implementing initial orientation estimation, full window for eo

acquisition

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

@@ -2165,7 +2165,7 @@ if (MORE_BUTTONS) {
 					);
 			// set initial orientation of the cameras from the sensors that see mpst of the matching pointers
 			// just for the LMA to start
-			DISTORTION_CALIBRATION_DATA.setInitialOrientation(true);
+			DISTORTION_CALIBRATION_DATA.setInitialOrientation(PATTERN_PARAMETERS, true);
 			return;
 		}
 
@@ -5871,7 +5871,7 @@ if (MORE_BUTTONS) {
     			DISTORTION_CALIBRATION_DATA.updateSetOrientation(null); // restore orientation from (enabled) image files
     			if (DEBUG_LEVEL>0) System.out.println("Setting sets orientation from per-grid image data");
     		}
-    		if (overwriteAll) DISTORTION_CALIBRATION_DATA.setInitialOrientation(overwriteAll);  // needed here? modify?
+    		if (overwriteAll) DISTORTION_CALIBRATION_DATA.setInitialOrientation(PATTERN_PARAMETERS, overwriteAll);  // needed here? modify?
 			if ((DEBUG_LEVEL>0) && (DISTORTION_CALIBRATION_DATA.gIS!=null)){
 				System.out.println("There are now "+DISTORTION_CALIBRATION_DATA.getNumberOfEstimated(true)+ "("+DISTORTION_CALIBRATION_DATA.getNumberOfEstimated(false)+") images with estimated orientation");
 			}
@@ -6255,7 +6255,7 @@ if (MORE_BUTTONS) {
 /* ======================================================================== */
 		if       (label.equals("Get Orientation")) {
 			DEBUG_LEVEL=MASTER_DEBUG_LEVEL;
-			if (DEBUG_LEVEL>0){
+			if (DEBUG_LEVEL>10) { // 0){
 				IJ.showMessage("disabled option");
 				return;
 			}
@@ -6278,11 +6278,22 @@ if (MORE_BUTTONS) {
 				System.out.println("GONIOMETER was initialized");
 			}
 			// initialize needed classes
-			DISTORTION_CALIBRATION_DATA=new DistortionCalibrationData( // images are not setup yet
-	        		EYESIS_CAMERA_PARAMETERS, //EyesisCameraParameters eyesisCameraParameters
-	        		GONIOMETER_PARAMETERS);
+			if (DISTORTION_CALIBRATION_DATA == null ) {
+				System.out.println("Initiaslizing DISTORTION_CALIBRATION_DATA");
+				DISTORTION_CALIBRATION_DATA=new DistortionCalibrationData( // images are not setup yet
+		        		EYESIS_CAMERA_PARAMETERS, //EyesisCameraParameters eyesisCameraParameters
+		        		GONIOMETER_PARAMETERS);
+
+			} else if (DEBUG_LEVEL>1){
+				System.out.println("DISTORTION_CALIBRATION_DATA was initialized");
+			}
 			if ((LENS_DISTORTIONS!=null) && (LENS_DISTORTIONS.fittingStrategy!=null)) {
 				LENS_DISTORTIONS.fittingStrategy.distortionCalibrationData=DISTORTION_CALIBRATION_DATA;
+				if (DEBUG_LEVEL>0){
+					System.out.println("Setting LENS_DISTORTIONS.fittingStrategy.distortionCalibrationData=DISTORTION_CALIBRATION_DATA");
+				}
+			} else if (DEBUG_LEVEL>0){
+				System.out.println("Was already set: LENS_DISTORTIONS.fittingStrategy.distortionCalibrationData=DISTORTION_CALIBRATION_DATA");
 			}
 
 			if (DEBUG_LEVEL>1){
@@ -6301,9 +6312,10 @@ if (MORE_BUTTONS) {
 					IJ.showMessage("Error",msg);
 					return;
 				}
+
 				LENS_DISTORTIONS=new Distortions(LENS_DISTORTION_PARAMETERS,PATTERN_PARAMETERS,REFINE_PARAMETERS,this.SYNC_COMMAND.stopRequested);
 				if (DEBUG_LEVEL>1){
-					System.out.println("Initiaslizing Distortions class");
+					System.out.println("Initiaslizing Distortions class (LENS_DISTORTIONS)");
 				}
 			} else if (DEBUG_LEVEL>1){
 				System.out.println("LENS_DISTORTIONS was initialized");
@@ -6324,10 +6336,13 @@ if (MORE_BUTTONS) {
 				return;
 			}
 			GONIOMETER_PARAMETERS.gridGeometryFile=gridPathname;
+			if (DEBUG_LEVEL > 0){
+				System.out.println("Using pattern file: "+gridPathname);
+			}
 
 // Find curernt orientation
 			double [] currentOrientation=GONIOMETER.estimateOrientation (
-					CAMERAS.getImages(1), // last acquired images with number of pointers detected>0
+					CAMERAS.getImages(1),       // last acquired images with number of pointers detected>0
 					DISTORTION_CALIBRATION_DATA, // DistortionCalibrationData distortionCalibrationData,
 					PATTERN_PARAMETERS,          //PatternParameters patternParameters, // should not be null
 					LENS_DISTORTIONS,            //Distortions lensDistortions, // should not be null
@@ -9871,7 +9886,22 @@ if (MORE_BUTTONS) {
 
 		PATTERN_PARAMETERS.debugLevel=MASTER_DEBUG_LEVEL;
 		EYESIS_CAMERA_PARAMETERS.updateNumstations (numStations);
-		DISTORTION_CALIBRATION_DATA=new DistortionCalibrationData( // new way for LWIR - initialize form dirs
+
+// Adding class here to use for orientation estimation - will not be needed?
+		if (GONIOMETER==null) {
+			GONIOMETER= new Goniometer(
+					CAMERAS, // CalibrationHardwareInterface.CamerasInterface cameras,
+					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
+			);
+		}
+
+		DISTORTION_CALIBRATION_DATA=new DistortionCalibrationData( // new way for LWIR - initialize from dirs
 				gridFileDirs,
 				sourceStationDirs,
 				gridFilter,
@@ -9889,7 +9919,7 @@ if (MORE_BUTTONS) {
 				);
 		// set initial orientation of the cameras from the sensors that see most of the matching pointers
 		// just for the LMA to start
-		DISTORTION_CALIBRATION_DATA.setInitialOrientation(true);
+		DISTORTION_CALIBRATION_DATA.setInitialOrientation(PATTERN_PARAMETERS, true);
 		return true;
 
 

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

@@ -771,7 +771,7 @@ horizontal axis:
 			throw new IllegalArgumentException(msg);
 		}
 
-		// remove unneeded, copied from updateFocusGrid()
+		// remove unneeded, copied from updateFocusGrid() Now it is not needed?
 		SimulationPattern.SimulParameters simulParameters = modifySimulParameters();
 		MatchSimulatedPattern.DistortionParameters distortionParameters = modifyDistortionParameters();
 
@@ -1007,6 +1007,10 @@ horizontal axis:
 		};
 		return result;
 	}
+
+
+
+
     public static class GoniometerParameters {
     	public String gridGeometryFile="";
     	public String initialCalibrationFile="";

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

@@ -6818,8 +6818,11 @@ public class MatchSimulatedPattern {
 				numPointerDetected++;
 			}
 		}
-		if (numPointerDetected>0) return pointersXY;
-		else return null;
+		if (numPointerDetected>0) {
+			return pointersXY;
+		}	else {
+			return null;
+		}
 	}
 
 	public static void setPointersXYUV(ImagePlus imp, double [][] pointersXYUV){

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

@@ -739,6 +739,7 @@ import ij.io.Opener;
 			int [] iUV={u1-this.U0, v1-this.V0};
 			return iUV;
 		}
+
 		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;
@@ -761,6 +762,31 @@ import ij.io.Opener;
 			return result;
 //			return this.gridGeometry[v1][u1];
 		}
+		public double[] getXYZ(
+				double [] uv,
+				boolean verbose,
+				int station){ // u=0,v=0 - center!
+			int iu = (int) Math.floor(uv[0]);
+			int iv = (int) Math.floor(uv[1]);
+			double fu = uv[0] - iu;
+			double fv = uv[1] - iv;
+			double [][] corn = new double [4][];
+			corn[0] = getXYZM(iu,     iv,     verbose, station);
+			corn[1] = getXYZM(iu + 1, iv,     verbose, station);
+			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)) {
+				System.out.println("Optical axis outside of te grid: TODO: modify getXYZM() to handle!");
+				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];
+			rslt_xyz[1] = (1-fu) * (1-fv) * corn[0][1] + fu * (1-fv) * corn[1][1] + (1-fu) * fv * corn[2][1] + fu * fv * corn[3][1];
+			rslt_xyz[2] = (1-fu) * (1-fv) * corn[0][2] + fu * (1-fv) * corn[1][2] + (1-fu) * fv * corn[2][2] + fu * fv * corn[3][2];
+			return rslt_xyz;
+		}
+
+
 		public int getGridIndex(int u, int v){ // u=0,v=0 - center!
 			int u1=u+this.U0;
 			int v1=v+this.V0;

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

@@ -77,7 +77,7 @@ public class LwirReader {
 	public static final int MAX_THREADS = 100; // combine from all classes?
 
 	public static final int FRAMES_AHEAD = 5;
-	
+
 	/** Logger for this class. */
 	private static final Logger LOGGER =
 			LoggerFactory.getLogger(LwirReader.class);
@@ -568,7 +568,7 @@ public class LwirReader {
    				fs.saveAsTiff(path);
 			}
 		}
-		
+
 		if (lrp.isShowImages()) {
 			if (imps_avg != null) {
 				for (ImagePlus imp: imps_avg) {
@@ -665,8 +665,13 @@ public class LwirReader {
 	   					"&TRIG_BITLENGTH=31*0"+
 	   					"&EXTERN_TIMESTAMP=1*0";
 	   		}
-
-
+	   		if (lrp.eo_full_window) {
+	   			urls[num_lwir+chn] +=
+	   					"&WOI_LEFT=0"+
+	   					"&WOI_TOP=0"+
+	   					"&WOI_WIDTH=2592"+
+	   					"&WOI_HEIGHT=1936";
+	   		}
 		}
 		for (int i = 0; i < urls.length; i++) {
 				LOGGER.debug("programLWIRCamera(): reading url " + urls[i]);

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

@@ -3378,15 +3378,52 @@ public class QuadCLT {
 						  }
 						  ///						  float [] pixels=(float []) imp_srcs[srcChannel].getProcessor().getPixels();
 
+						  float [] vign_pixels = eyesisCorrections.channelVignettingCorrection[srcChannel];
+						  if (pixels.length!=vign_pixels.length){
+//							  System.out.println("Vignetting data for channel "+srcChannel+" has "+vign_pixels.length+" pixels, image "+sourceFiles[nFile]+" has "+pixels.length);
+							  int woi_width =  Integer.parseInt((String) imp_srcs[srcChannel].getProperty("WOI_WIDTH"));
+							  int woi_height = Integer.parseInt((String) imp_srcs[srcChannel].getProperty("WOI_HEIGHT"));
+							  int woi_top =  Integer.parseInt((String) imp_srcs[srcChannel].getProperty("WOI_TOP"));
+							  int woi_left =  Integer.parseInt((String) imp_srcs[srcChannel].getProperty("WOI_LEFT"));
+							  int vign_width =  eyesisCorrections.pixelMapping.sensors[srcChannel].pixelCorrectionWidth;
+							  int vign_height = eyesisCorrections.pixelMapping.sensors[srcChannel].pixelCorrectionHeight;
+
+							  if (pixels.length != woi_width * woi_height){
+								  System.out.println("Vignetting data for channel "+srcChannel+" has "+vign_pixels.length+" pixels, < "+
+										  sourceFiles[nFile]+" has "+pixels.length);
+								  woi_width = width;
+								  woi_height = height;
+							  }
+							  if (vign_width < (woi_left + woi_width)) {
+								  System.out.println("Vignetting data for channel "+srcChannel+
+										  " has width + left ("+(woi_left+woi_width)+") > vign_width ("+vign_width+")");
+								  return null;
+							  }
+							  if (vign_height < (woi_top + woi_height)) {
+								  System.out.println("Vignetting data for channel "+srcChannel+
+										  " has height + top ("+(woi_top+woi_height)+") > vign_height ("+vign_width+")");
+								  return null;
+							  }
+							  if (pixels.length != woi_width * woi_height){
+								  System.out.println("Vignetting data for channel "+srcChannel+" has "+vign_pixels.length+" pixels, < "+
+										  sourceFiles[nFile]+" has "+pixels.length);
+								  return null;
+							  }
+							  vign_pixels = new float[woi_width * woi_height];
+							  for (int row = 0; row < woi_height; row++) {
+								  System.arraycopy(
+										  eyesisCorrections.channelVignettingCorrection[srcChannel], // src
+										  (woi_top + row) * vign_width + woi_left, // srcPos,
+										  vign_pixels,                             // dest,
+										  row * woi_width,                         // destPos,
+										  woi_width);                              // length);
+							  }
 
-						  if (pixels.length!=eyesisCorrections.channelVignettingCorrection[srcChannel].length){
-							  System.out.println("Vignetting data for channel "+srcChannel+" has "+eyesisCorrections.channelVignettingCorrection[srcChannel].length+" pixels, image "+sourceFiles[nFile]+" has "+pixels.length);
-							  return null; // not used in lwir
 						  }
 						  // TODO: Move to do it once:
 						  double min_non_zero = 0.0;
 						  for (int i=0;i<pixels.length;i++){
-							  double d = eyesisCorrections.channelVignettingCorrection[srcChannel][i];
+							  double d = vign_pixels[i];
 							  if ((d > 0.0) && ((min_non_zero == 0) || (min_non_zero > d))){
 								  min_non_zero = d;
 							  }
@@ -3395,7 +3432,7 @@ public class QuadCLT {
 
 						  System.out.println("Vignetting data: channel="+srcChannel+", min = "+min_non_zero);
 						  for (int i=0;i<pixels.length;i++){
-							  double d = eyesisCorrections.channelVignettingCorrection[srcChannel][i];
+							  double d = vign_pixels[i];
 							  if (d > max_vign_corr) d = max_vign_corr;
 							  pixels[i]*=d;
 						  }