Grid matching for secondary (LWIR) sensors

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

@@ -1520,9 +1520,10 @@ I* - special case when the subcamera is being adjusted/replaced. How to deal wit
     		for (;(endIndex<enabled.length) && !allImages && !enabled[endIndex];endIndex++); // advance over disabled images
     		GenericDialog gd=new GenericDialog("Select images "+startIndex+"..."+(endIndex-1));
     		for (int i=startIndex;i<endIndex;i++) if (allImages || enabled[i]){
-				gd.addCheckbox    (i+" - "+(this.distortionCalibrationData.gIP[i].enabled?"":"(disabled) ")+
+				gd.addCheckbox    (i+ " ("+this.distortionCalibrationData.gIP[i].getSetNumber()+
+						"."+this.distortionCalibrationData.gIP[i].getChannel()+")"+
+    		            " - "+(this.distortionCalibrationData.gIP[i].enabled?"":"(disabled) ")+
 						IJ.d2s(this.distortionCalibrationData.gIP[i].timestamp,6)+
-						": "+this.distortionCalibrationData.gIP[i].channel+
 						" matched "+this.distortionCalibrationData.gIP[i].matchedPointers+" pointers"+
 						", hinted state: "+((hintedMatch[i]<0)?"undefined":((hintedMatch[i]==0)?"failed":((hintedMatch[i]==1)?"orientation":"orientation and translation"))),
 						selection[i]);
@@ -1852,7 +1853,7 @@ I* - special case when the subcamera is being adjusted/replaced. How to deal wit
 //			gd.addCheckbox("Select images with estimated orientation", selectEstimated);
 //			gd.addCheckbox("Select new enabled images", selectNewEnabled);
 			if (this.distortionCalibrationData.hasSmallSensors()) {
-				gd.addMessage("=== Filter selection by High/Low resolution sensors (such as VNIR/LWIR)");
+				gd.addMessage("=== Filter selection by High/Low resolution sensors (such as EO/LWIR)");
 				gd.addCheckbox("Select high-res sensors", true);
 				gd.addCheckbox("Select low-res sensors", true);
 			}
@@ -1977,7 +1978,7 @@ I* - special case when the subcamera is being adjusted/replaced. How to deal wit
    	 * @param useParameters Select parameters for this series
    	 * @param askNextSeries Ask for next series number
    	 * @param zeroAndOther use 2 channels 0 and "other", propagate settings for channel 1 to all the rest
-   	 * For low/high res (LWIR/VNIR) - use first /other for each class
+   	 * For low/high res (LWIR/EO) - use first /other for each class
    	 * @return -2 - cancel, -1, done, otherwise - number of step to edit
    	 */
 
@@ -2055,7 +2056,7 @@ I* - special case when the subcamera is being adjusted/replaced. How to deal wit
 				// sub(other):    their group number - no, 0 - later add this.definedModesAll.length to master subcamera
 				// not zeroAndOther:
 				// non-sub - -1:
-				// sub(>0): subCam-1 (previous index) - will suggest any with smaller index - may be useless with lwir < vnir indices
+				// sub(>0): subCam-1 (previous index) - will suggest any with smaller index - may be useless with lwir < eo indices
 //				int subMaxNum = (this.distortionCalibrationData.isSubcameraParameter(parIndex) && (subCam > 0)) ? (zeroAndOther? 0 : (subCam-1)):-1;
 				int subMaxNum = -1;
 				if (this.distortionCalibrationData.isSubcameraParameter(parIndex)) { // only for subcamera parameters
@@ -2120,7 +2121,7 @@ I* - special case when the subcamera is being adjusted/replaced. How to deal wit
     	 * @param useParameters Select parameters for this series
     	 * @param askNextSeries Ask for next series number
     	 * @param zeroAndOther use 2 channels 0 and "other", propagate settings for channel 1 to all the rest
-    	 * Updated for more groups (up to 4 in LWIR/VNIR) - use 1 channel for each group, propagate to the rest of the group
+    	 * Updated for more groups (up to 4 in LWIR/EO) - use 1 channel for each group, propagate to the rest of the group
     	 * @return -2 - cancel, -1, done, otherwise - number of step to edit
     	 */
     	public int selectStrategyStep(
@@ -2187,7 +2188,7 @@ I* - special case when the subcamera is being adjusted/replaced. How to deal wit
 				for (int i=0;i<this.distortionCalibrationData.eyesisCameraParameters.numStations;i++) 	gd.addCheckbox("Station "+i, constrainByStation[i]);
 			}
 			if (this.distortionCalibrationData.hasSmallSensors()) {
-				gd.addMessage("Constrain (select/remove all) by High/Low resolution sensors (such as VNIR/LWIR)");
+				gd.addMessage("Constrain (select/remove all) by High/Low resolution sensors (such as EO/LWIR)");
 				gd.addCheckbox("Select high-res sensors", true);
 				gd.addCheckbox("Select low-res sensors", true);
 			}
@@ -2272,7 +2273,7 @@ I* - special case when the subcamera is being adjusted/replaced. How to deal wit
 					// sub(other):    their group number - no, 0
 					// not zeroAndOther:
 					// non-sub - -1:
-					// sub(>0): subCam-1 (previous index) - will suggest any with smaller index - may be useless with lwir < vnir indices
+					// sub(>0): subCam-1 (previous index) - will suggest any with smaller index - may be useless with lwir < eo indices
 //					int subMaxNum = (this.distortionCalibrationData.isSubcameraParameter(parIndex) && (subCam > 0)) ? (zeroAndOther? 0 : (subCam-1)):-1;
 					int subMaxNum = -1;
 					if (this.distortionCalibrationData.isSubcameraParameter(parIndex)) { // only for subcamera parameters

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

@@ -989,7 +989,9 @@ horizontal axis:
 		// TODO: Set initial values for the goniometer angles from the sensor
 		// (channel) number, average them if there are several in the list
 
-		lensDistortions.LevenbergMarquardt(false); // skip dialog
+		lensDistortions.LevenbergMarquardt(
+				false, // skip dialog
+				false); // new: dry_run use it here?
 		if (debug_level > 0)
 			System.out.println("Finished LMA at "
 					+ IJ.d2s(0.000000001 * (System.nanoTime() - startTime), 3));

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

@@ -5,9 +5,9 @@ import java.util.Properties;
 import com.elphel.imagej.cameras.EyesisSubCameraParameters;
 import com.elphel.imagej.common.WindowTools;
 
+import Jama.Matrix;
 import ij.IJ;
 import ij.gui.GenericDialog;
-import Jama.Matrix;
 
 //import EyesisCameraParameters;
 //import Distortions.EyesisSubCameraParameters;
@@ -97,24 +97,25 @@ import Jama.Matrix;
 			}
 		}
 	    public LensDistortionParameters(
-//	    		LensDistortionParameters lensDistortionParameters,
 	    		boolean isTripod,
 	    		boolean cartesian,
+	    		double  pixelSize,
+	    		double  distortionRadius,
 	            double [][] interParameterDerivatives, //partial derivative matrix from subcamera-camera-goniometer to single camera (12x21) if null - just values, no derivatives
 	    		double [] parVect,
 	    		boolean [] mask, // calculate only selected derivatives (all parVect values are still
 	    		int debugLevel
-//	    		boolean calculateDerivatives // calculate this.interParameterDerivatives -derivatives array (false - just this.values)
 	    		){
 	    	this.debugLevel=debugLevel;
 	    	lensCalcInterParamers( // changed name to move calcInterParamers method from enclosing class
 	    			this,
 		    		isTripod,
 		    		cartesian,
+		    		pixelSize,
+		    		distortionRadius,
 		            interParameterDerivatives, //partial derivative matrix from subcamera-camera-goniometer to single camera (12x21) if null - just values, no derivatives
 		    		parVect,
 		    		mask // calculate only selected derivatives (all parVect values are still
-//		    		boolean calculateDerivatives // calculate this.interParameterDerivatives -derivatives array (false - just this.values)
 		    		);
 	    }
 
@@ -197,6 +198,7 @@ import Jama.Matrix;
 			null   // r_od,
 			);
 		}
+		@Override
 		public LensDistortionParameters clone() {
 			return new LensDistortionParameters(
 					this.focalLength,
@@ -1861,6 +1863,8 @@ dPXmmc/dphi=
 	    		LensDistortionParameters lensDistortionParameters,
 	    		boolean isTripod,
 	    		boolean cartesian,
+	    		double  pixelSize,
+	    		double  distortionRadius,
 	            double [][] interParameterDerivatives, //partial derivative matrix from subcamera-camera-goniometer to single camera (12x21) if null - just values, no derivatives
 	    		double [] parVect,
 	    		boolean [] mask // calculate only selected derivatives (all parVect values are still
@@ -2056,6 +2060,10 @@ dPXmmc/dphi=
 //				System.out.println("interParameterDerivatives[0]="+sprintfArray(interParameterDerivatives[0]));
 			}
 	        double [] extrinsicParams=parametersFromMAMB(MA,MB); // all after 6 are 0;
+
+	        lensDistortionParameters.pixelSize =        pixelSize;
+	        lensDistortionParameters.distortionRadius = distortionRadius;
+
 	        lensDistortionParameters.distance=extrinsicParams[2];
 	        lensDistortionParameters.x0=extrinsicParams[0];
 	        lensDistortionParameters.y0=extrinsicParams[1];
@@ -2087,21 +2095,8 @@ dPXmmc/dphi=
 				lensDistortionParameters.r_od[i][0]=parVect[index++];
 				lensDistortionParameters.r_od[i][1]=parVect[index++];
 			}
-			/*
-			for (double [] row :lensDistortionParameters.r_xy){
-				row[0]=parVect[index++];
-				row[1]=parVect[index++];
-			}
-			for (double [] row :lensDistortionParameters.r_od){
-				row[0]=parVect[index++];
-				row[1]=parVect[index++];
-			}
-			*/
-///
-//			public double [][] r_xy=null; // only 6, as for the first term delta x, delta y ==0  
-//			public double [][] r_od=null; // ortho
 
-			lensDistortionParameters.recalcCommons(); // uncliding lensDistortionParameters.r_xyod
+			lensDistortionParameters.recalcCommons(); // uncluding lensDistortionParameters.r_xyod
 
 
 	        if (this.debugLevel>2){
@@ -2816,4 +2811,3 @@ dPXmmc/dphi=
 		public int getNumInputs(){return numInputs;}
 		public int getNumOutputs(){return numOutputs;}
 	}
- 
\ No newline at end of file

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

@@ -5476,7 +5476,7 @@ public class EyesisCorrectionParameters {
   			gd.addMessage     ("Unity up vector in camera coordinate system (x - right, y - up, z - to camera): {"+
   			this.vertical_xyz[0]+","+this.vertical_xyz[1]+","+this.vertical_xyz[2]+"}");
 
-  			gd.addTab         ("LWIR", "parameters for LWIR/VNIR 8-camera rig");
+  			gd.addTab         ("LWIR", "parameters for LWIR/EO 8-camera rig");
   			this.lwir.dialogQuestions(gd);
 
 //  			gd.buildDialog();

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

@@ -362,4 +362,12 @@ import java.util.Properties;
     		updateCartesian();
     		this.cartesian = cartesian;
     	}
+
+    	public double getPixelSize() {
+    		return this.pixelSize;
+    	}
+    	public double getDistortionRadius() {
+    		return this.distortionRadius;
+    	}
+
     }

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

@@ -496,12 +496,12 @@ public class LwirReader {
 		if (lrp.lwir_ffc) {
 			calibrate(lrp); // seems to work. test calibration duration and if any images are sent during calibration
 		}
-		int num_frames = lrp.avg_number + lrp.vnir_lag + 2 * lrp.max_frame_diff;
+		int num_frames = lrp.avg_number + lrp.eo_lag + 2 * lrp.max_frame_diff;
 		ImagePlus [][] imps = readAllMultiple(
 				num_frames,
 //				lrp.lwir_telemetry,
 				false, // final boolean show,
-				lrp.vnir_scale);
+				lrp.eo_scale);
 		if (imps == null) {
 			LOGGER.error("acquire(): failed to acquire images");
 			return null;
@@ -521,9 +521,9 @@ public class LwirReader {
 			LOGGER.warn(String.format("LWIR channel %d time from FFC: %.3f", chn, after_ffc[chn]));
 		}
 
-		int [] lags = new int [lrp.lwir_channels.length + lrp.vnir_channels.length];
+		int [] lags = new int [lrp.lwir_channels.length + lrp.eo_channels.length];
 		for (int i = 0; i < lags.length; i++) {
-			lags[i] = (i >= lrp.lwir_channels.length) ? lrp.vnir_lag : 0;
+			lags[i] = (i >= lrp.lwir_channels.length) ? lrp.eo_lag : 0;
 		}
 		ImagePlus [][] imps_sync =  matchSets(
 				imps,
@@ -605,10 +605,10 @@ public class LwirReader {
 
 	public boolean programLWIRCamera(LwirReaderParameters lrp) {
 		int lwir_master_port = 0;
-		int vnir_master_port = 0;
+		int eo_master_port = 0;
 		int num_lwir = lrp.lwir_channels.length;
-		int num_vnir = lrp.vnir_channels.length;
-		final String [] urls = new String [num_lwir + num_vnir];
+		int num_eo = lrp.eo_channels.length;
+		final String [] urls = new String [num_lwir + num_eo];
 		for (int chn:lrp.lwir_channels) {
 			urls[chn] = "http://"+lrp.lwir_ip+"/parsedit.php?immediate&sensor_port="+chn+
 					"&BITS=16"+
@@ -623,21 +623,21 @@ public class LwirReader {
 						"&XMIT_TIMESTAMP=1*0";
 			}
 		}
-		for (int chn:lrp.vnir_channels) {
+		for (int chn:lrp.eo_channels) {
 	   		int minExposure=10; // usec
 	   		int maxExposure=1000000; //usec
 	   		int minGain=(int) (0x10000*1.0);
 	   		int maxGain=(int) (0x10000*15.75);
 	   		int minScale=0;
 	   		int maxScale=(int) (0x10000*4.0);
-	   		int exposure= (int) (Math.round(1000*lrp.vnir_exposure_ms * lrp.vnir_exp_corr[chn]));
-	   		int autoExposureMax= (int) (Math.round(1000*lrp.vnir_max_autoexp_ms));
-	   		int gain=     (int) (Math.round(0x10000*lrp.vnir_gain_g));
-	   		int rScale=   (int) (Math.round(0x10000*lrp.vnir_gain_rg*lrp.vnir_gcorr_rbgb[3*chn+0]));
-	   		int bScale=   (int) (Math.round(0x10000*lrp.vnir_gain_bg*lrp.vnir_gcorr_rbgb[3*chn+1]));
-	   		int gScale=   (int) (Math.round(0x10000*                 lrp.vnir_gcorr_rbgb[3*chn+2]));
-	   		int autoExp=  lrp.vnir_autoexp?1:0;
-	   		int autoWB=   lrp.vnir_whitebal?1:0;
+	   		int exposure= (int) (Math.round(1000*lrp.eo_exposure_ms * lrp.eo_exp_corr[chn]));
+	   		int autoExposureMax= (int) (Math.round(1000*lrp.eo_max_autoexp_ms));
+	   		int gain=     (int) (Math.round(0x10000*lrp.eo_gain_g));
+	   		int rScale=   (int) (Math.round(0x10000*lrp.eo_gain_rg*lrp.eo_gcorr_rbgb[3*chn+0]));
+	   		int bScale=   (int) (Math.round(0x10000*lrp.eo_gain_bg*lrp.eo_gcorr_rbgb[3*chn+1]));
+	   		int gScale=   (int) (Math.round(0x10000*                 lrp.eo_gcorr_rbgb[3*chn+2]));
+	   		int autoExp=  lrp.eo_autoexp?1:0;
+	   		int autoWB=   lrp.eo_whitebal?1:0;
 	   		if (exposure<minExposure) exposure=minExposure; else if (exposure>maxExposure) exposure=maxExposure;
 	   		if (autoExposureMax<minExposure) autoExposureMax=minExposure; else if (autoExposureMax>maxExposure) autoExposureMax=maxExposure;
 	   		if (gain<minGain) gain= minGain ; else if (gain> maxGain) gain= maxGain;
@@ -645,9 +645,9 @@ public class LwirReader {
 	   		if (bScale<minScale) bScale= minScale ; else if (bScale> maxScale) bScale= maxScale;
 	   		if (gScale<minScale) gScale= minScale ; else if (gScale> maxScale) gScale= maxScale;
 
-	   		urls[num_lwir+chn] = "http://"+lrp.vnir_ip+"/parsedit.php?immediate&sensor_port="+chn+
+	   		urls[num_lwir+chn] = "http://"+lrp.eo_ip+"/parsedit.php?immediate&sensor_port="+chn+
 	   				"&COLOR="+COLOR_JP4+ // "*1"+ // JP4 always
-	   				"&QUALITY="+lrp.vnir_quality+ // "*0"+
+	   				"&QUALITY="+lrp.eo_quality+ // "*0"+
 	   				"&EXPOS="+exposure+ // "*0"+
 		   			"&AUTOEXP_EXP_MAX="+autoExposureMax+//"*0"+
 		   			"&AUTOEXP_ON="+autoExp+//"*0"+
@@ -659,7 +659,7 @@ public class LwirReader {
 	   				"&DAEMON_EN_TEMPERATURE=1";//"*0";
 
 
-	   		if (chn == vnir_master_port) {
+	   		if (chn == eo_master_port) {
 	   			urls[num_lwir+chn] += "&TRIG=4*0"+
 	   					"&TRIG_CONDITION=611669*0"+ // external input
 	   					"&TRIG_BITLENGTH=31*0"+