattern grid file (ground gtruth) is provided");
 		}
-		if ((configPaths[3] !=null) && (configPaths[3] != "")){ // load sensor
+		if ((configPaths[3] !=null) && !configPaths[3].equals("")){ // load sensor
 			if (distortions.fittingStrategy==null) return false; // Why?
 			if (DEBUG_LEVEL>0) System.out.println("Autoloading sensor calibration files "+configPaths[3]);
 			distortions.setDistortionFromImageStack(

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

@@ -25,6 +25,7 @@ package com.elphel.imagej.calibration;
 
 import java.io.File;
 import java.io.FilenameFilter;
+import java.util.Arrays;
 import java.util.Properties;
 
 import com.elphel.imagej.common.WindowTools;
@@ -223,8 +224,10 @@ import ij.gui.GenericDialog;
 			    return new File(current, name).isDirectory();
 			  }
 			});
+			// TODO:Sort set list
 			String [] sourceSets = new String[sourceFileSets.length];
 			for (int i=0;i<sourceSets.length;i++) sourceSets[i]=sourceFileSets[i].getPath();
+			Arrays.sort(sourceSets);
 			return sourceSets;
         }
 

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

@@ -520,6 +520,10 @@ public class Distortions {
 /*					double [] XYZM=patternParameters.getXYZM( // will throw if outside or masked out
 							fittingStrategy.distortionCalibrationData.gIP[imgNum].pixelsUV[pointNumber][0],
 							fittingStrategy.distortionCalibrationData.gIP[imgNum].pixelsUV[pointNumber][1]);*/
+					if ((targetXYZ[index]==null) || (XYZMP==null)) {
+						System.out.println("Null problem in imgNum="+imgNum+", point "+pointNumber);
+						continue;
+					}
 					this.targetXYZ[index][0]=XYZMP[0];
 					this.targetXYZ[index][1]=XYZMP[1];
 					this.targetXYZ[index][2]=XYZMP[2];
@@ -3293,6 +3297,7 @@ For each point in the image
 			int global_debug_level, // DEBUG_LEVEL
 			int debug_level // debug level used inside loops
 	){
+
 		int debugThreshold0=0;
 		int debugThreshold=2;
 		MatchSimulatedPattern matchSimulatedPattern = new MatchSimulatedPattern(64); // new instance, all reset, FFTSize=64 will not be used
@@ -3316,6 +3321,10 @@ For each point in the image
 		int numSuccess=0;
 		DistortionCalibrationData dcd=fittingStrategy.distortionCalibrationData;
 		for (int numGridImage=0;numGridImage<dcd.gIP.length;numGridImage++) {
+			if (numGridImage >= 1680)	{
+				System.out.println("Processing debug image "+numGridImage);
+				System.out.println("Processing debug image "+numGridImage);
+			}
 			int set_number = dcd.gIP[numGridImage].getSetNumber();
 			if ((set_number >= start_set) &&
 					(set_number <= end_set) &&
@@ -3338,6 +3347,17 @@ For each point in the image
 						}
 					}
 				}
+				if ((dcd.gIP[numGridImage].matchedPointers > 0) && !ignoreLaserPointers) { // just re-enable with the same shifts (will fail if pointers were just added, but it failed anyway) 
+					if (!dcd.gIP[numGridImage].enabled) {
+						if (this.debugLevel>0) {
+							System.out.println("Re-enabling grid #"+numGridImage+" that has pointer(s) with the previously set UVShiftRot =={0,0,0}");
+						}
+						dcd.gIP[numGridImage].enabled = true;
+						dcd.gIP[numGridImage].newEnabled = true;
+					}
+					continue;
+				}
+				
 				if (this.debugLevel>debugThreshold0) {
 					System.out.println("\n---- applyHintedGrids() image #"+numGridImage+" (imageNumber="+imageNumber+") "+
 							" dcd.gIP["+numGridImage+"].pixelsXY.length="+dcd.gIP[numGridImage].pixelsXY.length+
@@ -3385,7 +3405,6 @@ For each point in the image
 					System.out.println("++++++ BUG: in applyHintedGrids() failed in createUV_INDEX()");
 					continue;
 				}
-
 				double [] goniometerTiltAxial=dcd.getImagesetTiltAxial(numGridImage);
 				if ((goniometerTiltAxial==null) || Double.isNaN(goniometerTiltAxial[0])  || Double.isNaN(goniometerTiltAxial[1])){
 					if (this.debugLevel>0) {
@@ -3551,7 +3570,7 @@ For each point in the image
 	public int [][] getImageMarkers(int numGridImage){
 		String source_path=fittingStrategy.distortionCalibrationData.gIP[numGridImage].source_path;
 		if (source_path != null) {
-			final ImagePlus imp = new ImagePlus(source_path);
+			ImagePlus imp = new ImagePlus(source_path);
 			imp.show();
 			/*
 			Thread msg_box_thread  = new Thread() {
@@ -3580,6 +3599,25 @@ For each point in the image
 				System.out.println("This image does not have point marks - please mark it in "+source_path);
 				IJ.showMessage("This image does not have point marks - please mark it in "+source_path);
 				return null;
+				/*
+				
+				boolean mark_and_continue = IJ.showMessageWithCancel("Mark and Continue", "This image does not have point marks - please mark it in "+source_path);
+				
+				if (mark_and_continue) {
+					imp = new ImagePlus(source_path);
+					System.out.println("got it again!");
+					pointRoi = null;
+					if (imp.getRoi() instanceof PointRoi) {
+						pointRoi =  (PointRoi) imp.getRoi();
+					} else {
+						System.out.println("This image does not have point marks - please mark it in "+source_path);
+						IJ.showMessage("This image does not have point marks - please mark it in "+source_path);
+						return null;
+					}
+				} else {
+					return null;
+				}
+				*/
 			}
 			Point [] points = pointRoi.getContainedPoints();
 			int [][] ipoints = new int [points.length][2];

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

@@ -2016,6 +2016,9 @@ public class MatchSimulatedPattern {
 				ix = (interpolateXY[maxIndex][0] + j) % size;
 				for (int i = 0; i < 2; i++) {
 					iy = interpolateXY[maxIndex][1] + i; // next: OOB 2147483647
+					if (iy >= fft_complex.length) {
+						iy = fft_complex.length - 1; // was Index 17 out of bounds for length 17
+					}
 					interpolateAmplitudes[maxIndex][i][j] = Math.sqrt(fft_complex[iy][ix][0] * fft_complex[iy][ix][0]
 							+ fft_complex[iy][ix][1] * fft_complex[iy][ix][1]);
 					interpolatePhases[maxIndex][i][j] = Math.atan2(
@@ -7688,7 +7691,7 @@ public class MatchSimulatedPattern {
 		int shiftSelect = (((shifts[0][0] - coeff[0][2]) * (shifts[0][0] - coeff[0][2]) + (shifts[0][1] - coeff[1][2])
 				* (shifts[0][1] - coeff[1][2])) > ((shifts[1][0] - coeff[0][2]) * (shifts[1][0] - coeff[0][2])
 						+ (shifts[1][1] - coeff[1][2]) * (shifts[1][1] - coeff[1][2]))) ? 1 : 0;
-		if (this.debugLevel > 1) {
+		if (this.debugLevel > 0) {
 			double d1 = Math.sqrt((shifts[0][0] - coeff[0][2]) * (shifts[0][0] - coeff[0][2])
 					+ (shifts[0][1] - coeff[1][2]) * (shifts[0][1] - coeff[1][2]));
 			double d2 = Math.sqrt((shifts[1][0] - coeff[0][2]) * (shifts[1][0] - coeff[0][2])
@@ -8068,7 +8071,8 @@ public class MatchSimulatedPattern {
 					numCells++;
 				}
 			if (numCells > 0) {
-				setPatternGridArray(maxU - minU + 1, maxV - minV + 1);
+//				setPatternGridArray(maxU - minU + 1, maxV - minV + 1); // FIXME: Does nothing
+				this.PATTERN_GRID = setPatternGridArray(maxU - minU + 1, maxV - minV + 1); // FIXME: Does nothing
 				double[] xy = new double[2];
 				int[] uv = new int[2];
 				for (int i = 0; i < pixels[0].length; i++)

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

@@ -2,6 +2,7 @@ package com.elphel.imagej.calibration;
 import java.awt.Rectangle;
 import java.util.Properties;
 
+import com.elphel.imagej.common.PolynomialApproximation;
 import com.elphel.imagej.jp4.JP46_Reader_camera;
 
 /*
@@ -743,6 +744,7 @@ import ij.io.Opener;
 		public double[] getXYZM(int u, int v, boolean verbose, int station){ // u=0,v=0 - center!
 			int u1=u+this.U0;
 			int v1=v+this.V0;
+			double r2 = 0.25;
         	if ((v1<0) || (u1<0) || (v1 >= this.gridGeometry.length) || (u1 >= this.gridGeometry[0].length) ||
         			(this.gridGeometry[v1][u1][3]==0)) {
         		if ((this.debugLevel>1) && verbose && ((v1<0) || (u1<0) || (v1 >= this.gridGeometry.length) || (u1 >= this.gridGeometry[0].length))){
@@ -755,13 +757,68 @@ import ij.io.Opener;
         		return null;
         	}
         	if (this.stationZCorr==null) return this.gridGeometry[v1][u1];
-        	double [] result=this.gridGeometry[v1][u1].clone();
+        	double [] result = this.gridGeometry[v1][u1].clone();
 // use lower station if grid file does not have current
         	int useStation=(this.stationZCorr[v1][u1].length>station)?station:(this.stationZCorr[v1][u1].length-1);
         	result[2]+=this.stationZCorr[v1][u1][useStation];
 			return result;
-//			return this.gridGeometry[v1][u1];
 		}
+
+		/**
+		 * Use this for just initial orientation
+		 * @param u
+		 * @param v
+		 * @param verbose
+		 * @return {x,y,z}
+		 */
+		public double[] extrapolateXYZ(
+				double u,
+				double v,
+				boolean verbose){ // u=0,v=0 - center! No correction for stationZCorr - anyway it is not accurate outside
+			double u1 = u + this.U0;
+			double v1 = v + this.V0;
+			double r2 = 0.0001;
+			double [] result = null;
+			PolynomialApproximation pa = new PolynomialApproximation();
+			double [][][] data = new double[gridGeometry.length * gridGeometry[0].length][3][];
+			int di = 0;
+			for (int vg = 0; vg < gridGeometry.length; vg++) {
+				double dv2 = v1 - vg;
+				dv2 = dv2*dv2 + r2;;
+				for (int ug = 0; ug < gridGeometry[0].length; ug++) {
+					data[di][0] = new double[2];
+					data[di][0][0] = ug; 
+					data[di][0][1] = vg;
+					data[di][1] = new double[3];
+					data[di][2] = new double[1];
+					if ((gridGeometry[vg][ug] != null) && (gridGeometry[vg][ug][3] > 0.0)){
+						data[di][1][0] = gridGeometry[vg][ug][0]; // x 
+						data[di][1][1] = gridGeometry[vg][ug][1]; // y 
+						data[di][1][2] = gridGeometry[vg][ug][2]; // z
+						double du = u1 - ug;
+						data[di][2][0] = gridGeometry[vg][ug][3] / (du*du + dv2); 
+					}
+					di++;
+				}
+			}
+			double [][] coeff = pa.quadraticApproximation(
+					data,
+					true, // forceLinear,  // use linear approximation
+					null); // damping,
+			if (coeff== null) return null;
+			result = new double[3]; // out of grid, so all but x,y,z are 0.0;
+			for (int i = 0; i < 3; i++) {
+				result[i] = coeff[i][0]*u1 + coeff[i][1]*v1 + coeff[i][2]; 
+			}
+			/*
+        	if (this.stationZCorr==null) return result; // this.gridGeometry[v1][u1];
+// use lower station if grid file does not have current
+        	int useStation=(this.stationZCorr[v1][u1].length>station)?station:(this.stationZCorr[v1][u1].length-1);
+        	result[2]+=this.stationZCorr[v1][u1][useStation];
+        	*/
+			return result;
+		}		
+		
 		public double[] getXYZ(
 				double [] uv,
 				boolean verbose,
@@ -776,8 +833,11 @@ import ij.io.Opener;
 			corn[2] = getXYZM(iu,     iv + 1, verbose, station);
 			corn[3] = getXYZM(iu + 1, iv + 1, verbose, station);
 			if ((corn[0] == null) || (corn[1] == null) || (corn[2] == null) || (corn[3] == null)) {
+				if (verbose) {
 					System.out.println("Optical axis outside of the grid: TODO: modify getXYZM() to handle!");
-				return null;
+				}
+				return extrapolateXYZ (uv[0], uv[1], verbose);
+				//				return null;
 			}
 			double [] rslt_xyz = new double[3];
 			rslt_xyz[0] = (1-fu) * (1-fv) * corn[0][0] + fu * (1-fv) * corn[1][0] + (1-fu) * fv * corn[2][0] + fu * fv * corn[3][0];
@@ -915,7 +975,7 @@ import ij.io.Opener;
         	};
 			return result;
 		}
-		public double[] getXYZMPE(
+		public double[] getXYZMPE( // update this and other to interpolate
 				int u,
 				int v,
 				int station,

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

@@ -68,7 +68,7 @@ import java.util.Properties;
 		public int subcamera =   0;
 		public int sensor_port = 0;
 		public int subchannel =  0;
-
+		public boolean lwir =    false; // invert color for LWIR sensors
 
 		/*
 		 Modifying to accommodate for eccentricity of different terms (2 parameters per term) and elliptical shape (another 2 terms). When all are
@@ -115,7 +115,8 @@ import java.util.Properties;
     			double channelWeightDefault,
     			int subcamera,
     			int sensor_port,
-    			int subchannel
+    			int subchannel,
+    			boolean lwir     // LWIR camera with inverted color
     	){
     		this.decimateMasks = decimateMasks;
         	this.sensorWidth= sensorWidth;
@@ -158,7 +159,7 @@ import java.util.Properties;
 			this.subcamera = subcamera;
 			this.sensor_port = sensor_port;
 			this.subchannel = subchannel;
-
+			this.lwir =       lwir;
     		updateCartesian(); // set alternative
     	}
     	// defects are not cloned!
@@ -197,7 +198,8 @@ import java.util.Properties;
     	    		this.channelWeightDefault,
     				this.subcamera,
     				this.sensor_port,
-    				this.subchannel
+    				this.subchannel,
+    				this.lwir
     				);
     	}
     	public void setDefaultNonRadial(){
@@ -247,8 +249,7 @@ import java.util.Properties;
 			properties.setProperty(prefix+"subcamera",           this.subcamera+"");
 			properties.setProperty(prefix+"sensor_port",         this.sensor_port+"");
 			properties.setProperty(prefix+"subchannel",          this.subchannel+"");
-
-
+			properties.setProperty(prefix+"lwir",                this.lwir+"");
     	}
     	public void getProperties(String prefix,Properties properties){
     		getProperties(prefix,properties, -1);
@@ -333,7 +334,8 @@ import java.util.Properties;
 				this.sensor_port=Integer.parseInt(properties.getProperty(prefix+"sensor_port"));
 			if (properties.getProperty(prefix+"subchannel")!=null)
 				this.subchannel=Integer.parseInt(properties.getProperty(prefix+"subchannel"));
-
+			if (properties.getProperty(prefix+"lwir")!=null)
+				this.lwir=Boolean.parseBoolean(properties.getProperty(prefix+"lwir"));
     	}
     	public void setChannelWeightCurrent(
     			double weight){
@@ -363,9 +365,14 @@ import java.util.Properties;
     		this.cartesian = cartesian;
     	}
 
+    	public boolean isLWIR() {
+    		return this.lwir;
+    	}
+
     	public double getPixelSize() {
     		return this.pixelSize;
     	}
+    	
     	public double getDistortionRadius() {
     		return this.distortionRadius;
     	}

src/main/java/com/elphel/imagej/lwir/Lwir16Reader.java

@@ -88,7 +88,6 @@ public class Lwir16Reader {
 	public static final String SCRIPT_CAPTURE=  "capture_range.php"; // capture synchronized images
 	public static final String SCRIPT_RESET=    "reset_frames.php";  // Reset frame numbers
 	public static final String SCRIPT_WAIT=     "wait_frame.php";    // wait for absolute frame (positive) or skip frames (nefative)
-	
 	// will remove later
 	public static final String IMAGE_URL_FIRST="/towp/wait/img/save";     // next image name, same image number/time
 	public static final String SKIP_FRAME_URL= "/towp/wait/meta";          // Wait for the next frame, return meta data
@@ -288,38 +287,6 @@ public class Lwir16Reader {
    		}
    		startAndJoin(threads);
 
-   		/*
-		for (int chn = 0; chn < num_channels; chn++) {
-			int width =  sets[0][chn].getWidth();
-			int height = sets[0][chn].getHeight();
-			String title = sets[0][chn].getTitle()+"_average"+num_frames;
-			float [] pixels_avg = (float []) sets[0][chn].getProcessor().getPixels(); //null pointer
-			for (int n = 1; n < num_frames; n++) {
-				float [] pixels = (float []) sets[n][chn].getProcessor().getPixels();
-				for (int i = 0; i < pixels_avg.length; i++) {
-					pixels_avg[i] += pixels[i];
-				}
-			}
-			double scale = 1.0/num_frames;
-			for (int i = 0; i < pixels_avg.length; i++) {
-				pixels_avg[i] *= scale;
-			}
-			ImageProcessor ip=new FloatProcessor(width,height);
-			ip.setPixels(pixels_avg);
-			ip.resetMinAndMax();
-			imps_avg[chn]=  new ImagePlus(title, ip);
-			Properties properties0 = sets[0][chn].getProperties();
-			for (String key:properties0.stringPropertyNames()) {
-				imps_avg[chn].setProperty(key, properties0.getProperty(key));
-			}
-			imps_avg[chn].setProperty("average", ""+num_frames);
-			if (motorsPosition!=null) for (int m=0;m<motorsPosition.length;m++ ) {
-				imps_avg[chn].setProperty("MOTOR"+(m+1), ""+motorsPosition[m]);
-			}
-			ImagejJp4Tiff.encodeProperiesToInfo(imps_avg[chn]);
-			// TODO: Overwrite some properties?
-		}
-   		 */
 		return imps_avg;
 	}
 
@@ -744,6 +711,7 @@ public class Lwir16Reader {
 	    }
 
 	}
+	
 	public double getFutureTimestamnp (String ip, double delay) { // delay in seconds from master
 		if (lwirReaderParameters.getDebugLevel() > 0) {
 			System.out.println("Increasing delay by 3.0s when there is some printing");
@@ -797,22 +765,28 @@ public class Lwir16Reader {
 	 * @param lrp
 	 * @param delay
 	 * @param duration -1 - start only, 0 - stop only, >0 - start+stop (LWIR cameras)
-	 * @param duration_eo -1 - start only, 0 - stop only, >0 - start+stop (EO cameras)
+	 * @param duration_eo -1 - start only, 0 - stop only, >0 - start+stop (EO cameras). If stop only - will wait for both masters
 	 * @return <0 - error, >0 last frame of the master camera/port in sequence
 	 */
 	public int captureRange(LwirReaderParameters lrp, double delay, int duration, int duration_eo) {
+		boolean sync2eo = true;
 		int lwir_master_index = 0;
+		int eo_master_index = 4;
+		String [] all_ips = lrp.getAllIPs();
 		int num_lwir =      lrp.getLwirIPs().length;
 		int [] port_masks= getPortMasks(lrp);
-		double target_ts = getFutureTimestamnp (lrp.getLwirIP(lwir_master_index), delay);
+		String master_ip = all_ips[sync2eo? eo_master_index : lwir_master_index];
+		double target_ts = getFutureTimestamnp (master_ip, delay);
 		if (Double.isNaN(target_ts)) {
 			return -1;
 		}
-		String [] all_ips = lrp.getAllIPs();
 		String [] urls = new String [all_ips.length];
 		for (int i = 0; i < urls.length; i++) {
 			int dur = (i>= num_lwir)?duration_eo:duration;
 			urls[i]=String.format("http://%s/%s?sensor_port=0&ts=%f&m=%d&d=%d", all_ips[i], SCRIPT_CAPTURE, target_ts, port_masks[i], dur);
+			if ((dur == 0) && ((i==lwir_master_index) || (i==eo_master_index))){
+				urls[i] += "&wait";
+			}
 		}
 		boolean OK = true;
    		Document [] docs = collectXmlResponses(urls);
@@ -849,12 +823,19 @@ public class Lwir16Reader {
    		}
 		int master_frame = Integer.parseInt(((Node) 
 				(((Node) docs[lwir_master_index].getDocumentElement().getElementsByTagName("frame").item(0)).getChildNodes().item(0))).getNodeValue());
-		if (lrp.getDebugLevel() > 0) System.out.println(String.format("master_frame=%d(0x%x)", master_frame,master_frame));
+		if ((lrp.getDebugLevel() > 0) && ((duration==0) || (duration_eo==0)) ) {
+			System.out.println(String.format("master_frame=%d(0x%x)", master_frame,master_frame));
+   			for (int i = 0; i < urls.length; i++) {
+   				System.out.println(i+": "+urls[i]);
+   			}
+		}
+//		System.out.println("mater_frame = "+master_frame+", target_ts="+target_ts);
 		return master_frame;
 	}
 	
 	public boolean startStopCompressor(LwirReaderParameters lrp, boolean start, double delay) {
-		if (lrp.getDebugLevel() > 0) System.out.println("startStopCompressor() start="+start);
+//		if (lrp.getDebugLevel() > 0) System.out.println("startStopCompressor() start="+start);
+		if (lrp.getDebugLevel() > -1) System.out.println("startStopCompressor() start="+start);
 		int duration = start? -1: 0;
 		int end_frame = captureRange(lrp, delay, duration, duration);
 		if (end_frame < 0) return false;
@@ -1003,12 +984,13 @@ public class Lwir16Reader {
 		}
 		resetFrameBuffers(lrp); // actually only needed after stopping, here just in case
 		// start capturing frames into each camera buffer
-		int end_frame = captureRange(lrp, lrp.getAcquireDelay(), lrp.getAvgNumberLwir(),lrp.getAvgNumberEO());
+//		int end_frame = 
+		captureRange(lrp, lrp.getAcquireDelay(), lrp.getAvgNumberLwir(),lrp.getAvgNumberEO());
 
 //	public static final String IMAGE_URL_NEXT=  "/torp/next/wait/img/save"; // same image name, same image number/time
 //	public static final String IMAGE_URL_NEXT=  "/torp/wait/img/next/save"; // same image name, same image number/time
-		int [] port_masks= getPortMasks(lrp);
-		String [] all_IPs = lrp.getAllIPs();
+//		int [] port_masks= getPortMasks(lrp);
+//		String [] all_IPs = lrp.getAllIPs();
 		final int num_lwir = lrp.getLwirIPs().length;
 		final int avg_lwir = lrp.getAvgNumberLwir();
 		final int avg_eo =   lrp.getAvgNumberEO();
@@ -1076,7 +1058,9 @@ public class Lwir16Reader {
 				public void run() {
    					for (int chn = indxAtomic.getAndIncrement(); chn < num_channels; chn = indxAtomic.getAndIncrement()) {
    						if (imgs[chn] != null) {
-   							int num_frames = (chn < (num_lwir*IMGSRV_PORTS.length))? avg_lwir : avg_eo;
+   							boolean is_lwir = chn < (num_lwir*IMGSRV_PORTS.length);
+//   							int num_frames = (chn < (num_lwir*IMGSRV_PORTS.length))? avg_lwir : avg_eo;
+   							int num_frames = is_lwir? avg_lwir : avg_eo;
    							if (num_frames > 0) {
    								float [] pixels_avg = (float []) imgs[chn].getProcessor().getPixels();
    								double scale = 1.0/num_frames;
@@ -1090,6 +1074,9 @@ public class Lwir16Reader {
    								if (motorsPosition!=null) for (int m=0;m<motorsPosition.length;m++ ) {
    									imgs[chn].setProperty("MOTOR"+(m+1), ""+motorsPosition[m]);
    								}
+								imgs[chn].setProperty(
+										LwirReaderParameters.SENSOR_TYPE,
+										LwirReaderParameters.SENSOR_TYPES[is_lwir?1:0]);
    								ImagejJp4Tiff.encodeProperiesToInfo(imgs[chn]);
    							}
    						}
@@ -1098,6 +1085,29 @@ public class Lwir16Reader {
    			};
    		}
    		startAndJoin(threads);
+   		
+		if (dirpath != null) {
+			File  f_dir = new File(dirpath);
+			// get series path from the first channel file title
+			String first_name = imgs[0].getTitle();
+			String set_name = first_name.substring(0, first_name.lastIndexOf('_'));
+			String set_path = dirpath+Prefs.getFileSeparator()+set_name;
+			File  set_dir = new File(set_path);
+			set_dir.mkdirs(); // including parent
+			LOGGER.warn("Saving image set to: "+set_dir.getAbsolutePath());
+			for (ImagePlus imp:imgs) {
+				String fname = imp.getTitle();
+//				fname = fname.substring(0, fname.lastIndexOf('_')) + ".tiff"; // remove _average
+//				fname = fname.substring(0, fname.lastIndexOf('.')) + ".tiff"; // remove _average
+				fname = fname + ".tiff"; // remove _average
+   				FileSaver fs=new FileSaver(imp);
+   				String path=set_path+Prefs.getFileSeparator()+fname;
+   				IJ.showStatus("Saving "+path);
+   				LOGGER.info("LWIR_ACQUIRE: 'Saving "+path );
+   				fs.saveAsTiff(path);
+			}
+		}
+   		
 		if (lrp.isShowImages()) {
 			for (ImagePlus imp: imgs) {
 				imp.show();
@@ -1159,8 +1169,10 @@ public class Lwir16Reader {
 				img_numbers[i] = -1;
 			}
 			img_names[i] = (String) imps[i].getProperty("CONTENT_FILENAME");
+			if (lrp.getDebugLevel() > 0) {
 				LOGGER.warn("Seconds for "+i+" - "+img_seconds[i]+", number"+img_numbers[i]+", name "+img_names[i]);
 			}
+		}
 		// Make a sparse array for all lwir+eo channels with nulls for channels that are not measured. 
 		ImagePlus [] imps_all = new ImagePlus [all_IPs.length * IMGSRV_PORTS.length];
 		int indx = 0;
@@ -1307,7 +1319,7 @@ public class Lwir16Reader {
    				}
    			}
    		}
-		skipMasterFrames(two_IPs,  4); // make sure all previous parameters are applied
+		skipMasterFrames(two_IPs,  4); // make sure all previous parameters are applied // waits for both LWIR and EO
 		// second reset after cameras running synchronously
 		OK &= resetAllFrames(lrp);
 		skipMasterFrames(two_IPs,  1); 

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

@@ -31,6 +31,7 @@ import java.io.FilenameFilter;
 import java.util.Properties;
 
 import com.elphel.imagej.common.GenericJTabbedDialog;
+import com.elphel.imagej.readers.EyesisTiff;
 
 import ij.ImagePlus;
 import ij.Prefs;
@@ -41,6 +42,8 @@ public class LwirReaderParameters {
 	public final static String [] CAMERA_NAMES= {NAME_TALON,NAME_LWIR16};
 	public final static int []    BOSON_FFC_FRAMES= {2,4,8,16};
 	public final static int []    FFC_GROUPS=          {1,2,4};
+	public static final String [] SENSOR_TYPES = {"EO","LWIR"};
+	public static final String    SENSOR_TYPE =  "SENSOR_TYPE";
 	
 	private boolean parameters_updated =     false;
 	protected String  camera_name =          "Talon"; // "LWIR16";
@@ -94,7 +97,7 @@ public class LwirReaderParameters {
 	protected boolean show_images = false;
 
 	protected int     lwir_chn0 =             0; // not configurable
-	protected int     eo_chn0 =               4; // not configurable
+//	protected int     eo_chn0 =               4; // not configurable
 
 	public LwirReaderParameters() {
 		
@@ -104,6 +107,15 @@ public class LwirReaderParameters {
 		else if (NAME_LWIR16.equals(name)) camera_name = NAME_LWIR16;
 	}
 
+	public static boolean is_LWIR(String type) {
+		return ((type != null) && type.equals(SENSOR_TYPES[1]));
+	}
+	public static boolean is_EO(String type) {
+		return ((type != null) && type.equals(SENSOR_TYPES[1]));
+	}
+	public static String sensorName(boolean lwir) {
+		return SENSOR_TYPES[lwir?1:0];
+	}
 	
 	// --- interface methods
 	public int getAvgNumberLwir() {
@@ -126,7 +138,11 @@ public class LwirReaderParameters {
 	}
 
 	public int getEoChn0 () {
-		return eo_chn0;
+		return isLwir16() ? 16:4;// eo_chn0;
+	}
+	
+	public int getNumChannels() {
+		return 20;
 	}
 
 	public boolean is_LWIR(int width) {
@@ -134,6 +150,14 @@ public class LwirReaderParameters {
 	}
 
 	public boolean is_LWIR(ImagePlus imp){
+		// See if image has LwirReaderParameters.SENSOR_TYPE property, then use is_LWIR(String property_value),
+		// if not - use old width property
+		if (imp.getProperty("WOI_WIDTH")==null) {
+			EyesisTiff.decodeProperiesFromInfo(imp);
+		}
+		if (imp.getProperty(SENSOR_TYPE)!=null) {
+			return is_LWIR((String) imp.getProperty(SENSOR_TYPE));
+		}
 		return is_LWIR(imp.getWidth());
 	}