Commit 4587ba94 authored by Andrey Filippov's avatar Andrey Filippov
Browse files

fixing re-calibrate set with interAxisAngle

parent e54061b3

src/main/java/Aberration_Calibration.java

+22 −4
Original line number Diff line number Diff line
@@ -6281,6 +6281,7 @@ if (MORE_BUTTONS) { 
    		}

    		double tiltCenter=LENS_DISTORTIONS.fittingStrategy.distortionCalibrationData.gIS[imageSetNumber].goniometerTilt;

    		double axialCenter=LENS_DISTORTIONS.fittingStrategy.distortionCalibrationData.gIS[imageSetNumber].goniometerAxial;

    		double interCenter=LENS_DISTORTIONS.fittingStrategy.distortionCalibrationData.gIS[imageSetNumber].interAxisAngle;

    		int tiltNumSteps=1;

    		int axialNumSteps=21;

    		double tiltStep=0.25;
@@ -6296,6 +6297,7 @@ if (MORE_BUTTONS) { 
    		gd.addCheckbox("Ignore laser pointers", ignoreLaserPointers);

    		gd.addNumericField("Image set tilt", tiltCenter, 2,6,"degrees");

    		gd.addNumericField("Image set axial", axialCenter, 2,6,"degrees");

    		gd.addNumericField("Image set inter-axis", interCenter, 2,6,"degrees");

    		gd.addNumericField("Tilt number of steps", tiltNumSteps, 0,3,"");

    		gd.addNumericField("Axial number of steps", axialNumSteps, 0,3,"");

    		gd.addNumericField("Tilt scan step", tiltStep, 2,5,"degrees");
@@ -6308,6 +6310,7 @@ if (MORE_BUTTONS) { 
    		ignoreLaserPointers=      gd.getNextBoolean();

    		tiltCenter=               gd.getNextNumber();

    		axialCenter=              gd.getNextNumber();

    		interCenter=              gd.getNextNumber();

    		tiltNumSteps=       (int) gd.getNextNumber();

    		axialNumSteps=      (int) gd.getNextNumber();

    		tiltStep=                 gd.getNextNumber();
@@ -6318,13 +6321,18 @@ if (MORE_BUTTONS) { 
    		double [] initialAxial=   new double [axialNumSteps];

    		double [][] finalTilt =   new double [tiltNumSteps][axialNumSteps];

    		double [][] finalAxial=   new double [tiltNumSteps][axialNumSteps];

    		double [][] finalInter=   new double [tiltNumSteps][axialNumSteps];

    		double [][] finalError=   new double [tiltNumSteps][axialNumSteps];

    		for (int tiltIndex=0; tiltIndex<tiltNumSteps;tiltIndex++) initialTilt[tiltIndex]=tiltCenter+tiltStep*(tiltIndex-0.5*(tiltNumSteps-1));

    		for (int axialIndex=0;axialIndex<axialNumSteps;axialIndex++) initialAxial[axialIndex]=axialCenter+axialStep*(axialIndex-0.5*(axialNumSteps-1));

    		for (int tiltIndex=0; tiltIndex<tiltNumSteps;tiltIndex++) for (int axialIndex=0;axialIndex<axialNumSteps;axialIndex++) { 

    			LENS_DISTORTIONS.fittingStrategy.distortionCalibrationData.gIS[imageSetNumber].goniometerTilt=initialTilt[tiltIndex];

    			LENS_DISTORTIONS.fittingStrategy.distortionCalibrationData.gIS[imageSetNumber].goniometerAxial=initialAxial[axialIndex];

    			if (DEBUG_LEVEL>0) System.out.println("Image Set #"+imageSetNumber+" Initial tilt="+initialTilt[tiltIndex]+" Initial axial="+initialAxial[axialIndex]);

    			LENS_DISTORTIONS.fittingStrategy.distortionCalibrationData.gIS[imageSetNumber].interAxisAngle=interCenter; // no scanning, just use center value

    			

    			if (DEBUG_LEVEL>0) System.out.println("Image Set #"+imageSetNumber+

    												  " Initial tilt="+initialTilt[tiltIndex]+

    												  " Initial inter="+interCenter);

    			int [][] imageSets=LENS_DISTORTIONS.fittingStrategy.distortionCalibrationData.listImages(!processAllImages);

    			int [] imageSet=imageSets[imageSetNumber];

    			if (imageSet==null){
@@ -6368,10 +6376,12 @@ if (MORE_BUTTONS) { 
				if (LMA_OK) {

					finalTilt[tiltIndex][axialIndex]=LENS_DISTORTIONS.fittingStrategy.distortionCalibrationData.gIS[imageSetNumber].goniometerTilt;

					finalAxial[tiltIndex][axialIndex]=LENS_DISTORTIONS.fittingStrategy.distortionCalibrationData.gIS[imageSetNumber].goniometerAxial;

					finalInter[tiltIndex][axialIndex]=LENS_DISTORTIONS.fittingStrategy.distortionCalibrationData.gIS[imageSetNumber].interAxisAngle;

					finalError[tiltIndex][axialIndex]=LENS_DISTORTIONS.currentRMS;

				} else {

					finalTilt[tiltIndex][axialIndex]=initialTilt[tiltIndex];

					finalAxial[tiltIndex][axialIndex]=initialAxial[axialIndex];

					finalInter[tiltIndex][axialIndex]=interCenter;

					finalError[tiltIndex][axialIndex]=Double.NaN;

					if (DEBUG_LEVEL>0) System.out.println("----------------- LMA FAILED -------------------------");

				}
@@ -6388,12 +6398,19 @@ if (MORE_BUTTONS) { 
    		} 

			if (DEBUG_LEVEL>0) System.out.println("================ Image Set #"+imageSetNumber+" rms="+IJ.d2s(bestRMS, 6)+

					" final tilt="+finalTilt[bestTiltIndex][bestAxialIndex]+" ("+tiltCenter+": "+initialTilt[bestTiltIndex]+") " +

					" final axial="+finalAxial[bestTiltIndex][bestAxialIndex]+" ("+axialCenter+": "+initialAxial[bestAxialIndex]+")");

					" final axial="+finalAxial[bestTiltIndex][bestAxialIndex]+" ("+axialCenter+": "+initialAxial[bestAxialIndex]+")"+

					" final inter="+finalInter[bestTiltIndex][bestAxialIndex]+" ("+interCenter+": "+interCenter+")");









// repeat with the best indices			









			LENS_DISTORTIONS.fittingStrategy.distortionCalibrationData.gIS[imageSetNumber].goniometerTilt=finalTilt[bestTiltIndex][bestAxialIndex]; //initialTilt[bestTiltIndex];









			LENS_DISTORTIONS.fittingStrategy.distortionCalibrationData.gIS[imageSetNumber].goniometerAxial=finalAxial[bestTiltIndex][bestAxialIndex]; //initialAxial[bestAxialIndex];









			if (DEBUG_LEVEL>0) System.out.println("Image Set #"+imageSetNumber+" Initial tilt="+finalTilt[bestTiltIndex][bestAxialIndex]+" Initial axial="+finalAxial[bestTiltIndex][bestAxialIndex]);









			LENS_DISTORTIONS.fittingStrategy.distortionCalibrationData.gIS[imageSetNumber].interAxisAngle=finalInter[bestTiltIndex][bestAxialIndex];









			if (DEBUG_LEVEL>0) System.out.println(









					"Image Set #"+imageSetNumber+









					" Initial tilt="+finalTilt[bestTiltIndex][bestAxialIndex]+









					" Initial axial="+finalAxial[bestTiltIndex][bestAxialIndex]+









					" Initial inter="+finalInter[bestTiltIndex][bestAxialIndex]









							);









			int [][] imageSets=LENS_DISTORTIONS.fittingStrategy.distortionCalibrationData.listImages(!processAllImages);









			int [] imageSet=imageSets[imageSetNumber];









			if (imageSet==null){










@@ -6443,7 +6460,8 @@ if (MORE_BUTTONS) {















			if (DEBUG_LEVEL>0) System.out.println("================ Image Set #"+imageSetNumber+" rms="+IJ.d2s(bestRMS, 6)+









					" final tilt="+finalTilt[bestTiltIndex][bestAxialIndex]+" ("+tiltCenter+": "+initialTilt[bestTiltIndex]+") " +









					" final axial="+finalAxial[bestTiltIndex][bestAxialIndex]+" ("+axialCenter+": "+initialAxial[bestAxialIndex]+")");









					" final axial="+finalAxial[bestTiltIndex][bestAxialIndex]+" ("+axialCenter+": "+initialAxial[bestAxialIndex]+")" +









					" final inter="+finalInter[bestTiltIndex][bestAxialIndex]+" ("+interCenter+")");

















			return;









		}