Fixing old bug where sample coordinates did not match measured lens

center

src/main/java/Distortions.java

@@ -12398,7 +12398,7 @@ Which parameters affect which matrices
         public int getGoniometerHorizontalIndex(){return 6;}
         public int getGoniometerAxialIndex(){return 7;}
         public int getSensorWidth() { return this.sensorWidth;}
-        public int getSensorHeight() { return this.sensorWidth;}
+        public int getSensorHeight() { return this.sensorHeight;}
         public int getSensorWidth(int subCam) { return this.sensorWidth;} // for the future? different sensors
         public int getSensorHeight(int subCam) { return this.sensorHeight;}// for the future? different sensors
         public double getPixelSize(int subCamNumber){return  this.eyesisSubCameras[0][subCamNumber].pixelSize;} // use station 0's pixel size
@@ -13952,6 +13952,33 @@ Which parameters affect which matrices
 			this.flipVertical=flipVertical;
 			recalcCommons();
 		}
+		public void setIntrincicFromSubcamera(EyesisSubCameraParameters pars){
+			setLensDistortionParameters(
+					pars.focalLength,
+					pars.pixelSize,  //um
+					pars.distortionRadius, // mm
+					pars.distortionA8, // r^7
+					pars.distortionA7, // r^6
+					pars.distortionA6, // r^5
+					pars.distortionA5, // r^4
+					pars.distortionA,  // r^4
+					pars.distortionB,  // r^3
+					pars.distortionC,  // r^2
+					// orientation/position parameters
+					this.yaw,          // (keep) angle in degrees from perpendicular to the pattern, 0 - towards wall, positive - clockwise from top
+					this.pitch,        // (keep) angle in degrees from perpendicular to the pattern, 0 - towards wall, positive - up
+					this.roll,         // (keep) angle in degrees rotation around camera optical axis (perpendicular to pattern if yaw==0, pitch==0), positive - clockwise
+					this.x0,           // (keep) lens axis from pattern center, mm (to the right)
+					this.y0,           // (keep) lens axis from pattern center, mm (down)
+					this.z0,           // (keep) lens axis from pattern center, mm (away)
+					this.distance,     // (keep) distance from the lens input pupil to the pattern plane along the camera axis, mm
+					pars.px0,          //        center of the lens on the sensor, pixels
+					pars.py0,          // center of the lens on the sensor, pixels
+					this.flipVertical  // (keep)  acquired image is mirrored vertically (mirror used)
+			);
+		}
+		
+		
 		public void setLensDistortionParameters(LensDistortionParameters ldp
 		){
 			this.focalLength=ldp.focalLength;

src/main/java/FocusingField.java

@@ -765,6 +765,9 @@ public double [][] flattenSampleCoord(){
     for (int i=0;i<sampleCoord.length;i++) for (int j=0;j<sampleCoord[0].length;j++) flatSampleCoord[index++]= sampleCoord[i][j];
     return flatSampleCoord; // last dimension is not cloned
 }
+public double [][][] getSampleCoord(){
+	return this.sampleCoord;
+}
 public class MeasuredSample{
     public int [] motors = new int[3];
     public String timestamp;
@@ -2890,23 +2893,31 @@ public void stepLevenbergMarquardtAction(int debugLevel){//
 
 /**
 * Dialog to select Levenberg-Marquardt algorithm and related parameters
+* @param autoSel - disable default stop, suggest strategy 0
 * @return true if OK, false if canceled
+* 
 */
-public boolean selectLMAParameters(){
+public boolean selectLMAParameters(boolean autoSel){
 //     int numSeries=fittingStrategy.getNumSeries();
 //    boolean resetCorrections=false;
      GenericDialog gd = new GenericDialog("Levenberg-Marquardt algorithm parameters lens aberrations approxiamtion");
      
      //TODO: change to selection using series comments
 //     	gd.addNumericField("Fitting series number", this.currentStrategyStep, 0, 3," (-1 - current)");
+     int suggestStep=this.currentStrategyStep;
+     boolean suggestStopEachStep=this.stopEachStep;
+     	if (autoSel){
+     		suggestStep=0;
+     		suggestStopEachStep=false;
+     	}
     	FieldStrategies fs=fieldFitting.fieldStrategies;
         String [] indices=new String[fs.getNumStrategies()+1];
         indices[0]="current strategy";
         for (int i=0;i<fs.getNumStrategies();i++) {
         	indices[i+1]=i+": "+fs.getComment(i)+" ("+(fs.isStopAfterThis(i)?"STOP":"CONTINUE")+")";
         }
-        if (this.currentStrategyStep>=(indices.length-1)) this.currentStrategyStep=indices.length-2;
-        gd.addChoice("Fitting series", indices,indices[this.currentStrategyStep+1]);
+        if (suggestStep>=(indices.length-1)) suggestStep=indices.length-2; // last one
+        gd.addChoice("Fitting series", indices,indices[suggestStep+1]);
      	
         gd.addCheckbox("Debug df/dX0, df/dY0", false);
         gd.addNumericField("Debug Jacobian for point number", this.debugPoint, 0, 5,"(-1 - none)");
@@ -2920,7 +2931,7 @@ public boolean selectLMAParameters(){
         gd.addNumericField("Threshold lambda to fail", this.maxLambda, 5);
         gd.addNumericField("Maximal number of iterations", this.numIterations, 0);
 
-        gd.addCheckbox("Dialog after each iteration step", this.stopEachStep);
+        gd.addCheckbox("Dialog after each iteration step", suggestStopEachStep); //this.stopEachStep);
         gd.addCheckbox("Dialog after each iteration series", this.stopEachSeries);
         gd.addCheckbox("Dialog after each failure", this.stopOnFailure);
         gd.addCheckbox("Show modified parameters", this.showParams);
@@ -3995,12 +4006,13 @@ public void calculateGoodSamples(){
 public boolean LevenbergMarquardt(
 		FocusingFieldMeasurement measurement, // null in calibrate mode
 		boolean openDialog,
+		boolean autoSel,
 //		boolean filterZ, // for adjust mode
 		int debugLevel){
 	boolean calibrate=measurement==null;
 	double savedLambda=this.lambda;
 	this.debugLevel=debugLevel;
-	if (openDialog && !selectLMAParameters()) return false;
+	if (openDialog && !selectLMAParameters(autoSel)) return false;
 	this.startTime=System.nanoTime();
 	// create savedVector (it depends on parameter masks), restore from it if aborted
 //	fieldFitting.initSampleCorrVector(
@@ -5000,6 +5012,7 @@ public boolean LevenbergMarquardt(
     		boolean OK=LevenbergMarquardt(
     				measurement, 
     				false, // true, // open dialog
+    				true,// boolean autoSel,
     				debugLevel);
     		if (!OK){
         		if (debugLevel>1) System.out.println("testMeasurement() failed: LMA failed");
@@ -8675,7 +8688,7 @@ f_corr: d_fcorr/d_zcorr=0, other: a, reff, kx ->  ar[1], ar[2], ar[3],  ar[4]
     		System.out.println("qualBOptimize LMA failed");
     	}
 //    	zTxTy[0]-=best_qb_corr[0]; - absolute, no need to calculate best_qb_corr;
-    	this.qualBOptimizationResults=zTxTy;
+    	this.qualBOptimizationResults=zTxTy.clone();
     	return zTxTy;
     }
     

src/main/java/LensAdjustment.java

@@ -297,13 +297,13 @@ public class LensAdjustment {
         public double motorsPreSigma=3584.0; // when fitting parabola for focusing sharpness in the center, far measurements decay with this sigma
         public double maxLinearStep= 3584.0; // If there are insufficient measurements to fit parabola - make this step
         
-        public int scanStep=200;             // motor step (all 3 motors) in scan focus mode (signed value)
+        public int scanStep=320; // 200;             // motor step (all 3 motors) in scan focus mode (signed value)
         public int scanNumber=50;            // number of scanStep steps to run
-        public int scanNumberNegative=15;    // number of scanStep steps negative from the start 
-        public boolean scanHysteresis=true;  // scan both ways
+        public int scanNumberNegative=20; // 15;    // number of scanStep steps negative from the start 
+        public boolean scanHysteresis=false; // true;  // scan both ways
         public int scanHysteresisNumber=5;   // number of test points for the Hysteresis measurement
         
-        public boolean scanTiltEnable=true;  // enable scanning tilt
+        public boolean scanTiltEnable=false; //true;  // enable scanning tilt
         public boolean scanTiltReverse=false;  // enable scanning tilt in both directions
         public boolean scanMeasureLast=false;  // Calculate PSF after last move (to original position)
         public int scanTiltRangeX=14336;    // 4 periods